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Title: Microbial Community Dynamics within a Serpentinization-Influenced Aquifer : Characterization of Community Assembly Processes and Responses to Drilling-Induced Perturbations
Creator: Putman, Lindsay Irene
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Serpentinization is the hydrothermal alteration of ultramafic rock, which results in high pH, reducing fluids that are low in dissolved inorganic carbon, and have high levels of methane and hydrogen. While endemic microbial communities have been well-characterized from a variety of marine and terrestrial serpentinizing ecosystems, to date the ecological processes that contribute to microbial community assembly, community dynamics, and the impact of disturbances in serpentinizing environments...
Show moreSerpentinization is the hydrothermal alteration of ultramafic rock, which results in high pH, reducing fluids that are low in dissolved inorganic carbon, and have high levels of methane and hydrogen. While endemic microbial communities have been well-characterized from a variety of marine and terrestrial serpentinizing ecosystems, to date the ecological processes that contribute to microbial community assembly, community dynamics, and the impact of disturbances in serpentinizing environments have not yet been assessed. The work in this dissertation was performed at the Coast Range Ophiolite Microbial Observatory, CA, USA, where a series of wells were drilled in 2011 to access serpentinization-influenced fluids directly from the subsurface. Geochemical and 16S rRNA gene amplicon datasets were collected directly from these wells and a series of microcosm experiments were performed on fluids from the site. Samples collected over the course of six years were used to assess community assembly processes and the biogeochemical impacts of drilling fluid injection into the subsurface. A series of microcosm experiments were also performed to better understand the response of microbial populations to geochemical changes observed in situ following drilling. Results from this work will inform studies of biogeochemical dynamics relevant to modern and ancient Earth and extraterrestrial sites such as Mars. These data further our understanding of microbial community responses to environmental perturbations and provide information that will aid in the development of future drilling and monitoring projects focused on learning about life in the deep subsurface.
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Title: Modeling the movement of water, bacteria and nutrients across heterogeneous landscapes in the Great Lakes region using a process-based hydrologic model
Creator: Niu, Jie
Date: 2013
Collection: Electronic Theses & Dissertations
Description: The development and application of process-based hydrologic models (PBHMs) continues to be a topic of significant interest to the hydrologic community. Although numerous studies have applied PBHMs at small scales ranging from plot and field scales to small-watershed scales, the application of PBHMs to understand large-scale hydrology remains a topic that is relatively unexplored. Understanding controls on large-scale hydrology is key to climate change assessments and effective water resources...
Show moreThe development and application of process-based hydrologic models (PBHMs) continues to be a topic of significant interest to the hydrologic community. Although numerous studies have applied PBHMs at small scales ranging from plot and field scales to small-watershed scales, the application of PBHMs to understand large-scale hydrology remains a topic that is relatively unexplored. Understanding controls on large-scale hydrology is key to climate change assessments and effective water resources management; therefore, to quantify the nature and magnitude of fluxes in regional Great Lakes watersheds, we use a new distributed hydrologic model (PAWS+CLM). Here we describe the application of the model to several large watersheds in the State of Michigan including the Grand River, Saginaw Bay, Kalamazoo and Red Cedar River watersheds and evaluate model performance by comparing model results with different types of data including point measurements of streamflows, groundwater heads, soil moisture, soil temperature as well as remotely-sensed datasets for evapotranspiration (ET) and land water thickness equivalent (GRACE). We then report a budget analysis of major hydrologic fluxes and compute annual-average fluxes due to infiltration, ET, surface runoff, sublimation, recharge, and groundwater contributions to streams etc. as percentage of precipitation and use this information to understand the inter-annual variability of these fluxes and to quantify storage in these large watersheds. After testing the model for its ability to describe hydrologic fluxes and states, we describe the development of solute transport models at the watershed scale by using a mechanistic, reactive transport modeling framework in which the advection, dispersion and reaction steps are solved using an operator-splitting strategy. The solute transport models are tested extensively using available analytical solutions for different hydrologic domains and then applied to describe transport with surface - subsurface interactions and to describe the fate and transport of fecal indicator bacteria such as Escherichia coli in the Red Cedar River watershed in Michigan. Following the successful application of the bacterial fate and transport model, we describe detailed reactive transport modules for predicting the levels of nutrients (N and P). The models are tested using available field observations for the Kalamazoo River watershed in Michigan. The watershed-scale fate and transport modules are expected to aid management by quantifying the impacts of upstream watershed influences on water quality in downstream receiving water bodies such as lakes and oceans. Together with the flow modules they represent a comprehensive suite of process-based models to describe the terrestrial hydrologic cycle coupled with vegetation/land surface and biogeochemical processes.
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Title: Molecular epidemiology, pangenomic diversity, and comparative genomics of Campylobacter jejuni
Creator: Rodrigues, Jose Alexandre
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Campylobacter jejuni, the leading cause of bacterial gastroenteritis in the United States, is often resistant to commonly used antibiotics and has been classified as a serious threat to public health. Through this work, we sought to evaluate infection trends, quantify resistance frequencies, identify epidemiological factors associated with infection, and use whole-genome sequencing (WGS) as well as comparative phylogenomic and pangenomic approaches to understand circulating C. jejuni...
Show moreCampylobacter jejuni, the leading cause of bacterial gastroenteritis in the United States, is often resistant to commonly used antibiotics and has been classified as a serious threat to public health. Through this work, we sought to evaluate infection trends, quantify resistance frequencies, identify epidemiological factors associated with infection, and use whole-genome sequencing (WGS) as well as comparative phylogenomic and pangenomic approaches to understand circulating C. jejuni populations in Michigan. C. jejuni isolates (n=214) were collected from patients via an active surveillance system at four metropolitan hospitals in Michigan between 2011 and 2014. Among the 214 C. jejuni isolates, 135 (63.1%) were resistant to at least one antibiotic. Resistance was observed for all nine antibiotics tested yielding 11 distinct resistance phenotypes. Tetracycline resistance predominated (n=120; 56.1%) followed by resistance to ciprofloxacin (n= 49; 22.9%), which increased from 15.6% in 2011 to 25.0% in 2014. Notably, patients with ciprofloxacin resistant infections were more likely to report traveling in the past month (Odds Ratio (OR): 3.0; 95% confidence interval (CI): 1.37, 6.68) and international travel (OR: 9.8; 95% CI: 3.69, 26.09). To further characterize these strains, we used WGS to examine the pangenome and investigate the genomic epidemiology of this set of C. jejuni strains recovered from Michigan patients. Among the 214 strains evaluated, 83 unique multilocus sequence types (STs) were identified that were classified as belonging to 19 previously defined clonal complexes (CCs). Core-gene phylogenetic reconstruction based on 615 genes identified three clades, with Clade I comprising six subclades (IA-IF) and predominating (83.2%) among the strains. Because specific cattle-associated STs, such as ST-982, predominated among strains from Michigan patients, we also examined a collection of 72 C. jejuni strains from cattle recovered during an overlapping time period by WGS. Several phylogenetic analyses demonstrated that most cattle strains clustered separately within the phylogeny, but a subset clustered together with human strains. Hence, we used high quality single nucleotide polymorphism (hqSNP) profiling to more comprehensively examine those cattle and human strains that clustered together to evaluate the likelihood of interspecies transmission. Notably, this method distinguished highly related strains and identified clusters comprising strains from both humans and cattle. For instance, 88 SNPs separated a cattle and human strain that were previously classified as ST-8, while the human and cattle derived ST-982 strains differed by >200 SNP differences. These findings demonstrate that highly similar strains were circulating among Michigan patients and cattle during the same time period and highlight the potential for interspecies transmission and diversification within each host. In all, the data presented illustrate that WGS and pangenomic analyses are important tools for enhancing our understanding of the distribution, dissemination, and evolution of specific pathogen populations. Combined with more traditional phenotypic and genotypic approaches, these tools can guide the development of public health prevention and mitigation strategies for C. jejuni and other foodborne pathogens.
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Title: New insights in the urease activation process obtained by characterization of apourease complexes and the UreG accessory protein of Klebsiella aerogenes
Creator: Quiroz Valenzuela, Soledad De Los Ángeles
Date: 2008
Collection: Electronic Theses & Dissertations

Title: SOCIOECOLOGICAL PREDICTORS OF MICROBIOME VARIATION IN WILD POPULATIONS OF AFRICAN MAMMALS
Creator: Rojas, Connie A.
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Host-associated microbial communities (e.g. microbiomes) influence multiple aspects of their host’s phenotype. Over a decade of research shows that the microbiome can vary with both host factors and environmental factors. However, much of the existing literature has been limited to intestinal microbiomes and to laboratory and domesticated animals. Multi-body site and longitudinal analyses of the microbiomes of wild mammals are lacking. Here, I address these gaps in knowledge and use DNA...
Show moreHost-associated microbial communities (e.g. microbiomes) influence multiple aspects of their host’s phenotype. Over a decade of research shows that the microbiome can vary with both host factors and environmental factors. However, much of the existing literature has been limited to intestinal microbiomes and to laboratory and domesticated animals. Multi-body site and longitudinal analyses of the microbiomes of wild mammals are lacking. Here, I address these gaps in knowledge and use DNA sequencing to survey the microbiomes of a highly gregarious carnivore, the spotted hyena (Crocuta crocuta). Due to their complex societies, spotted hyenas offer an excellent model system for investigating how host physiology and ecology interact with the microbiome, and for elucidating the contributions of the microbiome to host function. In this dissertation, I leverage over three decades of data and samples collected by my adviser from wild hyenas residing in the Masai Mara National Reserve, Kenya (MMNR). Because this dissertation involved many collaborations with other scientists, I use the first person plural throughout this dissertation. In Chapter 1, I evaluate whether the microbiomes at six body-sites vary with host age, sex, and social rank in spotted hyenas, and find that the microbiome is distinct among body sites, and that this differentiation in microbiomes occurs early in life. For Chapter 2, I conduct a longitudinal analysis of the gut microbiome across 3 generations of spotted hyenas from 4 lineages, and elucidate the potential ways gut microbes may be contributing to their host’s digestion of animal carcasses. Findings show that the composition of the gut microbiome is highly variable across time, but its functional repertoire of genes is highly consistent. Furthermore, our analyses reveal that the abundances of bacterial taxa are associated with long-term ecological changes in livestock grazing, anthropogenic disturbance, and herbivore densities that occurred in the Masai Mara reserve. Chapter 3 inquires whether host social interactions and close associations between individuals shape gut microbiota similarity and diversity in a social group of spotted hyenas, which exhibit fission-fusion dynamics. Consistent with our hypothesis, close hyena affiliates share a greater number of bacterial types than hyena dyads that rarely encountered one another, but contrary to our hypothesis, more socially connected individuals do not harbor more diverse gut microbiotas than more isolated individuals. Chapter 4 compares the gut microbiomes of 11 species of sympatric African herbivores from the MMNR and Laikipia region in Kenya, and determines the relative influence of host diet and host phylogenetic relatedness in structuring the microbiome. My findings indicate that across distantly related hosts, herbivore gut microbiotas are strongly shaped by host phylogenetic relatedness and taxonomy, but among closely related hosts, host diet explains the most variation in the gut microbiota. Findings suggest that the gut microbiota is species-specific, but can be further modified by host ecology, including host diet and geography, especially among closely related host species. Overall, my dissertation provides novel insight regarding the factors shaping the gut microbiome in wild carnivores and herbivores, at individual, group-level, and ecosystem-wide scales.
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Title: SYNTHESIS AND CHARACTERIZATION OF BIOACTIVE GLASS-CERAMIC PARTICLES WITH ADVANCED ANTIBACTERIAL PROPERTIES FOR APPLICATIONS IN BONE REGENERATION
Creator: Pajares Chamorro, Natalia
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Bacterial infections are major surgical complications, which have worsened due to the continued evolution of drug-resistance. In coping with the decay of the antibiotic era, scientists eagerly search for alternative treatments. Multi-functional biomaterials capable of combating infections while triggering tissue regeneration are of great interest. For example, bioactive glasses have been regularly used to deliver drugs and regenerate tissue owed to their unique bone-bonding ability. Doping...
Show moreBacterial infections are major surgical complications, which have worsened due to the continued evolution of drug-resistance. In coping with the decay of the antibiotic era, scientists eagerly search for alternative treatments. Multi-functional biomaterials capable of combating infections while triggering tissue regeneration are of great interest. For example, bioactive glasses have been regularly used to deliver drugs and regenerate tissue owed to their unique bone-bonding ability. Doping the bioactive glass structure with broad-spectrum biocide ions such as Ag+ confers advanced antibacterial properties. The release of Ag+ is controlled by the degradation process of the glass network, maintaining the dose within a therapeutic window that is not cytotoxic to eukaryotic cells. Despite the extensive research performed on Ag-doped bioactive glasses, their regenerative properties in bone tissues have been rarely investigated. This thesis presents promising interactions between Ag-doped bioactive glass (Ag-BG) microparticles and osteoprogenitor cells, providing evidence of the ability to support bone regeneration. Ag-BG’s degradation provoked cell proliferation and cell differentiation in vitro and demonstrated healing of critical calvaria defects in mice after one month of implantation, thanks to the release of Si and Ca ions. Additionally, Ag-BG was antibacterial against Staphylococcus aureus (S. aureus), the most common cause of bone-degenerative diseases like osteomyelitis, and demonstrated low proclivity to induce resistance. The antibacterial potential originated from the degradation by-products of the structure. The mechanism of inhibition was built upon four main sources from higher to lower contribution: Ag+ release, oxidative stress, mechanical damage by nano-sized debris, and osmotic effect. In addition, Ag-BG was capable of restoring ineffective antibiotics with cell-wall-related inhibitory mechanisms by simple combinatorial therapies, rendering them effective in clearing infections. This unprecedented functionality of Ag-BG was expanded with antibiotic depots, where Ag-BG served as a carrier for an ineffective drug. Bioactive glass nanoparticles (BGNs) have been proposed to advance biological and antibacterial properties compared to their micro-sized counterparts. However, the challenges of producing BGNs with multifold metallic ions in a reproducible manner have limited their use. Here, the Stöber method was comprehensively studied to understand the effect of process variables on BGNs’ composition, structure, and morphology. The use of methanol as solvent and the early addition of metallic ion reagents before catalysis helped improved their cation incorporation within the glass network. Extended stirring was key to achieving the targeted composition and controlling the particle size. Monodispersed 10 nm Ag-doped BGNs (Ag-BGNs) were achieved. These Ag-BGNs were stronger antimicrobial weapons, providing bacterial inhibition within hours of treatment. The biological properties were not significantly advanced in the Ag-BGNs compared to Ag-BG; however, cell proliferation, differentiation, and bone re-growth were still provoked. These Ag-BGNs were used as fillers in hydrogel nanocomposites with natural matrices consisting of collagen type I or extracellular matrix. Ag-BGNs distributed homogeneously along the polymer fibrils and allowed polymerization within hours at physiological conditions. These materials hold potential for injectable devices, designing minimally invasive single-step treatment for debilitating bone infections while promoting tissue recovery.
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Title: THE IDENTIFICATION OF NOVEL AMINOGLYCOSIDE ADJUVANTS FOR THE ERADICATION OF PSEUDOMONAS AERUGINOSA BIOFILMS
Creator: Maiden, Michael M.
Date: 2018
Collection: Electronic Theses & Dissertations
Description: The Infectious Disease Society of America has named antimicrobial resistance the greatest global threat to human health. More than half of all infections are due to bacteria growing as biofilms, which are a community of cells enmeshed in a self-made matrix that can be up to 1000x more resistant conventional antimicrobials. Pseudomonas aeruginosa in particular, due to its numerous resistance mechanisms is a formable threat that often forms biofilms. Few new therapies have been developed to...
Show moreThe Infectious Disease Society of America has named antimicrobial resistance the greatest global threat to human health. More than half of all infections are due to bacteria growing as biofilms, which are a community of cells enmeshed in a self-made matrix that can be up to 1000x more resistant conventional antimicrobials. Pseudomonas aeruginosa in particular, due to its numerous resistance mechanisms is a formable threat that often forms biofilms. Few new therapies have been developed to combat P. aeruginosa, and our antibacterial arsenal continues to decline. One solution to this daunting problem are anti-resistance compounds or adjuvants, which enhance conventional antimicrobials, extending and improving their utility. Here, we describe three adjuvants, triclosan, oxyclozanide and melittin. We demonstrate that each synergizes with tobramycin against mature P. aeruginosa biofilms. We also define the mechanism of action of triclosan and oxyclozanide, as protonophores that inhibit efflux pump activity, rendering cells susceptible to tobramycin killing. These adjuvants could be used in conjunction with current therapies to both improve their effectiveness, extend their lifespan, and target cells in biofilms
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Title: The impact of lactobacillus and bacteriophage on group b streptococcus and the placental membranes
Creator: Shiroda, Megan
Date: 2019
Collection: Electronic Theses & Dissertations
Description: The human microbiota encompasses the microbes that live on and in the human body. While some body sites including the vaginal and intestinal tracts have been studied extensively for their role in human health, other body sites have been historically considered sterile and are less studied. One such site is the placental membranes that surround the fetus during pregnancy and serve as an important protective barrier during pregnancy. Several studies have established which bacteria are found in...
Show moreThe human microbiota encompasses the microbes that live on and in the human body. While some body sites including the vaginal and intestinal tracts have been studied extensively for their role in human health, other body sites have been historically considered sterile and are less studied. One such site is the placental membranes that surround the fetus during pregnancy and serve as an important protective barrier during pregnancy. Several studies have established which bacteria are found in this site, but few studies have been conducted to characterize their interactions in vitro or to understand their impact on the placental membranes. Further, our knowledge of the viral component of the microbiome in human health remains incomplete.In this dissertation, Lactobacillus, a well-studied probiotic in other body sites, was evaluated for its effect in the placental membranes. As these membranes were previously considered sterile, we sought to assess the ability of Lactobacillus to colonize these cells and evaluate its impact on them. A cell line model of the outermost layer of these membranes, the decidual cells, was used to establish that Lactobacillus can associate and impact a known cell signaling pathway, the Mitogen Activated Protein Kinase (MAPK) pathway, which is associated with inflammation and host cell death. Total protein level of p38, an important upstream protein in this pathway, was found to be significantly lower with Lactobacillus than in mock infection. These data suggest that Lactobacillus could maintain a commensal interaction in the placental membranes as described in other body sites. Lactobacillus is also known to inhibit pathogen invasion. Group B Streptococcus (GBS) can ascend from the vaginal tract to infect placental membranes, triggering premature birth or neonatal infection. Four Lactobacillus strains representing three species were characterized to assess their impact on two GBS strains (colonizing and invasive). We found live Lactobacillus does not affect GBS growth or biofilm production. L. gasseri increased association of both strains of GBS to the decidual cells but did not result in increased invasion of the cells. Instead, co-culture with Lactobacillus reduced host cell death. Secreted products of Lactobacillus drastically reduced growth in 35 GBS strains that broadly represent GBS diversity and could prevent biofilm formation; this inhibition was strain dependent. Unfortunately, increased GBS-induced host cell death with Lactobacillus supernatants was observed. Collectively, these data suggest that both live Lactobacillus and its supernatant could impact GBS interactions with the placental membranes.Bacteriophage are one of the most abundant members of the microbiome but their impact on opportunistic pathogens such as GBS remains unknown. As GBS can be isolated from gastrointestinal tract, we hypothesized fecal phage communities would inhibit the growth of GBS in vitro. Approximately 6% of the tested communities inhibited the growth of 35 GBS strains. To better understand differences in GBS strain inhibition, we examined capsule, sequence and clinical types of the strains. As no significant differences were found with these traits, we next examined Clustered Regularly Interspaced Palindromic Repeats (CRISPR), which serve as an adaptive immune system against invading foreign DNA by the acquisition of spacer sequences. GBS strains with fewer than nine spacer sequences were less likely to be lysed by a phage community than strains with more than sixteen spacers. We further hypothesized that presence of GBS in the corresponding bacterial component of each phage community would correlate to its ability to inhibit GBS growth. While this correlation did not exist across all GBS strains tested, sensitive strains of GBS were significantly more likely to be inhibited by phage communities with a lower abundance of GBS. Collectively, these data suggest that the phage component of the intestinal microbiome could impact GBS colonization. To further characterize these interactions, an individual bacteriophage should be isolated from these communities.
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Title: Transfer and inactivation of Salmonella during post-harvest processing of tomatoes
Creator: Wang, Haiqiang
Date: 2015
Collection: Electronic Theses & Dissertations
Description: Salmonella outbreaks have been historically linked to tomatoes, with cross-contamination during post-harvest processing having become a major public health concern. In response, a series of studies were developed to assess the extent to which dump tanks, conveyors, slicers, and dicers can spread Salmonella and other microorganisms. An evaluation of the microbiological quality of tomatoes and dump tank water was conducted during three visits to a local tomato packinghouse. At the beginning of...
Show moreSalmonella outbreaks have been historically linked to tomatoes, with cross-contamination during post-harvest processing having become a major public health concern. In response, a series of studies were developed to assess the extent to which dump tanks, conveyors, slicers, and dicers can spread Salmonella and other microorganisms. An evaluation of the microbiological quality of tomatoes and dump tank water was conducted during three visits to a local tomato packinghouse. At the beginning of whole-day processing and after 3 h of operation, bacteria and yeast/mold populations decreased < 2 logs on tomatoes, with these microbial counts greatly impacted by changes in organic load and sanitizer concentration during washing. When the spread of Salmonella was assessed during washing of tomatoes with various sanitizers and subsequent conveying in a pilot-scale packing line, ~ 90% of the original Salmonella inoculum transferred to sanitizer-free water. Acidified chlorine yielded the greatest Salmonella reduction on tomatoes (3.1 log CFU/g). After processing with sanitizers, Salmonella populations decreased to non-detectable levels (< 0.2 log CFU/100 cm2) on the equipment surfaces. Thereafter, Salmonella transfer was assessed during conveying of tomatoes with plastic, foam, or brush rollers. Overall, cross-contamination was greatest using foam, followed by plastic and brush rollers (P < 0.05). After 5 inoculated tomatoes were roller conveyed, 24 and 76% of all uninoculated subsequently conveyed tomatoes were cross-contaminated with Salmonella of 10 - 100 and 1 - 10 CFU/tomato, respectively, compared to 8% of 25 tomatoes using brush rollers.The next two studies focused on Salmonella transfer during slicing and dicing of tomatoes. For tomato slicing, one red round tomato was inoculated with Salmonella Typhimurium LT2 (~ 5 log CFU/g) and sliced using a manual or electric slicer, followed by 20 uninoculated tomatoes, all of which yielded quantifiable numbers of Salmonella after slicing. The quantitative data was fitted to a two-parameter exponential model (Y = A  e(B  X)). While significantly higher (P ≤ 0.05) percentages of Salmonella were transferred to wet (12.2%) as opposed to dry tomatoes (1.1%), with the variety of tomato also impacting transfer, post-contamination hold time, processing temperature and tomato slice thickness did not significantly impact the overall percentage of cells transferred. When one 0.9 kg batch of inoculated Roma tomatoes (~5 log CFU/g) was mechanically diced, followed by ten batches of uninoculated tomatoes, all uninoculated tomatoes yielded Salmonella, with populations exponentially decreasing from 3.3 to 1.1 log CFU/g. Flume tank washing in sanitizer-free water or water containing 80 ppm peroxyacetic acid, 80 ppm mixed peracid, or 80 ppm total chlorine decreased the Salmonella populations on diced tomatoes 1.3 ± 0.2, 2.3 ± 0.3, 2.4 ± 0.4, and 2.4 ± 0.1 log CFU/g, respectively. Spray sanitation on conveyor belts proved to be an effective way to enhance safety of diced tomatoes, with electrolyzed water being especially attractive due to its relatively low cost and ease of preparation.Finally, the impact of temperature, pH, and wash water organic load on Salmonella morphology and early-biofilm formation was assessed on different surfaces encountered in tomato packing houses. Both pH and temperature significantly affected the surface hydrophobicity of Salmonella. Early-biofilm formation on tomatoes was significantly affected by both time (P = 0.0004) and temperature (P < 0.0001). After 6 d, early-biofilms consistently developed on stainless steel and HDPE surface, with the former being more evenly distributed.
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Title: UNDERSTANDING DRIVERS OF PLANT MICROBIOME IN MICHIGAN AGRICULTURE : STUDIES OF THE APPLE ROOT ZONE AND COMMON BEAN SEEDS
Creator: Bintarti, Ari Fina
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Plant-associated microbial communities are crucial for plant health and fitness, and may enhance plant tolerance to various environmental stresses. As global climate change threatens crop production and increases demands on sustainable agriculture, harnessing the plant microbiome has become one potential strategy to address these issues. Thus, it is fundamental to understand the relative contributions of both the host plant as well as the environment in shaping the plant microbiome. Moreover,...
Show morePlant-associated microbial communities are crucial for plant health and fitness, and may enhance plant tolerance to various environmental stresses. As global climate change threatens crop production and increases demands on sustainable agriculture, harnessing the plant microbiome has become one potential strategy to address these issues. Thus, it is fundamental to understand the relative contributions of both the host plant as well as the environment in shaping the plant microbiome. Moreover, the response of plant microbiomes to stress and any consequences of microbiome stress responses for the host plants are poorly understood, though this information is critical to achieve a basis of knowledge for plant microbiome engineering. My research aimed to contribute to this knowledge by investigating the factors that structure root- and seed-associated microbial communities of two valuable crops for Michigan’s agricultural economy: apple and common bean. The first chapter of my dissertation aimed to assess the biogeography of bacterial, archaeal, fungal, and nematode communities in the root zone of apple trees, and to determine their relationships with each other and their changes over natural abiotic gradients across orchards. I also assessed the influence of plant cultivar on microbiome structure in the root zone. I found that root zone microbiome community structure was strongly affected by geographic location and edaphic properties of soil. The next chapter of my dissertation investigated the variability of seed endophyte community of common bean (Phaseolus vulgaris L.). My results showed that plant-to-plant variability under controlled growth conditions exceeded within-plant variability among seeds from different pods. My study developed protocols and added insights to the growing toolkit of approaches to understand the plant-microbiome engagements that support the health of agricultural and environmental ecosystems. The last chapter assessed the responses of common bean seed endophytes to drought stress in the field across two growing locations and four genotypes of common bean. To summarize, this work advances foundational knowledge of the seed microbiome as a critical component of the plant microbiome, and in the context of two key crops for Michigan agriculture.
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Title: WILDFIRE IMPACTS ON SOIL CARBON POOLS AND MICROBIAL COMMUNITIES IN MIXED-CONIFER FORESTS OF CALIFORNIA
Creator: Adkins, Jaron
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Forest ecosystems are important reservoirs for long term carbon (C) storage. Forests of the western United States account for 20-40% of total U.S. carbon C sequestration, and nearly half of the total C in these forests is stored in soil. However, many forests in the western U.S are experiencing wildfire conditions that diverge from historical fire regimes. Prior to Euro-American settlement, California’s mixed-conifer forests typically experienced frequent surface fires of low to moderate burn...
Show moreForest ecosystems are important reservoirs for long term carbon (C) storage. Forests of the western United States account for 20-40% of total U.S. carbon C sequestration, and nearly half of the total C in these forests is stored in soil. However, many forests in the western U.S are experiencing wildfire conditions that diverge from historical fire regimes. Prior to Euro-American settlement, California’s mixed-conifer forests typically experienced frequent surface fires of low to moderate burn severity, but, due to the combined effects of altered forest structure and climate change, now experience fires that are larger and more severe than historical conditions. Fires have numerous direct and indirect effects on the soil biological, chemical, and physical characteristics that influence the soil C cycle. Understanding how altered soil characteristics influence the cycling and persistence of soil C, and how they vary with severity, is important for managing forests for C storage and for predicting fire-climate feedbacks. My dissertation work incorporates observational and manipulative experiments to understand the direct and indirect effects of burn severity on soil C cycling and microbial communities over the short to intermediate term, with a particular focus on the distribution of soil C between active and slow cycling pools. Soil C can be conceptualized as discrete pools of variable persistence in soil. The active C pool is quickly decomposed, contributing to the return of CO2 to the atmosphere, whereas the non-active C pool is more stable and contributes to long term C storage. I leveraged a burn severity gradient resulting from a wildfire in a California mixed-conifer forest to determine the structure and kinetics of these C pools at an intermediate time point in post-fire recovery (i.e. three years). I found that the size of the non-active C pool was smaller in burned areas than unburned areas, and the kinetic rate of the non-active C pool was negatively related to burn severity. I also characterized the soil microbial communities across this severity gradient and identified the environmental characteristics responsible for differences. I found that fungal-to-bacterial ratio and oligotroph-to-copiotroph bacteria ratio decreased with burn severity, and these effects were driven by differences in live and dead tree basal area, soil nutrients, and pH. Leveraging another burn severity gradient, I then determined whether differences in microbial communities and soil C pools were related one-year post-fire in a mixed-conifer forest. I again found lower non-active C pool kinetic rates, and higher abundances of copiotrophic bacteria in burned compared to unburned areas. Differences in soil C pool kinetics were related to tree basal area, soil nutrients, and bacterial communities. I determined the short-term impacts of fire on soil C pools and cycling using lab experiments in which I manipulated soil heating intensity and pyrogenic organic matter (PyOM) additions. I found that high intensity soil heating can decrease microbial biomass C (MBC) accumulation, whereas PyOM had minimal effects on MBC in the short-term. Finally, I found that the size of the active C pool increased with soil heating intensity, while the kinetic rate of the non-active C pool decreased; PyOM primarily increased the size of the non-active C pool. Taken as a whole, my research suggests that fire induces short-term soil C losses by increasing the size of the active C pool, but, over the intermediate-term, residual soil C is more persistent. Fire severity is predicted to increase globally throughout the 21st century, and my research contributes to understanding how forest C storage will be affected by disrupted wildfire regimes.
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