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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
#1
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...
September 11, 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
#2
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
#3
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 (IODP) 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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
https://www.readbyqxmd.com/read/28396823/genomic-comparisons-of-a-bacterial-lineage-that-inhabits-both-marine-and-terrestrial-deep-subsurface-systems
#17
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
#18
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
#19
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
#20
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
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