How farming systems supply sufficient nitrogen (N) for high yields but with reduced N losses is a central challenge for reducing the tradeoffs often associated with N cycling in agriculture. This dissertation consists of three studies that assess how variability in organic farms across an agricultural landscape may yield insights for improving N cycling and for evaluating novel indicators of N availability. Pulses of N are common in agricultural systems and often result in N losses if N is not quickly captured by plants or soil microbes. But understanding of how root behavioral responses and microbial N dynamics interact following soil N pulses remains limited, especially in soil under field conditions relevant to actual agroecosystem processes. The first study examined rhizosphere responses to a soil N pulse in an organic farm soil. A novel combination of molecular and 15N isotopic techniques was used to investigate the response of tomato (Solanum lycopersicum L.) roots and soil N cycling to a pulse of inorganic N in an undisturbed soil patch on an organic farm. Tomato roots rapidly responded to and exploited the N pulse via upregulation of key N metabolism genes that comprise the core physiological response of roots to patchy soil N availability. The transient root gene expression response underscored the sensitivity of root N uptake to local N availability. Strong root activity limited accumulation of soil nitrate (NO3−) despite high rates of gross nitrification and allowed roots to out-compete soil microbes for uptake of the inorganic N pulse, even on the short time scale of a few days. Root expression of genes such as cytosolic glutamine synthetase, a key gene in root N assimilation, could serve as a "plant's eye view" of N availability when plant-soil N cycling is rapid, complementing more typical measures of N availability like soil inorganic N pools and bioassays of N mineralization potential. Much of the research geared toward improving N cycling takes place at research stations with fixed management factors and limited variation in soil characteristics. Better understanding of how the plant-soil-microbe interactions that underpin N availability, potential for N loss, and yields vary across working farms would help reveal how to simultaneously achieve high provisioning (yields) and regulating (low potential for N loss) ecosystem services in heterogeneous landscapes. A landscape approach was thus used in the second and third studies to assess crop yields, plant-soil N cycling, root gene expression, and soil microbial community activity and composition over the course of a tomato growing season on working organic farms in Yolo County, California, USA. The 13 selected fields were representative of organic tomato production in the local landscape and spanned a three-fold range of soil carbon (C) and N but had similar soil types, texture, and pH. Yields ranged from 22.9 to 120.1 Mg ha−1 with a mean similar to the county average (86.1 Mg ha−1), which included mostly conventionally-grown tomatoes. Substantial variability in soil inorganic N concentrations, tomato N, and root gene expression indicated a range of possible tradeoffs between yields and potential for N losses across the fields. Soil enzyme activities reflected distinct metabolic capacity in each field, such that soil C-cycling enzyme potential activities increased with inorganic N availability while those of soil N-cycling enzymes increased with soil C availability. Compared to potential enzyme activity, there was less variation in soil microbial community composition, likely reflecting the history of high soil disturbance and low ecological complexity in this landscape. The variation in potential activity of soil enzymes across the organic fields thus may be due to high plasticity of the resident microbial community to environmental conditions. Those fields in the landscape that showed evidence of tightly-coupled plant-soil N cycling, a desirable scenario in which high crop yields are supported by adequate N availability but low potential for N loss, had the highest total and labile soil C and N and received diverse types of organic matter inputs with a range of N availability. In these fields, elevated expression of cytosolic glutamine synthetase in roots (as evaluated in the first study), confirmed that plant N assimilation was high even when soil inorganic N pools were low. The on-farm approach provided a wide range of farming practices and soil characteristics to reveal how microbially-derived ecosystem functions can be effectively manipulated to enhance nutrient cycling capacity. Novel combinations of N cycling indicators (i.e. inorganic N along with soil microbial activity and root gene expression for N assimilation) would support adaptive management for improved N cycling on organic as well as conventional farms, and could overcome the uncertainty of managing N inputs accurately, especially when plant-soil N cycling is rapid.

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 sustainable intensification of agriculture relies on the efficient use of ecosystem services, particularly those provided by the microbial community. Managing for these ecosystem services can improve plant yields and reduce off-site impacts. For instance, increasing plant diversity is linked to positive effects on yield, and these beneficial effects are often mediated by the microbial community and the nutrient transformations it carries out. My dissertation has aimed to elucidate the mechanisms by which plant diversity improves agricultural production. In particular, I have focused on how changes to the amount and diversity of carbon (C) inputs affects soil microorganisms involved in the nitrogen (N) cycle. My work spans multiple scales of observation: from a global meta-analysis to mechanistic studies utilizing denitrification as a model system.In a global meta-analysis, I found that increasing plant diversity through intercropping yields a net increase in extracellular enzyme activity. This effect varied by plant species and soil type suggesting that increases in the quality of nutrient inputs mediates these positive effects on microbial activity. Then, I looked at how intercropping cover crops into corn affects soil nutrient pools and microbial activities in a field experiment. No effect of interseeding cover crops into corn was found on soil nutrient pools or microbial activities. However, by analyzing differences in relationships between nutrient pools and microbial activities at two locations throughout Michigan, I was able to describe how the availability of dissolved organic C (DOC) drives differences in microbial N-cycling processes. I then investigated how C availability drives activity in microbial hotspots within the soil by comparing differences in denitrification potential in bulk soil versus the rhizospheres of corn and interseeded cover crops. Here, I found that denitrification rates were increased in the rhizospheres of all plant types, and this effect varied depending on the species of plant. I was able to further differentiate the impact of DOC and microbial biomass C on the rhizosphere effect and found that C availability was the primary driver of differences in denitrification rates between rhizospheres. Since plants provide many different forms of C to soil microbes, it is important to understand how the chemistry of C inputs affects microbial activity. I used a series of C-substrate additions to determine how C chemistry affects denitrifiers. I found that amino acids and organic acids tended to stimulate the most nitrous oxide (N2O) production and reduction. Although management and site affected overall rates of denitrification, C-utilization patterns of microbes were mostly similar between locations. To identify the mechanisms responsible for these effects, I performed a final experiment to track how denitrifiers utilized different C compounds. The C substrates that stimulated the most complete reduce of N2O also were utilized with the lowest C-use efficiency (CUE). This suggests possible trade-offs between N2O reduction and CUE, with important implications for how to manage microbial communities.Overall, my work demonstrates that land management can impact microbial community activity by influencing the identity of soil C inputs. While the importance of increasing soil C inputs has been known, this dissertation supports the notion that the chemical identity of C inputs can exert significant controls on microbial activity. Moreover, by comparing microbial traits I highlight the importance of trade-offs in how microbially mediated C- and N cycling are coupled.

This book highlights the latest discoveries about the nitrogen cycle in the soil. It introduces the concept of nitrogen fixation and covers important aspects of nitrogen in soil and ecology such as its distribution and occurrence, soil microflora and fauna and their role in N-fixation. The importance of plant growth-promoting microbes for a sustainable agriculture, e.g. arbuscular mycorrhizae in N-fixation, is discussed as well as perspectives of metagenomics, microbe-plant signal transduction in N-ecology and related aspects. This book enables the reader to bridge the main gaps in knowledge and carefully presents perspectives on the ecology of biotransformations of nitrogen in soil.

Sustainability has a major part to play in the global challenge of continued development of regions, countries, and continents all around the World and biological nitrogen fixation has a key role in this process. This volume begins with chapters specifically addressing crops of major global importance, such as soybeans, rice, and sugar cane. It continues with a second important focus, agroforestry, and describes the use and promise of both legume trees with their rhizobial symbionts and other nitrogen-fixing trees with their actinorhizal colonization. An over-arching theme of all chapters is the interaction of the plants and trees with microbes and this theme allows other aspects of soil microbiology, such as interactions with arbuscular mycorrhizal fungi and the impact of soil-stress factors on biological nitrogen fixation, to be addressed. Furthermore, a link to basic science occurs through the inclusion of chapters describing the biogeochemically important nitrogen cycle and its key relationships among nitrogen fixation, nitrification, and denitrification. The volume then provides an up-to-date view of the production of microbial inocula, especially those for legume crops.

Agriculture transforms the environment. The simplification of agroecosystems structure increases the hazards of leaching, wind and water erosion, and volatilization of chemicals from soil. Soil nitrogen is of interest as a major crop nutrient, but also as a potential environmental pollutant. Knowledge about the behavior of soil nitrogen is desirable in order to optimize plant growth and crop yield and to minimize environmental side effects. This book also gives information about the function of biogeochemical barriers in the form of shelterbelts, which efficiently decrease the concentrations of various forms of nitrogen in ground water.

The large and rapidly expanding body ofliterature related to nitrogen cycling in both managed and native terrestrial ecosystems reflects the importance accorded to the behaviour of this vital and often limiting nutrient. Research at the organism, ecosystem and landscape levels commonly addresses questions concerning nitrogen acquisition, internal cycling and retention. Goals for this research include increased agricultural productivity and a better understanding of human impact on local, regional and global nitrogen cycles. Nitrogen cycle research in tropical regions has a long and distinguished history. Research on different aspects of nitrogen cycling in ecosystems of the tropics has been carried out in many regions. In relatively few instances has there, however, been a focus on the biogeochemical cycles at the ecosystem level. The meeting resulting in this volume was an attempt to bring together existing information on nitrogen cycling in ecosystems of Latin America and the Caribbean and discuss this in an ecosystem context.