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Title: The distribution and dynamics of resistance genes in soil microbiomes
Creator: Dunivin, Taylor Katherine
Date: 2019
Collection: Electronic Theses & Dissertations
Description: "The soil microbiome harbors immense microbial biodiversity that encodes important functions of interest to public health. These include functional genes that encode resistance to antibiotics and arsenic. In the case of antibiotic resistance, transfer from environmental strains to pathogens is a public health risk, and arsenic resistance and metabolisms are important for bioremediation as they impact the fate of arsenic in the environment. While these resistance genes are well-characterized...
Show more"The soil microbiome harbors immense microbial biodiversity that encodes important functions of interest to public health. These include functional genes that encode resistance to antibiotics and arsenic. In the case of antibiotic resistance, transfer from environmental strains to pathogens is a public health risk, and arsenic resistance and metabolisms are important for bioremediation as they impact the fate of arsenic in the environment. While these resistance genes are well-characterized in vitro, the full scope of their environmental distribution, diversity, and interspecies transfer is unknown. A better understanding of the diversity and distribution of resistance genes would provide insights into the potential for mitigation of public health problems such as arsenic contamination and antibiotic resistance. The work in this dissertation used a combination of cultivation-dependent and -independent techniques to better understand the dynamics and distributions of antibiotic and arsenic resistance genes in the environment. The influence of a disturbance on microbial antibiotic resistance and arsenic related genes was investigated by examining soils overlaying an underground coal mine fire in Centralia, PA. Additionally, soil meta-analyses were used to determine broader distributions patterns of these genes. These data and methods not only provide insights into the distributions and dynamics of antibiotic resistance and arsenic related genes in soil microbiomes but also provide a framework for future studies of other functional genes."--Page ii.
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Title: Biodegradation of emerging contaminants in agricultural soils and their impact on soil microbial communities
Creator: Thelusmond, Jean-Rene
Date: 2018
Collection: Electronic Theses & Dissertations
Description: The incomplete elimination of pharmaceuticals and personal care products (PPCPs) during wastewater treatment has resulted in their dissemination in agricultural soils. Biodegradation is a potential removal mechanism; however, the microorganisms and pathways involved are generally unknown. The current work examined the biodegradation of carbamazepine (CBZ), diclofenac (DCF), triclocarban (TCC), and triclosan (TCS) in agricultural soils under aerobic and anaerobic conditions. Solid phase...
Show moreThe incomplete elimination of pharmaceuticals and personal care products (PPCPs) during wastewater treatment has resulted in their dissemination in agricultural soils. Biodegradation is a potential removal mechanism; however, the microorganisms and pathways involved are generally unknown. The current work examined the biodegradation of carbamazepine (CBZ), diclofenac (DCF), triclocarban (TCC), and triclosan (TCS) in agricultural soils under aerobic and anaerobic conditions. Solid phase extraction and liquid chromatography tandem mass spectrometry were used for PPCP extraction and analysis. The soil microbial communities were investigated using 16S rRNA gene amplicon and shotgun sequencing. The first study examined CBZ biodegradation at three concentrations (50, 500, 5000 ng/g), under aerobic and anaerobic conditions, in two soils, using 16S rRNA gene amplicon sequencing and an approach to predict metagenomes (phylogenetic investigation of communities by reconstruction of unobserved states, PICRUSt). The most significant CBZ biodegradation occurred under aerobic conditions. PICRUSt revealed that one soil contained a greater abundance of xenobiotic degrading genes. Several phylotypes were enriched following CBZ degradation, including unclassified Sphingomonadaceae, Xanthomonadaceae and Rhodobacteraceae, as well as Sphingomonas, Aquicella and Microvirga. These phylotypes are considered putative CBZ degraders as they appear to be benefiting from CBZ biodegradation. The second study focused on DCF, CBZ and TCC biodegradation in four soils at concentrations typically detected in soils and biosolids (50 ng g -1) using 16S rRNA gene amplicon sequencing and PICRUSt. Rapid DCF removal (<7 days) was observed under aerobic conditions, with limited biodegradation under other conditions. CBZ and TCC degradation was slow (half-lives of 128-241 days and 165-190 days for CBZ and TCC). Phylotypes in the Proteobacteria, Gemmatimonadales and Actinobacteria were more abundant during DCF biodegradation. For CBZ, those in the Bacteroidetes, Actinobacteria, Proteobacteria and Verrucomicrobia were enriched during biodegradation. Actinobacteria and Proteobacteria were also enriched during TCC biodegradation. Such differences could indicate these microorganisms are associated with biodegradation. The impact on KEGG (Kyoto Encyclopedia of Genes and Genomes) metabolism pathways was also examined. Four pathways were positively impacted during DCF biodegradation. CBZ had a limited impact on the metabolic pathways. TCC removal was linked to genes associated with the degradation of simple and complex substrates. The third study examined CBZ, TCC and TCS biodegradation using shotgun sequencing and MG-RAST analysis. CBZ and TCC biodegradation was again slow, and TCS biodegradation was rapid. For each chemical, between three and ten phylotypes were enriched during biodegradation. The genera of previously reported CBZ, TCC or TCS degrading isolates were present; Rhodococcus (CBZ), Streptomyces (CBZ), Pseudomonas (CBZ, TCC, TCS), Sphingomonas (TCC, TCS), Methylobacillus (TCS) and Stenotrophomonas (TCS). From the analysis of xenobiotic degrading pathways, five KEGG pathways were the most dominant. This research indicates a number of phylotypes are likely involved in PPCP biodegradation in agricultural soils. Also, the work suggests that the phylotypes impacted are affected by the experimental conditions (e.g. PPCP concentration, soil type, incubation time). From the PPCPs examined, CBZ and TCC are highly recalcitrant and will likely remain in agricultural soils for extended periods of time.
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Title: Utilization and production of N₂0 by denitrifiers isolated from different soil environments and effect of pH on the rates and products of denitrification
Creator: Okereke, Gilbert Uwahamaka
Date: 1978
Collection: Electronic Theses & Dissertations

Title: Friendly Workers of the Soil : Ten Lessons
Creator: O.M. Scott & Sons
Date: 1921
Collection: Scotts Company Collection Monographs
Description: Includes: Foreword; An Invisible World; Fighting the Destroyers; Bacterial Armor; Friendly Helpers on the Farm; The Food of Plants; Conditions of Bacterial Life; The Soil Factory; The Waste of Nitrogen; Putting Plant Food into the Soil; and The Indispensable Condition.

Title: A study of the distribution of N̲a̲e̲g̲l̲e̲r̲i̲a̲ sp. in soil
Creator: Umeche, Ndu
Date: 1978
Collection: Electronic Theses & Dissertations

Title: Studies in denitrification
Creator: Edwards, Sarles F.
Date: 1903
Collection: Electronic Theses & Dissertations

Title: The initial steps of 2,4-dichlorophenoxyacetic acid (2,4-D) degradation in soil bacterial isolates
Creator: Sassanella, Timothy Martin
Date: 1998
Collection: Electronic Theses & Dissertations

Title: Identifying the activities of rhizosphere microbial communities using metatranscriptomics
Creator: Garoutte, Aaron
Date: 2016
Collection: Electronic Theses & Dissertations
Description: "Soil microbial communities carry out many functions, most of which are beneficial to the planet as well as to humans. Soil microbial communities control the biogeochemical cycling rates of key elements such as carbon, nitrogen, sulfur and phosphorous and can also aid in plant growth and disease defense. Microbial ecologists have studied the functional activities of microbial communities for decades often using laboratory incubations. Metagenomics has allowed the identification of the...
Show more"Soil microbial communities carry out many functions, most of which are beneficial to the planet as well as to humans. Soil microbial communities control the biogeochemical cycling rates of key elements such as carbon, nitrogen, sulfur and phosphorous and can also aid in plant growth and disease defense. Microbial ecologists have studied the functional activities of microbial communities for decades often using laboratory incubations. Metagenomics has allowed the identification of the microbes and the potentially functional genes in an environmental sample, but does not allow an assessment of activity. Direct observation of microbial community activity in the field is the desired strategy to build the foundational knowledge required to assess, predict and potentially manage soil microbial community activity. In this dissertation I combine the use of metagenomics with metatranscriptomics to identify functional activity of the microbial community in the soil and rhizosphere of candidate biofuel crops. First, I assessed the efficiency of a novel method of rRNA removal, called the duplex specific nuclease normalization, to remove the dominating rRNA from samples of total RNA, to allow greater sequence coverage of mRNA. While this method did result in about 17% non-rRNA, it did not provide a major gain in sequencing depth. I also established best practices for computational metatranscriptomic analysis, especially the importance of assembling short reads into longer contigs to improve annotation accuracy. Second, I examined the activity of the rhizosphere microbial community of switchgrass, a candidate biofuel crop, using a combination of metagenomics, metatranscriptomics and metaproteomics. I defined a minimum core of microbial community functions of both metagenomic and metatranscriptomic sequences to focus the analysis on the most common sequences that were expressed. Beyond the expected housekeeping functions, the ecologically important functions related to biogeochemical cycling expressed were glycoside hydrolases, ligninolytic enzymes, ammonia assimilation, phosphate metabolism and functions related to plant-microbe interactions were production of auxin, trehalose and ACC-deaminase. Ecologically important genes had lower abundance than housekeeping functions indicating that ecologically important genes may represent keystone functions. I also examined the effect of two plants, switchgrass and corn, on the presence and activity of microbial community functions at various distances from living roots using metagenomics and metatranscriptomics. The metagenomic data was able to differentiate between microbial communities associated with the two different crops and differentiate communities in direct contact with the roots versus those not in direct contact. The metatranscriptomic data was unable to differentiate between bulk and rhizosphere samples indicating others factors are stronger determinants of community transcription. I show that direct observation of the activity of microbial communities associated with biofuel crops in field collected samples is possible through metatranscriptomics and aided by metagenomics and metaproteomics. These data allow the detection of microbial activities related to biogeochemical cycling and plant microbe interactions as well as reveal differences in genetic potential across different soil treatments."--Pages ii-iii.
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Title: Antibiotic resistance and bacterial microbiome in lettuce-soil systems
Creator: Shen, Yike
Date: 2020
Collection: Electronic Theses & Dissertations
Description: Food safety challenges from emerging contaminants such as antibiotics and antibiotic resistance genes (ARGs) have received increasing attention due to rapid increases in their abundance in agroecosystems. This is particularly true in soil-vegetable systems as microbiomes and antibiotic resistomes of vegetables are important to their quality and safety and could be influenced by crop production with contaminated soil and water. Additionally, the food safety of vegetables may also drive...
Show moreFood safety challenges from emerging contaminants such as antibiotics and antibiotic resistance genes (ARGs) have received increasing attention due to rapid increases in their abundance in agroecosystems. This is particularly true in soil-vegetable systems as microbiomes and antibiotic resistomes of vegetables are important to their quality and safety and could be influenced by crop production with contaminated soil and water. Additionally, the food safety of vegetables may also drive consumers' preference and demand for certain food products (especially for labeled products such as USDA Organic, Raised Without Antibiotics, etc.). Using a soil-lettuce (Lactuca sativa) model system, the first study in this dissertation assessed how irrigation with antibiotics-contaminated water via overhead or soil-surface irrigation could influence bacterial communities and ARG profiles in lettuce shoots, roots, and soil, using 16S rRNA amplicon sequencing and high throughput qPCR techniques, respectively. The overall abundance and diversity of ARGs and bacteria associated with soil-surface irrigated lettuce shoots were lower than those under overhead irrigation, indicating soil-surface irrigation may have lower risks of producing food crops with high abundance of ARGs. ARG profiles and bacterial communities were sensitive to pharmaceutical exposure, but no consistent patterns of changes were observed. The second study examined the fate and transport of selected antibiotics through bulk soil, rhizosphere soil, and lettuce roots and shoots under soil-surface irrigation. Root concentration factors based on the antibiotic concentrations in bulk soil (RCFbs) were significantly higher than those based on antibiotic concentrations in rhizosphere soil (RCFrs) for ciprofloxacin, lincomycin, oxytetracycline, sulfamethoxazole, and tetracycline, similar for trimethoprim and tylosin, and lower for monensin. The third study investigated bacterial community assembly and ARG profiles in lettuce shoots, roots, rhizosphere soil, and bulk soil upon exposure to antibiotics. Bacterial communities were driven by stochastic processes upon exposure to low level antibiotics, and were more resilient in roots and rhizosphere soil than in bulk soil and shoots. The fourth study explored the importance of demographics, food-relevant habits, and foodborne disease perception to consumers' buy and pay preferences to labeled products by using conventional statistical and novel machine learning methods to analyze survey data. Consumers' willingness to buy or to pay more for certain labeled food products is dependent on certain demographic traits (e.g., urban living) and food-relevant habits (e.g., cooking fresh produce). Machine learning methods achieved sufficient prediction accuracy scores for estimating consumers' willingness to buy or to pay for labeled products, and thus could be useful tools for evaluating survey data and facilitating the development of strategies promoting healthy food production and consumption.
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Title: Linking plant communities to soil microbial communities and processes in old-fields
Creator: Broughton, Laura C.
Date: 2001
Collection: Electronic Theses & Dissertations

Title: Enhancement of soil aggregation by the combined influences of soil wetting and drying and root-microbial associations
Creator: Sissoko, Fagaye
Date: 1997
Collection: Electronic Theses & Dissertations

Title: Forensic soil bacterial profiling using 16S rRNA gene sequencing and diverse statistics
Creator: Hopkins, James MacKenzie
Date: 2014
Collection: Electronic Theses & Dissertations
Description: Evidentiary soil in an investigation can link an individual with the scene of a crime since the diversity and geospatial distribution of soils can make it highly probative. Recently, advanced techniques have been developed that allow a deeper investigation into bacterial communities and produce considerably more data than previous methods. This research used next-generation sequencing and statistical analyses to identify factors influencing soil bacterial communities and assess the...
Show moreEvidentiary soil in an investigation can link an individual with the scene of a crime since the diversity and geospatial distribution of soils can make it highly probative. Recently, advanced techniques have been developed that allow a deeper investigation into bacterial communities and produce considerably more data than previous methods. This research used next-generation sequencing and statistical analyses to identify factors influencing soil bacterial communities and assess the feasibility for their use forensically. Soil samples were collected from a variety of habitats over different distances, depths, and times, DNAs were extracted, the 16S rRNA gene amplified, and DNAs sequenced on a Roche 454 platform. Five statistical procedures--nonmetric multidimensional scaling, hierarchical cluster analysis, integral library shuffle, unique fraction method, and k-Nearest Neighbor--were used to compare differences or changes in bacterial communities. Multiple similar and diverse habitats were differentiated with both multivariate statistics and pairwise comparisons. Additionally, changes in communities were indicated over time, horizontal space, and depth. Multivariate statistics generally suggested similar relationships though not always consistent with pairwise comparisons, which showed analogous results though the unique fraction method always found fewer differences. k-Nearest Neighbor could be forensically useful based on the correct classification accuracy of `unknown' samples from a non-ideal training set. This research elucidates the potential of next-generation sequencing for soil investigation, how samples should be collected, and what statistics would be useful to analyze the data.
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Title: Spatial organization in soil bacterial communities
Creator: Blackwood, Christopher B.
Date: 2001
Collection: Electronic Theses & Dissertations

Title: Effect of selection on the structure of a 2,4-dichlorophenoxyacetate (2,4-D) degrading guild in soil
Creator: Dunbar, John M. (John Martin)
Date: 1996
Collection: Electronic Theses & Dissertations

Title: Factors influencing the production of nitrous oxide during denitrification
Creator: Firestone, Mary Kathryn
Date: 1978
Collection: Electronic Theses & Dissertations

Title: Short-term measurement of soil denitrification using C₂H₂ inhibition : response to anaerobiosis and the effect of the rhizosphere
Creator: Smith, Morgan Scott
Date: 1978
Collection: Electronic Theses & Dissertations

Title: Microbial profiling of soil for forensic applications
Creator: Smith, Ethan Scott Travis
Date: 2011
Collection: Electronic Theses & Dissertations
Description: Soil can be of tremendous evidentiary value in forensic investigations. Historically, soil evidence has been analyzed based on physical or chemical characteristics; however, microbial analysis has recently emerged as a possible way to better characterize soil samples. Within any given soil sample there are hundreds or thousands of species of microorganisms, each differing in abundance. This variation can potentially be assayed, producing a unique and comparable microbial "fingerprint" for...
Show moreSoil can be of tremendous evidentiary value in forensic investigations. Historically, soil evidence has been analyzed based on physical or chemical characteristics; however, microbial analysis has recently emerged as a possible way to better characterize soil samples. Within any given soil sample there are hundreds or thousands of species of microorganisms, each differing in abundance. This variation can potentially be assayed, producing a unique and comparable microbial "fingerprint" for questioned and known samples. The aim of this research was to examine the effectiveness of real-time PCR in the analysis of forensic soil samples. This was accomplished by collecting soil from four different locations around mid-Michigan over a one year period, extracting bacterial DNA, and targeting the 16S rRNA gene of different bacterial groups known to vary in abundance based on soil type. Several soil characteristics were examined including uniqueness among habitats, changes in bacterial communities over time, and the level of heterogeneity within a habitat. Multivariate statistical analysis was performed to determine the significance of each characteristic examined. Results showed that some habitats could be differentiated from one another using ADONIS and NMDS. Habitats had little variability at different depths; however the Agricultural Field and Marsh showed significant temporal variability. Given this, most habitats could still be distinguished from one another in a pairwise manner, which more truly reflects a forensic situation.
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Title: A study of coliforms and enterococci in soil
Creator: Cooper, Robert Chauncey
Date: 1953
Collection: Electronic Theses & Dissertations

Title: Contribution of microorganisms to zinc immobilization in soil
Creator: Zamani, Bahram
Date: 1983
Collection: Electronic Theses & Dissertations

Title: Studies of genera cytophaga-flavobacterium in context of the soil carbon cycle
Creator: Mayrberger, Jenifer M.
Date: 2011
Collection: Electronic Theses & Dissertations
Description: There is a great need to understand the global carbon cycle; with specific interest in the cycling of soil carbon. This need is two-fold and interconnected. The global climate change is in-part due to the loss of soil organic carbon and the reduced ability of soils to sequester carbon. Also, to maintain sustainable, high yielding agriculture, carbon loss from soil must be mitigated and in turn this can restore the ability of soils to sequester carbon. A specific group of bacteria, the...
Show moreThere is a great need to understand the global carbon cycle; with specific interest in the cycling of soil carbon. This need is two-fold and interconnected. The global climate change is in-part due to the loss of soil organic carbon and the reduced ability of soils to sequester carbon. Also, to maintain sustainable, high yielding agriculture, carbon loss from soil must be mitigated and in turn this can restore the ability of soils to sequester carbon. A specific group of bacteria, the Cytophaga-Flavobacterium (CF), are of interest in these contexts because evidence suggests that they have the potential to exacerbate the loss of organic carbon from soil. The CF are globally distributed, often detected as organisms responsible for degradation or organic compounds. Other research has demonstrated their active presence in soil, especially the zone around plant roots. Most importantly, these bacteria produce a large assortment of hydrolytic enzymes that can degrade complex carbohydrates. The first studies in this dissertation were intended to investigate the phylogenic diversity and distribution of CF in soil. CF specific clone libraries were generated to investigate a possible link between the CF and soils under different land management and use history, and thus different carbon contents. Also in this dissertation, we tested the hypothesis that Flavobacterium soil isolates would weaken, or degrade, remolded aggregates generated with xylan, a complex carbohydrate, in an effort to describe how Flavobacterium can be responsible for the loss of organic carbon from soil. While the initial studies were exploratory in design, some specific comparisons were made. The CF community from the agricultural soil was determined to be a subset of the communities found in the non-agricultural soils. When the CF communities from deciduous forest soil and fertilized deciduous forest soil were compared, no differences in phylogenetic diversity or distribution were identified. A significant difference in the phylogenetic distribution was detected when the CF community from conventionally tilled agricultural soils was compared to the community from a no-till agricultural management. The diversity of the community from the tilled soil was greater than the community from the no-till soil. Remolded aggregates composed with xylan were challenged with nine Flavobacterium spp. isolated from soil to test the hypothesis that they would degrade the xylan causing a reduction in the erosive strength of the remolded aggregates. In natural soils, increased breakage can lead to a loss of carbon from the soil. The erosive strength is a measure of how readily aggregates will break apart. These values are determined by eroding the aggregates in precision-machined soil aggregate erosion chambers and recording the length of time and amount of force required to remove layers of the aggregate. Using two measures of erosive strength, the highest recorded value, or peak erosive strength, and the total erosive strength for all layers of the aggregate, the aggregates treated with Flavobacterium spp. were compared to uninoculated controls. It was determined that six of the nine species significantly reduced the peak erosive strength and four species also reduced the total erosive strength. These data support the hypothesis that Flavobacterium spp. contribute to a loss of organic carbon from soil. These works can now be extended, using the same techniques, by investigating the role of Flavobacterium as part of the whole bacterial community, as well as investigating the influence of temperature on their degradation activity.
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