microbial communities in coastal sediments

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Microbial Communities in Coastal Sediments
Author : Salom Thanga
Publisher : Elsevier
Release Date : 2020-01-15
ISBN 10 : 9780128151655
Pages : 500 pages
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Microbial Communities in Coastal Sediments: Structure and Functions presents research gained on coastal microbiology over the past two decades. The book covers the source of organic matter, which is found to design sediment microbial communities, and goes on to consider the quality of this matter with regard to degradation in coastal sediment. The book explores human induced changes in coastal ecosystems, then later focuses on the availability of nutrients, source of persistent organic pollutants (POPs) in the sediment, and the sequencing of microbial structures and functions when using molecular tools. Despite the years of research, this is the first book to focus purely on coastal microbes in coastal ecosystems. As such, it is for gaining a better understanding of the diversity and functions of different types of microbes in coastal ecosystems across the globe. The book outlines the microbial community structure in marine sediments while also elaborating on the methods of assessment of the microbial community, making it of great relevance to aquatic microbiologists, marine ecologists, marine microbiologists, aquatic researchers, and scientists alike. Presents data on physico-chemical and biological features of coastal ecosystems and microbial community composition, allowing researchers to compare their data with pre-existing data Includes unique figures, schematic diagrams and photographs related to microbial processes of coastal ecosystems, providing a clear representation on the different aspects of microbial structure and functions Provides analytical methods and detailed molecular techniques for qualitative and quantitative analyses of microbial community structure, enabling scientists and students to follow the protocols provided in the book for assessment in their own research

Performance Assessment and Enrichment of Anaerobic Methane Oxidizing Microbial Communities from Marine Sediments in Bioreactors
Author : Susma Bhattarai Gautam
Publisher : CRC Press
Release Date : 2018-08-20
ISBN 10 : 0429826451
Pages : 22 pages
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Anaerobic oxidation of methane (AOM) coupled to sulfate reduction (AOM-SR) is a biological process mediated by anaerobic methanotrophs (ANME) and sulfate reducing bacteria. It has scientifi c and societal relevance in regulating the global carbon cycle and biotechnological application for treating sulfate-rich wastewater. This research aimed to enhance the recent knowledge on ANME distribution and its enrichment in different bioreactor confi gurations, i.e. membrane bioreactor (MBR), biotrickling fi lter (BTF) and high pressure bioreactor (HPB). Marine sediment from Ginsburg mud volcano, Gulf of Cadiz was used as inoculum in the BTF and MBR. The BTF operation showed the enrichment of ANME in the biofi lm, especially ANME-1 (40%) and ANME-2 (10%). Whereas, the dominancy of ANME-2 and Desulfosarcina aggregates was observed in the MBR. Moreover, HPB study was performed by using highly enriched ANME-2 community from Captain Arutyunov mud volcano. During the study of HPB at different temperature and pressure conditions, the incubation at 10 MPa pressure and 15 ̊C was observed to be the most suitable condition for the studied AOM-SR community. Furthermore, AOM-SR activity in the coastal sediments from marine Lake Grevelingen (the Netherlands) was explored and the microbial community was characterised which was dominated by ANME-3 among known ANME types.

Linking Molecular Microbiology and Geochemistry to Better Understand Microbial Ecology in Coastal Marine Sediments
Author : Brandi Kiel Reese
Publisher : N.A
Release Date : 2012
ISBN 10 :
Pages : 329 pages
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The overall objective of the research presented here was to combine multiple geochemical parameters and molecular characterizations to provide a novel view of active microbial community ecology of sediments in a large-river deltaic estuary. In coastal and estuarine environments, a large portion of benthic respiration has been attributed to sulfate reduction and implicated as an important mechanism in hypoxia formation. The use of high-resolution sampling of individual sediment cores and high throughput nucleic acid extraction techniques combined with 454 FLX sequencing provided a robust understanding of the metabolically active benthic microbial community within coastal sediments. This was used to provide further understanding and show the importance of simultaneously analyzing the connectivity of sulfur and iron cycling to the structure and function of the microbial population. Although aqueous sulfide did not accumulate in the sediments of the northern Gulf of Mexico, active sulfate reduction was observed in all locations sampled. Microbial recycling and sequestration as iron sulfides prevented the release of sulfide from the sediment. Prominent differences were observed between the sample locations and with depth into the sediment column. This study emphasized the importance of combining novel molecular techniques with simultaneous traditional geochemical measurements to show the interdependence of microbiology and geochemistry. In addition, this study highlights the need to consider microbial community biogeography along with small-scale variations in geochemistry and biology that impact the overall cycling of redox elements when constructing biogeochemical models in marine sediments.

The metabolic pathways and environmental controls of hydrocarbon biodegradation in marine ecosystems
Author : Joel E. Kostka,Andreas P. Teske,Samantha B. Joye,Ian Head
Publisher : Frontiers Media SA
Release Date : 2015-05-15
ISBN 10 : 2889193462
Pages : 329 pages
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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.

The Responses of Marine Microorganisms, Communities and Ecofunctions to Environmental Gradients
Author : Stefan M. Sievert
Publisher : Frontiers Media SA
Release Date : 2019-04-05
ISBN 10 : 2889458075
Pages : 329 pages
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Marine environments are fluid. Microorganisms living in the ocean experience diverse environmental changes over wide spatiotemporal scales. For microorganisms and their communities to survive and function in the ocean, they need to have the capacity to sense, respond to, adapt to and/or withstand periodic and sporadic environmental changes. This eBook collates a variety of recent research reports and theoretical discussions on the ecoenergetic strategies, community structure, biogeochemical and ecosystem functions as well as regulatory processes and mechanisms that marine microorganisms employ in response to environmental gradients and variations.

Performance Assessment and Enrichment of Anaerobic Methane Oxidizing Microbial Communities from Marine Sediments in Bioreactors
Author : Susma Bhattarai Gautam
Publisher : CRC Press
Release Date : 2018-09-03
ISBN 10 : 042982646X
Pages : 22 pages
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Anaerobic oxidation of methane (AOM) coupled to sulfate reduction (AOM-SR) is a biological process mediated by anaerobic methanotrophs (ANME) and sulfate reducing bacteria. It has scientifi c and societal relevance in regulating the global carbon cycle and biotechnological application for treating sulfate-rich wastewater. This research aimed to enhance the recent knowledge on ANME distribution and its enrichment in different bioreactor confi gurations, i.e. membrane bioreactor (MBR), biotrickling fi lter (BTF) and high pressure bioreactor (HPB). Marine sediment from Ginsburg mud volcano, Gulf of Cadiz was used as inoculum in the BTF and MBR. The BTF operation showed the enrichment of ANME in the biofi lm, especially ANME-1 (40%) and ANME-2 (10%). Whereas, the dominancy of ANME-2 and Desulfosarcina aggregates was observed in the MBR. Moreover, HPB study was performed by using highly enriched ANME-2 community from Captain Arutyunov mud volcano. During the study of HPB at different temperature and pressure conditions, the incubation at 10 MPa pressure and 15 ̊C was observed to be the most suitable condition for the studied AOM-SR community. Furthermore, AOM-SR activity in the coastal sediments from marine Lake Grevelingen (the Netherlands) was explored and the microbial community was characterised which was dominated by ANME-3 among known ANME types.

Interactions Between Macro- and Microorganisms in Marine Sediments
Author : Erik Kristensen
Publisher : American Geophysical Union
Release Date : 2005-01-14
ISBN 10 : 087590274X
Pages : 390 pages
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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.

The metabolic pathways and environmental controls of hydrocarbon biodegradation in marine ecosystems
Author : Joel E. Kostka,Andreas P. Teske,Samantha B. Joye,Ian Head
Publisher : Frontiers Media SA
Release Date : 2015-05-15
ISBN 10 : 2889193462
Pages : 329 pages
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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.

Ecology of Coastal Marine Sediments
Author : Simon Thrush,Judi Hewitt,Conrad Pilditch,Alf Norkko
Publisher : N.A
Release Date : 2021-02-12
ISBN 10 : 0198804768
Pages : 224 pages
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This accessible textbook provides an ideal point of entry into the field, providing basic information on the nature of soft-sediment ecosystems, examples of how and why we research them, the new questions these studies inspire, and the applications that ultimately benefit society.

Extracellular Enzymes, Microbes and Decomposition of Organic Matter in Coastal Mangrove Sediments
Author : Ling Luo
Publisher : Open Dissertation Press
Release Date : 2017-01-26
ISBN 10 : 9781361039922
Pages : 329 pages
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This dissertation, "Extracellular Enzymes, Microbes and Decomposition of Organic Matter in Coastal Mangrove Sediments" by Ling, Luo, 罗玲, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: Extracellular enzymes, primarily produced by microorganisms, affect ecosystem processes because of their essential role in degradation, transformation and mineralization of organic matter. However, such data on sediments in mangrove ecosystems are especially scanty. Therefore, there is a need to investigate extracellular enzymes in mangrove ecosystems in order to estimate the C cycling dynamics on a global scale. The objectives of this research were to investigate the activities of enzymes involved in C and nutrient cycling, to assess microbial nutrient acquisition by applying enzymatic stoichiometry, to delineate the relationships among enzyme activities, microbial parameters as well as decomposition of sediment organic matter (SOM) in a coastal mangrove of Hong Kong. Strong variations in activities of hydrolases (β-glucosidase (GLU), β-N-acetyl-glucosaminidase (NAG), and acid phosphatase (ACP) involved in C, N and P cycling, respectively), but not activity of phenol oxidase (PHO, degrading recalcitrant organic matter) have been observed. However, evident variations of PHO activity were found in rhizosphere and crab-affected sediments. Hydrolase activities are positively correlated to sediment C, N and P as well as bacterial abundance, suggesting a feedback and succession of microorganisms to limitation of natural resources. On the other hand, a significant correlation between ACP and PHO activity indicates SOM degradation is controlled by P availability. Coincidentally, the enzymatic stoichiometry also suggests that this ecosystem is extremely microbial P-limited. Moreover, at molecular level, the remarkable correlations between bacterial laccase-like communities (relating to SOM degradation) and sediment C: P as well as N: P have repeatedly suggested a P-limited condition for SOM-degrading microbial communities. Therefore, it can be known that the increase of P limitation will slow down SOM decomposition and thus protect C storage in this coastal mangrove ecosystem. Furthermore, the effects of N and biochar additions on SOM decomposition have been investigated. Relative to the controls, N addition has dual role in C storage since both loss and accumulation of organic C was observed in mangrove forest and intertidal zone sediments, respectively. Sediment organic C was slightly increased after biochar addition, although the increase of PHO and GLU activity indicates a trend of C loss. This contradictory phenomenon is probably due to the entrapped or adsorbed enzymes catalyzing the oxidation or hydrolysis of SOM. Although the information is still limited on this subject, the results of this study may help to better understand the potential strategies on preventing C loss in mangrove ecosystems. Overall, the thesis indicates that SOM in this coastal mangrove is microbial P-limitation, and SOM decomposition may be slowed down so as to sequester C into sediments if microbial P limitation is exacerbated. Therefore, in further study, the importance of P in SOM degradation and microbial communities should be considered for C cycling and climate change mitigation. DOI: 10.5353/th_b5610935 Subjects: Mangrove ecology

Microbial Mats
Author : Joseph Seckbach,Aharon Oren
Publisher : Springer Science & Business Media
Release Date : 2010-07-17
ISBN 10 : 9789048137992
Pages : 606 pages
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This book provides information about microbial mats, from early fossils to modern mats located in marine and terrestrial environments. Microbial mats – layered biofilms containing different types of cells – are most complex systems in which representatives of various groups of organisms are found together. Among them are cyanobacteria and eukaryotic phototrophs, aerobic heterotrophic and chemoautotrophic bacteria, protozoa, anoxygenic photosynthetic bacteria, and other types of microorganisms. These mats are perfect models for biogeochemical processes, such as the cycles of chemical elements, in which a variety of microorganisms cooperate and interact in complex ways. They are often found under extreme conditions and their study contributes to our understanding of extremophilic life. Moreover, microbial mats are models for Precambrian stromatolites; the study of modern microbial mats may provide information on the processes that may have occurred on Earth when prokaryotic life began to spread.

Biodiversity, Ecosystem Functioning, and Human Wellbeing
Author : Shahid Naeem
Publisher : Oxford University Press
Release Date : 2009-07-30
ISBN 10 : 0199547955
Pages : 368 pages
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In an age of accelerating biodiversity loss, this timely and critical volume summarizes recent advances in biodiversity-ecosystem functioning research and explores the economics of biodiversity and ecosystem services. The book starts by summarizing the development of the basic science and provides a meta-analysis that quantitatively tests several biodiversity and ecosystem functioning hypotheses. It then describes the natural science foundations of biodiversityand ecosystem functioning research including: quantifying functional diversity, the development of the field into a predictive science, the effects of stability and complexity, methods to quantifymechanisms by which diversity affects functioning, the importance of trophic structure, microbial ecology, and spatial dynamics. Finally, the book takes research on biodiversity and ecosystem functioning further than it has ever gone into the human dimension, describing the most pressing environmental challenges that face humanity and the effects of diversity on: climate change mitigation, restoration of degraded habitats, managed ecosystems, pollination, disease, and biological invasions.

The Marine Microbiome
Author : Lucas J. Stal,Mariana Silvia Cretoiu
Publisher : Springer
Release Date : 2016-06-03
ISBN 10 : 3319330004
Pages : 498 pages
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This book describes the state-of-the-art concerning the ‘marine microbiome’ and its uses in biotechnology. The first part discusses the diversity and ecology of marine microorganisms and viruses, including all three domains of life: Bacteria, Archaea, and Eukarya. It discusses whether marine microorganisms exist and, if so, why they might be unique. The second part presents selected marine habitats, their inhabitants and how they influence biogeochemical cycles, while the third discusses the utilization of marine microbial resources, including legal aspects, dissemination, and public awareness. The marine microbiome is the total of microorganisms and viruses in the ocean and seas and in any connected environment, including the seafloor and marine animals and plants. The diversity of microbial life remains unquantified and largely unknown, and could represent a hidden treasure for human society. Accordingly, this book is also intended to connect academics and industry, providing essential information for microbiologists from both fields.

The Estuarine Ecosystem
Author : Donald S. McLusky,M. Elliott,Michael Elliott
Publisher : Oxford University Press on Demand
Release Date : 2004-04-29
ISBN 10 : 0198525087
Pages : 214 pages
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For the inhabitants of many of the world's major towns & cities estuaries provide their first & nearest glimpse of a natural habitat. This text will be of use to advanced undergraduate & graduate students on a general ecology course, & to professional researchers in aquatic/marine ecology & environmental science.

Geochemistry of Marine Sediments
Author : David J. Burdige
Publisher : Princeton University Press
Release Date : 2020-08-04
ISBN 10 : 0691216096
Pages : 329 pages
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The processes occurring in surface marine sediments have a profound effect on the local and global cycling of many elements. This graduate text presents the fundamentals of marine sediment geochemistry by examining the complex chemical, biological, and physical processes that contribute to the conversion of these sediments to rock, a process known as early diagenesis. Research over the past three decades has uncovered the fact that the oxidation of organic matter deposited in sediment acts as a causative agent for many early diagenetic changes. Summarizing and discussing these findings and providing a much-needed update to Robert Berner's Early Diagenesis: A Theoretical Approach, David J. Burdige describes the ways to quantify geochemical processes in marine sediment. By doing so, he offers a deeper understanding of the cycling of elements such as carbon, nitrogen, and phosphorus, along with important metals such as iron and manganese. No other book presents such an in-depth look at marine sediment geochemistry. Including the most up-to-date research, a complete survey of the subject, explanatory text, and the most recent mathematical formulations that have contributed to our greater understanding of early diagenesis, Geochemistry of Marine Sediments will interest graduate students of geology, geochemistry, and oceanography, as well as the broader community of earth scientists. It is poised to become the standard text on the subject for years to come.

Marine Metagenomics
Author : Takashi Gojobori,Tokio Wada,Takanori Kobayashi,Katsuhiko Mineta
Publisher : Springer
Release Date : 2019-07-24
ISBN 10 : 9811381348
Pages : 271 pages
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This book presents the state-of-art marine metagenome research and explains the method of marine metagenomic analysis in an easy-to-understand manner. Changes in the marine environment due to global warming and pollution have become a major global problem. Maintaining a healthy marine ecosystem requires advanced environmental monitoring and assessment systems. As such, the book presents a novel metagenomic monitoring method, which has been developed for comprehensive analyses of the DNA of microorganisms living in seawater to further our understanding of the dynamics of the marine environment. The book can be used as a primer for new researchers and as a manual on experimental methods.

The Prokaryotes
Author : Edward F. DeLong,Stephen Lory,Erko Stackebrandt,Fabiano Thompson
Publisher : Springer
Release Date : 2014-11-19
ISBN 10 : 9783642301391
Pages : 1063 pages
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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.

Earth and Life Processes Discovered from Subseafloor Environments
Author : N.A
Publisher : Elsevier
Release Date : 2014-12-03
ISBN 10 : 0444626115
Pages : 822 pages
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The Integrated Ocean Drilling Program (IODP: 2000-2013) has provided crucial records of past and present processes and interactions within and between the biosphere, cryosphere, atmosphere, hydrosphere and geosphere. Research in IODP encompasses a wide range of fundamental and applied issues that affect society, such as global climate change, biodiversity, the origin of life, natural hazards involving the study of earthquakes processes, and the internal structure and dynamics of our planet. This compilation of major findings from the 2003-2013/14 phase of IODP, focusing on scientific results rather than description of data acquisition and early inferences, provides invaluable information. Anyone wondering what scientific drilling can achieve will gain quick understanding of the range of questions that are uniquely addressed with this methodology and the ways these data dovetail with other regional information. The excitement of breakthrough findings that occasionally accompanies a drilling project will be evident. IODP obtained unique records from the global ocean basins during the 2003-2013 program phase. This book highlights findings in three theme areas: Subseafloor life and the marine biosphere; Earth's changing environments; and Dynamics of the solid Earth. Each core or borehole log provides a window revealing insights that no other data achieve. Presents syntheses of key results from the Integrated Ocean Drilling Program Encompasses a wide range of issues that affect society Describes the Integrated Ocean Drilling Program and its expeditions

Deep Subsurface Microbiology
Author : Andreas Teske,Jennifer F. Biddle,Virginia P. Edgcomb, Axel Schippers
Publisher : Frontiers Media SA
Release Date : 2015-07-01
ISBN 10 : 2889195368
Pages : 329 pages
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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.