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Nitrogen is an essential element in biological systems, and one that often limits production in both aquatic and terrestrial systems. Due to its requirement in biological macromolecules, its acquisition and cycling have the potential to structure microbial communities, as well as to control productivity on the ecosystem scale. In addition, its versatile redox chemistry is the basis of complex biogeochemical transformations that control the inventory of fixed nitrogen, both in local environments and over geological time. Although many of the pathways in the microbial nitrogen cycle were described more than a century ago, additional fundamental pathways have been discovered only recently. These findings imply that we still have much to learn about the microbial nitrogen cycle, the organisms responsible for it, and their interactions in natural and human environments. Progress in nitrogen cycle research has been facilitated by recent rapid technological advances, especially in genomics and isotopic approaches. In this Research Topic, we reviewed the leading edge of nitrogen cycle research based on these approaches, as well as by exploring microbial processes in modern ecosystems.
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.
Human influence on the global nitrogen cycle (e.g., through fertilizer and wastewater runoff) has caused a suite of environmental problems including acidification, loss of biodiversity, increased concentrations of greenhouse gases, and eutrophication. These environmental risks can be lessened by microbial transformations of nitrogen; nitrification converts ammonia to nitrite and nitrate, which can then be lost to the atmosphere as N2 gas via denitrification or anammox. Microbial processes thus determine the fate of excess nitrogen and yet recent discoveries suggest that our understanding of these organisms is deficient. This dissertation focuses on microbial transformations of nitrogen in marine and estuarine systems through laboratory and field studies, using techniques from genomics, microbial ecology, and microbiology. Recent studies revealed that many archaea can oxidize ammonia (AOA; ammonia-oxidizing archaea), in addition to the well-described ammonia-oxidizing bacteria (AOB). Considering that these archaea are among the most abundant organisms on Earth, these findings have necessitated a reevaluation of nitrification to determine the relative contribution of AOA and AOB to overall rates and to determine if previous models of global nitrogen cycling require adjustment to include the AOA. I examined the distribution, diversity, and abundance of AOA and AOB in the San Francisco Bay estuary and found that the region of the estuary with low-salinity and high C:N ratios contained a group of AOA that were both abundant and phylogenetically distinct. In most of the estuary where salinity was high and C:N ratios were low, AOB were more abundant than AOA—despite the fact that AOA outnumber AOB in soils and the ocean, the two end members of an estuary. This study suggested that a combination of environmental factors including carbon, nitrogen, and salinity determine the niche distribution of the two groups of ammonia-oxidizers. In order to gain insight into the genetic basis for ammonia oxidation by estuarine AOA, we sequenced the genome of a new genus of AOA from San Francisco Bay using single cell genomics. The genome data revealed that the AOA have genes for both autotrophic and heterotrophic carbon metabolism, unlike the autotrophic AOB. These AOA may be chemotactic and motile based on numerous chemotaxis and motility-associated genes in the genome and electron microscopy evidence of flagella. Physiological studies showed that the AOA grow aerobically but they also oxidize ammonia at low oxygen concentrations and may produce the potent greenhouse gas N2O. Continued cultivation and genomic sequencing of AOA will allow for in-depth studies on the physiological and metabolic potential of this novel group of organisms that will ultimately advance our understanding of the global carbon and nitrogen cycles. Denitrifying bacteria are widespread in coastal and estuarine environments and account for a significant reduction of external nitrogen inputs, thereby diminishing the amount of bioavailable nitrogen and curtailing the harmful effects of nitrogen pollution. I determined the abundance, community structure, biogeochemical activity, and ecology of denitrifiers over space and time in the San Francisco Bay estuary. Salinity, carbon, nitrogen and some metals were important factors for denitrification rates, abundance, and community structure. Overall, this study provided valuable new insights into the microbial ecology of estuarine denitrifying communities and suggested that denitrifiers likely play an important role in nitrogen removal in San Francisco Bay, particularly at high salinity sites.
Presenting the first continental-scale assessment of reactive nitrogen in the environment, this book sets the related environmental problems in context by providing a multidisciplinary introduction to the nitrogen cycle processes. Issues of upscaling from farm plot and city to national and continental scales are addressed in detail with emphasis on opportunities for better management at local to global levels. The five key societal threats posed by reactive nitrogen are assessed, providing a framework for joined-up management of the nitrogen cycle in Europe, including the first cost-benefit analysis for different reactive nitrogen forms and future scenarios. Incorporating comprehensive maps, a handy technical synopsis and a summary for policy makers, this landmark volume is an essential reference for academic researchers across a wide range of disciplines, as well as stakeholders and policy makers. It is also a valuable tool in communicating the key environmental issues and future challenges to the wider public.
The nitrogen (N) cycle is one of the most important nutrient cycles on the planet, and many of its steps are performed by microbial organisms. During the cycling process, greenhouse gases are formed, including nitrous oxide and methane. In addition, the use of nitrogen fertilizers increases freshwater nitrate levels, causing pollution and human health problems. A greater knowledge of the microbial communities involved in nitrogen transformations is necessary to understand and counteract nitrogen pollution. This book - written by renowned researchers who are specialized in the most relevant and emerging topics in the field - provides comprehensive information on the new theoretical, methodological, and applied aspects of metagenomics and other 'omics' approaches used to study the microbial N cycle. The book provides a thorough account of the contributions of metagenomics to microbial N cycle background theory. It also reviews state-of-the-art investigative methods and explores new applications in water treatment, agricultural practices, climate change, among others. The book is recommended for microbiologists, environmental scientists, and anyone interested in microbial communities, metagenomics, metatranscriptomics, and metaproteomics of the microbial N cycle.
A full review of the latest research findings on microbes involved in conventional aerobic nitrification, anaerobic ammonia oxidation, and related processes. • Examines the four principal groups of nitrifying microbes including conventional aerobic bacterial ammonia oxidizers, recently discovered aerobic archaeal ammonia oxidizers, anaerobic ammonia-oxidizing planctomycetes, and nitrite-oxidizing bacteria. • Provides current information on the ecology, phylogeny, biochemistry, molecular biology, and genomics of each group of microbes. • Discusses the latest industrial applications of nitrification and anammox processes, and explores the ecology of nitrification in marine, freshwater, soil, and wastewater environments.
State-of-the-art update on methods and protocols dealing with the detection, isolation and characterization of macromolecules and their hosting organisms that facilitate nitrification and related processes in the nitrogen cycle as well as the challenges of doing so in very diverse environments. Provides state-of-the-art update on methods and protocols Deals with the detection, isolation and characterization of macromolecules and their hosting organisms Deals with the challenges of very diverse environments
During the past three decades there has been a large amount of research on biological nitrogen fixation, in part stimulated by increasing world prices of nitrogen-containing fertilizers and environmental concerns. In the last several years, research on plant--microbe interactions, and symbiotic and asymbiotic nitrogen fixation has become truly interdisciplinary in nature, stimulated to some degree by the use of modern genetic techniques. These methodologies have allowed us to make detailed analyses of plant and bacterial genes involved in symbiotic processes and to follow the growth and persistence of the root-nodule bacteria and free-living nitrogen-fixing bacteria in soils. Through the efforts of a large number of researchers we now have a better understanding of the ecology of rhizobia, environmental parameters affecting the infection and nodulation process, the nature of specificity, the biochemistry of host plants and microsymbionts, and chemical signalling between symbiotic partners. This volume gives a summary of current research efforts and knowledge in the field of biological nitrogen fixation. Since the research field is diverse in nature, this book presents a collection of papers in the major research area of physiology and metabolism, genetics, evolution, taxonomy, ecology, and international programs.
Nitrogen in the Marine Environment provides information pertinent to the many aspects of the nitrogen cycle. This book presents the advances in ocean productivity research, with emphasis on the role of microbes in nitrogen transformations with excursions to higher trophic levels. Organized into 24 chapters, this book begins with an overview of the abundance and distribution of the various forms of nitrogen in a number of estuaries. This text then provides a comparison of the nitrogen cycling of various ecosystems within the marine environment. Other chapters consider chemical distributions and methodology as an aid to those entering the field. This book discusses as well the enzymology of the initial steps of inorganic nitrogen assimilation. The final chapter deals with the philosophy and application of modeling as an investigative method in basic research on nitrogen dynamics in coastal and open-ocean marine environments. This book is a valuable resource for plant biochemists, microbiologists, aquatic ecologists, and bacteriologists.