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Fraxinus ash trees in North America a threatended by the invasive Agrilus planipennis, emerald ash borer (EAB). EAB infestation has wide ranging economic, cultural and ecological impacts upon the North American environment. This study aims to look at the biological impact that infestation of ash trees can have on the soil microbiome around the tree’s roots. A previous study has already examined the possible geochemical effects of the trees sampled, and by looking at the effects on the microbiome through 16S ribosomal sequencing, we hoped to gain some estimation of the effect imposed on microbiota surrounding the tree. With a combination of alpha, beta, and network analysis, we can see some possible changes within the rhizosphere associated to the health of trees. Alpha diversity was inconclusive as there was inconsistent data amongst our sampled set of trees. There is confounding points in the data pertaining to geographic differences in sample locations. However, when stratifying to sample locations, beta and network analyses show shifts in the microbiome are significant, with site 2 and 4 beta diversity showing a progression of microbiome makeup to change as health state changed. Differential networks between health states indicate a change in taxa between healthy and unhealthy tree rhizopheres exist. The network topography as well as the strength of edges between networks showed a difference in taxonomic makeup comparing health states with some phyla of note being Verrucomicrobia, Nitrospirae, and Acidobacteria. Because our sample size within each location was small, we recommend further studies be done to explore those differences.

The overall goal of my scientific pursuits has been to understand how the environment influences ecological systems and organismal biology and vice versa. Over the past two centuries humans have placed unprecedented demands on the Earth’s natural resources. As a result of these pressures, we have witnessed an accelerated loss of biodiversity and a dramatic alteration of ecological patterns and processes. These changes have potentially devastating consequences in the long-term and are a cause for instigating novel scientific investigation and ecological mediation. Thus, the aim of my doctoral research was to understand community dynamics and primary metabolisms of soil-dwelling microbes following a fire disturbance. Prescribed fire is a critical strategy for mitigating the effects of catastrophic wildfires. While the above-ground response to fire has been well-documented, fewer studies have addressed the effect of prescribed fire on soil microorganisms. As documented in Chapter 2, we set out to understand how soil microbial communities respond to prescribed fire. For this work we extensively sampled four plots (two burned, two controls) for 17 months in a mixed conifer forest in northern California, USA. Using amplicon sequencing, we found that prescribed fire significantly altered both fungal and bacterial community structure. We found that most differentially abundant fungal taxa had a positive fold-change, while differentially abundant bacterial taxa generally had a negative fold-change in burned plots. We tested the null hypothesis that these communities assembled due to neutral processes (i.e., drift and/or dispersal), finding that >90% of taxa fit this neutral prediction. However, a dynamic subcommunity composed of burn-associated indicator taxa that were positively differentially abundant was enriched for non-neutral ASVs, suggesting assembly via deterministic processes. In synthesizing these results, we identified 15 pyrophilous taxa with a significant and positive response to prescribed burns. Together, these results lay the foundation for building a process-driven understanding of microbial community assembly in the context of the classical disturbance regime of fire.Fires have a significant impact on soil carbon stocks because combustion transforms carbon into either CO2 or in the production of recalcitrant pyrogenic organic matter (PyOM). PyOM is chemically heterogeneous and composed of a spectrum of fixed organic carbon (C), ranging from living plant biomass to completely charred material and soot. Pyrogenic carbon can modify microbial activity via promotion of microbial metabolism of PyOM as an energy or nutrient source, alteration of physical and chemical properties of the soil, or by interference of microbial signaling. As documented in Chapter 3, we were interested in bacterial species whose metabolic activities were promoted by the PyOM generated by fire. We targeted and isolated post-fire bacteria which can utilize the complex carbon compounds, found in PyOM, from fire-affected soils collected from wildfire sites across Northern California, in addition to soil collected from our prescribed burn sites. We find two bacterial genera, Streptomyces sp. and Paraburkholderia sp., were the dominate species in our post-fire isolate collection, suggesting they have the metabolic potential to utilize carbon substrates found in PyOM. Further, preliminary experiments reveal that a post-fire isolate from our prescribed burn sites, Paraburkholderia caledonica F3, can grow on aromatic carbon substrates in the lab. Finally, genomic analyses reveal that Paraburkholderia caledonica F3 possess the metabolic potential to degrade a variety of complex aromatic carbon compounds found in PyOM. These findings provide an exciting and promising outlook for the application of these post-fire bacteria for bioremediation efforts following fire. Bioremediation utilizes the naturally occurring abilities of microorganisms (or plants) to break down harmful compounds and detoxify a polluted environment. Many of these organisms are native to these ecosystems, thus researchers are particularly interested in uncovering who these microorganisms are and how they can metabolically catabolize toxic compounds, such as aromatics and PAHs. While isolating organisms which are native to environments of interest poses its own challenges, we are still able to strategically and successful isolated these specialists in the laboratory. The arduous task arises in interpreting gene functions which have a phenotype under laboratory conditions. However, recent innovations in high-throughput analysis of mutant phenotypes have improved the rate at which researchers can predict gene functions. As documented in Chapter 4, we applied Random-Barcoded Transposon Sequencing to characterize the functional pathways of aromatic degradation in our laboratory isolate, Paraburkholderia caledonica F3. Here we validate the success of the generation of our Paraburkholderia caledonica F3 barcoded transposon insertion mutant library and propose fitness experiments with compounds of interest which are to follow.

Maintaining efficient plant yields is critical to protect agricultural output levels that can support the global population. Unfortunately, crop yields can be devastated by drought conditions, pathogen attacks, and abnormal root growth due to stress. Recycled wastewater (RWW) can be employed to alleviate drought conditions, however, this source of water can deliver a set of chemicals referred to as chemicals of emerging concern (CECs). These compounds can have deleterious effects on the soil microbiome associated with the crop plants, thus reducing crop yields. Pathogens can be addressed with the application of fungicidal agents, but these often have off target effects that impact the soil microbiome. Plant growth promoting rhizobacteria (PGPR) can interact with plants through root development pathways and ensure that plant root development continues or is altered to cope with the stressful conditions. In our studies we examined how CECs and off target effects from fungicidal agents impact the soil microbiome associated with plants. We also examined how the PGPR Bradyrhizobium japonicum interacts with plants to facilitate root development. Overall the results suggest that CECs and off-target effects of fungicidal agents can impact the soil microbiome and alter their community functions. It was also observed that PGPRs were able to facilitate root development through auxin transport pathways.

Flax is a dual-purpose crop for both the seeds and linseed oil; as with other major crops, abiotic stress imparted by both varying environmental conditions and climate change have significant effects on the plant’s viability. In particular, nutrient deprivation is well-characterized at both the phenotypic and molecular level in four varieties of flax (Bethune, Pl, S, and L). While, salt stress susceptibility and tolerance is much less understood in the aforementioned flax varieties. The primary aims of this project included: 1. characterize the phenotype and genotype of four flax varieties under salt stress to be compared to nutrient deprivation, 2. determine the transcriptomic changes of the four flax varieties under salt stress versus nutrient deprivation, and 3. characterize the flax soil microbiome (rhizosphere) to identify punitive plant growth promoting rhizobacteria (PGPR) and/or well-known PGPR. The first portion of the project focused on collecting data pertaining to several phenotypic metrics (height, branching, flowering, and seed setting/collection), as well as genotypic characteristics. Such genotypic regions of interested included LIS-1 to determine if this region was inserted under salt stress, as well as, characterize of several molecular markers (scaffold regions) to identify genotypic patterns specific to salt stress. While, the second portion consisted of RNA sequencing of Bethune, Pl, S and L under salt stress (0.08 M NaCl and 0.15 M NaCl). Additionally, RNA sequencing of S and L under nutrient deprivation was conducted. These data illustrated that many candidate transcripts are those implicated in general stress response, as there was not consistent differential expression per each stress condition within or between flax varieties. Finally, the third portion consisted of 16S ITS V4 sequencing which allowed for metagenomic analysis of the Bethune, Pl, S, and L soil microbiomes under 0.08 M NaCl, 0.015 M NaCl, and nutrient deprivation. This allowed for us to identify any novel microbes, those specific to either salt stress or nutrient deprivation, along with the impact of the flax genotype on the soil microbiome composition. Such analyses led to the discovery that the nutrient deprived samples for all four flax varieties have strong similarities in microbial diversity and abundance, but such a pattern was not observed for either salt stress condition. Collectively, all aspects of the project described above, allowed for identification of unique changes to each flax variety and support the notion that response to the abiotic stresses studied are dependent on the flax variety. The genomic analysis illustrated that there are noteworthy differences for salt stress versus nutrient stress for each variety. Transcriptomic profiling highlighted the fact that there are shared differentially expressed genes, indicative of general stress response. While, there is not a specific set of transcripts pertaining to each of the three stress conditions. Finally, the soil rhizosphere composition is dependent on both the stress condition and flax genotype. As some microbes are specific to only one flax variety, but the compositions are not synonymous per each stress across the four varieties.

Farmers utilize cover crops to manage weeds, amend nutrients, improve resiliency against pest and disease, and build soil health. One limitation to adoption is that we cannot predict well enough how different cover crop species affect weed management or soil health. Brassica cover crops are a well-studied group because of their potential for agriculturally and ecologically significant weed control. The functions of soil microbiomes could contribute to underlying mechanisms behind these weed responses. Two properties of brassica cover crops have substantial and differing effects on the soil microbiome and weed community: glucosinolate and carbon release through root exudation and biomass breakdown. Glucosinolates break down into biocidal isothiocyanates that have been found to effectively control weeds and soil pathogens. Carbon from cover crop biomass and root exudates also stimulate microbial activity and create more diverse resource pools, resulting in more diverse weed and microbial communities. This thesis assesses whether the soil microbiome differed under cover crop treatments (Chapter 1), and if differing weed and microbial responses could distinguish between carbon and glucosinolate as driving mechanisms (Chapter 2).

Microbial nitrogen cycling in hot desert soils is dominated by bursts of biogeochemical metabolic activity during short periods of water availability. Both edaphic traits of the soil ecosystem and the functional traits of the soil microbiome influence the transformation of nitrogen during this process. The aim of this research is to determine how soil bacteri and fungi transform mineral N and how air pollution in the form of atmospheric nitrogen deposition (N-dep) impacts nitrogen cycling. I used a set of desert field sites across a nitrogen deposition gradient in order to investigate soil microbiomes with increasing exposure to chronic atmospheric N-dep. In Chapter 1, I track bacterial and fungal communities over time in response to N addition to show patterns of community change corresponding to NO emissions. In Chapter 2, dry soils were taken from across the N-dep gradient and incubated with 15NH4 in the lab in order to stimulate nitrogen assimilation by soil bacteria. Using this heavy isotope substrate enriched nitrogen assimilating bacterial DNA with 15N, allowing me to determine the degree of growth using DNA-quantitative stable isotope probing (DNA-qSIP). I then sequenced the bacterial 16S ribosomal gene from this qSIP-processed DNA and analyzed the sequence data to calculate isotope incorporation by each bacterial species. I found that with increasing exposure to N-dep, there was a more phylogenetically diverse group of assimilators. Furthermore, assimilation of NH4 across the N-dep gradient was dominated by 5 bacterial orders: Rhizobiales, Burkholderiales, Frankiales, Cytophagales, and Sphingomonadales. In Chapter 3, rewetting experiments were performed at 4 desert field sites with increasing annual loads of N-dep in order to stimulate bacterial metabolic activity. Metagenomes were sequenced in order to determine which nitrogen cycling functional genes were present in the soil, and which genes increase in abundance during rewetting. I found that N-dep significantly altered the composition of genes related to denitrification and organic matter decomposition, although I did not find any significant patterns of gene abundance before and after rewetting. Overall, these experiments demonstrate that nitrogen deposition alters several aspects of the desert nitrogen cycle by changing the composition and gene inventory of soil bacteria.

The use of organic matter amendments (OMAs) is an ancient practice for improving agricultural soils, but our understanding of the microbial mechanisms by which benefits to soil ecosystems occur remains incomplete. The 1.6 million acres of almond orchards in California need effective and sustainable management practices that promote soil as a living ecosystem. This thesis examines OMAs in the context of emerging microbiome science, our current understanding of relevant soil processes as affected by OMAs, and the challenges involved in modeling nutrient cycling through the microbiome. Results from two research trials conducted in 2019-2021 to evaluate three soil health practices in almond agroecosystems are presented. First, a field trial explored the effects of an almond hull and shell amendment and off-ground harvest on soil C and N and soil microbial biomass in almond orchards. A 210-day incubation trial further evaluated the same amendment on soils with differing management histories by utilizing soil that had previously received a green waste compost OMA for three years. Results highlight the suitability of the almond hull and shell amendment as a soil health treatment, finding that it increased microbial respiration and microbial biomass without significantly affecting nitrogen immobilization. Soil with a history of past OMA application displayed higher microbial respiration, dissolved organic carbon, and net N mineralization than soil without that history when receiving a new amendment of almond hulls and shells. Decomposition of amendment residue progressed at nearly identical rates in the field trial and the incubation trial and exhibited characteristics comparable to forest litter layers. These findings add to our understanding of the processes by which OMAs impact the soil microbiome and our ability to utilize these processes to achieve specific outcomes.

Microbes are the life support system of the biosphere. Their metabolic activities have been tightly linked to establishing and maintaining core ecosystem processes around the globe, including the polar deserts of terrestrial Antarctica. Shaped by the continent’s extreme abiotic constraints and physical isolation, core ecosystem processes such as primary production and geochemical cycling often involve unique taxa with novel functional traits thus emphasizing the high conservational value of endemic microbiota. Up till now, microorganisms were rarely considered in Antarctic conservation frameworks despite growing concerns about complex environmental change and our anthropogenic footprint. Major gaps in biodiversity surveys and a general lack of understanding in the basic ecological concepts (niche and neutral) underlying the assemblage of Antarctic soil microbial communities has led to their poor protection status and regional sampling bias. Systematic retrieval of baseline data across the continent is therefore much needed, especially in Eastern Antarctica. In support of bridging this gap, we combined a comprehensive amplicon survey (>700 soil samples) with multivariate analyses and high-end modelling approaches to discern biogeographic patterns of polar soil bacteria, micro-eukarya and archaea throughout two coastal regions in Eastern Antarctica – the Windmill Islands and hyperarid Vestfold Hills. This thesis entails three simple but important mission statements: (1) to unveil the diversity of East Antarctic soil microbiota using a multi-domain approach; (2) to identify key edaphic drivers and threshold tipping points by advancing methods for quantifying multispecies responses to change along environmental gradients; and (3) to explore the influence of wind-driven dispersal as a new initiative for monitoring ecosystem change using a combination of dust samples and particulate trajectory modelling with historical climate data. Soil biodiversity profiles and co-occurrence networks found bacteria, micro-eukarya and archaea likely to be jointly responsible for molding the microbial backbone of Antarctic polar desert ecosystems. Species co-existence is proposed to be linked to tradeoffs between niche (environmental filtering and competition) and neutral (dispersal, speciation and drift) processes. However, the scales weighing these processes are heavily tipped in favor of strong niche-partitioning, which is expected given the harsh abiotic constraints. Bacteria (average Chao1 = 1427.57), the most strongly niche-driven (wPLN = 1.000, wNB = 17, 000 sequence variants) and the environment (79 physiochemical variables), for the first time, on the hyperarid Vestfold Hills soil microbiome. Moisture availability was primarily responsible for shaping the regional microbiome. Highest rates of compositional turnover were observed for rarer lineages of bacteria and micro-eukarya within the 10 – 12 % moisture range. Often the most responsive were taxa with phototrophic or nutrient-cycling capacities such as Cyanobacteria, Chlorophyta and Ochrophyta, which were detected in relatively high amounts within soil at Old Wallow (OW) and Rookery Lake (RL). High dispersal propensity of Chlorophyta (>75 %), based on dust biodiversity profiles (n = 25), generated some insight on the potential implications of wind-driven dispersal upon current ecosystem dynamics as Antarctica warms up. In theory, habitat expansion for micro-algal blooms via aeolian processes may lead to increased phototrophic capacity thereby resulting in potential competition for dominance between primary production strategies across Eastern Antarctica. Cascading events from this hypothetical scenario would be especially pertinent if aeolian deposition occurred within the vicinity of bird and seal colonies, like those found at OW and RL in the Vestfold Hills. When also taking into account the distinctive soil micro-eukaryotic and bacterial components at these two East Antarctic sites, OW and RL were recommended as conservation targets for further sampling and protection. Escalation of consequences from climate change and human activities are major threats to Antarctica’s unique biodiversity. In the coming century, strengthening of links between science and governance will be key towards forming a solid basis for future conservation planning and management across Antarctica. Integration of microbial data has been identified as crucial to this action. This thesis tackles one part of the equation by bringing attention to the vastly understudied coastal regions of Eastern Antarctica. More baseline surveys and research, however, are needed to capture the full scope of biodiversity offered by the Antarctic soil microbiome. This enormous effort would require sustained funding, increased international cooperation and greater year-round access to all regions.

Logging and forest conversion are occurring at alarming rates in the tropical forests of Southeast Asia. These disturbances alter soil chemistry, microbial diversity, and disrupt carbon cycling through shifts in litter decomposition. Direct links between microbial diversity and soil properties such as pH are well established; however, the indirect impacts of logging and forest conversion on microbial diversity and litter decomposition are poorly understood. We used surface (5 cm) soil to assess soil physicochemical properties, next-generation DNA sequencing to assess soil microbial diversity, and standardized litterbags to assess litter decomposition stabilization at five sites along a land use disturbance gradient in the tropical montane forests of Sabah state in eastern Malaysia. We used a hierarchical approach to explore how land use disturbance affects soil properties; how those soil properties in conjunction with land use disturbance affect soil microbial diversity; and how each of those factors affects litter decomposition and stabilization. We show that soil pH, total nitrogen, and bacterial diversity increase with time since disturbance; and sulfur, total carbon, percent sand, soil organic matter, and fungal diversity display a peaked response with peak around 100 years since the last disturbance. Fungal diversity is positively correlated with onsite forest cover, litter decomposition rate, and litter stabilization. Bacterial diversity shows a positive linear relationship with litter decomposition rates, but a peaked relationship with litter stabilization with peak around the mid-range of bacterial diversity. In summary, soils of the older forests harbor significantly greater microbial diversity and stabilize greater amounts of litter than soils of the younger forests and converted sites. Our results suggest that logging and forest conversion significantly affect soil microbial diversity and have lasting effects on carbon cycling in tropical montane forests.

It has been documented that beneficial plant-associated bacteria have contributed to disease suppression, growth promotion, and tolerance to abiotic stresses. Advances in high-throughput sequencing have allowed an increase in research regarding bacterial endophytes, which are microbes that colonize the interior of plants without causing disease. Practices associated with minimizing the use of off-farm resources, such as reduced tillage regimes and crop rotations, can cause shifts in plant-associated bacteria and its surrounding agroecosystem. Integrated crop–livestock systems are an option that can provide environmental benefits by implementing diverse cropping systems, incorporating perennial and legume forages and adding animal manure through grazing livestock. It has been found that crop-livestock systems can increase soil quality and fertility, reduce cost of herbicide use and improve sustainability, especially for farmers in poorer areas of the world. This work explores how crop-livestock systems that integrate chicken rotations can impact tomato plant growth, as well as soil and endophytic bacterial communities. Tomato plants were subjected to greenhouse and field studies where biomass was assessed, and bacterial communities were characterized through culture-dependent and -independent approaches.In greenhouse experiments, the greater percent of chicken grazed soil incorporated in the planting substrate, the greater the stunting of tomato seedlings. In the field study, bacterial communities differed significantly by sample origin and plant development stage, regardless of chicken grazing history. Our findings suggest stronger contribution of agricultural management practices during early plant stages on endophytic microbiome, as opposed to later on in the host lifecycle. Taxonomic composition of dominant groups of recovered endophytic bacterial isolates were consistent with those found by amplicon sequencing. Plots with history of chicken grazing had a significant increase of soil fertility and differentially abundant ASVs. Dominant phyla (Actinobacteria, Proteobacteria, Bacteroidetes and Firmicutes) of bacterial taxa identified were uniform between culture-dependent and -independent approaches from both greenhouse and field experiments. Most of the recovered isolates were found to be phylogenetically similar to formerly cultured plant endophytes and bacteria found in soil. However, some isolates were similar to bacteria recovered in human clinical settings. Further directions should focus on identification and elucidation of transmission of possible plant growth promoting bacteria, as well as human pathogens, found in crops grown in this type of agricultural management strategy. Moreover, the influence of stage in plant lifecycle on bacterial community composition under specific management strategies remains to be explored. This work provides insight into the influence of crop-livestock rotations on soil- and tomato plant-associated bacterial communities.

The expansion of urban areas in response to human population growth is occurring at a rapid pace. Urban areas encroach surrounding landscapes, creating a mosaic of patchy and dynamic development. Across the United States and in many parts of the world, turfgrass ecosystems are a primary groundcover in urban areas. When studied at larger scales, turf lawns coalesce into urban grasslands, a distinct vegetation type that can be studied, characterized, and compared to more well-studied ecosystems. To date, studies of urban grasslands have documented a general increase in soil carbon (C) and nitrogen (N) associated with managed turf, but fewer studies have focused on the microbial mediation of soil nutrient dynamics in these novel urban ecosystems. We sought to 1) search the literature for common turfgrass management practices that have been demonstrated to affect urban grassland soil microbiomes; 2) compare the microbiome composition, activity, and microbial biomass in a chronosequences of lawns established on either formerly agricultural- or forest-history soils to reference agricultural and forest history reference sites; and 3) elucidate the effect of litter quality on the lawn chronosequences to determine if there was an interaction with land-use history or the soil microbiome as might be suggested by current frameworks integrating litter quality, microbial physiology, and soil organic matter formation (e.g. MEMS and MIMICS). Cultural management practices, particularly mowing, are required to maintain quality turf and can alter nutrient cycling in the rhizosphere and at the soil surface depending on how clippings or fall leaf-litter is managed. We found significant shifts in soil microbiome composition when lawns were established on forest-history soils, but not agricultural-history soils. Compositional shifts were related to changing edaphic conditions, particularly pH, %N and %C as lawns aged. We found that short-term additions of litter did not alter the soil microbiome composition, but did affect soil microbial biomass and soil C and N. Relatively more-labile grass clippings stimulated soil C and N accumulation and lower-quality leaf litter increased soil microbial biomass. These observations agree with current soil organic matter models that explicitly consider microbial physiology. Overall, we found land-use history to be a highly significant, but relatively poor predictor of lawn soil microbiome composition. However, the nature of the patterns in lawns were influenced by the previous land-uses, and therefore may still be informative for understanding microbial composition and function at landscape scales. Soil physiochemical conditions, especially pH, were much stronger predictors of lawn microbiomes. Future land-use change studies would benefit from considerations of edaphic conditions rather than generalizations about vegetative cover. The continued study of urban grasslands and urban ecosystems is needed to advance the knowledge of these novel ecosystems and provide the basis for improving their sustainable management.

Plant pathologists must engage with diverse stakeholders and adopt multidisciplinary approaches to develop practical solutions to plant health problems. Two distinct projects were undertaken in this dissertation research, both requiring participatory and multidisciplinary approaches to address research objectives. The overarching objective of the first research project was to develop methods to improve soil and plant health on smallholder tomato farms in the Morogoro Region of Tanzania. Tomato is the main vegetable cash crop grown by smallholder farmers in this region and its production is constrained by plant diseases, limited access to improved tomato varieties, and poor soil health. Disease surveys were conducted in five villages to determine the most prevalent tomato diseases during both the wet and dry production seasons. The most commonly occurring foliar diseases in both seasons were early blight, bacterial spot/speck, viral diseases, and Septoria leaf spot. Ethnophytopathological activities were conducted to gather local disease knowledge in order to improve farmer and researcher communication and elucidate how farmers perceive key diseases. Mother and baby trials were conducted as a participatory crop improvement approach to introduce and evaluate tomato varieties in three villages. Mother trials were conducted in seven environments, and variance partitioning revealed significant genetic effects for all traits measured. Results from baby trials indicated that introduced varieties were locally acceptable to farmers, except for traits related to marketability. A participatory approach was used to improve soil health monitoring by participating farmers. Baseline soil characteristics were gathered from fifty tomato fields in the region, local soil knowledge was elicited from farmers and used to develop a soil health card, and farmers were trained on the use of a low cost soil test kit. Outcome Mapping was used to evaluate participation in mother and baby trials and soil health training. Results suggested that high stakeholder participation levels in mother and baby trials could predict future adoption of introduced cultivars, whereas evaluation of the soil health training indicated few differences in farmer participation and future use of the soil health test kit. The objective of the second research project was to evaluate and adapt anaerobic soil disinfestation (ASD) as a strategy for managing emerging soilborne diseases in high-value Midwestern vegetable production systems. ASD is an environmentally benign method for managing soilborne diseases in which a carbon source is added to soil, the soil is irrigated to saturation, and tarped with plastic mulch for several weeks. ASD studies, both field and growth chamber, were conducted to assess ASD for management of a tomato soilborne disease complex consisting of Verticillium wilt (Verticillium dahliae), corky root rot (Pyrenochaeta lycopersici), black dot root rot (Colletotrichum coccodes), and root knot nematodes (Meloidogyne spp.) and for management of root knot nematodes (Meloidogyne hapla) in lettuce and clubroot (Plasmodiophora brassicae) in mustard greens produced on muck soils. The impacts of ASD on soil bacterial communities were assessed using a high throughput sequencing approach. ASD impacted soilborne diseases and soil microbial communities in a carbon source and soil dependent manner.