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  • 1
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Evidence is growing that hydrothermal venting occurs not only along mid-ocean ridges but also on old regions of the oceanic crust away from spreading centres. Here we report the discovery of an extensive hydrothermal field at 30° N near the eastern intersection of the Mid-Atlantic Ridge ...
    Type of Medium: Electronic Resource
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  • 2
    Publication Date: 2023-03-14
    Description: Table 1 shows biogeochemical data collected from five depths in the CSW1.1 well at the Coast Range Ophiolite Microbial Observatory, California, USA during a one-day sampling event in June 2016. Included are latitude and longitude of the CSW1.1 well, depth each sample was collected, oxygen level and other water quality parameters such as pH, temperature, and oxidation reduction potential. Hydrogen sulfide was measured via spectrophotometric methods, and anions were measured using ion chromatography. Dissolved gases were measured using a gas chromatograph with a flame ionization detector. Data was collected to understand the fluid chemistry in this well that is quite extreme relative to typical waters at Earth's surface and used to inform both Gibbs energy calculations and microbiological analyses.
    Keywords: alkaliphiles; biogeochemical gradients; Bromide; California, USA; Carbon, inorganic, dissolved; Carbon monoxide; Chloride; CO2 sequestration; Conductivity, electrical; CROMO_CSW1.1; CSW1.1; Depth, well; depth profile; Gas chromatography - Flame Ionization Detection (GC-FID); gas flux; groundwater; Hydrogen; hydrogenotrophy; Hydrogen sulfide; Ion chromatography; Methane; Nitrate; Nitrite; Oxidation reduction (RedOx) potential; Oxygen; pH; Saturation; Serpentinization; Spectrophotometric; Sulfate; Temperature, water; Water sample; WS
    Type: Dataset
    Format: text/tab-separated-values, 85 data points
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  • 3
    Publication Date: 2024-04-20
    Description: We have measured microbial sulfate reduction rates by ultra sensitive radio tracer incubations in fluids from 11 wells of the actively serpentinizing the Coast Range ophiolite (CA, USA) and Samail ophiolite (Oman). We also determined environmental parameter of the serpentinizing fluids (pH, redox potential and chloride, sulfate, hydrogen, methane and organic acid conentrations. We also determiend the abundance of sulfate reducing taxa in the these fluids.
    Keywords: Binary Object; California_Coast_Ranges; California, USA; Coast_Range_Ophiolite; File content; Oman; ophiolites; radio-tracer; Semail_Oman; Semail_Ophiolite; Serpentinization; Sulfate reducing bacteria abundance; sulfate reduction rates
    Type: Dataset
    Format: text/tab-separated-values, 12 data points
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  • 4
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 9 (2018): 840, doi:10.3389/fmicb.2018.00840.
    Description: Earth’s subsurface environment is one of the largest, yet least studied, biomes on Earth, and many questions remain regarding what microorganisms are indigenous to the subsurface. Through the activity of the Census of Deep Life (CoDL) and the Deep Carbon Observatory, an open access 16S ribosomal RNA gene sequence database from diverse subsurface environments has been compiled. However, due to low quantities of biomass in the deep subsurface, the potential for incorporation of contaminants from reagents used during sample collection, processing, and/or sequencing is high. Thus, to understand the ecology of subsurface microorganisms (i.e., the distribution, richness, or survival), it is necessary to minimize, identify, and remove contaminant sequences that will skew the relative abundances of all taxa in the sample. In this meta-analysis, we identify putative contaminants associated with the CoDL dataset, recommend best practices for removing contaminants from samples, and propose a series of best practices for subsurface microbiology sampling. The most abundant putative contaminant genera observed, independent of evenness across samples, were Propionibacterium, Aquabacterium, Ralstonia, and Acinetobacter. While the top five most frequently observed genera were Pseudomonas, Propionibacterium, Acinetobacter, Ralstonia, and Sphingomonas. The majority of the most frequently observed genera (high evenness) were associated with reagent or potential human contamination. Additionally, in DNA extraction blanks, we observed potential archaeal contaminants, including methanogens, which have not been discussed in previous contamination studies. Such contaminants would directly affect the interpretation of subsurface molecular studies, as methanogenesis is an important subsurface biogeochemical process. Utilizing previously identified contaminant genera, we found that ∼27% of the total dataset were identified as contaminant sequences that likely originate from DNA extraction and DNA cleanup methods. Thus, controls must be taken at every step of the collection and processing procedure when working with low biomass environments such as, but not limited to, portions of Earth’s deep subsurface. Taken together, we stress that the CoDL dataset is an incredible resource for the broader research community interested in subsurface life, and steps to remove contamination derived sequences must be taken prior to using this dataset.
    Description: We wish to acknowledge the support of the Sloan Foundation and the Deep Carbon Observatory and the Department of Energy, Office of Fossil Energy (Colwell).
    Keywords: 16S rRNA ; Contamination ; Microbial survey ; Census of Deep Life ; Deep subsurface
    Repository Name: Woods Hole Open Access Server
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  • 5
    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 McGlynn, S. E., Glass, J. B., Johnson-Finn, K., Klein, F., Sanden, S. A., Schrenk, M. O., Ueno, Y., & Vitale-Brovarone, A. Hydrogenation reactions of carbon on Earth: linking methane, margarine, and life. American Mineralogist, 105(5), (2020): 599-608, doi:10.2138/am-2020-6928CCBYNCND.
    Description: Hydrogenation reactions are a major route of electron and proton flow on Earth. Interfacing geology and organic chemistry, hydrogenations occupy pivotal points in the Earth’s global geochemical cycles. Some examples of hydrogenation reactions on Earth today include the production and consumption of methane in both abiotic and biotic reactions, the reduction of protons in hydrothermal settings, and the biological synthesis and degradation of fatty acids. Hydrogenation reactions were likely important for prebiotic chemistry on the early Earth, and today serve as one of the fundamental reaction classes that enable cellular life to construct biomolecules. An understanding and awareness of hydrogenation reactions is helpful for comprehending the larger web of molecular and material inter-conversions on our planet. In this brief review we detail some important hydrogenation and dehydrogenation reactions as they relate to geology, biology, industry, and atmospheric chemistry. Such reactions have implications ranging from the suite of reactions on early Earth to industrial applications like the production of hydrocarbon fuel.
    Description: S.E.M. is supported by NSF Award 1724300 and JSPS KAKENHI Grant JP18H01325. A.V.B. is supported by ANR T-ERC, CNRS INSU-SYSTER, and Rita Levi Montalcini by MIUR. J.B.G. is supported by NASA Exobiology Grant NNX14AJ87G and 80NSSC19K0477. F.K. is supported by NSF-OCE award 1634032 and 1427274. M.O.S. is supported by the NASA Astrobiology Institute Rock-Powered Life Grant NNA15BB02A.
    Keywords: Hydrogenation ; Hydrogen ; Methane ; Carbon dioxide ; Carbon monoxide ; Redox ; Reduction ; Oxidation ; Earth in Five Reactions: A Deep Carbon Perspective
    Repository Name: Woods Hole Open Access Server
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  • 6
    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 Barry, P. H., De Moor, J. M., Chiodi, A., Aguilera, F., Hudak, M. R., Bekaert, D. V., Turner, S. J., Curtice, J., Seltzer, A. M., Jessen, G. L., Osses, E., Blamey, J. M., Amenabar, M. J., Selci, M., Cascone, M., Bastianoni, A., Nakagawa, M., Filipovich, R., Bustos, E., Schrenk, M. O. , Buongiorno, J., Ramírez, C. J., Rogers, T. J., Lloyd, K. G. & Giovannelli, D. The helium and carbon isotope characteristics of the Andean Convergent Margin. Frontiers in Earth Science, 10, (2022): 897267, https://doi.org/10.3389/feart.2022.897267.
    Description: Subduction zones represent the interface between Earth’s interior (crust and mantle) and exterior (atmosphere and oceans), where carbon and other volatile elements are actively cycled between Earth reservoirs by plate tectonics. Helium is a sensitive tracer of volatile sources and can be used to deconvolute mantle and crustal sources in arcs; however it is not thought to be recycled into the mantle by subduction processes. In contrast, carbon is readily recycled, mostly in the form of carbon-rich sediments, and can thus be used to understand volatile delivery via subduction. Further, carbon is chemically-reactive and isotope fractionation can be used to determine the main processes controlling volatile movements within arc systems. Here, we report helium isotope and abundance data for 42 deeply-sourced fluid and gas samples from the Central Volcanic Zone (CVZ) and Southern Volcanic Zone (SVZ) of the Andean Convergent Margin (ACM). Data are used to assess the influence of subduction parameters (e.g., crustal thickness, subduction inputs, and convergence rate) on the composition of volatiles in surface volcanic fluid and gas emissions. He isotopes from the CVZ backarc range from 0.1 to 2.6 RA (n = 23), with the highest values in the Puna and the lowest in the Sub-Andean foreland fold-and-thrust belt. Atmosphere-corrected He isotopes from the SVZ range from 0.7 to 5.0 RA (n = 19). Taken together, these data reveal a clear southeastward increase in 3He/4He, with the highest values (in the SVZ) falling below the nominal range associated with pure upper mantle helium (8 ± 1 RA), approaching the mean He isotope value for arc gases of (5.4 ± 1.9 RA). Notably, the lowest values are found in the CVZ, suggesting more significant crustal inputs (i.e., assimilation of 4He) to the helium budget. The crustal thickness in the CVZ (up to 70 km) is significantly larger than in the SVZ, where it is just ∼40 km. We suggest that crustal thickness exerts a primary control on the extent of fluid-crust interaction, as helium and other volatiles rise through the upper plate in the ACM. We also report carbon isotopes from (n = 11) sites in the CVZ, where δ13C varies between −15.3‰ and −1.2‰ [vs. Vienna Pee Dee Belemnite (VPDB)] and CO2/3He values that vary by over two orders of magnitude (6.9 × 108–1.7 × 1011). In the SVZ, carbon isotope ratios are also reported from (n = 13) sites and vary between −17.2‰ and −4.1‰. CO2/3He values vary by over four orders of magnitude (4.7 × 107–1.7 × 1012). Low δ13C and CO2/3He values are consistent with CO2 removal (e.g., calcite precipitation and gas dissolution) in shallow hydrothermal systems. Carbon isotope fractionation modeling suggests that calcite precipitation occurs at temperatures coincident with the upper temperature limit for life (122°C), suggesting that biology may play a role in C-He systematics of arc-related volcanic fluid and gas emissions.
    Description: This work was principally supported by the NSF-FRES award 2121637 to PB, KL, and JM. Field work was also supported by award G-2016-7206 from the Alfred P. Sloan Foundation and the Deep Carbon Observatory to PB, KL, DG, and JM. Additional support came from The National Fund for Scientific and Technological Development of Chile (FONDECYT) Grant 11191138 (The National Research and Development Agency of Chile, ANID Chile), and COPAS COASTAL ANID FB210021 to GJ. DG was partially supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program Grant Agreement No. 948972—COEVOLVE—ERC-2020-STG.
    Keywords: Helium ; Carbon ; SVZ ; CVZ ; Andes (Argentina and Chile)
    Repository Name: Woods Hole Open Access Server
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  • 7
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bekaert, D. V., Gazel, E., Turner, S., Behn, M. D., de Moor, J. M., Zahirovic, S., Manea, V. C., Hoernle, K., Fischer, T. P., Hammerstrom, A., Seltzer, A. M., Kulongoski, J. T., Patel, B. S., Schrenk, M. O., Halldórsson, S. A., Nakagawa, M., Ramírez, C. J., Krantz, J. A., Yücel, M., Ballentine, C. J., Giovannelli, D., Lloyd, K. G., Barry, P. H. High (3)He/(4)He in central Panama reveals a distal connection to the Galápagos plume. Proceedings of the National Academy of Sciences of the United States of America, 118(47), (2021): e2110997118, https://doi.org/10.1073/pnas.2110997118.
    Description: It is well established that mantle plumes are the main conduits for upwelling geochemically enriched material from Earth's deep interior. The fashion and extent to which lateral flow processes at shallow depths may disperse enriched mantle material far (〉1,000 km) from vertical plume conduits, however, remain poorly constrained. Here, we report He and C isotope data from 65 hydrothermal fluids from the southern Central America Margin (CAM) which reveal strikingly high 3He/4He (up to 8.9RA) in low-temperature (≤50 °C) geothermal springs of central Panama that are not associated with active volcanism. Following radiogenic correction, these data imply a mantle source 3He/4He 〉10.3RA (and potentially up to 26RA, similar to Galápagos hotspot lavas) markedly greater than the upper mantle range (8 ± 1RA). Lava geochemistry (Pb isotopes, Nb/U, and Ce/Pb) and geophysical constraints show that high 3He/4He values in central Panama are likely derived from the infiltration of a Galápagos plume–like mantle through a slab window that opened ∼8 Mya. Two potential transport mechanisms can explain the connection between the Galápagos plume and the slab window: 1) sublithospheric transport of Galápagos plume material channeled by lithosphere thinning along the Panama Fracture Zone or 2) active upwelling of Galápagos plume material blown by a “mantle wind” toward the CAM. We present a model of global mantle flow that supports the second mechanism, whereby most of the eastward transport of Galápagos plume material occurs in the shallow asthenosphere. These findings underscore the potential for lateral mantle flow to transport mantle geochemical heterogeneities thousands of kilometers away from plume conduits.
    Description: This work was principally supported by Grant G-2016-7206 from the Alfred P. Sloan Foundation and the Deep Carbon Observatory to P.H.B. We also acknowledge the NSF awards (1144559, 1923915, and 2015789) to P.H.B., which partially supported this work. S.Z. was supported by the Australian Research Council Grant DE210100084 and a University of Sydney Robinson Fellowship. D.G. was partially supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program Grant Agreement No. 948972—COEVOLVE—ERC-2020-STG. This study was also supported in part by NSF award No. EAR 1826673 to E.G. Folkmar Hauff is acknowledged for contributing to the analysis of the La Providencia samples at GEOMAR.
    Keywords: Helium ; Mantle plume ; Slab window ; Mantle flow ; Geochemistry
    Repository Name: Woods Hole Open Access Server
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  • 8
    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
    Repository Name: Woods Hole Open Access Server
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  • 9
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Barry, P. H., Nakagawa, M., Giovannelli, D., de Moor, J. M., Schrenk, M., Seltzer, A. M., Manini, E., Fattorini, D., di Carlo, M., Regoli, F., Fullerton, K., & Lloyd, K. G. Helium, inorganic and organic carbon isotopes of fluids and gases across the Costa Rica convergent margin. Scientific Data, 6(1), (2019): 284, doi: 10.1038/s41597-019-0302-4.
    Description: In 2017, fluid and gas samples were collected across the Costa Rican Arc. He and Ne isotopes, C isotopes as well as total organic and inorganic carbon concentrations were measured. The samples (n = 24) from 2017 are accompanied by (n = 17) samples collected in 2008, 2010 and 2012. He-isotopes ranged from arc-like (6.8 RA) to crustal (0.5 RA). Measured dissolved inorganic carbon (DIC) δ13CVPDB values varied from 3.55 to −21.57‰, with dissolved organic carbon (DOC) following the trends of DIC. Gas phase CO2 only occurs within ~20 km of the arc; δ13CVPDB values varied from −0.84 to −5.23‰. Onsite, pH, conductivity, temperature and dissolved oxygen (DO) were measured; pH ranged from 0.9–10.0, conductivity from 200–91,900 μS/cm, temperatures from 23–89 °C and DO from 2–84%. Data were used to develop a model which suggests that ~91 ± 4.0% of carbon released from the slab/mantle beneath the Costa Rican forearc is sequestered within the crust by calcite deposition with an additional 3.3 ± 1.3% incorporated into autotrophic biomass.
    Description: This work was principally supported by a grant (G-2016-7206) from the Alfred P. Sloan Foundation and the Deep Carbon Observatory to P.H.B. In addition, P.H.B. was supported by NSF grant 1144559 during a portion of this project. D.G. was supported by an NSF grant (MCB 15–17567) and an ELSI Origins Network (EON) research Fellowship, which is supported by a grant from the John Templeton Foundation. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the John Templeton Foundation. DG was also partially supported a Deep Life Modeling and Visualization Fellowship, which is supported by the Deep Carbon Observatory. This work was further supported in party by JSPS KAKENHI grants (JP17K14412, JP17H06105, JP17H02989) awarded to M.N., NSF OCE-1431598 and NASA Exobiology NNX16AL59G awarded to K.G.L. J.M.d.M. gratefully acknowledges funding from Universidad Nacional Costa Rica, the World Bank, and the Costa Rican Ley Transitorio 8933 used to acquire a laser carbon isotope system in collaboration with R. Sánchez-Murillo and G. Esquivel-Hernandez. M.N. produced the most data. We thank Patricia Barcala Dominguez for assistance with figure illustration. We thank Bruce Deck, Marten Wahlen and Keith Blackmon for analytical assistance at SIO. Finally, we acknowledge D. Hummer, T. Lopez, C.A. Pratt, Y. Alpízar Segura, A. Battaglia, P. Beaudry, G. Bini, M. Cascante, G. d’Errico, K. Fullerton, E. Gazel, G. González, S. A. Halldórsson, K. Iacovino, T. Ilanko, J.T. Kulongoski, M. Martínez, H. Miller, S. Ono, S. Patwardhan, C.J. Ramírez, F. Smedile, S. Turner, C. Vetriani, M. Yücel, C.J. Ballentine, T.P. Fischer, and D.R. Hilton, who were instrumental in proposal writing, sample collection, sample analysis and data analysis.
    Repository Name: Woods Hole Open Access Server
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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 Seyler, L. M., Brazelton, W. J., McLean, C., Putman, L. I., Hyer, A., Kubo, M. D. Y., Hoehler, T., Cardace, D., & Schrenk, M. O. . Carbon assimilation strategies in ultrabasic groundwater: clues from the integrated study of a serpentinization-influenced aquifer. mSystems, 5(2), (2020): e00607-00619, doi: 10.1128/mSystems.00607-19.
    Description: Serpentinization is a low-temperature metamorphic process by which ultramafic rock chemically reacts with water. Such reactions provide energy and materials that may be harnessed by chemosynthetic microbial communities at hydrothermal springs and in the subsurface. However, the biogeochemistry mediated by microbial populations that inhabit these environments is understudied and complicated by overlapping biotic and abiotic processes. We applied metagenomics, metatranscriptomics, and untargeted metabolomics techniques to environmental samples taken from the Coast Range Ophiolite Microbial Observatory (CROMO), a subsurface observatory consisting of 12 wells drilled into the ultramafic and serpentinite mélange of the Coast Range Ophiolite in California. Using a combination of DNA and RNA sequence data and mass spectrometry data, we found evidence for several carbon fixation and assimilation strategies, including the Calvin-Benson-Bassham cycle, the reverse tricarboxylic acid cycle, the reductive acetyl coenzyme A (acetyl-CoA) pathway, and methylotrophy, in the microbial communities inhabiting the serpentinite-hosted aquifer. Our data also suggest that the microbial inhabitants of CROMO use products of the serpentinization process, including methane and formate, as carbon sources in a hyperalkaline environment where dissolved inorganic carbon is unavailable.
    Description: We thank McLaughlin Reserve, in particular Paul Aigner and Cathy Koehler, for hosting sampling at CROMO and providing access to the wells, A. Daniel Jones and Anthony Schilmiller for their advice regarding metabolite extraction and mass spectrometry, Elizabeth Kujawinski for her guidance in metabolomics data analysis and interpretation, and Julia McGonigle, Christopher Thornton, and Katrina Twing for assistance with metagenomic and computational analyses.
    Keywords: Carbon assimilation ; Carbon fixation ; Formaldehyde ; Formate ; Methane ; Serpentinization
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