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Deep biosphere

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
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
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
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
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...
2016: Nature Microbiology
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
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
Paula J Mouser, Mikayla Borton, Thomas H Darrah, Angela Hartsock, Kelly C Wrighton
Horizontal drilling and hydraulic fracturing are increasingly used for recovering energy resources in black shales across the globe. Although newly drilled wells are providing access to rocks and fluids from kilometer depths to study the deep biosphere, we have much to learn about microbial ecology of shales before and after 'fracking'. Recent studies provide a framework for considering how engineering activities alter this rock-hosted ecosystem. We first provide data on the geochemical environment and microbial habitability in pristine shales...
November 2016: FEMS Microbiology Ecology
Mario López-Pérez, Nikole E Kimes, Jose M Haro-Moreno, Francisco Rodriguez-Valera
We have used two metagenomic approaches, direct sequencing of natural samples and sequencing after enrichment, to characterize communities of prokaryotes associated to particles. In the first approximation, different size filters (0.22 and 5 μm) were used to identify prokaryotic microbes of free-living and particle-attached bacterial communities in the Mediterranean water column. A subtractive metagenomic approach was used to characterize the dominant microbial groups in the large size fraction that were not present in the free-living one...
2016: Frontiers in Microbiology
Jonathan P Badalamenti, Zarath M Summers, Chi Ho Chan, Jeffrey A Gralnick, Daniel R Bond
Reaching a depth of 713 m below the surface, the Soudan Underground Iron Mine (Soudan, MN, USA) transects a massive Archaean (2.7 Ga) banded iron formation, providing a remarkably accessible window into the terrestrial deep biosphere. Despite organic carbon limitation, metal-reducing microbial communities are present in potentially ancient anoxic brines continuously emanating from exploratory boreholes on Level 27. Using graphite electrodes deposited in situ as bait, we electrochemically enriched and isolated a novel halophilic iron-reducing Deltaproteobacterium, 'Desulfuromonas soudanensis' strain WTL, from an acetate-fed three-electrode bioreactor poised at +0...
2016: Frontiers in Microbiology
Bibiana G Crespo, Philip J Wallhead, Ramiro Logares, Carlos Pedrós-Alió
High-throughput sequencing (HTS) techniques have suggested the existence of a wealth of species with very low relative abundance: the rare biosphere. We attempted to exhaustively map this rare biosphere in two water samples by performing an exceptionally deep pyrosequencing analysis (~500,000 final reads per sample). Species data were derived by a 97% identity criterion and various parametric distributions were fitted to the observed counts. Using the best-fitting Sichel distribution we estimate a total species richness of 1,568-1,669 (95% Credible Interval) and 5,027-5,196 for surface and deep water samples respectively, implying that 84-89% of the total richness in those two samples was sequenced, and we predict that a quadrupling of the present sequencing effort would suffice to observe 90% of the total richness in both samples...
2016: PloS One
Magnus Ivarsson, Anna Schnürer, Stefan Bengtson, Anna Neubeck
The recent recognition of fungi in the oceanic igneous crust challenges the understanding of this environment as being exclusively prokaryotic and forces reconsiderations of the ecology of the deep biosphere. Anoxic provinces in the igneous crust are abundant and increase with age and depth of the crust. The presence of anaerobic fungi in deep-sea sediments and on the seafloor introduces a type of organism with attributes of geobiological significance not previously accounted for. Anaerobic fungi are best known from the rumen of herbivores where they produce molecular hydrogen, which in turn stimulates the growth of methanogens...
2016: Frontiers in Microbiology
Maria G Pachiadaki, Vanessa Rédou, David J Beaudoin, Gaëtan Burgaud, Virginia P Edgcomb
The deep sedimentary biosphere, extending 100s of meters below the seafloor harbors unexpected diversity of Bacteria, Archaea, and microbial eukaryotes. Far less is known about microbial eukaryotes in subsurface habitats, albeit several studies have indicated that fungi dominate microbial eukaryotic communities and fungal molecular signatures (of both yeasts and filamentous forms) have been detected in samples as deep as 1740 mbsf. Here, we compare and contrast fungal ribosomal RNA gene signatures and whole community metatranscriptomes present in sediment core samples from 6 and 95 mbsf from Peru Margin site 1229A and from samples from 12 and 345 mbsf from Canterbury Basin site U1352...
2016: Frontiers in Microbiology
Li Zhang, Yan Wang, Jing Liang, Qinghao Song, Xiao-Hua Zhang
The deep-sea water of the South Pacific Gyre (SPG, 20°S-45°S) is a cold and ultra-oligotrophic environment that is the source of cold-adapted enzymes. However, the characteristic features of psychrophilic enzymes derived from culturable microbes in the SPG remained largely unknown. In this study, the degradation properties of 174 cultures from the deep water of the SPG were used to determine the diversity of cold-adapted enzymes. Thus, the abilities to degrade polysaccharides, proteins, lipids, and DNA at 4, 16, and 28 °C were investigated...
September 2016: Extremophiles: Life Under Extreme Conditions
Steffen L Jørgensen, Rui Zhao
The deep marine biosphere has over the past decades been exposed as an immense habitat for microorganisms with wide-reaching implications for our understanding of life on Earth. Recent advances in knowledge concerning this biosphere have been achieved mainly through extensive microbial and geochemical studies of deep marine sediments. However, the oceanic crust buried beneath the sediments, is still largely unexplored with respect to even the most fundamental questions related to microbial life. Here, we present quantitative and qualitative data related to the microbial inventory from 33 deeply buried basaltic rocks collected at two different locations, penetrating 300 vertical meters into the upper oceanic crust on the west flank of the Mid-Atlantic spreading ridge...
2016: Frontiers in Microbiology
Qingyang Hu, Duck Young Kim, Wenge Yang, Liuxiang Yang, Yue Meng, Li Zhang, Ho-Kwang Mao
The distribution, accumulation and circulation of oxygen and hydrogen in Earth's interior dictate the geochemical evolution of the hydrosphere, atmosphere and biosphere. The oxygen-rich atmosphere and iron-rich core represent two end-members of the oxygen-iron (O-Fe) system, overlapping with the entire pressure-temperature-composition range of the planet. The extreme pressure and temperature conditions of the deep interior alter the oxidation states, spin states and phase stabilities of iron oxides, creating new stoichiometries, such as Fe4O5 (ref...
June 9, 2016: Nature
Andrew David Beale, David Whitmore, Damian Moran
Most of the life with which humans interact is exposed to highly rhythmic and extremely predictable changes in illumination that occur with the daily events of sunrise and sunset. However, while the influence of the sun feels omnipotent to surface dwellers such as ourselves, life on earth is dominated, in terms of biomass, by organisms isolated from the direct effects of the sun. A limited understanding of what life is like away from the sun can be inferred from our knowledge of physiology and ecology in the light biosphere, but a full understanding can only be gained by studying animals from the dark biosphere, both in the laboratory and in their natural habitats...
June 4, 2016: Journal of Comparative Physiology. B, Biochemical, Systemic, and Environmental Physiology
Y Morono, F Inagaki
Over the past few decades, the subseafloor biosphere has been explored by scientific ocean drilling to depths of about 2.5km below the seafloor. Although organic-rich anaerobic sedimentary habitats in the ocean margins harbor large numbers of microbial cells, microbial populations in ultraoligotrophic aerobic sedimentary habitats in the open ocean gyres are several orders of magnitude less abundant. Despite advances in cultivation-independent molecular ecological techniques, exploring the low-biomass environment remains technologically challenging, especially in the deep subseafloor biosphere...
2016: Advances in Applied Microbiology
Sergei V Bukin, Olga N Pavlova, Andrei Y Manakov, Elena A Kostyreva, Svetlana M Chernitsyna, Elena V Mamaeva, Tatyana V Pogodaeva, Tamara I Zemskaya
The ability to compare the composition and metabolic potential of microbial communities inhabiting the subsurface sediment in geographically distinct locations is one of the keys to understanding the evolution and function of the subsurface biosphere. Prospective areas for study of the subsurface biosphere are the sites of hydrocarbon discharges on the bottom of the Lake Baikal rift, where ascending fluxes of gas-saturated fluids and oil from deep layers of bottom sediments seep into near-surface sediment. The samples of surface sediments collected in the area of the Posolskaya Bank methane seep were cultured for 17 months under thermobaric conditions (80°C, 5 MPa) with the addition of complementary organic substrate, and a different composition for the gas phase...
2016: Frontiers in Microbiology
Nadine M Boulotte, Steven J Dalton, Andrew G Carroll, Peter L Harrison, Hollie M Putnam, Lesa M Peplow, Madeleine Jh van Oppen
Reef-building corals possess a range of acclimatisation and adaptation mechanisms to respond to seawater temperature increases. In some corals, thermal tolerance increases through community composition changes of their dinoflagellate endosymbionts (Symbiodinium spp.), but this mechanism is believed to be limited to the Symbiodinium types already present in the coral tissue acquired during early life stages. Compelling evidence for symbiont switching, that is, the acquisition of novel Symbiodinium types from the environment, by adult coral colonies, is currently lacking...
April 19, 2016: ISME Journal
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