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Deep biosphere

Kevin W Becker, Felix J Elling, Jan M Schröder, Julius S Lipp, Tobias Goldhammer, Matthias Zabel, Marcus Elvert, Jörg Overmann, Kai-Uwe Hinrichs
The stratified water column of the Black Sea serves as a model ecosystem for studying the interactions of microorganisms with major biogeochemical cycles. Here we provide detailed analysis of isoprenoid quinones to study microbial redox processes in the ocean. In a continuum from the photic zone through the chemocline into deep anoxic sediments of the southern Black Sea, diagnostic quinones and inorganic geochemical parameters indicate niche segregation between redox processes and corresponding shifts in microbial community composition...
March 9, 2018: Applied and Environmental Microbiology
Aurèle Vuillemin, Daniel Ariztegui, Fabian Horn, Jens Kallmeyer, William D Orsi
For decades, microbial community composition in subseafloor sediments has been the focus of extensive studies. In deep lacustrine sediments however, the taxonomic composition of microbial communities remains undercharacterized. Greater knowledge on microbial diversity in lacustrine sediments would improve our understanding of how environmental factors, and resulting selective pressures, shape subsurface biospheres in marine and freshwater sediments. Using high-throughput sequencing of 16S rRNA genes across high resolution climate intervals covering the last 50,000 years in Laguna Potrok Aike, Argentina, we identified changes in microbial populations in response to both past environmental conditions and geochemical changes of the sediment during burial...
February 20, 2018: FEMS Microbiology Ecology
Jaime Cuevas, Ana Isabel Ruiz, Raúl Fernández
Clay and cement are known nano-colloids originating from natural processes or traditional materials technology. Currently, they are used together as part of the engineered barrier system (EBS) to isolate high-level nuclear waste (HLW) metallic containers in deep geological repositories (DGR). The EBS should prevent radionuclide (RN) migration into the biosphere until the canisters fail, which is not expected for approximately 103 years. The interactions of cementitious materials with bentonite swelling clay have been the scope of our research team at the Autonomous University of Madrid (UAM) with participation in several European Union (EU) projects from 1998 up to now...
February 21, 2018: Chemical Record: An Official Publication of the Chemical Society of Japan ... [et Al.]
D'Arcy R Meyer-Dombard, Caitlin P Casar, Alexander G Simon, Dawn Cardace, Matthew O Schrenk, Carlo A Arcilla
Terrestrial serpentinizing systems harbor microbial subsurface life. Passive or active microbially mediated iron transformations at alkaline conditions in deep biosphere serpentinizing ecosystems are understudied. We explore these processes in the Zambales (Philippines) and Coast Range (CA, USA) ophiolites, and associated surface ecosystems by probing the relevance of samples acquired at the surface to in situ, subsurface ecosystems, and the nature of microbe-mineral associations in the subsurface. In this pilot study, we use microcosm experiments and batch culturing directed at iron redox transformations to confirm thermodynamically based predictions that iron transformations may be important in subsurface serpentinizing ecosystems...
February 15, 2018: Extremophiles: Life Under Extreme Conditions
Emma Bell, Lynsay I Blake, Angela Sherry, Ian M Head, Casey R J Hubert
Endospores of thermophilic bacteria are found in cold and temperate sediments where they persist in a dormant state. As inactive endospores that cannot grow at the low ambient temperatures, they are akin to tracer particles in cold sediments, unaffected by factors normally governing microbial biogeography (e.g. selection, drift, mutation). This makes thermophilic endospores ideal model organisms for studying microbial biogeography since their spatial distribution can be directly related to their dispersal history...
February 2, 2018: Environmental Microbiology
Matthias Winkel, Julia Mitzscherling, Pier P Overduin, Fabian Horn, Maria Winterfeld, Ruud Rijkers, Mikhail N Grigoriev, Christian Knoblauch, Kai Mangelsdorf, Dirk Wagner, Susanne Liebner
Thawing submarine permafrost is a source of methane to the subsurface biosphere. Methane oxidation in submarine permafrost sediments has been proposed, but the responsible microorganisms remain uncharacterized. We analyzed archaeal communities and identified distinct anaerobic methanotrophic assemblages of marine and terrestrial origin (ANME-2a/b, ANME-2d) both in frozen and completely thawed submarine permafrost sediments. Besides archaea potentially involved in anaerobic oxidation of methane (AOM) we found a large diversity of archaea mainly belonging to Bathyarchaeota, Thaumarchaeota, and Euryarchaeota...
January 22, 2018: Scientific Reports
S L Cobain, D M Hodgson, J Peakall, P B Wignall, M R D Cobain
Macrofauna is known to inhabit the top few 10s cm of marine sediments, with rare burrows up to two metres below the seabed. Here, we provide evidence from deep-water Permian strata for a previously unrecognised habitat up to at least 8 metres below the sediment-water interface. Infaunal organisms exploited networks of forcibly injected sand below the seabed, forming living traces and reworking sediment. This is the first record that shows sediment injections are responsible for hosting macrofaunal life metres below the contemporaneous seabed...
January 10, 2018: Scientific Reports
Holly L Sewell, Anne-Kristin Kaster, Alfred M Spormann
The deep marine subsurface is one of the largest unexplored biospheres on Earth and is widely inhabited by members of the phylum Chloroflexi In this report, we investigated genomes of single cells obtained from deep-sea sediments of the Peruvian Margin, which are enriched in such Chloroflexi 16S rRNA gene sequence analysis placed two of these single-cell-derived genomes (DscP3 and Dsc4) in a clade of subphylum I Chloroflexi which were previously recovered from deep-sea sediment in the Okinawa Trough and a third (DscP2-2) as a member of the previously reported DscP2 population from Peruvian Margin site 1230...
December 19, 2017: MBio
Maren Ziegler, Víctor M Eguíluz, Carlos M Duarte, Christian R Voolstra
The association between corals and photosynthetic dinoflagellates (Symbiodinium spp.) is the key to the success of reef ecosystems in highly oligotrophic environments, but it is also their Achilles' heel due to its vulnerability to local stressors and the effects of climate change. Research during the last two decades has shaped a view that coral host-Symbiodinium pairings are diverse, but largely exclusive. Deep sequencing has now revealed the existence of a rare diversity of cryptic Symbiodinium assemblages within the coral holobiont, in addition to one or a few abundant algal members...
January 2018: ISME Journal
Mart Krupovic, Virginija Cvirkaite-Krupovic, Jaime Iranzo, David Prangishvili, Eugene V Koonin
Viruses of archaea represent one of the most enigmatic parts of the virosphere. Most of the characterized archaeal viruses infect extremophilic hosts and display remarkable diversity of virion morphotypes, many of which have never been observed among viruses of bacteria or eukaryotes. The uniqueness of the virion morphologies is matched by the distinctiveness of the genomes of these viruses, with ∼75% of genes encoding unique proteins, refractory to functional annotation based on sequence analyses. In this review, we summarize the state-of-the-art knowledge on various aspects of archaeal virus genomics...
January 15, 2018: Virus Research
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...
January 2018: Environmental Microbiology
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
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
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
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
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
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
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
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
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
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