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Hoffert M, Anderson RE, Reveillaud J, Murphy LG, Stepanauskas R, Huber JA. Genomic Variation Influences Methanothermococcus Fitness in Marine Hydrothermal Systems. Front Microbiol 2021; 12:714920. [PMID: 34489903 PMCID: PMC8417812 DOI: 10.3389/fmicb.2021.714920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/31/2021] [Indexed: 11/13/2022] Open
Abstract
Hydrogenotrophic methanogens are ubiquitous chemoautotrophic archaea inhabiting globally distributed deep-sea hydrothermal vent ecosystems and associated subseafloor niches within the rocky subseafloor, yet little is known about how they adapt and diversify in these habitats. To determine genomic variation and selection pressure within methanogenic populations at vents, we examined five Methanothermococcus single cell amplified genomes (SAGs) in conjunction with 15 metagenomes and 10 metatranscriptomes from venting fluids at two geochemically distinct hydrothermal vent fields on the Mid-Cayman Rise in the Caribbean Sea. We observed that some Methanothermococcus lineages and their transcripts were more abundant than others in individual vent sites, indicating differential fitness among lineages. The relative abundances of lineages represented by SAGs in each of the samples matched phylogenetic relationships based on single-copy universal genes, and genes related to nitrogen fixation and the CRISPR/Cas immune system were among those differentiating the clades. Lineages possessing these genes were less abundant than those missing that genomic region. Overall, patterns in nucleotide variation indicated that the population dynamics of Methanothermococcus were not governed by clonal expansions or selective sweeps, at least in the habitats and sampling times included in this study. Together, our results show that although specific lineages of Methanothermococcus co-exist in these habitats, some outcompete others, and possession of accessory metabolic functions does not necessarily provide a fitness advantage in these habitats in all conditions. This work highlights the power of combining single-cell, metagenomic, and metatranscriptomic datasets to determine how evolution shapes microbial abundance and diversity in hydrothermal vent ecosystems.
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Affiliation(s)
- Michael Hoffert
- Biology Department, Carleton College, Northfield, MN, United States.,Finch Therapeutics Group, Somerville, MA, United States
| | - Rika E Anderson
- Biology Department, Carleton College, Northfield, MN, United States
| | - Julie Reveillaud
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, University of Montpellier, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Institut de Recherche Pour le Développement, Montpellier, France
| | | | | | - Julie A Huber
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
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Grozeva NG, Klein F, Seewald JS, Sylva SP. Chemical and isotopic analyses of hydrocarbon-bearing fluid inclusions in olivine-rich rocks. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020; 378:20180431. [PMID: 31902341 PMCID: PMC7015310 DOI: 10.1098/rsta.2018.0431] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/30/2019] [Indexed: 06/10/2023]
Abstract
We examined the mineralogical, chemical and isotopic compositions of secondary fluid inclusions in olivine-rich rocks from two active serpentinization systems: the Von Damm hydrothermal field (Mid-Cayman Rise) and the Zambales ophiolite (Philippines). Peridotite, troctolite and gabbroic rocks in these systems contain abundant CH4-rich secondary inclusions in olivine, with less abundant inclusions in plagioclase and clinopyroxene. Olivine-hosted secondary inclusions are chiefly composed of CH4 and minor H2, in addition to secondary minerals including serpentine, brucite, magnetite and carbonates. Secondary inclusions in plagioclase are dominated by CH4 with variable amounts of H2 and H2O, while those in clinopyroxene contain only CH4. We determined hydrocarbon abundances and stable carbon isotope compositions by crushing whole rocks and analysing the released volatiles using isotope ratio monitoring-gas chromatography mass spectrometry. Bulk rock gas analyses yielded appreciable quantities of CH4 and C2H6 in samples from Cayman (4-313 nmol g-1 CH4 and 0.02-0.99 nmol g-1 C2H6), with lesser amounts in samples from Zambales (2-37 nmol g-1 CH4 and 0.004-0.082 nmol g-1 C2H6). Mafic and ultramafic rocks at Cayman exhibit δ13CCH4 values of -16.7‰ to -4.4‰ and δ13CC2H6 values of -20.3‰ to +0.7‰. Ultramafic rocks from Zambales exhibit δ13CCH4 values of -12.4‰ to -2.8‰ and δ13CC2H6 values of -1.2‰ to -0.9‰. Similarities in the carbon isotopic compositions of CH4 and C2H6 in plutonic rocks, Von Damm hydrothermal fluids, and Zambales gas seeps suggest that leaching of fluid inclusions may provide a significant contribution of abiotic hydrocarbons to deep-sea vent fluids and ophiolite-hosted gas seeps. Isotopic compositions of CH4 and C2H6 from a variety of hydrothermal fields hosted in olivine-rich rocks that are similar to those in Von Damm vent fluids further support the idea that a significant portion of abiotic hydrocarbons in ultramafic-influenced vent fluids is derived from fluid inclusions. This article is part of a discussion meeting issue 'Serpentinite in the Earth system'.
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Affiliation(s)
- Niya G. Grozeva
- Massachusetts Institute of Technology – Woods Hole Oceanographic Institution Joint Program in Oceanography, Cambridge, MA 02139, USA
| | - Frieder Klein
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Jeffrey S. Seewald
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Sean P. Sylva
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
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Haughton GA, Hayman NW, Searle RC, Le Bas T, Murton BJ. Volcanic-Tectonic Structure of the Mount Dent Oceanic Core Complex in the Ultraslow Mid-Cayman Spreading Center Determined From Detailed Seafloor Investigation. GEOCHEMISTRY, GEOPHYSICS, GEOSYSTEMS : G(3) 2019; 20:1298-1318. [PMID: 35860338 PMCID: PMC9285398 DOI: 10.1029/2018gc008032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/22/2019] [Accepted: 01/23/2019] [Indexed: 06/15/2023]
Abstract
The flanks of the ultraslow-spreading Mid-Cayman Spreading Center (MCSC) are characterized by domal massifs or oceanic core complexes (OCCs). The most prominent of these, Mount Dent, comprises lower-crustal and upper-mantle lithologies and hosts the Von Damm vent field ~12 km west of the axial deep. Here, presented autonomous underwater vehicle-derived swath sonar (multibeam) mapping and deep-towed side-scan sonar imagery lead to our interpretation that: (i) slip along the OCC-bounding detachment fault is ceasing, (ii) the termination zone, where detachment fault meets the hanging wall, is disintegrating, (iii) the domed surface of the OCC is cut by steep north-south extensional faulting, and (iv) the breakaway zone is cut by outward facing faults. The Von Damm vent field and dispersed pockmarks on the OCC's south flank further suggest that hydrothermal fluid flow is pervasive within the faulted OCC. On the axial floor of the MCSC, bright acoustic backscatter and multibeam bathymetry reveal: (v) a volcanic detachment hanging wall, (vi) a major fault rifting the southern flank of Mount Dent, and (vii) a young axial volcanic ridge intersecting its northern flank. These observations are described by a conceptual model wherein detachment faulting and OCC exhumation are ceasing during an increase in magmatic intrusion, brittle deformation, and hydrothermal circulation within the OCC. Together, this high-resolution view of the MCSC provides an instructive example of how OCCs, formed within an overall melt-starved ultraslow spreading center, can undergo magmatism, hydrothermal activity, and faulting in much the same way as expected in magmatically more robust slow-spreading centers elsewhere.
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Affiliation(s)
- G. A. Haughton
- School of Ocean and Earth SciencesUniversity of SouthamptonSouthamptonUK
| | - N. W. Hayman
- Institute for Geophysics, Jackson School for GeosciencesUniversity of TexasAustinTXUSA
| | - R. C. Searle
- Department of Earth SciencesDurham UniversityDurhamUK
| | - T. Le Bas
- National Oceanography CenterSouthamptonUK
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Bassez MP. Water near its Supercritical Point and at Alkaline pH for the Production of Ferric Oxides and Silicates in Anoxic Conditions. A New Hypothesis for the Synthesis of Minerals Observed in Banded Iron Formations and for the Related Geobiotropic Chemistry inside Fluid Inclusions. ORIGINS LIFE EVOL B 2018; 48:289-320. [PMID: 30091010 PMCID: PMC6244801 DOI: 10.1007/s11084-018-9560-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 06/24/2018] [Indexed: 11/27/2022]
Abstract
An alternative hypothesis for the origin of the banded iron formations and the synthesis of prebiotic molecules is presented here. I show the importance of considering water near its supercritical point and at alkaline pH. It is based on the chemical equation for the anoxic oxidation of ferrous iron into ferric iron at high-subcritical conditions of water and high pH, that I extract from E-pH diagrams drawn for corrosion purposes (Geophysical Research Abstracts Vol 15, EGU2013-22 Bassez 2013, Orig Life Evol Biosph 45(1):5-13, Bassez 2015, Procedia Earth Planet Sci 17, 492-495, Bassez 2017a, Orig Life Evol Biosph 47:453-480, Bassez 2017b). The sudden change in solubility of silica, SiO2, at the critical point of water is also considered. It is shown that under these temperatures and pressures, ferric oxides and ferric silicates can form in anoxic terrains. No FeII oxidation by UV light, neither by oxygen is needed to explain the minerals of the Banded Iron Formations. The intervention of any kind of microorganisms, either sulfate-reducing, or FeII-oxidizing or O2-producing, is not required. The chemical equation for the anoxic oxidation of ferrous iron is applied to the hydrolyses of fayalite, Fe2SiO4 and ferrosilite, FeSiO3. It is shown that the BIF minerals of the Hamersley Group, Western Australia, and the Transvaal Supergroup, South Africa, are those of fayalite and ferrosilite hydrolyses and carbonations. The dissolution of crustal fayalite and ferrosilite during water-rock interaction needs to occur at T&P just below the critical point of water and in a rising water which is undersaturated in SiO2. Minerals of BIFs which can then be ejected at the surface from venting arcs are ferric oxide hydroxides, hematite, FeIII-greenalite, siderite. The greenalite dehydrated product minnesotaite forms when rising water becomes supersaturated in SiO2, as also riebeckite and stilpnomelane. Long lengths of siderite without ferric oxides neither ferric silicates can occur since the exothermic siderite formation is not so much dependent in T&P. It is also shown that the H2 which is released during hydrolysis/oxidation of fayalite/ferrosilite can lead to components of life, such as macromolecules of amino acids which are synthesized from mixtures of (CO, N2, H2O) in Sabatier-Senderens/Fischer-Tropsch & Haber-Bosch reactions or microwave or gamma-ray excitation reactions. I propose that such geobiotropic synthesis may occur inside fluid inclusions of BIFs, in the silica chert, hematite, FeIII-greenalite or siderite. Therefore, the combination of high-subcritical conditions of water, high solubility of SiO2 at these T&P values, formation of CO also at these T&P, high pH and anoxic water, leads to the formation of ferric minerals and prebiotic molecules in the process of geobiotropy.
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Affiliation(s)
- Marie-Paule Bassez
- Institut de Technologie, Université de Strasbourg, 67400 Illkirch-Graffenstaden, Strasbourg, France.
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Amador ES, Bandfield JL, Brazelton WJ, Kelley D. The Lost City Hydrothermal Field: A Spectroscopic and Astrobiological Analogue for Nili Fossae, Mars. ASTROBIOLOGY 2017; 17:1138-1160. [PMID: 28910143 DOI: 10.1089/ast.2016.1606] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Low-temperature serpentinization is a critical process with respect to Earth's habitability and the Solar System. Exothermic serpentinization reactions commonly produce hydrogen as a direct by-product and typically produce short-chained organic compounds indirectly. Here, we present the spectral and mineralogical variability in rocks from the serpentine-driven Lost City Hydrothermal Field on Earth and the olivine-rich region of Nili Fossae on Mars. Near- and thermal-infrared spectral measurements were made from a suite of Lost City rocks at wavelengths similar to those for instruments collecting measurements of the martian surface. Results from Lost City show a spectrally distinguishable suite of Mg-rich serpentine, Ca carbonates, talc, and amphibole minerals. Aggregated detections of low-grade metamorphic minerals in rocks from Nili Fossae were mapped and yielded a previously undetected serpentine exposure in the region. Direct comparison of the two spectral suites indicates similar mineralogy at both Lost City and in the Noachian (4-3.7 Ga) bedrock of Nili Fossae, Mars. Based on mapping of these spectral phases, the implied mineralogical suite appears to be extensive across the region. These results suggest that serpentinization was once an active process, indicating that water and energy sources were available, as well as a means for prebiotic chemistry during a time period when life was first emerging on Earth. Although the mineralogical assemblages identified on Mars are unlikely to be directly analogous to rocks that underlie the Lost City Hydrothermal Field, related geochemical processes (and associated sources of biologically accessible energy) were once present in the subsurface, making Nili Fossae a compelling candidate for a once-habitable environment on Mars. Key Words: Mars-Habitability-Serpentinization-Analogue. Astrobiology 17, 1138-1160.
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Affiliation(s)
- Elena S Amador
- 1 Department of Earth and Space Sciences, University of Washington , Seattle, Washington
| | | | | | - Deborah Kelley
- 4 School of Oceanography, University of Washington , Seattle, Washington
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Anderson RE, Reveillaud J, Reddington E, Delmont TO, Eren AM, McDermott JM, Seewald JS, Huber JA. Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents. Nat Commun 2017; 8:1114. [PMID: 29066755 PMCID: PMC5655027 DOI: 10.1038/s41467-017-01228-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 08/30/2017] [Indexed: 02/01/2023] Open
Abstract
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.
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Affiliation(s)
- Rika E Anderson
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA.
- Department of Biology, Carleton College, Northfield, MN, 55057, USA.
| | - Julie Reveillaud
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Cirad UMR 117, Inra UMR 1309 ASTRE, Cirad Campus International de Baillarguet, Montpellier, France
| | - Emily Reddington
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Great Pond Foundation, Edgartown, MA, 02539, USA
| | - Tom O Delmont
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - A Murat Eren
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Jill M McDermott
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
- Department of Earth and Environmental Sciences, Lehigh University, Bethlehem, PA, 18015, USA
| | - Jeff S Seewald
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Julie A Huber
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
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