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https://www.readbyqxmd.com/read/29159878/arsenobetaine-an-ecophysiologically-important-organoarsenical-confers-cytoprotection-against-osmotic-stress-and-growth-temperature-extremes
#1
Tamara Hoffmann, Bianca Warmbold, Sander H J Smits, Britta Tschapek, Stefanie Ronzheimer, Abdallah Bashir, Chiliang Chen, Anne Rolbetzki, Marco Pittelkow, Mohamed Jebbar, Andreas Seubert, Lutz Schmitt, Erhard Bremer
Arsenic, a highly cytotoxic and cancerogenic metalloid, is brought into the biosphere through geochemical sources and anthropogenic activities. A global biogeochemical arsenic biotransformation cycle exists in which inorganic arsenic species are transformed into organoarsenicals, which are subsequently mineralized again into inorganic arsenic compounds. Microorganisms contribute to this biotransformation process greatly and one of the organoarsenicals synthesized and degraded in this cycle is arsenobetaine...
November 21, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29078310/methyl-compound-use-and-slow-growth-characterize-microbial-life-in-2-km-deep-subseafloor-coal-and-shale-beds
#2
Elizabeth Trembath-Reichert, Yuki Morono, Akira Ijiri, Tatsuhiko Hoshino, Katherine S Dawson, Fumio Inagaki, Victoria J Orphan
The past decade of scientific ocean drilling has revealed seemingly ubiquitous, slow-growing microbial life within a range of deep biosphere habitats. Integrated Ocean Drilling Program Expedition 337 expanded these studies by successfully coring Miocene-aged coal beds 2 km below the seafloor hypothesized to be "hot spots" for microbial life. To characterize the activity of coal-associated microorganisms from this site, a series of stable isotope probing (SIP) experiments were conducted using intact pieces of coal and overlying shale incubated at in situ temperatures (45 °C)...
October 31, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29045616/potential-impact-of-global-climate-change-on-benthic-deep-sea-microbes
#3
Roberto Danovaro, Cinzia Corinaldesi, Antonio Dell Anno, Eugenio Rastelli
Benthic deep-sea environments are the largest ecosystem on Earth, covering approximately 65% of the Earth surface. Microbes inhabiting this huge biome at all water depths represent the most abundant biological components and a relevant portion of the biomass of the biosphere, and play a crucial role in global biogeochemical cycles. Increasing evidence suggests that global climate changes are affecting also deep-sea ecosystems, both directly (causing shifts in bottom-water temperature, oxygen concentration and pH), and indirectly (through changes in surface oceans' productivity and in the consequent export of organic matter to the seafloor)...
October 13, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/29020741/the-sponge-microbiome-project
#4
Lucas Moitinho-Silva, Shaun Nielsen, Amnon Amir, Antonio Gonzalez, Gail L Ackermann, Carlo Cerrano, Carmen Astudillo-Garcia, Cole Easson, Detmer Sipkema, Fang Liu, Georg Steinert, Giorgos Kotoulas, Grace P McCormack, Guofang Feng, James J Bell, Jan Vicente, Johannes R Björk, Jose M Montoya, Julie B Olson, Julie Reveillaud, Laura Steindler, Mari-Carmen Pineda, Maria V Marra, Micha Ilan, Michael W Taylor, Paraskevi Polymenakou, Patrick M Erwin, Peter J Schupp, Rachel L Simister, Rob Knight, Robert W Thacker, Rodrigo Costa, Russell T Hill, Susanna Lopez-Legentil, Thanos Dailianis, Timothy Ravasi, Ute Hentschel, Zhiyong Li, Nicole S Webster, Torsten Thomas
Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales...
October 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28894932/genomic-insights-into-temperature-dependent-transcriptional-responses-of-kosmotoga-olearia-a-deep-biosphere-bacterium-that-can-grow-from-20-to-79%C3%A2-%C3%A2-c
#5
Stephen M J Pollo, Abigail A Adebusuyi, Timothy J Straub, Julia M Foght, Olga Zhaxybayeva, Camilla L Nesbø
Temperature is one of the defining parameters of an ecological niche. Most organisms thrive within a temperature range that rarely exceeds ~30 °C, but the deep subsurface bacterium Kosmotoga olearia can grow over a temperature range of 59 °C (20-79 °C). To identify genes correlated with this flexible phenotype, we compared transcriptomes of K. olearia cultures grown at its optimal 65 °C to those at 30, 40, and 77 °C. The temperature treatments affected expression of 573 of 2224 K. olearia genes. Notably, this transcriptional response elicits re-modeling of the cellular membrane and changes in metabolism, with increased expression of genes involved in energy and carbohydrate metabolism at high temperatures and up-regulation of amino acid metabolism at lower temperatures...
November 2017: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/28885627/ecological-and-genomic-profiling-of-anaerobic-methane-oxidizing-archaea-in-a-deep-granitic-environment
#6
Kohei Ino, Alex W Hernsdorf, Uta Konno, Mariko Kouduka, Katsunori Yanagawa, Shingo Kato, Michinari Sunamura, Akinari Hirota, Yoko S Togo, Kazumasa Ito, Akari Fukuda, Teruki Iwatsuki, Takashi Mizuno, Daisuke D Komatsu, Urumu Tsunogai, Toyoho Ishimura, Yuki Amano, Brian C Thomas, Jillian F Banfield, Yohey Suzuki
Recent single-gene-based surveys of deep continental aquifers demonstrated the widespread occurrence of archaea related to Candidatus Methanoperedens nitroreducens (ANME-2d) known to mediate anaerobic oxidation of methane (AOM). However, it is unclear whether ANME-2d mediates AOM in the deep continental biosphere. In this study, we found the dominance of ANME-2d in groundwater enriched in sulfate and methane from a 300-m deep underground borehole in granitic rock. A near-complete genome of one representative species of the ANME-2d obtained from the underground borehole has most of functional genes required for AOM and assimilatory sulfate reduction...
September 8, 2017: ISME Journal
https://www.readbyqxmd.com/read/28836742/thriving-or-surviving-evaluating-active-microbial-guilds-in-baltic-sea-sediment
#7
Laura A Zinke, Megan M Mullis, Jordan T Bird, Ian P G Marshall, Bo Barker Jørgensen, Karen G Lloyd, Jan P Amend, Brandi Kiel Reese
Microbial life in the deep subsurface biosphere is taxonomically and metabolically diverse, but it is vigorously debated whether the resident organisms are thriving (metabolizing, maintaining cellular integrity and expressing division genes) or just surviving. As part of Integrated Ocean Drilling Program Expedition 347: Baltic Sea Paleoenvironment, we extracted and sequenced RNA from organic carbon-rich, nutrient-replete and permanently anoxic sediment. In stark contrast to the oligotrophic subsurface biosphere, Baltic Sea Basin samples provided a unique opportunity to understand the balance between metabolism and other cellular processes...
August 24, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28812648/fungus-like-mycelial-fossils-in-2-4-billion-year-old-vesicular-basalt
#8
Stefan Bengtson, Birger Rasmussen, Magnus Ivarsson, Janet Muhling, Curt Broman, Federica Marone, Marco Stampanoni, Andrey Bekker
Fungi have recently been found to comprise a significant part of the deep biosphere in oceanic sediments and crustal rocks. Fossils occupying fractures and pores in Phanerozoic volcanics indicate that this habitat is at least 400 million years old, but its origin may be considerably older. A 2.4-billion-year-old basalt from the Palaeoproterozoic Ongeluk Formation in South Africa contains filamentous fossils in vesicles and fractures. The filaments form mycelium-like structures growing from a basal film attached to the internal rock surfaces...
April 24, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28790980/exploring-microdiversity-in-novel-kordia-sp-bacteroidetes-with-proteorhodopsin-from-the-tropical-indian-ocean-via-single-amplified-genomes
#9
Marta Royo-Llonch, Isabel Ferrera, Francisco M Cornejo-Castillo, Pablo Sánchez, Guillem Salazar, Ramunas Stepanauskas, José M González, Michael E Sieracki, Sabrina Speich, Lars Stemmann, Carlos Pedrós-Alió, Silvia G Acinas
Marine Bacteroidetes constitute a very abundant bacterioplankton group in the oceans that plays a key role in recycling particulate organic matter and includes several photoheterotrophic members containing proteorhodopsin. Relatively few marine Bacteroidetes species have been described and, moreover, they correspond to cultured isolates, which in most cases do not represent the actual abundant or ecologically relevant microorganisms in the natural environment. In this study, we explored the microdiversity of 98 Single Amplified Genomes (SAGs) retrieved from the surface waters of the underexplored North Indian Ocean, whose most closely related isolate is Kordia algicida OT-1...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28746759/is-de-extinction-special
#10
Henry T Greely
I have been involved with the current interest in de-extinction since early 2012, nearly its beginning. I have given a lot of thought to the potential risks and benefits of de-extinction. But only recently, after deep immersion in discussions around CRISPR-Cas9, the hottest new tool in bioscience since polymerase chain reaction, have I thought about a more fundamental question: how, if at all, is de-extinction special? Are "revived species" just another kind of genetically modified organism, raising essentially the same general concerns? I answer, for the most part, yes...
July 2017: Hastings Center Report
https://www.readbyqxmd.com/read/28720809/microbial-turnover-times-in-the-deep-seabed-studied-by-amino-acid-racemization-modelling
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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...
September 2017: ISME Journal
https://www.readbyqxmd.com/read/28419734/the-life-sulfuric-microbial-ecology-of-sulfur-cycling-in-marine-sediments
#20
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...
August 2017: Environmental Microbiology Reports
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