One of the central goals of the field of microbial biogeography is to better understand spatial patterns of microbial community diversity and how communities respond to gradients in environmental conditions, be they natural or anthropogenic in origin. The main aim of this thesis was to investigate how gradients in environmental conditions (i.e., across a mountain elevational gradient and across different land-use types) affect soil microbial community structure, diversity and functional traits, and to assess how these communities respond to differing environmental variables, using next-generation sequencing technologies. Elevation gradients are commonly used to explore impact climate impacts on biological communities since declines in temperature with increased elevation can generate substantial climate gradients over small spatial scales. However, inconsistent spatial patterns in soil bacterial community structure observed across elevation gradients imply that communities are affected by a variety of factors at different spatial scales. Here, I investigated the biogeography of soil bacteria across broad (i.e., a ~ 1500 m mountain elevation gradient) and fine sampling scales (i.e., both aspects of a mountain ridge) using 16S rRNA gene sequencing. Across equivalent distances, variation in bacterial community composition changed more with variation in site aspect than elevation. Bacterial community composition and richness were most strongly associated with soil pH, despite the large variability in multiple soil climate variables across the site. These findings highlight the need to incorporate knowledge of multiple factors, including site aspect and soil pH for the appropriate use of elevation gradients as a proxy to explore the impacts of climate change on microbial community composition. Similar to , inconsistent elevational patterns in soil fungal community diversity suggest that these communities are driven by a complex underlying mechanism. Thus, to enhance understanding of whether distinct biogeographic patterns can be distinguished between different microorganisms and how such gradients influence the potential interactions among individual taxa, I assessed variation in the co-occurrence of different fungal taxa at different elevations along the aforementioned mountain ridge, using fungal internal transcribed spacer (ITS1) DNA sequencing. Fungal community composition changed significantly along the gradient, and their co-occurrences were less frequent with increasing elevation. Such changes with elevation were associated with soil nutrient concentrations, likely driven by the relative ability of different taxa to compete for nutrients at different environmental concentrations. Evidence of nutrient-driven shifts in fungal community diversity and function in soil will enhance our understanding of underground nutrient cycling and the likely impacts of climate change and agricultural disturbance on soil microbial communities. To further explore gradients in the functional potential of soil bacterial communities along an elevation gradient, I devised a method to 'infer' metagenomics data from bacterial 16S rRNA gene sequences. I evaluated the applicability of my 'inferred metagenomics' approach, by comparing bacterial community composition derived from the original bacterial data to communities derived only from the 400 taxa for which genomic information is available. The results generated from these two datasets were highly similar, suggesting that the subset of 'inferred' community was largely reflective of that of the wider environmental community. Further analysis indicates that bacteria with larger genome size appear to prevail across the elevation gradient, suggesting that microorganisms might successfully cope with harsh or various environmental conditions by retaining a larger burden of potential genes and related functions. These findings highlight the potential for using inferred genomic information, based on bacterial 16S rRNA gene data, to generate a general functional trait-based picture of microbial biogeographical patterns. Apart from studies on elevational patterns of soil microbial communities, many other environmental gradients impact distributions of bacterial communities, including gradients of anthropogenic disturbance. Therefore, I studied how pastoral land management practices affect soil bacteria, both in agricultural soils and adjacent forest fragments along 21 transects bisecting pasture-forest boundaries. Decreased compositional dispersion of bacterial communities in the grazed pasture soils resulting in a net loss of diversity caused by community homogenisation after forest-to-pasture conversion. Additionally, a greater richness of pastureonly taxa for sites with a fence on the boundary between the two land uses revealed that boundary fences play an important role in protecting the integrity of soil bacterial communities in forests surrounded by agricultural land via restricting livestock invasion. The observed variation in bacterial community richness and composition was most related to changes in soil physicochemical variables commonly associated with agricultural fertilisation. Overall, my findings demonstrate clear, and potentially detrimental, effects of agricultural disturbance on bacterial communities in forest soils adjacent to pastoral land. This thesis reports the findings of a comprehensive evaluation of the impact of different environmental gradients on soil microbial community composition and functional potential, encompassing sample data collected across different spatial scales and land use types, as well as between different microbial phylogenetic groups. These results confirm that spatial patterns in both bacterial and fungal community structure are driven by various interacting environmental variables related with natural gradients or agricultural disturbances.

Several textbooks and edited volumes are currently available on general soil fertility but‚ to date‚ none have been dedicated to the study of “Sustainable Carbon and Nitrogen Cycling in Soil.” Yet this aspect is extremely important, considering the fact that the soil, as the ‘epidermis of the Earth’ (geodermis)‚ is a major component of the terrestrial biosphere. This book addresses virtually every aspect of C and N cycling, including: general concepts on the diversity of microorganisms and management practices for soil, the function of soil’s structure-function-ecosystem, the evolving role of C and N, cutting-edge methods used in soil microbial ecological studies, rhizosphere microflora, the role of organic matter (OM) in agricultural productivity, C and N transformation in soil, biological nitrogen fixation (BNF) and its genetics, plant-growth-promoting rhizobacteria (PGPRs), PGPRs and their role in sustainable agriculture, organic agriculture, etc. The book’s main objectives are: (1) to explain in detail the role of C and N cycling in sustaining agricultural productivity and its importance to sustainable soil management; (2) to show readers how to restore soil health with C and N; and (3) to help them understand the matching of C and N cycling rules from a climatic perspective. Given its scope, the book offers a valuable resource for educators, researchers, and policymakers, as well as undergraduate and graduate students of soil science, soil microbiology, agronomy, ecology, and the environmental sciences. Gathering cutting-edge contributions from internationally respected researchers, it offers authoritative content on a broad range of topics, which is supplemented by a wealth of data, tables, figures, and photographs. Moreover, it provides a roadmap for sustainable approaches to food and nutritional security, and to soil sustainability in agricultural systems, based on C and N cycling in soil systems.

The functioning of terrestrial ecosystems is entirely dependent on the activity of autotrophic primary producers and microbial decomposers, and how they are affected by climate, mineralogy and anthropogenic change. Ecosystem ecology has classically focused on how allocation and community composition of plant primary producers may alter predictions of future ecosystem functioning in the face of environmental change. Little attention has been paid to allocation and community composition of microbial decomposers. The functioning of microbial decomposers has been considered implicitly, in the context of plant traits; primarily plant biomass chemistry. However, soil microbial communities represent a vast diversity of taxa spanning multiple kingdoms of life and an array of functional groups. It is not only likely, but probable that understanding ecological aspects of soil microbial community structure, activity, and allocation will fundamentally change how we understand and predict ecosystem function in the future. In chapters 1-3 of this dissertation, I explicitly considered how microbial activities varied based on microbial community structure and the resulting impacts for biogeochemical cycling. Specifically, in chapters 1 and 2, I manipulated the relative abundance of symbiotic root fungi to demonstrate that competition between symbionts and free-living decomposers for nitrogen slowed soil carbon cycling. In chapter 3, I scaled how nitrogen is partitioned between plants, mycorrhizas and free-living decomposer microbes to demonstrate how shifts in microbial community structure could explain how forests productivity is sustained over centuries. In chapter 4, I developed a microbial allocation framework that explicitly considers microbial resource environments. I demonstrated that past microbial allocation frameworks based on plant ecological mechanisms cannot explain allocation patterns of decomposer microbial life. Throughout this dissertation I attempt to put soil microbial life in an explicit ecological context that challenges current understanding of ecosystem process and will allow for deeper understanding and prediction of ecosystem functioning. Incorporating microbial community structure, allocation, and simple ecological mechanisms into models will improve the predictive power of ecosystem ecology.

Microbial communities play an essential role in carrying out the biogeochemical cycles that sustain life on Earth, yet we know very little about their ecology. One question of particular interest is how environmental conditions shape microbial community structure (i.e., the types of organisms found in the community and their relative abundance), and whether such changes in structure are related to biogeochemical function. It is the aim of this dissertation to address this question via the examination of carbon (C) and nitrogen (N) cycling in wetland ecosystems, which due to their diverse hydrology have a profound influence on biogeochemical cycles. With respect to N cycling, the community structure of denitrification- and dissimilatory nitrate reduction to ammonium (DNRA)-capable organisms was evaluated in response to changes in resource availability, specifically organic matter (OM) and nitrate (NO3-), using an in situ field manipulation. Interactive regulation of microbial community composition was exhibited in both groups, likely due to variation in C substrate preferences and NO3- utilization efficiency. Subsequent experimentation considering only denitrification revealed that resource regulation of activity rates was mediated through changes in denitrifier community composition. The resource regulation of wetland C cycling also was evaluated using an in situ OM manipulation. OM characteristics (e.g., degree of decomposition) affected microbial extracellular enzyme activity (EEA) and changed the community structure of bacteria, archaea, and methanogens. These changes were linked with carbon dioxide and methane production via a conceptual model diagramming the importance of microbial community structure and EEA in greenhouse gas production. The investigation of C cycling in wetlands was extended to consider an important global change threat: saltwater intrusion into freshwater tidal wetlands. Bacterial community structure and EEA were examined along a natural salinity gradient. Salinity was strongly associated with bacterial community structure and positively correlated with EEA. These results suggested that salinity-induced increases in decomposition were responsible for reduced soil OM content in more saline wetlands. This work demonstrates that microbial communities in wetlands are structured by environmental conditions including resource availability and salinity. Further, the research provides evidence that environmental regulation of important biogeochemical processes in wetlands (e.g., methanogensis, denitrification, etc.) is mediated through changes in microbial community structure.