ASSESSING THE IMPACT OF COMPOST AMENDMENT FOR MANAGING NEMATODES AND THE HEALTH OF MINERAL SOIL UNDER CARROT PRODUCTION By Alemayehu Workalemahu Habteweld A DISSERTATION Submitted to Michigan State University in partial fulfillment of the requirements for the degree of Hort iculture - Doctor of Philosophy 2015 ABSTRACT ASSESSING THE IMPACT OF COMPOST AMENDMENT FOR MANAGING NEMATODES AND THE HEALTH OF MINERAL SOIL UNDER CARROT PRODUCTION By Alemayehu Workalemahu Habteweld he main goal was to develop integrated compost amendment strategies for managing soil nutrient, nematodes, soil health, and carrot yield and quality. - - - sandy clay loam soil - increased SI from 50 % in Cupar. Higher rates of AC treatments increased soil respiration. Although compost amendments increased yield in 2013 in Sugarsnax 54, most compost amendments decreas ed yield in 2012. The variable responses relative to compost rate, source and time suggest that the effect of compost based amendments on the soil food web structure and the ecosystem services it provides point away from a one - size - fits - all approach. - The hypothesis was Lower rates of urea mixed with higher rate of PC increased soil biological activity. However, there was no difference among the treatments in carrot yield. In addition, no changes in EI due to treatments were detected. In a third experiment, how compost works in sterilized soil was used to simulate biologically degraded soil under glasshouse conditions o ver three months; however, it appeared that a longer time is needed for compost to be effective. As part of understanding variable responses and integrated amendment use efficiency, a weighted nematode guild abundance concept was introduce to integrate th e fertilizer use efficiency (FUE) and soil food web models for better resolution of agroecological analysis relative to soil health. Integrating weighted nematode guild abundance and agronomic data into the FUE model showed that most of the compost treatme nts were significantly greater than the control. Collectively, the findings help build a foundation up on which soil health - related industry priorities can be addressed through understanding the biological and physi c ochemical basis of the changes and desig ning potential solutions that fit variable soil conditions. iv To Abnet and Bethel v ACKNOWLEDGEMENTS I would like to take this opportunity to thank people who helped me to succeed in the course of my study. Without their guidance, help and patience, I would have never been able to accomplish the work of this Dissertation. First, I would like to thank Dr. Haddish Melakeberhan for giving me the opportunity and the means to pursue a Doctoral Degre e. I am also grateful for his excellent academic support, encouragement, and enthusiasm, which made this Dissertation possible, and for his patience in process. I thank my advisory committee members, Dr. Daniel Brainard, Dr. Mathieu Ngouajio, Dr. Sasha Kra vchenko and Dr. Parwinder Grewal for their academic support, encouragement, guidance and constructive suggestions through these years. I am thankful to Dr. Zin Thu Zar Maung for her friendship and support, I want to thank I would like to thank Michigan State University AgBioResearch through Dr. Haddish Melakeber Hatch project (#1792) , the C ollege of Agriculture and Natural Resources, the Graduate School , the Department of Horticulture, Michigan Carrot Commission , Michigan Vegetable Council, and John L. Arend Excellence in Graduate Student Research Scholarshi p for financial support for my program. I am also thankful for And many, many thank s to my wife Abnet and my daughter Bethel for their love, support, encouragement and patience during the st ressful times. vi TABLE OF CONTENTS LIST OF TABLES ................................ ................................ ................................ ......................... ix LIST OF FIGURES ................................ ................................ ................................ ...................... xv KEY TO SYMBOLS OR AB BREVIATIONS ................................ ................................ ........... xxi CHAPTER 1 ................................ ................................ ................................ ................................ ... 1 INTRODUCTION AND REVIEW OF LITERATURE ................................ ............................ 1 CHAPTER 2 ................................ ................................ ................................ ................................ ... 8 GENERAL MATERIALS AND METHODS ................................ ................................ ............ 8 Plot establishment and maintenance ................................ ................................ ....................... 8 Soil sampling ................................ ................................ ................................ .......................... 9 Nematode extraction, identification and abundance ................................ ............................... 9 Nematode community indices ................................ ................................ ............................... 10 Soil food web condition, trophic ratios and fertility index ................................ ................... 10 Soil respiration and physicochemical properties ................................ ................................ .. 11 Carrot yield and quality ................................ ................................ ................................ ........ 12 Multiple factor analysis ................................ ................................ ................................ ......... 12 CHAPTER 3 ................................ ................................ ................................ ................................ . 14 EFFECTS OF PLANT AND ANIMAL WASTE - BASED COMPOST AMENDMENTS ON NEMATODES, SOIL PROPERTIES, AND YIELD AND QUALITY OF FRESH MARKET AND PROCESSING CARROT CULTIVARS ................................ ................................ ........ 1 4 Abstract ................................ ................................ ................................ ................................ . 14 Introduction ................................ ................................ ................................ ........................... 15 Materials and methods ................................ ................................ ................................ .......... 18 Experimental design and treatments ................................ ................................ ................. 18 Data analysis ................................ ................................ ................................ ..................... 20 Results ................................ ................................ ................................ ................................ ... 22 Composition and abundance of nematode trophic groups ................................ ................ 22 Nematode community indices ................................ ................................ ........................... 27 Soil food web condition, trophic ratios and fertility index ................................ ............... 29 Soil respiration and physicochemica l properties ................................ .............................. 32 Carrot yield and quality ................................ ................................ ................................ .... 37 Discussion ................................ ................................ ................................ ............................. 43 CHAPTER 4 ................................ ................................ ................................ ................................ . 51 EFFECTS OF INTEGRATED APPLICATION OF PLANT - BASED COMPOST AND UREA ON SOIL FOOD WEB, SOIL PROPERTIES, AND YIELD AND QUALITY OF A PROCESSING CARROT CULTIVAR ................................ ................................ .................... 51 Abstract ................................ ................................ ................................ ................................ . 51 Introduction ................................ ................................ ................................ ........................... 52 vii Materials and Methods ................................ ................................ ................................ .......... 54 Experimental design and treatments ................................ ................................ ................. 54 Data analysis ................................ ................................ ................................ ..................... 55 Results ................................ ................................ ................................ ................................ ... 57 Composition and abundance of nematode trophic groups ................................ ................ 57 Nematode community indices ................................ ................................ ........................... 62 Soil food web condition, trophic ratios and fertility index ................................ ............... 62 Physicochemical properties and soil respiration ................................ ............................... 64 Carrot yield and quality ................................ ................................ ................................ .... 67 Relationships among nematode trophic, soil, and yield variables ................................ .... 69 Relationships among abundant herbivores and yield ................................ ........................ 70 Discussion ................................ ................................ ................................ ............................. 73 CHAPTER 5 ................................ ................................ ................................ ................................ . 79 EFFECTS OF PLANT - AND ANIMAL WASTE - BASED COMPOST AMENDMENTS, AND SOIL STERILIZATION ON NEMATODES, SOIL PROPERTIES, AND YIELD OF A FRESH MARKET CARROT CULTIVAR UNDER GLASSHOUSE CONDITIONS .......... 79 Abstract ................................ ................................ ................................ ................................ . 79 Introduction ................................ ................................ ................................ ........................... 80 Materials and methods ................................ ................................ ................................ .......... 81 Soil samples ................................ ................................ ................................ ...................... 81 Experimental design and treatments ................................ ................................ ................. 82 Nematode extraction, identification and abundance ................................ ......................... 84 Carrot yield ................................ ................................ ................................ ....................... 84 Data analysis ................................ ................................ ................................ ..................... 84 Results ................................ ................................ ................................ ................................ ... 85 Nematode composition and abundance ................................ ................................ ............ 85 Nematode community indices ................................ ................................ ........................... 86 Soil food web indices, trophic ratios and fertility index ................................ ................... 89 Soil properties and soil respiration ................................ ................................ ................... 92 Carrot yield ................................ ................................ ................................ ....................... 99 Relationships between nematodes and soil properties ................................ .................... 104 Discussion ................................ ................................ ................................ ........................... 107 CHAPTER 6 ................................ ................................ ................................ ............................... 111 SECOND MODIFICATION OF THE FERTILIZER USE EFFICIENCY (FUE) MODEL INTEGRATING WEIGHT ED NEMATODE GUILDS FOR BROADER USE IN SOIL HEALTH MANAGEMENT ................................ ................................ ................................ ... 111 Abstract ................................ ................................ ................................ ............................... 111 Introduction ................................ ................................ ................................ ......................... 112 Materials and methods ................................ ................................ ................................ ........ 115 Experimental design and treatments ................................ ................................ ............... 115 Soil sampling, and nematode extraction, identification and enumeration ...................... 116 Soil pH, organic matter and carrot yield ................................ ................................ ......... 117 Integrati ng FUE and soil food web models concepts ................................ ..................... 117 Second modification of the FUE model ................................ ................................ ........... 119 Statistical analysis of data fitted to the second modification of the FUE model ............ 121 viii Results ................................ ................................ ................................ ................................ . 121 Discussion ................................ ................................ ................................ ........................... 131 CHAPTER 7 ................................ ................................ ................................ ............................... 136 GENERAL DISCUSSION AND CONCLUSIONS ................................ ............................... 136 APPENDICES ................................ ................................ ................................ ............................ 144 APPENDIX A: SUPPORTING DATA ................................ ................................ .................. 145 APPENDIX B: CARROT FIELD SURVEY ................................ ................................ ......... 152 APPENDIX C: VOUCHER SPECIMENS ................................ ................................ ............. 168 BIBLIOGRAPHY ................................ ................................ ................................ ....................... 171 ix LIST OF TABLES Table 3.1. Average soil pH, macro (%) and micro nutrient contents (ppm) of animal (AC) andplant compost (PC) and rates at which they were applied (kg/ha) in sandy clay loam soil and planted with Cupar and Sugarsnax 54 carrot cultivars in 2012 - 2014. ................................ .......... 20 Table 3.2. List of nematode genera detected in AC and PC compost, urea and non - amended check plots in sandy clay loam soil in 2012 - 2014 growing seasons. Numbers within brackets represent c - p vales following Bongers and Bongers (1998). ................................ ........................ 23 Table 3.3. Probability values (Pr > F) of treatment (TR), time (T), and interaction of treatment and time (TR*T) effects for nematode trophic abundances, non - herbivore and total nematodes, nematode community and soil food web indices, trophic group r atios and soil physicochemical properties for field plots amended with AC and PC, and standard urea application and non - amended check in sandy clay loam soil planted with Cupar and Sugarsnax 54 cultivars in 2012 - 2013. ................................ ................................ ................................ ................................ .............. 24 Table 3.4. Means abundance of herbivores (HV), bacterivores (BV), fungivores (FV) and predators (PR) nematode trophic groups, non - herbivore (NHV) and total nematode s (TL) per 100 cc of soils at the studied treatments in Cupar plots across 2012 and 2013 growing seasons. ..... 27 Table 3.5. Means across all sampling time points of the Shannon - diversity indices, and maturity index (MI) at the studied treatment s in Cupar and Sugarsnax 54 cultivars across 2012 and 2013 growing seasons. ................................ ................................ ........ 29 Table 3.6. Soil food web structure index (SI) from plots amended with plant (PC) and animal (AC) composts and standard urea application, and non - amended check in Cupar plots in sandy clay loam soil at 0, and132 and 133 DAP in 2012 and 2013 growing seasons, respectively. ...... 30 Table 3.7. Rate of soil respirations (µg CO 2 - C g - 1 day - 1 ) from plots amended with animal (AC) and plant (PC) composts and standard urea application and non - amende d check in sandy clay loam soil at planting (0) and at 132 and 133 days after planting (DAP) in Cupar, and at 78 and 79 DAP in Sugarsnax 54 in 2012 and 2013 growing seasons. ................................ .......................... 33 Table 3.8. Soil pH, and phosphorus (P) and nitrate - nitrogen (NO 3 - N) contents (ppm) in Cupar plots amended with animal (AC) and plant (PC) composts, standard urea application and non - amended check in sandy clay loam soil at planting (0 ) and at 132 and 133 days after planting (DAP) in 2012 - 2013 growing seasons. ................................ ................................ ......................... 35 x Table 3.9. Soil pH, phosphorus (P), potassium (K) and nitrate - nitrogen (NO 3 - N) contents (ppm) and soil organic matter (% OM) in Sugarsnax 54 plots amended with animal (AC) and plant (PC) composts, standard urea application and non - amended check in sandy clay loam soil at plan ting (0 ) and at 78 and 79 days after planting (DAP) in 2012 - 2013 growing seasons. ........................ 36 Table 4.1. Integrated application of urea an d plant compost (PC) at varying ratios to supply the recommended nitrogen (N) for processing carrot cultivars. Treatments are different combinations of N levels coming from urea and PC to provide the recommended nitrogen amount. ............... 55 Table 4.2. Average soil pH, macro (%) and micro nutrients (ppm) of plant compost (PC) and rates at which they were applied (kg/ha) in sandy loam soil and planted with a processing carrot - 2014 growing seasons. ................................ ................................ ......... 56 Table 4.3. List of nematode genera detected in plots amended with integrated application of urea and PC at different levels to supply 135 kg N/ha recommended for processing carrot varieties, standard urea, and non - amended check plots in sandy loam soil in 2012 - 2014 growing seasons. Numbers within brac kets represent c - p values following Bongers and Bongers (1998). ............. 58 Table 4.4. Probability values (Pr > F) of treatment (TR), time (T), and interaction of treatment and time (TR*T) effects for nematode trophic group abundances, non - herbivore and total nematodes, nematode community and soil food web indices, trophic group ratios, soil respiration and soil physicochemical properties fo r field plots amended with integrated application of urea and PC at different levels to supply 135 kg N/ha and standard urea application and non - amended check in sandy loam soil in 2012 - 2014. ................................ ................................ ........................ 60 Table 4.5. Interaction effects of different levels of urea and PC combined to supply 135 kg N/ha, standard urea and growing seasons (2012, 2013 and 2014) on the abundance of nematode trophic groups (herbivores, bacterivores, fungivores, omnivores and predators) per 100 cc soils. Treatments show the proportion of nitrogen coming from urea and PC to supply 135 kg N/ha recommended for Cupar. ................................ ................................ ................................ .............. 61 Table 4.6. Means across all sampling time points of the enrichment index (EI), structure index (SI), basal index (BI) and channel index (CI) at the studied treatments across 2012, 2013 and 2014 growing seasons. ................................ ................................ ................................ .................. 63 Table 4.7. Soil pH, nitrate - nitrogen (NO 3 - N) and calcium (Ca) contents (ppm) in plots amended with integrated application of urea and PC to supply 135 kg N/ha recommended for Cupar, standard urea application and non - amended check in sandy loam soil at planting (0) and at 132 and 133 days after planting (DAP) in 2012 - 2013 growing seasons. ................................ ............ 65 xi Table 5.1. Average soil pH, macro (%) and micro nutrient contents (ppm) of animal (AC) and plant compost (PC) and rates of application (kg/ha) in 2012 and 2013. ................................ ....... 83 Table 5.2. List of nematode genera detected in AC and PC amendments, standard urea and non - amended c heck in pots filled with 960 g non - sterilized sandy clay loam soil planted with Sugarsnax 54 at planting and 86 days later at harvest in 2012 and 2013 glasshouse experiments. Numbers within brackets represent c - p vales following Bongers and Bongers (1998). ............... 87 Table 5.3. Mean numbers of herbivores, bacterivores, fungivores, predators and omnivores nematode trophic groups abundances in 100 cc of soil amended with animal (AC) and plant (PC) composts, standard urea and non - amended check in pots filled with 960 g of non - sterilized sandy clay loam soil planted with Sugarsnax 54 at planting b and at harvest c (86 DAP) across 2012 and 2013 glas shouse experiments. ................................ ................................ ................................ ....... 88 Table 5.4. The effect of animal (AC) and plant (PC) composts at different rates, standard urea and non - amended check on Shannon - filled with 960 g of non - sterilized sandy clay loam soil planted with Sugarsnax 54 at planting b and at harvest c (86 DAP) in 2012 and 2013 glasshouse experiments. ................................ .......... 88 Table 5.5. The effect of animal (AC) and plant (PC) composts at different rates, standard urea and non - amended check on maturity indices (PPI, MI and MI25) in pots filled with 960 g of non - sterilized sandy clay loam soil planted with Sugarsnax 54 at planting b and at harvest c (86 DAP) in 2012 and 2013 experiments. ................................ ................................ ................................ ..... 89 Table 5.6. The effect of animal (AC) and plant (PC) composts at different rates, standard urea and non - amended check on food web enrichment (EI) and structure (SI), basal index (BI), and channel index (CI ) in pots filled with 960 g of non - sterilized sandy clay loam soil planted with Sugarsnax 54 at planting b and at harvest c (86 DAP) in 2012 and 2013 experiments. .................. 90 Table 5.7. The effect of animal (AC) and plant (PC) composts at different rates, standard urea and non - amended check on fungivores - to - bacterivores ratio (FV/BV), sum of bacterivores and fungivores - to - herbivores ((BV + FV)/HV) and fertility index (FI= PPI/MI) in pots filled with 960 g of non - sterilized sandy clay loam soil planted with Sugarsnax 54 at planting b and at harvest c (86 DAP) in 2012 and 2013 experiments. ................................ ................................ ....... 90 Table.5.8. Soil pH, moisture content (% MO) and phosphorus (P), potassium (K), calcium (Ca), Magnesium (Mg) contents (ppm), cation exchange capacity (CEC) (100 me/100g), organic matt er (% OM), nitrate - nitrogen (NO 3 - N) (ppm), ammonium - nitrogen (NH 4 - N) (ppm) and soil respiration (SR) (µ CO 2 - C per gram per day) in animal (AC) and plant (PC) composts amendments at different rates, standard urea and non - amended check in pots filled with 9 60 g of xii sterilized (S) and non - sterilized (NS) sandy clay loam soil planted with Sugarsnax 54 at planting b and at harvest c (86 DAP) in 2012 glasshouse experiments. ................................ ......................... 93 Table 5.9. Soil pH, moisture (% MO) and phosphorus (P), potassium (K), calcium (Ca), Magnesium (Mg) contents (ppm), and cation exchange capacity (CEC) (100 me/100g), organic matter (% OM), nitrate - nitrogen (NO 3 - N) (pp m), ammonium - nitrogen (NH 4 - N) (ppm) and soil respiration (SR) (µ CO 2 - C per gram per day) in animal (AC) and plant (PC) composts amendments at different rates, standard urea and non - amended check in pots filled with 960 g of sterilized (S) and non - steriliz ed (NS) sandy clay loam soil planted with Sugarsnax 54 at planting b and at harvest c (86 DAP) in 2013 glasshouse experiments. ................................ ......................... 96 Table 5.10. The effect of animal (AC) and plant (PC) compost amendment at different rates, standard urea and non - amended check on carrot root fresh weight (RFW), root dry weight (RDW), shoot fresh weight (SFW), shoot dry weight (SDW) and root - to - shoot dr y weight ratio (RD/SD) in pots filled with 960 g of sterilized (S) and non - sterilized (NS) sandy clay loam soil planted with Sugarsnax 54 after 86 days in 2012 experiments. ................................ .................. 102 Table 5.11. The effect of animal (AC) and plant (PC) compost amendment at different rates, standard urea and non - amended check on carrot root fresh weight (RFW), root dry weight (RDW), shoot fresh weight (SFW ), shoot dry weight (SDW) and root - to - shoot dry weight ratio (RD/SD) in pots filled with 960 g of sterilized (S) and non - sterilized (NS) sandy clay loam soil planted with Sugarsnax 54 after 86 days in 2013 experiments. ................................ .................. 103 Table 6.1. Soil organic matter (% OM), soil pH, and marketable and unmarketable carrots (T/ha) in Cupar plots amended with animal (AC) and plant (PC) composts at different rates (kg N/ha), standard urea application and non - amended check in sandy clay loam soil at planting (0) and at 132 and 133 days after planting (DAP) in 2012 - 2013 growing season for % OM and pH, and in 2012 - 2014 growing seasons for carrot yield ( T/ha). ................................ ................................ ... 124 Table 6.2. Soil organic matter (% OM), Soil pH, and marketable and unmarketable carrots (T/ha) in Sugarsnax 54 plots a mended with animal (AC) and plant (PC) composts at different rates (kg N/ha), standard urea application and non - amended check in sandy clay loam soil at planting (0) and at 78 and 79 days after planting (DAP) in 2012 - 2013 growing seasons. ............................. 125 Table A - 1 . Nematode trophic groups, and non - herbivores and total nematodes abundances in 100 cc of soil amended with AC and PC containing 135, 204 and 270, and 112, 168 and 224 kg N/ha for Cupar and Sugarsnax 54, respectively, and standard urea application a and non - amended check in sandy clay loam soil in 2012 - 2014, and 2012 and2013 growing seasons for Cupar and Sugarsnax 54, respectively ................................ ................................ ................................ ........... 14 5 Table A - 2 . Omnivore nematodes abundance in 100 cc of soil amended with animal (AC) and plant (PC) composts containing 135, 203 and 270 kg N/ha and standard urea application xiii supplying 135 kg N/ha and non - amended check for Cupar in sandy clay loam soil at different days after planting in 2012 - 2013 growing seasons ................................ ................................ ...... 14 6 Table A - 3 . Omnivore nematodes abundance in 100 cc of soil amended with animal (AC) and plant (PC) composts containing 112, 168 and 224 kg N/ha and standard urea application supplying 112 kg N/ha and non - amended check for S ugarsnax 54 in sandy clay loam soil at different days after planting in 2012 - 2013 growing seasons ................................ ....................... 14 7 Table A - 4 . Plant - parasitic index (PPI) values obtained from plots amended with animal (AC) and plant (PC) composts containing 112, 168 and 224 kg N/ha a nd standard urea application supplying 112 kg N/ha and non - amended check for Sugarsnax 54 in sandy clay loam soil at different days after planting in 2012 - 2013 growing seasons ................................ ....................... 14 8 Table A - 5 . Soil food web structure index (SI) in plots amended with animal (AC) and plant (PC) composts containing 135, 203 and 270 kg N/ha and standard urea application supplying 135 kg N/ha and non - amended check in Cupar plots in sandy clay loam soil at different days after planting in 2012 - 2013 growing seasons ................................ ................................ ...................... 149 Table B - 1 . Carrot quality of five randomly selected carrots from each 2 hectares portion of the carrot farm sites ................................ ................................ ................................ ............................ 155 Table B - 2. List of nematode genera from herbivore, bacterivore, fungivore, omnivore and predator trophic groups detected during the field survey. Numbers within brackets represent c - p values following Bongers and Bongers (1998) ................................ ................................ ............ 159 Table B - 3. Abundance of herbivores (HV), bacterivores (BV), fungivores (FV), and omnivores (OV), non - herbivores (NHV), and total nematodes per 100 cc soil of the four selected carrot fields. The proportion of root lesion nematodes was expressed as a percent of herbivores (Pr/HV) and as percent of total nematodes (Pr/TL) ................................ ................................ ................... 1 60 Table B - N 0, and nematode community maturity expressed as plant - parasitic index (PPI), maturity index for free - living nematodes (MI) and maturity index of free - living nematodes with c - p 2 to 5 values for the carrot fields ................................ ................................ ................................ ............ 16 1 Table B - 5. Soil food web enrichment (E I), structure (SI), basal (BI) conditions and channel index (CI) calculated for the carrot fields. Nematode trophic group ratios were expressed as fungivores (FV) - to - bacterivores (BV), and fungivores plus bacterivores - to - herbivores ((FV + BV)/HV), and the fertility index (FI) expressed as PPI/MI of the selected fields ................................ ............... 162 Table C - 1. List of voucher specimens a of nematode genera identified from the experimental samples and mounted on glass slides. The specimens were from MSU Teaching and Research center, Holt, MI, USA (N 43 0 0 0 0 2012 - 2014 growing seasons. The samples are stored in the Agricultural Nematology Laboratory, Department of Horticulture at MSU ................................ ................................ ............................ 1 68 xiv Table C - 2. List of additional photographed and documented nematode genera identified from MSU Teaching Research Center, Holt, MI, USA (N 43 0 85 0 42 0 0 from 2012 - 2014 growing seasons ................................ ................. 17 0 xv LIST OF FIGURES Figure 3.1. Soil food web condition in plots planted with Cupar (A) and Sugarsnax 54 (B) and amende d with plant (PC) and animal (AC) compost, standard urea and non - amended check in sandy clay loam soil at planting (May, June) and harvest (August, October) in 2012 - 2014 and 2012 - 2013 growing seasons for Cupar and Sugarsnax 54, respectively. In Cupar plot s, numbers 1 - 3 refer PC at a rate of 135, 203 and 270 kg N/ha, respectively and 4 - 6 refer AC at a rate 135, 203 and 270 kg N/ha, respectively, 7 and 8 refer urea and check, respectively. In Sugarsnax 54 plots, numbers 1 - 3 refer PC at a rate of 112, 168 and 224 kg N/ha, respectively and 4 - 6 refer AC at a rate 112, 168 and 224 kg N/ha, respectively, 7 and 8 refer urea and check, respectively. .... 31 Figure 3.2. Effect of - - ................................ ....... 38 Figure 3.3. Multiple factor analysis of the variables where Dimension 1 (Dim 1) and Dimension 2 (Dim 2) represent the first and second best summary of varia bility of the information, respectively. (A) The relationships between abundance of nematode trophic groups (Gc) (bacterivores (BV), fungivores (FV), omnivores (OV), predators (PR), sum of omnivores and predators (OP), herbivores (HV) (Yeats et al., 1993)) and non - herbivore (FL) and total (TL) nematodes, and nematode guilds c - p 1 bacterivores (BV1), c - p 2 bacterivores (BV2), sum of c - p 3 and c - p 4 (BV34), c - p 2 herbivores (HV2) and sum of c - p 3 to c - p 5 herbivores (HV345) (Bongers, 1990; Bongers and Bonger s, 1998) and soil properties (Gc2) (soil pH (pH) , organic matter percentage (OM), nitrate - nitrogen (NO 3 - N), ammonium - nitrogen (NH 4 - N),calcium (Ca), magnesium (Mg), phosphorus (P), potassium (K), moisture percent (MO), bulk density (BD), cation exchange ca pacity (CEC) and porosity (PO). (B) The relationship among soil food web indices and trophic group ratios (Gc1) ((FV/BV)=FV) and ((FV + BV)/HV=FBP), soil physicochemical properties (Gc2) and carrot yield and quality (Gc3) (stunt (STU), forks (FO), rots ( RO), cracks (CRA), marketable (MC), total unmarketable carrots (UNC) and root dry - to - shoot dry weight ratio (RDSD)) from treatments with plant (PC) and animal (AC) compost, standard urea (UR) and non - amended check (CK) in Cupar plots in 2012 and 2013 growi ng seasons. ................................ ................................ ................................ ................................ ......... 40 Figure 3.4. Multiple factor analysis of the variables where Dimension 1 (Dim 1) and Dimension 2 (Dim 2) represent the first and second best summary of variability of the information, respectively. (A) The relationships between abundance of nematode trophic groups (Gc1)(bacterivores (BV), fungivores (FV), omnivores (OV), predators (PR), sum of omnivores and predators (OP), herbivores (HV) (Yeats et al., 1993)) and non - herbivore (FL) and total (TL) nematodes, and nematode guilds c - p 1 bacterivores (BV1), c - p 2 bacterivores (BV2), sum of c - p xvi 3 and c - p 4 (BV34), c - p 2 herbivores (HV2) and sum of c - p 3 to c - p 5 herbivore s (HV345) (Bongers, 1990; Bongers and Bongers, 1998) and soil properties (Gc2) (soil pH (pH) , organic matter percentage (OM), nitrate - nitrogen (NO 3 - N), ammonium - nitrogen (NH 4 - N),calcium (Ca), magnesium (Mg), phosphorus (P), potassium (K), moisture percent (MO), bulk density (BD), cation exchange capacity (CEC) and porosity (PO). (B) The relationship among soil food web indices and trophic group ratios (Gc1)((FV/BV)=FV) and ((FV + BV)/HV=FBP), soil physicochemical properties (Gc2) and carrot yield and qual ity (Gc3)(stunt (STU), forks (FO), rots (RO), cracks (CRA), marketable (MC), total unmarketable carrots (UNC) and root dry - to - shoot dry weight ratio (RDSD)) from treatments with plant (PC) and animal (AC) compost, standard urea (UR) and non - amended check ( CK) in Sugarsnax 54 plots in 2012 and 2014 growing seasons. ................................ ................................ ................................ ........................... 42 Figure 4.1. Soil food web condition in plots amended with integrat ed application of urea and PC, standard urea and non - amended check in sandy loam soil at planting (May, June) and harvest (October) in 2012 - 2014 growing seasons. Numbers 1 - 6 represent treatments: 1= Urea alone, 2= 3:1 ratio of urea and PC, 3= 1:1 ratio of urea and PC, 4= 1:3 ratio of urea and PC, 5= PC alone and 6= non - amended check. ................................ ................................ ................................ ......... 64 Figure 4.2. Means across all sampling time points of soil phosphorus content at the studied treatments across 2012, 2013 and 2014 growing seasons. Bars with different letters are statistically significant at P < 0.05 . ................................ ............................... 66 Figure 4.3. Means across all sampling time points of soil respiration at the studied treatments across 2012, 2013 and 2014 growing s easons. Bars with different letters are statistically significant at P < 0.05 . ................................ ................................ .................. 67 Figure 4.4. Effect of treatments on mean carrot yield by category (marketable, stunts, cracks, forks and rots) in 2012, 2013 and 2014. There was no significant difference in quality category at P ................................ ................................ ................................ ........ 68 Figure 4.5. Multiple factor analysis of the variables where Dimension 1 (Dim 1) and Dimension 2 (Dim 2) represent the first and second best summary of variabili ty of the information, respectively. (A) Relationships among abundance of nematode trophic groups (Gc1) (bacterivores (BV), fungivores (FV), omnivores (OV), predators (PR), sum of omnivores and predators (OP), herbivores (HV) )(Yeats et al., 1993), and non - herbivore (FL) and total (TL) nematodes, and nematode guilds c - p 1 bacterivores (BV1), c - p 2 bacterivores (BV2), sum of c - p 3 and c - p 4 (BV34), c - p 2 herbivores (HV2) and sum of c - p 3 to c - p 5 herbivores (HV345) (Bongers and Bongers, 1998) and soil prope rties (Gc2) (soil pH (pH) , organic matter percentage (OM), nitrate - nitrogen (NO 3 - N), ammonium - nitrogen (NH 4 - N),calcium (Ca), magnesium (Mg), phosphorus (P), potassium (K), moisture percent (MO), bulk density (BD), cation exchange capacity (CEC) and porosi ty (PO). (B) Relationships of soil food web indices and trophic groups (Gc1) ((FV/BV)=FV) and ((FV + BV)/HV=FBP), soil properties (Gc2), and carrot yield and xvii quality (Gc3) (stunt (STU), forks (FO), rots (RO), cracks (CRA), marketable (MC), total unmarketab le carrots (UNC) and root dry - to - shoot dry weight ratio (RDSD)) from plots amended with integrated application of urea and plant compost. ................................ ................................ 71 Figure 4.6. Multiple factor analysis of the variables where Dimension 1 (Dim 1) and Dimension 2 (Dim 2) represent the first and second best summary of variability of the information, respectively. (A) Relationships among carrot yield and qualit y expressed as fresh weight (Gc1) ( (stunt (STU), forks (FO), rots (RO), cracks (CRA), marketable (MC), total unmarketable carrots (UNC) and root dry weight (RDW) and abundant herbivores (Gc2) ( Malenchus , MAL; Tylenchus , TYL; Helicotylenchus , HEL; Pratylen chus , PRA). (B) Relationships among carrot yield and quality (Gc1) expressed as number and abundant herbivores nematodes (Gc2) from plots amended with integrated application of urea and plant compost. ................................ ........ 72 Figure 5.1. Faunal profiles representing the structure (SI) and enrichment (EI) conditions of the soil food web in pots filled with non - sterilized sandy clay loam soil planted with Sugarsnax 54 cultivar in 2012 and 2013 glasshouse experiments. Pots were amended with animal compost (AC) and plant compost (PC) at different rates, standard urea and non - amended check. Numbers represent: 1 - 3= PC adjusted at 112, 168 and 224 kg N/ha, respe ctively; 4 - 6= AC adjusted to supply 112, 168 and 224 kg N/ha, respectively, 7= urea and 8= non - amended check. ................ 91 Figure 5.2. Mult iple factor analysis of the variables where Dimension 1 (Dim 1) and Dimension 2 (Dim 2) represent the first and second best summary of variability of the information, respectively. (A) The relationship among abundance of nematode trophic groups (Gc1) (bac terivores (BV), fungivores (FV), omnivores (OV), predators (PR) and herbivores (HV) (Yeats et al., 1993)) and soil properties (Gc2) (soil pH (pH) , organic matter percentage (OM), nitrate - nitrogen (NO3N), ammonium - nitrogen (NH4N),calcium (Ca), magnesium (M g), phosphorus (P), potassium (K), moisture percent (MO) and cation exchange capacity (CEC) in 2012. (B) The relationship among soil food web indices, trophic group ratios ((FV/BV)=FB) and ((FV + BV)/HV=FB.P) (Gc1), soil properties (Gc), and carrot yield ( Gc3) (root fresh weight (RFW), root dry weight (RDW), shoot fresh weight (SFW), shoot dry weight (SDW) and root dry - to - shoot dry weight ratios (RDSD)) in 2012 from glasshouse experiment. ......................... 105 Figure 5.3. Multiple factor analysis of the variables where Dimension 1 (Dim 1) and Dimension 2 (Dim 2) represent the first and second best summary of variability of the information, respectivel y. (A) The relationship among abundance of nematode trophic groups (bacterivores (BV), fungivores (FV), omnivores (OV), predators (PR) and herbivores (HV) (Yeats et al., 1993)) and soil properties (soil pH (pH) , organic matter percentage (OM), nitrate - ni trogen (NO3N), ammonium - nitrogen (NH4N),calcium (Ca), magnesium (Mg), phosphorus (P), potassium (K), moisture percent (MO) and cation exchange capacity (CEC) in 2013. (B) The relationship among soil food web indices and, trophic group ratios (Gc1) ((FV/BV) =FB) and ((FV + BV)/HV=FB.P), soil properties (Gc), and carrot yield (Gc3) (root fresh weight (RFW), root dry weight (RDW), shoot fresh weight (SFW), shoot dry weight (SDW) and root dry - to - shoot dry weight ratios (RDSD)) in 2013 from glasshouse experiment. ................................ .... 106 xviii Figure 6.1. Fertilizer use efficiency (FUE) model and its modification. (a) Four hypothetical categories of FUE derived from host productivity/nematode/nutrient interactions (Melakeberhan, 2006) with permission from Brill and (b) modified FUE model applied to assess the effect of soil amendment on the relationships between nematode trophic groups (excluding plant - parasitic) and yield or soil parameters (Melakeberhan and Avendaño, 2008) with permission Springer. . 113 Figure 6.2. Functional guilds of soil nematodes characterized by feeding habit and by life history characteristics expressed along a colonizer - persister (c - p) scale (After Bongers & Bongers, 1998). Indicator guilds of soil food web conditions (basal, structured and enriched) are designated and weightings of the guilds along the structure and enrichment trajectories are provided for determination of the enrichment index (EI) and structure index (SI) of the food web (Source: Ferris et al., 2001) with permission from Elsevier. ................................ ...................... 114 Figure 6.3. The second modification of FUE model that integrated concepts of modified FUE and soil food web models to assess the effect of soil am endment on the relationships between nematode functional guilds as indicator of soil health and other agronomic parameters. Data points that fall above the controls (100 %) will show an increase/improvement in tested agronomic parameters (A and B) and soil health status (B and D). Data points in Quadrant B would be best - case scenario, in Quadrant C would be worst - case scenario, and those Quadrant A and D provide a choice of improving soil health or yield, respectively (After Melakeberhan and Avendaño, 2008) with permission from Springer. ................................ ................................ ...... 118 Figure 6.4. Effects of compost types and rate of application data plotted on the modified - modi fied FUE model for Cupar carrot cultivar at planting in May 2012, and harvest in October 2012 and 2013 growing seasons for organic matter and soil pH. - - N - - - ................................ ................................ ................................ ..................... 12 7 Figure 6.5. Effects of compost types and rate of application data plotte d on the modified - modified FUE model for Cupar carrot cultivar for marketable and unmarketable (UNC) carrots at harvest in October 2012, 2013 and 2014 growing seasons. - - N - - - ................................ ................................ ................................ ................................ 128 Figure 6.6. Effects of compost types and rate of application data plotted on the modified - modified FUE model for Sugarsnax 54 carrot cultivar at planting in May 2012, and harvest in xix August 2012 and 2013 growing seasons for organic matter and soil pH. - - N - - - ................................ ................................ ................................ ..................... 129 Figure 6.7. Effects of compost types and rate of application data plotted on the modified - modified FUE model for Sugarsnax 54 carrot cultivar for marketable and unmarketable (UNC) carrots at harvest in August 2012 and 2013 growi ng seasons. - - N - - - ................................ ................................ ................................ ..................... 130 Figure 6.8. Soil food web condition in plots planted with Cupar (A) and Sugarsnax 54 (B) and amended with plant (PC) and animal (AC) compost, standard urea and non - amended check in sandy clay loam soil at plantin g (May, June) and harvest (August, October) in 2012 - 2014 and 2012 - 2013 growing seasons for Cupar and Sugarsnax 54, respectively. In Cupar plots, numbers 1 - 3 refer PC at a rate of 135, 203 and 270 kg N/ha, respectively and 4 - 6 refer AC at a rate 135, 203 a nd 270 kg N/ha, respectively, 7 and 8 refer urea and check, respectively. In Sugarsnax 54 plots, numbers 1 - 3 refer PC at a rate of 112, 168 and 224 kg N/ha, respectively and 4 - 6 refer AC at a rate 112, 168 and 224 kg N/ha, respectively, 7 and 8 refer urea and check, respectively (Source: Chapter 3). ................................ ................................ ................................ .................... 134 Figure 7.1. The long - term impact of conventional and alternative management practices on soil health, environmental quality and yield ................................ ................................ ...................... 138 Figure A - 1 . Effect of plant (PC) and animal (AC) compost containing 135, 203 and 270 kg N/ha for Cupar, standard urea (UR) (293 kg/ ha) to supply 135 kg N/h a and non - amended check (CK) on carrot yield and quality in sandy clay loam so il in 2012 - 2014 growing seasons ................... 150 Figure A - 2 . Ten soil sampling spots for the glasshouse experiment from the field experiment site in 2012 and 2013 ................................ ................................ ................................ .......................... 15 1 Figure B - 1. - - - xx ................................ ................................ ............................... xxi KEY TO SYMBOLS OR ABBREVIATIONS - - - - xxii 1 CHAPTER 1 INTRODUCTION AND REVIEW OF LITERA TURE Michigan is one of the main producers of fresh market and processing carrot varieties in the USA (Hausbeck, 2008). Herbivore nematodes Berney a nd Bird, 1992 Northern root - knot ( Meloidogyne hapla Chitwood, 1949 ), carrot cyst ( Heterodera carotae Jones, 1950 ), root lesion ( Pratylenchus penetrans Cobb, 1917 ) and pin ( Paratylenchus spp . Micoletzky 1922) nematodes were ident ified as major problems in Michigan carrot production systems. Northern r oot - knot, carrot cyst and lesion nematodes are highly problematic in muck soils. Paratylenchus projectus and P. hamatus exist mainly in mineral and muck soils, respectively (Hausbeck, 2008) . N orthern root - knot and carrot cyst nematodes are considered as the most damaging nematodes under Michigan conditions (Berney and Bird, 1992 ; Melakeberhan et al., 2007; Hausbeck, 2008 ). In the face of Food Quality Protection Act - driven r estrictions on broad spectrum nematicides and no commercially available nematode resistant carrot cultivars, multi - purpose aspects of organic soil amendments have the potential to be sustainable alternatives for managing nematodes and soil health (Abawi an d Widmer, 2000; Melakeberhan et al., 2007, Zasada et al., 2008; Mennan et al., 2010). Organic soil amendments encompassing green manure, cover crops, animal manure and compost are among the promising alternatives to conventional soil fertility management p ractices . In addition, they suppress diseases and pests, and improve d carrot yield and quality (Bulluck III et al., 2002a; Wang et al., 2004; Nahar et al., 2006; Briar et al., 2007). Organic soil amendments are also known to improve soil conditions and e cosystem services provided by soil food web (Bardgett and Cook, 1998; Ferris et al., 2001). Managing soil 2 food web functions is important to utilizing essential ecosystem services such as nutrient cycling, and pest suppression that require the activities o f appropriate functional guilds (Ingham et al., 1985; Ferris et al., 1998; Sánchez - Moreno and Ferris, 2007; Ferris et al., 2012). This can be maintained through consistent supply of organic amendments to the soil (Ferris et al., 2004; Ferris and Bongers, 2 006; Ferris, 2010). Apart from sustaining the soil food web, soil organic amendments are known to improve retention of essential nutrients for plant growth and soil water holding capacity ( Pimentel et al., 2005; Zasada et al., 2008; Glover et al., 2010; Me nnan et al., 2010). microbial biomass Briar et al., 2007; Forge and Kempler, 2009; Ferris et al., 2012 - 3 - Sánchez and Richard, 2009 ). Nematodes have several attributes to be considered as bioi ndicators of soil ecosystem change (Bongers and Bongers, 1998). They are the most abundant multicellular organisms and occur across multiple trophic levels in the soil food web (Bongers and Ferris, 1999). Their function in the soil is easily inferred from their mouth structure (Yeates et al., 1993). They can generally be categorized in to five trophic groups : herbivores, bacterivores, fungivores, omnivores and predators (Yeates et al., 1993). There are nematode extraction procedures (Ritz 4 and Trudgill, 199 9) that can c apture diverse nematode species and yield high intrinsic information from a given soil sample (Bongers and Bongers, 1998; Bongers and Ferris, 1999) . Nematodes have also diverse life history characteristics ranging from r - strategists (colonize rs) with c - p 1 (colonizer - persister) characterized by short generation time, high fecundity, and high toleran ce to disturbances to k - strategists (persisters) with c - p 5 characterized by long generation time, low fecundity, and greater sensitiv y to disturbance . Th ese characteristics make nematodes useful bioindicators (Bongers, 1990; Bongers and Bongers, 1998). There are a number of nematode - based indices that assess the structure and function of soil ecosystems. Diversity indices such as Shannon practices on the diversity and richness of nematodes. The Maturity I ndex ( MI ) provides information on the condition o f an ecosystem based on the composition of the nematode community (Bongers, 1990; Neher et al., 2005). The value of the MI varies from less than 2 in disturbed condition s to 4 in undisturbed condition s (Bongers and Bongers, 1998). Weighted nematode guild b ased soil food web indices have been developed to assess soil ecosystem health (Ferris et al., 2001; Berkelmans et al., 2003; Ferris and Matute, 2003, S á nchez - Moreno and Ferris, 2007; Knight et al., 2013). These include s tructure (SI), Enrichment (EI), bas al (BI) and channel (CI ) indices. SI uses functional guilds to assess the soil food web conditions as affected by stress or by disturbance. P resence of functional guilds with c - p values 3 - 5 indicates structured soil ecosystem with greater trophic links while c - p values 1 - 2 indicates degraded conditions with fewer trophic links. EI is a measure of turnover of opportunistic bacterivore and fungivore nematodes and whether the soil environment is nitrogen enriched or depleted (Ferris et al., 2001). BI is a m easure of general opportunistic bacterivore and fungivore 5 nematodes and describes if the soil food web i s diminished due to stress either from nutrient depletion or disturbances. CI measures opportunistic grazers feeding on fungi and bacteria to determine a predominant decomposition pathway. The nematode trophic ratios (fungivores - to - bacterivores, and fungivores plus bacterivores - to - herbivores) have also been used to compare predominant decomposition pathways of the soil food web in previous studies (Freck man and Ettema, 1993; Wasilewska, 1994). Melakeberhan (2006) emphasized cross - disciplinary and integrated decision making approach and develop ed the Fertilizer Use Efficiency ( FUE ) model . The FUE separates the relationships among plant growth, herbivore nematode parasitism, nutrient deficiency and toxicity. The model describes treatment outcome as a percent of control (untreated check) and graphically expresses data in four quadrants from best to worst case scenarios. Later, the FUE model was modified to include assessment of beneficial nematodes and agronomic parameters (Melakeberhan and Anvenda ñ o, 2008). This modification helps to explain soil ecosystem change when assessing efficiency of soil am endments that simultaneously suppress herbivore nematode s and promote the beneficial nematodes (Melakeberhan, 2010). information is available on the impact of specific com post types and rates of applications . The impacts of 6 Hence, the main goal of this research was to develop compost amendment strateg ies for nutrient, nematode and soil health management to improved carrot yield and quality. The working hypotheses were: i - - iii - - integrating the concepts of FUE and nematode - based soil food web models will improve the power of FUE model for integrated a nalysis of soil health and agronomic parameters . In Chapter 3, the objective was to compare the effects of AC and PC composts and rates on herbivore and non - herbivore nematodes, soil fo od web conditions, soil biological and carrot cultivars in sandy clay loam soil. In Chapter 4, I compared the effects of integrated application of di fferent levels of PC and urea on oil biological and physicochemical properties, and yield and quality of Cupar in a sandy loam soil. In Chapter 5, t he effects of different rates of AC and PC on - assessed on sterilized and non - sterilized soils under 7 glasshouse condition s . The study was extended to integrat e the concepts of FUE and the food web models described in Chapter 6. 8 CHAPTER 2 GENERAL MATERIALS AN D METHODS Plot establishment and maintenance Field experiments were established at the Michigan State University (MSU) Horticulture Teaching and Rese arch Center in Holt, Michigan. Each plot was 3.72 meter square (3.05 m x 1.22 m) separated by 1.83 m wide guard rows between their length and 1.52 m between their widths. The field had been used for mixed vegetables and soybean production in 2010 and 2011 growing season, respectively. The field soil had above optimum phosphorus (P) and potassium (K) levels and did not receive P and K fertilizers . The field was tilled to the depth of 30 cm and amendment treatments were uniformly applied, spread to each plot by hand and mixed to 10 cm soil depth using an RTR2548 rototiller (Land Pride, Assaria, KS, USA) before planting. Seeds were planted using MasterMacc planter (Market Farm Implement, Friedens, PA, USA) with 4 rows set 25 cm apart at a rate of 1 seed every 5 cm and every 2.5 cm in - row spacing for Cupar and Sugarsnax 54, respectively. The seeding rate was equivalent to 640,000 and 1,200 ,000 seeds/ha for Cupar and Sugarsnax 54, respectively. Throughout the duration of the experiment, weed control measures were done per recommended standard herbicides for carrots and hand weeding (Zandstra, 2011). Herbicides consisted of preemergenc application of linuron (0.56 kg a.i/ha) 1 to 2 weeks after carrot planting, and postemergence application of linuron (0.56 kg a.i/ha) and clethodim (0.1 kg a.i/ha) applied at 4 to 6 weeks after carrot planting. Plots were irrigated with sprinkler irrigation system set for an hour every day until the carrots emerged and for 4 hours as required after carrot emergence. Experiments on Cupar, the processing variety , were completed 132 DAP in 2012 growing season (Chapter 3 and 4), and 133 DAP in 2013 and 9 2014 growing seasons. The experiment s on Sugarsnax 54, the fresh market variety , were c ompleted 78 DAP in 2012, and 79 DAP in 2013. Soil sampling In 2012, 2013 and 2014, six soil cores per plot were collected at 0 - 25 cm soil depth of root zone in the center two rows using a sampling cone (AMES companies, Inc. , Camp Hill, PA, USA ) at Nematode extraction, identification and abundance N 100 cc of soil - using a semi - automatic elutriator as described earlier (Avendaño et al., 2003) and fixed in double TAF solution (14 ml 40% formalin: 4 ml tri - ethanolamine: 91 ml distilled water) (Hooper, 1986). All nematodes in each sample were counted using an inverted microscope (Accu - scope Inc, Commack, NY, USA) at 400X magnification and identified at genus level following diagnostic keys by Bongers (1994) and the University of Nebraska Lincoln nematode identification website (http:nematode.unl.edu/konzlistbutt.htm). E ach identified genus was assigned to a herbivore, bacterivore, fungivore, omnivore or predator trophic group (Yeates et al., 1993; Okada and Kadota, 2003) and to a colonizer - persister (c - p) groups ranging from r - strategists (colonizers) with c - p 1 as short generation time, high fecundity, tolerant to disturbances to k - strategists 10 (persisters) with c - p 5 as long generation time, low fecundity, sensitive to disturbance, also make them an extremely useful indicator organisms (Bongers, 1990; Bongers and Bongers , 1998). Permanent slides of voucher specimens were prepared following methods described by De Grisse (1969) and photographed. The permananent mounts and digital pictures are stored in the Agricultural Nematology Labaoratory, Department of Hoticulture, at Michigan State University (Tables C - 1 and C - 2 ). Nematode community indices MI of c - p 1 to 5 nematodes and MI of c - p 2 to 5 of free - living nematodes (MI25) were calculated to measure soil ecosystem disturbance level s . Separate plant - parasitic index (PPI) w as calculated by including c - p 2 to c - p 5 plant - parasitic nematode genera. MI, MI25 and PPI were calculated as weighted mean frequency, mathematically expressed as where vi = c - p value assigned to family i , fi = frequency of family i in the s ample, and n = total number of individuals in sample (Bongers, 1990). - ], where Pi is the proportion of taxa in the total population (Shannon and Weaver, 1949), Hill N1 was used to compare number of abundant genera within the community, respect ively. Soil food web condition, trophic ratios and fertility index The effect of treatments on soil food web indices was measured as described by Ferris et al. (2001). BI, CI, EI and SI were calculated based on the weighted abundance of nematodes guilds k s n s k e n e k b n b ) where k is the specific weight of each guild and n is the relative frequency of each nematode functional 11 guild in the soil sample using the following formulae: BI = 100[b/(e+s+b)], SI = 100[s/(s + b)] and EI = 100[e/(e + b)]. CI = 100[0.8(c - p 2 fungivores)/ ( 3.2 (c - p 1 bacterivores) + 0.8(c - p 2 fungivores))], was calculated based on the ratio of fungivores of c - p 2 with the decomposer guilds (fungivores of c - p 2 and b acterivores of c - p 1). The soil food web structure and function was graphically described as function of EI (measure of opportunistic bacterivores and fungivores in the community) and SI (indicator of food web status affected by stress or disturbance) as d escribed by Ferris et al. (2001) . In addition to CI, fungivores - to - bacterivores (fungivores/bacterivores) (Freckman and Ettema, 1993), and fungivores and bacterivores - to - herbivores ( (fungivores + bacterivores)/herbivores) (Wasilewska, 1994) ratios were use d to compare predominant nutrient mineralization pathway s . Fertility index (FI = PPI/MI) was calculated as a measure of changes in the functioning of the soil in response to treatments (Bongers et al., 1997). Soil respiration and physicochemical properti es The rate of CO 2 emission from the soil samples was used as an indicator of relative soil respiration and of level of biological activity (Ettema et al., 1998; Ferris and Matute, 2003; Treonis et al., 2010). Fifteen grams of fresh soil sample per plot wa s incubated in 237 ml glass jars at 22 0 C for 7 days at field soil moisture content during sampling (Treonis et al., 2010). The CO 2 concentration of a 0.5 ml headspace gas sample was withdrawn from the jar through a rubber stopper using 1 ml syringe. The c oncentration was determined after 7 days of incubation using an infrared gas analyzer (LI - 820, LI - COR, Inc., Lincoln, NE, USA; Zibilske, 1994) and expressed as µg CO 2 - C per gram of soil per day. Soil chemical properties such as pH, phosphorus, potassium, c alcium, magnesium, soil organic matter, nitrate - nitrogen (NO 3 - N), ammonium - nitrogen (NH 4 - N) and cation exchange capacity were determined at MSU Soil and 12 Plant Nutrient Laboratory using standard procedures (Huffman and Barbarick, 1981; Nelson, 1983). Soil m oisture content at sampling time, soil bulk density and chemical properties were measured to determine the effects of treatments on soil properties. Soil moisture content in each sample was determined by weight loss after oven drying the soil samples 104 0 C for 24 h. Bulk density was measure d on pre - plant, and harvest soil samples by drying core soils ( 3 cm h eight and 5 cm diameter) at 104 0 C for 24 hours (Blake and Hartge, 1986). Carrot yield and quality All carrots from the center two rows were harvested using spading fork (True Temper, AMES companies, Inc. , Camp Hill, PA, USA ). The roots with tops still attached were washed with a garden hose, counted and graded (Anon, 1965). Carrots were categorized as marketable when the length was greater tha n or equal to 13 cm and the diameter at the shoulder was greater than 2 cm for Sugarsnax 54 and 2.5 cm for Cupar cultivars and without defects. Carrots were graded as unmarketable when carrots were stunt ed (length < 13 cm and diameter at the shoulder < 2 c m for Sugarsnax 54 and 2.5 cm for Cupar ) or had defects such as cracks, fork ing and rot ting (Anon, 1965). Five marketable quality carrots were randomly selected from each plot, and roots and shoots were placed in separate paper bags for fresh and dry weigh t determination. Dry weight was determined after the roots and shoots had been dried at 66 0 C for 12 days (Hochmuth et al., 2006). Multiple factor analysis Multiple factor analysis (Escofier and Pagès, 1994 ) was performed using R v. 3.1.0 to describe the relationships among abundance of nematode trophic groups and soil physicochemical properties. The relationship among soil physicochemical properties, and soil food web indices, 13 trophic ratios and yield parameters were also analyzed. M ultiple factor analys is allows obtaining the best linear combinations of the original variables where Dimension 1 and 2 represent the first and second best summary of variability of the information, respectively. Variables closest to the horizontal axis and the unit circle are best correlated with Dimension 1 (Dim 1) and those closer to vertical axis and unit circle are best correlated with Dimension 2 (Dim 2) . The variables closer to - 1 on each axis are negatively correlated and vice versa . 14 CHAPTER 3 EFFECTS OF PLANT AND ANIMAL WASTE - BASED COMPOST AMENDM ENTS ON NEMATODES, SOIL P ROPERTIES, AND YIELD AND QUALITY OF FRESH MARKET AND PROCESSIN G CARROT CULTIVARS Abstract - soil samples - . As expected, AC amendments increased soil pH, phosphorus, potassium , and organic matter compared with the controls after two years. Except for PC at 168 kg N / ha and AC at 112 kg N/ha, compost treatments decreased Sugarsnax 54 marketable yield compared with urea in 2012. However, all compost amendment treatments increased marketable and total carrot yield of Sugarsnax 54 compared with the controls in 2013. SI was positively correlated with soil respiration, calcium, magnesium, cation exchange capacity, organic matter and soil pH, but negatively correlated with total unmarke table carrot yield, and fertility and basal indices. Overall , the findings support the working hypothesis and suggest that the compost related increase in soil food web struct ure may lead to increasing ecosystem services provided by the soil food web. 15 Introduction Organic soil amendments improve soil food web structure and function and ecosystem services (Bardgett and Cook, 1998; Ferris et al., 2001; Hooper et al., 2005). The stewardship of the functions of soil food web is fundamental to optimizing essential ecosystem services such as nutrient mineralization and pest regulations (Ingham et al., 1985; Ferris et al., 1998; Sánchez - Moreno and Ferris, 2007; Ferris et al., 2012). S ufficient biomass and activity of appropriate functional guilds in the soil food web are required to provide adequate levels of various ecosystem services (Ferris et al., 2001). This can be achieved through a consistent supply of new organic material such as compost to the soil (Ferris et al., 2004; Ferris and Bongers, 2006; Ferris, 2010). Moreover, increased organic matter is usually associated with higher soil moisture content, greater retention of essential minerals and improved soil health (Pimentel et al., 2005; Zasada et al., 2008; G lover et al., 2010; Mennan and Melakeberhan , 2010). Compost is one of the most commonly used organic amendments , and has been shown to increase soil organic matter, nutrient content and microbial biomass, suppresses pests and improve overall soil health (Bulluck et al., 2002a; Briar et al., 2007; Forge and Kempler, 2009; Ferris et al., 2012). For example, addition of compost increased soil organic matter, total nitrogen, available phosphorus , exchangeable potassium , availab le water content and porosity of the soil (Pinamonti, 1998). Nahar et al. (2006) also reported compost amendment significantly increased particulate organic matter. However, little is known about the effects of different sources and rates of composts on or ganisms that drive the soil ecosystem functions (Pinamonti, 1998; Briar et al., 2007; Forge and Kempler, 2009). As the most abundant metazoan in terrestrial ecosystems, nematodes are considered as an important component of the soil biotic community and an indicator of soil ecosystem change 16 (Bongers and Bongers, 1998; Porazinska et al., 1999). Nematodes have a central position in the soil food web and they respond to nutrient enrichment, environmental perturbation, and recovery from disturbance (Bongers and Bongers, 1998). They also play a key role in decomposition and nutrient mineralization (Ingham et al., 1985; Ferris and Matute, 2003; Wang et al., 2004; Neher et al., 2012). Presence of a range of life strategy characteristics also makes nematodes useful i ndicator organism (Bongers, 1990; Bongers and Bongers, 1998). Trophic group (herbivores, bacterivores, fungivores, omnivores and predators) abundances, non - herbivores and total useful indicators of ecosystem productivity and change (Nahar et al., 2006; Wang et al., 2006; Cheng and Grewal, 2009; Knight et al., 2013). The MI, a measure of soil disturbance level, has values usually lower than 2 in agroecosystems with frequent farm operations and agrochemical inputs , and up to 4 in natural and undisturbed ecosystems (Bongers and Bongers, 1998). Furthermore, a range of soil food web indices based on the nematode community have been developed to assess soil ecosystem health (Ferris et al., 2001; Berkelmans et al., 2003; Ferris and Matute, 2003, Sanchez - Moreno and Ferris, 2007; Knight et al., 2013). These include SI indicator of lack of, or recovery from, environmental stress and/or resource depletion which contribute to abundance of predators and omnivores. Sanchez - Moreno et al. (2009) found that highest SI in plots treated with compost and cover cr ops compared with conventionally treated plots . SI values are usually low in agroecosystems because of physical and agrochemical distrubance s (Fiscus and Neher, 2002; Berkelmans et al., 2003; Tenuta and Ferris, 2004; Ferris, 2010; Briar et al., 2011). EI r eflects the resource availability of the soil food web. BI is an indicator of soil food webs that are diminished due to stress. CI indicates the percentage of 17 opportunistic grazers feeding on fungi or bacteria, and the predominant decomposition pathway (Fe rris et al., 2001). In addition to CI, fungivores - to - bacterivores (Freckman and Ettema, 1993), and fungivores and bacterivores - to - herbivores (Wasilewska, 1994) ratios can be used to compare predominant nutrient mineralization pathways. - Berney and Bird, 1992 Abawi and Widmer, 2000). Compost amendments are among the promising alternatives to conventional soil fertility management practices, whi ch can provide additional benefits such as suppression of diseases and pests, and improved carrot yield and quality (Bulluck III et al., 2002a; Wang et al., 2004; Nahar et al., 2006; Briar et al., 2007). Bulluck et al. (2002a) reported that cotton - gin tra sh compost application increased bacterivore nematodes in a field cultivated with tomatoes. The abundance of bacterivore, fungivore, omnivore and predator nematodes were increased while herbivore nematodes decreased in composted dairy manure treated plots (Nahar et al., 2006). Similarly, horse manure compost application increased the abundance of total nematodes and the relative abundance of bacterivores, but decreased the relative abundance of herbivores (Lie et al., 2010). However, Ferris et al. (2012) fo und that abundance of bacterivores and fungivores were not affected by green - waste compost application. agronomic benefits, the effect of compost on nematode community has been less studied. Moreover , l 18 Therefore, the objectives of the study reported in this chapter were to compare the effects of AC and PC and rates on soil food web conditions, soil biological and physicochemical properties, and carrot yield and quality of Cupar and Sugarsnax 54 in sandy clay loam soil. I hypothesized Materials and methods Ex perimental design and treatments A repeated field experiment w as conducted at Michigan State University (MSU) Horticulture Teaching and Research Center in Holt, Michigan (N 43 0 0 854 m elevated) in a Colwood - Brookston sandy clay loam (fine - loamy, mixed, mesic Type, Haplaquolls - Argiaquolls, Anon, 1977) with 54 % sand, 25 % silt and 21 % clay. PC from lea ves left to decompose for more than ten years and AC from cow manure - based compost ( Dairy Doo , Sears, MI, USA) were used as organic a mendments. PC was obtained from MSU Student Organic Farm, Holt, MI, USA and AC purchased from Morgan Composting, Inc., Sears, MI, USA (Table 3.1). Urea was the standard inorganic source. Compost was applied on dry matter basis and reported as average of three years (Table 3.1). Treatments for Cupar were 12.0 Mg/ha (1X), 18.0 Mg/ ha (1.5X) and 24.0 Mg/ha (2X) of PC and 9.6 Mg/ha (1X), 14.4 Mg/ha (1.5X) and 19.2 Mg/ha (2X) of AC where 1X was estimated to supply 135 kg N/ha which is a recommended N for proce ssing carrot cultivars. It is assumed that between 10 % and 50 % of N is available in the first season after application (Sanchez and 19 Richard, 2009). A total of 293 kg urea (46 - 0 - 0) /ha (135 kg N/ha) was applied in three split applications (3 0 kg N/ha, 4 5 kg N/ha and 4 5 kg N/ha) when carrot petiole nitrate content was below thres holds established by Warncke (1997 ) . Treatments for Sugarsnax 54 were 12.0 Mg/ha (X), 18.0 Mg/ha (1.5X) and 24.0 Mg/ha (2X) of PC and 8.7 Mg/ha (X), 13.0 Mg/ha (1.5X) and 17.4 Mg/ha (2X) of AC where X was adjusted at a rate of 112 kg N/ha which is a recommended N for fresh market carrot varieties (0.112 N Mg/ha) and urea (46 - 0 - 0) was applied as 0.243 Mg (0.112 Mg N/ha) per plot before planting. The experiment was randomized complete block design with four replications. The contents of macronutrients (nitrogen, phosphorus, potassium, s odium, and sulfur ) and micronutrients (Iron, Zinc, Copper) were significantly higher in AC than in PC (Table 3.1). On the other hand, calcium and alumin um were significantly higher in PC than in AC. However, there were no statistical differences in percentage of organic matter, total carbon and carbon - to - nitrogen ratio (C: N) between AC and PC . Methods pertaining to soil sampling, nematode extraction, ide ntification and nematode community, ecosystem disturbance and soil food web indices, were described in the General Materials and Methods S ection (Chapter 2). Similarly, methods used to measure soil respiration, soil physicochemical properties, and carrot y ield and quality were stated in Chapter 2. 20 Table 3 . 1 . Average soil pH, macro (%) and micro nutrient contents (ppm) of animal (AC) and plant compost (PC) and rates at which they were applied (kg/ha) in sandy clay loam soil and planted with Cupar and Sugarsnax 54 carrot cultivars in 2012 - 2014. pH and nutrients Cupar Sugarsnax 54 Content Rate (kg/ha) Content Rate (kg/ha) AC PC AC PC AC PC AC PC pH 8.4 a e 7.8 a na a na 9.2 b a 7.9 b b na na Macronutrients (%) Nitrogen 1.5 a 1.1 b 135.0 135.0 1.3 a 1.0 b 112.0 112.0 Phosphorus 0.6 a 0.1 b 57.0 12.0 0.6 a 0.1 b 52.0 12.0 Potassium 1.5 a 0.3 b 135.0 36.0 1.5 a 0.3 b 130.0 36.0 Calcium 3.0 b 3.8 a 287.0 457.0 2.9 b 4.0 a 252.0 478.0 Magnesium 0.7 a 0.8 a 67.0 96.0 0.7 b 0.9 a 61.0 11.0 Sodium 0.2 a 0.02 b 19.0 2.0 0.2 a 0.02 b 17.0 2.0 Sulfur 0.4 a 0.2 b 38.0 24.0 0.4 a 0.2 b 35.0 24.0 OM c 29.2 a 25.2 a 27740.0 3005.0 27 a 23 a 2348.0 2750.0 Carbon 16.9 a 14.6 a 1530.0 1755.0 16 a 14 a 1391.0 1674.0 C : N d 11.3 a 13.3 a na na 12 a 14 a na na Micronutrients (ppm) Iron 6306.8 a 5248.1 b 57.0 60.0 6052.3 a 5307.0 b 52.0 60.0 Zinc 188.4 a 77.6 b 2.0 1.0 188.3 a 82.6 b 2.0 1.0 Manganese 348.2 a 324.2 a 3.0 4.0 344.8 a 329.6 a 3.0 4.0 Copper 102.1 a 28.8 b 1.0 0.4 101.5 a 30.6 b 1.0 0.3 Boron 23.9 a 27.3 a 0.2 0.4 24.4 a 27.1 a 0.2.0 0.3 Aluminum 1896.2b 2663.2 a 19.0 36.0 1936.1 b 2843.5 a 17.0 36.0 a Rate was not available because pH and C/N ratio cannot be expressed as a rate of application. b pH value obtained only from 2013. c percent of organic matter. d carbon - to - nitrogen ratio. e Means with different letters in rows within each carrot variety indicat e statistical difference at P < 0.05. Data analysis Nematode taxa and trophic group abundances were expressed on an absolute basis (number of nematodes in a taxon i per 100 cc of fresh soil). Nematode population abundance data were transformed as ln (x+1) prior to statistical analysis to normalize the variance in the data . U ntransformed arithmetic means are presented here in . Treatments were compared for 21 nematode trophic groups, community indices, soil food web indices, trophic group ratios, fertility index, soil physi c ochemical and yield variables. Statistical analysis was conducted using the PROC MIXED procedure of SAS. The statistical model consisted of fixed effects of amendments and time and the interaction between them and random effects of blocks and block by amendment interaction. The interaction between blocks and amendments was used as an error term to test the effect of amendments. The effect of time was addressed using the repeated measures approach with REPEATED statement of the PROC MIXED. Aikaike information criterion was used to select the optimal variance - covariance structure for the repeated measures analysis. Data were tested separately fo r 2014 to validate the positive results observed in 2013 in Cupar plots using same repeated measure procedures. Yield data were compared using one - way analysis of variance (PROC MIXED, SAS ver 9.3, SAS Institute, 2012, Cary, NC , USA ). The statistical mode l consisted of fixed effect of amendments and a random effect of block. F - values were obtained using appropriate error term in the model. Two types of statistical analysis were conducted for SI. First, the SI values were compared following a standard ANOVA and mean separations (Table 3 .6). Second, SI values were plotted to the food web model (Fig. 3 .1). Then, SI values were tested for statistical difference from 50 % (cut off point for structured soil food web) using one - tail t - The means o f the treatments with statistical difference from 50 % are noted by asterisks (*). Comparison among the amendment sources (AC, PC, urea and non - amended check) was done using contrasts in SAS by comparing values before soil amendments in 2012 (0 DAP) and at the end of the two years experiment in 2013 (133 DAP). The nutrient sources were also compared at the beginning of the experiment and the end of the 2014 experiment. Data were analyzed for each carrot variety separately due to differences in amount of ame ndments applied 22 and 133 DAP for Cupar and about 79 DAP for Sugarsnax 54 length of growing season . When the interaction effect of treatments and sampling time was significant, the result was presented . Otherwise, I presented only significant main effects of the treatments. The probability level P < 0.05 was regarded as significant. Results Composition and abundance of nematode trophic groups A total of 15 herbivores, 16 bacterivores, 5 fungivores, 7 omnivores and 6 predator genera were detected in all of th e soil samples collected from Sugarsnax 54 and Cupar plots over the three - year period (Table 3.2). Panagrolaimus, Rhabditis, Acrobeloides, Eucephalobus, Heterocephalobus and Plectus from bacterivores , Aphelenchus, Filenchus and Aphelenchoides from fungivor es , and Basiria and Tylenchus from herbivores were among the most frequently encountered nematode genera. Acrobeles, Pristionchus, Prodorylaimus, Tripyla, Hemicyclophora, Hoplolaimus, Helicotylenchus , and Xiphinema occurred less frequently. Rhabditis , Panagrolaimus , Acrobeloides , Eucephalobus , Heterocephalobus and Plectus were the most abundant bacterivores, and Aphelenchoides , Aphelenchus , and Filenchus were the most abundant fungivores nematode genera. Among herbivores, Tylenchus was the most abundant genus. Omnivores and predators were less abundant in both cultivars except in Cupar at 133 DAP in 2013 and 2014. The average number of herbivores, bacterivores, fungivores, omnivores, and predators per 100 cc of soil was 19, 8, 14, 0.4 and 0.1, and 17, 18 , 21, 0.4 and 0.3 in Sugarsnax 54 and Cupar plots, respectively (Table A - 1). . 23 Table 3 . 2 . List of nematode genera detected in AC and PC compost, urea and non - amended check plots in sandy clay loam soil in 2012 - 2014 growing seasons. Numbers within brackets represent c - p vales following Bongers and Bongers (1998). Herbivores Bacterivores Fungivores Omnivores Predators Basiria (2) Eumonhystera (1) Aphelenchoides (2) Eudorylaimus (4) Trypila (3) Boleodorus (2) Mesorhabditis (1) Aphelenchus (2) Mesodorylaimus (4) Clarkus (4) Cephalenchus (2) Panagrolaimus (1) Ditylenchus (2) Microdorylaimus (4) Mononchus (4) Malenchus (2) Pellioditis (1) Filenchus (2) Pungentus (4) Mylonchulus (4) Paratylenchus (2) Pristionchus (1) Tylencholaimellus (4) Thonus (4) Prionchulus (4) Psilenchus (2) Rhabditis (1) Aporcelaimellus (5) Nygolaimus (5) Tylenchus (2) Acrobeles (2) Prodorylaimus (5) Dolichorynchus (3) Acrobeloides (2) Helicotylenchus (3) Cephalobus (2) Hemicycliophora (3) Cervidellus (2) Heterodera (J2) (3) Eucephalobus (2) Hoplolaimus (3) Heterocephalobus (2) Pratylenchus (3) Plectus (2) Tylenchorhynchus (3) Microlaimus (3) Xiphinema (5) Prismatolaimus (3) Alaimus (4) 24 Table 3 . 3 . Probability values (Pr > F) of treatment (TR), time (T), and interaction of treatment and time (TR*T) effects for nematode trophic abundances, non - herbivore and total nematodes, nematode community and soil food web indices, trophic group ratios and soil physicochemical properties for field plots amended with AC and PC, and standard urea application and non - amended check in sandy clay loam soil planted with Cupar and Sugarsnax 54 cultivars in 2012 - 2013. Probability > F Variables Cupar Sugarsnax 54 Treatment Time Treatment x time Treatment Time Treatment x time Trophic groups Herbivores 0.51 <0.0001 0.56 0.44 <0.0001 0.96 Bacterivores 0.014 <0.0001 0.39 0.78 <0.0001 0.76 Fungivores 0.031 <0.0001 0.18 0.76 <0.0001 0.08 Omnivores 0.001 <0.0001 0.04 0.6 <0.0001 0.003 Predators 0.32 <0.0001 0.98 0.43 0.004 0.73 Non - herbivores 0.02 <0.0001 0.11 0.72 <0.0001 0.66 Total nematodes 0.02 <0.0001 0.15 0.93 <0.0001 0.69 Diversity indices H' a 0.02 <0.0001 0.41 0.014 <0.0001 0.39 Hill's N1 0.061 <0.0001 0.4 0.004 <0.0001 0.48 Hill's N0 0.21 <0.0001 0.46 0.38 <0.0001 0.78 Maturity indices PPI 0.25 <0.0001 0.84 0.43 <0.0001 0.0074 MI 0.03 <0.0001 0.41 0.11 <0.0001 0.71 MI25 0.36 <0.0001 0.28 0.47 <0.0001 0.17 Food web indices EI 0.73 <0.0001 0.89 0.78 <0.0001 0.24 SI 0.41 <0.0001 0.02 0.49 0.1 0.65 BI 0.7 <0.0001 0.84 0.43 <0.0001 0.24 CI 0.06 <0.0001 0.8 0.21 <0.0001 0.33 Trophic group ratio FV/BV b 0.15 <0.0001 0.24 0.82 <0.0001 0.5 (FV+BV)/HV c 0.46 <0.0001 0.28 0.03 <0.0004 0.31 SR d 0.11 <0.0001 0.78 0.04 <0.0001 0.027 25 Variables Probability > F Cupar Sugarsnax 54 Treatment Time Treatment x time Treatment Time Treatment x time Soil physicochemical properties Bulk density 0.99 <0.0001 0.89 0.49 <0.0001 0.91 Porosity 0.99 <0.0001 0.89 0.97 <0.0001 0.74 Moisture 0.51 <0.0001 0.76 0.7 <0.0001 0.74 Soil pH 0.73 <0.0001 0.014 0.27 <0.0001 0.01 Phosphorus 0.12 <0.0001 0.042 0.36 <0.0001 0.01 Potassium 0.57 <0.0001 0.16 0.04 <0.0001 <0.0001 Calcium 0.4 <0.0001 0.71 0.69 <0.0001 0.54 Magnesium 0.17 <0.0001 0.64 0.8 <0.0001 0.9 Organic m atter 0.75 <0.0001 0.53 0.28 <0.0001 0.0004 NO 3 - N <0.0001 0.23 <0.0001 0.0017 <0.0001 0.03 NH 4 - N 0.54 <0.0001 0.37 0.08 <0.0001 0.67 CEC 0.28 <0.0001 0.89 0.73 <0.0001 0.88 a Shannon - Weaver diversity index (Shannon & Weaver, 1949). b Fungivores - to - bacterivores ratio (Freckman and Ettema, 1993).. c Fungivores plus bacterivores - to - herbivores ratio (Wasilewska, 1994). d Rate of soil respiration. Abundances of omnivores were significantly affected by the interaction of treatment and time in Sugarsnax 54 and in Cupar plots in 2012 and 2013 (Table 3.3). However, the interaction was not significant in Cupar in 2014. In Cupar, omnivores were significantly higher in non - amended check compared with the rest of the treatments at 0 DAP in 2012 (Table A - 2) . However, omnivores were significantly lower in PC at 270 kg N/ha and urea plots. In 2012 at 132 DAP, PC at 270 kg N/ha, and AC at 135 and 270 kg N/ha significantly increased omnivores compared with PC at 135 kg N/ha, AC at 203 kg N/ha, urea and non - amended check. All compos t treatments significantly increased omnivores compared with urea and non - amended check at 133 DAP in 2013. Treatments with highest rate of PC and AC (270 kg N/ha) 26 significantly increased omnivores compared with treatments with lower rates of composts (135 and 203 kg N/ha) at 133 DAP in 2013. In Sugarsnax 54, there was no significant difference in omnivores among the treatments in 2012 sampling dates, but PC at 168 kg N/ha significantly increased omnivores compared with urea in 2013 (Table A - 3 ). There wa s no interaction effect of treatment and time on herbivores, bacterivores, fungivores and predators in both cultivars (Table 3.3). However, there was significant treatment effect on bacterivores, fungivores, total non - herbivores and total nematodes abunda nce in Cupar plots (Table 3.4). Overall, AC at 270 kg N/ha significantly increased bacterivores compared with all of the treatments , except PC at 203 kg N/ha and urea. PC at 203 kg N/ha, AC at 135 and 270 kg N/ha, urea and non - amended check significantly i ncreased fungivores compared with PC at 135 kg N/ha and AC at 203 kg N/ha. There was no significant difference in the abundance of herbivore and predator nematode s among the soil amendment treatments. PC at 203 kg N/ha and AC at 270 kg N/ha significantly i ncreased non - herbivores compared with the rest of the treatments. PC at 203 kg N/ha, AC at 135 and 270 kg N/ha, and non - amended check significantly increased total nematodes compared with PC at 135 and 270 kg N/ha. Time had significant effect on the abunda nce of all trophic groups in both cultivars ( p < 0.05) (Table 3.3). Abundance of all trophic groups except omnivores in Cupar, non - herbivores and total nematodes tended to decrease with time. The nematode community was dominated by c - p 2 herbivore and non - herbivores nematode at all sampling dates in bot h cultivars. In Cupar, the proportions of c - p 4 nematodes increased in compost amended plots compared with urea amended plots at 133 DAP in 2013. The proportion of persister nematodes (c - p 3 to c - p 5) increased over time in compost amended more than in ure a amended plots in 2014. 27 Table 3 . 4 . Means abundance of herbivores (HV), bacterivores (BV), fungivores (FV) and predators (PR) nematode trophic groups, non - herbivore (NHV) and total nematodes (TL) per 100 cc of soils at the studied treatments in Cupar plots across 2012 and 2013 growing seasons. Amendments Rate (kg N/ha) HV BV FV PR NHV TL PC 135 15 a a 14 b 18 b 0.4 a 26 c 40 b 203 18 a 19 ab 25 a 0.4 a 44 a 62 a 270 16 a 15 b 16 b 0.1 a 30 c 45 b AC 135 18 a 18 b 24 a 0.4 a 39 bc 56 a 203 19 a 13 b 18 b 0.3 a 32 bc 51 ab 270 15 a 24 a 21 a 0.5 a 45 a 61 a Urea 135 15 a 20 ab 21 a 0.3 a 40 bc 56 ab Check 0 19 a 18 b 23 a 0.3 a 39 bc 59 a a Means within columns followed by same letter(s) are not significantly different at P < 0.05 . The abundance of omnivores at 0 DAP in 2012 was significantly higher in non - amended check than in PC and urea in Cupar plots. However, PC and AC significantly increased omnivores compared with urea and non - amended check at 133 DAP in 2013. Both PC and AC also significantly increased omnivores at 133 DAP in 2013 compared with 0 DAP in 2012 and the same effect was observed in 2014. AC significantly increased non - herbivores and total nematodes compared with non - amended check at 133 DA P in 2013. There was no significant difference in the trophic groups among the amendment sources in Sugarsnax 54. Nematode community indices PPI was significantly affected by the interaction of treatment and time in Sugarsnax 54. PPI was significantly low er in 2013 than in 2012 sampling times in all of the treatments. AC at 135 kg N/ha significantly increased PPI compared with the rest of the treatments in 2014 (Table A - 4) . There was no significant treatment and time interaction effect on diversity indice 28 However, t here was significant effect of time in all the above indices in both cultivars (Table 3.3). Urea significantly decreased MI compared with the r est of the treatments in Cupar (Table 3.5). PC at 203 kg N/ha, and AC at 135 and 203 kg N/ha significantly increased MI compared with PC at 135 and 270 kg N/ha, and AC at 270 kg N/ha in Cupar (Table 3.5). In Sugarsnax 54, PC at 112 kg N/ha and urea signifi N/ha, AC at 224 kg N/ha and non - amended check. Similarly, PC at 112 kg N/ha and urea N/ha and non - amended check. In Cupar plots, PC, AC and non - amended check had higher MI at 133 DAP in 2013 compared with 0 DAP in 2012. Similarly, PC and AC significantly increased MI25 at 133 DAP 133 DAP in 2013 compared with 0 DAP in 2012. In Cupar, PC, AC and non - amended check had significantly lower PPI at 133 DAP in 2013 compared with 0 DAP in 2012. AC significantly increased MI (1.69 vs 1.94) at 133 DAP in 2013 compared with 0 DA P in 2012 in Cupar plots . In 2014, PC, AC and non - amended check significantly increased MI and MI25 at 133 DAP compared with 0 DAP. Non - amended check significantly increased MI compared to urea at 133 DAP. 29 Table 3 . 5 . Means across all sampling time points of the Shannon - diversity indices, and maturity index (MI) at the studied treatments in Cupar and Sugarsnax 54 cultivars across 2012 and 2013 growing seasons. Amendments Carrot cultivar Sugarsnax 54 Cupar Rate (Kg N/ha) H' Hill's N1 Rate (Kg N/ha) MI PC 112 2.17 a a 8.94 a 135 1.98 b 168 2.02 b 7.78 b 203 2.09 a 224 1.99 b 7.81 b 270 2.02 b AC 112 2.03 b 7.84 b 235 2.05 a 168 2.08 ab 8.30 ab 203 2.07 a 224 2.02 b 7.89 b 270 2.00 b Urea 112 2.16 a 8.83 a 135 1.91 c Check 0 1.96 b 7.45 b 0 1.99 b a Means within columns followed by same letter (s) are not significantly different at P < 0.05 LSD . Soil food web condition, trophic ratios and fertility index Fertility index, fungivores - to - bacterivores and decomposers - to - herbivores ratios, EI, BI and CI were not affected by the interaction of treatment and time in both varieties (Table 3.3). There was no significant difference in EI, BI and CI among the treatments. SI was significantly affected by the interaction of treatment and time in Cupar, but such effect was not observed in Sugarsnax 54. At 0 DAP in 2013, SI was significantly higher in AC at 270 kg N/ha, but significantly lower in PC at 203 and 270 kg N/ha compared with the rest of the treatments. In Cupar, all compost treatments except AC at 203 kg N/ha significantly increased SI at 132 DAP compared with 0 DAP in 2012, but this effect was not observed in urea and non - amen ded check (Table s 3.6 and A - 5 ). All the treatments including urea and non - amended check had higher SI at 133 DAP compared with 0 DAP in 2013. SI was significantly greater than 50 % in all compost amendments except AC at 203 kg N/ha at 132 DAP in 2013, but such effect was not observed in 30 urea and non - amended check. Similarly, all of the compost amendments except AC 270 kg N/ha and non - amended check were greater than 50 % SI at 133 DAP in 2014 (Fig. 3.1). In 2014, PC and AC significantly increased SI and sign ificantly decreased BI at harvest compared to pre - plant samples. At most of the sampling dates, the food web was enriched (EI > 50) in all of the treatments (Fig. 3.1) . Faunal profile analysis revealed that compost amended plots showed greater food web st ructure over time, but such effect was not observed in Sugarsnax 54 (Fig. 3.1A & B). Although there was slight progression at the end of 2012 growing season, soil food web became more structured in all compost treatments except AC at 203 kg N/ha and PC at 270 kg N/ha at the end of 2013 and 2014 growing seasons , respectively . Table 3 . 6 . Soil food web structure index (SI) from plots amended with plant (PC) and animal (AC) composts and standard urea application, and non - amended check in Cupar plots in sandy clay loam soil at 0, and132 and 133 DAP in 2012 and 2013 growing seasons, respectively. Amendments Rate (kg N/ha) SI 2012 2013 0 132 0 133 PC 135 7.5 aC a 24.5 aB 6.8 bC 72.8 aA 203 7.6 aC 32.4 aB 2.1 cC 82.6 aA 270 4.0 aB 29.9 aA 0 cB 74.2 aA AC 135 11.9 aC 31.6 aB 2.2 bC 80.6 aA 203 8.6 aC 35.3aC 3.5bC 68.4 aA 270 8.1 aC 23.4 aB 10.4 aB 78.7 aA Urea 135 17.0 aB 9.1 aB 5.5 bB 51.4 aA Check 0 21.2 aBC 6.3 aBC 3.3 bC 59.6 aA a Means with different lower case letters within columns and different upper case letters across rows indicate significant difference at P < 0.05 . 31 Figure 3 . 1 . Soil food web condition in plots planted with Cupar (A) and Sugarsnax 54 (B) and amended with plant (PC) and animal (AC) compost, standard urea and non - amended check in sandy clay loam soil at planting (May, June) and harvest (August, October) in 2012 - 20 14 and 2012 - 2013 growing seasons for Cupar and Sugarsnax 54, respectively. In Cupar plots, numbers 1 - 3 refer PC at a rate of 135, 203 and 270 kg N/ha, respectively and 4 - 6 refer AC at a rate 135, 203 and 270 kg N/ha, respectively, 7 and 8 refer urea and ch eck, respectively. In Sugarsnax 54 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 1* 2* 3* 4* 5 6* 7 8 1 2 3 4 5 6 7 8 1* 2* 3 4* 5* 6* 7 8* 0 50 100 0 50 100 Enrichment Index (%) Structure Index (%) May-12 Oct-12 May-13 Oct-13 A A B C D 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 0 50 100 0 50 100 Enrichment index (%) Structre index (%) May-12 Aug-12 May-13 Aug-13 B A B C D 32 Figure 3.1 . plots, numbers 1 - 3 refer PC at a rate of 112, 168 and 224 kg N/ha, respectively and 4 - 6 refer AC at a rate 112, 168 and 224 kg N/ha, respectively, 7 and 8 refer urea and check, respectively. *Treatments significantly increased SI from 50 % using one - tail t - test at = 0.05 for Cupar plots in 2013 and 2014 growing seasons . Soil respiration and physicochemical properties There were no significant effects of interaction effects of treatment and time, and treatment on soil respiration in Cupar, but treatment and interaction effects were significant in Sugarsnax 54 (Table 3.3). Soil respiration was significantly higher in AC at 168 and 224 kg N/ha plots at harvest in 2013 compared with all the oth er treatments . Soil respiration rate was also significantly higher at harvest in 2013 compared with at planting and at harvest in 2012 and at planting in 2013 (Table 3.7). Phosphorus, soil pH and NO 3 - N , and organic matter and potassium were significantly affected by the interaction of treatment and time in both cultivars and Sugarsnax 54, respectively (Table 3.3). Phosphorus content of the soil was significantly higher in all of the AC treatments than i n urea, non - amended check and PC treatments at 2013 harvest in both cultivars (Tables 3.8 and 3.9). Compost treatments significantly increased soil pH while urea decreased it in both cultivars at harvest in 2013 compared with the previous sampling dates. S oil pH was also significantly lower in urea compared with compost treatments and non - amended check at the end of 2013 growing season in both cultivars (Tables 3.8 and 3.9). 33 Table 3 . 7 . Rate of soil respi rations (µg CO 2 - C g - 1 day - 1 ) from plots amended with animal (AC) and plant (PC) composts and standard urea application and non - amended check in sandy clay loam soil at planting ( 0 ) and at 132 and 133 days after planting ( DAP ) in Cupar, and at 78 and 79 DAP in Sugarsnax 54 in 2012 and 2013 growing seasons. a Nitrogen rate (kg N/ha) applied from each treatments. b Means with different lower case letters in columns within each cultivar and different upper case letters across rows indicate significant difference at P < 0.05 . Cultivar Year DAP Nutrient sources and rate of application s PC AC Urea Check 135 a 203 270 135 203 270 135 0 Cupar 2012 0 3.2 aA b 3.3 aA 3.9 aA 4.7 aA 4.3 aA 3.1 aA 4.7 aA 2.7 aA 132 6.4 aA 5.2 aA 5.1 aA 5.9 aA 6.2 aA 3.9 aA 6.0 aA 5.2 aA 2013 0 2.7 aA 2.9 aA 3.6 aA 2.6 aA 2.7 aA 2.5 aA 2.8 aA 2.3 aA 133 2.9 aA 3.6 aA 5.0 aA 3.8 aA 4.6 aA 6.5 aA 3.5 aA 3.7 aA Sugarsn ax 54 2012 0 112 168 224 112 168 224 112 0 3.3 aA 3.5 aA 3.3 aA 3.5 aA 3.1 bA 3.3 bA 3.5 aA 3.0 aA 78 2.8 aA 2.4 aA 3.6 aA 3.4 aA 4.0 bA 3.4 bA 3.9 aA 2.8 aA 2013 0 2.9 aA 2.8 aA 3.2 aA 3.0 aA 3.0 bA 3.1 bA 2.6 aA 2.8 aA 79 4.2 aB 3.4 aB 3.7 aB 4.5 aB 6.8 aA 7.9 aA 2.6 aB 2.9 aB 34 In Sugarsnax 54, AC treatments significantly increased potassium compared with PC treatments, urea and non - amended check at harvest in 2013. Urea significantly increased NO 3 - N compared with the rest of the treatments at harvest in 2012 and in 2013 in Cupar, but such effect was observed only in 2013 at harvest in Sugarsnax 54. Similarly, urea significantly increased NO 3 - N at harvest in 2012 and in 2013 compared with at planting time in Cupar (Table 3.8). However, urea significantly increased NO 3 - N only at harvest in 2013 compared with at harvest in 2012 and planting time in 2013 in Sugarsnax 54. PC at 168 kg N/ha, and AC at 112 and 224 kg N/ha significantly increased organic matter compared with urea and non - amended check at harvest in 2013 in Su garsnax 54. 35 Table 3 . 8 . Soil pH, and phosphorus (P) and nitrate - nitrogen (NO 3 - N) contents (ppm) in Cupar plots amended with animal (AC) and plant (PC) composts, standard urea application and non - amended check in sandy clay loam soil at planting ( 0 ) and at 132 and 133 days after planting (DAP) in 2012 - 2013 growing seasons. Variables Year DAP Nutrient sources and rate of application s PC AC Urea Check 135 a 203 270 135 203 270 135 0 pH 2012 0 7.2 bA b 7.2 bA 7.2bA 7.1bA 7.2bA 7.2bA 7.3aA 7.1bA 132 7.3 bAB 7.1 bAB 7.5abA 7.2bAB 7.2bAB 7.2bAB 6.8cB 7.2aAB 2013 0 7.5 bA 7.4 bA 7.5abA 7.4bA 7.5bA 7.5bA 7.4abA 7.4aA 133 7.7 aA 7.7 aA 7.7aA 7.7aA 7.7aA 7.7aA 7.2bB 7.6aA P 2012 0 53.5 bA 57.5 bA 55.0 aA 46.5 bA 55.5 bA 49.8 cA 57.8aA 57.3aA 132 57.0 aA 65.3 aA 55.3 aA 54.8 aA 64.0 aA 57.5 bA 59.8aA 54.3abA 2013 0 43.0 cB 51.7 bA 46.7 bAB 41.7 cB 54.0 bA 50.0 cAB 49bAB 45.7bAB 133 47.0 abB 52.0 abB 50.3 abB 49.8 abB 81.0 aA 84.7 aA 48.3bB 44.7bB NO 3 - N 2012 0 6.6 aAB 9.2 aAB 5.5 aAB 4.8 aB 5.0 aAB 7.4 aAB 8.4 bA 7.0 aAB 132 1.6 aB 2.0 aB 2.3 aB 1.3 aB 2.0 aB 1.6 aB 31.7 aA 1.6 aB 2013 0 4.3 aAB 6.2 aAB 4.0 aB 4.3 aAB 5.0 aAB 4.1 aAB 7.2 bA 4.3 aAB 133 0.7 aB 1.5 aB 0.8 aB 1.0 aB 1.8 aB 3.3 aB 29.4 aA 1.1 aB a Nitrogen rate (kg N/ha) applied from each treatments. b Means with different lower case letters in columns within each soil variable and different upper case letters across rows indicate significant difference at P < 0.05 . 36 Table 3 . 9 . Soil pH, phosphorus (P), potassium (K) and nitrate - nitrogen (NO 3 - N) contents (ppm) and soil organic matter ( % OM) in Sugarsnax 54 plots amended with animal (AC) and plant (PC) composts, standard urea application and non - amended check in sandy clay loam soil at planting ( 0 ) and at 78 and 79 days after planting (DAP) in 2012 - 2013 growing seasons. Variables Year DAP Nutrient sources and rate of applications PC AC Urea Check 112 a 168 224 112 168 224 112 0 pH 2012 0 7.3 bAB b 7.3 bAB 7.2 bAB 7.4 aA 7.4 bAB 7.3 bAB 7.2 aB 7.3 bAB 78 7.3 bA 7.3 bA 7.3 abA 7.3 bA 7.4 bA 7.4 bA 7.2 aA 7.3 bA 2013 0 7.3 bA 7.3 bA 7.3 abA 7.3 bA 7.3 bA 7.2 bA 7.2 aA 7.3 bA 79 7.5 aA 7.6 aA 7.4 aA 7.6 aA 7.6 aA 7.5 aA 7.0 bB 7.5 aA P 2012 0 80.0 bA 82.8 bA 80.5 aA 80.0 bA 76.0 bA 74.8 cA 82.0 abA 83.5 bA 78 89.5 aA 94.3 aA 89.3 aA 101.0 aA 101 aA 90.5 bA 89.5 aA 92.0 aA 2013 0 78.0 bA 76.3 bA 75.0 aA 80.7 bA 81.0 bA 79.3 cA 74.3 bA 71.7 bA 79 73.3 bB 76.3 bB 75.3 aB 103.7 aA 109.7 aA 121.3 aA 70.7 bB 75.3 bB K 2012 0 154.0 aA 162.0 aA 156.3 aA 149.0 bA 148.0 cA 145.3 bA 165.5 aA 163.8 aA 78 143.5 aB 157.5 abAB 146.3 bB 160.3 bAB 163.5 bA 164.3 bA 152.3 aAB 147.3 bAB 2013 0 124.3 aA 115.0 cA 114.0 bA 114.3 cA 130.0 cA 121.7 cA 124.7 bA 114.7 cA 79 125.0 aB 137.3 bB 117.0 bB 204.3 aA 218.7 aA 224.3 aA 125.3 bB 116.7 cB % OM 2012 0 3.1 aB 3.2 aA 3.0 aB 3.2 aA 3.1 aB 3.0 aB 3.1 aB 3.1 aB 78 2.3 cA 2.4 cA 2.3 cA 2.4 cA 2.3 cA 2.3 cA 2.2 cA 2.2dA 2013 0 2.8 bA 2.7 bA 2.7 bA 2.8 bA 2.8 bA 2.7 bA 2.6 bA 2.8 bA 79 2.7 bAB 2.9 abA 2.8 abAB 3.0 abA 2.9 abA 3.1 aA 2.5 bB 2.6 cB NO 3 - N 2012 0 6.2 aB 9.0 aA 6.0 aB 7.7 aB 6.4 aB 7.7 aB 9.1 aA 9.4 aA 78 2.8 bAB 2.9 cAB 2.2 bAB 3.5 bA 2.1 bB 2.7 bAB 4.0 cA 2.9 cAB 2013 0 5.9 aAB 7.5 aAB 4.9 aB 5.6 abAB 8.3 aA 6.0 aAB 5.2 bAB 5.1 bAB 79 1.4 bB 1.6 dB 0.9 cB 3.7 bB 3.1 bB 3.8 abB 20.1 aA 1.2 cB a Nitrogen rate (kg N/ha) applied from each treatments . b Means with different lower case letters in columns with in each soil variable and different upper case letters across rows indicate significant difference at P < 0.05 . 37 Carrot yield and quality There were no significant difference s in carrot yield and quality among the treatments and nutrient sources in Cupar in the three growing seasons (Fig. A - 1) , but significant difference was observed in Sugarsnax 54 in 2012 and in 2013. PC at 168 kg N/ha and AC at 112 kg N/ha showed comparable marketable carrot yield to urea in 2012 , but all other compost treatments had lower yield than the urea control . In 2013, compost amendments significantly increased both marketable and total carrot yields compared with urea and non - amended check (Fig. 3.2 ). The number of stunted carrots was significantly lower in urea compared with the rest of the treatments in Cupar in 2013. In 2012, PC at 168 kg N/ha and urea significantly increased the number of marketable carrots compared with the rest of the treatment s in Sugarsnax 54 . In Sugarsnax 54, the total number of unmarketable carrots in 2012 was the highest in PC at 112 kg N/ha . 38 Figure 3 . 2 . Effect of - - a a a a a a b b 0 5 10 15 20 25 30 112 168 224 112 168 224 112 0 PC AC UR CK Yield (T/ha) Nutrient sources and rates of applications Sugarsnax 54 2013 Rots Forks Cracks Stunts Marketable B A b a b ab b b a b 0 5 10 15 20 25 30 112 168 224 112 168 224 112 0 PC AC UR CK Yield (T/ha) Nutrient sources and rates of applications Sugarsnax 54 2012 Rots Forks Cracks Stunts Marketable 39 Multifactor analyses of nematode, soil and yield variables showed correlation patterns. In Cupar plots, calcium, cation exchange ca pacity and soil pH were negatively correlated while fungivores, bacterivores, c - p 1 bacterivores, c - p 2 bacterivores non - herbivores and total nematodes were positively correlated with Dimension 1 (Fig. 3.3A) . Porosity was negatively correlated while bulk d ensity and soil moisture content were positively correlated with Dimension 2 (Fig. 3.3A). Cation exchange capacity, calcium, magnesium and omnivores were positively correlated to each other while negatively correlated with c - p 2 herbivores, sum of c - p 3 to c - p 5 herbivores and total herbivores. Soil pH was negatively correlated with c - p 1 bacterivores, c - p 2 bacterivores, total bacterivores, non - herbivores, and total nematodes. As illustrated in Fig. 3.3B, calcium, cation exchange capacity, organic matter, SI, stunt carrots and soil pH were negatively correlated while fertility index, ammonium - nitrogen, bulk density, and cracked, rot ten , forked, unmarketable and total carrots were positively correlated with Dimension 1. CI was negatively correlated while EI was positively correlated with Dimension 2. Cation exchange capacity, calcium, organic matter, stunt ednes s, SI and soil pH were positively correlated to each other while negatively correlated with fertility index, and cracked, rot ten , forked, unmarketable and total carrots. CI was negatively correlated with EI and NO 3 - N . BI and fungivores - to - bacterivores ratios were negatively correlated with marketable carrots and magnesium, and NO 3 - N . 40 Figure 3 . 3 . Multiple factor analysis of the variables where Dimension 1 (Dim 1) and Dimension 2 (Dim 2) represent the first and second best summary of variability of the information, respectively. (A) T he relationships between abundanc e of nematode trophic groups (Gc) (bacterivores (BV), fungivores (FV), omnivores (OV), predators (PR), sum of omnivores and predators (OP), herbivores (HV) (Yeats et al., 1993)) and non - herbivore (FL) and total (TL) nematodes, and nematode guilds c - p 1 bac terivores (BV1), c - p 2 bacterivores (BV2), sum of c - p 3 and c - p 4 (BV34), c - p 2 herbivores (HV2) and sum of c - p 3 to c - p 5 herbivores (HV345) (Bongers, 1990; Bongers and Bongers, 1998) and soil properties (Gc2) (soil pH (pH) , organic matter percentage (O M), nitrate - nitrogen (NO 3 - N), ammonium - nitrogen (NH 4 - N),calcium (Ca), magnesium (Mg), phosphorus (P), potassium (K), moisture percent (MO), bulk density (BD), cation exchange capacity (CEC) and porosity (PO) . (B) T he relationship among soil food web indi ces and trophic group ratios (Gc1) ((FV/BV)=FV) and ((FV + BV)/HV=FBP) , soil physicochemical properties (Gc2) and carrot yield and quality (Gc3) (stunt (STU), forks (FO), rots (RO), cracks (CRA), marketable (MC), total unmarketable carrots (UNC) and root d ry - to - shoot dry weight ratio (RDSD)) from treatments with plant (PC) and animal (AC) compost, standard urea (UR) and non - amended check (CK) in Cupar plots in 2012 and 2013 growing seasons. 41 In Sugarsnax 54 (Fig. 3.4A), c - p 1 bacterivores, c - p 2 bacterivores, bacterivores, fungivores, c - p herbivores, herbivores, non - herbivores and total nematodes were positively correlated with Dimension 1. Calcium, magnesium, cation exchange capacity and soil pH were positively correlated with Dimension 2. Amo ng the soil variables, bulk density and NH 4 - N were positively correlated to each other but negatively correlated with porosity, organic matter, nitrate - nitrogen, c - p 2 bacterivores, and sum of c - p 3 to c - p 5 herbivores. As illustrated in Fig. 3.4B, fertili ty index, bulk density, ammonium - nitrogen, unmarketable carrots and soil moisture content were negatively correlated while marketable carrots, organic matter, and stunt and rot ten carrots were positively correlated with Dimension 1. Calcium, cation exchang e capacity and CI were positively correlated with Dimension 2. Soil moisture content, unmarketable carrots, bulk density, ammonium - nitrogen and fertility index were positively correlated to each other, but negatively correlated with rot ting , stunt ing and marketable carrots, and organic matter. Magnesium, BI and CI were positively correlated to each other but negatively correlated to EI, soil respiration and SI. Soil pH and cracked carrots were positively correlated to each other, but negatively correlated with forked carrots. 42 Figure 3 . 4 . Multiple factor analysis of the variables where Dimension 1 (Dim 1) and Dimension 2 (Dim 2) represent the first and second best summary of variability of the information, respectively. (A) T he relationships between abundance of nematode trophic groups (Gc1) (bacterivores (BV), fungivores (FV), omnivores (OV), predators (PR), sum of omnivores and predators (OP), herbivo res (HV) (Yeats et al., 1993)) and non - herbivore (FL) and total (TL) nematodes, and nematode guilds c - p 1 bacterivores (BV1), c - p 2 bacterivores (BV2), sum of c - p 3 and c - p 4 (BV34), c - p 2 herbivores (HV2) and sum of c - p 3 to c - p 5 herbivores (HV345) (Bon gers, 1990; Bongers and Bongers, 1998) and soil properties (Gc2) (soil pH (pH) , organic matter percentage (OM), nitrate - nitrogen (NO 3 - N), ammonium - nitrogen (NH 4 - N),calcium (Ca), magnesium (Mg), phosphorus (P), potassium (K), moisture percent (MO), bulk de nsity (BD), cation exchange capacity (CEC) and porosity (PO) . (B) T he relationship among soil food web indices and trophic group ratios (Gc1) ((FV/BV)=FV) and ((FV + BV)/HV=FBP) , soil physicochemical properties (Gc2) and carrot yield and quality (Gc3) (stun t (STU), forks (FO), rots (RO), cracks (CRA), marketable (MC), total unmarketable carrots (UNC) and root dry - to - shoot dry weight ratio (RDSD)) from treatments with plant (PC) and animal (AC) compost, standard urea (UR) and non - amended check (CK) in Sugarsn ax 54 plots in 2012 and 2014 growing seasons. 43 Discussion The outcomes of this study were partially in line with the hypothesis that compost amendment treatments increased omnivores compared with urea and non - amended check at the end of the growing seasons. As expected , higher compost rates significantly increased omnivores compared with lower rates of PC and AC at 133 DAP in 2013. However, compost type had no effect on omnivores. The more structured soil food web condition compared with 50 % in comp ost amendments show s the positive effect of compost (Fig. 3.1). Supporting the hypothesis, AC amendment treatments increased soil chemical proprieties as AC contained greater concentration of nutrients such as phosphorus and soil respiration . PC at 168 kg N/ha and AC at 112 kg N/ha produced yield as high as the urea in 2012 , but most of compost treatments decreased marketable carrot yield. In contrast to this, Sugarsnax 54 marketable carrot yield was higher in all compost amendment treatments than in urea a nd non - amended check in 2013. Number of omnivores was significantly different at the end of the growing seasons among the treatments in both cultivars. Their increase in abundance showed that reduced soil disturbance level (Bongers, 1990; Bongers and Bonge rs, 1998). This is consistent with other studies (Nahar et al., 2006; Lie et al., 2010), where compost amendment increased omnivores over time. Similar trend was observed in both cultivars, but the trends in Sugarsnax 54 were not as strong as those in Cupa r. This could be due to the short growing season (79 DAP) as omnivores nematodes normally require 95 to 130 days to complete a life cycle (McSorley, 2012). Throughout this study, omnivores nematodes were low in urea plots perhaps due to the toxic effect o f nitrogenous compounds (e.g. NH 3 ) that urea is known to release (N a har et al., 2006; Ferris, 2010; Ferris et al., 2012). Increase in omnivores can be explained by either compost 44 favoring omnivores or lack of toxicity associated with mineral fertilizer app lication (Fiscus and Neher, 2002; Ferris et al., 2012). There was no significant difference in bacterivores, fungivores, predators and herbivores trophic groups, and non - herbivores and total nematode abundance through time in both cultivars. However, signi ficant treatment effects were observed on bacterivores, fungivores, non - herbivores and total nematodes in Cupar, but with no clear difference among compost amendments and the controls. Exceptions were that AC at 270 kg N/ha showed significant increase in b acterivores compared with non - amended check, and PC at 203 kg N/ha and AC at 270 kg N/ha significantly increased non - herbivores nematodes compared with urea and non - amended check. Consistent with the present results, Ferris et al. (2012) reported that comp ost amendment alone did not increase c - p 1 and c - p 2 nematodes. In contrast, addition of compost with low C:N ratio (< 20:1) at least temporarily increased bacterivores (Bulluck III et al., 2002a; Ferris and Matute, 2003; Briar et al., 2011). Lack of signi ficant increase in bacterivores and fungivores following compost addition in this study could have been due to inadequate sampling intervals to detect possible short term peaks in nematode abundance with short generation time. Bacterivore generation time is usually around ten days (Sánchez - Moreno et al., 2011). Another possibility could be that soil factors such as soil pH suppressed bacterivores and fungivores directly or indirectly suppressing their microbial food base. The negative correlation between s ome of the soil physicochemical properties and nematode trophic groups supported the later explanation (Fig. 3.3 A ). The increase in non - herbivore nematodes in PC at 168 and AC 270 kg N/ha can be explained by the relatively higher number of bacterivores and fungivores in those treatments. Low abundance of bacterivores and fungivores may reflect diminished potential of nutrient mineralization (Ferris et al., 2001; Ferris et al., 2004). 45 In this study, there was no significant effect of treatments on HV. Organi c amendments may release chemicals detrimental to herbivores (Akhatar and Malik, 2000; Zasada et al., 2008 ; ). Similarly, Melakeberhan et al. (2007) and Mennan and Melakeberhan, (2010) found that application of recycled municipal biosolid had suppressive effect on Meloidogyne hapla . Differential effect of compost that favored the abundance of c - p 2 herbivores , especially Tylenchus and Filenchus , while suppressing c - p 3 plant - parasitic nematode Pratylenchus spp . was report ed previously (Briar et al., 2011). Other field and glasshouse experiments have also revealed that the effect of compost is dependent on the species of herbivores, amendment type and/or other environmental factors (McSorley & Gallaher, 19 97; Kimpinski et a l., 2003; Ren o et al., 2011). To my knowledge, there are only a few studies available to explain the impact of soil mineral contents ( e.g. calcium, magnesium, potassium) on herbivores. Soil calcium and magnesium content had negative correlation with soybe an cyst nematode (Avendaño et al., 2004) and the impact of mineral fertilizer applications on herbivore nematode suppression highlighted elsewhere (Coyne et al., 2004). Hence, multiple factor analysis result suggests that the inconsistent effects of both c ompost and inorganic fertilizer applications on nematode trophic groups could be due to variations in soil conditions in previous studies. SI was greater than 50 % in compost amended plots compared with urea at the end the growing seasons in 2013 and in 2 014 . There was no significant differential effect of compost types and rates of applications on SI in this study. All of the treatments increased SI over time. Similarly, there was also no significant effect of compost amendments, compost types and rate of applications on EI, BI and CI. 46 Soil nematode faunal profile showed that compost amendments improved soil food web structure over time and led to a balanced bacterial - fungal decomposition channel ( Q uadrant B) at the end of 2013 - 2014 growing seasons (Fig.3 .1). However, the same trend was observed for the urea and untreated controls. The significant increase of SI from 50 % in compost amendments in t he nematode faunal profile of the present study suggests that compost amendments improve d soil food web structure with greater trophic links. A high degree of connectivity reflects a result of ant functional redundancy in the regulatory process and functional resilience to perturbation (Ferris et al., 2012). The results of the present study s howed that the higher rates of AC (AC at 168 and 224 kg N/ha) increased soil respiration compared with all of the other treatments at 79 DAP in 2013 growing season and at 0 and 78 DAP in 2012, and 0 DAP in 2013 in Sugarsnax 54 (Table 3.7) . This suggests in creased soil biological activity. In related studies, organic soil amendment increased rate of soil respiration compared with non - amended controls (Gunapala et al., 1998; Treonis et al., 2010). However, increased soil respiration was observed in treatment s containing compost blended with wheat straw, but not from treatments with inorganic fertilizer and compost alone (Ferris and Matute, 2003). Improved soil respiration observed here might be attributed to increased labile organic matter associated to AC (T able 3.1). Higher phosphorus and potassium in AC than in PC , urea and non - amended check treatments is likely to be due high contents of these elements in t he AC source (Table 3.1) . Contrary to expectation, compost rate had no detectable impact on soil moi sture content and bulk density (Nahar et al., 2006) . Compost amendments increased soil pH compared with urea in 2013 growing season. Similarly, all AC treatments and PC at 168 kg N/ha increased organic matter compared with urea and non - amended check after two years in Sugarsnax 54 plots while 47 urea increased NO 3 - N compared with all compost amendments and non - amended check in both cultivars (Tables 3.8 and 3.9). Other studies have shown that addition of compost increased soil organic matter and soil nut rients compared with synthetic fertilizers (Bulluck III et al., 2002b; Briar et al., 2007). In contrast, Nahar et al. (2006) reported that compost amendment did not increase organic matter compared with non - amended check after two years. Continuous annual applications of compost are required to cause significant improvement in soil properties (Shiralipour et al., 1992). Thus, it is not surprising that these changes were not observed in all compost treatments in my study . Urea increased end - of - season soil N O 3 - N and reduced soil pH compared with compost amendments and non - amended check in both cultivars. Consistent with these finding s , Briar et al. (2007) found higher soil NO 3 - N in conventional system receiving chemical fertilizers. Urea hydrolysis and subseq uent nitrification result in release of hydrogen ion (H + ) may lead to decline in soil pH in urea plots. Previ o us s tudies have shown that urea decr eased while compost amendment increased soil pH (Bulluck III et al., 2002b; Li et al., 2010). Compost addition s raised the pH of acid soils by forming aluminum complex and increasing base saturation (Shiralipour et al., 1992; Van den Berghe and Hue, 1999). Decline in soil pH induced by synthetic fertilizer application is known to reduce soil biodiversity and promo te some pathogens, reduce yield and affect overall soil health (Singh et al., 2013). Although urea decreased soil pH compared with the compost treatments, which supports the established adverse effects of urea on soil environments , the soil pH in my experimental field was above optimum for carrots (Swiader and Ware, 2002). The expectation was that compost treat ments would have greater quality of carrots compared with urea and non - amended check treatments because of the positive effect of compost 48 amend ments on nutrient availability , physical properties, and pest suppression (Abawi and Widmer, 2000; Akhtar and Malik, 2000). In the present study , there was no difference in total yield and carrot quality among compost amendments, urea and non - amended check in Cupar in all years (Fig. 3.2). However, all compost treatments other than PC at 168 kg N/ha and AC at 112 kg N/ha had lower marketable yield compared with the urea control in 2012 growing season in Sugarsnax 54. In contrast to this, urea and non - amende d check was significantly low in marketable and total carrots in 2013. Lower yield in 2012 in some compost treatments may have been due to lower available N relative to the urea control (Table 3.8) . H owever , more frequent soil N sampling would have been re quired to test this hypothesis. In contrast, higher yields in compost amended plots compared to urea controls in 2013 were unlikely due to higher levels of N, and more likely due to either changes in other chemical characteristics (higher pH or higher K), improvements in (undetected) soil physical properties, or reductions in pest abundance. With respect to herbivore nematodes, their abundance was low ( less than 20 individuals / 100 cc of soil , Table 3.4) and there was no significant difference in their ab undance among compost treatments and urea . Apart from their low abundance, the herbivore nematodes population was dominated by root hair feeders that can cause less carrot damage. Hence, the difference observed in carrot yield is unlikely due to herbivore nematodes . Although short - term yield increases associated with chemical content of nutrients can be dramatic when compared to unfertilized controls, d etection of yield increases due to physical properties in fields amended with compost usually requires th ree to five years of continuous application (Parr et al., 1992; ). Compost treatments increased total carrot yield and decreased unmarketable carrots (e.g. fork ing , stunt ing ) and some of the weed species compared to non - composted fields 49 in Michigan, USA (Brainard and Noyes, 2012). Besides, compost's positive impact on yield, lower negative environmental impact and better soil biological health and activity (Bulluck III et al. , 2002b, Briar et al., 2007; Briar et al., 2011) may enhance the importance of compost amendment as a soil health management practice in agroecosystems. Results from m ultiple factor analysis revealed some key correlation s between soil food web indices and carrot yield and quality. SI was positively correlated with soil pH, organic matter, calcium, cation exchange capacity while negatively correlated with almost all of the unmarketable carrot parameter s ( e.g., rot ting , fork ing and crack ing ), bulk density and fertility index in Cupar plots (Fig. 3.3B). High soil organic matter improves microbial activity, increase nutrient reserves and soil aggregates and water holding capacity (Pimentel et al., 2005; Forge and Kempler, 2009) . This lead s to improved carrot yie ld and quality. Similarly, cation exchange capacity improves nutrient retention capacity of soil , enabling a more steady release of nutrients which improve plant growth. Knight et al. (2013) reported that soil parameters such as clay and soil organic matte r as soil heath indicators and lettuce productivity though SI was not correlated with these parameters. In Sugarsnax 54, SI was positively correlated with soil respiration (indicator of soil biological activity level) and EI (a measure of nutrient avail ability), and negatively correlated with BI (indicators of stressed soil condition) and CI (slow decomposition pathway). SI increase is linked to improved soil biological activities and nutrient availability while SI decrease is linked to stressed soil con ditions and slow mineralization process (Fig. 3. 4B ; Ferris et al. 2001; Ferris and Matute, 2003). EI was negatively correlated with CI in Cupar plots, and positively correlated with SI, soil respiration, but negatively correlated with BI and CI in Sugarsna x 54. Berkelmans et al. (2003) suggested that SI and BI may be more suitable as general indicators for 50 the soil health status . H igh BI would indicate poor ecosystem health while a high SI would indicate a well - regulated, healthy ecosystem. In a related stu dy, EI was proposed to be used as an indicator of soil heath and plant productivity because of its predictive value of high nutrient availability to plants (Knight et al., 2013). In conclusion, this research provided an opportunity to compare the effect of compost amendments on nematode community structure, soil food web, soil physicochemical and biological properties, and carrot yield and quality. The analys e s indicated that compost amendments increased soil food web structure compared with 50 % over tim e . Moreover, higher rate of AC improve soil biological activities. Compost treatment generally increased soil mineral contents and soil pH which could have positive impact on soil fertility. In the contrary, urea decreased soil pH and increase NO 3 - N . Multi ple factor result revealed the importance of soil food web indices in describing soil health status and carrot yield and quality, suggesting SI, EI, BI and CI in combination can be used to describe the soil health conditions under different management prac tices. Overall, the results partially support the tested hypothesis and suggest that the compost based improvements in soil food web structure may lead to increases in ecosystem services provided by the soil food web. 51 CHAPTER 4 EFFECTS OF INTEGRATE D APPLICA TION OF PLANT - BASED COMPOST AND UREA ON SOIL FOOD WE B, SOIL PROPERTIES, AND YIELD AND QUALIT Y OF A PROCESSING CARROT CULTIVAR Abstract - - soil samples - - - - - Malenchus and Helicotylencus abundance were negatively correlated with carrot fresh weight of most categories such as fork ing and crack ing . Overall, results suggest that integrating lower rates of urea and higher rates of PC are likely to increase soil biological activity, pH and pho sphorus content. 52 Introduction - - 53 - Bongers and Bongers, 1998; Ferris et al., 2001 Nematodes are also considered as a powerful indictor of soil ecosystem change (Freckman and Ettema, 1993; Wasilewska, 1994; Ferris and Matute, 2003; Ferris et al., 2004; Cheng and Grewal, 2009; Knight et al., 2013). Ferris et al. (2001) developed a faunal profile analysis that relates soil nematode community to soil food web structure and function. This model uses a graphic representation of the relationship between the nematode EI (a measure of opportunistic bacterivore and fungivore nematodes) and SI (indicator of food web state affected b y stress or disturbanc e ) to describe the soil community profile in four quadrants. While there are several studies on the impact of organic amendments and inorganic fertilizer effects on nematode community, soil fertility and plant productivity (Bulluck I II et al., 2002a; Briar et al., 2007), the impact of mixed compost - fertilizer application s on soil nematodes community structure and overall soil food web health has been less studied. The objectives of this study were to compare the effects of mixed appl ication of different levels of PC and urea on nematode community structure soil food web health, soil biological and physicochemical 54 properties, and yield and quality of a processing carrot cultivar Cupar in a sandy loam soil. The central hypothesis of thi s study was that Materials and Methods Experimental design and treatments A field experiment was conducted at Michigan State University (MSU) Horticulture Teaching and Research Center in Holt, Michigan (N 42 0 0 elevated) in a Marlette fine sandy loam (fine - loamy, mixed, mesic Glossoboric Hapludalfs, Anon, 1977) during 2012 - 2014 growing seasons. Carrots were grown in the f ield and amended with composted manure in 2010 and 2011 growing seasons. The study was designed to test the effects of mixed application s of different ratios of u - PC was obtained from MSU Student Organic Farm, Holt, MI, USA. PC levels were applied on dry matter basis and reported as average of the 2012 - 2014 growing seasons (Table 4.2). Standard urea (135 kg N/ha) and non - amended check were included as controls. randomized complete block design with four replications. 55 Table 4 . 1 . Integrated application of urea and plant compost (PC) at varying ratios to supply the recommended nitrogen (N) for proc essing carrot cultivars. Treatments are different combinations of N levels coming from urea and PC to provide the recommended nitrogen amount. Treatment Ratio a Amount of N (kg/ha) Actual rate (Mg/ha) Urea PC Urea PC 1 1:0 135 0 0.29 0 2 3:1 101 34 0.22 3 3 1:1 67.5 67.5 0.15 6 4 1:3 34 101 0.07 9 5 0:1 0 135 0 12 6 C heck 0 0 0 0 a The portion of N source applied as urea and PC ratio to provide a total of 135 kg N/ha. Methods pertaining to soil sampling, nematode extraction, identification and nematode community, ecosystem disturbance and soil food web indices, were described in the General Materials and Methods S ection (Chapter 2). Similarly, methods used to measure so il respiration, soil physicochemical properties, and carrot yield and quality were stated in Chapter 2. Data analysis Nematode taxa and trophic group abundances were expressed on an absolute basis (number of nematodes in a taxon i per 100 cc of fresh soil ). Nematode abundance data were transformed as ln (x+1) prior to statistical analysis to normalize variance, but untransformed arithmetic means are presented here in . Treatments were compared for nematode trophic groups, community indices, soil food web i ndices, trophic group ratios, fertility index, soil and yield variables. Statistical analysis was conducted using the PROC MIXED procedure of SAS. The statistical model consisted of fixed effects of amendments and time and the interaction between them and random effects of blocks and block by amendment interaction. The interaction between blocks and amendments was used as an error term to test the effect of amendments. The effect of time was addressed using the repeated measures approach with REPEATED state ment of the 56 PROC MIXED. Aikaike information criterion was used to select the optimal variance - covariance structure for the repeated measures analysis. Two types of statistical analysis were conducted for SI. First, the SI values were compared following a s tandard ANOVA and mean separations (Table 4.6). Second, SI values were plotted to the food web model (Fig. 4.1). Then, SI values were tested for statistical difference from 50 % ( cut off point of the soil food web structure ) using one - tail t - 0. 05. The means of the treatments with statistical difference from 50 % are noted by asterisks (*). Table 4 . 2 . Average soil pH, macro (%) and micro nutrients (ppm) of plant compost (PC) and rates at which they w ere applied (kg/ha) in sandy loam soil and planted with a processing carrot - 2014 growing seasons. pH and nutrients Content Rate (kg/ha) pH 7.8 na a Macronutrients (%) Nitrogen 1.1 135 Phosphorus 0.1 12 Potassium 0.3 36 Calcium 3.8 457 Magnesium 0.8 96 Sodium 0.02 2 Sulfur 0.2 24 OM b 25.2 3005 Carbon 14.6 1755 C : N c 13.3 na Micronutrients (ppm) Iron 5248.1 60 Zinc 77.6 1 Manganese 324.2 4 Copper 28.8 0.4 Boron 27.3 0.4 Aluminum 2663.2 36 a Rates was not available because pH and C/N ratio cannot be expressed as a rate of application. b Percent of organic matter. c Carbon - to - nitrogen ratio. 57 Treatments were compared for yield parameters using one - way analysis of variance (PROC MIXED, SAS ver 9.3, SAS Institute, 2012, Cary, NC , USA ). The statistical model consisted of fixed effect of amendments and a random effect of block and block by amendmen t. The interaction between blocks and amendments was used as an error term to test the effect of amendments. First, the data was analyzed by the interaction of treatment and sampling time. When the effect of the interaction was not significant, the data we re analyzed by the interaction of treatment and year, and presented. Interactive effects of amendment and time are presented in results only when significant . Otherwise, I have presented only significant interaction effect s of treatment and year and main e ffects of treatment. The probability level P < 0.05 was regarded as significant. Results Composition and abundance of nematode trophic groups A total of 51 nematode genera were identified in the plots throughout the study period (Table 4.3). The number of genera identified as herbivores, bacterivores, fungivores, omnivores and predators were 17, 16, 6, 7 and 5, respectively. On average, 23, 27, 21, 1.4 and 0.4 per 100 cc of soil individuals of herbivore, bacterivore, fungivore, omnivore and predator trophic groups, respectively, were obtained in the three - year period. Among herbivore nematodes, Malenchus, Pratylenchus, Helicotylenchus and Tylenchus were the most abundant genera and represent ed 11, 11, 24 and 36 %, respectively. Mesorhabditis, Microlaimus, Acrobeloides and Rhabditis represented 10, 10, 21 and 22 % of the bacterivores, respectively. Filenchus and Aphelenchus represented 33 and 46 % of fungivores, respectively. The abundances of o mnivores and predators were generally low representing less than 3 % of the total nematode community. 58 Table 4 . 3 . List of nematode genera detected in plots amended with integrated application of urea and PC at different levels to supply 135 kg N/ha recommended for processing carrot varieties, standard urea, and non - amended check plots in sandy loam soil in 2012 - 2014 growing seasons. Numbers within brackets represent c - p values following Bongers and Bonger s (1998). Herbivores Bacterivores Fungivores Omnivores Predators Basiria (2) Eumonhystera (1) Aphelenchoides (2) Eudorylaimus (4) Tripyla (3) Boleodorus (2) Mesorhabditis (1) Aphelenchus (2) Mesodorylaimus (4) Clarkus (4) Cephalenchus (2) Panagrellus (1) Ditylenchus (2) Microdorylaimus (4) Mylonchulus (4) Malenchus (2) Panagrolaimus (1) Filenchus (2) Pungentus (4) Prionchulus (4) Paratylenchus (2) Pellioditis (1) Diphtherophora (3) Thonus (4) Nygolaimus (5) Psilenchus (2) Pristionchus (1) Tylencholaimellus (4) Aporcelaimellus (5) Tylenchus (2) Rhabditis (1) Prodorylaimus (5) Dolichorynchus (3) Acrobeloides (2) Helicotylenchus (3) Cephalobus (2) Hemicycliophora (3) Cervidellus (2) Heterodera (J2) (3) Eucephalobus (2) Pratylenchus (3) Heterocephalobus (2) Rotylenchus (3) Plectus (2) Tylenchorhynchus (3) Microlaimus (3) Trichodorus(4) Prismatolaimus (3) Longidorus (5) Alaimus (4) Xiphinema (5) 59 Nematode trophic group abundance was not affected by the interaction of treatment and time, and treatment, but significantly affected by time (Table 4.4). However, herbivores, bacterivores and predators were significantly affected by interaction effect of treatment and year (Table 4.5). All of the treatments, except urea and PC at 1:3 ratio, significantly increased herbivores in 2014 compared with 2012. However, it should be noted that the lack of increase in herbivores in urea and PC at 1:3 treatment was associated with higher initial abundance of herbivore nematode s in that treatment, rather than lower final herbivore abundance . All of the treatments, except urea alone application, significantly decreased bacterivores in 2014 compared with 2012. Urea sign ificantly increased predator nematode s compared with the rest of the treatments in 2012 while PC alone significantly increased them compared with the rest of the treatments in 2013. Urea alone, and urea and PC at 3:1 ratio significantly increased predators compared with urea and PC at 1:1 ratio and non - amended check treatments in 2014. All of the treatments, except urea, significantly decreased non - herbivores nematodes in 2013 than 2012. Only urea and PC at 1:1 ratio significantly decreased non - herbivores i n 2014 than in 2012. However, there was no significant difference in abundance of non - herbivores among the treatments between 2013 and 2014. Urea and PC at 1:3 ratio significantly decreased total nematode abundance in 2013 compared with 2012. 60 Table 4 . 4 . Probability values (Pr > F) of treatment (TR), time (T), and interaction of treatment and time (TR*T) effects for nematode trophic group abundances, non - herbivore and total nematodes, nematode community and soil food web indices, trophic group ratios, soil respiration and soil ph ysicochemical properties for field plots amended with integrated application of urea and PC at different levels to supply 135 kg N/ha and standard urea application and non - amended check in sandy loam soil in 2012 - 2014. Variables Probability >F TR T TR*T Trophic groups Herbivores 0.95 <0.0001 0.60 Bacterivores 0.95 <0.0001 0.67 Fungivores 0.93 <0.0001 0.77 Omnivores 0.86 <0.0001 0.35 Predators 0.48 <0.0001 0.82 Non - herbivores 0.98 <0.0001 0.62 Total nematodes 0.97 <0.0001 0.89 Diversity indices H' a 0.99 <0.0001 0.2 Hill's N1 0.97 <0.0001 0.29 Hill's N0 0.99 <0.0001 0.44 Ecological disturbance indices PPI 0.91 <0.0001 0.43 MI 0.67 <0.0001 0.48 MI25 0.13 <0.0001 0.64 FI b 0.91 <0.0001 0.15 Food web indices FI 0.63 0.0012 0.49 SI 0.041 <0.0001 0.48 BI 0.623 <0.0001 0.61 CI 0.94 <0.0001 0.48 Trophic group ratios FV/BV c 0.86 <0.0001 0.64 (FV+BV)/HV d 0.85 <0.0001 0.03 Soil respiration 0.02 <0.0001 0.53 61 Variables Probability >F TR T TR*T Soil physicochemical properties Bulk density 0.45 <0.0001 0.98 Porosity 0.26 <0.0001 0.98 Moisture 0.28 <0.0001 0.73 Soil pH 0.18 <0.0001 0.01 Phosphorus 0.02 0.005 0.74 Potassium 0.69 <0.0001 0.42 Calcium 0.48 <0.0001 0.03 Magnesium 0.74 <0.0001 0.55 Organic matter 0.23 <0.0001 0.54 Nitrate - nitrogen 0.02 <0.0001 <0.0001 Ammonium - nitrogen 0.43 <0.0001 0.99 Cation exchange capacity 0.62 <0.0001 0.55 a Shannon - Weaver diversity index (Shannon and Weaver, 1949). b Fertility index (PPI/MI) (Bongers et al., 1997). c Fungivores - to - bacterivores ratio (Freckman and Ettema, 1993). d Decomposers - to - herbivores ratio (Wasilewska, 1994). Table 4 . 5 . Interaction effects of different levels of urea and PC combined to supply 135 kg N/ha, standard urea and growing seasons (2012, 2013 and 2014) on the abundance of nematode trophic groups (herbivores, bacterivores, fungivores, omnivores and predators) per 100 cc soils. Treatments show the proportion of nitrogen coming from urea and PC to supply 135 kg N/ha recommended for Cupar. TR a Herbivores Bacterivores Fungivores 2012 2013 2014 2012 2013 2014 2012 2013 2014 1:0 11 aB b 15 aB 43 aA 41 aA 17 aB 21 aAB 31 aA 13 aA 16 aA 3:1 10 aB 15 aB 32 aA 45 aA 12 aB 19 aB 37 aA 14 aA 13 aA 1:1 17 aB 24 aAB 32 aA 47 aA 14 aB 17 aB 36 aA 15 aA 16 aA 1:3 18 aA 15 aA 32 aA 45 aA 17 aB 29 aB 40 aA 13 aB 14 aAB 0:1 13 aB 17 aAB 42 aA 41 aA 16 aB 19 aB 36 aA 14 aA 16 aA Check 9 aB 22 aB 39 aA 49 aA 17 aB 17 aB 32 aA 12 aA 15 aA 62 Table 4.5 (Con t ) TR a Omnivores Predators 2012 2013 2014 2012 2013 2014 1:0 1 aA 1 aA 1 aA 1 aA 0 bB 1 aA 3:1 1 aA 1 aA 1 aA 0 bB 0.1 bB 1 aA 1:1 1 aA 1 aA 2 aA 0.1 bA 0.3 bA 0.5 bA 1:3 1 aA 1 aA 2 aA 0.2 bB 0.3 bB 0.8 abA 0:1 2 aA 1 aA 2 aA 0.3 bB 0.6 aA 0.9 abA Check 1 aA 1 aA 3 aA 0.2 bA 0.5 bA 0.6 bA a Treatments that showed the portion of N source applied as urea and PC ratio to provide a total of 135 kg N/ha. b Means with different lower case letters within columns and different upper case letters across rows within trophic groups indicate the significant differe nce at P < 0.05 using . Nematode community indices were not affected by the interaction of treatment and time or by treatment effect, but they were treatment and year. MI was significantly higher in non - amended check, and urea and PC at 1:1 ratio in 2014 compared with 2012. However, all of the treatments si gnificantly increased MI25 in 2014 compared with 2012. There was no significant difference in PPI and fertility index among 2012, but no significant difference was abserved indices. Soil food web condition, trophic ratios and fertility index Soil food web indices (BI, EI, SI and CI) and fertility index were not affected by the interaction of treatment and time, but sum of fungivores and bacterivores - to - herbivores ratio were affected. All of the soil food web indices except SI, the trophic group ratios and fertility 63 index were not affected by treatment . However , all the soil food web indices, trophic ratios and fertility in dex were affected by time (Table 4.4). All of the treatments significantly decreased fungivores + bacterivores - to - herbivores ratio over time. Overall, urea, urea and PC at 3:1 ratio, and PC significantly increased SI compared with urea and PC 1:1 and 1:3 r atios, and non - amendd check . Urea and PC at 1:3 ratio significantly decreased SI compared with all of the treatments (Table 4.6). EI and SI were significantly affected by the interaction of treatment and year, but such effect was not observed in BI and CI. Urea and PC at 1:3 ratio significantly increased EI in 2014 compared with 2012 and 2013 . Urea and PC at 1:3 ratio also significantly increased EI compared with non - amended check in 2014. All of the treatments significantly increased SI in 2014 compared wi th 2012. Table 4 . 6 . Means across all sampling time points of the enrichment index (EI), structure index (SI), basal index (BI) and channel index (CI) at the studied treatments across 2012, 2013 and 2014 growin g seasons. Treatments a EI SI BI CI 1:0 70 a b 41 a 24 a 28 a 3:1 70 a 39 a 24 a 30 a 1:1 67 a 37 b 27 a 34 a 1:3 68 a 31 c 27 a 30 a 0:1 66 a 41 a 27 a 37 a Check 68 a 37 b 25 a 28 a a Treatments that showed the portion of N source applied as urea and PC ratio to provide a total of 135 kg N/ha. b Means within columns followed by same letter(s) are not significantly different at P < 0.05 . The results of soil food web analysis from samples collected at planting and at harvest are presented in (Fig. 4.1). Except urea in 2013, all of the treatments resulted in data falling in Quadrant A (poorly structured soil food webs) at planting in all years. Similarly, all of the treatments resulted in data falling in Quadrant A at harvest in 2013. At harvest in 2013, urea and 64 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3* 4 5* 6 0 50 100 0 50 100 Enrichment Index (%) Structure index (%) May-12 Oct-12 May-13 Oct-13 14-Jun 14-Oct A B D C PC resulted in data falling in Quadrant B, enriched and maturing food web. All of the treatments had maturing and enriched food webs at harvest in 2014, but only PC al one , and urea and PC at 1:1 ratio showed greater than 50 % food web structure (Fig. 4.1) . Figure 4 . 1 . Soil food web condition in plots amended with integrated application of urea and PC, standard urea and n on - amended check in sandy loam soil at planting (May, June) and harvest (October) in 2012 - 2014 growing seasons. Numbers 1 - 6 represent treatments: 1= Urea alone, 2= 3:1 ratio of urea and PC, 3= 1:1 ratio of urea and PC, 4= 1:3 ratio of urea and PC, 5= PC a lone and 6= non - amended check. *Treatments significantly increased SI from 50 % using one - tail t - test at 0.05 for 2014 growing season. Physicochemical properties and soil respiration Soil pH, calcium and NO 3 - N were significantly affected by the interaction of treatment and time while soil respiration and other soil physicochemical properties were not affected 65 (Tables 4.4 and 4.7). Soil respiration and NO 3 - N was significantly affected by treatment while soil respiration and all of the soil physicochemical properties were affected by time. Table 4 . 7 . Soil pH, nitrate - nitrogen (NO 3 - N) and calcium (Ca) contents (ppm) in plots amended with integrated applicatio n of urea and PC to supply 135 kg N/ha recommended for Cupar , standard urea application and non - amended check in sandy loam soil at planting ( 0 ) and at 132 and 133 days after planting (DAP) in 2012 - 2013 growing seasons. Var iable s YR DAP Treatments as a ra tio of urea and PC 1:0 a 3:1 1:1 1:3 0:1 C heck pH 2012 0 6.8 bB b 6.8 bB 7.2 bA 7.0 bAB 7.2 bA 7.2 cA 132 6.4 cB 6.8 bAB 7.4 abA 7.2 bA 7.3 bA 7.3 abcA 2013 0 6.9 bA 7 .0 abA 7.4 abA 7.2 bA 7.3 bA 7.4 bA 132 6.7 bB 7.1 aAB 7.5 aA 7.4 aA 7.6 aA 7.5 abA NO 3 - N 2012 0 1.4 dAB 0.6 cB 0. 8 cAB 0.5 cB 0.7 cB 1.5 cA 132 29.2 aA 2.9 bB 3.0 bB 3.7 abB 4.6 bB 3.0 bB 2013 0 5.3 cA 5.4 aA 6.0 aA 5.4 aA 6.5 aA 7.2 aA 132 17.5 bA 2. 6 bB 3.4 bB 4. 6 aB 3.8 bB 2.7b B Ca 2012 0 1159.7 b 1120. 7 b 1263.3 ab 1139. 3 b 1192.7 b 1295. 7 b 132 1057.3 b 1126. 7 b 1287. 7 ab 1193.7 b 1307.3 ab 1303.7 b 2013 0 1111.3 b 1108. 7 b 1246. 7 b 1152.3 b 1345.3 ab 1406.3 a 132 1243.3 a 1242. 3 a 1471.3 a 1388.3a 1423.0 a 1450.3 a a Treatments expressed as urea - to - PC ratio. b Means with different lower case letters within columns and different upper case letters across rows indicate the significant difference at P < 0.05 . Urea significantly decreased soil pH at harvest in 2012 compared with at planting in 2012, but such effect was not observed between samples collected at planting and at harvest in 2013. Soil pH was the lowest at harvest in 2012 compared with the rest of th e sampling dates in urea treated plots. All of the integrated applications did not significantly increase soil pH at harvest compared with that at planting in 2012. However, urea and PC at 1:3 ratio, and PC significantly increased soil pH at harvest in 201 3 compared with at planting and harvest in 2012, and at planting in 2013 . Soil pH in urea, and urea and PC at 3:1 ratio treatments was significantly lower compared with all of the other treatments including non - amended check at planting in 2012. However, o nly urea significantly decreased soil pH at harvest compared with all of the 66 treatments in 2012. There was no significant difference in soil pH among the treatments at planting in 2013, except urea significantly decreased soil pH at harvest compared with a ll of the other treatments (Table 4.7). All of the treatments significantly increased soil NO 3 - N content at harvest compared with at planting in 2012 (Table 4.7). In 2013, urea significantly increased NO 3 - N at harvest compared with at planting . T he integr ated treatments , except urea and PC at 1:3 ratio, and non - amended check , significantly decreased NO 3 - N at harvest than that at planting in 2013 . Non - amended check had significantly higher NO 3 - N compared with all of the treatments except urea at planting in 2012. Urea significantly increased soil NO 3 - N content compared with all of the treatments at harvests in 2012 and 2013. Figure 4 . 2 . Means across all sampling time points of soil phosphorus content at the studied treatments across 2012, 2013 and 2014 growing seasons. Bars with different letters are statistically significant at P < 0.05 . There was no treatment effect on soil calcium content at harvest in 2012. All treatments , except PC a nd non - amended check, significantly increased soil calcium content at harvest in 2013 compared with at planting in 2013. Urea, and urea and PC at 3:1 ratio significantly b b ab a a a 0 5 10 15 20 25 1:0 3:1 1:1 1:3 0:1 Check Phosphorus (ppm) Treatments 67 increased soil calcium content at harvest in 2013 compared with at planting and at har vest in 2012, and at planting in 2013. There was no significant difference in soil calcium content among the treatments in all of the sampling dates. Urea, urea and PC at 3:1 ratio significantly decreased soil phosphorus content compared with all of the tr eatments (Fig. 4.2) . PC, urea and PC at 1:3, and 1:1 ratios significantly increased soil respiration compared with the rest of the treatments (Fig. 4.3). Figure 4 . 3 . Means across all sampling time points of soil respiration at the studied treatments across 2012, 2013 and 2014 growing seasons. Bars with different letters are statistically significant at P < 0.05 . Carrot yield and quality Carrot quan tity and quality were not affected by the treatment s in any year d ue to high variability in carrot yield, making it difficult to come to any conclusion about effects on carrot yield . b b a a a b 0 1 2 3 4 5 6 7 1:0 3:1 1:1 1:3 0:1 Check µg CO 2 - C g - 1 day - 1 Treatments 68 Figure 4 . 4 . Effect of treatments on mean carrot yield by category (marketable, stunts, cracks, forks and rots) in 2012, 2013 and 2014. There was no significant difference in quality category at P < 0.05 . 0 20 40 60 80 100 120 1:0 3:1 1:1 1:3 0:1 Check Yield (T/ha) Treatments 2012 Rots Forks Cracks Stunts Marketable 0 10 20 30 40 50 60 70 80 1:0 3:1 1:1 1:3 0:1 Check Yield (T/ha) Treatments 2013 Rots Forks Cracks Stunts Marketable 0 10 20 30 40 50 60 1:0 3:1 1:1 1:3 0:1 Check Yield (T/ha) Treatments 2014 Rots Forks Cracks Stunts Marketable 69 Relationships among nematode trophic , soil, and yield variables Multiple factor analyses of nematodes, soil and yield variables showed correlation patterns. C - p 1 bacterivores and total bacterivores were negatively correlated with Dimension1 while total herbivores, c - p 2 herbivores and sum of c - p 3 to c - p 5 herbivores and soil moisture content were positively correlated with Dimension 2 (Fig. 4.5A). Cation exchange capacity, calcium, magnesium and porosity were positively correlated to each other while negatively correlated with soil moisture content an d bulk density. Potassium was negatively correlated with soil pH and sum of c - p 3 to c - p 5 herbivores. C - p 2 bacterivores, total bacterivores, fungivores, non - herbivores and total nematodes were positively correlated with each other. As illustrated in Fi g. 4.5B, cation exchange capacity and calcium were positively correlated while stunt ing w as negatively correlated with Dimension 1. CI, fungivores - to - bacterivores ratio and BI were positively while EI, phosphorus, soil organic matter and rot ting were negat ively correlated with dimension 2. SI, pH and porosity were positively correlated with each other, but negatively correlated with fork ing , soil moisture content, bulk density, NH 4 - N and potassium. C arrot c rack ing , potassium, NH 4 - N, and BI were positively c orrelated . M agnesium was negatively correlated with sum of fungivores and bacterivores - to - herbivores, fertility index, and unmarketable and total carrots. 70 Relationships among abundant herbivores and yield Carrot fresh weight of all categories except stunted and rotten carrots were positively correlated while Malenchus and Helicotylenchus were negatively correlated with Dimension 1 (Fig. 4.6A). Pratylenchus and carrot stunt ing were positively correlated while rot ting w as negatively correlated with Dimension 2. As illustrated in (Fig. 4.6B), the number of marketable carrots w as positively correlated with Dimension 1. Malenchus was negatively correlated with the number of cracked and forked carrots ; whereas , Helicotylenchus was positively correlated with the number of rotten carrots. Tylenchus and Pratylenchus were negatively correlated with Dimension 1 and Dimension 2, respectively. 71 Figure 4 . 5 . Multiple factor analysis of the variables where Dimension 1 (Dim 1) and Dimension 2 (Dim 2) represent the first and second best summary of variability of the information, respectively. (A) R elationships among abundance of nem atode trophic groups (Gc1) (bacterivores (BV), fungivores (FV), omnivores (OV), predators (PR), sum of omnivores and predators (OP), herbivores (HV) )(Yeats et al., 1993), and non - herbivore (FL) and total (TL) nematodes, and nematode guilds c - p 1 bacterivo res (BV1), c - p 2 bacterivores (BV2), sum of c - p 3 and c - p 4 (BV34), c - p 2 herbivores (HV2) and sum of c - p 3 to c - p 5 herbivores (HV345) (Bongers and Bongers, 1998) and soil properties (Gc2) (soil pH (pH) , organic matter percentage (OM), nitrate - nitrogen (NO 3 - N), ammonium - nitrogen (NH 4 - N),calcium (Ca), magnesium (Mg), phosphorus (P), potassium (K), moisture percent (MO), bulk density (BD), cation exchange capacity (CEC) and porosity (PO) . (B) R elationships of soil food web indices and trophic groups (Gc1) ((FV/BV)=FV) and ((FV + BV)/HV=FBP), soil properties (Gc2) , and carrot yield and quality (Gc3) (stunt (STU), forks (FO), rots (RO), cracks (CRA), marketable (MC), total unmarketable carrots (UNC) and root dry - to - shoot dry weight ratio (RDSD)) from plots amended with integrated application of urea and plant compost. 72 Figure 4 . 6 . Multiple factor analysis of the variables where Dimension 1 (Dim 1) and Dimension 2 (Dim 2) represent the first and second best summary of variability of the information, respectively. (A) R elationships among carrot yield and quality expressed as fresh weight (Gc1) ( (stunt (STU), forks (FO), rots (RO), cracks (CRA), marketabl e (MC), total unmarketable carrots (UNC) and root dry weight (RDW) and abundant herbivores (Gc2) ( Malenchus , MAL; Tylenc h us , TYL; Helicotylenchus , HEL; Pratylenchus , PRA) . (B) R elationships among carrot yield and quality (Gc1) expressed as number and abund ant herbivores nematodes (Gc2) from plots amended with integrated application of urea and plant compost. 73 Discussion Wang et al. (2006) have reported that nitrogen fertilizer application increased the percentage of herbivores, b ut organic amendments are known to reduce herbivores (Melakeberhan et al., 2007; Mennan and Melakeberhan, 2010). Variable experimental conditions make generalization of outcomes of compost and other organic amendments difficult (Akhtar and Malik, 2000; Ren , except urea application decreased bacterivores in 2014 compared with 2012 while bacterivores were unchanged in urea plots (Table 4.5). This result was partially consistent with Li et al. (2010), who showed increased bacterivores in nitrogen fertilized treatments. In contrast to this, nitrogen fertilization did not increase bacterivores (Ferris and Matute, 2003). Addition of compost with low C: N ratio, as in the present study, at least temporarily increase d opportuni stic bacterivores , probably due to high microbial activity (Bulluck III et al., 2002a; Briar et al., 2011). However, other studies showed compost had no effect or decreased non - herbivores (Cheng and Grewal, 2009; Ferris et al., 2012). Since omnivores and predators are sensitive to agrochemicals (Fiscus and Neher, 2002) , the ir low number s from urea treatment s in the present study were expected . It is assumed that integrated applications reduce d the negative effect of inorganic fertilizer application (Gruzed eva et al., 2007; Lie et al., 2010). Moreover, integrated application enhances microbial activities and improves soil physicochemical properties ( Lazcano et al., 2013). MI was higher in non - amended check (2.1 vs 1.8), and urea and PC at 1:1 ratio (2.1 vs 1.7) in 2014 than in 2012. In contrast , urea application reduced MI in previous studies (Bongers 74 et al., 1997; Ferris, 2010). MI offers possibilities to measure changes in the functioning of the soil ecosystem as result of disturbance and subsequent recovery (Bongers and Bongers, 1998). Hence, the improved MI in urea and PC at 1:1 ratio and non - amende d check suggest s improved soil conditions. suggests decreased nematode diversity over time. In contrast to this, both inorganic and organic amendments did not affect n ematode diversity in previous studies (Bulluck III et al., 2002a; Cheng et al., 2008). However, Okada and Harada (2007) observed organic amendments increased nematode diversity due to increase in non - herbivores. The impact of inorganic fertilization on SI did not conform to expectations. U rea, urea and PC at 3:1 ratio, and PC significantly increased SI compared with all of the treatments while urea and PC at 1:3 ratio significantly decreased SI compared with all of the treatments (Table 4.6). I expected tha t as urea rate decreases, SI increases due to increase in omnivores and predators (Bongers and Ferris, 1999; Okada and Harada, 2007; Lie et al., 2010). The SI increase in urea and integrated application with higher rate of urea in the present study needs f urther investigation. However , consistent with my finding that compost amendment increased SI in Sanchez - Moreno et al. (2009) (Table 4.6) . This may be due to increase in food base for omnivores and predators driven by compost amendment. Analyses of the so il conditions revealed that the soil food web structure progressed overtime (Fig. 4.1). All treatments including the controls had maturing and enriched food webs at harvest in 2014, where treatments with PC alone, and urea and PC at 1:1 ratio significantly increased SI from 50 % . EI represents availability of nutrients in the soil to support the opportunistic nematodes as observed in this study (Ferris et al., 2001). SI values are usually low 75 in agroecosystems because of physical and/or chemical disturbance of the soil ( Fiscus and Neher, 2002; Berkelmans et al., 2003; Briar et al., 2011). The r elatively more structured soil food web in PC, and urea and PC at 1:1 ratio may show reduced soil disturbance. Urea treatment significantly decreased soil pH, but the other treatments increased soil pH overtime. After two years of the experiment, soil pH was low in urea plots compared with the other treatments except urea and PC at 3:1 ratio. Consistent to my finding s , other studies showed that urea decreased soil pH wh ile compost amendment increased it (Bulluck III et al., 2002b; Li et al., 2010). Compost additions raise the pH of acid soils by forming aluminum complex and increasing base saturation (Shiralipour et al., 1992; Van den Berghe and Hue, 1999). Inorganic nit rogen fertilizer s lower soil pH that, in turn, adversely affect soil biodiversity, overall soil health and crop yield (Singh et al., 2013). However, increase in soil pH due to integrated application with higher rates of PC and PC alone is desirable, especially in acidic soils (Singh et al., 2013). Urea application increased residual soil NO 3 - N at the end of the season compared with the rest of the tr eatments in cluding non - amended control . Consistent with my finding s , Briar et al. (2007) found higher soil NO 3 - N in conventional system receiving inorganic fertilizers. In 2012, urea application resulted in significantly higher NO 3 - N at harvest, suggestin g that NO 3 - N loses to the environment. Surprisingly, most of the integrated applications had higher NO 3 - N at planting in 2013 compared with at planting and at harvest in 2012. This indicat es residual effect of PC that makes nitrate available to the subsequ ent growing seasons through decomposition (Sánchez and Richard, 2009). Urea, urea and PC at 3:1 ratio decreased soil phosphorus content compared with the rest of the treatments except urea and PC at 1:1 ratio (Fig. 4.2). This suggests that integrated 76 appl ications supplies other plant nutrients that inorganic fertilizers may not. In addition to delivering nutrients present in commercial fertilizers, compost includes nutrients that are sometimes not applied in adequate quantities by farmers ( e.g. manganese , zinc, and sulfur) . Compost can serve as insurance against potential yield limit ing nutrients ( Bulluck III et al., 2002b). Moreover, the integrated application reduce s the non - nutrient components of compost compared with compost alone treatments that allevi ate unintended consequences ( . This study revealed that PC, and urea and PC at 1:3 and 1:1 ratios significantly increased soil respiration compared with the rest of the treatments, indicating improved soil biological activity as I expected (Fig. 4.3). Ferris and Matute (2003) found improved soil respiration in treatments containing compost blended with wheat straw, but not from treatments with inorganic fertilizer and compost alone . Consistent with my result s, organic soil amendment increased rates of soil respiration compared with non - amended check (Gunapala et al., 1998; Treonis et al., 2010). I expected greater quality of carrots from plots treated with integrated application du e to reduced nitrogen fertilizer that support early growth, and improvement in soil physicochemical properties and pest suppression from PC (Abawi and Widmer, 2000; ). In my study, yield response was highly variable . In previous studies, i ntegrated application increased plant growth, yield, quality and soil fertility (Ahmed et al., 2006; Mahmoud et al., 2009). Keeling et al. (2003) also reported integrated application of nitrogen fertilizer with compost improved nitr ogen utilization efficiency. Although I did not see yield increase in integrated application in this study, the benefits of enhanced biological activities and 77 the anticipated reduction of negative environmental damage provide basis for further studies to t est impact of integrated application on carrot yield and quality. S um of c - p 3 to 5 herbivores were negatively correlated with potassium and positively correlated with soil pH. Total herbivore nematode abundance was also positively correlated with soil or ganic matter (Fig. 4.5A) . Increase organic matter resulted in increased nutrient status and enhance d biological activity which promotes plant growth, and subsequently increases in herbivores (Bonger et al., 1990; Pimentel et al., 2005; Forge and Kempler, 2 009). Negative correlation of potassium with herbivores suggests suppressive effect on herbivore nematodes (Coyne et al., 2004). Previous studies also showed the combination of SI, EI, CI and BI could be use to describe the soil health status and plant pro ductivity (Berkelmans et al., 2003; Knight et al., 2013). The multiple factor analysis between the most abundant nematodes and carrot yield parameters showed correlation pattern s . Malenchus and Helicotylencus were negatively correlated with carrot fresh w eight of all categories except carrot stunting and rot ting while Helicotylenchus was positively correlated with rotting (Fig. 4.6A and 4.6B ). However, considering that Malenchus is a root hair feeder (Yeates et al., 1993; Bongers and Bongers, 1998), its ne gative correlation with carrot yield suggests the need for further investigation to avoid carrot damage from underestimated herbivore nematodes. In conclusion, the positive impact of urea and PC at 1:1 ratio on MI, SI and herbivores, the increasing trend of omnivore nematode s as PC rate increases, and negative impact of urea on structure and soil food web conditions. PC and integrated application mixed with higher rates of PC, increased soil pH, nutrient content and soil biological activity levels while urea decreased 78 soil pH and increase d NO 3 - N. The negative correlation between Malenchus with carrot yield indicates the need for further investigation to prevent potential yield loses from underestimated nematode groups. Although I did not see yield increase in integrated application in this study, the benefits of enhanced biological activit ies, and increase in soil pH and nutrient contents together with the anticipated reduction in negative environmental damage would encourage further studies . One of the areas of the research could be mixing different compost types with inorganic fertilizers to exploit integrated application in carrot production systems. 79 CHAPTER 5 EFFECTS OF PLANT - AND ANIMAL WASTE - BASED COMPOST AMENDMENTS, AND SOIL STERILIZATION ON NEM ATODES, SOIL PROPERTIES, AND YIEL D OF A FRESH MARKET CARROT CULTIVAR UNDE R G LASS HOUSE CONDITIONS Abstract A comparative study was conducted using sterilized and non - sterilized soils to test the effects of plant and animal compost amendments on nematode community structure, soil food web conditions, soil properties and growth of fresh market carrot cultivar The overarching question here was to know how compost amendments work under severe biological degradation . in a glasshouse in 2012 and 2013 - soil samples - - Generally soil sterilization increased most of the measured soil nutrients and CO 2 evolution while decreasing soil pH, suggesting heating during soil sterilization enhances decomposition of organic matter. Carrot growth was stunted. Overall, results did not support the initial hypothesis that compost amendments will improve nematode community structure, soil food web condition, soil properties, and carrot yield in degraded soil compared with urea and non - amended check. Perhaps, reinoculating the sterilized soil with a small amount of control soil could have made a difference. 80 Introduction - Berney and Bird, 1992 Abawi and Widmer, 2000). Developing soil amendment - based alternatives for suppressing herbivores, other pests and diseases while improving soil quality are highly desired by conventional and organic carrot and other vegetable production systems. These include organic soil amendments such as green manure, cover crops, animal manure and compost (Abawi and Widmer, 2000; Wang et al., 2004; Briar et al., 2007) and a range of soil sterilization methods (Malowany and Newton, 1947; McNamara et al., 2003; Compost is one of the most commonly used organic amendments for increasing soil organic matter, nutrient content and microbial biomass, suppresses pest species, and improv es overall soil health (Forge and Kempler, 2009; Ferris et al., 2012). As part of a project initiated to develop appropriate compost amendment strategy for nutrient, nematode and soil health management that will lead to improved carrot yield and quality, I tested the effects of PC and AC at different rate of applications on nematode community, soil food web structure, soil physicochemical changes, and carrot yield and quality under field condition (Chapter 3). As the most abundant metazoan in terrestrial ec osystems, nematodes are considered as an important component of the soil biotic community and an important indicator of soil ecosystem services (Bongers and Bongers, 1998; Porazinska et al., 1999; Ferris et al., 2001; Wang et al., 2006; S á nchez - Moreno and Ferris, 2007; Cheng and Grewal, 2009; Knight et al., 2013). 81 In order to address the overarching priorities of suppressing herbivore nematodes and other pests and diseases while improving soil quality using compost in conventional and organic production s ystems, there is a need to consider the production practices. For example, carrot productions naturally has high disturbance on soils for creating the fine seedbed and to reduce weeds and pests (Brainard et al., 2012) and frequent application of broad rang e of agricultural inputs often add to soil biological degradation ( ). Under these circumstances, it is necessary to know if compost application will reverse biologically degraded soils. Therefore, the objective of the study was to (1) compare the performance of PC and AC sources in improving nematode community structure, soil food web structure, soil properties, and growth of Sugarsnax 54 under sterilized and non - sterilized conditions. I hypothesize d Materials and methods Soil samples Soil for this experiment was collected from Michigan State University (MSU) Horticulture Teaching and Research center, Holt, Michigan (N 43 0 0 m elevated) in September 2012 and October 2013. The soil is characterized as a Colwood - Brookston sandy clay loam (fine - loamy, mixed, mesic Type, Haplaquolls - Argiaquolls, Anon, 1977) with 54 % sand, 25 % silt and 2 1 % clay. This was the same field where the experiments in Chapter 3 were conducted. Approximately 64 liters of bulk soil sample was shoveled from the top15 to 20 cm depth (Melakeberhan et al., 2007) from 10 randomly selected spots from the guard rows each year (Fig. A - 2), homogenized, filled in containers and transported to Agricultural Nematology Laboratory cold room set at 5 0 C. In order to eliminate preexisting 82 organisms, half of it was sterilized using an autoclave (AMSCO, ERIE, Pennsylvania, USA) at 1 20 0 C and 22 psi for 16 hr in MSU Department of Plant Biology soil sterilization facility (De la peña et al, 2013). Experimental design and treatments The experiment was conducted from December 21, 2012 to March 15, 2013 and repeated from October 18, 201 3 to January 15, 2014 in MSU Plant Science glasshouse facility. Composts used for these experiments were the same with that were used in 2012 and 2013 field experiments for Sugarsnax 54 carrot cultivar. PC and AC (Dairy Doo, Sears, MI, USA) were used as or ganic amendments. PC was obtained from MSU Student Organic Farm, Holt, MI, USA and AC purchased from Morgan Composting, Inc., Sears, MI, USA (Table 5.1). Standard urea equivalent to 243 kg/ha which is recommended for Sugarsnax 54 carrot cultivar and non - am ended check were included as controls. a hectare contains 2, 600,000 kg of soil used in many laboratories for nutrient recommendations. This technique was used to matc h the recommended amount of soil amendments used in my field experiment (Burden and Sims, 1999). A total of 64 experimental units (8 treatments x 2 soils x 4 replications) were used. Each pot received 960 g of either sterilized or non - soil sterilized soils before applying the amendments to each pot. Compost with nutrient composition reported in Table 5.1 was applied on dry matter basis. In 2012 experiment, the treatments were: 83 Table 5 . 1 . Average soil pH, macro (%) and micro nutrient contents (ppm) of animal (AC) and plant compost (PC) and rates of application (kg/ha) in 2012 and 2013. pH and nutrients Compost nutrient composition and rate Content Rate (kg/ha) AC PC AC PC pH 9.2 a a 7.9 a b na b na Macronutrients (%) Nitrogen 1.3 a 1.0 b 112 112 Phosphorus 0.6 a 0.1 b 52 12 Potassium 1.5 a 0.3 b 130 36 Calcium 2.9 b 4.0 a 252 478 Magnesium 0.7 b 0.9 a 61 11 Sodium 0.2 a 0.02 b 17 2 Sulfur 0.4 a 0.2 b 35 24 OM c 27 a 23 a 2348 2750 Carbon 16 a 14 a 1391 1674 C : N d 12a 14 a na na Micronutrients (ppm) Iron 6052.3 a 5307.0 b 52 60 Zinc 188.3 a 82.6 b 2 1 Manganese 344.8 a 329.6 a 3 4 Copper 101.5 a 30.6 b 1 0.3 Boron 24.4 a 27.1 a 0.2.0 0.3 Aluminum 1936.1 b 2843.5 a 17 36 a pH value obtained only from 2013. b Rate was not available because pH and C/N ratio cannot be expressed as a rate of application. c percent of organic matter. d carbon - to - nitrogen ratio. e Means with different letters across rows indicate statistical difference at P < 0.05. 6 g (X), 9 g (1.5X) and 12 g (2X) of PC and 4 g (X), 6 g (1.5X) and 8 g (2X) of AC where X was adjusted at a rate of 112 kg N/ha which is a recommended N for fresh market carr ot varieties and urea (46 - 0 - 0) was applied as 0.1 g per pot which is equivalent to 112 kg N/ha. The 2013 treatments were: 4 g (X), 7 g (1.5X) and 9 g (2X) of PC and 4 g (X), 6 g (1.5X) and 8 g (2X) of AC and urea (46 - 0 - 0) was applied as 0.1 g per pot. The treatments were applied to each pot and 84 mixed to the soil. Each pot was water to saturation 1 hour prior transplanting two - week old carrot seedlings (Melakeberhan et al., 2007). Pots were monitored every day and watered as needed throughout the experiment. Treatments were arranged in randomized complete block design (RCBD) with four replications on glasshouse bench. The experiments were terminated 86 DAP. Nematode extraction, identification and abundance In order to establish base line information, n - using a semi - automatic elutriator as described earlier (Avendaño et al., 2003). Methods pertaining to soil sampling, nematode extraction, i dentification and nematode community, ecosystem disturbance and soil food web indices, were described in the General Materials and Methods section (Chapter 2). Similarly, methods used to measure soil respiration, soil physicochemical properties, and carrot yield and quality were stated in Chapter 2. C arrot yield After 86 days, carrots were uprooted from each pot. The root and shoot were weighted separately for fresh weight and placed in a separate paper bags for dry weight determination. The dry weight determinations were made after the roots and shoots had been d ried to constant weight at 66 0 C (Hochmuth et al., 2006). Data analysis Treatments were compared for nematode trophic groups, community indices, soil food web indices, trophic group ratios, fertility index (PPI/MI), soil and yield variables. Statistical analysis was conducted using the PROC MIXED procedure of SAS. The statisti cal model consisted of 85 fixed effects of amendments and soil (sterilized and non - sterilized) and the interaction between them, and random effects of block. Comparisons were performed by using two - way analysis of variance for soil and yield parameters accoun ting soil sterilization and treatments as factors of the experiment. Treatments were compared using one - way analysis of variance (Proc Mixed, SAS ver 9.3, SAS Institute, 2012, Cary, NC , USA ) for nematode data because nematodes were not extracted from ste rilized soil. F - values were obtained using appropriate error term in the models. Multiple comparisons were adjusted to Tukey - Kramer when F is not significant to perform the preplanned comparisons. Prior to analysis; nematode population abundance was transf ormed to ln (x+1) to meet the assumptions of normality and equal variances, but untransformed arithmetic means are presented. The probability level P < 0.05 was regarded as significant. Results Nematode composition and abundance A total of 29 nematode gen era were detected from soil samples in 2012 and 2013 (Table 5.2). The nematode genera detected from herbivore, bacterivore, fungivore, predator and omnivore trophic groups were 8, 13, 4, 1 and 3, respectively. Eudorylaimus , Cephalobus and Cervidellus were detected only in 2012, and Basiria , Acrobeles , Alaimus and Mononchus were detected only in 2013 soil samples. Tylenchus, Acrobeloides , and Aphelenchus and Filenchus were the most abundant herbivore, bacterivore and fungivore genera, respectively. Overall, the abundance of omnivores and predators were low, and nematode abundance was higher in 2012 compared with 2013 samples. Nematodes were not detected in sterilized soil in both 2012 and 2013 soil samples. 86 Herbivores were significantly higher at planting co mpared with AC at 168 kg N/ha, urea and check at harvest in 2012 (Table 5.3). Similarly, bacterivores were significantly higher at planting compared with all the treatments at harvest in 2012. Fungivores were significantly higher at planting and AC at 112 and 224 kg N/ha at harvest in 2012 compared with the rest of the treatments. In 2013, herbivores and Fungivores were significantly higher at planting compared with all of the treatments at harvest. In both years, there was no significant difference in omni vores and predators among the treatments. Nematode community indices Shannon - Weaver diversity index was significantly higher at planting and AC at 112 and 224 kg N/ha, urea and non - amended check at harvest compared with the rest of the treatments in 2012 ( at 112 kg N/ha, AC at 224 kg N/ha, urea and non - amended check compared wi th AC at 168 kg significantly higher at planting compared with all of the t reatments at harvest. There were no significant differences in MI and MI25 at planting and harvest samples, and among the treatments in 2012 and 2013 (Table 5.5). There was also no significant difference in PPI at planting and harvest, and among the treatm ents in 2012. PPI was significantly higher at planting compared with the rest of the treatments at harvest in 2013. 87 Table 5 . 2 . List of nematode genera detected in AC and PC amendments, standard u rea and non - amended check in pots filled with 960 g non - sterilized sandy clay loam soil planted with Sugarsnax 54 at planting and 86 days later at harvest in 2012 and 2013 glasshous e experiments. Numbers within brackets represent c - p vales following Bonger s and Bongers (1998). Herbivores Bacterivores Fungivores Predators Omnivores Basiria a (2) Mesorhabditis (1) Ditylenchus (2) Mononchus a (4) Eudorylaimus (4) b Cephalenchus (2) Panagrolaimus (1) Aphelenchoides (2) Thonus (4) Malenchus (2) Pellioditis c (1) Aphelenchus (2) Aprocelaimellus(5) Paratylenchus (2) Pristionchus a (1) Filenchus (2) Psilenchus (2) Rhabditis (1) Tylenchus (2) Acrobeles a (2) Heterodera (3) Acrobeloides (2) Pratylenchus (3) Cephalobus c (2) Cervidellus c (2) Eucephalobus (2) Heterocephalobus (2) Plectus (2) Alaimus a (4) a D etected only in 2013. b D etected only at harvest in 2012 experiment . c Detected only in 2012. 88 Table 5 . 3 . Mean number s of herbivores, bacterivores, fungivores, predators and omnivores nematode trophic groups abundances in 100 cc of soil amended with animal (AC) and plant (PC) composts, standard urea and non - amended check in pots filled with 960 g of non - sterilized sandy clay loam soil planted with Sugarsnax 54 at planting b and at harvest c (86 DAP) across 2012 and 2013 glasshouse experiments. AM a Rate (kg N/ha) HV BV FV PR OV b 10 a d 52 a 42 a 0 1 PC 112 c 3 b 14 b 25 b 0 1 168 4 b 12 bc 22 b 0 0 224 3 b 6 bc 14 b 0 1 AC 112 3 b 15 b 19 b 0 0 168 1 b 5 c 3 c 0 0 224 4 b 13 b 21 b 0 0 Urea 112 2 b 14 b 15 b 0 0 Check 0 2 b 15 b 14 b 0 0 a Amendments. b Planting samples c Harvest samples d Means within columns followed by same letter(s) are not significantly different at P < 0.05 . Table 5 . 4 . The effect of animal (AC) and plant (PC) composts at different rates, standard urea and no n - amended check on Shannon - filled with 960 g of non - sterilized sandy clay loam soil planted with Sugarsnax 54 at planting b and at harvest c (86 DAP) in 2012 and 2013 glasshouse experiments. AM a Rate (Kg N/ha) H' N1 N0 H' N1 N0 2012 2013 b 2.49 a d 12.12 a 15 a 1.50 a 5.40 a 8 a PC 112 c 1.88 ab 7.88 abc 10 ab 0.97 a 3.41 a 3 b 168 1.86 ab 6.47 bc 9 abc 0.87 a 3.34 a 3 b 224 2.00 ab 7.40 bc 8 bc 0.91 a 2.82 a 2 b AC 112 2.13 a 8.50 ab 10 ab 1.26 a 3.75 a 3 b 168 1.12 b 4.17 c 4 c 0.86 a 2.74 a 2 b 224 2.21 a 9.22 ab 11 ab 1.40 a 4.54 a 4 b Urea 112 2.13 a 8.40 ab 9 abc 1.17 a 3.95 a 3 b Check 0 2.08 a 8.19 ab 8 bc 1.14 a 3.81 a 3 b a Amendments. b Planting samples . c Harvest samples . d Means within columns followed by same letter(s) are not significantly different at P < 0.05 . 89 Table 5 . 5 . The effect of animal (AC) and plant (PC) composts at different rates, standard urea and non - amended check on maturity indices (PPI, MI and MI25) in pots filled with 960 g of non - sterilized sandy clay loam soil planted with Sugarsnax 54 at planting b and at harvest c (86 DAP) in 2012 and 2013 experiments. AM a Rate (Kg N/ha ) PPI MI MI25 PPI MI MI25 2012 2013 b 2.13 a d 1.75 a 2.02 a 2.00 a 1.80 a 2.00 a PC 112 c 2.08 a 1.95 a 2.00 a 0.00 b 1.89 a 2.00 a 168 2.26 a 1.81 a 2.00 a 0.00 b 1.56 a 2.00 a 224 2.25 a 1.97 a 2.00 a 0.00 b 1.92 a 2.00 a AC 112 2.10 a 1.92 a 2.00 a 0.00 b 2.00 a 2.00 a 168 2.00 a 1.92 a 2.00 a 0.00 b 2.44 a 2.50 a 224 2.05 a 1.94 a 2.00 a 0.50 b 1.84 a 2.00 a Urea 112 2.17 a 1.87 a 2.00 a 0.00 b 1.94 a 2.00 a Check 0 2.04 a 1.87 a 2.00 a 0.00 b 1.20 a 2.00 a a Amendments. b Planting samples . c Harvest samples . d Means within columns followed by same letter(s) are not significantly different at P < 0.05 . Soil food web indices, trophic ratios and fertility index There were no significant differences in soil foo d web indices between at planting and at harvest samples in 2012. However, PC at 168 kg N/ha and non - amended check were significantly higher in EI compared with PC at 112 and 224 kg N/ha, and AC at 112 kg N/ha in 2013 (Table 5.6). This result was supported by the faunal profile analysis where only a few data points fell in Quadrant A, but most data points fell in Quadrant D (Fig. 5.1). Similarly, there was no significant difference in fungivores - to - bacterivores and fungivores plus bacterivores - to - herbivores ratios and fertility index between planting and harvest samples, and among the treatments in 2012 and 2013 (Table 5.7). 90 Table 5 . 6 . The effect of animal (AC) and plant (PC) composts at different rates, stand ard urea and non - amended check on food web enrichment (EI) and structure (SI), basal index (BI), and channel index (CI) in pots filled with 960 g of non - sterilized sandy clay loam soil planted with Sugarsnax 54 at planting b and at harvest c (86 DAP) in 2012 and 2013 experiments. AM a Rate (kg N/ha) EI SI BI CI EI SI BI CI 2012 2013 b 67 a d 4 a 32 a 29 a 65 ab 5 a 27 a 42 a PC 112 c 52 a 3 a 47 a 75 a 30 c 0 a 52 a 60 a 168 59 a 1 a 40 a 63 a 75 a 0 a 25 a 36 a 224 51 a 11 a 47 a 72 a 33 c 0 a 67 a 78 a AC 112 50 a 3 a 49 a 61 a 39 bc 0 a 61 a 100 a 168 44 a 0 a 56 a 51 a 47 abc 25 a 40 a 78 a 224 47 a 0 a 53 a 72 a 58 abc 0 a 42 a 66 a Urea 112 53 a 0 a 47 a 62 a 46 abc 0 a 54 a 82 a Check 0 53 a 2 a 46 a 54 a 75 a 0 a 24 a 21 a a Amendments. b Planting samples . c Harvest samples . d Means within columns followed by same letter(s) are not significantly different at P < 0.05 . Table 5 . 7 . The effect of animal (AC) and plant (PC) composts at different rates, standard urea and non - amended check on fungivores - to - bacterivores ratio (FV/BV), sum of bacterivores and fungivores - to - herbivores ((BV + FV)/HV) and fertility index (FI= PPI/MI) in pots filled with 960 g of non - steri lized sandy clay loam soil planted with Sugarsnax 54 at planting b and at harvest c (86 DAP) in 2012 and 2013 experiments. AM a Rate (Kg N/ha) FV/BV (BV+FV)/HV FI FV/BV (BV+FV)/HV FI 2012 2013 b 0.75 a d 13.24 a 1.22 a 1.40 a 1.10 a 3.36 a PC 112 c 2.02 a 11.70 a 1.07 a 0.28 a 0.21 a 0.00 a 168 2.43 a 19.97 a 1.33 a 0.53 a 0.40 a 0.00 a 224 2.32 a 5.14 a 1.15 a 0.96 a 0.96 a 0.00 a AC 112 1.22 a 12.98 a 1.09 a 1.56 a 1.17 a 0.00 a 168 1.83 a 3.75 a 1.04 a 0.75 a 0.38 a 0.00 a 224 1.68 a 12.73 a 1.06 a 1.67 a 1.25 a 0.63 a Urea 112 1.33 a 23.25 a 1.16 a 0.47 a 0.23 a 0.00 a Check 0 1.14 a 14.10 a 1.09 a 0.72 a 0.54 a 0.00 a a Amendments. b Planting samples . c Harvest samples . d Means within columns followed by same letter(s) are not significantly different at P < 0.05 . 91 Figure 5 . 1 . Faunal profiles representing the structure (SI) and enrichment (EI) conditions of the soil food web in pots filled with non - sterilized sandy clay loam soil planted with Sugarsnax 54 cultivar in 2012 and 2013 glasshouse experiments. Pots were amended with animal compost (AC) and plant compost (PC) at different rates, standard urea and non - amended check. Numbers represent: 1 - 3= PC adjusted at 112, 168 and 224 kg N/ha, respectively; 4 - 6= AC adjusted to supply 112, 168 and 224 kg N/ha, respectively, 7= urea an d 8= non - amended check. 1 2 3 4 5 6 7 8 0 50 100 0 50 100 Enrichment index (%) Structural index (%) 2012 Preplant Harvest 1 2 3 4 5 6 7 8 0 50 100 0 50 100 Enrichment index (%) Structural index (%) 2013 Preplant Harvest 92 Soil properties and soil respiration All of the AC treatments significantly increased soil pH on sterilized soil at harvest compared with at planting in 2012. In 2013, all of the treatments significantly increased soil pH on sterilized soil at harvest compared with at planting. In non - sterili zed soil, however, only AC at 224 kg N/ha significantly increased soil pH compared with AC at 168 kg N/ha and urea in 2013. AC at 224 kg N/ha significantly increased soil pH at harvest compared with at planting in 2013. Generally, soil sterilization decre ased soil pH in these experiments except in AC at 168 kg N /ha and urea (Tables 5.8 and 5.9). All of the treatments increased soil phosphorus content on non - sterilized soil at harvest compared with that at planting in 2013, but only AC at 224 kg N/ha had s uch effect in 2012. All of the AC treatments increased phosphorus compared with urea. In 2012, soil phosphorus was generally higher at harvest than at planting in all treatments including urea and non - amended check on sterilized soil. However, PC at 224 kg N/ha and all of the AC treatments increased soil phosphorus content on sterilized soil in 2013. 93 Table . 5 . 8 . Soil pH, moisture content ( % MO) and phosphorus (P), potassium (K), calcium (Ca), Magnesium (Mg) contents (ppm), cation exchange capacity (CEC) (100 me/100g), organic matter ( % OM), nitrate - nitrogen (NO 3 - N) (ppm), ammonium - nitrogen (NH 4 - N) (ppm) and soil respiration (SR) (µ CO 2 - C per gram per day) in animal (AC) and plant (PC) composts amendment s at different rates, standard urea and non - amended check in pots filled with 960 g of sterilized (S) and non - sterilized (NS) sandy clay loam soil planted with Sugarsnax 54 at planting b and at harvest c (86 DAP) in 2012 glasshouse experiments. AM a Rate (kg N/ha) pH % MO P K S NS S NS S NS S NS b 7.3 bB d 7.5 dA 8.4 a 10.6 a 72.8 c 71.6 b 135.8 a 136.6 a PC 112 c 7.4 abB 7.7 abcA 7.0 aB 10.3 aA 77.0 bcA 68.7 bB 115.3 de 119.3 b 168 7.5 abB 7.8 abcA 8.0 a 9.3 ab 79.0 bcA 68.0 bB 112.7 de 115.0 b 224 7.4 abB 7.8 abA 8.5 a 7.3 b 83.0 abA 73.3 abB 120.0 bcde 123.0 ab AC 112 7.6 a 7.7 abc 6.4 aB 9.4 abA 82.0 abA 72.0 abB 129.7 ab 121.3 b 168 7.5 a 7.6 dc 7.2 a 9.1 ab 82.0 abA 72.7 abB 129.0 abc 126.3 a 224 7.5 aB 7.8 aA 7.5 a 6.6 b 85.7 aA 76.3 aB 125.7 abcd 136.3 a Urea 112 7.4 ab 7.6 bcd 6.3 a 8.6 ab 79.3 bA 69.3 bB 109.7 e 113.0 b Check 0 7.4 abB 7.7 abcA 8.7 a 8.2 ab 82.0 abA 70.7 abB 111.7 e 112.3 b 94 Table 5 .8 (con t AM a Rate (kg N/ha) Ca Mg CEC S NS S NS S NS 1332 b 1317.4 b 274.8 aB 336.8 aA 9.3 b 9.72 b PC 112 1348.3 b 1385.7 ab 263.3 ab 287.0 b 9.2 b 9.60 b 168 1366.3 b 1360.0 b 253.0 ab 261.3 b 9.2 b 9.30 b 224 1349.0 b 1507.7 a 262.7 ab 316.3 b 9.2 bB 10.5 aA AC 112 1391.3 ab 1368.0 b 258.0 ab 287.0 b 9.4 b 9.50 b 168 1419.7 ab 1369.7 b 250.7 ab 293.0 b 9.5 b 9.60 b 224 1350.0 b 1404.0 ab 239.7 b 276.7 b 9.1 b 9.70 b Urea 112 1353.3 b 1342.7 b 240.0 b 275.0 b 9.0 b 9.30 b Check 0 1371.3 b 1354.0 b 243.7 b 263.7 b 9.2 b 9.30 b AM a Rate (kg N/ha) % OM NO 3 - N NH 4 - N SR S NS S NS S NS S NS b 2.02 a d 2.10 b 20.18 c 21.50 b 20.36 aA 1.64 aB 6.00 aA 3.10 aB PC 112 c 2.10 a 2.10 b 44.20 abA 28.20 bB 5.70 b 2.40 a 4.90 a 3.10 a 168 2.00 a 2.10 b 45.80 abA 21.00 bB 5.70 b 2.80 a 4.70 abA 2.30 aB 224 2.00 aB 2.20 aA 40.30 bA 26.70 bB 5.10 b 2.70 a 4.20 ab 3.20 a AC 112 2.10 a 2.20 a 44.20 abA 25.40 bB 7.30 bA 2.60 aB 4.00 ab 3.20 a 168 2.00 a 2.10 b 47.10 abA 25.00 bB 8.80 bA 2.50 aB 3.90 ab 3.00 a 224 2.00 a 2.10 ab 39.50 b 30.60 b 7.40 bA 2.70 aB 4.70 ab 2.90 a Urea 112 2.00 a 2.00 b 52.70 a 69.30 a 8.20 bA 2.60 aB 3.60 abA 1.70 aB Check 0 2.00 a 2.10 ab 40.90 b 31.60 b 5.30 b 2.70 a 2.90 b 2.60 a a Amendments. b Planting samples . c Harvest samples . d Means with different lower case letters within columns and different upper case letters between soil conditions (S vs. NS) within each variable indicate the significant difference at P < 0.05 . 95 All of the PC treatments, urea and non - amended check decreased soil potassium content at harvest compared with at planting in 2012. However, there was no significant difference among all of the AC treatments at harvest compared with planting in 2012. In 20 13, all of the treatments except PC at 168 kg N/ha and urea increased soil potassium content on sterilized soil at harvest compared with at planting (Tables 5.8 and 5.9). On non - sterilized soil, only AC at 168 and 224 kg N/ha increased soil potassium conte nt at harvest compared with at planting in 2012. However, only AC at 224 kg N/ha increased potassium at harvest on non - sterilized soil in 2013. There was no difference in calcium content on sterilized soil in both years. PC at 224 kg N/ha increased soil calcium content at harvest in 2012 compared with that at planting, but calcium content decreased in all of the treatments at harvest compared with at planting in 2013. Magnesium was lower in AC at 224 kg N/ha, urea and non - amended check at harvest tha n at planting in 2012 (Table 5.8). All of the treatments increased magnesium content at harvest in 2013 (Table 5.9). Similarly, magnesium content was low in non - sterilized soil in all the treatments at harvest compared with at planting in 2012. However, on ly PC and AC at 224 kg N/ha, and non - amended check were low in magnesium at harvest than at planting in 2013. 96 Table 5 . 9 . Soil pH, moisture ( % MO) and phosphorus (P), potassium (K), calcium (Ca), Magnesium (Mg) contents (ppm), and cation exchange capacity (CEC) (100 me/100g), organic matter ( % OM), nitrate - nitrogen (NO 3 - N) (ppm), ammonium - nitrogen (NH 4 - N) (ppm) and soil respiration (SR) (µ CO 2 - C per gram per day) in animal (AC) and plant (PC) composts amendmen ts at different rates, standard urea and non - amended check in pots filled with 960 g of sterilized (S) and non - sterilized (NS) sandy clay loam soil planted with Sugarsnax 54 at planting b and at harvest c (86 DAP) in 2013 glasshouse experiments. AM a Rate (kg N/ha) pH % MO P K S NS S NS S NS S NS b 7.10 bB d 7.80 aA 13.20 a 10.20 b 52.70 b 45.30 d 101.00 b 119.33 b PC 112 c 7.60 aB 7.90 aA 13.10 a 14.50 a 85.70 a 79.70 abc 127.00 a 128.30 ab 168 7.50 aB 7.90 aA 13.40 a 13.90 a 83.30 a 75.30 bc 120.30 ab 127.00 ab 224 7.60 a 7.70 a 14.40 a 14.00 a 86.70 a 83.70 abc 129.00 a 133.70 ab AC 112 7.70 aB 8.00 aA 13.90 a 13.40 a 85.00 a 87.00 a 135.00 a 132.30 ab 168 7.70 a 7.90 ab 13.10 a 13.40 a 84.70 a 86.70 a 133.70 a 133.70 ab 224 7.60 a 7.70 a 13.90 a 13.50 a 91.00 a 84.30 ab 134.00 a 143.70 a Urea 112 7.60 a 7.80 a 13.20 a 14.00 a 87.30 aA 74.30 cB 119.70 ab 130.00 ab Check 0 7.60 a 7.80 a 13.70 a 13.20 a 83.30 a 79.30 abc 128.00 a 129.30 ab 97 Table 5 AM a Rate (kg N/ha) Ca Mg CEC S NS S NS S NS 1520.70 aB 1720.70 aA 246.00 bB 378.67 aA 9.90 aB 12.10 aA PC 112 1496.70 a 1491.00 b 337.70 a 355.30 ab 10.60 a 10.70 b 168 1468.00 a 1524.70 b 321.30 a 348.30 ab 10.30 a 10.90 b 224 1430.00 a 1475.70 b 325.30 a 333.00 b 10.20 a 10.50 b AC 112 1492.00 a 1487.70 b 341.30 a 348.70 ab 10.70 a 10.70 b 168 1408.00 a 1451.30 b 320.30 a 343.70 ab 10.10 a 10.50 b 224 1411.30 a 1520.00 b 317.30 a 338.70 b 10.00 a 10.80 b Urea 112 1446.00 a 1563.70 b 312.30 aB 355.00 abA 10.10 aB 11.10 bA Check 0 1455.00 a 1489.70 b 309.00 a 322.70 b 10.20 a 10.50 b AM a Rate (kg N/ha) % OM NO 3 - N NH 4 - N SR S NS S NS S NS S NS b 1.60 b d 1.60 b 2.40 c 3.30 c 15.70 aA 1.90 bB 10.59 aA 1.97 cB PC 112 c 2.50 a 2.70 a 66.70 aA 31.20 abB 2.80 b 1.40 b 1.98 b 6.32 b 168 2.60 a 2.70 a 57.10 abA 29.00 abB 2.80 b 1.20 b 2.12 b 1.94 c 224 2.60 a 2.70 a 54.50 ab 45.40 ab 2.80 b 7.70 a 4.25 b 4.04 bc AC 112 2.50 a 2.60 a 46.30 b 26.60 bc 4.40 b 1.30 b 2.58 b 2.01 c 168 2.60 a 2.70 a 38.20 b 42.80 ab 3.00 b 1.20 b 3.81 b 2.03 c 224 2.70 a 2.60 a 49.70 ab 45.70 ab 4.30 b 1.30 b 3.48 b 3.26 bc Urea 112 2.40 aB 2.70 aA 67.70 a 55.80 a 5.50 b 1.10 b 2.12 b 2.12 c Check 0 2.40 a 2.50 a 53.00 ab 36.60 ab 5.00 b 3.90 ab 1.76 b 2.56 c a Amendments. b Planting samples . c Harvest samples . d Means with different lower case letters within columns and different upper case letters between soil conditions (S vs. NS) within each variable indicate the significant difference at P < 0.05 . 98 In sterilized soil, there was no difference in cation exchange capacity between planting and harvest samples and among the treatments at harvest in both years (Tables 5.8 and 5.9). There was also no difference in soil orga nic matter between planting and harvest samples, and among the treatments at harvest soil in 2012, but all of the treatments increased soil organic matter at harvest compared with at planting in 2013. Soil sterilization decreased soil cation exchange capac ity and organic matter in PC at 224 kg N/ha and urea in 2012 and 2013, respectively. In non - sterilized soil, PC at 224 kg N/ha increased cation exchange capacity at harvest than at planting in 2012. However, all of the treatments were low in cation excha nge capacity at harvest than at planting in 2013. PC at 224 and AC at 112 kg N/ha increased soil organic matter at harvest than at planting in 2012. Similarly, PC at 224 kg N/ha and AC at 112 kg N/ha increased soil organic matter at harvest compared with P C at 112 and 168 kg N/ha, AC at 168 kg N/ha, and urea in 2012. However, all the treatments increased soil organic matter at harvest than at planting in 2013. All of the treatments increased soil NO 3 - N content on sterilized soil at harvest compared with that at planting in 2012 and 2013 (Tables 5.8 and 5.9). Among the treatments, PC at 224 kg N/ha and AC at 112 kg N/ha significantly increased NO 3 N compared with PC at 112 and 168 kg N/ha, and non - amended control on sterilized soil at harvest in 2012. In co ntrast to this, PC at 112 kg N/ha and urea significantly increased NO 3 - N compared with PC at 224 kg N/ha and AC at 112 kg N/ha in 2013. Soil sterilization increased NO 3 - N content in all of PC treatments, AC at 112 and 168 kg N/ha in 2012. On non - sterilized soil, only urea significantly increased NO 3 - N compared with the rest of the treatments in 2012. Similar to this, urea increased NO 3 - M 99 compared with AC at 112 kg N/ha in 2013. In 2013, the effect of soil sterilization was observed only in PC at 112 and 168 kg N/ha. In sterilized soil, NH 4 - N decreased in all treatments at harvest compared with at planting, but there were no differences among the treatments at harvest in 2012 and 2013. Soil sterilization significantly increased NH 4 - N at planting, in all of th e AC treatments and urea in 2012, but such effect was observed only at planting in 2013. On non - sterilized soil, there was no significant difference in NH 4 - N between planting and harvest soil samples in 2012. Similarly, there was no significant difference among the treatments at harvest in 2012. However, PC at 224 kg N/ha significantly increased NH 4 - N compared with all of the treatments except non - amended check in 2013. Soil respiration was significantly higher at planting compared with non - amended check, a nd all of the treatments on sterilized soil at harvest in 2012 and 2013, respectively. On non - sterilized soil, there was no significant difference between planting and harvest samples, and among the treatments in 2012. In 2013, PC at 112 kg N/ha significa ntly increased soil respiration in non - sterilized soil compared with at planting, and all of the treatments except PC and AC at 224 kg N/ha. Soil sterilization increased soil respiration in PC at 168 kg N/ha, and urea in 2013, but there was no such effect in 2012. Carrot yield There were no treatment and soil sterilization effects on root fresh and dry weight in 2012 (Table 5.10). However, AC at 224 kg N/ha, significantly increased shoot fresh weight on sterilized soil compared with non - amended check in 20 12. In non - sterilized soil, PC at 224 kg N/ha and AC at 112 and 224 kg N/ha significantly increased shoot fresh weight compared with urea and non - amended check. PC at 112 kg N/ha and AC at 224 kg N/ha significantly increased 100 shoot dry weight on sterilized soil compared with non - amended check. However, all the treatments except urea significantly increased shoot dry weight on non - sterilized soil compared with non - amended check in 2012. PC at 168 kg N/ha and AC at 168 kg N/ha significantly increased root - to - s hoot dry weight ratio on sterilized soil compared with non - amended control in 2012. However, AC at 224 kg N/ha significantly increased root - to - shoot dry weight ratio compared with all of the treatments in 2012. Soil sterilization significantly increased sh oot fresh weight in urea treatment in 2012, but no effect of soil sterilization observed in shoot dry weight and root - to - shoot dry weight ratio. In 2013 on sterilized soil, PC at 224 kg N/ha significantly increased root fresh weight compared with all of th e treatment except AC at 112 and 224 kg N/ha (Table 5.11). Soil sterilization significantly increased root dry weight in AC at 112 and 224 kg N/ha. However, soil sterilization decreased root dry weight in urea and increased root fresh weight in PC and AC a t 224 kg N/ha and urea. In 2013 in non - sterilized soil, AC at 224 kg N/ha significantly increased root fresh weight compared with AC at 168 kg N/ha, urea and non - amended check (Table 5.11). All of the treatments significantly increased root fresh weight co mpared with non - amended check in 2013. However, there were no significant differences among the treatments including the cobtrols in root dry weight. In 2013 in sterilized soil, AC at 112 and 224 kg N/ha, and PC at 224 kg N/ha significantly increased shoo t fresh weight compared with AC at 168 kg N/ha, urea and non - amended check (Table 5.11). PC at 112 kg N/ha also significantly increased shoot fresh weight compared with urea and non - amended check. Soil sterilization significantly increased shoot fresh weig ht in PC at 112 and 224 kg N/ha and AC 112 kg N/ha. However, soil sterilization had no 101 significant effect on shoot dry weight and root - to - shoot dry weight ratio. There was no significant difference in shoot fresh weight among the treatments on non - sterili zed soil in 2013. 102 Table 5 . 10 . The effect of animal (AC) and plant (PC) compost amendment at different rates, standard urea and non - amended check on carrot root fresh weight (RFW), root dry weight (RDW ), shoot fresh weight (SFW), shoot dry weight (SDW) and root - to - shoot dry weight ratio (RD/SD) in pots filled with 960 g of sterilized (S) and non - sterilized (NS) sandy clay loam soil planted with Sugarsnax 54 after 86 days in 2012 experiments. TR RFW RDW SFW SDW RD/SD AM a S NS S NS S NS S NS S NS PC 112 b 0.60 a c 0.81 a 0.22 a 0.28 a 0.65ab 0.49 ab 0.47 a 0.39 a 0.44 ab 0.79 b 168 0.91 a 0.61 a 0.34 a 0.23 a 0.56 ab 0.59 ab 0.35 ab 0.53 a 0.95 a 0.45 b 224 0.46 a 0.92 a 0.21 a 0.34 a 0.58 ab 0.87 a 0.41 ab 0.49 a 0.48 ab 0.70 b AC 112 0.61 a 1.02 a 0.28 a 0.36 a 0.51 ab 0.65 a 0.35 ab 0.54 a 0.93 ab 0.75 b 168 0.85 a 1.13 a 0.33 a 0.42 a 0.51 ab 0.59 ab 0.37 ab 0.45 a 0.98 a 0.93 b 224 0.63 a 0.83 a 0.33 a 0.34 a 0.69 a 0.69 a 0.51a 0.44 a 0.68 ab 1.17 a Urea 112 0.17 a 0.23 a 0.09 a 0.11 a 0.61 abA 0.27 bB 0.43 abA 0.17 abB 0.27 ab 0.51 b Check 0 0.25 a 0.14 a 0.11 a 0.09 a 0.34b 0.27 b 0.21 b 0.14 b 0.21 b 0.36 b a Amendments. b values expressed in gram (g). c Means with different lower case letters within columns and different upper case letters between soil conditions (S vs. NS) wi th each variable indicate the significant difference at P < 0.05 . 103 Table 5 . 11 . The effect of animal (AC) and plant (PC) compost amendment at different rates, standard urea and non - amended check on carrot root fresh weight (RFW), root dry weight (RDW), shoot fresh weight (SFW), shoot dry weight (SDW) a nd root - to - shoot dry weight ratio (RD/SD) in pots filled with 960 g of sterilized (S) and non - sterilized (NS) sandy clay loam soil planted with Sugarsnax 54 after 86 days in 2013 experiments. AM a Rate (kg N/ha) RFW RDW SFW SDW RD/SD S NS S NS S NS S NS S NS PC 112 b 6.73 bc c 4.87 ab 1.78 abc 1.52 a 3.59 abA 2.63 aB 0.66 a 0.54 a 2.84 a 2.82 a 168 6.90 bc 4.74 ab 1.56 bcd 1.14 a 3.07 abc 2.45 a 0.52 a 0.43 a 3.03 a 2.77 a 224 10.17 aA 4.69 abB 1.73 abcd 1.51 a 3.77 aA 2.82 aB 0.68 a 0.59 a 2.83 a 2.65 a AC 112 7.55 abc 4.55 ab 2.42 aA 1.14 aB 4.02 aA 2.88 aB 0.77 a 0.58 a 3.24 a 1.99 a 168 4.89 dc 5.29 ab 1.19 cd 1.6 a 2.77 bc 2.86 a 0.69 a 0.49 a 1.95 a 3.36 a 224 8.66 abA 4.83 abB 2.13 abA 1.23 aB 3.77 a 2.87 a 0.63 a 0.46 a 3.29 a 2.81 a Urea 112 3.61 dB 7.37 aA 0.99 dB 1.91 aA 2.45 c 3.15 a 0.45 a 0.68 a 2.48 a 3.07 a Check 0 4.94 cd 4.28b 1.72 abcd 1.24 a 2.48 c 2.28 a 0.69 a 0.42 a 3.23 a 3.15 a a Amendments. b values expressed in gram (g). c Means with different lower case letters within columns and different upper case letters between soil conditions (S vs. NS) within each variable indicate the significant difference at P < 0.05 . 104 Relationships between nematodes and soil properties T he multifactor analysis results revealed correlation pattern in nematode trophic groups, nematode community and food web indices, soil and yield parameters in 2012 and 2013. In 2012, bacterivores, fungivores, and herbivores were positively while NH 4 - N negatively correlated with Dimension 1 (Fig. 5.2A). CEC was positively correlated with Dimension 2. Calcium and soil pH were positively correlated each other while negatively correlated with soil moisture content. Herbivores, fungivores, omniv ores and bacterivores positively correlated with each other while negatively correlated with NH 4 - N. As illustrated in Fig. 5.2B, there was also a correlation pattern in soil food web indices, soil properties and yield parameters. Soil calcium, potassium an d magnesium contents, and cation exchange capacity were positively correlated with each other and Dimension 1 (Fig. 5.2B). Most of the yield parameters positively correlated to each other while negatively correlated with soil nitrate - nitrogen and Dimension 2 (Fig. 5.2B). BI, CI and NH 4 - N were negatively correlated with EI and decomposers - to - herbivores ration. In 2013, soil magnesium and calcium contents, cation exchange capacity, bacterivores, and fungivores were positively correlated while nitrate - nitrogen , soil moisture, phosphorus and organic matter contents negatively correlated with Dimension 1 (Fig. 5.3A). Omnivores and predators positively correlated with Dimension 2 while negatively correlated to soil pH. Calcium and magnesium contents and cation exc hange capacity were positively correlated while soil phosphorus, nitrate - nitrogen, moisture and organic matter contents negatively correlated with Dimension 1 (Fig. 5.3B). BI and CI positively correlated to each other, but negatively correlated with SI and EI. Root fresh and shoot fresh weights, and shoot dry weight was positively correlated each other while negatively correlated with soil phosphorus, nitrate - nitrogen, moisture and organic matter contents (Fig. 5.3B). 105 Figure 5 . 2 . Multiple factor analysis of the variables where Dimension 1 (Dim 1) and Dimension 2 (Dim 2) represent the first and second best summary of variability of the information, respectively. (A) T he relationship among abundance of nematode trophic groups (Gc1) (bacterivores (BV), fungivores (FV), omnivores (OV), predators (PR) and herbivores (HV) (Yeats et al., 1993)) and soil properties (Gc2) (soil pH (pH) , organic matter percentage (OM), nitrate - nitrogen (NO3N), ammonium - nitrogen (NH4N),calcium (Ca), magnesium (Mg), phosphorus (P), potassium (K), moisture percent (MO) and cation exchange capacity (CEC) in 2012 . (B) T he relationship among soil food web indices, trophic group ratios ((FV/BV)=FB) an d ((FV + BV)/HV=FB.P) (Gc1), soil properties (Gc) , and carrot yield (Gc3) (root fresh weight (RFW), root dry weight (RDW), shoot fresh weight (SFW), shoot dry weight (SDW) and root dry - to - shoot dry weight ratios (RDSD)) in 2012 from glasshouse experiment. 106 Figure 5 . 3 . Multiple factor analysis of the variables where Dimension 1 (Dim 1) and Dimension 2 (Dim 2) represent the first and second best summary of variability of the information, re spectively. (A) T he relationship among abundance of nematode trophic groups (bacterivores (BV), fungivores (FV), omnivores (OV), predators (PR) and herbivores (HV) (Yeats et al., 1993)) and soil properties (soil pH (pH) , organic matter percentage (OM), n itrate - nitrogen (NO3N), ammonium - nitrogen (NH4N),calcium (Ca), magnesium (Mg), phosphorus (P), potassium (K), moisture percent (MO) and cation exchange capacity (CEC) in 2013 . (B) T he relationship among soil food web indices and, trophic group ratios (Gc1) ((FV/BV)=FB) and ((FV + BV)/HV=FB.P), soil properties (Gc) , and carrot yield (Gc3) (root fresh weight (RFW), root dry weight (RDW), shoot fresh weight (SFW), shoot dry weight (SDW) and root dry - to - shoot dry weight ratios (RDSD)) in 2013 from glasshouse ex periment. 107 Discussion Tylenchus, Acrobeloides , and Aphelenchus and Filenchus were the most abundant herbivore, bacterivore and fungivore genera, respectively. These nematode genera were also among the most abundant nematodes extracted in the field experiment data collected from same treatments reported in Chapter 3. All of these g enera belong to c - p 2 nematodes, which have stress tolerance ability (Bongers and Bongers, 1998). Overall, the abundance of omnivores and predators were low, may be due to unfavorable soil condition in the pots or short experimental period (86 days) as th ese nematodes normally require up to 130 days to reproduce (McSorley, 2012). The multiple factor analysis result supports the former argument that NH 4 - N and NO 3 - N were negatively correlated with the nematode trophic groups (Fig. 5.2A and 5.3A). Nematode ab undance was higher in 2012 compared with 2013 samples at harvest. Nematodes were not detected in sterilized soil in both 2012 and 2013 soil samples because of either lack of recolonization from the air and tap water or they are below detection level requir ing longer period of time depending of the area of recovery (Yeates et al., 1991; Yeates and van der Meulen, 1996). The alternative explanation could be soil sterilization alters the soil chemistry in ways that inhibit fast colonization by the nematodes (T revors, 1996; Shaw et al., 1999; Ferris, 2010). Indeed, soil sterilization increased soil NO 3 - N and NH 4 - N and both of which were negatively correlated with nematodes. Herbivores, bacterivores and fungivores were higher at planting before the treatments wer e applied in non - planting. However, there were no differences in MI, MI25, EI, SI, BI, CI, fungivores - to - bacterivores and fungivores plus bacterivores - to - herbivores ratios and fertility index among the 108 treatments in both years except PPI was higher at planting in 2013. The food web was basal in most of the data points, suggesting stress ed soil condition with where fungal feeders dominated decomposition pathway and degraded soil food web (Ferris et al., 2001). The result of the present study showed that generally compost amendments increased soil pH in sterilized and non - sterilized soils , and soil sterilization generally decreased soil pH. This is contrary to some of the previous studies that showed increase in soil pH due accumulation of ammonium as a result of decomposition of dead microorganisms and the loss of ammonium oxidizing bacte ria (Tanaka et al., 2003). However, the results are partially in line with my field experiments that compost amendments increased soil pH (Chapter 3). However, Skipper and Westermann (1973) and Shaw et al. (1999) reported that decreased in soil pH due to r elease of organic acids from organic matter. The variable effects of soil sterilization could be due to differences in soil characteristics (Williams - Linera and Ewel, 1984; Shaw et al., 1999). AC had greater effect in increasing soil phosphorus content tha n urea. This supported the result of the field experiment from the same treatments (Chapter 3). Soil sterilization also increased soil phosphorus content may be either due to break down of organic phosphorus or increase in solubility of organic phosphorus that will be broken down later (Malowany and Newton, 1947). Treatments had variable effects on soil potassium content though these treatments increased potassium in the field experiment (Chapter 3). Soil sterilization had no effect on soil potassium conten t. Previous reports were also inconsistent on the effect of soil sterilization on potassium content (Salonius et al., 1967; Skipper and Westermann, 1973). Similar to previous studies, soil sterilization had no effect on soil calcium content (Skipper and Westermann, 1973; Williams - Linera and Ewel, 1984). Treatment effect was variable on soil magnesium content though these treatments had no effect on soil magnesium 109 content in the field (Chapter 3). Similarly, effect of sterilization was not consistent on m agnesium content in other studies (Salonius et al., 1967; Williams - Linera and Ewel, 1984). The results showed that only PC at 224 kg N/ha increased cation exchange capacity on non - sterilized soil in 2012. Eno and Popenoe (1964) reported that soil steriliza tion had no effect on cation exchange capacity as observed in the present study. Similarly, all of these treatments did not increase or decrease cation exchange capacity in 2 years field data (Chapter 3). The increase in cation exchange capacity in PC at 2 24 kg N/ha in the glasshouse may be attributed to high calcium content of PC that increased with the rate of application (Table 5.1). Effects of soil amendments were not consistent on soil organic matter that showed increase only in 2013. However, compost amendments increased soil organic matter after 2 years of the experiment (Chapter 3). Over all soil sterilization did not decrease soil organic matter though studies showed organic matter decreased due to decomposition as a result of heating during soil st erilization (Malowany and Newton, 1947; Skipper and Westermann, 1973). Different studies have shown that soil sterilization increased NO 3 - N gradually as I found here (Malowany and Newton, 1947; Salonius et al., 1967). The results in non - sterilized soil wer e consistent with my field data that only urea significantly increased NO 3 - N compared with plant and animal compost amendments (Chapter 3). Consistent to the result of the field experiment, compost amendments did not increase NH 4 - N in the glasshouse (Chapt er 3). However, soil sterilization increased soil NH 4 - N. Previous reports showed that soil sterilization increased NH 4 - N compare with non - sterilized soil because of the decomposition of organic matter (Malowany and Newton, 1947; Salonius et al., 1967; Trev ors, 1996). The significant increase in soil respiration in sterilized soil at planting in the present study may be due to initial release of CO 2 due to decarboxylation of organic matter (McNamara et al., 110 2003). Otherwise, substrate induced respiration ra tes generally reduced relative to the control due to decreased microbial activity (Ramsay and Bawden, 1983). Compost amendments and urea increased shoot fresh and dry weight compared with non - amended check on both sterilized and non - sterilized soils in 201 2. However, compost amendments generally increased root fresh and dry weight, and shoot fresh weight compared with urea and non - amended check on sterilized soil, but such effect was not observed on non - sterilized soil. In conclusion, the nematode genera d ominated by c - p 2 herbivores and non - herbivores in non - sterilized soil in both years. Omnivores and predators almost non - existent on non - sterilized soil may be because of unfavorable soil condition in the pots that affect their reproduction or short experi ment time that was no long enough for these nematodes to complete their life cycle. The soil food web analysis also revealed that the food web was basal in most of the data points, suggesting stressed soil condition with fungal dominated decomposition path way and degraded soil food web. Nematodes were not detected in sterilized soil at planting and harvest in both years because of either lack of recolonization from the air and tap water or they are below detection level which requires longer period of time depending on recovery conditions. It could also be because of the effect of soil sterilization on the soil chemical and physical properties that inhibit the fast colonization by nematodes. Soil sterilization, generally, increased the contents of measured n utrients. Soil sterilization decreased soil pH may be due to release of organic acids from soil organic matter. I also found soil sterilization increased CO 2 evolution in sterilized soil. Carrot fresh and dry weights were small due to the stunt carrot grow th. These results generally suggest that the effect of compost amendments may not be observed in severe biologically degraded soil in the short - term. 111 CHAPTER 6 SECOND MODIFICATION OF THE FERTILIZER US E EFFICIENCY (FUE) MODEL INTEGRATING WEIGHTED NEMATODE GUILDS FO R BROADER USE IN SOI L HEALTH MANAGEMENT Abstract The objective in this chapter was to integrate the concepts of FUE and soil food web models and test FUE model resolution power on integrated cross - disciplinary decision - making. To accomplish this, I used da ta from field experiments conducted - - where the effects of different rates of - - 112 Introduction As the most abundant metazoan on the planet , nematodes are excellent indicators of changes in soil ecosystem (Bongers and Bongers, 1998). Nematodes are also central players in the soil food web and nutrient cycling processes (Ingham et al., 1985; Ferris et al., 2001). The latter point is particularl y significant in the development of integrated and sustainable soil nutrient and agroecosystem management practices (Ferris et al., 2001; Yeates et al., 2009). In pest and disease as well as soil nutrient management practices in the prevailing agroecosystems influence nematodes (Bulluck III et al., 2002 a ; Wang et al., 2006; Neher, 2010; Melakeberhan et al., 2015). For example, most nematode management in agricultur al practices are focused on suppressing herbivore nematodes. Moreover, most pest and disease management , and increasing crop yield by modifying the plant and/or the soil (Melakeberhan, 1997; Baligar et al., 2001; Good et al., 2004) and do not factor benefi cial nematodes and their role in nutrient cycling (Ingham et al., 1985; Neher et al., 2012). In order to utilize the best attributes of nematodes, it is necessary to consider the current soil and nutrient management practices designed to improve crop yield and/or suppress nematodes and other pests and diseases (Melakeberhan, 2006). For the most part, they are applied to manage one factor or another and do not consider integrated outcomes (Melakeberhan and Avendaño, 2008). In other words, they test the hypot hesis that either crop yield will increase and/ or pest will be suppressed as opposed to testing whether there are quantifiable relationships that will lead to assessing integrated efficiency . Such an approach es need to account for ecosystem functions and p rocesses where agrobiological, physicochemical , economic and 113 environmental efficiencies can be separated (Melakeberhan, 2010). This can be achieved using the Fertilizer Use Efficiency (FUE) model (Melakeberhan, 2006). The FUE model, which separates the re lationships among plant growth, herbivore nematode parasitism, nutrient deficiency and toxicity, allows cross - disciplinary and integrated decision - making (Melakeberhan, 2006). It calculates treatment outcome as a percent of control (untreated check) and gr aphically expresses data in four quadrants from best ( Quadrant A) to worst case ( Quadrant D) scenarios (Fig. 6 .1a). The FUE model was modified to include assessment of beneficial nematodes and soil physicochemical properties ( Fig. 6 .1b , Melakeberhan and Anvenda ñ o, 2008). Such integrated analysis links nematology and cross - disciplinary gaps in testing agriculturally and ecologically sustainable management practices ( Melakeberhan and Avendaño, 2008 ; Melakeberhan, 2010 ). Figure 6 . 1 . Fertilizer use efficiency (FUE) model and its modification. (a) Four hypothetical categories of FUE derived from host productivity/nematode/nutrient interactions (Melakeberhan, 2006) with permission from B rill and (b) modified FUE model applied to assess the effect of soil amendment on the relationships between nematode trophic groups (excluding plant - parasitic) and yield or soil parameters (Melakeberhan and Avenda ñ o, 2008) with permission Springer. a b 114 The n ematode - base d Ferris et al. (2001) soil food web model describes soil condition s from best (Quadrant B) to worst (Quadrant D) case scenarios for agroecosystem suitability and nutrient cycling potential (Fig. 6.2). It uses a graphic representation of the relationship between the nematode EI (a measure of opportunistic bacterivore and f ungivore nematodes) and SI (indicator of food web state affected by stress or disturbance) to describe the soil community profile in four quadrants. Figure 6 . 2 . Functional guilds of soil nematodes chara cterized by feeding habit and by life history characteristics expressed along a colonizer - persister (c - p) scale (After Bongers & Bongers, 1998). Indicator guilds of soil food web conditions (basal, structured and enriched) are designated and weightings of the guilds along the structure and enrichment trajectories are provided for determination of the enrichment index (EI) and structure index (SI) of the food web (Source: Ferris et al., 2001) with permission from Elsevier. Apart from the possibility for cro ss - disciplinary and integrated analysis, the graphical presentation of FUE model creates an opportunity to demonstrate changes not apparent in the calculation of nematode indices. However, the FUE model and its modification are based on 115 numbers of nematode s, but not functional guilds. On the other hand, soil food web model Therefore, the objective of the study was to integrate the concepts of FUE and soil food web models and test FUE model resolution power on integrated agroecological analysis. Materials and methods Experimental design and treatments A field study was conducted to investigate the effects of PC and AC on nematode community structure, herbivores suppression and soil pro perties, and yield and quality of - AC was purchased from Morgan Composting, Inc., Sears, MI, USA, and PC was obtained from MSU Student Organic Farm, Holt, MI, USA. The characteristics of the composts are presented in Chapter 3 (Table 3.1). The experiment was conducted at Michigan State University (MSU) Horticulture Teaching and Research Center in Holt, Michigan (N 43 0 0 - Brookston sandy clay loam (fine - loamy, mixed, mesic Type, Haplaquolls - Argiaquolls, Anon, 1977) with 54 % sand, 25 % silt and 21 % clay. Compost treatments were adjusted to supply 135, 203 and 270 kg N/ha, and 112, 168 and 224 kg N/ha for Cupar and Sugarsnax 54, respectively. Standard ur ea (135 and 112 kg N/ha for - amended check were included as controls. Treatments were arranged in randomized complete block design with four replications. Each p lot was 3.72 meter square. Treatments were appli ed, distributed uniformly by hand and mixed to a depth of 30 cm using an RTR2548 rototiller (Land Pride, Assaria, KS, USA) before planting. Carrot seeds were planted at the rate s of 640,000 and 1, 200,000 seeds/ha for Cupar and Sugarsnax 54, respectively, using MasterMacc planter (Market Farm Implement, 116 Friedens, PA, USA). Throughout the duration of the experiment, weed control measures were taken as per recommended standard herbicides for carrots and hand weeding. Herbicides consisted of preemergenc applic ation of linuron (0.56 kg a.i/ha) 1 to 2 weeks after carrot planting, and postemergence application of linuron (0.56 kg a.i/ha) and clethodim (0.1 kg a.i/ha) applied at 4 to 6 weeks after carrot planting. Plots were irrigated with sprinkler irrigation syst em set for an hour every day until the carrots emerged and for 4 hours as required after carrot emergence. Experiments for Cupar were completed 132 and 133 DAP in 2012, and 2013 and 2014 growing seasons, respectively, and Experiment for Sugarsnax 54 were completed 78 and 79 DAP in 2012 and 2013 growing seasons, respectively. Soil sampling, and nematode extraction, identification and enumeration In 2012, 2013 and 2014, six soil cores per plot were collected at 0 - 25 cm soil depth of root zone from the c enter two rows using a sampling cone (AMES companies, Inc., Camp Hill, PA, USA) at planting (May, June) and at harvest (October) . ( Avendaño et al., 2003) and fixed according to Hooper (1986). Nematodes were identified under inverted microscope (Accu - scope Inc, Commack, NY, USA) at 400X magnification at genus level following diagnostic keys by Bongers (1994) and the University of Nebra ska Lincoln nematode identification website (http:nematode.unl.edu/konzlistbutt.htm). Each identified nematode was assigned to a colonizer - presister (c - p) scale according to Bongers & Bongers (1998). 117 Soil pH, organic matter and carrot yield Soil organic matter and soil pH, and marketable and unmarketable carrot yield were selected as a measure of integrated efficiency of the treatments. Soil pH and organic matter were determined from 2012 and 2013 samples by the MSU Soil and Plant Nutrient La boratory using standard procedures (Huffman & Barbarick, 1981; Nelson, 1983). Carrots were harvested from the center two rows using spading fork (True Temper, AMES companies, Inc ., Camp Hill, PA, USA ) and washed with a garden hose. Carrots were categorized and counted as marketable and unmarketable following USDA standards (Anon, 1965). Integrating FUE and soil food web models concepts The original FUE model is centered on managing the impact of herbivore nematodes (Melakeberhan, 2006). It was modified to integrate beneficial nematodes trophic groups with link s to agronomic, economic and soil health parameters (Melakeberhan and Avendaño, 2008). o n of nematode guilds concept (Ferris et al., 2001). The Ferris et al. (2001) model evaluates the soil food web and soil conditions by identifying three food web conditions as basal, enriche d and structured. Soil food web model The second modification of the FUE model (Fig. 6 .3), proposed herein, in tegrates nematode guilds concept of Bongers & Bongers (1998) and weightings of nematode guilds (Ferris et al., 2001). Nematode guild concept refers the assemblage of nematode species with similar biological attributes and response to environmental conditio ns as described by Ferris et al. (2001). As described in Ferris et al. (2001) weighting system integrates nutrient transfer 118 during the life course, organism longevity, food web complexity, individual biomass and disruption - sensitivity of functional guilds. Figure 6 . 3 . The second modification of FUE model that integrated concepts of modified FUE and soil food web models to assess the effect of soil amendment on the relationships between nematode functional guilds as indicator of soil health and other agronomic parameters. Data points that fall abo ve the controls (100 %) will show an increase/improvement in tested agronomic parameters (A and B) and soil health status (B and D). Data points in Quadrant B would be best - case scenario, in Quadrant C would be worst - case scenario, and those Quadrant A and D provide a choice of improving soil health or yield, respectively (After Melakeberhan and Avendaño, 2008) with permission from Springer. Unlike the soil food web model, the enrichment and structure components of the food web are not treated separately i n the second modification of FUE model . The total nematode assemblage is treated in the concept of trophic connectance in food web of increasing complexity as the system matures or becomes progressive ly simpl e as the system degrades. The assumption is that the food web in healthy soils will contain all the nematode functional groups including c - p 1 nematodes which are present in all habitats from disturbed to the most stable tropical forest, fruits and carcasses (Bongers and Bongers, 1998). This explains fo od webs of higher complexity Efficient for agronomic parameters, but inefficient for improving soil health Efficient for agronomic parameters and improving soil health Ine fficient for agronomic parameters and improving soil health Ine fficient for agronomic parameters, but efficient for improving soil health Weighted nematode guilds abundance as % of control Agronomic parameters as % of control 100 0 100 A B C D 119 contain representatives of food webs of lower complexity (Bongers and Bongers, 1998). As Ferris et al. (2012) stated, a healthy soil food web should sustain nematodes of different life strategies . These include those with feedi ng behaviors ranging from fast - growing and fast - breeding bacteria - feeding nematodes at the bottom of the food chain, to those slow growing, long generation and low fecundity predaceous nematodes at the top. Second modification of the FUE model Weighted nematode guilds abundance that includes all nematode guilds in the calculations was proposed (Fig. 6 .3). Ferris et al. (2001) weighting systems for c - p 2 up to c - p 5 nematodes were adopted and introduced a new weight for c - p 1 nematodes. The Ferris et al. (2001) weightings of nematode guilds in structure trajectory reflect the postulated degree of trophic connectance in food webs of increasing complexity as the system matures or progressive food web simplicity as the system degrades. They assumed that troph ic links ( l ) increase as a constant fraction of square of the number of species ( s s 2 constant and s is the number of species. Based on the available data, they established the formula for weightings of c - p values which is 0.8*(0.5*(n+1)) 2 where n is the c - fraction of increase in food web complexity with each increment in c - p class. Using this concept and formula, a new weight was introduced for the c - p1 nematodes different from the weight given by Ferris et al. (2001). C - p 1 nematode received weight (0.8*(0.5*(0+1)) 2 = 0.2) based on their indicator role in the structured food web though Ferris et al. (2001) assigned the weight (3.2) to c - p 1nematodes based on their responsiveness to nutrient enric hment. Their weight (0.2) is reasonable to weight their presence and abundance in structured food web and undisturbed soil. I n the calculation s, weighted nematode guilds abundance received the following weights based on their presence and 120 abundance in heal thy soil assumed to have structured soil food web. The weights will be c - p 1= 0.2, c - p 2 = 0.8, c - p 3 = 1.8, c - p 4 = 3.2 and c - p 5 = 5. Weights of nematode guild for each treatment were calculated as: Weighted nematode guilds abundance = (0.2*total no. cp1) + (0.8*total no. cp2) + (1.8*total no. of cp3) + (3.2*total no. cp4) + (5*total no. cp5) [1] Fitting the data to the second modification of the FUE model Before plotting the data, values will be standardized as percent of control as fol lows: Weighted nematode guilds abundance as % of control Agronomic or soil parameter of interest as % of control After calculating weighted nematode guild abundance and other agronomic parameters as a percent of control, the y are plotted on x - axis ( weighted nematode guild abundance ) and y - axis ( agronomic parameters and other parameters) for analysis of integrated efficiency (Fig. 6 .3). Best case scenario would be if data points fell in Quadrant B, where the agronomic parameter s and soil health condition are improved. Worst case scenario would be if data points fell in Quadrant C , where agronomic parameters and soil health status are not improved. Data points that fall in Quadrants A and D are half efficient and will require com plementary intervention to improve soil health status or other agronomic parameters, respectively. The second modification 121 - Statistical analysis of data fitted to the second modification of the FUE model Two types of statistical analyses were conducted. First, data used in this study were analyzed following the standard ANOVA and mean separations (Tables 6.1 and 6.2). Second, t he weighted nematode guilds abundance (x - axis) and agronomic parameters (y - axis) data points were expressed on a percent of control basis and fitted to the FUE mod el (Figs. 6.4 6.7). The data fitted to the FUE model were then tested for statistical difference from the control (100 %) using one - tail t - The means of the treatments with statistical difference from 100 % are noted by asteris k s (*). Results The previous data analysis (Chapter 3) showed that compost treatments significantly increased soil pH in Cupar at harvest in 2013 compared with at planting in 2012 (Table 6.1). However, urea decreased soil pH at harvest in 2013 c ompared with at planting in 2012. Urea also significantly decreased soil pH at harvest in 2012 and 2013 compared with all of the compost treatments. There was no significant difference in soil organic matter, marketable and unmarketable carrots among the t reatments. In Sugarsnax 54, all of the compost amendments significantly increased soil pH at harvest 2013 compared with at planting in 2012 (Table 6.1). Urea significantly decreased soil pH at harvest in 2013 compared with at planting in 2012. PC at 168 k g N/ha, and AC at 112 and 224 kg N/ha significantly increased organic matter compared with urea and non - amended check in Sugarsnax 54 at harvest in 2013. PC at 168 kg N/ha and AC at 112 kg N/ha showed 122 comparable marketable carrot yield to urea in 2012. In 2013, compost amendments significantly increased marketable carrot yields compared with urea and non - amended check (Table 6.2). In 2012, almost all of the soil samples were generally lower in organic matter relative to non - amended check before the treatme nts were applied in Cupar (Fig. 6.4). At the same time, weighted nematode guilds abundance was lower in all of the compost treatments except PC at 135 N/ha and AC at 135 and 270 kg N/ha relative to non - amended check in Cupar (Fig. 6.4). However, all compo st amendments except PC and AC at 135 kg N/ha increased organic matter at harvest 2013. Comparing these data points with the control (100 %) showed that all of the AC treatments and PC at 270 kg N/ha were significantly greater than 100 % at harvest (Octob er) in 2013 (Fig. 6.4). Similarly, all of the compost amendments increased weighted nematode guilds abundance except PC at 135 kg N/ha and AC at 203 kg N/ha at harvest in 2012. Weighted nematode guilds abundance in all of the treatments was not different from 100 % at harvest in 2012. At harvest in 2013, PC at 203 kg N/ha and AC at 270 kg N/ha were significantly greater than 100 %. Similarly, weighted nematode guilds abundance at harvest in 2014 as significantly greater than 100 % in all of the compost ame ndments except PC at 270 kg N/ha and AC at 203 kg N/ha. Such effect was not observed in urea (Fig. 6.4 and 6.5). Organic matter and weighted nematode guilds abundance in all compost amendments were greater than in the check at harvest in 2013 (Fig. 6.4). M oreover, the effects of AC amendments on both organic matter and weighted nematode guilds were greater compared with the PC amendments except PC at 270 kg N/ha. Although urea increased organic matter in 2012 relative to the check, it decreased in 2013. Fur thermore, urea decreased or did not affect weighted nematode guilds abundance compared with non - amended check in 2012 and 2013. 123 At planting in 2012, soil pH was higher in all compost treatments compared with non - amended check in Cupar. However, all of the compost treatments except AC at 135 kg N /ha had lower weighted nematode guilds abundance compared with the non - amended check at planting in 2012 (Fig. 6.4). However, all compost amendments except PC at 203 kg N/ha, had higher or same level of soil pH comp ared with non - amended check at harvest in 2012. The t - test comparison showed that PC and AC at 270 kg N/ha plots and urea had significantly higher soil pH than 100 % at the beginning. However, PC at 135 kg N/ha and AC at 270 kg N/ha, significantly increase d soil pH while urea significantly decreased it at harvest in 2013 (Fig. 6. 4). All compost increased soil pH at harvest in 2013. However, urea decreased soil pH compared with the non - amended check in 2012 and 2013. All compost amendments, except PC at 135 and 270 kg N/ha in 2012 and PC at 270 kg N/ha, increased marketable carrots relative to non - amended check (Fig. 6.5). However, the comparison showed that none of the treatments were significantly greater than 100 % in marketable and unmarketable carrot in 2012. PC at 203 kg N/ha was greater than 100 % in marketable carrots in 2013. In 2014, PC at 135 and 203 kg N/ha were greater than 100 % in 2014 (Fig. 6.5). Overall, all of compost treatments except PC at 203 and AC at 203 kg N/ha reduced unmarketable car rots relative to non - amended check in all years. However, urea increased unmarketable yield relative to the check in 2013 and 2014. The comparison with 100 % showed that PC at 135 and 270 kg N/ha, and AC at 135 kg N/ha significantly decreased unmarketable carrots in 2013. Such significant decrease in unmarketable carrots was observed in PC at 135 kg N/ha while urea increased it (Fig. 6.5). All of compost amendments, except PC at 135 kg N/ha in 2012 and PC at 270 kg N/ha, in 2014 increased weighted nematode guilds abundance relative to non - amended check. However, urea decreased weighted nematode guilds abundance in all years relative to non - amended check. 124 Table 6 . 1 . Soil organic matter (% OM), soil pH, and marketable and unmarketable carrots (T/ha) in Cupar plots amended with animal (AC) and plant (PC) composts at different rates (kg N/ha), standard urea application and non - amended check in sandy clay loam soil at planting ( 0 ) and at 132 and 133 days after planting (DAP) in 2012 - 2013 growing season for % OM and pH, and in 2012 - 2014 growing seasons for carrot yield (T/ha). AM a Rate (Kg N/ha) % OM pH Marketable Unmarketable 2012 2013 2012 2013 2012 2013 2014 2012 2013 2014 DAP DAP DAP 0 132 0 133 0 132 0 133 132 133 132 133 132 133 PC 135 1.6 1.8 2.4 2.1 7.2 bA b 7.3 bAB 7.5 bA 7.7 aA 35 56 35 46 14 13 203 1.7 1.9 2.3 2.0 7.2 bA 7.1 bAB 7.4 bA 7.7 aA 59 64 34 46 23 16 270 1.7 2.0 2.4 2.2 7.2bA 7.5bA 7.5 bA 7.7 aA 30 58 19 51 14 18 AC 135 1.7 1.9 2.3 2.1 7.1bA 7.2bAB 7.4 bA 7.7 aA 59 56 24 43 15 20 203 1.7 2.0 2.4 2.2 7.2bA 7.2bAB 7.5 bA 7.7 aA 44 54 26 52 17 22 270 1.6 2.0 2.3 2.2 7.2bA 7.2bAB 7.5 bA 7.7 aA 44 52 31 52 15 21 Urea 135 1.7 2.0 2.4 1.9 7.3aA 6.8cB 7.4 abA 7.2 bB 56 54 26 47 23 26 Check 0 1.8 1.9 2.4 1.9 7.1bA 7.2bAB 7.4 aA 7.6 aA 44 52 23 51 19 21 a Amend m ents. b Means with different lower case letters in rows within each variable and different upper case letters within columns indicate significant difference at P < 0.05 . 125 Table 6 . 2 . Soil organic matter (% OM), Soil pH, and marketable and unmarketable carrots (T/ha) in Sugarsnax 54 plots amended with animal (AC) and plant (PC) composts at different rates (kg N/ha), standard urea application and non - amended check in sandy clay loam soil at planting ( 0 ) and at 78 and 79 days after planting (DAP) in 2012 - 2013 growing seasons. AM a Rate (Kg N/ha) % OM pH Marketable Unmarketable 2012 2013 2012 2013 2012 2013 2012 2013 DAP DAP DAP DAP DAP DAP 0 78 0 79 0 78 0 79 78 79 0 79 PC 135 3.1 aB b 2.3 cA 2.8 bA 2.7 bAB 7.3 bAB 7.3 bA 7.3 bA 7.5 aA 3 b 16 a 16 9 203 3.2 aA 2.4 cA 2.7 bA 2.9 abA 7.3 bAB 7.3 bA 7.3 bA 7.6 aA 11 a 18 a 16 8 270 3.0 aB 2.3 cA 2.7 bA 2.8 abAB 7.2 bAB 7.3 abA 7.3 abA 7.4 aA 4 b 17 a 16 9 AC 135 3.2 aA 2.4 cA 2.8 bA 3.0 abA 7.4 aA 7.3 bA 7.3 bA 7.6 aA 7 ab 17 a 19 8 203 3.1 aB 2.3 cA 2.8 bA 2.9 abA 7.4 bAB 7.4 bA 7.3 bA 7.6 aA 3 b 17 a 16 10 270 3.0 aB 2.3 cA 2.7 bA 3.1 aA 7.3 bAB 7.4 bA 7.2 bA 7.5 aA 5 b 17 a 17 9 Urea 135 3.1 aB 2.2 cA 2.6 bA 2.5 bB 7.2 aB 7.2 aA 7.2 aA 7.0 bB 10 a 11 b 17 7 Check 0 3.1 aB 2.2dA 2.8 bA 2.6 cB 7.3 bAB 7.3 bA 7.3 bA 7.5 aA 6 b 11 b 15 6 a Amendm e nts. b Means with different lower case letters in rows within each variable and different upper case letters within columns indicate significant difference at P < 0.05 . 126 In Sugarsnax 54, all compost treatments increased organic matter at harvest while urea decreased it relative to non - amended check at harvest in 2012 and 2013 (Fig. 6.6). There was no significant difference from 100 % in soil organic matter at the beginning of 2012 and at the end of 2012 growing season. However, all compost amendments were greater than 100 % at harvest in 2013, but such effect was not observed in urea (Fig. 6.6). All compost amendments except PC at 168 and 224 kg N/ha, increased weighted nem atode guilds abundance at harvest in 2012 and 2013. At harvest in 2012, weighted nematode guilds abundance in PC at 168 and 224 kg N/ha was significantly lower than 100%. At harvest in 2013, weighted nematode guild abundance was significantly greater in AC at 224 kg N/ha than 100 % (Fig. 6.6). Soil pH in compost amendments was not different from 100 %, but urea was significantly lower than 100 %. With regard to Sugarsnax 54 carrot yield, PC at 112 and 224 kg N/ha, and AC at 112, 168 and 224 kg N/ha, decrea sed marketable carrots relative to non - amended check in 2012. However, all compost amendments increased marketable carrots relative to non - amended check in 2013 (Fig. 6.7). Contrary to this, all the compost treatments increased total unmarketable carrots r elative to non - amended check in 2012 and 2013 (Fig. 6.7). Marketable carrots in 2012 in PC at 112 kg N/ha was significantly lower than 100 % while higher in PC at 168 kg N/ha and in urea treatments. In 2013, marketable carrot in all of the compost amendmen ts was greater than 100 %, but urea did not show such result (Fig. 6.7). Unmarketable carrots was greater than 100 % in AC at 112 kg N/ha in 2012. However, all of the compost treatments, except PC at 168 kg N/ha and AC at 112 kg N/ha, increased unmarketabl e carrot in 2013 (Fig. 6.7). 127 Figure 6 . 4 . Effects of compost types and rate of application data plotted on the modified - modified FUE model for Cupar carrot cultivar at planting in May 2012, and harvest in October 2012 and 2013 growing seasons for organic matter and soil pH. - - N - - 1 2 * 3 4 5 6 * 7 8 1 2 3 4 5 6 7 8 1 * 2 * 3 * * 4 * * 5 * * 6 * * 7 8 80 100 120 0 50 100 150 200 250 300 Organic matter as % of control Weighted nematode guilds abundance as % of control May 12 Oct 12 Oct 13 1 2 3* 4 5 6* 7* 8 1 2 * 3* 4 5 6 * 7 8 1 * * 2 * 3 * 4 * 5 * 6 * * 7* 8 90 100 110 0 50 100 150 200 250 300 Soil pH as % of control Weighted nematode guilds abundance as % of control May-12 Oct-12 Oct-13 128 - *Treatments with subscripts and superscripts asterisks (*) indicate significantly different form 100 % for weighted nematode guilds abundance, and soil organic matter and soil pH, respectively, using one - tailed t - Figure 6 . 5 . Effects of compost types and rate of application data plotted on the modified - modified FUE model for Cupar carrot cultivar for marketable and unmarketable (UNC) carrots at harvest in October 2012, 2013 and 2014 growing seasons. - - 1 2 * 3 4 5 6 * 7 8 1 * 2 * * 3 * 4 5 * 6 * 7 8 1 * * 2 * * 3 4 * 5 6 * 7 8 0 100 200 0 100 200 300 Marketable carrots as % of control Weighted nematode guilds as % of control Oct-12 Oct-13 Oct-14 1 2 3 4 5 6 7 8 1* 2 3* 4* 5 6 7 8 1* 2 3 4 5 6 7 8 0 100 200 0 100 200 300 UNC as % of control Weighted nematode guilds abundance as % of control Oct-12 Oct-13 Oct-14 129 N - - - *Treatments with subscripts and superscripts asterisks (*) indicate significantly different form 100 % for weighted nematode guilds abundance, and marketable and UNC carrots, respectively, using one - tailed t - Figure 6 . 6 . Effects of compost types and rate of application data plotted on the modified - modified FUE model for Sugarsnax 54 carrot cultivar at planting in May 2012, and harvest in August 2012 and 2013 growing seasons for organic matter and soil pH. - - 1 2 3 4 5 6 7 8 1 2 * 3 * 4 5 6 7 8 1 2* 3* 4* 5* 6 * * 7 8 80 100 120 0 50 100 150 200 250 Organic matter as % of control Weighted nematode guilds abundance as % of control May 12 Aug 12 Aug 13 1 2 3 4 5 6 7 8 1 2 * 3 * 4 5 6 7 8 1 2 3 4 5 6 * 7* 8 80 100 120 0 50 100 150 200 250 Soil pH as % of control Weighted nematode guilds abundance as % of control May-12 Aug-12 Aug-13 130 N - - - *Treatments with subscripts and superscripts asterisks (*) indicate significantly different f orm 100 % for weighted nematode guilds abundance, and soil organic matter and soil pH, respectively, using one - tailed t - Figure 6 . 7 . Effects of compost types and rate of application data plotted on the modified - modified FUE model for Sugarsnax 54 carrot cultivar for marketable and unmarketable (UNC) carrots at harvest in August 2012 and 2013 growing seasons. - - 1* 2 * * 3 * 4 5 6 7* 8 1* 2* 3* 4* 5* 6 * * 7 8 0 100 200 0 50 100 150 200 250 Marketable carrots as % of control Weighted nematode guilds as % of control Aug-12 Aug-13 1 2 * 3 * 4* 5 6 7 8 1* 2 3* 4 5* 6 * * 7 8 0 100 200 0 50 100 150 200 250 UNC as % of control Weighted nematode guilds as % of control Aug-12 Aug-13 131 N - - - *Treatments with subscripts and superscripts asterisks (*) indicate significantly different form 100 % for weighted nematode guilds abundance, and marketable and UNC carrots, respectively, using one - tailed t - Discussion The second modification of the FUE model introduces weighted nematode guilds to describe the integrated efficiency of compost amendment use outcomes in four possible categorie s. Best case scenario would be if the weighted nematode guilds data points fell in Quadrant B, indicating that the agronomic parameters and soil health conditions of the prescribed treatments are desirable. Worst case scenario would be if data points fell in Quadrant C, indicating that the compost amendment treatments have resulted in an undesirable outcome for soil health and crop yield expectations. Data that fall in Quadrants A and D would indicate the need for complementary intervention to improve soil health and agronomic parameters, respectively. Fitting the weighted nematode guilds data to the second modification of the FUE model showed that organic matter, soil pH and marketable carrot data points of compost amendment treatments fell in Quadrant B w hile data points of urea treatments fell in either in Quadrant A or Quadrant C in Cupar. Most unmarketable carrots data points from the compost amendment treatments fell in Quadrant D while data points from the urea treatments fell in Quadrant A. These res ults show that compost amendments are efficient in increasing organic matter, soil pH and marketable carrot yield, and improving soil health. These results were not only in line with 132 soil health condition diagnosed in the soil food web evaluation using Fer ris et al. (2001) model, but also allow integrated analysis of agronomic parameters. In Sugarsnax 54, organic matter and soil pH data points from compost amended treatments fell in either Quadrant A or Quadrant B while data points from urea treatments fel l in Quadrant C. Unlike in Cupar, data points of PC at 168 and 224 kg N/ha amendments fell in Quadrant A. Thus, suggesting that the compost amendments were efficient in improving soil organic matter and soil pH. Such conclusions would not have been possibl e without the integrated analysis the modifications introduced into the FUE model. All of the compost amendment treatments increased unmarketable carrots relative to non - amended check in 2012 and 2013. While this suggests the need for intervention to impr ove marketable carrots yield, it is necessary to consider how factors such as soil compaction, coarse texture, undecomposed organic debris or fluctuations in nutrient and moisture content may be contributing to producing unmarketable carrot (Guteziet, 2001 ; Walker, 2004). In Cupar, statistical analysis of the effect of compost amendments, urea and non - amended check on organic matter, marketable and unmarketable carrots showed no significant differences (Table 6.1). However, plotting the data on FUE model s howed differences that were not explained in the statistical analysis. This allowed seeing difference between compost types which was not apparent in the means through statistical analysis. Moreover, comparison of the data points with 100 % revealed most of the data points were greater than 100 % for most of compost amendments at the end of the growing seasons. I found consistent results with my previous statistical analysis that those significant differences in organic matter and marketable carrots among the treatments in Sugarsnax 54 are clearly seen on FUE model (Table 6.2 and Fig. 6.6). In 2012, PC at 168 kg N/ha and urea were significantly higher in marketable carrots compared with 133 the rest of the treatments in Sugarsnax 54. Also, urea and non - amended check were significantly decreased marketable carrot yield compared with compost amendments in 2013, these results are clearly apparent on second modification of the FUE model. Therefore, FUE model is powerful in separating both significant and non - signifi cant, but meaningful differences in both agronomic parameters and soil health condition. Weighted nematode guild analysis was also in line with the result of faunal profile analysis obtained from this data set (Chapter 3). Data points of compost amendments fell in Quadrant B while those of urea fell in Quadrant A and B (Fig. 6.6A). The interpretation of the data in the second modification of the FUE model here is the best case scenario that showed compost amendments were efficient in agronomic parameters an d soil health condition. Similar interpretation as the best case scenario following Ferris et al. (2001) that the soil food web was enriched and maturing in compost treatments in Cupar. Although data from Sugarsnax 54 did not overlap with the faunal profil e analysis, the second modification of the FUE model further separates the data points that show slight differences among compost treatments, and between compost treatments and urea (Fig. 6.6B). These show that the second modification of the FUE model not only describing the effect of management practices on soil health, but also allow integration of other agronomic parameters for cross - disciplinary decision making. The model helps to identify and monitor changes in soil conditions, thereby creating the nec essary bridges to disciplinary gaps (Melakeberhan and Avendaño, 2008). 134 Figure 6 . 8 . Soil food web condition in plots planted with Cupar (A) and Sugarsnax 54 (B) and amended with plant (PC) and animal (AC) compost, standard urea and non - amended check in sandy clay loam soil at planting (May, June) and harvest (August, October) in 2012 - 201 4 and 2012 - 2013 growing seasons for Cupar and Sugarsnax 54, respectively. In Cupar plots, numbers 1 - 3 refer PC at a rate of 135, 203 and 270 kg N/ha, respectively and 4 - 6 refer AC at a rate 135, 203 and 270 kg N/ha, respectively, 7 and 8 refer urea and che ck, respectively. In Sugarsnax 54 plots, numbers 1 - 3 refer PC at a rate of 112, 168 and 224 kg N/ha, respectively and 4 - 6 refer AC 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 1* 2* 3* 4* 5 6* 7 8 1 2 3 4 5 6 7 8 1* 2* 3 4* 5* 6* 7 8* 0 50 100 0 50 100 Enrichment Index (%) Structure Index (%) May-12 Oct-12 May-13 Oct-13 June-14 Oct-14 A A B C D 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 0 50 100 0 50 100 Enrichment index(%) Structure index (%) May-12 Aug-12 May-13 Aug-13 B A B D C 135 at a rate 112, 168 and 224 kg N/ha, respectively, 7 and 8 refer urea and check, respectively (Source: Chapter 3 ). *Treatments significantly increased SI from 50 % using one - tail t - in 2013 and 2014 growing seasons. In conclusion, the second modification of the FUE model integrated the concepts of FUE and soil food web mo dels for enhanced diagnostic power of the impacts of soil amendment management practices. In order to fully assess soil health, the modification needed the power of integrating nematode functions by giving different weights to the presence and abundance of nematode guilds. A new guild weight (0.2) was assigned for c - p 1 nematodes which is proportional to their indicator value in soil health, which is different from the weight given by Ferris et al. (2001). The second modification of the analysis in the present study showed that the new modification impr oved the explanatory power of the FUE model towards integrated soil health analysis. Thus, second modification of FUE model creates a road map for cross - and multidisciplinary applications of soil amendment - based management practices. 136 CHAPTER 7 GENERAL DIS CUSSION AND CONCLUSI ONS The goal of my Dissertation was to develop integrated compost amendment use strategy for managing soil nutrient, nematodes, soil health, and carrot yield and quality in potentially benefits such as increasing organic matter, nutrient supply and pest suppression are well known (Pinamonti, 1998; Abawi and Widmer, al., 2011, McSorley, 2011). Mo reover, little information is available on the impact of specific compost types and rates of applications on herbivore nematode suppression, nematode community structure, soil food web conditions, overall soil health, and carrot yield and quality. This is particularly important when considering the growing environmental concerns relative to nematicide/pesticide use that have negative impact on soil organisms, which drive the soil food web and nutrient transformations and for which nematodes are excellent in dicators (Ingham et al., 1985; Bongers and Bongers, 1998; Ferris et al., 2001; Ferris et al., 2010). In order to address the multitude of challenges and gaps, it is necessary to recognize the need for generating integrated data sets and developing models t hat explain variable responses and efficiencies of soil amendment experimental outcomes for better cross - disciplinary applications. The thrust of my Dissertation has been to understand the relationships among plant - and animal - based organic amendments, har mful and beneficial nematode communities, and changes in soil ecosystem services under fresh market and processing carrot production in mineral soils under field and controlled conditions. Among my significant findings include identifying the a) complexiti es of the shifts in nematode community structure relative to animal - and plant - based organic amendments and rates of applications; b) interactions of integrated plant - based organic 137 amendment and conventional fertilizer; c) challenges associated with introd ucing compost in biologically degraded soil; and d) parameters necessary to integrate the soil food web and fertilizer use efficiency models for greater cross - disciplinary applications. I also did a one - time minor survey as part of relating the nematode co mmunities in my experimental field to what may be happening in the carrot production fields (Appendix B). Compost amendment integrated with inorganic fertilizer used as alternatives to conventional managements in my study improved soil health as reflecte d in the presence and abundance of omnivores and predators that represent the higher trophic level of the soil food web. Potentially, this will lead to long - term healthy environmental quality and better yield (Fig. 7.1). The presence of higher trophic leve ls in the soil food web indicates higher biological interactions and trophic links in soils typical of carrot production shows the kinds of biological changes that may occur in such soils. This provides basis for developing better strategic use of compost than currently exist. On the other hand, urea application in my study negatively affected the soil biology and soil physicochemical properties. The soil food web dominated by bacterivores and fungivores that ultimately lead to ecosystem disservices, w hich in turn cause poor soil health and environmental quality, and yield reduction. The reduction of the higher trophic level of soil food web, and decline in MI, biological activity levels, soil pH and nutrients observed in my study from urea treated plot s may reflect what is happening in conventional carrot production systems (Fig. 7.1). 138 - - - - - - - - - - - - - Figure 7 . 1 . The long - term impact of conventional and alternative management practices on soil health, environmental quality and yield 139 As mentioned earlier, the overall results of this study supported the value of nematodes as indicators of ecosystem change. In Chapter 3, I compared the effect of compost types and rates of applications on soil food web conditions, soil physicochemical and biological properties, and carrot yield and quality. Compost amendments increased omnivore nematodes over time in Cupar, th e processing cultivar. This was reflected by the more structured soil food web with greater trophic links with potential pest regulatory ecosystem services. However, the positive impact of compost on soil food web structure was not observed in Sugarsnax 54 , the fresh market cultivar. It is likely that the growing season may have been too short for the omnivore nematodes to reproduce (McSorley, 2012). This, in turn, may explain some of the sources of variability when assessing the benefits of compost applica tion relative to cultivar differences. My findings in Chapter 3 also pointed out variabilities relative to compost rate and time. The increased CO 2 levels after two years under the higher rates of AC suggests improve soil biological activity. Similarly, t he general increase in soil mineral contents in AC amendments over time suggests positive impact on soil fertility and chemistry. To the contrary, urea decreased soil pH and increase NO 3 - N. The positive impacts on soil food web structure, soil biological a ctivities and soil nutrient contents over time suggest the need for repeated compost application to see the benefits. Moreover, the variable effects of compost rate suggest a rate - dependent response and provide a road map to getting accurate outcomes. The time, nutrient source and compost rate of application described herein explain why the hypothesis that compost amendment would improve nematode community structure, soil biological and physicochemical properties, and increase carrot yield and quality was p artially true. Finding a balance among nutrient supply, N in particular, sources and rates, environmental safety, and crop quality and yield is very challenging. For the most part, Chapter 4 140 was designed to address the challenge of finding a balance by applying urea and PC mixed at different proportions. As in Chapter 3, the there were variabilities in nematode community structure and soil food web conditions. For example, SI increased in urea alone, and urea and PC at 3:1 ratios, contradicts with previo us studies (Fiscus and Neher, 2002; Ferris, 2010). However, MI, a measure of changes in the functioning of the soil ecosystem relative to disturbance (Bongers, 1990; Bongers and Bongers, 1998) and SI, a measure of greater trophic links (Ferris et al., 200 1) improved over time when urea and PC were applied at 1:1 ratio compared with urea alone (Fig. 4.1). It is promising that the lower urea rate and integrated with PC enhanced biological activity level, and increased soil pH and nutrients. This is an appeal ing alternative to inorganic fertilizers only for meeting crop requirements and reducing environmental damages (Sikora and Enkiri, 2001). Promoting the PC and urea mix could be a good alternative to urea alone as urea decreased soil pH and increased NO 3 - N, which leaches to the water table and causes environmental damages (Oberson et al., 1996; Gunapala and Scow, 1998; Kaur et al., 2005; Pimentel et al., 2005). Although yield increase was not observed in the integrated urea and PC application study, the ben efits of enhanced biological activities, and increase in soil pH and nutrient contents together with the anticipated reduction of environmental damage point to the need for further studies to understand the linkages among the different interacting factors influencing crop yield. It is known that herbivore nematodes affect plant growth and reduce yield by interfering with water and nutrient uptake (Melakeberhan, 1997). Previous studies have shown that root hair feeders contribute to increase in microbial act ivity by eliciting leakage of metabolites from roots, but do not seem to cause measurable plant damage (Bardgett et al., 1999; Yeates et al., 1999; Verschoor, 2002; Ferris et al., 2010). Whether or not the negative correlation of the abundance of 141 Malenchus , a root hair feeder, with carrot yield may be similar to the previous studies is not clear. The glasshouse study using sterilized and non - sterilized soil was designed to simulate how biologically degraded soils would respond to compost application (Chapte r 5). The stunted carrot yield and c - p 2 group dominated nematode community on non - sterilized soil regardless of the treatments indicate other experimental conditions may not have been ideal for determining the effects of the treatments in the glasshouse e xperiment. The absence of nematodes on sterilized soil may be attributed to the soil physical and chemical property changes due to sterilization, which results in conditions that inhibit or slow recolonization. Perhaps, reinoculating the sterilized soil wi th a small amount of control soil could have made a difference. One possible reason could be increased concentration of NH 4 - N and NO 3 - N after soil sterilization that negatively correlated with nematode trophic groups in non - sterilized soil. Soil sterilizat ion increased most of the measured soil nutrients while decrease soil pH. Designing cross - disciplinary and integrated analyses tools are necessary to promote both agronomic and soil health benefits. As described in Chapter 6, I have developed a weighted g uild approach to modify the FUE model and integrate it with the soil food web model. The FUE model separates nutrient deficiency and toxicity from nematode parasitism and agrobiological efficiency. The soil food web model describes soil nutrient cycling re lative to availability and agroecosystem suitability using nematode community analyses. Nematodes of different guilds have different biological attributes, respond differently to environmental perturbation (Bongers and Bongers, 1998) and indicate health of the soil (Ferris et al., 2001). The guild weights reflect increasing complexity as the system matures or progressive simplicity as the system degrades (Ferris et al., 2001). The assumption is that food webs of 142 higher complexity contain representatives of food webs of lower complexity (Bongers and Bongers, 1998; Ferris et al., 2001). My including the guild functions in the modification of the FUE model shows promising and interesting results in explaining the soil health conditions as in soil food web mode l while addressing additional agronomic parameters of interest. This builds an integrated soil health analysis tool that creates a road map for cross - disciplinary applications of soil amendment - based management practices (Melakeberhan and Avendaño, 2008). The major highlights of the outcomes of the hypotheses that I tested can be summarized as follows: The first hypothesis was partially true as shown by the improved soil food web in Cupar and soil potassium and phosphorus, and soil respiration in the highe r rates of AC. In Sugarsnax 54, although some compost amendments had comparable marketable and total yield compared with that of urea in 2012, all of compost amendments were higher in marketable carrot yield in 2013. The findings pointed out variabilities relative to compost rate, source and time, and suggest compost based improvements in soil food web structure may lead to increase in ecosystem services provided by the soil food web. The second hypothesis was also partially true as shown by im proved soil biological activity and phosphorus content in the lower rates of urea and integrated with higher rates of PC. This is an appealing alternative to inorganic fertilizers for meeting crop requirements and improving soil health. The outcomes of the two hypotheses pointed to variable responses, a major challenge when dealing with soil amendment studies and the soil biological and physicochemical changes they drive and their collective impact on crop yield and quality (McSorley, 2011). My developing t he second modification of the FUE model and integrating it with soil food web model adds more power to integrated and cross - disciplinary analysis of variable responses in soil health management. This new model separates data points that reflect 143 efficiencie s of compost amendments on soil health, and soil pH, organic matter and carrot yield and quality. Hence, the model serves as an important tool to identify areas of targeted intervention. Moreover, the powers of the new model will be critical to understandi ng the gaps when dealing with rehabilitating soils with severe biological degradations. Collectively, the information that I have generated is a significant step towards addressing the industry priorities through understanding the biological and physicoche mical basis of the changes in soil health and designing potential solutions tha t fit variable soil conditions. 144 APPENDICES 145 APPENDIX A : SUPPORTING DATA Table A - 1 . Nematode trophic groups, and non - herbivores and total nematodes abundances in 100 cc of soil amended with AC and PC containing 135, 204 and 270, and 112, 168 and 224 kg N/ha for Cupar and Sugarsnax 54, respectively, and standard urea application a and non - amended check in s andy clay loam soil in 2012 - 2014, and 2012 and2013 growing seasons for Cupar and Sugarsnax 54, respectively. Trophic groups Processing variety Fresh market variety Mean Mean Herbivores 17.0 (0 - 69) b 19.0 (9 - 46) Bacterivores 18.0 (2 - 120) 8.0 (1 - 64) Fungivores 21.0 (0 - 214) 14.0 (1 - 53) Omnivores 0.4 (0 - 10) 0.4 (0 - 4) Predators 0.3 (0 - 2) 0.1 (0 2) Non - herbivores 40.0 (1 - 258) 26.0 (6 - 105) Total nematodes 57.0 (2 - 304) 45.0 (7 - 142) a 293 and 243 kg/ha urea supplying 135 kg N/ha and 112 kg N/ha for Cupar and Sugarsnax 54 cultivars, respectively. b Range of nematodes abundance in 100 cc of soil. 146 Table A - 2 . Omnivore nematodes abundance in 100 cc of soil amended with animal (AC) and plant (PC) composts containing 135, 203 and 270 kg N/ha and standard urea application supplying 135 kg N/ha and non - amended check for Cupar in sandy clay loam soil at different days after planting in 2012 - 2013 growing seasons. Amendments Rate (kg N/ha) Number of omnivores per 100 cc of soil Days after planting 2012 2013 0 32 62 96 132 0 30 62 94 133 PC 135 1 bB a 0 aB 0 bB 1 bB 1 bB 1aB 0 aB 0 bB 1 aB 5 bA 203 1 bB 0 aB 0 bB 1bB 2 bA 0 aB 0 aB 2 aA 1 aB 5 bA 270 0 cC 0 aC 1 aB 3 aA 3 aA 0 aC 1 aB 1 bB 1 aB 10 aA AC 135 1 bC 0 aD 0 bD 2 aBC 3 aB 0 aD 1 aC 1 bC 1 aC 7 bA 203 1 bB 0 aB 0 bB 1 bB 2 bA 1 aB 0 aB 2aA 0 aB 7 bA 270 1 bC 0 aC 0 bC 0 bC 3 aB 1 aC 1 aC 1 bC 1 aC 10 aA Urea 135 0 cB 0 aB 0 bB 1 bA 0 bB 0 aB 0 aB 1 bA 0 aB 2 cA Check 0 2 aA 0 aB 1 aB 1 bB 1 bB 1 aB 0 aB 1 bB 1 aB 3 cA a Means with different lower case letters within columns and different upper case letters across rows indicate significant difference at P < 0.05. 147 Table A - 3 . Omnivore nematodes abundance in 100 cc of soil amended with animal (AC) and plant (PC) composts containing 112, 168 and 224 kg N/ha and standard urea application supplying 112 kg N/ha and non - amended check for Sugarsnax 54 in sandy clay loam so il at different days after planting in 2012 - 2013 growing seasons. Amendments Rate (kg N/ha) Number of omnivores per 100 cc of soil Days after planting 2012 2013 0 32 62 78 0 30 62 79 PC 112 0.5 aB a 0.0 aB 0.3 aB 0.0 aB 0.0 bB 0.8 abB 1.8 aA 0.3 abB 168 0.0 aB 0.0 aB 0.0 aB 0.0 aB 0.5 abAB 0.0 bB 0.5 bAB 1.0 aA 224 0.3 aB 0.0 aB 0.3 aB 0.0 aB 0.5 abB 0.3 bB 2.0 aA 0.3 abB AC 112 0.3 aB 0.0 aB 0.0 aB 0.0 aB 0.8 abAB 0.3 bB 1.3 aA 0.5 abAB 168 0.3 aB 0.0 aB 0.0 aB 0.0 aB 1.3 aA 0.8 abAB 0.0 bB 0.3 abB 224 0.0 aA 0.0 aA 0.0 aA 0.3 aA 0.5 abA 0.8 abA 0.3 bA 0.5 abA Urea 112 1.0 aA 0.0 aA 0.0 aA 0.0 aA 0.5 abA 0.5 abA 0.0 bA 0.0 bA Check 0 0.8 aAB 0.0 aB 0.0 aB 0.0 aB 0.3 bB 1.3 aA 0.0 bB 0.3 abB a Means with different lower case letters within columns and different upper case letters across rows indicate the significant difference at P < 0.05. 148 Table A - 4 . Plant - parasitic index (PPI) values obtained from plots amended with animal (AC) and pla nt (PC) composts containing 112, 168 and 224 kg N/ha and standard urea application supplying 112 kg N/ha and non - amended check for Sugarsnax 54 in sandy clay loam soil at different days after planting in 2012 - 2013 growing seasons. Amendments Rate (kg N/ha) Plant - parasitic index a Days after planting 2012 2013 0 32 62 78 0 30 62 79 PC 112 2.7 aA b 2.5 abBC 2.4 aB 2.5 aBC 2.4 aB 2.1 aC 2.3 aC 2.2 abC 168 2.5 aA 2.5 abA 2.6 aB 2.5 aA 2.2 aB 2.2 aB 2.2 abB 2.2 abB 224 2.3 bA 2.4 bA 2.4 aA 2.1 bB 2.2 aB 2.1 aB 2.1 bB 2.1 bB AC 112 2.3 bB 2.5 abA 2.6 aA 2.5 aA 2.3 aB 2.3 aB 2.3 aB 2.3 abB 168 2.4 bB 2.7 aA 2.7 aA 2.3 aAB 2.3 aC 2.3 aC 2.2 abC 2.4 aB 224 2.6 aA 2.5 abA 2.5 aA 2.4 aA 2.2 aB 2.4 aA 2.2 abB 2.2 abB Urea 112 2.3 bB 2.6 abA 2.6 aA 2.4 aB 2.3 aB 2.3 aB 2.2 abB 2.2 abB Check 0 2.5 aA 2.5 abA 2.5 aA 2.4 aA 2.3 aB 2.2 aB 2.1 bB 2.1 bB a Plant - parasitic nematodes index (PPI) which expresses the maturity of plant - parasitic nematodes with c - p 2 to c - p 5 (Bongers, 1990). b Means with different lower case letters within columns and different upper case letters across rows indicate the significant difference at P < 0.05. 149 Table A - 5 . Soil food web structure index (SI) in plots amended with animal (AC) and plant (PC) composts containing 135, 203 and 270 kg N/ha and standard urea application supplying 135 kg N/ha and non - amended check in Cupar plots in sandy clay loam soil at different days after planting in 2012 - 2013 growing seasons. Struct ure index (SI) AM a Rate (kg N/ha) Days after planting 2012 2013 0 32 62 96 132 0 30 62 94 133 PC 135 7.5 aC b 8.7aB 7.1 aC 8.0 bC 24.5 aB 6.8 bC 30.2 aB 11.0 aB 15.9 aB 72.8 aA 203 7.6 aC 3.2 aC 0.0 aC 10.6 bC 32.4 aB 2.1cC 9.9 bC 51.6 aB 26.9 aB 82.6 aA 270 4.0 aB 5.9 aB 17.6 aA 41.6 aA 29.9 aA 0 cB 19.1 abA 39.2 aA 16.9 aB 74.2 aA AC 135 11.9 aC 3.4 aC 3.7 aC 16.7 abC 31.6 aB 2.2 bC 38.6 aB 38.0 aB 38.8 aB 80.6 aA 203 8.6 aC 15.2 aC 8.7 aC 20.6 abC 35.3 aC 3.5 bC 36.0 aB 36.9 aB 11.5 aC 68.4 aA 270 8.1 aC 7.1 aC 2.5 aC 2.6 bC 23.4 aB 10.4 aB 25.4 aB 26.1 aB 20.4 aB 78.7 aA Urea 135 17.0 aB 8.1 aB 11.3 aB 10.3 abB 9.1 aB 5.5 bB 15.0 abB 11.0 aB 10.3 aB 51.4 aA Check 0 21.2 aBC 19.0 aBC 9.1 aBC 12.9 abBC 6.3 aBC 3.3 bC 17.0 abBC 32.0 aB 17.9 aBC 59.6 aA a Amendments. b Means with different lower case letters within columns and different upper case letters across rows indicate significant difference at P < 0.05. 150 Figure A - 1 . Effect of plant (PC) and animal (AC) compost containing 135, 203 and 270 kg N/ha for Cupar, standard urea (UR) (293 kg/ ha) to supply 135 kg N/ha and non - amended check (CK) on carrot yield and quality in sandy clay loam soil in 2012 - 2014 growing seasons. 151 Figure A - 2 . Ten soil sampling spots for the glasshouse experiment from the field experiment site in 2012 and 2013. 152 APPENDIX B : CARROT FIELD SURVE Y Abstract - The objective of this preliminary study was to identify economically important herbivore nematodes and associated soil health conditions in selected Michigan carrot production areas. A survey of four fields indicated that 153 Introduction Michigan is the second and fourth producer of fresh market and processing carrots in the USA, respectively (Hausbeck, 2008). galls, cracks, forks and stunts that reduce marketable yield ( Walker, 2004; . They may also increase secondary infection by other pathogens (LaMondia, 2006). Herbivore nematodes are common problems in Michigan carrots producing areas though there are a few published works on carrot nematodes (Hausbeck, 2008). Northern root - knot ( Meloidogyne hapla Chitwood, 1949 ), carrot cyst ( Heterodera carotae Jones, 1950 ), root lesion ( Pratylenchus penetrans Cobb, 1917 ) and pi n ( Paratylenchus spp . Micoletzky 1922) nematodes were identified from Michigan carrot fields (Berney and Bird, 1992; Hausbeck, 2008). Northern root - knot and carrot cyst nematodes are considered as the most damaging under Michigan conditions (Berney and Bir d, 1992). conditions though efficient herbivore management requires identifying predominant herbivore nematodes before taking any management decisions. Knowing the prese nce and abundance of herbivores helps to understand the impact of management practices on herbivores abundance and their potential threats, and overall soil health condition. Moreover, nematodes management should consider simultaneous suppression of herbiv ores and promotion of beneficial nematodes represented by bacterivores, fungivores, omnivores and predators. Keeping the beneficial nematodes in the soil is important because nematodes are the most abundant multicellular organisms on the earth occurring a t multiple trophic levels that can represent soil food web and play a key role in nutrient cycling (Bongers and Bongers, 1998; 154 Ferris et al., 2001; Ferris et al., 2004; Neher et al., 2012). Thus, investigating the association between herbivores, and nemato de community and food web indices in on - farm practices could be useful to develop appropriate management strategies. This further enables growers to understand the impact of their management practices on the soil health status. Generating information on th e impact of the management practices on herbivores and non - herbivores nematode management practices. A total of four carrot fields that have alleged herbivores nematodes problems, but with no formal sampling for nematode identification were selected (Table B - 1). One of the fields was located in Mason and the other three were in Oceana counties in Michigan. These Counties are among the major carrot producing regio ns in the State (Hausbeck, 2008). Generating such data will give insight to growers and county agents on potentially damaging herbivores nematodes. The overall goal of this project was to identify the presence of economically important herbivore nematode genera and their abundance in the selected fields. I also described the soil health status of the fields using nematode community analysis. 155 Table B - 1. Carrot quality of five randomly selected carrots from each 2 hectares portion of the carrot farm sites. Site County Sample # Forks Marketable 1 1 2 3 Mason 2 4 1 3 1 4 4 2 3 2 3 2 1 5 0 Oceana 2 5 0 3 5 0 4 5 0 3 1 2 3 Oceana 2 0 5 3 0 5 4 2 3 4 Oceana 1 1 4 2 1 4 3 1 4 4 1 4 5 0 5 Materials and Methods Field selection and soil sampling The field survey was conducted in four selected carrot fields in September 2014. Soil samples were collected from four carrot fields in Mason and Oceana Counties based on the t not sampled before for nematode analysis. The range of the sampled fields was 8 to 10 hectares. Each carrot field was approximately divided into 2 hectares. From each 2 hectares portion of the farm one composite soil sample containing 20 soil cores using zig - zag sampling pattern was collected. Each soil core was collected close to the carrot root to increase chance of getting herbivores. I collected 5, 4, 4 and 5 composite soil samples from site 1, 2, 3 and 4, respectively (Table B - 1). I have also randomly collected 5 carrots from each 2 hectare portion and categorized them as stunt, fork, crack or rot carrots following carrot grade standards (Anon, 1965). The composite soil and carrot samples were 156 transported to Agricultural Nematology La boratory, Department of Horticulture, Michigan State University and stored at 5 0 C. Nematodes extraction , identification and enumeration Within 3 days, the nematodes were extracted from 100 cc of soil using a semi - automatic elutriator as described earlier (Avendaño et al . , 2003). The nematodes were fixed in double TAFF solution as described by Hooper (1986). Then, they were enumerated and identified at genus level following diagnostic keys by Bongers (1994) and the University of Nebraska Lincoln nematode id entification website (http:nematode.unl.edu/konzlistbutt.htm). Nematodes were assigned to a herbivore, bacterivore, fungivore, omnivore or predator trophic group according to Yeates et al. (1993) and Okada and Kadota (2003) and a c - p value was assigned acc ording to Bongers and Bongers (1998). Nematode community and food web analysis. Shannon - and maturity indices (MI, MI25 and PPI) (Bongers, 1990) were calculated to study the nematodes diversity and community structure, respectively. EI, SI, BI and CI were ca lculated and the soil food web condition was graphically described as function of EI and SI as described in Ferris et al. (2001). Nematode trophic group ratios such as fungivores - to - bacterivores (Freckman and Ettema, 1993) and fungivores plus bacterivores - to - herbivores (Wasilewska, 1994) were calculated to know a predominant nutrient mineralization pathway. Fertility index (FI = PPI/MI) was also calculated as a measure of changes in the functioning of the soil ecosystem (Bongers et al., 1997). 157 Data anal ysis Statistical analyses of all data were conducted using SAS ver 9.3 (SAS Institute, 2012, Cary, NC). The general linear Model (Proc GLM) was used to obtain F values for completely randomized design using the appropriate error term in the model. Nematode taxa and trophic group abundances were expressed on an absolute basis (number of nematodes in a taxon i per 100 cc of fresh soil). Dependent variables were the abundance of nematode trophic groups, non - herbivore and total nematodes, percentage of lesion nematode in non - herbivores and total nematodes, nematode community and food web indices, fertility index (PPI/MI), and trophic ratios. Independent variable was the carrot field site. Multiple comparisons were adjusted to Tukey - Kramer when F - value is not si gnificant to perform the preplanned comparisons. Prior to analysis; nematode population abundance was transformed to ln (x+1) to meet the assumptions of normality and equal variances, but untransformed arithmetic means are presented. The probability level P < 0.05 was regarded as significant. Result Carrot quality The randomly selected carrots from each 2 - ha carrot field were categorized based on their quality and grouped into marketable and unmarketable (Table B - 1). The percent of unmarketable carrots wer e 44, 100, 20 and 16 in site 1, 2, 3 and 4, respectively. Visually, rot carrots were very common in site 2 compared with the rest of the study sites. Stunt and cracks were not detected from any of the fields. Nematode genera and abundance This survey revealed the presence of 38 nematode genera, 9, 16, 6, 6 and 1 genera from herbivore, bacterivore, fungivore, omnivore and predator trophic group, respectively, from the 158 four study sites (Table B - 2). Total nematodes abundance ranges from 35 to 203 individuals per 100 cc of soil. The abundance of herbivores in average was 19, 44, 36 and 45 for site 1, 2, 3 and 4, respectively. Bacterivores abundance was 45, 44, 78 and 110 individuals for site 1, 2, 3 and 4, respectively. The abundance of fungivo res was generally low referring 6, 11, 9 and 11 in site 1, 2, 3 and 4, respectively. Abundance of omnivores was 10, 8, 4 and 2 individuals in site 1, 2, 3 and 4, respectively. Among the herbivores, Basiria, Cephalenchus and Psilenchus were detected only in site 1, 2 and 3. Malenchus detected only from site 2 and 4. Tylenchus was detected in all sites except site 2. Xiphinema and Tylenchorynchus were detected in site 2 and 3, respectively. But, root lesion nematode was detected in all of the study sites. The abundance of root lesion nematodes in average was 19, 43, 33, 35 individuals per 100 cc of soil in site 1, 2, 3 and 4, respectively. Herbivore nematodes, Basiria , Cepahenchus, Malenchus, Psilenchus and Tylenchus of the epidermal cell and root hair feeders were less than four individuals per 100 cc of soil. Single individual of ectoparasitic herbivore nematodes from Tylenchorynchus and Xiphinema genera were detected only in a single sample from site 3 and 2, respectively. On average, 4 individuals of ectop arasitic herbivore, Helicotylenchus were detected in site 4 in 3 out of five soil samples. There was significant difference in herbivores nematodes among the study sites (Table B - 3). The abundance of herbivores were significantly higher in site 4 compared with the rest of the sites. Similarly, bacterivores abundance was significantly higher in site 4 compared with site 1 and site 2. However, there was no significant difference in fungivores, omnivores, and predators among the study sites though the abundanc e of omnivores was greater in site 1 and site 2. 159 Table B - 2. List of nematode genera from herbivore, bacterivore, fungivore, omnivore and predator trophic groups detected during the field survey. Numbers within brackets represent c - p values followin g Bongers and Bongers (1998). Herbivores Bacterivores Fungivores Omnivores Predators Basir i a(2) Eumonhystera (1) Aphelenchoides (2) Eudorylaimus (4) Prionchulus (4) Cephalenchus (2) Mesorhabditis (1) Aphelenchus (2) Mesodorylaimus (4) Malenchus(2) Panagrolaimus(1) Ditylenchus (2) Microdorylaimus (4) Psilenchus (2) Rhabditis (1) Filenchus (2) Thonus (4) Tylenchus (2) Acrobeles (2) Dipht h erophora (3) Aporcelaimellus (5) Helicotylenchus (3) Acrobeloides (2) Tylencholaimellus (4) Pratylenchus (3) Cephalobus (2) Tylenchorhynchus (3) Cervidellus (2) Xiphinema (5) Chiloplacus (2) Eucephalobus (2) Heterocephalobus (2) Plectus (2) Wilsonema (2) Microlaimus (3) Prismatolaimus (3) Alaimus (4) 160 Non - herbivore and total nematodes were significantly higher in site 4 compared with site 1 and site 2 (Table B - 3). Total nematodes were significantly higher in site 3 compared with site 1. The most abundant herbivore nematode was root lesio n nematodes in all of the study sites representing 98, 99, 92 and 78 % of total herbivore nematodes in site 1, 2, 3 and 4, respectively. This percentage was significantly higher in site 1, 2 and 3 compared with site 4. Root lesion nematodes were also repre senting 25, 42, 25 and 21 % of the total nematode abundance in site 1, 2, 3 and 4, respectively (Table B - 3). Table B - 3. Abundance of herbivores (HV), bacterivores (BV), fungivores (FV), and omnivores (OV), non - herbivores (NHV), and total nematodes per 100 cc soil of the four selected carrot fields. The proportion of root lesion nematodes was expressed as a percent of herbivores (Pr/HV) and as percent of total nematodes (Pr/TL). Site HV BV FV OV NHV TL Pr/HV (%) Pr/TL (%) 1 19 b a 45 b 6 10 62 b 82 c 98 a 25 2 44 b 44 b 11 8 62 b 106 bc 99 a 42 3 36 b 78 ab 9 4 91 ab 127 ab 92 a 25 4 45 a 110 a 11 2 123 a 169 a 78 b 21 a Means within columns followed by same letter(s) are not significantly different at P < 0.05. Nematode community indices There was no significant difference in nematode diversity among the study sites though B - 4). PPI was significantly higher in site 1 and 2 compared wi th site 4. MI was significantly higher in site 2 compared with site 3 and 4. MI was also significantly higher in Site 1 compared with site 4. MI25 was significantly higher in site 1 compared with site 3 and 4. Similarly, MI25 was significantly higher in si te 2 compared with site 4. 161 Table B - 4. N0, and nematode community maturity expressed as plant - parasitic index (PPI), maturity index for free - living nematodes (MI) and maturity index of free - living nematodes wit h c - p 2 to 5 values for the carrot fields. Site Diversity indices Maturity indices H' Hills N1 Hills N0 PPI MI MI25 1 2.38 11.60 15.00 2.98 a a 2.19 ab 2.59 2 2.23 9.67 16.00 3.00 a 2.23 a 2.50 3 2.43 11.65 16.50 2.93 ab 1.81 bc 2.25 4 2.39 11.23 17.00 2.83 b 1.73 c 2.11 a Means within columns followed by same letter(s) are not significantly different at P < 0.05. Food web indices , trophic ratios and fertility index None of soil food web indices were significantly different among the study sites except SI (Table B - 5). SI was significantly higher in site 1 and 2 compared with site 4. Overall, CI was low (< 50 %) in all the sites indicating predominant bacterial decompo sition pathway. The soil food web analysis indicated that the soil food web was enriched in all of the study sites, but structured only in site 1 and 2. The soil food web condition was maturing (Quadrant B) in site 1 and 2, but disturbed (Quadrant A) in si te 3 and 4 (Fig. B - 1). There was no significant difference in fungivores - to - bacterivores ratio, but fungivores + bacterivores - to - herbivores ratio was significantly lower in site 2 compared with the rest of the study sites (Table B - 5). Fertility index was s ignificantly low in site 1 and 2 compared with site 4, but significantly low in site 2 compared with site 3. 162 Table B - 5. Soil food web enrichment (EI), structure (SI), basal (BI) conditions and channel index (CI) calculated for the carrot fields. Nemat ode trophic group ratios were expressed as fungivores (FV) - to - bacterivores (BV), and fungivores plus bacterivores - to - herbivores ((FV + BV)/HV), and the fertility index (FI) expressed as PPI/MI of the selected fields. Site Food web indices Trophic ratio s BI CI EI SI FV/BV (FV+BV)/HV FI 1 21.73 a a 4.86 a 66.16 a 56.95 a 0.13 2.31 a 1.39 bc 2 27.36 a 11.61 a 56.43 a 58.09 a 0.23 1.20 b 1.35 c 3 24.04 a 6.56 a 71.52 a 34.58 ab 0.12 3.05 a 1.64 ab 4 28.45 a 7.19 a 68.42 a 19.35 b 0.10 2.74 a 1.66 a a Means within columns followed by same letter(s) are not significantly different at P < 0.05. 163 Figure B - 1. - - - 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 0 50 100 0 50 100 Enrichment index (%) Structure index (%) A A B C D 1 2 3 4 0 50 100 0 50 100 Enrichment index (%) Structure index (%) Site 1 Site 2 Site 3 Site 4 B A B C D 164 Discussion The abundance of the herbivore nematodes genera were less than 5 individuals per 100 cc of soil except root lesion nematodes and the numbers in average range between 19 in site 1 and 43 in site 2. Root lesion nematodes were the predominant herbivore genera comprising 98, 99, 92 and 78 % of the herbivores in site 1, 2, 3 and 4, respectively. In previous study M. hapla , P. penetrans , H. carotae and Paratylenchus spp. were reported from Michigan carrot fields (Berney and Bird, 1992; Hausbeck, 2008). Root lesion nematodes are known to cause serious damage on vegetables (LaMondia, 2006; Bao and Ne her, 2011). The above - ground symptoms such as wilting and patches observed and greater carrot damages (Table B - 1) in site 2 possibly associated with root lesion nematodes which represented 99 and 40 % of the herbivores and total nematodes community, respec tively. The abundance of non - herbivores and total nematodes was higher in site 4 compared with site 1 and 2 due to high number of bacterivores (Table B - 3), suggesting disturbed soil system. Bacterivores are more abundant in disturbed soils (Bongers, 1990, Bongers and Bongers, 1998). Apart from this, MI, MI25 and SI values were low in site 4 compared with the other sites, suggesting a relatively disturbed soil condition (Bongers, 1990; Ferris et al., 2001). The lower PPI in site 4 and higher in the other si tes were because of lower abundance (78 % of herbivores) of root lesion nematodes in site 4. Greater abundance of root - lesion nematodes in site 1 and 2 which are considered as relatively stable could be improved soil condition that can increase carrot grow th that supports more root lesion nematodes, or the past management practices favor root lesion nematodes. Some winter cover crops such as winter rye and vetch are good host for root lesion nematodes may increase the nematodes pressure on carrots, and pote ntially reduce yield as observed in site 2 (Abawi and Ludwig, 1995; Bao and Neher, 2011). 165 The soil food web analysis indicated that the soil food web was disturbed in site 3 and 4 (Quadrant A), but maturing in site 1 and 2 (Quadrant B) (Fig. B - 1), suggest ing the soil food web with greater trophic links and potential pest suppression ecosystem services in site 1 and 2 (Ferris et al., 2001; Sánchez - Moreno and Ferris, 2007). The lower fertility index value in site 1 (1.39) and 2 (1.34) compared with site 4 (1 .66), suggesting surplus of nutrients with high microbial activity in site 1 and 2, but severely nutrient - enriched in site 4 (Bongers et al., 1997). SI values are usually low in agroecosystems because of soil disturbance as a result of tillage and applicat ion of agrochemicals (Berkelmans et al., 2003; Briar et al., 2011; Fiscus and Neher, 2002 ) while structured in natural undisturbed ecosystems (Ferris et al., 2001). Hence, the nematode community analysis revealed differences in soil health condition among the study sites. Root lesion nematode is one of the most prevalent herbivores with wide host range (Castillo and Volvas, 2007; Bao and Neher, 2011) and their threshold level may vary with changes in weather conditions, crop cultivars and other environment al factors (Ferris, 1978). In some states, root lesion nematode above 100 individuals per 100 cc of soil is considered as economic threshold level with potential yield reduction (Bao and Neher, 2011). With this standard, the threshold level for root lesio n nematode did not reach to economic threshold level in our study that ranges between 7 - 60 individuals per 100 cc of soil. However, my result suggests the presence of potential damage of carrots from root lesion nematodes and a need for appropriate managem ent strategy to keep root lesion nematodes at lower density to avoid economic damages. Because of the restrictions on broad spectrum nematicides, alternative nematode management practice is required. Rotation to non - host crops can substantially reduce the 166 nematode population (Belair, 1996; Viaene and Abawi, 1998; LaMonda, 2006) though difficult because of the wide host range of root lesion nematodes that includes weeds (Bao and Neher, 2011). Some of the cover crops used in Michigan vegetable production sys tems such as winter rye and vetch are good hosts for root lesion nematodes. Therefore, the use of these cover crops in fields infested with these nematodes could increase pressure on subsequent crops and potentially reduce yield. In contrast, cover crop such as white clover was associated with the reduction of lesion nematode density in Vermont vegetable farms (Bao and Neher, 2011). Using Saia oat, Polynema marigold and sudangrass in rotation or as green manure reduced the number of lesion nematodes (LaMo ndia, 2006; Hooks et al., 2010). Also, annual ryegrass and wheat were poor hosts for root lesion nematodes (Kimpinski and Sanderson, 2004). This shows that knowing the presence of herbivore nematodes in a particular field and selecting appropriate cover/ r otation crops are important steps in nematode management. Use of cover crops with suppressive effect to more than one herbivore nematodes will have greater impact. For example, using sudangrass and Polynema marigold has suppressive to both root lesion and root - knot nematodes (Viaene and Abawi, 1998; Kimpinski and Sanderson, 2004; LaMondia, 2006). The other option to control root lesion nematodes could be use of compost amendments. Animal manure reduced the number of root - lesion nematodes (Maharn et al., 20 08, 2009; Bao and Neher, 2011). Annual application of spent mushroom compost prior to planting reduced the number of root lesion nematodes (LaMondia et al., 1999; LaMondia, 2006). Organic amendments can also be effective at controlling diseases and nematod es through the release of toxic compounds (Widmer and Abawi, 2000), or by providing more suitable habitable environment for antagonists of nematodes (LaMondia et al., 1999; Kerry, 2000). 167 In conclusion, i This further suggests that lesion nematodes could be predominant in this area accounting the similarities in cropping system, soil typ e and climatic conditions. However, nematode taxa that were not recovered in these carrot fields do not necessarily mean they do not occur and infest carrots. - - - 168 APPENDIX C : VOUCHER SPECIMENS Table C - 1. List of voucher specimens a of nematode genera identified from the experimental samples and mounted on glass slide s. The specimens were from MSU Teaching and Research center, Ho lt , MI , USA ( N 43 0 0 0 0 ) from 2012 - 2014 growing seasons . The samples are stored in the Agricultural Nematology Laboratory, Department of Horticulture at MSU. Slide N o Nematode genera Number of individuals Developmental stage 1 Acrobeloides 1 Juvenile 2 Acrobeloides 1 Female 3 Aphelenchus 1 Juvenile 4 Aphelenchus 1 Juvenile 5 Aphelenchus 1 Female 6 Aporcelaimellus 1 Juvenile 7 Aporcelaimellus 1 Juvenile 8 Aporcelaimellus 1 Juvenile 9 Aporcelaimellus 1 Female 10 Aporcelaimellus 1 Female 11 Cephalobus 1 Male 12 Clarkus 1 Juvenile 13 Clarkus 1 Juvenile 14 Clarkus 1 Juvenile 15 Diphtherophpra 1 Juvenile 16 Eucephalobus 1 Female 17 Filenchus 1 Juvenile 18 Helicotylenchus 1 Female 19 Helicotylenchus 1 Juvenile 20 Heterocephalobus 1 Female 21 Heterocephalobus 1 Juvenile 22 Mesodorylaimus 1 Juvenile 23 Mesodorylaimus 1 Juvenile 24 Mesodorylaimus 1 Juvenile 25 Mesodorylaimus 1 Female 26 Mesodorylaimus 1 Female 27 Mesodorylaimus 1 Female 28 Microdorylaimus 1 Juvenile 29 Nygolaimus 1 Juvenile 169 Table C - 1 (con t Slide N o Nematode genera Number of individuals Developmental stage 30 Panagrolaimus 1 Juvenile 31 Plectus 1 Juvenile 32 Psilenchus 1 Female 33 Pungentus 1 Juvenile 34 Pungentus 1 Juvenile 35 Pungentus 1 Female 36 Rhabditis 1 Juvenile 37 Rhabditis 1 Female 38 Rhabditis 1 Juvenile 39 Rhabditis 1 Female 40 Thonus 1 Juvenile 41 Thonus 1 Juvenile 42 Thonus 1 Male 43 Thonus 1 Juvenile 44 Tylencholaimellus 1 Female 45 Tylenchus 1 Female 46 Tylenchus 1 Female 47 Tylenchus 1 Female 48 Tylenchus 1 Female 49 Tylenchus 1 Female 50 Tylenchus 1 Female 51 Tylenchus 1 Female a Pictures of the voucher specimens were filed in Room 256, Agr icultural Nematology Laboratory , Department of Horticulture at MSU . 170 Table C - 2. List of additional photographed and documented nematode genera identified from MSU Teaching Research Center, Holt, MI, USA ( N 43 0 0 42 0 0 ) from 2012 - 2014 growing seasons. Nematode genera Acrobeles Heterocephalobus Psilenchus Acrobeloides Heterodera Pungentus Alaimus Hoplolaimus Rhabditis Aphelenchoides Longidorus Thonus Aphelenchus Malenchus Trichodorus Aporcelaimellus Mesodorylaimus Trypila Basiria Mesorhabditis Tylencholaimellus Boleodorus Microdorylaimus Tylenchorhynchus Cephalenchus Microlaimus Tylenchus Cephalobus Mononchus Xiphinema Cervidellus Mylonchulus Clarkus Nygolaimus Diphtherophora Panagrolaimus Ditylenchus Paratylenchus Dolichorynchus Pellioditis Eucephalobus Plectus Eudorylaimus Prionchulus Eumonhystera Prismatolaimus Filenchus Pristionchus Helicotylenchus Prodorylaimus 171 B IBL I OGRAPHY 172 BIBLIOGRAPHY Abawi, G. S. and Ludwing, J. W. 1995. Host efficiency of 16 cover crops to the lesion nematode. Phytopathology 85: 1554. Abawi, G.S. and Widmer, T.L. 2000. 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