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https://www.readbyqxmd.com/read/28419734/the-life-sulfuric-microbial-ecology-of-sulfur-cycling-in-marine-sediments
#1
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
#2
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
#3
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 10, 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
#4
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
#5
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
#6
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
#7
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...
March 3, 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
#8
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
#9
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
#10
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
#11
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
https://www.readbyqxmd.com/read/28115547/proteomic-and-mutant-analysis-of-the-co2-concentrating-mechanism-of-hydrothermal-vent-chemolithoautotroph-thiomicrospira-crunogena
#12
Mary Mangiapia, Terry-René W Brown, Dale Chaput, Edward Haller, Tara L Harmer, Zahra Hashemy, Ryan Keeley, Juliana Leonard, Paola Mancera, David Nicholson, Stanley Stevens, Pauline Wanjugi, Tania Zabinski, Chongle Pan, Kathleen M Scott
Many autotrophic microorganisms are likely to adapt to scarcity in dissolved inorganic carbon (DIC; CO2 + HCO3(-) + CO3(2-)) with CO2 concentrating mechanisms (CCM) that actively transport DIC across the cell membrane to facilitate carbon fixation. Surprisingly, DIC transport has been well studied among cyanobacteria and microalgae only. The deep-sea vent gammaproteobacterial chemolithoautotroph Thiomicrospira crunogena has a low-DIC inducible CCM, though the mechanism for uptake is unclear, as homologs to cyanobacterial transporters are absent...
April 1, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/27992585/effect-of-nickel-levels-on-hydrogen-partial-pressure-and-methane-production-in-methanogens
#13
Anna Neubeck, Susanne Sjöberg, Alex Price, Nolwenn Callac, Anna Schnürer
Hydrogen (H2) consumption and methane (CH4) production in pure cultures of three different methanogens were investigated during cultivation with 0, 0.2 and 4.21 μM added nickel (Ni). The results showed that the level of dissolved Ni in the anaerobic growth medium did not notably affect CH4 production in the cytochrome-free methanogenic species Methanobacterium bryantii and Methanoculleus bourgensis MAB1, but affected CH4 formation rate in the cytochrome-containing Methanosarcina barkeri grown on H2 and CO2...
2016: PloS One
https://www.readbyqxmd.com/read/27940647/gaia-and-her-microbiome
#14
John F Stolz
The Gaia Hypothesis, proposed 50 years ago, posits that the Earth's biosphere, atmosphere, hydrosphere, and lithosphere interact as a cybernetic system, maintaining the long-term habitability of the planet. The resulting chemical composition of the atmosphere, oceans, and crust is unique as compared to the other planets of our solar system, and due to the presence of life. Together these components comprise the biosphere, the life support system of the planet, with most of the essential processes carried out by microbes...
December 8, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27905827/modeling-pn2-through-geological-time-implications-for-planetary-climates-and-atmospheric-biosignatures
#15
E E Stüeken, M A Kipp, M C Koehler, E W Schwieterman, B Johnson, R Buick
Nitrogen is a major nutrient for all life on Earth and could plausibly play a similar role in extraterrestrial biospheres. The major reservoir of nitrogen at Earth's surface is atmospheric N2, but recent studies have proposed that the size of this reservoir may have fluctuated significantly over the course of Earth's history with particularly low levels in the Neoarchean-presumably as a result of biological activity. We used a biogeochemical box model to test which conditions are necessary to cause large swings in atmospheric N2 pressure...
December 2016: Astrobiology
https://www.readbyqxmd.com/read/27896730/scaling-up-the-phylogenetic-detection-of-lateral-gene-transfer-events
#16
Cheong Xin Chan, Robert G Beiko, Mark A Ragan
Lateral genetic transfer (LGT) is the process by which genetic material moves between organisms (and viruses) in the biosphere. Among the many approaches developed for the inference of LGT events from DNA sequence data, methods based on the comparison of phylogenetic trees remain the gold standard for many types of problem. Identifying LGT events from sequenced genomes typically involves a series of steps in which homologous sequences are identified and aligned, phylogenetic trees are inferred, and their topologies are compared to identify unexpected or conflicting relationships...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27875689/extreme-diversity-of-diplonemid-eukaryotes-in-the-ocean
#17
Olga Flegontova, Pavel Flegontov, Shruti Malviya, Stephane Audic, Patrick Wincker, Colomban de Vargas, Chris Bowler, Julius Lukeš, Aleš Horák
The world's oceans represent by far the largest biome, with great importance for the global ecosystem [1-4]. The vast majority of ocean biomass and biodiversity is composed of microscopic plankton. Recent results from the Tara Oceans metabarcoding study revealed that a significant part of the plankton in the upper sunlit layer of the ocean is represented by an understudied group of heterotrophic excavate flagellates called diplonemids [5, 6]. We have analyzed the diversity and distribution patterns of diplonemid populations on the extended set of Tara Oceans V9 18S rDNA metabarcodes amplified from 850 size- fractionated plankton communities sampled across 123 globally distributed locations, for the first time also including samples from the mesopelagic zone, which spans the depth from about 200 to 1,000 meters...
November 21, 2016: Current Biology: CB
https://www.readbyqxmd.com/read/27814034/dining-in-the-deep-the-feeding-ecology-of-deep-sea-fishes
#18
Jeffrey C Drazen, Tracey T Sutton
Deep-sea fishes inhabit ∼75% of the biosphere and are a critical part of deep-sea food webs. Diet analysis and more recent trophic biomarker approaches, such as stable isotopes and fatty-acid profiles, have enabled the description of feeding guilds and an increased recognition of the vertical connectivity in food webs in a whole-water-column sense, including benthic-pelagic coupling. Ecosystem modeling requires data on feeding rates; the available estimates indicate that deep-sea fishes have lower per-individual feeding rates than coastal and epipelagic fishes, but the overall predation impact may be high...
January 3, 2017: Annual Review of Marine Science
https://www.readbyqxmd.com/read/27807346/sulfur-mass-independent-fractionation-in-subsurface-fracture-waters-indicates-a-long-standing-sulfur-cycle-in-precambrian-rocks
#19
L Li, B A Wing, T H Bui, J M McDermott, G F Slater, S Wei, G Lacrampe-Couloume, B Sherwood Lollar
The discovery of hydrogen-rich waters preserved below the Earth's surface in Precambrian rocks worldwide expands our understanding of the habitability of the terrestrial subsurface. Many deep microbial ecosystems in these waters survive by coupling hydrogen oxidation to sulfate reduction. Hydrogen originates from water-rock reactions including serpentinization and radiolytic decomposition of water induced by decay of radioactive elements in the host rocks. The origin of dissolved sulfate, however, remains unknown...
October 27, 2016: Nature Communications
https://www.readbyqxmd.com/read/27787948/forest-ecosystems-of-temperate-climatic-regions-from-ancient-use-to-climate-change
#20
REVIEW
Frank S Gilliam
I. II. III. IV. V. References SUMMARY: Humans have long utilized resources from all forest biomes, but the most indelible anthropogenic signature has been the expanse of human populations in temperate forests. The purpose of this review is to bring into focus the diverse forests of the temperate region of the biosphere, including those of hardwood, conifer and mixed dominance, with a particular emphasis on crucial challenges for the future of these forested areas. Implicit in the term 'temperate' is that the predominant climate of these forest regions has distinct cyclic, seasonal changes involving periods of growth and dormancy...
October 27, 2016: New Phytologist
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