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Khawaja N, Hortal Sánchez L, O'Sullivan TR, Bloema J, Napoleoni M, Klenner F, Beinlich A, Hillier J, John T, Postberg F. Laboratory characterization of hydrothermally processed oligopeptides in ice grains emitted by Enceladus and Europa. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2024; 382:20230201. [PMID: 38736335 DOI: 10.1098/rsta.2023.0201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 01/30/2024] [Indexed: 05/14/2024]
Abstract
The Cassini mission provided evidence for a global subsurface ocean and ongoing hydrothermal activity on Enceladus, based on results from Cassini's mass spectrometers. Laboratory simulations of hydrothermal conditions on icy moons are needed to further constrain the composition of ejected ice grains containing hydrothermally altered organic material. Here, we present results from our newly established facility to simulate the processing of ocean material within the temperature range 80-150°C and the pressure range 80-130 bar, representing conditions suggested for the water-rock interface on Enceladus. With this new facility, we investigate the hydrothermal processing of triglycine (GGG) peptide and, for the first time, analyse the extracted samples using laser-induced liquid beam ion desorption (LILBID) mass spectrometry, a laboratory analogue for impact ionization mass spectrometry of ice grains in space. We outline an approach to elucidate hydrothermally processed GGG in ice grains ejected from icy moons based on characteristic differences between GGG anion and cation mass spectra. These differences are linked to hydrothermal processing and thus provide a fingerprint of hydrothermal activity on extraterrestrial bodies. These results will serve as important guidelines for biosignatures potentially obtained by a future Enceladus mission and the SUrface Dust Analyzer (SUDA) instrument onboard Europa Clipper. This article is part of the theme issue 'Dust in the Solar System and beyond'.
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Affiliation(s)
- Nozair Khawaja
- Department of Planetary Sciences and Remote Sensing, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
- Institute of Space Systems, University of Stuttgart , Stuttgart 70569, Germany
| | - Lucía Hortal Sánchez
- Department of Planetary Sciences and Remote Sensing, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
| | - Thomas R O'Sullivan
- Department of Planetary Sciences and Remote Sensing, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
| | - Judith Bloema
- Department of Planetary Sciences and Remote Sensing, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
| | - Maryse Napoleoni
- Department of Planetary Sciences and Remote Sensing, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
| | - Fabian Klenner
- Department of Earth and Space Sciences, University of Washington , Seattle, WA 98195, USA
| | - Andreas Beinlich
- Department of Mineralogy and Petrology, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
| | - Jon Hillier
- Department of Planetary Sciences and Remote Sensing, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
| | - Timm John
- Department of Mineralogy and Petrology, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
| | - Frank Postberg
- Department of Planetary Sciences and Remote Sensing, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
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Utzman PH, Mays VP, Miller BC, Fairbanks MC, Brazelton WJ, Horvath MP. Metagenome mining and functional analysis reveal oxidized guanine DNA repair at the Lost City Hydrothermal Field. PLoS One 2024; 19:e0284642. [PMID: 38718041 PMCID: PMC11078426 DOI: 10.1371/journal.pone.0284642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
The GO DNA repair system protects against GC → TA mutations by finding and removing oxidized guanine. The system is mechanistically well understood but its origins are unknown. We searched metagenomes and abundantly found the genes encoding GO DNA repair at the Lost City Hydrothermal Field (LCHF). We recombinantly expressed the final enzyme in the system to show MutY homologs function to suppress mutations. Microbes at the LCHF thrive without sunlight, fueled by the products of geochemical transformations of seafloor rocks, under conditions believed to resemble a young Earth. High levels of the reductant H2 and low levels of O2 in this environment raise the question, why are resident microbes equipped to repair damage caused by oxidative stress? MutY genes could be assigned to metagenome-assembled genomes (MAGs), and thereby associate GO DNA repair with metabolic pathways that generate reactive oxygen, nitrogen and sulfur species. Our results indicate that cell-based life was under evolutionary pressure to cope with oxidized guanine well before O2 levels rose following the great oxidation event.
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Affiliation(s)
- Payton H. Utzman
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Vincent P. Mays
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Briggs C. Miller
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Mary C. Fairbanks
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - William J. Brazelton
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Martin P. Horvath
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
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Brabender M, Henriques Pereira DP, Mrnjavac N, Schlikker ML, Kimura ZI, Sucharitakul J, Kleinermanns K, Tüysüz H, Buckel W, Preiner M, Martin WF. Ferredoxin reduction by hydrogen with iron functions as an evolutionary precursor of flavin-based electron bifurcation. Proc Natl Acad Sci U S A 2024; 121:e2318969121. [PMID: 38513105 PMCID: PMC7615787 DOI: 10.1073/pnas.2318969121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/14/2024] [Indexed: 03/23/2024] Open
Abstract
Autotrophic theories for the origin of metabolism posit that the first cells satisfied their carbon needs from CO2 and were chemolithoautotrophs that obtained their energy and electrons from H2. The acetyl-CoA pathway of CO2 fixation is central to that view because of its antiquity: Among known CO2 fixing pathways it is the only one that is i) exergonic, ii) occurs in both bacteria and archaea, and iii) can be functionally replaced in full by single transition metal catalysts in vitro. In order to operate in cells at a pH close to 7, however, the acetyl-CoA pathway requires complex multi-enzyme systems capable of flavin-based electron bifurcation that reduce low potential ferredoxin-the physiological donor of electrons in the acetyl-CoA pathway-with electrons from H2. How can the acetyl-CoA pathway be primordial if it requires flavin-based electron bifurcation? Here, we show that native iron (Fe0), but not Ni0, Co0, Mo0, NiFe, Ni2Fe, Ni3Fe, or Fe3O4, promotes the H2-dependent reduction of aqueous Clostridium pasteurianum ferredoxin at pH 8.5 or higher within a few hours at 40 °C, providing the physiological function of flavin-based electron bifurcation, but without the help of enzymes or organic redox cofactors. H2-dependent ferredoxin reduction by iron ties primordial ferredoxin reduction and early metabolic evolution to a chemical process in the Earth's crust promoted by solid-state iron, a metal that is still deposited in serpentinizing hydrothermal vents today.
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Affiliation(s)
- Max Brabender
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
| | - Delfina P. Henriques Pereira
- Microcosm Earth Center, Research Group for Geochemical Protozymes, Max Planck Institute for Terrestrial Microbiology and Philipps University, Marburg35032, Germany
| | - Natalia Mrnjavac
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
| | - Manon Laura Schlikker
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
| | - Zen-Ichiro Kimura
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
- Department of Civil and Environmental Engineering, National Institute of Technology, Kure College, Kure, Hiroshima737-8506, Japan
| | - Jeerus Sucharitakul
- Department of Biochemistry, Chulalongkorn University, Patumwan, Bangkok10330, Thailand
| | - Karl Kleinermanns
- Institute for Physical Chemistry, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
| | - Harun Tüysüz
- Max Planck Institute for Coal Research, Department of Heterogeneous Catalysis, Mülheim an der Ruhr45470, Germany
| | - Wolfgang Buckel
- Max Planck Institute for Terrestrial Microbiology, Marburg35043, Germany
- Laboratory for Microbiology, Department of Biology, Philipps University, Marburg35043, Germany
- Center for Synthetic Microbiology SYNMIKRO, Philipps University, Marburg35043, Germany
| | - Martina Preiner
- Microcosm Earth Center, Research Group for Geochemical Protozymes, Max Planck Institute for Terrestrial Microbiology and Philipps University, Marburg35032, Germany
| | - William F. Martin
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
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Song Y, Beyazay T, Tüysüz H. Effect of Alkali- and Alkaline-Earth-Metal Promoters on Silica-Supported Co-Fe Alloy for Autocatalytic CO 2 Fixation. Angew Chem Int Ed Engl 2024; 63:e202316110. [PMID: 38127486 DOI: 10.1002/anie.202316110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 12/23/2023]
Abstract
Hydrothermal vents harbor numerous microbial communities rich in reduced carbon species such as formate, acetate, and hydrocarbons. Such essential chemicals for life are produced by H2 -dependent CO2 reduction, where serpentinization provides continuous H2 and thermal energy. Here, we show that silica-supported bimetallic Co-Fe alloys, naturally occurring minerals around serpentinite, can convert CO2 and H2 O to key metabolic intermediates of the acetyl coenzyme A pathway such as formate (up to 72 mM), acetate, and pyruvate under mild hydrothermal vent conditions. Long-chain hydrocarbons up to C6 including propene are also detected, just as in the Lost City hydrothermal field. The effects of promoters on structural properties and catalytic functionalities of the Co-Fe alloy are systematically investigated by incorporating a series of alkali and alkaline earth metals including Na, Mg, K, and Ca. Alkali and alkaline earth metals resulted in higher formate concentrations when dissolved in water and increased reaction pH, while alkaline earth metals also favored the formation of insoluble hydroxides and carbonates similar to the constituent minerals of the chimneys at the Lost City hydrothermal fields.
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Affiliation(s)
- Youngdong Song
- Department of Heterogeneous Catalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Tuğçe Beyazay
- Department of Heterogeneous Catalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Harun Tüysüz
- Department of Heterogeneous Catalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
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5
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Schwander L, Brabender M, Mrnjavac N, Wimmer JLE, Preiner M, Martin WF. Serpentinization as the source of energy, electrons, organics, catalysts, nutrients and pH gradients for the origin of LUCA and life. Front Microbiol 2023; 14:1257597. [PMID: 37854333 PMCID: PMC10581274 DOI: 10.3389/fmicb.2023.1257597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/04/2023] [Indexed: 10/20/2023] Open
Abstract
Serpentinization in hydrothermal vents is central to some autotrophic theories for the origin of life because it generates compartments, reductants, catalysts and gradients. During the process of serpentinization, water circulates through hydrothermal systems in the crust where it oxidizes Fe (II) in ultramafic minerals to generate Fe (III) minerals and H2. Molecular hydrogen can, in turn, serve as a freely diffusible source of electrons for the reduction of CO2 to organic compounds, provided that suitable catalysts are present. Using catalysts that are naturally synthesized in hydrothermal vents during serpentinization H2 reduces CO2 to formate, acetate, pyruvate, and methane. These compounds represent the backbone of microbial carbon and energy metabolism in acetogens and methanogens, strictly anaerobic chemolithoautotrophs that use the acetyl-CoA pathway of CO2 fixation and that inhabit serpentinizing environments today. Serpentinization generates reduced carbon, nitrogen and - as newer findings suggest - reduced phosphorous compounds that were likely conducive to the origins process. In addition, it gives rise to inorganic microcompartments and proton gradients of the right polarity and of sufficient magnitude to support chemiosmotic ATP synthesis by the rotor-stator ATP synthase. This would help to explain why the principle of chemiosmotic energy harnessing is more conserved (older) than the machinery to generate ion gradients via pumping coupled to exergonic chemical reactions, which in the case of acetogens and methanogens involve H2-dependent CO2 reduction. Serpentinizing systems exist in terrestrial and deep ocean environments. On the early Earth they were probably more abundant than today. There is evidence that serpentinization once occurred on Mars and is likely still occurring on Saturn's icy moon Enceladus, providing a perspective on serpentinization as a source of reductants, catalysts and chemical disequilibrium for life on other worlds.
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Affiliation(s)
- Loraine Schwander
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Max Brabender
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Natalia Mrnjavac
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Jessica L. E. Wimmer
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Martina Preiner
- Microcosm Earth Center, Max Planck Institute for Terrestrial Microbiology and Philipps-Universität, Marburg, Germany
| | - William F. Martin
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
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Weber JM, Marlin TC, Prakash M, Teece BL, Dzurilla K, Barge LM. A Review on Hypothesized Metabolic Pathways on Europa and Enceladus: Space-Flight Detection Considerations. Life (Basel) 2023; 13:1726. [PMID: 37629583 PMCID: PMC10456045 DOI: 10.3390/life13081726] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Enceladus and Europa, icy moons of Saturn and Jupiter, respectively, are believed to be habitable with liquid water oceans and therefore are of interest for future life detection missions and mission concepts. With the limited data from missions to these moons, many studies have sought to better constrain these conditions. With these constraints, researchers have, based on modeling and experimental studies, hypothesized a number of possible metabolisms that could exist on Europa and Enceladus if these worlds host life. The most often hypothesized metabolisms are methanogenesis for Enceladus and methane oxidation/sulfate reduction on Europa. Here, we outline, review, and compare the best estimated conditions of each moon's ocean. We then discuss the hypothetical metabolisms that have been suggested to be present on these moons, based on laboratory studies and Earth analogs. We also detail different detection methods that could be used to detect these hypothetical metabolic reactions and make recommendations for future research and considerations for future missions.
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Affiliation(s)
- Jessica M. Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA (B.L.T.); (K.D.); (L.M.B.)
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7
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Tyne RL, Barry PH, Lawson M, Lloyd KG, Giovannelli D, Summers ZM, Ballentine CJ. Identifying and Understanding Microbial Methanogenesis in CO 2 Storage. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37327355 DOI: 10.1021/acs.est.2c08652] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Carbon capture and storage (CCS) is an important component in many national net-zero strategies. Ensuring that CO2 can be safely and economically stored in geological systems is critical. To date, CCS research has focused on the physiochemical behavior of CO2, yet there has been little consideration of the subsurface microbial impact on CO2 storage. However, recent discoveries have shown that microbial processes (e.g., methanogenesis) can be significant. Importantly, methanogenesis may modify the fluid composition and the fluid dynamics within the storage reservoir. Such changes may subsequently reduce the volume of CO2 that can be stored and change the mobility and future trapping systematics of the evolved supercritical fluid. Here, we review the current knowledge of how microbial methanogenesis could impact CO2 storage, including the potential scale of methanogenesis and the range of geologic settings under which this process operates. We find that methanogenesis is possible in all storage target types; however, the kinetics and energetics of methanogenesis will likely be limited by H2 generation. We expect that the bioavailability of H2 (and thus potential of microbial methanogenesis) will be greatest in depleted hydrocarbon fields and least within saline aquifers. We propose that additional integrated monitoring requirements are needed for CO2 storage to trace any biogeochemical processes including baseline, temporal, and spatial studies. Finally, we suggest areas where further research should be targeted in order to fully understand microbial methanogenesis in CO2 storage sites and its potential impact.
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Affiliation(s)
- R L Tyne
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - P H Barry
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | | | - K G Lloyd
- University of Tennessee, Knoxville, Tennessee 37996, United States
| | - D Giovannelli
- University of Naples Federico II, Naples 80138 Italy
| | - Z M Summers
- LanzaTech, Skokie, Illinois 60077, United States
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Seeburger R, Higgins PM, Whiteford NP, Cockell CS. Linking Methanogenesis in Low-Temperature Hydrothermal Vent Systems to Planetary Spectra: Methane Biosignatures on an Archean-Earth-like Exoplanet. ASTROBIOLOGY 2023; 23:415-430. [PMID: 37017441 DOI: 10.1089/ast.2022.0127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In this work, the viability of the detection of methane produced by microbial activity in low-temperature hydrothermal vents on an Archean-Earth-like exoplanet in the habitable zone is explored via a simplified bottom-up approach using a toy model. By simulating methanogens at hydrothermal vent sites in the deep ocean, biological methane production for a range of substrate inflow rates was determined and compared to literature values. These production rates were then used, along with a range of ocean floor vent coverage fractions, to determine likely methane concentrations in the simplified atmosphere. At maximum production rates, a vent coverage of 4-15 × 10-4 % (roughly 2000-6500 times that of modern Earth) is required to achieve 0.25% atmospheric methane. At minimum production rates, 100% vent coverage is not enough to produce 0.25% atmospheric methane. NASA's Planetary Spectrum Generator was then used to assess the detectability of methane features at various atmospheric concentrations. Even with future space-based observatory concepts (such as LUVOIR and HabEx), our results show the importance of both mirror size and distance to the observed planet. Planets with a substantial biomass of methanogens in hydrothermal vents can still lack a detectable, convincingly biological methane signature if they are beyond the scope of the chosen instrument. This work shows the value of coupling microbial ecological modeling with exoplanet science to better understand the constraints on biosignature gas production and its detectability.
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Affiliation(s)
- Rhys Seeburger
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
- Institute for Astronomy, University of Edinburgh, Royal Observatory, Blackford Hill, Edinburgh, UK
- Max Planck Institute for Astronomy, Heidelberg, Germany
| | - Peter M Higgins
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
- Institute for Astronomy, University of Edinburgh, Royal Observatory, Blackford Hill, Edinburgh, UK
- Department of Earth Sciences, University of Toronto, Toronto, Canada
| | - Niall P Whiteford
- Institute for Astronomy, University of Edinburgh, Royal Observatory, Blackford Hill, Edinburgh, UK
- Centre for Exoplanet Science, University of Edinburgh, Edinburgh, UK
- American Museum of Natural History, New York, New York, USA
| | - Charles S Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
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Twing KI, Ward LM, Kane ZK, Sanders A, Price RE, Pendleton HL, Giovannelli D, Brazelton WJ, McGlynn SE. Microbial ecology of a shallow alkaline hydrothermal vent: Strýtan Hydrothermal Field, Eyjafördur, northern Iceland. Front Microbiol 2022; 13:960335. [PMID: 36466646 PMCID: PMC9713835 DOI: 10.3389/fmicb.2022.960335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/05/2022] [Indexed: 10/20/2023] Open
Abstract
Strýtan Hydrothermal Field (SHF) is a submarine system located in Eyjafördur in northern Iceland composed of two main vents: Big Strýtan and Arnarnesstrýtan. The vents are shallow, ranging from 16 to 70 m water depth, and vent high pH (up to 10.2), moderate temperature (T max ∼70°C), anoxic, fresh fluids elevated in dissolved silica, with slightly elevated concentrations of hydrogen and methane. In contrast to other alkaline hydrothermal vents, SHF is unique because it is hosted in basalt and therefore the high pH is not created by serpentinization. While previous studies have assessed the geology and geochemistry of this site, the microbial diversity of SHF has not been explored in detail. Here we present a microbial diversity survey of the actively venting fluids and chimneys from Big Strýtan and Arnarnesstrýtan, using 16S rRNA gene amplicon sequencing. Community members from the vent fluids are mostly aerobic heterotrophic bacteria; however, within the chimneys oxic, low oxygen, and anoxic habitats could be distinguished, where taxa putatively capable of acetogenesis, sulfur-cycling, and hydrogen metabolism were observed. Very few archaea were observed in the samples. The inhabitants of SHF are more similar to terrestrial hot spring samples than other marine sites. It has been hypothesized that life on Earth (and elsewhere in the solar system) could have originated in an alkaline hydrothermal system, however all other studied alkaline submarine hydrothermal systems to date are fueled by serpentinization. SHF adds to our understandings of hydrothermal vents in relationship to microbial diversity, evolution, and possibly the origin of life.
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Affiliation(s)
- Katrina I. Twing
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, United States
- Department of Microbiology, Weber State University, Ogden, UT, United States
| | - L. M. Ward
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Department of Geosciences, Smith College, Northampton, MA, United States
| | - Zachary K. Kane
- Department of Microbiology, Weber State University, Ogden, UT, United States
| | - Alexa Sanders
- Department of Microbiology, Weber State University, Ogden, UT, United States
| | - Roy Edward Price
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - H. Lizethe Pendleton
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, United States
| | - Donato Giovannelli
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - William J. Brazelton
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, United States
| | - Shawn E. McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Center for Sustainable Resource Science, RIKEN, Saitama, Japan
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10
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Narrowing gaps between Earth and life. Proc Natl Acad Sci U S A 2022; 119:e2216017119. [PMID: 36288265 PMCID: PMC9674954 DOI: 10.1073/pnas.2216017119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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11
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Metabolic Strategies Shared by Basement Residents of the Lost City Hydrothermal Field. Appl Environ Microbiol 2022; 88:e0092922. [PMID: 35950875 PMCID: PMC9469722 DOI: 10.1128/aem.00929-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
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. IMPORTANCE The Lost City hydrothermal field is an iconic example of a microbial ecosystem fueled by energy and carbon from Earth's mantle. Uplift of mantle rocks into the seafloor can trigger a process known as serpentinization that releases molecular hydrogen (H2) and creates unusual environmental conditions where simple organic carbon molecules are more stable than dissolved inorganic carbon. This study provides an initial glimpse into the kinds of microbes that live deep within the seafloor where serpentinization takes place, by sampling hydrothermal fluids exiting from the Lost City chimneys. The metabolic strategies that these microbes appear to be using are also shared by microbes that inhabit other sites of serpentinization, including continental subsurface environments and natural springs. Therefore, the results of this study contribute to a broader, interdisciplinary effort to understand the general principles and mechanisms by which serpentinization-associated processes can support life on Earth and perhaps other worlds.
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Comparative Metagenomics Highlight a Widespread Pathway Involved in Catabolism of Phosphonates in Marine and Terrestrial Serpentinizing Ecosystems. mSystems 2022; 7:e0032822. [PMID: 35913189 PMCID: PMC9426474 DOI: 10.1128/msystems.00328-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Serpentinizing hydrothermal systems result from water circulating into the subsurface and interacting with mantle-derived rocks notably near mid-ocean ridges or continental ophiolites. Serpentinization and associated reactions produce alkaline fluids enriched in molecular hydrogen, methane, and small organic molecules that are assumed to feed microbial inhabitants. In this study, we explored the relationships linking serpentinization to associated microbial communities by comparative metagenomics of serpentinite-hosted systems, basalt-hosted vents, and hot springs. The shallow Prony bay hydrothermal field (PBHF) microbiome appeared to be more related to those of ophiolitic sites than to the Lost City hydrothermal field (LCHF) microbiome, probably because of the meteoric origin of its fluid, like terrestrial alkaline springs. This study emphasized the ubiquitous importance of a set of genes involved in the catabolism of phosphonates and highly enriched in all serpentinizing sites compared to other ecosystems. Because most of the serpentinizing systems are depleted in inorganic phosphate, the abundance of genes involved in the carbon-phosphorus lyase pathway suggests that the phosphonates constitute a source of phosphorus in these ecosystems. Additionally, hydrocarbons such as methane, released upon phosphonate catabolism, may contribute to the overall budget of organic molecules in serpentinizing systems. IMPORTANCE This first comparative metagenomic study of serpentinite-hosted environments provides an objective framework to understand the functioning of these peculiar ecosystems. We showed a taxonomic similarity between the PBHF and other terrestrial serpentinite-hosted ecosystems. At the same time, the LCHF microbial community was closer to deep basalt-hosted hydrothermal fields than continental ophiolites, despite the influence of serpentinization. This study revealed shared functional capabilities among serpentinite-hosted ecosystems in response to environmental stress, the metabolism of abundant dihydrogen, and the metabolism of phosphorus. Our results are consistent with the generalized view of serpentinite environments but provide deeper insight into the array of factors that may control microbial activities in these ecosystems. Moreover, we show that metabolism of phosphonate is widespread among alkaline serpentinizing systems and could play a crucial role in phosphorus and methane biogeochemical cycles. This study opens a new line of investigation of the metabolism of reduced phosphorus compounds in serpentinizing environments.
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Henriques Pereira DP, Leethaus J, Beyazay T, do Nascimento Vieira A, Kleinermanns K, Tüysüz H, Martin WF, Preiner M. Role of geochemical protoenzymes (geozymes) in primordial metabolism: specific abiotic hydride transfer by metals to the biological redox cofactor NAD . FEBS J 2021; 289:3148-3162. [PMID: 34923745 PMCID: PMC9306933 DOI: 10.1111/febs.16329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/09/2021] [Accepted: 12/17/2021] [Indexed: 12/17/2022]
Abstract
Hydrogen gas, H2, is generated in serpentinizing hydrothermal systems, where it has supplied electrons and energy for microbial communities since there was liquid water on Earth. In modern metabolism, H2 is converted by hydrogenases into organically bound hydrides (H–), for example, the cofactor NADH. It transfers hydrides among molecules, serving as an activated and biologically harnessed form of H2. In serpentinizing systems, minerals can also bind hydrides and could, in principle, have acted as inorganic hydride donors—possibly as a geochemical protoenzyme, a ‘geozyme’— at the origin of metabolism. To test this idea, we investigated the ability of H2 to reduce NAD+ in the presence of iron (Fe), cobalt (Co) and nickel (Ni), metals that occur in serpentinizing systems. In the presence of H2, all three metals specifically reduce NAD+ to the biologically relevant form, 1,4‐NADH, with up to 100% conversion rates within a few hours under alkaline aqueous conditions at 40 °C. Using Henry's law, the partial pressure of H2 in our reactions corresponds to 3.6 mm, a concentration observed in many modern serpentinizing systems. While the reduction of NAD+ by Ni is strictly H2‐dependent, experiments in heavy water (2H2O) indicate that native Fe can reduce NAD+ both with and without H2. The results establish a mechanistic connection between abiotic and biotic hydride donors, indicating that geochemically catalysed, H2‐dependent NAD+ reduction could have preceded the hydrogenase‐dependent reaction in evolution.
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Affiliation(s)
| | - Jana Leethaus
- Institute for Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
| | - Tugce Beyazay
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | | | - Karl Kleinermanns
- Institute for Physical Chemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Harun Tüysüz
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - William F Martin
- Institute for Molecular Evolution, Heinrich Heine University, Düsseldorf, Germany
| | - Martina Preiner
- Department of Ocean Systems, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands.,Department of Earth Sciences, Utrecht University, The Netherlands
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14
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Wimmer JLE, Xavier JC, Vieira ADN, Pereira DPH, Leidner J, Sousa FL, Kleinermanns K, Preiner M, Martin WF. Energy at Origins: Favorable Thermodynamics of Biosynthetic Reactions in the Last Universal Common Ancestor (LUCA). Front Microbiol 2021; 12:793664. [PMID: 34966373 PMCID: PMC8710812 DOI: 10.3389/fmicb.2021.793664] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/24/2021] [Indexed: 12/02/2022] Open
Abstract
Though all theories for the origin of life require a source of energy to promote primordial chemical reactions, the nature of energy that drove the emergence of metabolism at origins is still debated. We reasoned that evidence for the nature of energy at origins should be preserved in the biochemical reactions of life itself, whereby changes in free energy, ΔG, which determine whether a reaction can go forward or not, should help specify the source. By calculating values of ΔG across the conserved and universal core of 402 individual reactions that synthesize amino acids, nucleotides and cofactors from H2, CO2, NH3, H2S and phosphate in modern cells, we find that 95-97% of these reactions are exergonic (ΔG ≤ 0 kJ⋅mol-1) at pH 7-10 and 80-100°C under nonequilibrium conditions with H2 replacing biochemical reductants. While 23% of the core's reactions involve ATP hydrolysis, 77% are ATP-independent, thermodynamically driven by ΔG of reactions involving carbon bonds. We identified 174 reactions that are exergonic by -20 to -300 kJ⋅mol-1 at pH 9 and 80°C and that fall into ten reaction types: six pterin dependent alkyl or acyl transfers, ten S-adenosylmethionine dependent alkyl transfers, four acyl phosphate hydrolyses, 14 thioester hydrolyses, 30 decarboxylations, 35 ring closure reactions, 31 aromatic ring formations, and 44 carbon reductions by reduced nicotinamide, flavins, ferredoxin, or formate. The 402 reactions of the biosynthetic core trace to the last universal common ancestor (LUCA), and reveal that synthesis of LUCA's chemical constituents required no external energy inputs such as electric discharge, UV-light or phosphide minerals. The biosynthetic reactions of LUCA uncover a natural thermodynamic tendency of metabolism to unfold from energy released by reactions of H2, CO2, NH3, H2S, and phosphate.
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Affiliation(s)
- Jessica L. E. Wimmer
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Joana C. Xavier
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Andrey d. N. Vieira
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Delfina P. H. Pereira
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jacqueline Leidner
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Filipa L. Sousa
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Karl Kleinermanns
- Department of Chemistry, Institute of Physical Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Martina Preiner
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - William F. Martin
- Department of Biology, Institute of Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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15
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McMahon S, Ivarsson M, Wacey D, Saunders M, Belivanova V, Muirhead D, Knoll P, Steinbock O, Frost DA. Dubiofossils from a Mars-analogue subsurface palaeoenvironment: The limits of biogenicity criteria. GEOBIOLOGY 2021; 19:473-488. [PMID: 33951268 DOI: 10.1111/gbi.12445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/12/2021] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
The search for a fossil record of Earth's deep biosphere, partly motivated by potential analogies with subsurface habitats on Mars, has uncovered numerous assemblages of inorganic microfilaments and tubules inside ancient pores and fractures. Although these enigmatic objects are morphologically similar to mineralized microorganisms (and some contain organic carbon), they also resemble some abiotic structures. Palaeobiologists have responded to this ambiguity by evaluating problematic filaments against checklists of "biogenicity criteria". Here, we describe material that tests the limits of this approach. We sampled Jurassic calcite veins formed through subseafloor serpentinization, a water-rock reaction that can fuel the deep biosphere and is known to have occurred widely on Mars. At two localities ~4 km apart, veins contained curving, branched microfilaments composed of Mg-silicate and Fe-oxide minerals. Using a wide range of analytical techniques including synchrotron X-ray microtomography and scanning transmission electron microscopy, we show that these features meet many published criteria for biogenicity and are comparable to fossilized cryptoendolithic fungi or bacteria. However, we argue that abiotic processes driven by serpentinization could account for the same set of lifelike features, and report a chemical garden experiment that supports this view. These filaments are, therefore, most objectively described as dubiofossils, a designation we here defend from criticism and recommend over alternative approaches, but which nevertheless signifies an impasse. Similar impasses can be anticipated in the future exploration of subsurface palaeo-habitats on Earth and Mars. To avoid them, further studies are required in biomimetic geochemical self-organization, microbial taphonomy and micro-analytical techniques, with a focus on subsurface habitats.
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Affiliation(s)
- Sean McMahon
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
- School of Geosciences, Grant Institute, University of Edinburgh, Edinburgh, UK
| | - Magnus Ivarsson
- Department of Paleobiology, Swedish Museum of Natural History, Stockholm, Sweden
| | - David Wacey
- Centre for Microscopy Characterisation and Analysis, The University of Western Australia, Perth, WA, Australia
| | - Martin Saunders
- Centre for Microscopy Characterisation and Analysis, The University of Western Australia, Perth, WA, Australia
| | - Veneta Belivanova
- Department of Paleobiology, Swedish Museum of Natural History, Stockholm, Sweden
| | - David Muirhead
- School of Geosciences, King's College, University of Aberdeen, Aberdeen, UK
| | - Pamela Knoll
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
| | - Oliver Steinbock
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
| | - Daniel A Frost
- Department of Earth & Planetary Science, University of California, Berkeley, CA, USA
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16
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Microbial Diversity and Function in Shallow Subsurface Sediment and Oceanic Lithosphere of the Atlantis Massif. mBio 2021; 12:e0049021. [PMID: 34340550 PMCID: PMC8406227 DOI: 10.1128/mbio.00490-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The marine lithospheric subsurface is one of the largest biospheres on Earth; however, little is known about the identity and ecological function of microorganisms found in low abundance in this habitat, though these organisms impact global-scale biogeochemical cycling. Here, we describe the diversity and metabolic potential of sediment and endolithic (within rock) microbial communities found in ultrasmall amounts (101 to 104 cells cm−3) in the subsurface of the Atlantis Massif, an oceanic core complex on the Mid-Atlantic Ridge that was sampled on International Ocean Discovery Program (IODP) Expedition 357. This study used fluorescence-activated cell sorting (FACS) to enable the first amplicon, metagenomic, and single-cell genomic study of the shallow (<20 m below seafloor) subsurface of an actively serpentinizing marine system. The shallow subsurface biosphere of the Atlantis Massif was found to be distinct from communities observed in the nearby Lost City alkaline hydrothermal fluids and chimneys, yet similar to other low-temperature, aerobic subsurface settings. Genes associated with autotrophy were rare, although heterotrophy and aerobic carbon monoxide and formate cycling metabolisms were identified. Overall, this study reveals that the shallow subsurface of an oceanic core complex hosts a biosphere that is not fueled by active serpentinization reactions and by-products.
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17
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Bristow TF, Grotzinger JP, Rampe EB, Cuadros J, Chipera SJ, Downs GW, Fedo CM, Frydenvang J, McAdam AC, Morris RV, Achilles CN, Blake DF, Castle N, Craig P, Des Marais DJ, Downs RT, Hazen RM, Ming DW, Morrison SM, Thorpe MT, Treiman AH, Tu V, Vaniman DT, Yen AS, Gellert R, Mahaffy PR, Wiens RC, Bryk AB, Bennett KA, Fox VK, Millken RE, Fraeman AA, Vasavada AR. Brine-driven destruction of clay minerals in Gale crater, Mars. Science 2021; 373:198-204. [PMID: 34244410 DOI: 10.1126/science.abg5449] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 05/28/2021] [Indexed: 11/02/2022]
Abstract
Mars' sedimentary rock record preserves information on geological (and potential astrobiological) processes that occurred on the planet billions of years ago. The Curiosity rover is exploring the lower reaches of Mount Sharp, in Gale crater on Mars. A traverse from Vera Rubin ridge to Glen Torridon has allowed Curiosity to examine a lateral transect of rock strata laid down in a martian lake ~3.5 billion years ago. We report spatial differences in the mineralogy of time-equivalent sedimentary rocks <400 meters apart. These differences indicate localized infiltration of silica-poor brines, generated during deposition of overlying magnesium sulfate-bearing strata. We propose that destabilization of silicate minerals driven by silica-poor brines (rarely observed on Earth) was widespread on ancient Mars, because sulfate deposits are globally distributed.
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Affiliation(s)
- T F Bristow
- Eobiology Branch, NASA Ames Research Center, Moffett Field, CA 94035, USA.
| | - J P Grotzinger
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - E B Rampe
- Astromaterials Research and Exploration Science Division, NASA Johnson Space Center, Houston, TX 77058, USA
| | - J Cuadros
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - S J Chipera
- Planetary Science Institute, Tucson, AZ 85719, USA
| | - G W Downs
- Department of Geosciences, University of Arizona, Tucson, AZ 85721, USA
| | - C M Fedo
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN 37996, USA
| | - J Frydenvang
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - A C McAdam
- Solar System Exploration Division, NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA
| | - R V Morris
- Astromaterials Research and Exploration Science Division, NASA Johnson Space Center, Houston, TX 77058, USA
| | - C N Achilles
- Solar System Exploration Division, NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA
| | - D F Blake
- Eobiology Branch, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - N Castle
- Planetary Science Institute, Tucson, AZ 85719, USA
| | - P Craig
- Planetary Science Institute, Tucson, AZ 85719, USA
| | - D J Des Marais
- Eobiology Branch, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - R T Downs
- Department of Geosciences, University of Arizona, Tucson, AZ 85721, USA
| | - R M Hazen
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC 20015, USA
| | - D W Ming
- Astromaterials Research and Exploration Science Division, NASA Johnson Space Center, Houston, TX 77058, USA
| | - S M Morrison
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC 20015, USA
| | - M T Thorpe
- Jacobs Technology-Jacobs JETS Contract, Astromaterials Research and Exploration Science Division, at NASA Johnson Space Center, Houston, TX 77058, USA
| | - A H Treiman
- Lunar and Planetary Institute, Universities Space Research Association, Houston, TX 77058, USA
| | - V Tu
- Jacobs Technology-Jacobs JETS Contract, Astromaterials Research and Exploration Science Division, at NASA Johnson Space Center, Houston, TX 77058, USA
| | - D T Vaniman
- Planetary Science Institute, Tucson, AZ 85719, USA
| | - A S Yen
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - R Gellert
- Department of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - P R Mahaffy
- Solar System Exploration Division, NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA
| | - R C Wiens
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - A B Bryk
- Department of Earth and Planetary Science, University of California Berkeley, Berkeley, CA 94720, USA
| | - K A Bennett
- U.S. Geological Survey, Astrogeology Science Center, Flagstaff, AZ 86001, USA
| | - V K Fox
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - R E Millken
- Department of Earth, Environmental Sciences and Planetary Sciences, Brown University, Providence, RI 02912, USA
| | - A A Fraeman
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - A R Vasavada
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
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18
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Lingam M. Theoretical Constraints Imposed by Gradient Detection and Dispersal on Microbial Size in Astrobiological Environments. ASTROBIOLOGY 2021; 21:813-830. [PMID: 33902321 DOI: 10.1089/ast.2020.2392] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The capacity to sense gradients efficiently and acquire information about the ambient environment confers many advantages such as facilitating movement toward nutrient sources or away from toxic chemicals. The amplified dispersal evinced by organisms endowed with motility is possibly beneficial in related contexts. Hence, the connections between information acquisition, motility, and microbial size are explored from an explicitly astrobiological standpoint. By using prior theoretical models, the constraints on organism size imposed by gradient detection and motility are elucidated in the form of simple heuristic scaling relations. It is argued that environments such as alkaline hydrothermal vents, which are distinguished by the presence of steep gradients, might be conducive to the existence of "small" microbes (with radii of ≳0.1 μm) in principle, when only the above two factors are considered; other biological functions (e.g., metabolism and genetic exchange) could, however, regulate the lower bound on microbial size and elevate it. The derived expressions are potentially applicable to a diverse array of settings, including those entailing solvents other than water; for example, the lakes and seas of Titan. The article concludes with a brief exposition of how this formalism may be of practical and theoretical value to astrobiology.
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Affiliation(s)
- Manasvi Lingam
- Department of Aerospace, Physics and Space Science, Florida Institute of Technology, Melbourne, Florida, USA
- Institute for Theory and Computation, Harvard University, Cambridge, Massachusetts, USA
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19
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Russell MJ. The "Water Problem"( sic), the Illusory Pond and Life's Submarine Emergence-A Review. Life (Basel) 2021; 11:429. [PMID: 34068713 PMCID: PMC8151828 DOI: 10.3390/life11050429] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 04/30/2021] [Accepted: 05/01/2021] [Indexed: 01/10/2023] Open
Abstract
The assumption that there was a "water problem" at the emergence of life-that the Hadean Ocean was simply too wet and salty for life to have emerged in it-is here subjected to geological and experimental reality checks. The "warm little pond" that would take the place of the submarine alkaline vent theory (AVT), as recently extolled in the journal Nature, flies in the face of decades of geological, microbiological and evolutionary research and reasoning. To the present author, the evidence refuting the warm little pond scheme is overwhelming given the facts that (i) the early Earth was a water world, (ii) its all-enveloping ocean was never less than 4 km deep, (iii) there were no figurative "Icelands" or "Hawaiis", nor even an "Ontong Java" then because (iv) the solidifying magma ocean beneath was still too mushy to support such salient loadings on the oceanic crust. In place of the supposed warm little pond, we offer a well-protected mineral mound precipitated at a submarine alkaline vent as life's womb: in place of lipid membranes, we suggest peptides; we replace poisonous cyanide with ammonium and hydrazine; instead of deleterious radiation we have the appropriate life-giving redox and pH disequilibria; and in place of messy chemistry we offer the potential for life's emergence from the simplest of geochemically available molecules and ions focused at a submarine alkaline vent in the Hadean-specifically within the nano-confined flexible and redox active interlayer walls of the mixed-valent double layer oxyhydroxide mineral, fougerite/green rust comprising much of that mound.
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Affiliation(s)
- Michael J Russell
- Dipartimento di Chimica, Università degli Studi di Torino, via P. Giuria 7, 10125 Turin, Italy
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20
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Mueller RC, Peach JT, Skorupa DJ, Copié V, Bothner B, Peyton BM. An emerging view of the diversity, ecology and function of Archaea in alkaline hydrothermal environments. FEMS Microbiol Ecol 2021; 97:6021323. [PMID: 33501490 DOI: 10.1093/femsec/fiaa246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 12/01/2020] [Indexed: 11/15/2022] Open
Abstract
The described diversity within the domain Archaea has recently expanded due to advances in sequencing technologies, but many habitats that likely harbor novel lineages of archaea remain understudied. Knowledge of archaea within natural and engineered hydrothermal systems, such as hot springs and engineered subsurface habitats, has been steadily increasing, but the majority of the work has focused on archaea living in acidic or circumneutral environments. The environmental pressures exerted by the combination of high temperatures and high pH likely select for divergent communities and distinct metabolic pathways from those observed in acidic or circumneutral systems. In this review, we examine what is currently known about the archaea found in thermoalkaline environments, focusing on the detection of novel lineages and knowledge of the ecology, metabolic pathways and functions of these populations and communities. We also discuss the potential of emerging multi-omics approaches, including proteomics and metabolomics, to enhance our understanding of archaea within extreme thermoalkaline systems.
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Affiliation(s)
- Rebecca C Mueller
- Department of Chemical and Biological Engineering, Montana State University,Bozeman, MT 59717, PO Box 173920, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
| | - Jesse T Peach
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, PO Box 173400, USA
| | - Dana J Skorupa
- Department of Chemical and Biological Engineering, Montana State University,Bozeman, MT 59717, PO Box 173920, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
| | - Valerie Copié
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, PO Box 173400, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, PO Box 173400, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
| | - Brent M Peyton
- Department of Chemical and Biological Engineering, Montana State University,Bozeman, MT 59717, PO Box 173920, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
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21
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do Nascimento Vieira A, Kleinermanns K, Martin WF, Preiner M. The ambivalent role of water at the origins of life. FEBS Lett 2020; 594:2717-2733. [PMID: 32416624 DOI: 10.1002/1873-3468.13815] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/29/2020] [Accepted: 05/07/2020] [Indexed: 12/15/2022]
Abstract
Life as we know it would not exist without water. However, water molecules not only serve as a solvent and reactant but can also promote hydrolysis, which counteracts the formation of essential organic molecules. This conundrum constitutes one of the central issues in origin of life. Hydrolysis is an important part of energy metabolism for all living organisms but only because, inside cells, it is a controlled reaction. How could hydrolysis have been regulated under prebiotic settings? Lower water activities possibly provide an answer: geochemical sites with less free and more bound water can supply the necessary conditions for protometabolic reactions. Such conditions occur in serpentinising systems, hydrothermal sites that synthesise hydrogen gas via rock-water interactions. Here, we summarise the parallels between biotic and abiotic means of controlling hydrolysis in order to narrow the gap between biochemical and geochemical reactions and briefly outline how hydrolysis could even have played a constructive role at the origin of molecular self-organisation.
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Affiliation(s)
| | | | - William F Martin
- Institute for Molecular Evolution, University of Düsseldorf, Germany
| | - Martina Preiner
- Institute for Molecular Evolution, University of Düsseldorf, Germany
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22
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Microbial Residents of the Atlantis Massif's Shallow Serpentinite Subsurface. Appl Environ Microbiol 2020; 86:AEM.00356-20. [PMID: 32220840 PMCID: PMC7237769 DOI: 10.1128/aem.00356-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 03/21/2020] [Indexed: 12/25/2022] Open
Abstract
The International Ocean Discovery Program Expedition 357—“Serpentinization and Life”—utilized seabed drills to collect rocks from the oceanic crust. The recovered rock cores represent the shallow serpentinite subsurface of the Atlantis Massif, where reactions between uplifted mantle rocks and water, collectively known as serpentinization, produce environmental conditions that can stimulate biological activity and are thought to be analogous to environments that were prevalent on the early Earth and perhaps other planets. The methodology and results of this project have implications for life detection experiments, including sample return missions, and provide a window into the diversity of microbial communities inhabiting subseafloor serpentinites. The Atlantis Massif rises 4,000 m above the seafloor near the Mid-Atlantic Ridge and consists of rocks uplifted from Earth’s lower crust and upper mantle. Exposure of the mantle rocks to seawater leads to their alteration into serpentinites. These aqueous geochemical reactions, collectively known as the process of serpentinization, are exothermic and are associated with the release of hydrogen gas (H2), methane (CH4), and small organic molecules. The biological consequences of this flux of energy and organic compounds from the Atlantis Massif were explored by International Ocean Discovery Program (IODP) Expedition 357, which used seabed drills to collect continuous sequences of shallow (<16 m below seafloor) marine serpentinites and mafic assemblages. Here, we report the census of microbial diversity in samples of the drill cores, as measured by environmental 16S rRNA gene amplicon sequencing. The problem of contamination of subsurface samples was a primary concern during all stages of this project, starting from the initial study design, continuing to the collection of samples from the seafloor, handling the samples shipboard and in the lab, preparing the samples for DNA extraction, and analyzing the DNA sequence data. To distinguish endemic microbial taxa of serpentinite subsurface rocks from seawater residents and other potential contaminants, the distributions of individual 16S rRNA gene sequences among all samples were evaluated, taking into consideration both presence/absence and relative abundances. Our results highlight a few candidate residents of the shallow serpentinite subsurface, including uncultured representatives of the Thermoplasmata, Acidobacteria, Acidimicrobia, and Chloroflexi. IMPORTANCE The International Ocean Discovery Program Expedition 357—“Serpentinization and Life”—utilized seabed drills to collect rocks from the oceanic crust. The recovered rock cores represent the shallow serpentinite subsurface of the Atlantis Massif, where reactions between uplifted mantle rocks and water, collectively known as serpentinization, produce environmental conditions that can stimulate biological activity and are thought to be analogous to environments that were prevalent on the early Earth and perhaps other planets. The methodology and results of this project have implications for life detection experiments, including sample return missions, and provide a window into the diversity of microbial communities inhabiting subseafloor serpentinites.
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Genomic Evidence for Formate Metabolism by Chloroflexi as the Key to Unlocking Deep Carbon in Lost City Microbial Ecosystems. Appl Environ Microbiol 2020; 86:AEM.02583-19. [PMID: 32033949 PMCID: PMC7117926 DOI: 10.1128/aem.02583-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/31/2020] [Indexed: 02/06/2023] Open
Abstract
Primitive forms of life may have originated around hydrothermal vents at the bottom of the ancient ocean. The Lost City hydrothermal vent field, fueled by just rock and water, provides an analog for not only primitive ecosystems but also potential extraterrestrial rock-powered ecosystems. The microscopic life covering the towering chimney structures at the Lost City has been previously documented, yet little is known about the carbon cycling in this ecosystem. These results provide a better understanding of how carbon from the deep subsurface can fuel rich microbial ecosystems on the seafloor. The Lost City hydrothermal field on the Mid-Atlantic Ridge supports dense microbial life on the lofty calcium carbonate chimney structures. The vent field is fueled by chemical reactions between the ultramafic rock under the chimneys and ambient seawater. These serpentinization reactions provide reducing power (as hydrogen gas) and organic compounds that can serve as microbial food; the most abundant of these are methane and formate. Previous studies have characterized the interior of the chimneys as a single-species biofilm inhabited by the Lost City Methanosarcinales, but they also indicated that this methanogen is unable to metabolize formate. The new metagenomic results presented here indicate that carbon cycling in these Lost City chimney biofilms could depend on the metabolism of formate by Chloroflexi populations. Additionally, we present evidence for metabolically diverse, formate-utilizing Sulfurovum populations and new genomic and phylogenetic insights into the unique Lost City Methanosarcinales. IMPORTANCE Primitive forms of life may have originated around hydrothermal vents at the bottom of the ancient ocean. The Lost City hydrothermal vent field, fueled by just rock and water, provides an analog for not only primitive ecosystems but also potential extraterrestrial rock-powered ecosystems. The microscopic life covering the towering chimney structures at the Lost City has been previously documented, yet little is known about the carbon cycling in this ecosystem. These results provide a better understanding of how carbon from the deep subsurface can fuel rich microbial ecosystems on the seafloor.
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McCaig AM, Früh-Green GL, Kelemen P, Teagle DAH. Serpentinite in the Earth system. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020; 378:20190332. [PMID: 31902338 PMCID: PMC7015303 DOI: 10.1098/rsta.2019.0332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/12/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Andrew M. McCaig
- School of Earth and Environment, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | | | - Peter Kelemen
- Lamont-Doherty Earth Observatory, Palisades, NY, USA
- Earth and Environmental Sciences, Columbia University, New York, NY, USA
| | - Damon A. H. Teagle
- Ocean and Earth Science, University of Southampton, National Oceanography Centre Southampton, European Way, Southampton SO14 3ZH, UK
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