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https://www.readbyqxmd.com/read/28720809/microbial-turnover-times-in-the-deep-seabed-studied-by-amino-acid-racemization-modelling
#1
Stefan Braun, Snehit S Mhatre, Marion Jaussi, Hans Røy, Kasper U Kjeldsen, Christof Pearce, Marit-Solveig Seidenkrantz, Bo Barker Jørgensen, Bente Aa Lomstein
The study of active microbial populations in deep, energy-limited marine sediments has extended our knowledge of the limits of life on Earth. Typically, microbial activity in the deep biosphere is calculated by transport-reaction modelling of pore water solutes or from experimental measurements involving radiotracers. Here we modelled microbial activity from the degree of D:L-aspartic acid racemization in microbial necromass (remains of dead microbial biomass) in sediments up to ten million years old. This recently developed approach (D:L-amino acid modelling) does not require incubation experiments and is highly sensitive in stable, low-activity environments...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28713355/respiratory-pathways-reconstructed-by-multi-omics-analysis-in-melioribacter-roseus-residing-in-a-deep-thermal-aquifer-of-the-west-siberian-megabasin
#2
Sergey Gavrilov, Olga Podosokorskaya, Dmitry Alexeev, Alexander Merkel, Maria Khomyakova, Maria Muntyan, Ilya Altukhov, Ivan Butenko, Elizaveta Bonch-Osmolovskaya, Vadim Govorun, Ilya Kublanov
Melioribacter roseus, a representative of recently proposed Ignavibacteriae phylum, is a metabolically versatile thermophilic bacterium, inhabiting subsurface biosphere of the West-Siberian megabasin and capable of growing on various substrates and electron acceptors. Genomic analysis followed by inhibitor studies and membrane potential measurements of aerobically grown M. roseus cells revealed the activity of aerobic respiratory electron transfer chain comprised of respiratory complexes I and IV, and an alternative complex III...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28677247/major-phylum-level-differences-between-porefluid-and-host-rock-bacterial-communities-in-the-terrestrial-deep-subsurface
#3
Lily Momper, Brandi Kiel Reese, Laura Zinke, Greg Wanger, Magdalena R Osburn, Duane Moser, Jan P Amend
Earth's deep subsurface biosphere (DSB) is home to a vast number and wide variety of microorganisms. Although difficult to access and sample, deep subsurface environments have been probed through drilling programs, exploration of mines, and sampling of deeply-sourced vents and springs. In an effort to understand the ecology of deep terrestrial habitats, we examined bacterial diversity in the Sanford Underground Research Facility (SURF), the former Homestake gold mine, in South Dakota, USA. Whole genomic DNA was extracted from deeply-circulating groundwater and corresponding host rock (at a depth of 1...
July 5, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28676800/atribacteria-from-the-subseafloor-sedimentary-biosphere-disperse-to-the-hydrosphere-through-submarine-mud-volcanoes
#4
Tatsuhiko Hoshino, Tomohiro Toki, Akira Ijiri, Yuki Morono, Hideaki Machiyama, Juichiro Ashi, Kei Okamura, Fumio Inagaki
Submarine mud volcanoes (SMVs) are formed by muddy sediments and breccias extruded to the seafloor from a source in the deep subseafloor and are characterized by the discharge of methane and other hydrocarbon gasses and deep-sourced fluids into the overlying seawater. Although SMVs act as a natural pipeline connecting the Earth's surface and subsurface biospheres, the dispersal of deep-biosphere microorganisms and their ecological roles remain largely unknown. In this study, we investigated the microbial communities in sediment and overlying seawater at two SMVs located on the Ryukyu Trench off Tanegashima Island, southern Japan...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28676652/anaerobic-consortia-of-fungi-and-sulfate-reducing-bacteria-in-deep-granite-fractures
#5
Henrik Drake, Magnus Ivarsson, Stefan Bengtson, Christine Heim, Sandra Siljeström, Martin J Whitehouse, Curt Broman, Veneta Belivanova, Mats E Åström
The deep biosphere is one of the least understood ecosystems on Earth. Although most microbiological studies in this system have focused on prokaryotes and neglected microeukaryotes, recent discoveries have revealed existence of fossil and active fungi in marine sediments and sub-seafloor basalts, with proposed importance for the subsurface energy cycle. However, studies of fungi in deep continental crystalline rocks are surprisingly few. Consequently, the characteristics and processes of fungi and fungus-prokaryote interactions in this vast environment remain enigmatic...
July 4, 2017: Nature Communications
https://www.readbyqxmd.com/read/28674200/the-deep-hot-biosphere-twenty-five-years-of-retrospection
#6
Daniel R Colman, Saroj Poudel, Blake W Stamps, Eric S Boyd, John R Spear
Twenty-five years ago this month, Thomas Gold published a seminal manuscript suggesting the presence of a "deep, hot biosphere" in the Earth's crust. Since this publication, a considerable amount of attention has been given to the study of deep biospheres, their role in geochemical cycles, and their potential to inform on the origin of life and its potential outside of Earth. Overwhelming evidence now supports the presence of a deep biosphere ubiquitously distributed on Earth in both terrestrial and marine settings...
July 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28588569/methane-dynamics-in-a-tropical-serpentinizing-environment-the-santa-elena-ophiolite-costa-rica
#7
Melitza Crespo-Medina, Katrina I Twing, Ricardo Sánchez-Murillo, William J Brazelton, Thomas M McCollom, Matthew O Schrenk
Uplifted ultramafic rocks represent an important vector for the transfer of carbon and reducing power from the deep subsurface into the biosphere and potentially support microbial life through serpentinization. This process has a strong influence upon the production of hydrogen and methane, which can be subsequently consumed by microbial communities. The Santa Elena Ophiolite (SEO) on the northwestern Pacific coast of Costa Rica comprises ~250 km(2) of ultramafic rocks and mafic associations. The climatic conditions, consisting of strongly contrasting wet and dry seasons, make the SEO a unique hydrogeological setting, where water-rock reactions are enhanced by large storm events (up to 200 mm in a single storm)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28586679/the-deep-sea-under-global-change
#8
Roberto Danovaro, Cinzia Corinaldesi, Antonio Dell'Anno, Paul V R Snelgrove
The deep ocean encompasses 95% of the oceans' volume and is the largest and least explored biome of Earth's Biosphere. New life forms are continuously being discovered. The physiological mechanisms allowing organisms to adapt to extreme conditions of the deep ocean (high pressures, from very low to very high temperatures, food shortage, lack of solar light) are still largely unknown. Some deep-sea species have very long life-spans, whereas others can tolerate toxic compounds at high concentrations; these characteristics offer an opportunity to explore the specialized biochemical and physiological mechanisms associated with these responses...
June 5, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28524866/succession-in-the-petroleum-reservoir-microbiome-through-an-oil-field-production-lifecycle
#9
Adrien Vigneron, Eric B Alsop, Bartholomeus P Lomans, Nikos C Kyrpides, Ian M Head, Nicolas Tsesmetzis
Subsurface petroleum reservoirs are an important component of the deep biosphere where indigenous microorganisms live under extreme conditions and in isolation from the Earth's surface for millions of years. However, unlike the bulk of the deep biosphere, the petroleum reservoir deep biosphere is subject to extreme anthropogenic perturbation, with the introduction of new electron acceptors, donors and exogenous microbes during oil exploration and production. Despite the fundamental and practical significance of this perturbation, there has never been a systematic evaluation of the ecological changes that occur over the production lifetime of an active offshore petroleum production system...
May 19, 2017: ISME Journal
https://www.readbyqxmd.com/read/28419734/the-life-sulfuric-microbial-ecology-of-sulfur-cycling-in-marine-sediments
#10
REVIEW
Kenneth Wasmund, Marc Mußmann, Alexander Loy
Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes...
April 17, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28396823/genomic-comparisons-of-a-bacterial-lineage-that-inhabits-both-marine-and-terrestrial-deep-subsurface-systems
#11
Sean P Jungbluth, Tijana Glavina Del Rio, Susannah G Tringe, Ramunas Stepanauskas, Michael S Rappé
It is generally accepted that diverse, poorly characterized microorganisms reside deep within Earth's crust. One such lineage of deep subsurface-dwelling bacteria is an uncultivated member of the Firmicutes phylum that can dominate molecular surveys from both marine and continental rock fracture fluids, sometimes forming the sole member of a single-species microbiome. Here, we reconstructed a genome from basalt-hosted fluids of the deep subseafloor along the eastern Juan de Fuca Ridge flank and used a phylogenomic analysis to show that, despite vast differences in geographic origin and habitat, it forms a monophyletic clade with the terrestrial deep subsurface genome of "Candidatus Desulforudis audaxviator" MP104C...
2017: PeerJ
https://www.readbyqxmd.com/read/28396389/subduction-zone-forearc-serpentinites-as-incubators-for-deep-microbial-life
#12
Oliver Plümper, Helen E King, Thorsten Geisler, Yang Liu, Sonja Pabst, Ivan P Savov, Detlef Rost, Thomas Zack
Serpentinization-fueled systems in the cool, hydrated forearc mantle of subduction zones may provide an environment that supports deep chemolithoautotrophic life. Here, we examine serpentinite clasts expelled from mud volcanoes above the Izu-Bonin-Mariana subduction zone forearc (Pacific Ocean) that contain complex organic matter and nanosized Ni-Fe alloys. Using time-of-flight secondary ion mass spectrometry and Raman spectroscopy, we determined that the organic matter consists of a mixture of aliphatic and aromatic compounds and functional groups such as amides...
April 25, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28367144/reactivation-of-deep-subsurface-microbial-community-in-response-to-methane-or-methanol-amendment
#13
Pauliina Rajala, Malin Bomberg
Microbial communities in deep subsurface environments comprise a large portion of Earth's biomass, but the microbial activity in these habitats is largely unknown. Here, we studied how microorganisms from two isolated groundwater fractures at 180 and 500 m depths of the Outokumpu Deep Drillhole (Finland) responded to methane or methanol amendment, in the presence or absence of sulfate as an additional electron acceptor. Methane is a plausible intermediate in the deep subsurface carbon cycle, and electron acceptors such as sulfate are critical components for oxidation processes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28350381/metagenome-sequencing-and-98-microbial-genomes-from-juan-de-fuca-ridge-flank-subsurface-fluids
#14
Sean P Jungbluth, Jan P Amend, Michael S Rappé
The global deep subsurface biosphere is one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the Juan de Fuca Ridge subseafloor. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs)...
March 28, 2017: Scientific Data
https://www.readbyqxmd.com/read/28335808/potential-for-hydrogen-oxidizing-chemolithoautotrophic-and-diazotrophic-populations-to-initiate-biofilm-formation-in-oligotrophic-deep-terrestrial-subsurface-waters
#15
Xiaofen Wu, Karsten Pedersen, Johanna Edlund, Lena Eriksson, Mats Åström, Anders F Andersson, Stefan Bertilsson, Mark Dopson
BACKGROUND: Deep terrestrial biosphere waters are separated from the light-driven surface by the time required to percolate to the subsurface. Despite biofilms being the dominant form of microbial life in many natural environments, they have received little attention in the oligotrophic and anaerobic waters found in deep bedrock fractures. This study is the first to use community DNA sequencing to describe biofilm formation under in situ conditions in the deep terrestrial biosphere. RESULTS: In this study, flow cells were attached to boreholes containing either "modern marine" or "old saline" waters of different origin and degree of isolation from the light-driven surface of the earth...
March 23, 2017: Microbiome
https://www.readbyqxmd.com/read/28256106/distribution-of-anaerobic-carbon-monoxide-dehydrogenase-genes-in-deep-subseafloor-sediments
#16
T Hoshino, F Inagaki
Carbon monoxide (CO) is the simplest oxocarbon generated by the decomposition of organic compounds, and it is expected to be in marine sediments in substantial amounts. However, the availability of CO in the deep subseafloor sedimentary biosphere is largely unknown even though anaerobic oxidation of CO is a thermodynamically favourable reaction that possibly occurs with sulphate reduction, methanogenesis, acetogenesis and hydrogenesis. In this study, we surveyed for the first time the distribution of the CO dehydrogenase gene (cooS), which encodes the catalytic beta subunit of anaerobic CO dehydrogenase (CODH), in subseafloor sediment-core samples from the eastern flank of the Juan de Fuca Ridge, Mars-Ursa Basin, Kumano Basin, and off the Shimokita Peninsula, Japan, during Integrated Ocean Drilling Program (IODP) Expeditions 301, 308 and 315 and the D/V Chikyu shakedown cruise CK06-06, respectively...
May 2017: Letters in Applied Microbiology
https://www.readbyqxmd.com/read/28229521/microbial-potential-for-carbon-and-nutrient-cycling-in-a-geogenic-supercritical-carbon-dioxide-reservoir
#17
Adam J E Freedman, BoonFei Tan, Janelle R Thompson
Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO2 , harbor a 'deep carbonated biosphere' with carbon cycling potential. We sampled subsurface fluids from scCO2 -water separators at a natural scCO2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content...
February 22, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28220112/predominance-of-viable-spore-forming-piezophilic-bacteria-in-high-pressure-enrichment-cultures-from-1-5-to-2-4-km-deep-coal-bearing-sediments-below-the-ocean-floor
#18
Jiasong Fang, Chiaki Kato, Gabriella M Runko, Yuichi Nogi, Tomoyuki Hori, Jiangtao Li, Yuki Morono, Fumio Inagaki
Phylogenetically diverse microorganisms have been observed in marine subsurface sediments down to ~2.5 km below the seafloor (kmbsf). However, very little is known about the pressure-adapted and/or pressure-loving microorganisms, the so called piezophiles, in the deep subseafloor biosphere, despite that pressure directly affects microbial physiology, metabolism, and biogeochemical processes of carbon and other elements in situ. In this study, we studied taxonomic compositions of microbial communities in high-pressure incubated sediment, obtained during the Integrated Ocean Drilling Program (IODP) Expedition 337 off the Shimokita Peninsula, Japan...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28158920/the-geobiological-nitrogen-cycle-from-microbes-to-the-mantle
#19
REVIEW
A L Zerkle, S Mikhail
Nitrogen forms an integral part of the main building blocks of life, including DNA, RNA, and proteins. N2 is the dominant gas in Earth's atmosphere, and nitrogen is stored in all of Earth's geological reservoirs, including the crust, the mantle, and the core. As such, nitrogen geochemistry is fundamental to the evolution of planet Earth and the life it supports. Despite the importance of nitrogen in the Earth system, large gaps remain in our knowledge of how the surface and deep nitrogen cycles have evolved over geologic time...
May 2017: Geobiology
https://www.readbyqxmd.com/read/28128071/the-geomycology-of-elemental-cycling-and-transformations-in-the-environment
#20
REVIEW
Geoffrey Michael Gadd
Geomicrobiology addresses the roles of microorganisms in geological and geochemical processes, and geomycology is a part of this topic focusing on the fungi. Geoactive roles of fungi include organic and inorganic transformations important in nutrient and element cycling, rock and mineral bioweathering, mycogenic biomineral formation, and metal-fungal interactions. Lichens and mycorrhizas are significant geoactive agents. Organic matter decomposition is important for cycling of major biomass-associated elements, e...
January 2017: Microbiology Spectrum
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