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  • 1
    Unknown
    Lausanne : Frontiers
    Keywords: Terrestrial deep biosphere ; Eukaryotes ; Groundwater ; microbiome ; Heavy metal resistance ; MINE ; Nitrogen Cycle ; Iron oxidation ; Methane ; cave
    Description / Table of Contents: 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.
    Pages: Online-Ressource (141 Seiten)
    ISBN: 9782889451791
    Language: English
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  • 2
    Keywords: Marine Biogeochemistry ; Carbon ; organic matter ; river ; estuarine ; marine ; atmosphere ; dynamics ; ecosystem ; interface ; transition
    Description / Table of Contents: Editorial: Integrative Research on Organic Matter Cycling across Aquatic Gradients / Nicholas D. Ward. doi: 10.3389/fmars.2017.00131 --- Influence of Major Storm Events on the Quantity and Composition of Particulate Organic Matter and the Phytoplankton Community in a Subtropical Estuary, Texas / Nicolas E. Reyna, Amber K. Hardison and Zhanfei Liu. doi: 10.3389/fmars.2017.00043 --- The Fate of Carbon in Sediments of the Xingu and Tapajós Clearwater Rivers, Eastern Amazon / Dailson J. Bertassoli, André O. Sawakuchi, Henrique O. Sawakuchi, Fabiano N. Pupim, Gelvam A. Hartmann, Michael M. McGlue, Cristiano M. Chiessi, Matthias Zabel, Enno Schefuß, Tatiana S. Pereira, Rudney A. Santos, Samantha B. Faustino, Paulo E. Oliveira and Denise C. Bicudo. doi: 10.3389/fmars.2017.00044 --- Flux of Dissolved and Particulate Low-Temperature Pyrogenic Carbon from Two High-Latitude Rivers across the Spring Freshet Hydrograph / Allison N. Myers-Pigg, Patrick Louchouarn and Roman Teisserenc. doi: 10.3389/fmars.2017.00038 --- Environmental Drivers of Dissolved Organic Matter Molecular Composition in the Delaware Estuary / Helena Osterholz, David L. Kirchman, Jutta Niggemann and Thorsten Dittmar. doi: 10.3389/feart.2016.00095 --- Molecular and Optical Properties of Tree-Derived Dissolved Organic Matter in Throughfall and Stemflow from Live Oaks and Eastern Red Cedar / Aron Stubbins, Leticia M. Silva, Thorsten Dittmar and John T. Van Stan. doi: 10.3389/feart.2017.00022 --- Composition and Transformation of Dissolved Organic Matter in the Baltic Sea / Michael Seidel, Marcus Manecki, Daniel P. R. Herlemann, Barbara Deutsch, Detlef Schulz-Bull, Klaus Jürgens and Thorsten Dittmar. doi: 10.3389/feart.2017.00031 --- Evaluation of Primary Production in the Lower Amazon River Based on a Dissolved Oxygen Stable Isotopic Mass Balance / William C. Gagne-Maynard, Nicholas D. Ward, Richard G. Keil, Henrique O. Sawakuchi, Alan C. Da Cunha, Vania Neu, Daimio C. Brito, Diani F. Da Silva Less, Joel E. M. Diniz, Aline De Matos Valerio, Milton Kampel, Alex V. Krusche and Jeffrey E. Richey. doi: 10.3389/fmars.2017.00026 --- Surface Gradients in Dissolved Organic Matter Absorption and Fluorescence Properties along the New Zealand Sector of the Southern Ocean / Eurico J. D'Sa and Hyun-cheol Kim. doi: 10.3389/fmars.2017.00021 --- The Genesis and Exodus of Vascular Plant DOM from an Oak Woodland Landscape / Peter J. Hernes, Robert G. M. Spencer, Rachael Y. Dyda, Anthony T. O'Geen and Randy A. Dahlgren. doi: 10.3389/feart.2017.00009 --- Carbon Dioxide Emissions along the Lower Amazon River / Henrique O. Sawakuchi, Vania Neu, Nicholas D. Ward, Maria de Lourdes C. Barros, Aline M. Valerio, William Gagne-Maynard, Alan C. Cunha, Diani F. S. Less, Joel E. M. Diniz, Daimio C. Brito, Alex V. Krusche and Jeffrey E. Richey. doi: 10.3389/fmars.2017.00076 --- Short-Term Dissolved Organic Carbon Dynamics Reflect Tidal, Water Management, and Precipitation Patterns in a Subtropical Estuary / Peter Regier and Rudolf Jaffé. doi: 10.3389/fmars.2016.00250 --- Impact of Wetland Decline on Decreasing Dissolved Organic Carbon Concentrations along the Mississippi River Continuum / Shuiwang Duan, Yuxiang He, Sujay S. Kaushal, Thomas S. Bianchi, Nicholas D. Ward and Laodong Guo. doi: 10.3389/fmars.2016.00280 --- Microbially-Mediated Transformations of Estuarine Dissolved Organic Matter / Patricia M. Medeiros, Michael Seidel, Scott M. Gifford, Ford Ballantyne, Thorsten Dittmar, William B. Whitman and Mary Ann Moran. doi: 10.3389/fmars.2017.00069 --- Dissolved Organic and Inorganic Carbon Flow Paths in an Amazonian Transitional Forest / Vania Neu, Nicholas D. Ward, Alex V. Krusche and Christopher Neill. doi: 10.3389/fmars.2016.00114
    Pages: Online-Ressource (201 Seiten)
    ISBN: 9782889452125
    Language: English
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  • 3
    Keywords: Geomicrobiology ; deep biosphere ; IODP ; ocean crust ; iron oxidation ; sulfate reduction ; hydrothermal vents
    Description / Table of Contents: Igneous oceanic crust is one of the largest potential habitats for life on earth, and microbial activity supported by rock-water-microbe reactions in this environment can impact global biogeochemical cycles. However, our understanding of the microbiology of this system, especially the subsurface “deep biosphere” component of it, has traditionally been limited by sample availability and quality. Over the past decade, several major international programs (such as the Center for Dark Energy Biosphere Investigations, the current International Ocean Discovery Program and its predecessor Integrated Ocean Drilling Program, and the Deep Carbon Observatory) have focused on advancing our understanding of life in this cryptic, yet globally relevant, biosphere. Additionally, many field and laboratory research programs are examining hydrothermal vent systems –a seafloor expression of seawater that has been thermally and chemically altered in subseafloor crust – and the microbial communities supported by these mineral-rich fluids. The Frontiers in Microbiology 3 September 2017 | Recent Advances in Geomicrobiology of the Ocean Crust papers in this special issue bring together recent discoveries of microbial presence, diversity and activity in these dynamic ocean environments. Cumulatively, the articles in this special issue serve as a tribute to the late Dr. Katrina J. Edwards, who was a pioneer and profound champion of studying microbes that “rust the crust”. This special issue volume serves as a foundation for the continued exploration of the subsurface ocean crust deep biosphere.
    Pages: Online-Ressource (326 Seiten)
    ISBN: 9782889452835
    Language: English
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  • 4
    Keywords: microbiology ; carbon cycle ; B vitamins ; cobalamin ; thiamin ; Pyridoxin ; Trace metals ; Molybdenum ; Vanadium ; Nickel ; Copper ; Coenzymes
    Description / Table of Contents: In the last three decades, research has extensively focused on the role of Fe and other mineral nutrients in regulating biological processes, ranging from the surface to the deep ocean. This has produced major breakthroughs in our understanding of the fundamental role of those bioactive elements on the carbon, nitrogen and sulfur cycles and ecosystem function. However, biological processes cannot be entirely sustained by that small set of chemical elements, and new scientific evidence suggests that trace metals other than Fe (e.g., Co, Mo and Ni) as well as essential organic growth factors (e.g., vitamins) may also be crucial in most aquatic systems.
    Pages: Online-Ressource (109 Seiten)
    ISBN: 9782889195466
    Language: English
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  • 5
    Keywords: deep subsurface ; marine sediment ; deep biosphere ; ocean crust ; subseafloor sediment ; Methane ; Peru margin ; Hydrogen ; acetogenesis ; sulfate reduction ; microbiology
    Description / Table of Contents: 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.
    Pages: Online-Ressource (303 Seiten)
    ISBN: 9782889195367
    Language: English
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  • 6
    Unknown
    Lausanne : Frontiers
    Keywords: hydrothermal vents ; extremophiles ; marine sediments ; Guaymas basin ; microbial biogeography ; microbiology
    Description / Table of Contents: Hydrothermally influenced microbial habitats and communities represent a much wider spectrum of geological setting, chemical in-situ regimes, and biotic community than the classical examples from basalt-hosted black smoker chimneys at active mid-ocean spreading centers. Hydrothermal vent ecosystems now include hydrothermally heated and chemically altered sediments, microbiota fueled by serpentinization reactions, and low-temperature vents with unusual menus of electron donors. Novel marine provinces and hydrothermal areas are being charted and explored, such as new hydrothermal vent systems in the Arctic, around Antarctica, in the Western Pacific and in the Indian Ocean. Novel environmental gradients and niches provide habitats for unusual or unprecedented microorganisms and microbial ecosystems. The discovery of novel extremophiles such as Aciduliprofundum and the Nanoarchaeota underscores that hydrothermal vent microbial communities can no longer be characterized as assemblages of only “typical” sulfur oxidizers, methanogens and heterotrophs. Different stages of hydrothermal activity, from early onset to peak activity, gradual decline, and persistence of cold and fossil vent sites, correspond to different colonization waves by microorganisms as well as megafauna. This research topic will continue to stretch the limits of hydrothermal vent microbiology, and also provide a forum for the chemical and microbial linkages of hydrothermal vents to the ocean water column and the ocean crust or sedimentary subsurface.
    Pages: Online-Ressource (286 Seiten)
    ISBN: 9782889196821
    Language: English
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  • 7
    Keywords: microbial ecology ; biogeochemistry ; stoichiometry ; Climate Change ; soil microbiology ; elemental fluxes ; Respiration ; aquatic microbiology ; microbiology
    Description / Table of Contents: Advances in next generation sequencing technologies, omics, and bioinformatics are revealing a tremendous and unsuspected diversity of microbes, both at a compositional and functional level. Moreover, the expansion of ecological concepts into microbial ecology has greatly advanced our comprehension of the role microbes play in the functioning of ecosystems across a wide range of biomes. Super-imposed on this new information about microbes, their functions and how they are organized, environmental gradients are changing rapidly, largely driven by direct and indirect human activities. In the context of global change, understanding the mechanisms that shape microbial communities is pivotal to predict microbial responses to novel selective forces and their implications at the local as well as global scale. One of the main features of microbial communities is their ability to react to changes in the environment. Thus, many studies have reported changes in the performance and composition of communities along environmental gradients. However, the mechanisms underlying these responses remain unclear. It is assumed that the response of microbes to changes in the environment is mediated by a complex combination of shifts in the physiological properties, single-cell activities, or composition of communities: it may occur by means of physiological adjustments of the taxa present in a community or selecting towards more tolerant/better adapted phylotypes. Knowing whether certain factors trigger one, many, or all mechanisms would greatly increase confidence in predictions of future microbial composition and processes. This Research Topic brings together studies that applied the latest molecular techniques for studying microbial composition and functioning and integrated ecological, biogeochemical and/or modeling approaches to provide a comprehensive and mechanistic perspective of the responses of micro-organisms to environmental changes. This Research Topic presents new findings on environmental parameters influencing microbial communities, the type and magnitude of response and differences in the response among microbial groups, and which collectively deepen our current understanding and knowledge of the underlying mechanisms of microbial structural and functional responses to environmental changes and gradients in both aquatic and terrestrial ecosystems. The body of work has, furthermore, identified many challenges and questions that yet remain to be addressed and new perspectives to follow up on.
    Pages: Online-Ressource (263 Seiten)
    ISBN: 9782889197231
    Language: English
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  • 8
    Unknown
    Lausanne : Frontiers
    Keywords: nitrogen cycle ; microbial ecology ; nitrogen fixation ; denitrification ; Anammox ; nitrification ; microbiology
    Description / Table of Contents: Nitrogen is an essential element in biological systems, and one that often limits production in both aquatic and terrestrial systems. Due to its requirement in biological macromolecules, its acquisition and cycling have the potential to structure microbial communities, as well as to control productivity on the ecosystem scale. In addition, its versatile redox chemistry is the basis of complex biogeochemical transformations that control the inventory of fixed nitrogen, both in local environments and over geological time. Although many of the pathways in the microbial nitrogen cycle were described more than a century ago, additional fundamental pathways have been discovered only recently. These findings imply that we still have much to learn about the microbial nitrogen cycle, the organisms responsible for it, and their interactions in natural and human environments. Progress in nitrogen cycle research has been facilitated by recent rapid technological advances, especially in genomics and isotopic approaches. In this Research Topic, we reviewed the leading edge of nitrogen cycle research based on these approaches, as well as by exploring microbial processes in modern ecosystems.
    Pages: Online-Ressource (175 Seiten)
    ISBN: 9782889194124
    Language: English
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  • 9
    Keywords: bacteriophages ; environmental disturbance ; phage ecology ; aquatic microbiology ; phage therapy ; metaviromes ; evolution ; microarrays ; microbiology
    Description / Table of Contents: Viruses infect numerous microorganisms including, predominantly, Bacteria (bacteriophages or phages) but also Archaea, Protists, and Fungi. They are the most abundant and ubiquitous biological entities on Earth and are important drivers of ecosystem functioning. Little is known, however, about the vast majority of these viruses of microorganisms, or VoMs. Modern techniques such as metagenomics have enabled the discovery and description of more presumptive VoMs than ever before, but also have exposed gaps in our understanding of VoM ecology. Exploring the ecology of these viruses – which is how they interact with host organisms, the abiotic environment, larger organisms, and even other viruses across a variety of environments and conditions – is the next frontier. Integration of a growing molecular understanding of VoMs with ecological studies will expand our knowledge of ecosystem dynamics. Ecology can be studied at multiple levels including individual organisms, populations, communities, whole ecosystems, and the entire biosphere. Ecology additionally can consider normal, equilibrium conditions or instead perturbations. Perturbations are of particular interest because measuring the effect of disturbances on VoM-associated communities provides important windows into how VoMs contribute to ecosystem dynamics. These disturbances in turn can be studied through in vitro, in vivo, and in situ experimentation, measuring responses by VoM-associated communities to changes in nutrient availability, stress, physical disruption, seasonality, etc., and could apply to studies at all ecological levels. These are considered here across diverse systems and environments.
    Pages: Online-Ressource (95 Seiten)
    ISBN: 9782889194483
    Language: English
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  • 10
    Unknown
    Lausanne : Frontiers
    Keywords: climate ; Climate Change ; marine mammals ; predators ; seabirds ; trophic interactions
    Description / Table of Contents: Climate change affects all components of marine ecosystems. For endothermic top predators, i.e. seabirds and marine mammals, these impacts are often complex and mediated through trophic relationships. In this Research Topic, leading researchers attempt to identify patterns of change among seabirds and marine mammals, and the mechanisms through which climate change drives these changes.
    Pages: Online-Ressource (180 Seiten)
    ISBN: 9782889197361
    Language: English
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