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  • 1
    In: The ISME Journal, Springer Science and Business Media LLC, Vol. 13, No. 7 ( 2019-7), p. 1750-1762
    Type of Medium: Online Resource
    ISSN: 1751-7362 , 1751-7370
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2019
    detail.hit.zdb_id: 2299378-2
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  • 2
    In: Environmental Microbiology, Wiley, Vol. 21, No. 10 ( 2019-10), p. 3816-3830
    Abstract: Hydrogen (H 2 ) is enriched in hot springs and can support microbial primary production. Using a series of geochemical proxies, a model to describe variable H 2 concentrations in Yellowstone National Park (YNP) hot springs is presented. Interaction between water and crustal iron minerals yields H 2 that partition into the vapour phase during decompressional boiling of ascending hydrothermal fluids. Variable vapour input leads to differences in H 2 concentration among springs. Analysis of 50 metagenomes from a variety of YNP springs reveals that genes encoding oxidative hydrogenases are enriched in communities inhabiting springs sourced with vapour‐phase gas. Three springs in the Smokejumper (SJ) area of YNP that are sourced with vapour‐phase gas and with the most H 2 in YNP were examined to determine the fate of H 2 . SJ3 had the most H 2 , the most 16S rRNA gene templates and the greatest abundance of culturable hydrogenotrophic and autotrophic cells of the three springs. Metagenomics and transcriptomics of SJ3 reveal a diverse community comprised of abundant populations expressing genes involved in H 2 oxidation and carbon dioxide fixation. These observations suggest a link between geologic processes that generate and source H 2 to hot springs and the distribution of organisms that use H 2 to generate energy.
    Type of Medium: Online Resource
    ISSN: 1462-2912 , 1462-2920
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2019
    detail.hit.zdb_id: 2020213-1
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    American Society for Microbiology ; 2009
    In:  Applied and Environmental Microbiology Vol. 75, No. 13 ( 2009-07), p. 4620-4623
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 75, No. 13 ( 2009-07), p. 4620-4623
    Abstract: Degenerate primers for the [FeFe] hydrogenase ( hydA ) were developed and used in PCRs to examine hydA in microbial mats that inhabit saltern evaporative ponds in Guerrero Negro (GN), Mexico. A diversity of deduced HydA was discovered that revealed unique variants, which may reflect adaptation to the environmental conditions present in GN.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    RVK:
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2009
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2013
    In:  Microbial Ecology Vol. 66, No. 2 ( 2013-8), p. 268-280
    In: Microbial Ecology, Springer Science and Business Media LLC, Vol. 66, No. 2 ( 2013-8), p. 268-280
    Type of Medium: Online Resource
    ISSN: 0095-3628 , 1432-184X
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2013
    detail.hit.zdb_id: 1462065-0
    detail.hit.zdb_id: 188257-0
    SSG: 12
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  • 5
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 87, No. 2 ( 2021-01-04)
    Abstract: Serpentinization can generate highly reduced fluids replete with hydrogen (H 2 ) and methane (CH 4 ), potent reductants capable of driving microbial methanogenesis and methanotrophy, respectively. However, CH 4 in serpentinized waters is thought to be primarily abiogenic, raising key questions about the relative importance of methanogens and methanotrophs in the production and consumption of CH 4 in these systems. Herein, we apply molecular approaches to examine the functional capability and activity of microbial CH 4 cycling in serpentinization-impacted subsurface waters intersecting multiple rock and water types within the Samail Ophiolite of Oman. Abundant 16S rRNA genes and transcripts affiliated with the methanogenic genus Methanobacterium were recovered from the most alkaline (pH, 〉 10), H 2 - and CH 4 -rich subsurface waters. Additionally, 16S rRNA genes and transcripts associated with the aerobic methanotrophic genus Methylococcus were detected in wells that spanned varied fluid geochemistry. Metagenomic sequencing yielded genes encoding homologs of proteins involved in the hydrogenotrophic pathway of microbial CH 4 production and in microbial CH 4 oxidation. Transcripts of several key genes encoding methanogenesis/methanotrophy enzymes were identified, predominantly in communities from the most hyperalkaline waters. These results indicate active methanogenic and methanotrophic populations in waters with hyperalkaline pH in the Samail Ophiolite, thereby supporting a role for biological CH 4 cycling in aquifers that undergo low-temperature serpentinization. IMPORTANCE Serpentinization of ultramafic rock can generate conditions favorable for microbial methane (CH 4 ) cycling, including the abiotic production of hydrogen (H 2 ) and possibly CH 4 . Systems of low-temperature serpentinization are geobiological targets due to their potential to harbor microbial life and ubiquity throughout Earth’s history. Biomass in fracture waters collected from the Samail Ophiolite of Oman, a system undergoing modern serpentinization, yielded DNA and RNA signatures indicative of active microbial methanogenesis and methanotrophy. Intriguingly, transcripts for proteins involved in methanogenesis were most abundant in the most highly reacted waters that have hyperalkaline pH and elevated concentrations of H 2 and CH 4 . These findings suggest active biological methane cycling in serpentinite-hosted aquifers, even under extreme conditions of high pH and carbon limitation. These observations underscore the potential for microbial activity to influence the isotopic composition of CH 4 in these systems, which is information that could help in identifying biosignatures of microbial activity on other planets.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    RVK:
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2021
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 6
    In: The ISME Journal, Springer Science and Business Media LLC, Vol. 15, No. 4 ( 2021-04), p. 1121-1135
    Abstract: Metagenome assembled genomes (MAGs) and single amplified genomes (SAGs) affiliated with two distinct Methanobacterium lineages were recovered from subsurface fracture waters of the Samail Ophiolite, Sultanate of Oman. Lineage Type I was abundant in waters with circumneutral pH, whereas lineage Type II was abundant in hydrogen rich, hyperalkaline waters. Type I encoded proteins to couple hydrogen oxidation to CO 2 reduction, typical of hydrogenotrophic methanogens. Surprisingly, Type II, which branched from the Type I lineage, lacked homologs of two key oxidative [NiFe]-hydrogenases. These functions were presumably replaced by formate dehydrogenases that oxidize formate to yield reductant and cytoplasmic CO 2 via a pathway that was unique among characterized Methanobacteria, allowing cells to overcome CO 2 /oxidant limitation in high pH waters. This prediction was supported by microcosm-based radiotracer experiments that showed significant biological methane generation from formate, but not bicarbonate, in waters where the Type II lineage was detected in highest relative abundance. Phylogenetic analyses and variability in gene content suggested that recent and ongoing diversification of the Type II lineage was enabled by gene transfer, loss, and transposition. These data indicate that selection imposed by CO 2 /oxidant availability drove recent methanogen diversification into hyperalkaline waters that are heavily impacted by serpentinization.
    Type of Medium: Online Resource
    ISSN: 1751-7362 , 1751-7370
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2299378-2
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  • 7
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2017
    In:  Proceedings of the National Academy of Sciences Vol. 114, No. 27 ( 2017-07-03), p. 6895-6903
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 114, No. 27 ( 2017-07-03), p. 6895-6903
    Abstract: 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. Furthermore, it has become apparent that much of this life is dependent on lithogenically sourced high-energy compounds to sustain productivity. A vast diversity of uncultivated microorganisms has been detected in subsurface environments, and we show that H 2 , CH 4 , and CO feature prominently in many of their predicted metabolisms. Despite 25 years of intense study, key questions remain on life in the deep subsurface, including whether it is endemic and the extent of its involvement in the anaerobic formation and degradation of hydrocarbons. Emergent data from cultivation and next-generation sequencing approaches continue to provide promising new hints to answer these questions. As Gold suggested, and as has become increasingly evident, to better understand the subsurface is critical to further understanding the Earth, life, the evolution of life, and the potential for life elsewhere. To this end, we suggest the need to develop a robust network of interdisciplinary scientists and accessible field sites for long-term monitoring of the Earth’s subsurface in the form of a deep subsurface microbiome initiative.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
    RVK:
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2017
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    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2022
    In:  Proceedings of the National Academy of Sciences Vol. 119, No. 42 ( 2022-10-18)
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 119, No. 42 ( 2022-10-18)
    Abstract: Little is known of acetogens in contemporary serpentinizing systems, despite widely supported theories that serpentinite-hosted environments supported the first life on Earth via acetogenesis. To address this knowledge gap, genome-resolved metagenomics was applied to subsurface fracture water communities from an area of active serpentinization in the Samail Ophiolite, Sultanate of Oman. Two deeply branching putative bacterial acetogen types were identified in the communities belonging to the Acetothermia (hereafter, types I and II) that exhibited distinct distributions among waters with lower and higher water–rock reaction (i.e., serpentinization influence), respectively. Metabolic reconstructions revealed contrasting core metabolic pathways of type I and II Acetothermia, including in acetogenic pathway components (e.g., bacterial- vs. archaeal-like carbon monoxide dehydrogenases [CODH], respectively), hydrogen use to drive acetogenesis, and chemiosmotic potential generation via respiratory (type I) or canonical acetogen ferredoxin-based complexes (type II). Notably, type II Acetothermia metabolic pathways allow for use of serpentinization-derived substrates and implicate them as key primary producers in contemporary hyperalkaline serpentinite environments. Phylogenomic analyses indicate that 1) archaeal-like CODH of the type II genomes and those of other serpentinite-associated Bacteria derive from a deeply rooted horizontal transfer or origin among archaeal methanogens and 2) Acetothermia are among the earliest evolving bacterial lineages. The discovery of dominant and early-branching acetogens in subsurface waters of the largest near-surface serpentinite formation provides insight into the physiological traits that likely facilitated rock-supported life to flourish on a primitive Earth and possibly on other rocky planets undergoing serpentinization.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
    RVK:
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2022
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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  • 9
    In: Journal of Geophysical Research: Biogeosciences, American Geophysical Union (AGU), Vol. 126, No. 10 ( 2021-10)
    Abstract: Highly serpentinized subsurface rocks exhibit steep redox gradients and host microbial cell abundances that vary 〉 6 orders of magnitude Low rates of microbial sulfate reduction in rock cores are inferred to result in optical darkening and sulfide overprinting of the mineralogy Widespread andradite garnet, abundant ferroan brucite, and rare carbonate are targets for future spatially resolved life‐detection efforts
    Type of Medium: Online Resource
    ISSN: 2169-8953 , 2169-8961
    Language: English
    Publisher: American Geophysical Union (AGU)
    Publication Date: 2021
    detail.hit.zdb_id: 3094167-2
    detail.hit.zdb_id: 2220777-6
    SSG: 16,13
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  • 10
    Online Resource
    Online Resource
    Frontiers Media SA ; 2023
    In:  Frontiers in Microbiology Vol. 14 ( 2023-7-3)
    In: Frontiers in Microbiology, Frontiers Media SA, Vol. 14 ( 2023-7-3)
    Abstract: Serpentinization reactions produce highly reduced waters that have hyperalkaline pH and that can have high concentrations of H 2 and CH 4 . Putatively autotrophic methanogenic archaea have been identified in the subsurface waters of the Samail Ophiolite, Sultanate of Oman, though the strategies to overcome hyperalkaline pH and dissolved inorganic carbon limitation remain to be fully understood. Here, we recovered metagenome assembled genomes (MAGs) and applied a metapangenomic approach to three different Methanobacterium populations to assess habitat-specific functional gene distribution. A Type I population was identified in the fluids with neutral pH, while a Type II and “Mixed” population were identified in the most hyperalkaline fluids (pH 11.63). The core genome of all Methanobacterium populations highlighted potential DNA scavenging techniques to overcome phosphate or nitrogen limitation induced by environmental conditions. With particular emphasis on the Mixed and Type II population found in the most hyperalkaline fluids, the accessory genomes unique to each population reflected adaptation mechanisms suggesting lifestyles that minimize niche overlap. In addition to previously reported metabolic capability to utilize formate as an electron donor and generate intracellular CO 2 , the Type II population possessed genes relevant to defense against antimicrobials and assimilating potential osmoprotectants to provide cellular stability. The accessory genome of the Mixed population was enriched in genes for multiple glycosyltransferases suggesting reduced energetic costs by adhering to mineral surfaces or to other microorganisms, and fostering a non-motile lifestyle. These results highlight the niche differentiation of distinct Methanobacterium populations to circumvent the challenges of serpentinization impacted fluids through coexistence strategies, supporting our ability to understand controls on methanogenic lifestyles and adaptations within the serpentinizing subsurface fluids of the Samail Ophiolite.
    Type of Medium: Online Resource
    ISSN: 1664-302X
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
    detail.hit.zdb_id: 2587354-4
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