Download or read book Phylogenetic Characterization of Subsurface Sediment Microbial Communities written by Paul A. Vescio and published by . This book was released on 2000 with total page 190 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Deep Subsurface Microbiology written by Andreas Teske and published by Frontiers Media SA. This book was released on 2015-07-01 with total page 305 pages. Available in PDF, EPUB and Kindle. Book excerpt: Deep subsurface microbiology is a highly active and rapidly advancing research field at the interface of microbiology and the geosciences; it focuses on the detection, identification, quantification, cultivation and activity measurements of bacteria, archaea and eukaryotes that permeate the subsurface biosphere of deep marine sediments and the basaltic ocean and continental crust. The deep subsurface biosphere abounds with uncultured, only recently discovered and – at best - incompletely understood microbial populations. In spatial extent and volume, Earth's subsurface biosphere is only rivaled by the deep sea water column. So far, no deep subsurface sediment has been found that is entirely devoid of microbial life; microbial cells and DNA remain detectable at sediment depths of more than 1 km; microbial life permeates deeply buried hydrocarbon reservoirs, and is also found several kilometers down in continental crust aquifers. Severe energy limitation, either as electron acceptor or donor shortage, and scarcity of microbially degradable organic carbon sources are among the evolutionary pressures that have shaped the genomic and physiological repertoire of the deep subsurface biosphere. Its biogeochemical role as long-term organic carbon repository, inorganic electron and energy source, and subduction recycling engine continues to be explored by current research at the interface of microbiology, geochemistry and biosphere/geosphere evolution. This Research Topic addresses some of the central research questions about deep subsurface microbiology and biogeochemistry: phylogenetic and physiological microbial diversity in the deep subsurface; microbial activity and survival strategies in severely energy-limited subsurface habitats; microbial activity as reflected in process rates and gene expression patterns; biogeographic isolation and connectivity in deep subsurface microbial communities; the ecological standing of subsurface biospheres in comparison to the surface biosphere – an independently flourishing biosphere, or mere survivors that tolerate burial (along with organic carbon compounds), or a combination of both? Advancing these questions on Earth’s deep subsurface biosphere redefines the habitat range, environmental tolerance, activity and diversity of microbial life.

Download or read book Microbiology of the Terrestrial Deep Subsurface written by Penny S. Amy and published by CRC Press. This book was released on 2018-01-10 with total page 368 pages. Available in PDF, EPUB and Kindle. Book excerpt: Obtaining and analyzing samples is challenging in subsurface science. This first-of-its-kind reference book addresses accomplishments in this field-from drilling to sample work-up. A collaborative approach is taken, involving the efforts of microbiologists, geochemists, hydrologists, and drilling and mining experts to present a comprehensive view of subsurface research. The text provides practical information about obtaining, analyzing, and evaluating subsurface materials; the current status of subsurface microbial ecology; and describes several applications that will interest a variety of readers, including engineers, physical, and life scientists.

Download or read book Phylogenetic and Physiological Characterization of Deep biosphere Microorganisms in El gygytgyn Crater Lake Sediments written by Janine Heise and published by . This book was released on 2017 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The existence of diverse and active microbial ecosystems in the deep subsurface - a biosphere that was originally considered devoid of life - was discovered in multiple microbiological studies. However, most of the studies are restricted to marine ecosystems, while our knowledge about the microbial communities in the deep subsurface of lake systems and their potentials to adapt to changing environmental conditions is still fragmentary. This doctoral thesis aims to build up a unique data basis for providing the first detailed high-throughput characterization of the deep biosphere of lacustrine sediments and to emphasize how important it is to differentiate between the living and the dead microbial community in deep biosphere studies. In this thesis, up to 3.6 Ma old sediments (up to 317 m deep) of the El'gygytgyn Crater Lake were examined, which represents the oldest terrestrial climate record of the Arctic. Combining next generation sequencing with detailed geochemical characteristics and other environmental parameters, the ...

Download or read book Phylogenetic and Physiological Characterization of Deep biosphere Microorganisms in El gygytgyn Crater Lake Sediments written by Janine Heise and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The existence of diverse and active microbial ecosystems in the deep subsurface - a biosphere that was originally considered devoid of life - was discovered in multiple microbiological studies. However, most of the studies are restricted to marine ecosystems, while our knowledge about the microbial communities in the deep subsurface of lake systems and their potentials to adapt to changing environmental conditions is still fragmentary. This doctoral thesis aims to build up a unique data basis for providing the first detailed high-throughput characterization of the deep biosphere of lacustrine sediments and to emphasize how important it is to differentiate between the living and the dead microbial community in deep biosphere studies. In this thesis, up to 3.6 Ma old sediments (up to 317 m deep) of the El'gygytgyn Crater Lake were examined, which represents the oldest terrestrial climate record of the Arctic. Combining next generation sequencing with detailed geochemical characteristics and other environmental parameters, the...

Download or read book Phylogenetic Characterization of Microbial Communities from Carbon Tetrachloride Contaminated Soil written by Cynthia K. Brinkman and published by . This book was released on 2006 with total page 74 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book STRUCTURE AND FUNCTION OF SUBSURFACE MICROBIAL COMMUNITIES AFFECTING RADIONUCLIDE TRANSPORT AND BIOIMMOBILIZATION written by and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The objectives of this project were to: (1) isolate and characterize novel anaerobic prokaryotes from subsurface environments exposed to high levels of mixed contaminants (U(VI), nitrate, sulfate), (2) elucidate the diversity and distribution of metabolically active metal- and nitrate-reducing prokaryotes in subsurface sediments, and (3) determine the biotic and abiotic mechanisms linking electron transport processes (nitrate, Fe(III), and sulfate reduction) to radionuclide reduction and immobilization. Mechanisms of electron transport and U(VI) transformation were examined under near in situ conditions in sediment microcosms and in field investigations at the Oak Ridge Field Research Center (ORFRC), in Oak Ridge, Tennessee, where the subsurface is exposed to mixed contamination predominated by uranium and nitrate. A total of 20 publications (16 published or 'in press' and 4 in review), 10 invited talks, and 43 contributed seminars/ meeting presentations were completed during the past four years of the project. PI Kostka served on one proposal review panel each year for the U.S. DOE Office of Science during the four year project period. The PI leveraged funds from the state of Florida to purchase new instrumentation that aided the project. Support was also leveraged by the PI from the Joint Genome Institute in the form of two successful proposals for genome sequencing. Draft genomes are now available for two novel species isolated during our studies and 5 more genomes are in the pipeline. We effectively addressed each of the three project objectives and research highlights are provided. Task I - Isolation and characterization of novel anaerobes: (1) A wide range of pure cultures of metal-reducing bacteria, sulfate-reducing bacteria, and denitrifying bacteria (32 strains) were isolated from subsurface sediments of the Oak Ridge Field Research Center (ORFRC), where the subsurface is exposed to mixed contamination of uranium and nitrate. These isolates which are new to science all show high sequence identity to sequences retrieved from ORFRC subsurface. (2) Based on physiological and phylogenetic characterization, two new species of subsurface bacteria were described: the metal-reducer Geobacter daltonii, and the denitrifier Rhodanobacter denitrificans. (3) Strains isolated from the ORFRC show that Rhodanobacter species are well adapted to the contaminated subsurface. Strains 2APBS1 and 116-2 grow at high salt (3% NaCl), low pH (3.5) and tolerate high concentrations of nitrate (400mM) and nitrite (100mM). Strain 2APBS1 was demonstrated to grow at in situ acidic pHs down to 2.5. (4) R. denitrificans strain 2APBS1 is the first described Rhodanobacter species shown to denitrify. Nitrate is almost entirely converted to N2O, which may account for the large accumulation of N2O in the ORFRC subsurface. (5) G. daltonii, isolated from uranium- and hydrocarbon-contaminated subsurface sediments of the ORFRC, is the first organism from the subsurface clade of the genus Geobacter that is capable of growth on aromatic hydrocarbons. (6) High quality draft genome sequences and a complete eco-physiological description are completed for R. denitrificans strain 2APBS1 and G. daltonii strain FRC-32. (7) Given their demonstrated relevance to DOE remediation efforts and the availability of detailed genotypic/phenotypic characterization, Rhodanobacter denitrificans strain 2APBS1 and Geobacter daltonii strain FRC-32 represent ideal model organisms to provide a predictive understanding of subsurface microbial activity through metabolic modeling. Tasks II and III-Diversity and distribution of active anaerobes and Mechanisms linking electron transport and the fate of radionuclides: (1) Our study showed that members of genus Rhodanobacter and Geobacter are abundant and active in the uranium and nitrate contaminated subsurface. In the contaminant source zone of the Oak Ridge site, Rhodanobacter spp. are the predominant, active organisms detected (comprising 50% to 100% of rRNA detected). (2) We demonstrated for the first time that the function of microbial communities can be quantified in subsurface sediments using messenger RNA assays (molecular proxies) under in situ conditions. (3) Active Geobacteraceae were identified and phylogenetically characterized from the cDNA of messenger RNA extracted from ORFRC subsurface sediment cores. Multiple clone sequences were retrieved from G. uraniireducens, G. daltonii, and G. metallireducens. (4) Results show that Geobacter strain FRC-32 is capable of growth on benzoate, toluene and benzene as the electron donor, thereby providing evidence that this strain is physiologically distinct from other described members of the subsurface Geobacter clade. (5) Fe(III)-reducing bacteria transform structural Fe in clay minerals from their layer edges rather than from their basal surfaces.

Download or read book The Prokaryotes written by Edward F. DeLong and published by Springer. This book was released on 2014-10-13 with total page 567 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Prokaryotes is a comprehensive, multi-authored, peer reviewed reference work on Bacteria and Achaea. This fourth edition of The Prokaryotes is organized to cover all taxonomic diversity, using the family level to delineate chapters. Different from other resources, this new Springer product includes not only taxonomy, but also prokaryotic biology and technology of taxa in a broad context. Technological aspects highlight the usefulness of prokaryotes in processes and products, including biocontrol agents and as genetics tools. The content of the expanded fourth edition is divided into two parts: Part 1 contains review chapters dealing with the most important general concepts in molecular, applied and general prokaryote biology; Part 2 describes the known properties of specific taxonomic groups. Two completely new sections have been added to Part 1: bacterial communities and human bacteriology. The bacterial communities section reflects the growing realization that studies on pure cultures of bacteria have led to an incomplete picture of the microbial world for two fundamental reasons: the vast majority of bacteria in soil, water and associated with biological tissues are currently not culturable, and that an understanding of microbial ecology requires knowledge on how different bacterial species interact with each other in their natural environment. The new section on human microbiology deals with bacteria associated with healthy humans and bacterial pathogenesis. Each of the major human diseases caused by bacteria is reviewed, from identifying the pathogens by classical clinical and non-culturing techniques to the biochemical mechanisms of the disease process. The 4th edition of The Prokaryotes is the most complete resource on the biology of prokaryotes. The following volumes are published consecutively within the 4th Edition: Prokaryotic Biology and Symbiotic Associations Prokaryotic Communities and Ecophysiology Prokaryotic Physiology and Biochemistry Applied Bacteriology and Biotechnology Human Microbiology Actinobacteria Firmicutes Alphaproteobacteria and Betaproteobacteria Gammaproteobacteria Deltaproteobacteria and Epsilonproteobacteria Other Major Lineages of Bacteria and the Archaea

Download or read book Phylogenetic Characterization of Subsurface Bacteria by Analysis of 16S Ribosomal RNA and Gyrase B Gene Sequences and Phenotypic Profiles written by Dianne M. Fair and published by . This book was released on 1997 with total page 460 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Geomicrobes Life in Terrestrial Deep Subsurface written by Malin Bomberg and published by Frontiers Media SA. This book was released on 2017-07-17 with total page 143 pages. Available in PDF, EPUB and Kindle. Book excerpt: The deep subsurface is, in addition to space, one of the last unknown frontiers to human kind. A significant part of life on Earth resides in the deep subsurface, hiding great potential of microbial life of which we know only little. The conditions in the deep terrestrial subsurface are thought to resemble those of early Earth, which makes this environment an analog for studying early life in addition to possible extraterrestrial life in ultra-extreme conditions. Early microorganisms played a great role in shaping the conditions on the young Earth. Even today deep subsurface microorganisms interact with their geological environment transforming the conditions in the groundwater and on rock surfaces. Essential elements for life are richly present but in difficultly accessible form. The elements driving the microbial deep life is still not completely identified. Most of the microorganisms detected by novel molecular techniques still lack cultured representatives. Nevertheless, using modern sequencing techniques and bioinformatics the functional roles of these microorganisms are being revealed. We are starting to see the differences and similarities between the life in the deep subsurface and surface domains. We may even begin to see the function of evolution by comparing deep life to life closer to the surface of Earth. Deep life consists of organisms from all known domains of life. This Research Topic reveals some of the rich diversity and functional properties of the great biomass residing in the deep dark subsurface.

Download or read book Role of the Terrestrial Subsurface in Shaping Geothermal Spring Microbial Communities written by Sara Tin and published by . This book was released on 2011 with total page 9 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this study, we explored the possibility that dispersal from terrestrial subsurface sources "seeds" the development of geothermal spring microbial assemblages. We combined microscopy and culture-independent molecular approaches to survey the bacterial diversity of spring source waters in Yellowstone National Park, Lassen Volcanic National Park, and Russia's Kamchatka peninsula. Microscopic analysis uncovered clear evidence of microbial cells from spring sources in all three regions. Analysis of source water phylogenetic diversity identified members of all bacteria groups found previously in downstream sediments, as well as many other phylogenetic groups. Closely related or identical 16S sequences were determined from the source waters of geographically distant, chemically distinct springs, and we found no association between spring water chemistry and microbial diversity. In the source waters of two different Yellowstone springs, we also discovered a phylogenetic group of uncultured Firmicutes never before reported in geothermal habitats that were closely related to uncultured bacteria found in the hyper-arid Atacama Desert. Altogether, our results suggest geothermal features can be connected via the subsurface over long distances and that subsurface sources provide a potentially diverse source of microorganisms for downstream surface mat communities.

Download or read book Microbial Communities in Pristine and Tetrachloroethylene contaminated Aquifer Sediment written by Merry Shannon Riley-Buckley and published by . This book was released on 2001 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Phylogenetic Analysis of the Microbial Communities of Soils in the La Brea Asphalt Seeps and PAH Contaminated Rhizoplane written by Ian Nathaniel Balcom and published by . This book was released on 2007 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Characterization of Bacterial Communities of Riverbank Sediments Contaminated with Polycylcic Aromatic Hydrocarbons written by Gloria Patricia Johnston and published by . This book was released on 2014 with total page 27 pages. Available in PDF, EPUB and Kindle. Book excerpt: Microbial community structure and function are important to ecological processes and to the surrounding physical and chemical environment. Microbes also respond to changes in environmental conditions by oxidizing and transforming pollutants. Sediment contamination is a worldwide problem, yet there is a gap of information about geochemistry and structure of microbial communities in riverbank sediments impacted by long-term pollution. Characterizing the bacterial community in contaminated sediments is critical because it might reveal that some species have adapted to pollution and others can use the xenobiotic as energy and/or carbon sources. We measured high concentrations of polycyclic aromatic hydrocarbons (PAH) in riverbank sediments of the Mahoning River (Ohio, USA) derived from both pyrolytic and petrogenic sources, ranking this sediment as one of the most polluted aquatic ecosystems worldwide. A very high ecological risk to aquatic organisms, even at what was previously considered an unpolluted site was found. Multivariate statistics revealed that bacterial communities followed a temporal and spatial pattern similarly to that found in uncontaminated aquatic environments. PAHs, metals, sulfate, pH, and moisture represented a strong geochemical gradient that likely influenced community composition. Phylogenetic analysis of the 16S rDNA gene revealed groups of bacteria including d-proteobacteria, firmicutes, and bacteriodetes. Some members of these groups have been described as important in PAH degradation. Analysis of the dsrAB gene revealed that most sequences were closely affiliated with unknown, uncultured sulfate reducing bacteria (SRB). Two PAHs were used as models to measure their disappearance over time under sulfate reducing conditions and when a humic acid analogue (anthraquinone-2,6-disulfonate [AQDS]) was added to sediments. After 40-days of anaerobic incubation phenanthrene and fluorene degradation with AQDS was greatly increased in comparison to sediments undergoing natural attenuation. The presence of PAH-degrading and SRB indicated that degradation was likely a biotic mediated process. My research demonstrated that bacterial communities respond to intensive and extensive pollution and are driven by environmental conditions to different extents. In response, microbial communities likely used sulfate and humics for energy and PAHs as carbon sources, contributing to biogeochemical cycling of sulfur and carbon, and providing an important ecosystem function translated as degradation of PAHs.

Download or read book The Molecular Phylogenetic Analysis of Naturally Occurring Hyperthermophilic Microbial Communities written by Gene Stephen Wickham and published by . This book was released on 1995 with total page 410 pages. Available in PDF, EPUB and Kindle. Book excerpt:

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

Download or read book Microbial Life of the Deep Biosphere written by Jens Kallmeyer and published by Walter de Gruyter. This book was released on 2014-04-01 with total page 329 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over the last two decades, exploration of the deep subsurface biosphere has developed into a major research area. New findings constantly challenge our concepts of global biogeochemical cycles and the ultimate limits to life. In order to explain our observations from deep subsurface ecosystems it is necessary to develop truly interdisciplinary approaches, ranging from microbiology and geochemistry to physics and modeling. This book aims to bring together a wide variety of topics, covering the broad range of issues that are associated with deep biosphere exploration. Not only does the book present case studies of selected projects, but also treats questions arising from our current knowledge. Despite nearly two decades of research, there are still many boundaries to exploration caused by technical limitations and one section of the book is devoted to these technical challenges and the latest developments in this field. This volume will be of high interest to biologists, chemists and earth scientists all working on the deep biosphere.