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Microbial Community Diversity Associated With Carbon And Nitrogen Cycling In Permeable Marine Sediments
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Book Synopsis Microbial Community Diversity Associated with Carbon and Nitrogen Cycling in Permeable Marine Sediments by : Evan M. Hunter
Download or read book Microbial Community Diversity Associated with Carbon and Nitrogen Cycling in Permeable Marine Sediments written by Evan M. Hunter and published by . This book was released on 2006 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Microbial Communities in Coastal Sediments by : Salom Gnana Thanga Vincent
Download or read book Microbial Communities in Coastal Sediments written by Salom Gnana Thanga Vincent and published by Elsevier. This book was released on 2021-06-02 with total page 208 pages. Available in PDF, EPUB and Kindle. Book excerpt: A concise reference on the structural composition and function of microbial communities in coastal environments, especially in relation to natural and anthropogenic impacts. Microbial Communities in Coastal Sediments presents twenty years of coastal microbiology research, grounding it as a vital development in the field of microbial ecology. It is the first book to focus exclusively on the complex microbial ecology and its function in rest of the marine environment. The book outlines the structure, function, and assessment of microbial communities in marine sediments while exploring practical methods of assessment. It is an invaluable resource to aquatic microbiologists, marine ecologists, marine microbiologists, aquatic researchers, and graduate students in this field. Microbial Communities in Coastal Sediments begins with an examination of nutrient sources in the coastal context with a focus on organic matter inputs. The quantity and quality of organic matter in coastal sediments and their impacts on the composition and formation of microbial communities is discussed. The book explores the consequences of anthropogenic changes and human activity on microbial ecology and nutrient cycling. Sections on nutrient availability, green house gas production and biodegradation of persistent organic pollutants provide essential details. Molecular research techniques and methods for assessing microbial community structure and function in coastal sediments are also covered. - Explores the interplay of physicochemical and biological features of coastal ecosystems on microbial community composition to provide a template of comparison for field research - Includes unique figures, schematic diagrams and photographs related to microbial processes of coastal ecosystem to clearly represent different aspects of microbial structure and functions - Provides analytical methods and detailed molecular techniques for qualitative and quantitative analyses of microbial community structure
Book Synopsis Interactions Between Macro- and Microorganisms in Marine Sediments by :
Download or read book Interactions Between Macro- and Microorganisms in Marine Sediments written by and published by American Geophysical Union. This book was released on 2005-01-14 with total page 391 pages. Available in PDF, EPUB and Kindle. Book excerpt: Marine sediments support complex interactions between macro-and microorganisms that have global implications for carbon and nutrient cycles. What is the state of the science on such interactions from coastal and estuarine environments to the deep sea? How does such knowledge effect environmental management? And what does future research hold in store for scientists, engineers, resource managers, and educators?Interactions between Macro- and Microorganisms in Marine Sediments responds to these questions, and more, by focusing on:? Interactions between plants, microorganisms, and marine sediment? Interactions between animals, microorganisms, and marine sediment? Interactions between macro- and microorganisms and the structuring of benthic communities? Impact of macrobenthic activity on microbially-mediated geochemical cycles in sediments? Conceptual and numeric models of diagenesis that incorporate interactions between macro- and microorganismsHere is an authoritative overview of the research, experimentation and modeling approaches now in use in our rapidly evolving understanding of life in marine sediments.
Book Synopsis Microbial Nitrogen Cycling Dynamics in Coastal Systems by : Annika Carlene Mosier
Download or read book Microbial Nitrogen Cycling Dynamics in Coastal Systems written by Annika Carlene Mosier and published by Stanford University. This book was released on 2011 with total page 232 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Chemical Ecology of Marine Microbial Communities by : Alyssa Marie Demko
Download or read book Chemical Ecology of Marine Microbial Communities written by Alyssa Marie Demko and published by . This book was released on 2021 with total page 216 pages. Available in PDF, EPUB and Kindle. Book excerpt: Marine sediments cover ~70% of the earth and host rich and diverse microbial communities. These microbial communities play an integral role in global nutrient cycling and the food web. They can be both a source of disease and/or an agent of mitigation through the natural products they produce, which can have cascading impacts on community structure and ecosystem function. Despite their importance, marine sediment microbes remain woefully understudied. The goal of this dissertation was to use next generation sequencing technology and newly developed bioinformatic pipelines to gain insight into these complex communities. First, I sought to reevaluate the 1% culturability paradigm by comparing sediment microbial communities using culture-dependent and culture-independent techniques. This comparative approach not only highlighted that >1% of sediment bacteria could be cultured, but also revealed the biases associated with culture-independent methods. Thirty-nine genera were identified in culture that were not detected with culture-independent methods, including some taxa that were fairly divergent from known cultured representatives. Next, I wanted to assess connections between sediment microbial communities, the sediment metabolome and sediment characteristics across varying spatial scales. To do this, microbial communities were sampled at three spatial scales, 1 m2 quadrats, 10 m transects, and sites across a 12 km2 area. Additionally, a small molecule in situ resin capture (SMIRC) method was employed to capture the metabolome present in sediments. The results from this study indicate that microbial diversity significantly increases with spatial scale and that sediment characteristics, such as grain size and nitrate concentrations, are significantly correlated with microbial communities. The SMIRC method was able to capture natural products and revealed the vast chemical landscape of marine sediments, much of which remains unexplored. Finally, I sought to evaluate how microbial communities in marine sediments vary in relation to the surrounding benthic environment by comparing fringing and back reefs of Mo'orea, French Polynesia. Even within a small area, ~1 km2, fringing and back reef sediment communities were distinct from each other. Back reefs exhibited greater richness and diversity in the microbial communities while fringing reefs had greater metabolomic richness. Supervised correlative analyses identified connections between microbes, metabolites and environmental characteristics such as nutrient concentration. Many of the taxa identified in the network analyses belong to relatively unknown lineages, providing important insight into the role these lineages may be playing in their communities. In conclusion, the results of this dissertation provide fundamental baseline information about the microbial communities and metabolites associated with marine sediments.
Book Synopsis The metabolic pathways and environmental controls of hydrocarbon biodegradation in marine ecosystems by : Joel E. Kostka
Download or read book The metabolic pathways and environmental controls of hydrocarbon biodegradation in marine ecosystems written by Joel E. Kostka and published by Frontiers Media SA. This book was released on 2015-05-15 with total page 196 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biodegradation mediated by indigenous microbial communities is the ultimate fate of the majority of oil hydrocarbon that enters the marine environment. The aim of this Research Topic is to highlight recent advances in our knowledge of the pathways and controls of microbially-catalyzed hydrocarbon degradation in marine ecosystems, with emphasis on the response of microbial communities to the Deepwater Horizon oil spill in the Gulf of Mexico. In this Research Topic, we encouraged original research and reviews on the ecology of hydrocarbon-degrading bacteria, the rates and mechanisms of biodegradation, and the bioremediation of discharged oil under situ as well as near in situ conditions.
Book Synopsis Methods for the Study of Deep-Sea Sediments, Their Functioning and Biodiversity by : Roberto Danovaro
Download or read book Methods for the Study of Deep-Sea Sediments, Their Functioning and Biodiversity written by Roberto Danovaro and published by CRC Press. This book was released on 2009-12-21 with total page 460 pages. Available in PDF, EPUB and Kindle. Book excerpt: For years scientists viewed the deep sea as calm, quiet, and undisturbed, with marine species existing in an ecologically stable and uniform environment. Recent discoveries have completely transformed that understanding and the deep sea is recognized as a complicated and dynamic environment with a rich diversity of marine species. Carefully designe
Book Synopsis Biogeography of Nitrogen-cycling Microbial Communities in San Francisco Bay by : Jessica Audrey Lee
Download or read book Biogeography of Nitrogen-cycling Microbial Communities in San Francisco Bay written by Jessica Audrey Lee and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Nitrogen is an essential element to all of life on earth, and its bioavailability in the environment is governed by the activities of microorganisms that transform nitrogen species through redox processes such as denitrification, nitrification, and anammox. In this study, we survey the nitrogen-cycling microbial populations in the sediments of San Francisco Bay, using diverse DNA-based methods to address questions about microbial population dynamics across space, time, and the environmental gradients typical of an estuary. Our results include: a comparison of the abundance and community structures of nirK-type and nirS-type denitrifying bacteria; a novel use of next-generation sequencing for surveying functional gene diversity in the environment and a demonstration of machine-learning techniques for identifying ecological trends in that sequence data; and finally, deep sequencing of the 16S rRNA gene to survey and compare several N-cycling functional communities at once. Overall, we observe strong spatial structure in each nitrogen-cycling functional group as well as in the total microbial community, a strong response of all groups to salinity and to sediment nitrogen content, and marked differences in the temporal variability of communities in different sites. This survey of microbial diversity in San Francisco Bay contributes to our understanding of the processes influencing sediment biota in the estuary, and forms a foundation for future studies in the functioning of these nitrogen-cycling communities.
Book Synopsis Subterranean Estuaries by : Carlos Rocha
Download or read book Subterranean Estuaries written by Carlos Rocha and published by Frontiers Media SA. This book was released on 2023-01-19 with total page 289 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over recent decades, it has become widely recognized that water exchange between coastal aquifers and the ocean is an important component of the hydrologic cycle. Twenty years have passed since Willard S. Moore (Moore, 1999) introduced the term ‘subterranean estuary’ (STE) to identify those zones within coastal aquifers where fresh groundwater mixes with surface saltwater. Like open-water estuaries, STEs regulate the transfer of chemicals to the sea under the seashore by submarine groundwater discharge (SGD). This subterranean reactive node in the land-ocean exchange pathway has a physical, even if elusive, structure created by a combination of temporally and spatially variable mass transfer across the groundwater-ocean interface and dynamic flow processes. Many case studies have shown that SGD is a key material link between coastal watersheds and the sea and indeed spatially resolved budgets of radioactive tracers in shelf waters suggest it is the dominant bulk water flux to coastal zones globally. Clearly, STE outflow as SGD is a large source of biogeochemically active solutes to shelf seas, meaning that elemental budgets for these waters have to be revised in order to account for the new input. But how? Recognizing the global prevalence and potential environmental and societal impact of SGD, numerous attempts to quantify chemical inputs into the ocean through this pathway have been published over the past 40 years. However, the role of the STE in modulating chemical fluxes to coastal waters has been generally oversimplified, making a comprehensive analysis of cause and effect relationships between SGD inputs and ecosystem dynamics merely indicative. Unfortunately, we still lack a mechanistic understanding of the processes that control the interaction between allochthonous chemical delivery and autochthonous recycling in the STE that drive compositional variability of SGD flows. Like that applied to open-water estuaries, a general practical and theoretical framework is needed – one that captures the structure and biogeochemistry of STEs and allows more accurate understanding of the chemical composition of SGD outflows, while simultaneously providing for a typological basis that provides solid support for extrapolation of local SGD chemical flux measurements to regional, and from these to global, scale. A comprehensive and critical review of the current state-of-the-art would reveal that progress requires: a) improved variable-density groundwater flow models that provide more accurate predictions and insights into the flow, salt transport, and mixing dynamics in STEs; b) quantitative understanding of the physicochemical and temporal drivers of saline groundwater seepage and composition; and c) better knowledge of the microbial ecology of STEs and links to marine, freshwater, and terrestrial drivers of STE dynamics. Significant research effort has been devoted to addressing these knowledge gaps. It is now time to provide a focused synopsis of these efforts. We propose a combination of cutting-edge original research, systematic, practice and policy reviews, methods and hypothesis and theory articles, tied together by a direction-setting perspective analysis to generate a comprehensive and accurate scientific foundation supporting environmental managers, scientists, and other stakeholders to assess SGD feedbacks on coastal ecosystem functioning and resilience and implement successful coastal management policies.
Book Synopsis Microbial Processes and Carbon Cycling in the Ocean by : Nianzhi Jiao
Download or read book Microbial Processes and Carbon Cycling in the Ocean written by Nianzhi Jiao and published by Nova Science Publishers. This book was released on 2008 with total page 108 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses recent progress in microbial oceanography with emphasis on microbial processes and mechanisms related to carbon cycling in the ocean, including the newly recognised microbial light utilisation in the surface ocean, archaeal carbon fixation and methane oxidation in the deep ocean and sediment, as well as lysis of host organisms by viroplankton and its influence on carbon cycling in the water column. Key functional groups of microorganisms include Prochlorococcus which possess unique photosynthesis pigments, the divinyl chlrophylls; Aerobic anoxygenic phototrophic bacteria (AAPB) which possess bacterial chlorophyll a; Rhodopsin containing proteobacteria (PR); Nonthermophilic crenarchaeota, which use ammonia as a major energy source for autotrophic growth; and the ANME groups of archaea which oxidize methane for energy. Recent findings have challenged to the conventional concepts and theories. To face these challenges the authors propose novel models based on an understanding of newly discovered microbial processes. For carbon cycling in the surface ocean, a conceptual model is proposed based on light bio-utilisation where bacteriochlorophyll a induced anoxygenic phototrophy and proteiorhodopsin based proton pump are included.
Book Synopsis Marine Microbiome and Biogeochemical Cycles in Marine Productive Areas by : Alejandro A. Murillo
Download or read book Marine Microbiome and Biogeochemical Cycles in Marine Productive Areas written by Alejandro A. Murillo and published by Frontiers Media SA. This book was released on 2020-01-16 with total page 179 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Microbial Community Composition and Organic Carbon Cycling in Permanently Cold Marine Sediments (Svalbard) by : Sabrina Neill Powell
Download or read book Microbial Community Composition and Organic Carbon Cycling in Permanently Cold Marine Sediments (Svalbard) written by Sabrina Neill Powell and published by . This book was released on 2002 with total page 92 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Microbial Diversity and Resources in Tidal Flats by : Xue-Wei Xu
Download or read book Microbial Diversity and Resources in Tidal Flats written by Xue-Wei Xu and published by Frontiers Media SA. This book was released on 2024-06-06 with total page 232 pages. Available in PDF, EPUB and Kindle. Book excerpt: Tidal flats are widely distributed worldwide, occupying at least 127,921 km2, of which 70% are located in coastal areas of Asia, and North and South America. As a confluence of terrestrial and marine ecosystems, tidal flat is dually influenced by these two ecosystems and becomes one of the most productive ecosystems. Rhythmic changes of environmental factors (e.g., salinity, temperature, dissolved oxygen, illumination intensity, ocean current, etc.) and frequent disturbances of human behaviour enhance organic matter as well as nitrogen, phosphorus, and sulfur compounds in tidal flats. Furthermore, tidal flats have various important ecosystem functions, including climate regulation, shoreline stabilization, carbon fixation, pollutant degradation, etc.
Book Synopsis Microbial Communities of Coastal Eutrophic Systems by : Savvas Genitsaris
Download or read book Microbial Communities of Coastal Eutrophic Systems written by Savvas Genitsaris and published by Frontiers Media SA. This book was released on 2021-12-31 with total page 161 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Scenarios and Responses to Future Deep Oil Spills by : Steven A. Murawski
Download or read book Scenarios and Responses to Future Deep Oil Spills written by Steven A. Murawski and published by Springer. This book was released on 2019-07-04 with total page 542 pages. Available in PDF, EPUB and Kindle. Book excerpt: It has often been said that generals prepare for the next war by re-fighting the last. The Deepwater Horizon (DWH) oil spill was unlike any previous – an underwater well blowout 1,500 meters deep. Much has been learned in the wake of DWH and these lessons should in turn be applied to both similar oil spill scenarios and those arising from “frontier” explorations by the marine oil industry. The next deep oil well blowout may be at 3,000 meters or even deeper. This volume summarizes regional (Gulf of Mexico) and global megatrends in marine oil exploration and production. Research in a number of key areas including the behavior of oil and gas under extreme pressure, impacts on biological resources of the deep sea, and the fate of oil and gas released in spills is synthesized. A number of deep oil spills are simulated with detailed computer models, and the likely effects of the spills and potential mitigation measures used to combat them are compared. Recommended changes in policies governing marine oil exploration and development are proposed, as well as additional research to close critical and emerging knowledge gaps. This volume synthesizes state-of-the-art research in deep oil spill behavior and response. It is thus relevant for government and industry oil spill responders, policy formulators and implementers, and academics and students desiring an in-depth and balanced overview of key issues and uncertainties surrounding the quest for deep oil and potential impacts on the environment.
Book Synopsis Linking Ecosystem Function to Microbial Diversity by : Anne E. Bernhard
Download or read book Linking Ecosystem Function to Microbial Diversity written by Anne E. Bernhard and published by Frontiers Media SA. This book was released on 2016-10-20 with total page 161 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding the link between microbial diversity and ecosystem processes is a fundamental goal of microbial ecologists, yet we still have a rudimentary knowledge of how changes in diversity affect nutrient cycling and energy transfer in ecosystems. Due to the complexity of the problem, many published studies on this topic have been conducted in artificial or manipulated systems. Although researchers have begun to expose some possible mechanisms using these approaches, most have not yet been able to produce conclusive results that relate directly to natural systems. The few studies that have explored the link between diversity and activity in natural systems have typically focused on specific nutrient cycles or processes, such as nitrification, denitrification, and organic carbon degradation pathways, and the microbes that mediate them. What we have learned from these studies is that there are often strong associations between the physical and chemical features of the environment, the composition of the microbial communities, and their activities, but the rules that govern these associations have not been fully elucidated. These earlier studies of microbial diversity and processes in natural systems provide a framework for additional studies to broaden our understanding of the role of microbial diversity in ecosystem function. The problem is complex, but with recent advances in sequencing technology, -omics, and in-situ measurements of ecosystem processes and their applications to microbial communities, making direct connections between ecosystem function and microbial diversity seems more tractable than ever.
Book Synopsis Investigating Marine Microbial Metabolism and Diversity of Arctic Ecosystems by : David Colatriano
Download or read book Investigating Marine Microbial Metabolism and Diversity of Arctic Ecosystems written by David Colatriano and published by . This book was released on 2021 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The world's oceans are essential for sustaining life on Earth and harbour a vast diversity of organisms. Marine microbes play crucial roles in global biogeochemical cycling and are at the base of marine food webs. Due to the technical difficulties associated with sampling northern marine systems, relatively little is known about the microbial community composition and metabolism of these ecosystems. In this thesis work, the community composition and metabolism of northern marine ecosystems, including the Saint Lawrence Estuary, North Water and Canada Basin were described using meta-omic techniques. In the Saint Lawrence Estuary, differences in microbial community structure, metabolic lifestyles and carbon and nitrogen processing pathways were observed between the surface and deep waters. In the North Water, two distinct microbial communities with different taxonomic compositions and differing nutrient acquisition and resource allocation strategies were identified on either side of the polar mixed layer, and a third distinct community was described in the bottom waters. Functional and taxonomic analyses of the North Water polar mixed layer communities suggest a microbial community more typically associated with waters that undergo pulses of primary production on the Canadian side, while the community on the Greenland side was more typical of waters associated with a more steady level of primary production. In the Canada Basin, metagenomics was used to construct 360 Arctic Ocean metagenome assembled genomes. The analysis of six Chloroflexi MAGs revealed their potential for terrestrial derived aromatic compound degradation and that this metabolic capacity was acquired, at least in part, by lateral gene transfer from terrestrial organisms. To facilitate the meta-omic analyses performed in this thesis, a novel method to isolate microbial community DNA and proteins from the same environmental sample preserved in RNAlater was also developed. This thesis not only describes the microbial community composition and metabolism of northern marine systems over a broad geographic range, but also adds to the growing metagenomic and metaproteomic resource-base that can be used to develop and test hypotheses about northern marine microbial systems. Additionally, this work has implications for our understanding of how climate change may affect northern marine ecosystems.
