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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
#1
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
#2
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...
February 3, 2017: Geobiology
https://www.readbyqxmd.com/read/28128071/the-geomycology-of-elemental-cycling-and-transformations-in-the-environment
#3
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
#4
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) which actively transport DIC across the cell membrane to facilitate carbon fixation. Surprisingly, DIC transport has only been well-studied among cyanobacteria and microalgae. 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...
January 23, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/27992585/effect-of-nickel-levels-on-hydrogen-partial-pressure-and-methane-production-in-methanogens
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/27766749/the-sequence-capture-by-hybridization-a-new-approach-for-revealing-the-potential-of-mono-aromatic-hydrocarbons-bioattenuation-in-a-deep-oligotrophic-aquifer
#13
Magali Ranchou-Peyruse, Cyrielle Gasc, Marion Guignard, Thomas Aüllo, David Dequidt, Pierre Peyret, Anthony Ranchou-Peyruse
The formation water of a deep aquifer (853 m of depth) used for geological storage of natural gas was sampled to assess the mono-aromatic hydrocarbons attenuation potential of the indigenous microbiota. The study of bacterial diversity suggests that Firmicutes and, in particular, sulphate-reducing bacteria (Peptococcaceae) predominate in this microbial community. The capacity of the microbial community to biodegrade toluene and m- and p-xylenes was demonstrated using a culture-based approach after several hundred days of incubation...
October 21, 2016: Microbial Biotechnology
https://www.readbyqxmd.com/read/27761134/microbial-sulfate-reduction-potential-in-coal-bearing-sediments-down-to-2-5-km-below-the-seafloor-off-shimokita-peninsula-japan
#14
Clemens Glombitza, Rishi R Adhikari, Natascha Riedinger, William P Gilhooly, Kai-Uwe Hinrichs, Fumio Inagaki
Sulfate reduction is the predominant anaerobic microbial process of organic matter mineralization in marine sediments, with recent studies revealing that sulfate reduction not only occurs in sulfate-rich sediments, but even extends to deeper, methanogenic sediments at very low background concentrations of sulfate. Using samples retrieved off the Shimokita Peninsula, Japan, during the Integrated Ocean Drilling Program (IODP) Expedition 337, we measured potential sulfate reduction rates by slurry incubations with (35)S-labeled sulfate in deep methanogenic sediments between 1276...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27721813/cyanobacterial-diazotrophy-and-earth-s-delayed-oxygenation
#15
Stephanie L Olson, Christopher T Reinhard, Timothy W Lyons
The redox landscape of Earth's ocean-atmosphere system has changed dramatically throughout Earth history. Although Earth's protracted oxygenation is undoubtedly the consequence of cyanobacterial oxygenic photosynthesis, the relationship between biological O2 production and Earth's redox evolution remains poorly understood. Existing models for Earth's oxygenation cannot adequately explain the nearly 2.5 billion years delay between the origin of oxygenic photosynthesis and the oxygenation of the deep ocean, in large part owing to major deficiencies in our understanding of the coevolution of O2 and Earth's key biogeochemical cycles (e...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27630628/size-and-carbon-content-of-sub-seafloor-microbial-cells-at-landsort-deep-baltic-sea
#16
Stefan Braun, Yuki Morono, Sten Littmann, Marcel Kuypers, Hüsnü Aslan, Mingdong Dong, Bo B Jørgensen, Bente Aa Lomstein
The discovery of a microbial ecosystem in ocean sediments has evoked interest in life under extreme energy limitation and its role in global element cycling. However, fundamental parameters such as the size and the amount of biomass of sub-seafloor microbial cells are poorly constrained. Here we determined the volume and the carbon content of microbial cells from a marine sediment drill core retrieved by the Integrated Ocean Drilling Program (IODP), Expedition 347, at Landsort Deep, Baltic Sea. To determine their shape and volume, cells were separated from the sediment matrix by multi-layer density centrifugation and visualized via epifluorescence microscopy (FM) and scanning electron microscopy (SEM)...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27623198/evidence-for-seismogenic-hydrogen-gas-a-potential-microbial-energy-source-on-earth-and-mars
#17
Sean McMahon, John Parnell, Nigel J F Blamey
UNLABELLED: The oxidation of molecular hydrogen (H2) is thought to be a major source of metabolic energy for life in the deep subsurface on Earth, and it could likewise support any extant biosphere on Mars, where stable habitable environments are probably limited to the subsurface. Faulting and fracturing may stimulate the supply of H2 from several sources. We report the H2 content of fluids present in terrestrial rocks formed by brittle fracturing on fault planes (pseudotachylites and cataclasites), along with protolith control samples...
September 2016: Astrobiology
https://www.readbyqxmd.com/read/27595198/microbial-metabolisms-in-a-2-5-km-deep-ecosystem-created-by-hydraulic-fracturing-in-shales
#18
Rebecca A Daly, Mikayla A Borton, Michael J Wilkins, David W Hoyt, Duncan J Kountz, Richard A Wolfe, Susan A Welch, Daniel N Marcus, Ryan V Trexler, Jean D MacRae, Joseph A Krzycki, David R Cole, Paula J Mouser, Kelly C Wrighton
Hydraulic fracturing is the industry standard for extracting hydrocarbons from shale formations. Attention has been paid to the economic benefits and environmental impacts of this process, yet the biogeochemical changes induced in the deep subsurface are poorly understood. Recent single-gene investigations revealed that halotolerant microbial communities were enriched after hydraulic fracturing. Here, the reconstruction of 31 unique genomes coupled to metabolite data from the Marcellus and Utica shales revealed that many of the persisting organisms play roles in methylamine cycling, ultimately supporting methanogenesis in the deep biosphere...
September 5, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27559333/distribution-and-niche-separation-of-planktonic-microbial-communities-in-the-water-columns-from-the-surface-to-the-hadal-waters-of-the-japan-trench-under-the-eutrophic-ocean
#19
Takuro Nunoura, Miho Hirai, Yukari Yoshida-Takashima, Manabu Nishizawa, Shinsuke Kawagucci, Taichi Yokokawa, Junichi Miyazaki, Osamu Koide, Hiroko Makita, Yoshihiro Takaki, Michinari Sunamura, Ken Takai
The Japan Trench is located under the eutrophic Northwestern Pacific while the Mariana Trench that harbors the unique hadal planktonic biosphere is located under the oligotrophic Pacific. Water samples from the sea surface to just above the seafloor at a total of 11 stations including a trench axis station, were investigated several months after the Tohoku Earthquake in March 2011. High turbidity zones in deep waters were observed at most of the sampling stations. The small subunit (SSU) rRNA gene community structures in the hadal waters (water depths below 6000 m) at the trench axis station were distinct from those in the overlying meso-, bathy and abyssopelagic waters (water depths between 200 and 1000 m, 1000 and 4000 m, and 4000 and 6000 m, respectively), although the SSU rRNA gene sequences suggested that potential heterotrophic bacteria dominated in all of the waters...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27548228/pressure-as-a-limiting-factor-for-life
#20
Rachael Hazael, Filip Meersman, Fumihisa Ono, Paul F McMillan
Facts concerning the stability and functioning of key biomolecular components suggest that cellular life should no longer be viable above a few thousand atmospheres (200-300 MPa). However, organisms are seen to survive in the laboratory to much higher pressures, extending into the GPa or even tens of GPa ranges. This is causing main questions to be posed concerning the survival mechanisms of simple to complex organisms. Understanding the ultimate pressure survival of organisms is critical for food sterilization and agricultural products conservation technologies...
August 17, 2016: Life
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