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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.
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.
The study of estuaries and coasts has seen enormous growth in recent years, since changes in these areas have a large effect on the food chain, as well as on the physics and chemistry of the ocean. As the coasts and river banks around the world become more densely populated, the pressure on these ecosystems intensifies, putting a new focus on environmental, socio-economic and policy issues. Written by a team of international expert scientists, under the guidance of Chief Editors Eric Wolanski and Donald McClusky, the Treatise on Estuarine and Coastal Science, Ten Volume Set examines topics in depth, and aims to provide a comprehensive scientific resource for all professionals and students in the area of estuarine and coastal science Most up-to-date reference for system-based coastal and estuarine science and management, from the inland watershed to the ocean shelf Chief editors have assembled a world-class team of volume editors and contributing authors Approach focuses on the physical, biological, chemistry, ecosystem, human, ecological and economics processes, to show how to best use multidisciplinary science to ensure earth's sustainability Provides a comprehensive scientific resource for all professionals and students in the area of estuarine and coastal science Features up-to-date chapters covering a full range of topics
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.
From the Chapman & Hall Microbiology Series this unique resource offers specific experimental and practical applications of mathematical modeling in microbial ecology. The text presents a variety of systems, ranging from subcellular systems to ecosystems, and shows how to test whether the models provide a good representation of the system. The book also encourages further development and application of modeling to burgeoning problems associated with microbial ecology, such as the pollution and destruction of pesticides and herbicides.
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
Nitrogen discharge to the coastal environment has been increasing, posing the threat of accelerated eutrofication. Considerable research has been conducted in recent years to examine the impact of the nitrogen loading in coastal ecosystems. Based on proceedings from a SCOPE symposium held at the University of Aarhus in July of 1985, this volume covers a variety of up-to-date developments in research on nitrogen cycling in coastal marine environments. Topics include the role of nitrogen in algal productivity, regeneration of nutrients in the water column and the sediments, and the flow of nitrogen in coastal ecosystems.