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  • 1
    Publication Date: 2022-05-25
    Description: Author Posting. © National Academy of Sciences, 2006. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 103 (2006): 3846-3851, doi:10.1073/pnas.0600035103.
    Description: Studies of deeply buried, sedimentary microbial communities and associated biogeochemical processes during Ocean Drilling Program Leg 201 showed elevated prokaryotic cell numbers in sediment layers where methane is consumed anaerobically at the expense of sulfate. Here, we show that extractable archaeal rRNA, selecting only for active community members in these ecosystems, is dominated by sequences of uncultivated Archaea affiliated with the Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group, whereas known methanotrophic Archaea are not detectable. Carbon flow reconstructions based on stable isotopic compositions of whole archaeal cells, intact archaeal membrane lipids, and other sedimentary carbon pools indicate that these Archaea assimilate sedimentary organic compounds other than methane even though methanotrophy accounts for a major fraction of carbon cycled in these ecosystems. Oxidation of methane by members of Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group without assimilation of methane–carbon provides a plausible explanation. Maintenance energies of these subsurface communities appear to be orders of magnitude lower than minimum values known from laboratory observations, and ecosystem-level carbon budgets suggest that community turnover times are on the order of 100–2,000 years. Our study provides clues about the metabolic functionality of two cosmopolitan groups of uncultured Archaea.
    Description: This work was supported by Deutsche Forschungsgemeinschaft (to J.S.L., R.A., M.E., and K.-U.H. at Research Center for Ocean Margins and Grant Hi 616/4 to K.U.-H.); National Aeronautics and Space Administration Astrobiology Institute Grants NNA04CC06A (to J.E.B. and C.H.H. at Pennsylvania State University), NCC 2-1275 (to M.A.L., K.G.L., K.B.S., H.F.F., A.T., and K.-U.H. at the University of Rhode Island), and NCC 2-1054 (to M.L.S. and A.T. at the Marine Biological Laboratory); the G. Unger Vetlesen Foundation; U.S. Department of Energy Grant DE-FG02-93ER20117; and NSF Grant MCB03-48492. J.F.B. was supported by NSF Integrative Graduate Education and Research Traineeship Program Grant DGE-9972759 and a Schlanger fellowship from the Joint Oceanographic Institutions (JOI). M.A.L. was supported in part by postcruise support from JOI.
    Keywords: Anaerobic methanotrophy ; Deep biosphere ; FISH–secondary ion MS ; Intact polar lipids ; Stable carbon isotopes
    Repository Name: Woods Hole Open Access Server
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  • 2
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author(s), 2014. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in FEMS Microbiology Ecology 91 (2015): 1-11, doi:10.1093/femsec/fiu016.
    Description: Environmental gradients generate countless ecological niches in deep-sea hydrothermal vent systems, which foster diverse microbial communities. The majority of distinct microbial lineages in these communities occur in very low abundance. However, the ecological role and distribution of rare and abundant lineages, particularly in deep, hot subsurface environments, remains unclear. Here, we use 16S rRNA tag sequencing to describe biogeographic patterning and microbial community structure of both rare and abundant archaea and bacteria in hydrothermal vent systems. We show that while rare archaeal lineages and almost all bacterial lineages displayed geographically restricted community structuring patterns, the abundant lineages of archaeal communities displayed a much more cosmopolitan distribution. Finally, analysis of one high-volume, high-temperature fluid sample representative of the deep hot biosphere described a unique microbial community that differed from microbial populations in diffuse flow fluid or sulfide samples, yet the rare thermophilic archaeal groups showed similarities to those that occur in sulfides. These results suggest that while most archaeal and bacterial lineages in vents are rare and display a highly regional distribution, a small percentage of lineages, particularly within the archaeal domain, are successful at widespread dispersal and colonization.
    Description: Funding for this work was provided by a grant from the NASA Astrobiology Institute to the Carnegie Institution of Washington.
    Description: 2015-12-05
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  • 3
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 1114, doi:10.1038/s41467-017-01228-6.
    Description: Little is known about evolutionary drivers of microbial populations in the warm subseafloor of deep-sea hydrothermal vents. Here we reconstruct 73 metagenome-assembled genomes (MAGs) from two geochemically distinct vent fields in the Mid-Cayman Rise to investigate patterns of genomic variation within subseafloor populations. Low-abundance populations with high intra-population diversity coexist alongside high-abundance populations with low genomic diversity, with taxonomic differences in patterns of genomic variation between the mafic Piccard and ultramafic Von Damm vent fields. Populations from Piccard are significantly enriched in nonsynonymous mutations, suggesting stronger purifying selection in Von Damm relative to Piccard. Comparison of nine Sulfurovum MAGs reveals two high-coverage, low-diversity MAGs from Piccard enriched in unique genes related to the cellular membrane, suggesting these populations were subject to distinct evolutionary pressures that may correlate with genes related to nutrient uptake, biofilm formation, or viral invasion. These results are consistent with distinct evolutionary histories between geochemically different vent fields, with implications for understanding evolutionary processes in subseafloor microbial populations.
    Description: R.E.A. was supported by a NASA Postdoctoral Fellowship with the NASA Astrobiology Institute. This work was supported by a NASA Astrobiology Science and Technology for Exploring Planets (ASTEP) grant NNX-327 09AB75G and a grant from Deep Carbon Observatory's Deep Life Initiative to J.A.H. and J.S.S., and the NSF Science and Technology Center for Dark Energy Biosphere Investigations (C-DEBI). Ship and vehicle time in 2012 was supported by the NSF-OCE grant OCE-1061863 to J.S.S.
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  • 4
    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Marlow, J., Anderson, R., Reysenbach, A.-L., Seewald, J., Shank, T., Teske, A., Wanless, V., & Soule, S. New opportunities and untapped scientific potential in the abyssal ocean. Frontiers in Marine Science, 8, (2022): 798943, https://doi.org/10.3389./fmars.2021.798943
    Description: The abyssal ocean covers more than half of the Earth’s surface, yet remains understudied and underappreciated. In this Perspectives article, we mark the occasion of the Deep Submergence Vehicle Alvin’s increased depth range (from 4500 to 6500 m) to highlight the scientific potential of the abyssal seafloor. From a geologic perspective, ultra-slow spreading mid-ocean ridges, Petit Spot volcanism, transform faults, and subduction zones put the full life cycle of oceanic crust on display in the abyss, revealing constructive and destructive forces over wide ranges in time and space. Geochemically, the abyssal pressure regime influences the solubility of constituents such as silica and carbonate, and extremely high-temperature fluid-rock reactions in the shallow subsurface lead to distinctive and potentially unique geochemical profiles. Microbial residents range from low-abundance, low-energy communities on the abyssal plains to fast growing thermophiles at hydrothermal vents. Given its spatial extent and position as an intermediate zone between coastal and deep hadal settings, the abyss represents a lynchpin in global-scale processes such as nutrient and energy flux, population structure, and biogeographic diversity. Taken together, the abyssal ocean contributes critical ecosystem services while facing acute and diffuse anthropogenic threats from deep-sea mining, pollution, and climate change.
    Description: We would like to thank the National Science Foundation for their support through grants NSF 2009117 and 2129431 to SAS.
    Keywords: Abyssal ocean ; Geochemistry ; Microbiology ; Geology ; Ecology
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  • 5
    Publication Date: 2022-05-26
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 6 (2018): 19, doi:10.1186/s40168-018-0411-x.
    Description: The microbial endosymbionts of two species of vestimentiferan tubeworms (Escarpia sp. and Lamellibrachia sp.2) collected from an area of low-temperature hydrothermal diffuse vent flow at the Mid-Cayman Rise (MCR) in the Caribbean Sea were characterized using microscopy, phylogenetic analyses, and a metagenomic approach. Bacteria, with a typical Gram negative cell envelope contained within membrane-bound vacuoles, were observed within the trophosome of both tubeworm species. Phylogenetic analysis of the 16S rRNA gene and ITS region suggested MCR individuals harbored highly similar endosymbionts that were 〉 98% identical, with the exception of two symbionts that showed a 60 bp insertion within the ITS region. All sequences from MCR endosymbionts formed a separate well-supported clade that diverged from those of symbionts of seep and vent vestimentiferans from the Pacific, Gulf of Mexico, and Mediterranean Sea. The metagenomes of the symbionts of two specimens of each tubeworm species were sequenced, and two distinct Gammaproteobacteria metagenome-assembled genomes (MAGs) of more than 4 Mbp assembled. An Average Nucleotide Identity (ANI) of 86.5% between these MAGs, together with distinct 16S rRNA gene and ITS sequences, indicate the presence of multiple endosymbiont phylotypes at the MCR, with one MAG shared between one Escarpia and two Lamellibrachia individuals, indicating these endosymbionts are not specific to either host species. Genes for sulfur and hydrogen oxidation, nitrate reduction (assimilatory and dissimilatory), glycolysis and the Krebs cycle, peptide, sugar, and lipid transporters, and both rTCA and CBB carbon fixation cycles were detected in the MAGs, highlighting key and shared functions with symbiont metagenomes of the vestimentiferans Riftia, Tevnia, and Ridgeia from the Pacific. The potential for a second hydrogen oxidation pathway (via a bidirectional hydrogenase), formate dehydrogenase, a catalase, and several additional peptide transporters were found exclusively in the MCR endosymbiont MAGs. The present study adds new evidence that tubeworm endosymbionts can potentially switch from autotrophic to heterotrophic metabolism, or may be mixotrophic, presumably while free-living, and also suggests their versatile metabolic potential may enable both the host and symbionts to exploit a wide range of environmental conditions. Together, the marked gene content and sequence dissimilarity at the rRNA operon and whole genome level between vent and seep symbionts suggest these newly described endosymbionts from the MCR belong to a novel tubeworm endosymbiont genera, introduced as Candidatus Vondammii.
    Description: This work was supported by a NASA Astrobiology Science and Technology for Exploring Planets (ASTEP) grant NNX-32709AB75G to JAH, a grant from the Deep Carbon Observatory’s Deep Life Initiative to JAH, the NSF Science and Technology Center for Dark Energy Biosphere Investigations (C-DEBI contribution 412) and a mobility research grant from GDR3692 'Génomique environnementale' to JR. Ship and vehicle time was supported by NSF-OCE grant OCE-1061863 to colleagues Chris German and Jeff Seewald.
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  • 6
    Publication Date: 2022-12-06
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Anderson, R., Graham, E., Huber, J., & Tully, B. Microbial populations are shaped by dispersal and recombination in a low biomass subseafloor habitat. MBio, 13(4), (2022): e0035422, https://doi.org/10.1128/mbio.00354-22.
    Description: The subseafloor is a vast habitat that supports microorganisms that have a global scale impact on geochemical cycles. Many of the endemic microbial communities inhabiting the subseafloor consist of small populations under growth-limited conditions. For small populations, stochastic evolutionary events can have large impacts on intraspecific population dynamics and allele frequencies. These conditions are fundamentally different from those experienced by most microorganisms in surface environments, and it is unknown how small population sizes and growth-limiting conditions influence evolution and population structure in the subsurface. Using a 2-year, high-resolution environmental time series, we examine the dynamics of microbial populations from cold, oxic crustal fluids collected from the subseafloor site North Pond, located near the mid-Atlantic ridge. Our results reveal rapid shifts in overall abundance, allele frequency, and strain abundance across the time points observed, with evidence for homologous recombination between coexisting lineages. We show that the subseafloor aquifer is a dynamic habitat that hosts microbial metapopulations that disperse frequently through the crustal fluids, enabling gene flow and recombination between microbial populations. The dynamism and stochasticity of microbial population dynamics in North Pond suggest that these forces are important drivers in the evolution of microbial populations in the vast subseafloor habitat.
    Description: This work was supported by NSF OCE-1062006, OCE-1745589, and OCE-1635208 to J.A.H. The Gordon and Betty Moore Foundation sponsored observatory components at North Pond through grant GBMF1609. The Center for Dark Energy Biosphere Investigations (C-DEBI) (OCE-0939564) supported J.A.H. and B.J.T. This is C-DEBI contribution 598.
    Keywords: Microbial evolution ; Subseafloor ; Allele frequency ; Dispersal
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  • 7
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e109696, doi:10.1371/journal.pone.0109696.
    Description: The deep-sea hydrothermal vent habitat hosts a diverse community of archaea and bacteria that withstand extreme fluctuations in environmental conditions. Abundant viruses in these systems, a high proportion of which are lysogenic, must also withstand these environmental extremes. Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, collected by size fractionation of high temperature fluids from a diffuse flow hydrothermal vent. We detected a high enrichment of mobile elements and proviruses in the cellular fraction relative to microorganisms in other environments. We observed a relatively high abundance of genes related to energy metabolism as well as cofactors and vitamins in the viral fraction compared to the cellular fraction, which suggest encoding of auxiliary metabolic genes on viral genomes. Moreover, the observation of stronger purifying selection in the viral versus cellular gene pool suggests viral strategies that promote prolonged host integration. Our results demonstrate that there is great potential for hydrothermal vent viruses to integrate into hosts, facilitate horizontal gene transfer, and express or transfer genes that manipulate the hosts’ functional capabilities.
    Description: Funding for sequencing of the viral metagenome was provided by the Gordon and Betty Moore Foundation. All other funding was provided by a NASA Astrobiology Institute grant through Cooperative Agreement NNA04CC09A to the Geophysical Laboratory at the Carnegie Institution for Science. R.A. was funded by a NSF Graduate Research Fellowship through NSF grant number DGE-0718124, an NSF IGERT grant to the University of Washington Astrobiology Program, and the ARCS Foundation.
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  • 8
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Thomas, E., Anderson, R. E., Li, V., Rogan, L. J., & Huber, J. A. Diverse viruses in deep-sea hydrothermal vent fluids have restricted dispersal across ocean basins. Msystems, 6(3), (2021): e00068-21, https://doi.org/10.1128/mSystems.00068-21.
    Description: In the ocean, viruses impact microbial mortality, regulate biogeochemical cycling, and alter the metabolic potential of microbial lineages. At deep-sea hydrothermal vents, abundant viruses infect a wide range of hosts among the archaea and bacteria that inhabit these dynamic habitats. However, little is known about viral diversity, host range, and biogeography across different vent ecosystems, which has important implications for how viruses manipulate microbial function and evolution. Here, we examined viral diversity, viral and host distribution, and virus-host interactions in microbial metagenomes generated from venting fluids from several vent sites within three different geochemically and geographically distinct hydrothermal systems: Piccard and Von Damm vent fields at the Mid-Cayman Rise in the Caribbean Sea, and at several vent sites within Axial Seamount in the Pacific Ocean. Analysis of viral sequences and clustered regularly interspaced short palindromic repeat (CRISPR) spacers revealed highly diverse viral assemblages and evidence of active infection. Network analysis revealed that viral host range was relatively narrow, with very few viruses infecting multiple microbial lineages. Viruses were largely endemic to individual vent sites, indicating restricted dispersal, and in some cases, viral assemblages persisted over time. Thus, we show that hydrothermal vent fluids are home to novel, diverse viral assemblages that are highly localized to specific regions and taxa.
    Description: Funding for E.T. was provided by Carleton College. R.E.A. was supported by a NASA Postdoctoral Fellowship with the NASA Astrobiology Institute. This work was supported by a NASA Exobiology grant 80NSSC18K1076 to R.E.A. and J.A.H., a NASA Astrobiology Science and Technology for Exploring Planets (ASTEP) grant NNX-327 09AB75G, and a grant from Deep Carbon Observatory's Deep Life Initiative to J.A.H., the NSF Science and Technology Center for Dark Energy Biosphere Investigations (C-DEBI) to J.A.H., and the Gordon and Betty Moore Foundation grant GBMF3297 to J.A.H. Samples were collected from the Mid-Cayman Rise with the assistance of the captains and crew of the R/V Atlantis and R/V Falkor as well as ROVs Jason and Nereus. For Mid-Cayman Rise, ship and vehicle time in 2012 were supported by the NSF-OCE grant OCE-1061863 to Chris German and Jeff Seewald and in 2013 by the Schmidt Ocean Institute during cruise FX008-2013 aboard the R/V Falkor. Samples collected from Axial Seamount were collected with the assistance of the captains and crew of the R/V Falkor, R/V Thompson, and R/V Brown as well as the ROV ROPOS and Jason groups, and in 2013 the Schmidt Ocean Institute during cruise FK010-2013 aboard the R/V Falkor.
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  • 9
    Publication Date: 2023-02-25
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Brazelton, W. J., McGonigle, J. M., Motamedi, S., Pendleton, H. L., Twing, K. I., Miller, B. C., Lowe, W. J., Hoffman, A. M., Prator, C. A., Chadwick, G. L., Anderson, R. E., Thomas, E., Butterfield, D. A., Aquino, K. A., Fruh-Green, G. L., Schrenk, M. O., & Lang, S. Q. Metabolic strategies shared by basement residents of the lost city hydrothermal field. Applied and Environmental Microbiology, 88(17), (2022): e00929-22, https://doi.org/10.1128/aem.00929-22.
    Description: Alkaline fluids venting from chimneys of the Lost City hydrothermal field flow from a potentially vast microbial habitat within the seafloor where energy and organic molecules are released by chemical reactions within rocks uplifted from Earth’s mantle. In this study, we investigated hydrothermal fluids venting from Lost City chimneys as windows into subseafloor environments where the products of geochemical reactions, such as molecular hydrogen (H2), formate, and methane, may be the only available sources of energy for biological activity. Our deep sequencing of metagenomes and metatranscriptomes from these hydrothermal fluids revealed a few key species of archaea and bacteria that are likely to play critical roles in the subseafloor microbial ecosystem. We identified a population of Thermodesulfovibrionales (belonging to phylum Nitrospirota) as a prevalent sulfate-reducing bacterium that may be responsible for much of the consumption of H2 and sulfate in Lost City fluids. Metagenome-assembled genomes (MAGs) classified as Methanosarcinaceae and Candidatus Bipolaricaulota were also recovered from venting fluids and represent potential methanogenic and acetogenic members of the subseafloor ecosystem. These genomes share novel hydrogenases and formate dehydrogenase-like sequences that may be unique to hydrothermal environments where H2 and formate are much more abundant than carbon dioxide. The results of this study include multiple examples of metabolic strategies that appear to be advantageous in hydrothermal and subsurface alkaline environments where energy and carbon are provided by geochemical reactions.
    Description: This work was supported by NSF awards to W.J.B. and S.Q.L. (OCE-1536702/1536405), the NASA Astrobiology Institute Rock-Powered Life team, a NASA Postdoctoral fellowship to J.M.M., the Swiss National Science Foundation, and the Deep Carbon Observatory.
    Keywords: Acetogenesis ; Formate ; Hydrogenase ; Hydrothermal ; Metagenomics ; Methanogenesis ; Serpentinization ; Sulfate reduction
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  • 10
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Moulana, A., Anderson, R. E., Fortunato, C. S., & Huber, J. A. Selection is a significant driver of gene gain and loss in the pangenome of the bacterial genus Sulfurovum in geographically distinct deep-sea hydrothermal vents. Msystems, 5(2), (2020): e00673-19, doi:10.1128/mSystems.00673-19.
    Description: Microbial genomes have highly variable gene content, and the evolutionary history of microbial populations is shaped by gene gain and loss mediated by horizontal gene transfer and selection. To evaluate the influence of selection on gene content variation in hydrothermal vent microbial populations, we examined 22 metagenome-assembled genomes (MAGs) (70 to 97% complete) from the ubiquitous vent Epsilonbacteraeota genus Sulfurovum that were recovered from two deep-sea hydrothermal vent regions, Axial Seamount in the northeastern Pacific Ocean (13 MAGs) and the Mid-Cayman Rise in the Caribbean Sea (9 MAGs). Genes involved in housekeeping functions were highly conserved across Sulfurovum lineages. However, genes involved in environment-specific functions, and in particular phosphate regulation, were found mostly in Sulfurovum genomes from the Mid-Cayman Rise in the low-phosphate Atlantic Ocean environment, suggesting that nutrient limitation is an important selective pressure for these bacteria. Furthermore, genes that were rare within the pangenome were more likely to undergo positive selection than genes that were highly conserved in the pangenome, and they also appeared to have experienced gene-specific sweeps. Our results suggest that selection is a significant driver of gene gain and loss for dominant microbial lineages in hydrothermal vents and highlight the importance of factors like nutrient limitation in driving microbial adaptation and evolution.
    Description: We thank Julie Reveillaud and Emily Reddington for support in the collection and generation of metagenomic data, Chip Breier, David Butterfield, Bill Chadwick, Chris German, Jim Holden, Jill McDermott, and Jeff Seewald for sample collection support at sea, and Jaclyn Saunders for discussions regarding arsenate reductase. A.M. was supported by Carleton College. R.A. was supported by a NASA Postdoctoral Fellowship with the NASA Astrobiology Institute. This work was supported by a NASA Exobiology grant 80NSSC18K1076 to R.A. and J.A.H., a NASA Astrobiology Science and Technology for Exploring Planets (ASTEP) grant NNX-327 09AB75G and a grant from Deep Carbon Observatory’s Deep Life Initiative to J.A.H., the NSF Science and Technology Center for Dark Energy Biosphere Investigations (C-DEBI) to J.A.H., and the Gordon and Betty Moore Foundation grant GBMF3297 to J.A.H. Samples were collected from the Mid-Cayman Rise with the assistance of the captains and crew of the R/V Atlantis and R/V Falkor as well as ROVs Jason and Nereus. For Mid-Cayman Rise, ship and vehicle time in 2012 were supported by the NSF-OCE great OCE-1061863 to Chris German and Jeff Seewald and in 2013 by the Schmidt Ocean Institute during cruise FK008-2013 aboard the R/V Falkor. Samples collected from Axial Seamount were collected with the assistance of the captains and crew of the R/V Falkor, R/V Thompson, and R/V Brown as well as the ROV ROPOS and Jason groups, and in 2013 the Schmidt Ocean Institute during cruise FK010-2013 aboard the R/V Falkor.
    Keywords: Hydrothermal vents ; Metagenomics ; Pangenome
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