There can be little doubt that there are truly colossal challenges associated with providing food, fibre and energy for an expanding world population without further accelerating already rapid rates of biodiversity loss and undermining the ecosystem processes on which we all depend. These challenges are further complicated by rapid changes in climate and its additional direct impacts on agriculture, biodiversity and ecological processes. There are many different viewpoints about the best way to deal with the myriad issues associated with land use intensification and this book canvasses a number of these from different parts of the tropical and temperate world. Chapters focus on whether science can suggest new and improved approaches to reducing the conflict between productive land use and biodiversity conservation. Who should read this book? Policy makers in regional, state and federal governments, as well as scientists and the interested lay public.

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.

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.

General introduction; Land use impact on the stability of soil microbial community composition and enzyme activities to heat shock; Shifts in microbial community composition and physiological profiles across a gradient of induced soil degradation (GRIND); Development and validation of a soil quality index based on the equilibrium between soil organic matter and biochemical properties in an undisturbed forest ecosystem. The objectives of this thesis were to evaluate the responses of soil microbial communities to physical and chemical disturbances, and associate these responses with soil functional stability and changes in soil quality. The first study consisted of application of heat shocks (HS) to soils with contrasting land use history to evaluate differences in the stability of soil enzymes (laccase, cellulase and fluorescein diacetate hydrolysis) and microbial community composition as determined by phospholipid fatty acid (PLFA) analysis. The conversion of land use from forest to agriculture resulted in a new microbial community that was less functionally stable. Loss of stability was indicated by the reduced of laccase and cellulase activities in the agricultural soil, which suggested a less diverse community of microorganisms capable of producing these enzymes. The second study examined changes in microbial community composition and diversity that occurred across a gradient of soil disturbance. Disturbances were simulated by tillage events applied at different intensities to a 12-year-old fallow area. These treatments caused degradation of several soil physico-chemical properties, and alterations in microbial structure based on PLFA and terminal restriction fragment length polymorphism (T-RFLP) analyses, and in metabolic potential based on community level physiological profiles (CLPPs). Multivariate ordination of soil properties revealed the formation of a linear gradient of soil degradation that was significantly correlated with CLPPs, but not with T-RFLP and PLFA profiles. Nevertheless, changes observed in microbial community structure were significantly associated with decreases in soil organic C and field hydraulic conductivity. The third study demonstrated that undisturbed forest soils from western Oregon express an equilibrium between soil organic matter and biochemical properties. A model fitted through multiple regression analysis showed that phosphatase activity and microbial biomass were able to explain 97% of the soil organic C in these soils. This equilibrium was disrupted when a soil from an old-growth site was submitted to chemical stresses (Cu addition or pH alteration) and physical disturbances (wet-dry or freeze-thaw cycles). The magnitude of this disruption was consistently expressed by the ratio between soil C predicted by the model (Cp), and soil C that was measured (Cm). This ratio is proposed as biochemically-based index of soil quality.