1
|
Peña-Salinas ME, Speth DR, Utter DR, Spelz RM, Lim S, Zierenberg R, Caress DW, Núñez PG, Vázquez R, Orphan VJ. Thermotogota diversity and distribution patterns revealed in Auka and JaichMaa 'ja 'ag hydrothermal vent fields in the Pescadero Basin, Gulf of California. PeerJ 2024; 12:e17724. [PMID: 39175749 PMCID: PMC11340630 DOI: 10.7717/peerj.17724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 06/20/2024] [Indexed: 08/24/2024] Open
Abstract
Discovering new deep hydrothermal vent systems is one of the biggest challenges in ocean exploration. They are a unique window to elucidate the physical, geochemical, and biological processes that occur on the seafloor and are involved in the evolution of life on Earth. In this study, we present a molecular analysis of the microbial composition within the newly discovered hydrothermal vent field, JaichMaa 'ja 'ag, situated in the Southern Pescadero Basin within the Gulf of California. During the cruise expedition FK181031 in 2018, 33 sediment cores were collected from various sites within the Pescadero vent fields and processed for 16S rRNA amplicon sequence variants (ASVs) and geochemical analysis. Correlative analysis of the chemical composition of hydrothermal pore fluids and microbial abundances identified several sediment-associated phyla, including Thermotogota, that appear to be enriched in sediment horizons impacted by hydrothermal fluid flow. Comparative analysis of Thermotogota with the previously explored Auka hydrothermal vent field situated 2 km away displayed broad similarity between the two locations, although at finer scales (e.g., ASV level), there were notable differences that point to core-to-core and site-level factors revealing distinct patterns of distribution and abundance within these two sediment-hosted hydrothermal vent fields. These patterns are intricately linked to the specific physical and geochemical conditions defining each vent, illuminating the complexity of this unique deep ocean chemosynthetic ecosystem.
Collapse
Affiliation(s)
- Manet E. Peña-Salinas
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Baja California, Mexico
- Laboratorio de Astrobiología, Instituto de Astronomía, Universidad Nacional Autónoma de México, Ensenada, Baja California, Mexico
| | - Daan R. Speth
- Division of Microbial Ecology, Center for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States
| | - Daniel R. Utter
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States
| | - Ronald M. Spelz
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Baja California, Mexico
| | - Sujung Lim
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States
| | - Robert Zierenberg
- Department of Earth and Planetary Sciences, University of California, Davis, Davis, California, United States
| | - David W. Caress
- Science Division, Monterey Bay Aquarium Research Institute, Moss Landing, California, United States
| | - Patricia G. Núñez
- Laboratorio de Astrobiología, Instituto de Astronomía, Universidad Nacional Autónoma de México, Ensenada, Baja California, Mexico
| | - Roberto Vázquez
- Laboratorio de Astrobiología, Instituto de Astronomía, Universidad Nacional Autónoma de México, Ensenada, Baja California, Mexico
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States
| |
Collapse
|
2
|
Lissenberg CJ, McCaig AM, Lang SQ, Blum P, Abe N, Brazelton WJ, Coltat R, Deans JR, Dickerson KL, Godard M, John BE, Klein F, Kuehn R, Lin KY, Liu H, Lopes EL, Nozaka T, Parsons AJ, Pathak V, Reagan MK, Robare JA, Savov IP, Schwarzenbach EM, Sissmann OJ, Southam G, Wang F, Wheat CG, Anderson L, Treadwell S. A long section of serpentinized depleted mantle peridotite. Science 2024; 385:623-629. [PMID: 39116218 DOI: 10.1126/science.adp1058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 06/18/2024] [Indexed: 08/10/2024]
Abstract
The upper mantle is critical for our understanding of terrestrial magmatism, crust formation, and element cycling between Earth's solid interior, hydrosphere, atmosphere, and biosphere. Mantle composition and evolution have been primarily inferred by surface sampling and indirect methods. We recovered a long (1268-meter) section of serpentinized abyssal mantle peridotite interleaved with thin gabbroic intrusions. We find depleted compositions with notable variations in mantle mineralogy controlled by melt flow. Dunite zones have predominantly intermediate dips, in contrast to the originally steep mantle fabrics, indicative of oblique melt transport. Extensive hydrothermal fluid-rock interaction is recorded across the full depth of the core and is overprinted by oxidation in the upper 200 meters. Alteration patterns are consistent with vent fluid composition in the nearby Lost City hydrothermal field.
Collapse
Affiliation(s)
- C Johan Lissenberg
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, UK
| | - Andrew M McCaig
- School of Earth and Environment, University of Leeds, Leeds, UK
| | - Susan Q Lang
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Peter Blum
- International Ocean Discovery Program, Texas A&M University, College Station, TX, USA
| | - Natsue Abe
- Japan Agency for Marine-Earth Science and Technology, Yokohama, Japan
| | | | - Rémi Coltat
- Instituto Andaluz de Ciencias de la Tierra, CSIC-UGR, Granada, Spain
| | - Jeremy R Deans
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS, USA
| | - Kristin L Dickerson
- Department of Earth and Planetary Sciences, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Marguerite Godard
- Geosciences Montpellier, CNRS, University of Montpellier, Montpellier, France
| | - Barbara E John
- Department of Geology and Geophysics, University of Wyoming, Laramie, WY, USA
| | - Frieder Klein
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Rebecca Kuehn
- Institute of Geosciences and Geography, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Kuan-Yu Lin
- Department of Earth Sciences, University of Delaware, Newark, DE, USA
| | - Haiyang Liu
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Ethan L Lopes
- Department of Geophysics, Stanford University, Stanford, CA, USA
| | - Toshio Nozaka
- Department of Earth Sciences, Okayama University, Okayama, Japan
| | - Andrew J Parsons
- School of Geography, Earth and Environmental Sciences, University of Plymouth, Plymouth, UK
| | - Vamdev Pathak
- Department of Geology, Central University of Punjab, Bathinda, India
| | - Mark K Reagan
- Department of Earth and Environmental Sciences, University of Iowa, Iowa City, IA, USA
| | - Jordyn A Robare
- School of Molecular Sciences, Arizona State University, Phoenix, AZ, USA
| | - Ivan P Savov
- School of Earth and Environment, University of Leeds, Leeds, UK
| | | | | | - Gordon Southam
- School of the Environment, The University of Queensland, St. Lucia, QLD, Australia
| | - Fengping Wang
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education; and School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, China
| | - C Geoffrey Wheat
- Global Undersea Research Unit, University of Alaska Fairbanks, Moss Landing, CA, USA
| | | | - Sarah Treadwell
- Department of Communication, University of North Dakota, Grand Forks, ND, USA
- Blue Marble Space Institute of Science, Seattle, WA, USA
| |
Collapse
|
3
|
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'.
Collapse
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
| |
Collapse
|
4
|
Li R, Xi B, Wang X, Li Y, Yuan Y, Tan W. Anaerobic oxidation of methane in landfill and adjacent groundwater environments: Occurrence, mechanisms, and potential applications. WATER RESEARCH 2024; 255:121498. [PMID: 38522398 DOI: 10.1016/j.watres.2024.121498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/08/2024] [Accepted: 03/19/2024] [Indexed: 03/26/2024]
Abstract
Landfills remain the predominant means of solid waste management worldwide. Widespread distribution and significant stockpiles of waste in landfills make them a significant source of methane emissions, exacerbating climate change. Anaerobic oxidation of methane (AOM) has been shown to play a critical role in mitigating methane emissions on a global scale. The rich methane and electron acceptor environment in landfills provide the necessary reaction conditions for AOM, making it a potentially low-cost and effective strategy for reducing methane emissions in landfills. However, compared to other anaerobic habitats, research on AOM in landfill environments is scarce, and there is a lack of analysis on the potential application of AOM in different zones of landfills. Therefore, this review summarizes the existing knowledge on AOM and its occurrence in landfills, analyzes the possibility of AOM occurrence in different zones of landfills, discusses its potential applications, and explores the challenges and future research directions for AOM in landfill management. The identification of research gaps and future directions outlined in this review encourages further investigation and advancement in the field of AOM, paving the way for more effective waste stabilization, greenhouse gas reduction, and pollutant mitigation strategies in landfills.
Collapse
Affiliation(s)
- Renfei Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; School of Environment, Tsinghua University, Beijing 100084, PR China.
| | - Xiaowei Wang
- Department of Environmental Science and Engineering, Beijing Technology and Business University, Beijing 100048, PR China
| | - Yanjiao Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Ying Yuan
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Wenbing Tan
- State Key Laboratory of Environmental Criteria and Risk Assessment, and State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Scott KM, Payne RR, Gahramanova A. Widespread dissolved inorganic carbon-modifying toolkits in genomes of autotrophic Bacteria and Archaea and how they are likely to bridge supply from the environment to demand by autotrophic pathways. Appl Environ Microbiol 2024; 90:e0155723. [PMID: 38299815 PMCID: PMC10880623 DOI: 10.1128/aem.01557-23] [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] [Indexed: 02/02/2024] Open
Abstract
Using dissolved inorganic carbon (DIC) as a major carbon source, as autotrophs do, is complicated by the bedeviling nature of this substance. Autotrophs using the Calvin-Benson-Bassham cycle (CBB) are known to make use of a toolkit comprised of DIC transporters and carbonic anhydrase enzymes (CA) to facilitate DIC fixation. This minireview provides a brief overview of the current understanding of how toolkit function facilitates DIC fixation in Cyanobacteria and some Proteobacteria using the CBB and continues with a survey of the DIC toolkit gene presence in organisms using different versions of the CBB and other autotrophic pathways (reductive citric acid cycle, Wood-Ljungdahl pathway, hydroxypropionate bicycle, hydroxypropionate-hydroxybutyrate cycle, and dicarboxylate-hydroxybutyrate cycle). The potential function of toolkit gene products in these organisms is discussed in terms of CO2 and HCO3- supply from the environment and demand by the autotrophic pathway. The presence of DIC toolkit genes in autotrophic organisms beyond those using the CBB suggests the relevance of DIC metabolism to these organisms and provides a basis for better engineering of these organisms for industrial and agricultural purposes.
Collapse
Affiliation(s)
- Kathleen M. Scott
- Integrative Biology Department, University of South Florida, Tampa, Florida, USA
| | - Ren R. Payne
- Integrative Biology Department, University of South Florida, Tampa, Florida, USA
| | - Arin Gahramanova
- Integrative Biology Department, University of South Florida, Tampa, Florida, USA
| |
Collapse
|
7
|
Hart R, Cardace D. Mineral Indicators of Geologically Recent Past Habitability on Mars. Life (Basel) 2023; 13:2349. [PMID: 38137950 PMCID: PMC10744562 DOI: 10.3390/life13122349] [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: 10/07/2023] [Revised: 11/25/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
We provide new support for habitable microenvironments in the near-subsurface of Mars, hosted in Fe- and Mg-rich rock units, and present a list of minerals that can serve as indicators of specific water-rock reactions in recent geologic paleohabitats for follow-on study. We modeled, using a thermodynamic basis without selective phase suppression, the reactions of published Martian meteorites and Jezero Crater igneous rock compositions and reasonable planetary waters (saline, alkaline waters) using Geochemist's Workbench Ver. 12.0. Solid-phase inputs were meteorite compositions for ALH 77005, Nakhla, and Chassigny, and two rock units from the Mars 2020 Perseverance rover sites, Máaz and Séítah. Six plausible Martian groundwater types [NaClO4, Mg(ClO4)2, Ca(ClO4)2, Mg-Na2(ClO4)2, Ca-Na2(ClO4)2, Mg-Ca(ClO4)2] and a unique Mars soil-water analog solution (dilute saline solution) named "Rosy Red", related to the Phoenix Lander mission, were the aqueous-phase inputs. Geophysical conditions were tuned to near-subsurface Mars (100 °C or 373.15 K, associated with residual heat from a magmatic system, impact event, or a concentration of radionuclides, and 101.3 kPa, similar to <10 m depth). Mineral products were dominated by phyllosilicates such as serpentine-group minerals in most reaction paths, but differed in some important indicator minerals. Modeled products varied in physicochemical properties (pH, Eh, conductivity), major ion activities, and related gas fugacities, with different ecological implications. The microbial habitability of pore spaces in subsurface groundwater percolation systems was interrogated at equilibrium in a thermodynamic framework, based on Gibbs Free Energy Minimization. Models run with the Chassigny meteorite produced the overall highest H2 fugacity. Models reliant on the Rosy Red soil-water analog produced the highest sustained CH4 fugacity (maximum values observed for reactant ALH 77005). In general, Chassigny meteorite protoliths produced the best yield regarding Gibbs Free Energy, from an astrobiological perspective. Occurrences of serpentine and saponite across models are key: these minerals have been observed using CRISM spectral data, and their formation via serpentinization would be consistent with geologically recent-past H2 and CH4 production and sustained energy sources for microbial life. We list index minerals to be used as diagnostic for paleo water-rock models that could have supported geologically recent-past microbial activity, and suggest their application as criteria for future astrobiology study-site selections.
Collapse
Affiliation(s)
- Roger Hart
- Department of Physics and Engineering, Community College of Rhode Island, Lincoln, RI 02865, USA
- Department of Geosciences, University of Rhode Island, Kingston, RI 02881, USA;
| | - Dawn Cardace
- Department of Geosciences, University of Rhode Island, Kingston, RI 02881, USA;
| |
Collapse
|
8
|
Alibaglouei M, Trutschel LR, Rowe AR, Sackett JD. Complete genome sequence of Halomonas sp. strain M1, a thiosulfate-oxidizing bacterium isolated from a hyperalkaline serpentinizing system, Ney Springs. Microbiol Resour Announc 2023; 12:e0050823. [PMID: 37906025 PMCID: PMC10652883 DOI: 10.1128/mra.00508-23] [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: 06/13/2023] [Accepted: 09/28/2023] [Indexed: 11/02/2023] Open
Abstract
We report the full genome sequence of Halomonas sp. strain M1, isolated from a continental high pH serpentinizing spring in northern California, USA. The 3.7 Mb genome has a G + C content of 54.13%, encodes 3,354 protein-coding genes, and provides insights into the metabolic potential for sulfur oxidation.
Collapse
Affiliation(s)
- Mehdi Alibaglouei
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Leah R. Trutschel
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Annette R. Rowe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Joshua D. Sackett
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| |
Collapse
|
9
|
Trutschel LR, Rowe AR, Sackett JD. Complete genome sequence of Roseinatronobacter sp. strain S2, a chemolithoheterotroph isolated from a pH 12 serpentinizing system. Microbiol Resour Announc 2023; 12:e0028823. [PMID: 37584560 PMCID: PMC10508151 DOI: 10.1128/mra.00288-23] [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: 04/04/2023] [Accepted: 07/13/2023] [Indexed: 08/17/2023] Open
Abstract
Here, we report the complete genome sequence for Roseinatronobacter sp. S2, a sulfur-oxidizing heterotroph isolated from a serpentinizing system in Northern California. The S2 genome is 4.4 Mb and contains 4,570 protein-encoding genes. This organism contains the genes necessary for sulfur species oxidation and complete ethylmalonyl and pentose phosphate pathways.
Collapse
Affiliation(s)
- Leah R. Trutschel
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Annette R. Rowe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Joshua D. Sackett
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| |
Collapse
|
10
|
Magnuson E, Altshuler I, Freyria NJ, Leveille RJ, Whyte LG. Sulfur-cycling chemolithoautotrophic microbial community dominates a cold, anoxic, hypersaline Arctic spring. MICROBIOME 2023; 11:203. [PMID: 37697305 PMCID: PMC10494364 DOI: 10.1186/s40168-023-01628-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/19/2023] [Indexed: 09/13/2023]
Abstract
BACKGROUND Gypsum Hill Spring, located in Nunavut in the Canadian High Arctic, is a rare example of a cold saline spring arising through thick permafrost. It perennially discharges cold (~ 7 °C), hypersaline (7-8% salinity), anoxic (~ 0.04 ppm O2), and highly reducing (~ - 430 mV) brines rich in sulfate (2.2 g.L-1) and sulfide (9.5 ppm), making Gypsum Hill an analog to putative sulfate-rich briny habitats on extraterrestrial bodies such as Mars. RESULTS Genome-resolved metagenomics and metatranscriptomics were utilized to describe an active microbial community containing novel metagenome-assembled genomes and dominated by sulfur-cycling Desulfobacterota and Gammaproteobacteria. Sulfate reduction was dominated by hydrogen-oxidizing chemolithoautotrophic Desulfovibrionaceae sp. and was identified in phyla not typically associated with sulfate reduction in novel lineages of Spirochaetota and Bacteroidota. Highly abundant and active sulfur-reducing Desulfuromusa sp. highly transcribed non-coding RNAs associated with transcriptional regulation, showing potential evidence of putative metabolic flexibility in response to substrate availability. Despite low oxygen availability, sulfide oxidation was primarily attributed to aerobic chemolithoautotrophic Halothiobacillaceae. Low abundance and transcription of photoautotrophs indicated sulfur-based chemolithoautotrophy drives primary productivity even during periods of constant illumination. CONCLUSIONS We identified a rare surficial chemolithoautotrophic, sulfur-cycling microbial community active in a unique anoxic, cold, hypersaline Arctic spring. We detected Mars-relevant metabolisms including hydrogenotrophic sulfate reduction, sulfur reduction, and sulfide oxidation, which indicate the potential for microbial life in analogous S-rich brines on past and present Mars. Video Abstract.
Collapse
Affiliation(s)
- Elisse Magnuson
- Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, QC Canada
| | - Ianina Altshuler
- MACE Laboratory, ALPOLE, School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nastasia J. Freyria
- Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, QC Canada
| | - Richard J. Leveille
- Department of Earth and Planetary Sciences, McGill University, Montreal, QC Canada
- Geosciences Department, John Abbott College, Ste-Anne-de-Bellevue, QC Canada
| | - Lyle G. Whyte
- Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, QC Canada
| |
Collapse
|
11
|
Popall RM, Postec A, Lecoeuvre A, Quéméneur M, Erauso G. Metabolic challenges and key players in serpentinite-hosted microbial ecosystems. Front Microbiol 2023; 14:1197823. [PMID: 37555067 PMCID: PMC10404738 DOI: 10.3389/fmicb.2023.1197823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/29/2023] [Indexed: 08/10/2023] Open
Abstract
Serpentinite-hosted systems are amongst the most challenging environments for life on Earth. Serpentinization, a geochemical alteration of exposed ultramafic rock, produces hydrothermal fluids enriched in abiotically derived hydrogen (H2), methane (CH4), and small organic molecules. The hyperalkaline pH of these fluids poses a great challenge for metabolic energy and nutrient acquisition, curbing the cellular membrane potential and limiting electron acceptor, carbon, and phosphorous availability. Nevertheless, serpentinization supports the growth of diverse microbial communities whose metabolic make-up might shed light on the beginning of life on Earth and potentially elsewhere. Here, we outline current hypotheses on metabolic energy production, carbon fixation, and nutrient acquisition in serpentinizing environments. A taxonomic survey is performed for each important metabolic function, highlighting potential key players such as H2 and CH4 cycling Serpentinimonas, Hydrogenophaga, Methanobacteriales, Methanosarcinales, and novel candidate phyla. Methodological biases of the available data and future approaches are discussed.
Collapse
Affiliation(s)
| | | | | | | | - Gaël Erauso
- Aix-Marseille Univ, Univ Toulon, CNRS, IRD, MIO, Marseille, France
| |
Collapse
|
12
|
Konrad R, Vergara-Barros P, Alcorta J, Alcamán-Arias ME, Levicán G, Ridley C, Díez B. Distribution and Activity of Sulfur-Metabolizing Bacteria along the Temperature Gradient in Phototrophic Mats of the Chilean Hot Spring Porcelana. Microorganisms 2023; 11:1803. [PMID: 37512975 PMCID: PMC10385741 DOI: 10.3390/microorganisms11071803] [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: 04/12/2023] [Revised: 07/06/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
In terrestrial hot springs, some members of the microbial mat community utilize sulfur chemical species for reduction and oxidization metabolism. In this study, the diversity and activity of sulfur-metabolizing bacteria were evaluated along a temperature gradient (48-69 °C) in non-acidic phototrophic mats of the Porcelana hot spring (Northern Patagonia, Chile) using complementary meta-omic methodologies and specific amplification of the aprA (APS reductase) and soxB (thiosulfohydrolase) genes. Overall, the key players in sulfur metabolism varied mostly in abundance along the temperature gradient, which is relevant for evaluating the possible implications of microorganisms associated with sulfur cycling under the current global climate change scenario. Our results strongly suggest that sulfate reduction occurs throughout the whole temperature gradient, being supported by different taxa depending on temperature. Assimilative sulfate reduction is the most relevant pathway in terms of taxonomic abundance and activity, whereas the sulfur-oxidizing system (Sox) is likely to be more diverse at low rather than at high temperatures. Members of the phylum Chloroflexota showed higher sulfur cycle-related transcriptional activity at 66 °C, with a potential contribution to sulfate reduction and oxidation to thiosulfate. In contrast, at the lowest temperature (48 °C), Burkholderiales and Acetobacterales (both Pseudomonadota, also known as Proteobacteria) showed a higher contribution to dissimilative sulfate reduction/oxidation as well as to thiosulfate metabolism. Cyanobacteriota and Planctomycetota were especially active in assimilatory sulfate reduction. Analysis of the aprA and soxB genes pointed to members of the order Burkholderiales (Gammaproteobacteria) as the most dominant and active along the temperature gradient for these genes. Changes in the diversity and activity of different sulfur-metabolizing bacteria in photoautotrophic microbial mats along a temperature gradient revealed their important role in hot spring environments, especially the main primary producers (Chloroflexota/Cyanobacteriota) and diazotrophs (Cyanobacteriota), showing that carbon, nitrogen, and sulfur cycles are highly linked in these extreme systems.
Collapse
Affiliation(s)
- Ricardo Konrad
- Department of Molecular Genetics and Microbiology, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago 8331150, Chile
| | - Pablo Vergara-Barros
- Department of Molecular Genetics and Microbiology, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago 8331150, Chile
- Millennium Institute Center for Genome Regulation (CGR), Santiago 8370186, Chile
| | - Jaime Alcorta
- Department of Molecular Genetics and Microbiology, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago 8331150, Chile
- Millennium Institute Center for Genome Regulation (CGR), Santiago 8370186, Chile
| | - María E Alcamán-Arias
- Department of Oceanography, University of Concepcion, Concepcion 4030000, Chile
- Center for Climate and Resilience Research (CR)2, Santiago 8370449, Chile
- Escuela de Medicina, Universidad Espíritu Santo, Guayaquil 0901952, Ecuador
| | - Gloria Levicán
- Biology Department, Chemistry and Biology Faculty, University of Santiago of Chile, Santiago 9170022, Chile
| | - Christina Ridley
- Department of Molecular Genetics and Microbiology, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago 8331150, Chile
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago 8331150, Chile
- Millennium Institute Center for Genome Regulation (CGR), Santiago 8370186, Chile
- Center for Climate and Resilience Research (CR)2, Santiago 8370449, Chile
| |
Collapse
|
13
|
Holden JF, Sistu H. Formate and hydrogen in hydrothermal vents and their use by extremely thermophilic methanogens and heterotrophs. Front Microbiol 2023; 14:1093018. [PMID: 36950162 PMCID: PMC10025317 DOI: 10.3389/fmicb.2023.1093018] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/20/2023] [Indexed: 03/08/2023] Open
Abstract
Extremely thermophilic methanogens in the Methanococci and heterotrophs in the Thermococci are common in deep-sea hydrothermal vents. All Methanococci use H2 as an electron donor, and a few species can also use formate. Most Methanococci have a coenzyme F420-reducing formate dehydrogenase. All Thermococci reduce S0 but have hydrogenases and produce H2 in the absence of S0. Some Thermococci have formate hydrogenlyase (Fhl) that reversibly converts H2 and CO2 to formate or an NAD(P)+-reducing formate dehydrogenase (Nfd). Questions remain if Methanococci or Thermococci use or produce formate in nature, why only certain species can grow on or produce formate, and what the physiological role of formate is? Formate forms abiotically in hydrothermal fluids through chemical equilibrium with primarily H2, CO2, and CO and is strongly dependent upon H2 concentration, pH, and temperature. Formate concentrations are highest in hydrothermal fluids where H2 concentrations are also high, such as in ultramafic systems where serpentinization reactions occur. In nature, Methanococci are likely to use formate as an electron donor when H2 is limiting. Thermococci with Fhl likely convert H2 and CO2 to formate when H2 concentrations become inhibitory for growth. They are unlikely to grow on formate in nature unless formate is more abundant than H2 in the environment. Nearly all Methanococci and Thermococci have a gene for at least one formate dehydrogenase catalytic subunit, which may be used to provide free formate for de novo purine biosynthesis. However, only species with a membrane-bound formate transporter can grow on or secrete formate. Interspecies H2 transfer occurs between Thermococci and Methanococci. This and putative interspecies formate transfer may support Methanococci in low H2 environments, which in turn may prevent growth inhibition of Thermococci by its own H2. Future research directions include understanding when, where, and how formate is used and produced by these organisms in nature, and how transcription of Thermococci genes encoding formate-related enzymes are regulated.
Collapse
|
14
|
Yoshida-Takashima Y, Takaki Y, Yoshida M, Zhang Y, Nunoura T, Takai K. Genomic insights into phage-host interaction in the deep-sea chemolithoautotrophic Campylobacterota, Nitratiruptor. ISME COMMUNICATIONS 2022; 2:108. [PMID: 37938718 PMCID: PMC9723563 DOI: 10.1038/s43705-022-00194-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2023]
Abstract
The genus Nitratiruptor represents one of the most numerically abundant chemolithoautotrophic Campylobacterota populations in the mixing zones of habitats between hydrothermal fluids and ambient seawater in deep-sea hydrothermal environments. We isolated and characterized four novel temperate phages (NrS-2, NrS-3, NrS-4, and NrS-5) having a siphoviral morphology, infecting Nitratiruptor strains from the Hatoma Knoll hydrothermal field in the southern-Okinawa Trough, Japan, and conducted comparative genomic analyses among Nitratiruptor strains and their phages. The Nitratiruptor temperate phages shared many potential core genes (e.g., integrase, Cro, two structural proteins, lysozyme, and MazG) with each other despite their diverse morphological and genetic features. Some homologs of coding sequences (CDSs) of the temperate phages were dispersed throughout the non-prophage regions of the Nitratiruptor genomes. In addition, several regions of the phage genome sequences matched to spacer sequences within clustered regularly interspaced short palindromic repeats (CRISPR) in Nitratiruptor genomes. Moreover, a restriction-modification system found in a temperate phage affected an epigenetic feature of its host. These results strongly suggested a coevolution of temperate phages and their host genomes via the acquisition of temperate phages, the CRISPR systems, the nucleotide substitution, and the epigenetic regulation during multiple phage infections in the deep-sea environments.
Collapse
Affiliation(s)
- Yukari Yoshida-Takashima
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan.
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Mitsuhiro Yoshida
- Deep-Sea Bioresource Research Group, Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Yi Zhang
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Takuro Nunoura
- Deep-Sea Bioresource Research Group, Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Ken Takai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| |
Collapse
|
15
|
Abstract
Little is known of acetogens in contemporary serpentinizing systems, despite widely supported theories that serpentinite-hosted environments supported the first life on Earth via acetogenesis. To address this knowledge gap, genome-resolved metagenomics was applied to subsurface fracture water communities from an area of active serpentinization in the Samail Ophiolite, Sultanate of Oman. Two deeply branching putative bacterial acetogen types were identified in the communities belonging to the Acetothermia (hereafter, types I and II) that exhibited distinct distributions among waters with lower and higher water-rock reaction (i.e., serpentinization influence), respectively. Metabolic reconstructions revealed contrasting core metabolic pathways of type I and II Acetothermia, including in acetogenic pathway components (e.g., bacterial- vs. archaeal-like carbon monoxide dehydrogenases [CODH], respectively), hydrogen use to drive acetogenesis, and chemiosmotic potential generation via respiratory (type I) or canonical acetogen ferredoxin-based complexes (type II). Notably, type II Acetothermia metabolic pathways allow for use of serpentinization-derived substrates and implicate them as key primary producers in contemporary hyperalkaline serpentinite environments. Phylogenomic analyses indicate that 1) archaeal-like CODH of the type II genomes and those of other serpentinite-associated Bacteria derive from a deeply rooted horizontal transfer or origin among archaeal methanogens and 2) Acetothermia are among the earliest evolving bacterial lineages. The discovery of dominant and early-branching acetogens in subsurface waters of the largest near-surface serpentinite formation provides insight into the physiological traits that likely facilitated rock-supported life to flourish on a primitive Earth and possibly on other rocky planets undergoing serpentinization.
Collapse
|
16
|
Brazelton WJ, McGonigle JM, Motamedi S, Pendleton HL, Twing KI, Miller BC, Lowe WJ, Hoffman AM, Prator CA, Chadwick GL, Anderson RE, Thomas E, Butterfield DA, Aquino KA, Früh-Green GL, Schrenk MO, Lang SQ. 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: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/28/2022] [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.
Collapse
Affiliation(s)
| | - Julia M. McGonigle
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
| | - Shahrzad Motamedi
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | | | - Katrina I. Twing
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Briggs C. Miller
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - William J. Lowe
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | | | - Cecilia A. Prator
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Grayson L. Chadwick
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Rika E. Anderson
- Department of Biology, Carleton College, Northfield, Minnesota, USA
| | - Elaina Thomas
- Department of Biology, Carleton College, Northfield, Minnesota, USA
| | - David A. Butterfield
- Joint Institute for the Study of Atmosphere and Ocean, University of Washington, Seattle, Washington, USA
| | | | | | - Matthew O. Schrenk
- Department of Earth and Environmental Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Susan Q. Lang
- School of the Earth, Ocean, and Environment, University of South Carolina, Columbia, South Carolina, USA
| |
Collapse
|
17
|
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.
Collapse
|
18
|
MacKenzie SM, Neveu M, Davila AF, Lunine JI, Cable ML, Phillips-Lander CM, Eigenbrode JL, Waite JH, Craft KL, Hofgartner JD, McKay CP, Glein CR, Burton D, Kounaves SP, Mathies RA, Vance SD, Malaska MJ, Gold R, German CR, Soderlund KM, Willis P, Freissinet C, McEwen AS, Brucato JR, de Vera JPP, Hoehler TM, Heldmann J. Science Objectives for Flagship-Class Mission Concepts for the Search for Evidence of Life at Enceladus. ASTROBIOLOGY 2022; 22:685-712. [PMID: 35290745 PMCID: PMC9233532 DOI: 10.1089/ast.2020.2425] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 01/21/2022] [Indexed: 05/07/2023]
Abstract
Cassini revealed that Saturn's Moon Enceladus hosts a subsurface ocean that meets the accepted criteria for habitability with bio-essential elements and compounds, liquid water, and energy sources available in the environment. Whether these conditions are sufficiently abundant and collocated to support life remains unknown and cannot be determined from Cassini data. However, thanks to the plume of oceanic material emanating from Enceladus' south pole, a new mission to Enceladus could search for evidence of life without having to descend through kilometers of ice. In this article, we outline the science motivations for such a successor to Cassini, choosing the primary science goal to be determining whether Enceladus is inhabited and assuming a resource level equivalent to NASA's Flagship-class missions. We selected a set of potential biosignature measurements that are complementary and orthogonal to build a robust case for any life detection result. This result would be further informed by quantifications of the habitability of the environment through geochemical and geophysical investigations into the ocean and ice shell crust. This study demonstrates that Enceladus' plume offers an unparalleled opportunity for in situ exploration of an Ocean World and that the planetary science and astrobiology community is well equipped to take full advantage of it in the coming decades.
Collapse
Affiliation(s)
| | - Marc Neveu
- Department of Astronomy, University of Maryland, College Park, Maryland, USA
- Solar System Exploration Division, NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
| | - Alfonso F. Davila
- Division of Space Science and Astrobiology, NASA Ames Research Center, Moffett Field, California, USA
| | - Jonathan I. Lunine
- Department of Astronomy, Cornell University, Ithaca, New York, USA
- Carl Sagan Institute, Cornell University, Ithaca, New York, USA
| | - Morgan L. Cable
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | | | - Jennifer L. Eigenbrode
- Solar System Exploration Division, NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
| | - J. Hunter Waite
- Space Science and Engineering Division, Southwest Research Institute, San Antonio, Texas, USA
| | - Kate L. Craft
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | - Jason D. Hofgartner
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Chris P. McKay
- Division of Space Science and Astrobiology, NASA Ames Research Center, Moffett Field, California, USA
| | - Christopher R. Glein
- Space Science and Engineering Division, Southwest Research Institute, San Antonio, Texas, USA
| | - Dana Burton
- Department of Anthropology, George Washington University, Washington, District of Columbia, USA
| | | | - Richard A. Mathies
- Chemistry Department and Space Sciences Laboratory, University of California, Berkeley, Berkeley, California, USA
| | - Steven D. Vance
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Michael J. Malaska
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Robert Gold
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | - Christopher R. German
- Department of Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Krista M. Soderlund
- Institute for Geophysics, Jackson School of Geosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Peter Willis
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | | | - Alfred S. McEwen
- Lunar and Planetary Lab, University of Arizona, Tucson, Arizona, USA
| | | | - Jean-Pierre P. de Vera
- Space Operations and Astronaut Training, MUSC, German Aerospace Center (DLR), Cologne, Germany
| | - Tori M. Hoehler
- Division of Space Science and Astrobiology, NASA Ames Research Center, Moffett Field, California, USA
| | - Jennifer Heldmann
- Division of Space Science and Astrobiology, NASA Ames Research Center, Moffett Field, California, USA
| |
Collapse
|
19
|
Modeling Virus and Bacteria Populations in Europa’s Subsurface Ocean. Life (Basel) 2022; 12:life12050620. [PMID: 35629289 PMCID: PMC9147769 DOI: 10.3390/life12050620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 12/11/2022] Open
Abstract
The search for life in the universe is often informed by the study of “extreme” environments on Earth, which provide analogs for habitable locations in the Solar System, and whose microbial inhabitants may therefore also serve as analogs for potential life forms in extraterrestrial milieus. Recent work has highlighted the ubiquity and importance of viral entities in terrestrial ecosystems, which calls for a greater understanding of the roles that viruses might play in hypothetical extraterrestrial biomes. While some studies have modeled the dynamics of viral and bacterial populations in icy ocean environments on Earth, previous work has yet to apply these findings to icy ocean worlds such as Jupiter’s moon Europa. It is commonly theorized that hydrothermal vents on Europa could produce the necessary reductants for chemosynthesis to take place on the ocean bottom. In the case that Europa’s ocean is a reductant-limited environment, how might reductants and organic matter reach the sub-ice region to power a more easily accessible ecosystem? Here, we propose a ‘viral elevator,’ a mechanism that functions similarly to the ‘viral shunt’ in Earth’s oceans, which could create and shuttle dissolved organic matter (DOM) to a hypothetical sub-ice biosphere through viral carriers. Current models of Europa’s ocean currents and stratification support the movement of DOM to the sub-ice biosphere. We adapt an existing model for bacterial and viral population dynamics in Earth’s Arctic sea ice to Europa and use parameters from various Arctic-based studies as proxies for Europa’s environment. We find that viral burst size has the most significant effect on the virus-to-bacteria ratio (VBR) and system longevity in closed systems (such as brine pockets within Europa’s icy crust), with higher burst sizes clearly increasing both. When applying our model to an open system with an influx of DOM from the viral elevator, we found that a steady-state system is attainable, with resulting sub-ice biofilms on the order of 0.1 mm thick (global equivalent layer). This has implications for future searches for life on Europa, given that life directly under the ice will be easier to detect and observe than life near the ocean bottom.
Collapse
|
20
|
Shu WS, Huang LN. Microbial diversity in extreme environments. Nat Rev Microbiol 2022; 20:219-235. [PMID: 34754082 DOI: 10.1038/s41579-021-00648-y] [Citation(s) in RCA: 126] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 01/02/2023]
Abstract
A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa, survive and thrive in extreme environments. These unique and reduced-complexity ecosystems offer a tremendous opportunity for studying the structure, function and evolution of natural microbial communities. Marker gene surveys have resolved patterns and ecological drivers of these extremophile assemblages, revealing a vast uncultured microbial diversity and the often predominance of archaea in the most extreme conditions. New omics studies have uncovered linkages between community function and environmental variables, and have enabled discovery and genomic characterization of major new lineages that substantially expand microbial diversity and change the structure of the tree of life. These efforts have significantly advanced our understanding of the diversity, ecology and evolution of microorganisms populating Earth's extreme environments, and have facilitated the exploration of microbiota and processes in more complex ecosystems.
Collapse
Affiliation(s)
- Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, People's Republic of China.
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China.
| |
Collapse
|
21
|
Pan J, Xu W, Zhou Z, Shao Z, Dong C, Liu L, Luo Z, Li M. Genome-resolved evidence for functionally redundant communities and novel nitrogen fixers in the deyin-1 hydrothermal field, Mid-Atlantic Ridge. MICROBIOME 2022; 10:8. [PMID: 35045876 PMCID: PMC8767757 DOI: 10.1186/s40168-021-01202-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/24/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND Deep-sea hydrothermal vents represent unique ecosystems that redefine our understanding of the limits of life. They are widely distributed in deep oceans and typically form along mid-ocean ridges. To date, the hydrothermal systems in the Mid-Atlantic Ridge south of 14°S remain barely explored, limiting our understanding of the microbial community in this distinct ecosystem. The Deyin-1 is a newly discovered hydrothermal field in this area. By applying the metagenomic analysis, we aim at gaining much knowledge of the biodiversity and functional capability of microbial community inhabiting this field. RESULTS In the current study, 219 metagenomic assembled genomes (MAGs) were reconstructed, unveiling a diverse and variable community dominated by Bacteroidetes, Nitrospirae, Alpha-, Delta-, and Gammaproteobacteria in the active and inactive chimney samples as well as hydrothermal oxide samples. Most of these major taxa were potentially capable of using reduced sulfur and hydrogen as primary energy sources. Many members within the major taxa exhibited potentials of metabolic plasticity by possessing multiple energy metabolic pathways. Among these samples, different bacteria were found to be the major players of the same metabolic pathways, further supporting the variable and functionally redundant community in situ. In addition, a high proportion of MAGs harbored the genes of carbon fixation and extracellular carbohydrate-active enzymes, suggesting that both heterotrophic and autotrophic strategies could be essential for their survival. Notably, for the first time, the genus Candidatus Magnetobacterium was shown to potentially fix nitrogen, indicating its important role in the nitrogen cycle of inactive chimneys. Moreover, the metabolic plasticity of microbes, diverse and variable community composition, and functional redundancy of microbial communities may represent the adaptation strategies to the geochemically complex and fluctuating environmental conditions in deep-sea hydrothermal fields. CONCLUSIONS This represents the first assembled-genome-based investigation into the microbial community and metabolism of a hydrothermal field in the Mid-Atlantic Ridge south of 14°S. The findings revealed that a high proportion of microbes could benefit from simultaneous use of heterotrophic and autotrophic strategies in situ. It also presented novel members of potential diazotrophs and highlighted the metabolic plasticity and functional redundancy across deep-sea hydrothermal systems. Video abstract.
Collapse
Affiliation(s)
- Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong People’s Republic of China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Xiamen, People’s Republic of China
| | - Zhichao Zhou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong People’s Republic of China
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Xiamen, People’s Republic of China
| | - Chunming Dong
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Xiamen, People’s Republic of China
| | - Lirui Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong People’s Republic of China
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Xiamen, People’s Republic of China
- School of Marine Sciences, Nanjing University of Information Science & Technology, 210044 Nanjing, People’s Republic of China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong People’s Republic of China
| |
Collapse
|
22
|
Chadwick GL, Skennerton CT, Laso-Pérez R, Leu AO, Speth DR, Yu H, Morgan-Lang C, Hatzenpichler R, Goudeau D, Malmstrom R, Brazelton WJ, Woyke T, Hallam SJ, Tyson GW, Wegener G, Boetius A, Orphan VJ. Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea. PLoS Biol 2022; 20:e3001508. [PMID: 34986141 PMCID: PMC9012536 DOI: 10.1371/journal.pbio.3001508] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 04/15/2022] [Accepted: 12/08/2021] [Indexed: 11/25/2022] Open
Abstract
The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor. A comparative genomics study of anaerobic methanotrophic (ANME) archaea reveals the genetic "parts list" associated with the repeated evolutionary transition between methanogenic and methanotrophic metabolism in the archaeal domain of life.
Collapse
Affiliation(s)
- Grayson L. Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (GLC); (VJO)
| | - Connor T. Skennerton
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Rafael Laso-Pérez
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Andy O. Leu
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Daan R. Speth
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Hang Yu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Connor Morgan-Lang
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Roland Hatzenpichler
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Danielle Goudeau
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Rex Malmstrom
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - William J. Brazelton
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Tanja Woyke
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Steven J. Hallam
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada
- Department of Microbiology & Immunology, University of British Columbia, British Columbia, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada
- Life Sciences Institute, University of British Columbia, British Columbia, Canada
| | - Gene W. Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Gunter Wegener
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Antje Boetius
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (GLC); (VJO)
| |
Collapse
|
23
|
Smith AR, Mueller R, Fisk MR, Colwell FS. Ancient Metabolisms of a Thermophilic Subseafloor Bacterium. Front Microbiol 2021; 12:764631. [PMID: 34925271 PMCID: PMC8671834 DOI: 10.3389/fmicb.2021.764631] [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] [Received: 08/25/2021] [Accepted: 10/22/2021] [Indexed: 11/13/2022] Open
Abstract
The ancient origins of metabolism may be rooted deep in oceanic crust, and these early metabolisms may have persisted in the habitable thermal anoxic aquifer where conditions remain similar to those when they first appeared. The Wood–Ljungdahl pathway for acetogenesis is a key early biosynthetic pathway with the potential to influence ocean chemistry and productivity, but its contemporary role in oceanic crust is not well established. Here, we describe the genome of a novel acetogen from a thermal suboceanic aquifer olivine biofilm in the basaltic crust of the Juan de Fuca Ridge (JdFR) whose genome suggests it may utilize an ancient chemosynthetic lifestyle. This organism encodes the genes for the complete canonical Wood–Ljungdahl pathway, but is potentially unable to use sulfate and certain organic carbon sources such as lipids and carbohydrates to supplement its energy requirements, unlike other known acetogens. Instead, this organism may use peptides and amino acids for energy or as organic carbon sources. Additionally, genes involved in surface adhesion, the import of metallic cations found in Fe-bearing minerals, and use of molecular hydrogen, a product of serpentinization reactions between water and olivine, are prevalent within the genome. These adaptations are likely a reflection of local environmental micro-niches, where cells are adapted to life in biofilms using ancient chemosynthetic metabolisms dependent on H2 and iron minerals. Since this organism is phylogenetically distinct from a related acetogenic group of Clostridiales, we propose it as a new species, Candidatus Acetocimmeria pyornia.
Collapse
Affiliation(s)
- Amy R Smith
- Department of Science, Mathematics, and Computing, Bard College at Simon's Rock, Great Barrington, MA, United States.,Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States.,College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
| | - Ryan Mueller
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
| | - Martin R Fisk
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
| | - Frederick S Colwell
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
| |
Collapse
|
24
|
Takamiya H, Kouduka M, Suzuki Y. The Deep Rocky Biosphere: New Geomicrobiological Insights and Prospects. Front Microbiol 2021; 12:785743. [PMID: 34917063 PMCID: PMC8670094 DOI: 10.3389/fmicb.2021.785743] [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] [Received: 09/29/2021] [Accepted: 11/08/2021] [Indexed: 12/02/2022] Open
Abstract
Rocks that react with liquid water are widespread but spatiotemporally limited throughout the solar system, except for Earth. Rock-forming minerals with high iron content and accessory minerals with high amounts of radioactive elements are essential to support rock-hosted microbial life by supplying organics, molecular hydrogen, and/or oxidants. Recent technological advances have broadened our understanding of the rocky biosphere, where microbial inhabitation appears to be difficult without nutrient and energy inputs from minerals. In particular, microbial proliferation in igneous rock basements has been revealed using innovative geomicrobiological techniques. These recent findings have dramatically changed our perspective on the nature and the extent of microbial life in the rocky biosphere, microbial interactions with minerals, and the influence of external factors on habitability. This study aimed to gather information from scientific and/or technological innovations, such as omics-based and single-cell level characterizations, targeting deep rocky habitats of organisms with minimal dependence on photosynthesis. By synthesizing pieces of rock-hosted life, we can explore the evo-phylogeny and ecophysiology of microbial life on Earth and the life’s potential on other planetary bodies.
Collapse
Affiliation(s)
- Hinako Takamiya
- Department of Earth and Planetary Science, The University of Tokyo, Bunkyo, Japan
| | - Mariko Kouduka
- Department of Earth and Planetary Science, The University of Tokyo, Bunkyo, Japan
| | - Yohey Suzuki
- Department of Earth and Planetary Science, The University of Tokyo, Bunkyo, Japan
| |
Collapse
|
25
|
Wang X, Pecoraro L. Diversity and Co-Occurrence Patterns of Fungal and Bacterial Communities from Alkaline Sediments and Water of Julong High-Altitude Hot Springs at Tianchi Volcano, Northeast China. BIOLOGY 2021; 10:894. [PMID: 34571771 PMCID: PMC8464750 DOI: 10.3390/biology10090894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/28/2021] [Accepted: 09/07/2021] [Indexed: 12/03/2022]
Abstract
The Julong high-altitude volcanic hot springs in northeast China are of undeniable interest for microbiological studies due to their unique, extreme environmental conditions. The objective of this study was to provide a comprehensive analysis of the unexplored fungal and bacterial community composition, structure and networks in sediments and water from the Julong hot springs using a combination of culture-based methods and metabarcoding. A total of 65 fungal and 21 bacterial strains were isolated. Fungal genera Trichoderma and Cladosporium were dominant in sediments, while the most abundant fungi in hot spring water were Aspergillus and Alternaria. Bacterial communities in sediments and water were dominated by the genera Chryseobacterium and Pseudomonas, respectively. Metabarcoding analysis revealed significant differences in the microorganism communities from the two hot springs. Results suggested a strong influence of pH on the analyzed microbial diversity, at least when the environmental conditions became clearly alkaline. Our analyses indicated that mutualistic interactions may play an essential role in shaping stable microbial networks in the studied hot springs. The much more complicated bacterial than fungal networks described in our study may suggest that the more flexible trophic strategies of bacteria are beneficial for their survival and fitness under extreme conditions.
Collapse
Affiliation(s)
- Xiao Wang
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Lorenzo Pecoraro
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| |
Collapse
|
26
|
Hoffert M, Anderson RE, Reveillaud J, Murphy LG, Stepanauskas R, Huber JA. Genomic Variation Influences Methanothermococcus Fitness in Marine Hydrothermal Systems. Front Microbiol 2021; 12:714920. [PMID: 34489903 PMCID: PMC8417812 DOI: 10.3389/fmicb.2021.714920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/31/2021] [Indexed: 11/13/2022] Open
Abstract
Hydrogenotrophic methanogens are ubiquitous chemoautotrophic archaea inhabiting globally distributed deep-sea hydrothermal vent ecosystems and associated subseafloor niches within the rocky subseafloor, yet little is known about how they adapt and diversify in these habitats. To determine genomic variation and selection pressure within methanogenic populations at vents, we examined five Methanothermococcus single cell amplified genomes (SAGs) in conjunction with 15 metagenomes and 10 metatranscriptomes from venting fluids at two geochemically distinct hydrothermal vent fields on the Mid-Cayman Rise in the Caribbean Sea. We observed that some Methanothermococcus lineages and their transcripts were more abundant than others in individual vent sites, indicating differential fitness among lineages. The relative abundances of lineages represented by SAGs in each of the samples matched phylogenetic relationships based on single-copy universal genes, and genes related to nitrogen fixation and the CRISPR/Cas immune system were among those differentiating the clades. Lineages possessing these genes were less abundant than those missing that genomic region. Overall, patterns in nucleotide variation indicated that the population dynamics of Methanothermococcus were not governed by clonal expansions or selective sweeps, at least in the habitats and sampling times included in this study. Together, our results show that although specific lineages of Methanothermococcus co-exist in these habitats, some outcompete others, and possession of accessory metabolic functions does not necessarily provide a fitness advantage in these habitats in all conditions. This work highlights the power of combining single-cell, metagenomic, and metatranscriptomic datasets to determine how evolution shapes microbial abundance and diversity in hydrothermal vent ecosystems.
Collapse
Affiliation(s)
- Michael Hoffert
- Biology Department, Carleton College, Northfield, MN, United States.,Finch Therapeutics Group, Somerville, MA, United States
| | - Rika E Anderson
- Biology Department, Carleton College, Northfield, MN, United States
| | - Julie Reveillaud
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, University of Montpellier, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Institut de Recherche Pour le Développement, Montpellier, France
| | | | | | - Julie A Huber
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| |
Collapse
|
27
|
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.
Collapse
|
28
|
Altair T, Borges LGF, Galante D, Varela H. Experimental Approaches for Testing the Hypothesis of the Emergence of Life at Submarine Alkaline Vents. Life (Basel) 2021; 11:777. [PMID: 34440521 PMCID: PMC8401828 DOI: 10.3390/life11080777] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/21/2021] [Accepted: 07/28/2021] [Indexed: 11/17/2022] Open
Abstract
Since the pioneering experimental work performed by Urey and Miller around 70 years ago, several experimental works have been developed for approaching the question of the origin of life based on very few well-constructed hypotheses. In recent years, attention has been drawn to the so-called alkaline hydrothermal vents model (AHV model) for the emergence of life. Since the first works, perspectives from complexity sciences, bioenergetics and thermodynamics have been incorporated into the model. Consequently, a high number of experimental works from the model using several tools have been developed. In this review, we present the key concepts that provide a background for the AHV model and then analyze the experimental approaches that were motivated by it. Experimental tools based on hydrothermal reactors, microfluidics and chemical gardens were used for simulating the environments of early AHVs on the Hadean Earth (~4.0 Ga). In addition, it is noteworthy that several works used techniques from electrochemistry to investigate phenomena in the vent-ocean interface for early AHVs. Their results provided important parameters and details that are used for the evaluation of the plausibility of the AHV model, and for the enhancement of it.
Collapse
Affiliation(s)
- Thiago Altair
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos 13560-970, Brazil
| | - Luiz G. F. Borges
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-100, Brazil; (L.G.F.B.); (D.G.)
| | - Douglas Galante
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-100, Brazil; (L.G.F.B.); (D.G.)
| | - Hamilton Varela
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos 13560-970, Brazil
| |
Collapse
|
29
|
Procaryotic Diversity and Hydrogenotrophic Methanogenesis in an Alkaline Spring (La Crouen, New Caledonia). Microorganisms 2021; 9:microorganisms9071360. [PMID: 34201651 PMCID: PMC8307142 DOI: 10.3390/microorganisms9071360] [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: 05/17/2021] [Revised: 06/17/2021] [Accepted: 06/19/2021] [Indexed: 01/01/2023] Open
Abstract
(1) Background: The geothermal spring of La Crouen (New Caledonia) discharges warm (42 °C) alkaline water (pH~9) enriched in dissolved nitrogen with traces of methane, but its microbial diversity has not yet been studied. (2) Methods: Cultivation-dependent and -independent methods (e.g., Illumina sequencing and quantitative PCR based on 16S rRNA gene) were used to describe the prokaryotic diversity of this spring. (3) Results: Prokaryotes were mainly represented by Proteobacteria (57% on average), followed by Cyanobacteria, Chlorofexi, and Candidatus Gracilibacteria (GN02/BD1-5) (each > 5%). Both potential aerobes and anaerobes, as well as mesophilic and thermophilic microorganisms, were identified. Some of them had previously been detected in continental hyperalkaline springs found in serpentinizing environments (The Cedars, Samail, Voltri, and Zambales ophiolites). Gammaproteobacteria, Ca. Gracilibacteria and Thermotogae were significantly more abundant in spring water than in sediments. Potential chemolithotrophs mainly included beta- and gammaproteobacterial genera of sulfate-reducers (Ca. Desulfobacillus), methylotrophs (Methyloversatilis), sulfur-oxidizers (Thiofaba, Thiovirga), or hydrogen-oxidizers (Hydrogenophaga). Methanogens (Methanobacteriales and Methanosarcinales) were the dominant Archaea, as found in serpentinization-driven and deep subsurface ecosystems. A novel alkaliphilic hydrogenotrophic methanogen (strain CAN) belonging to the genus Methanobacterium was isolated, suggesting that hydrogenotrophic methanogenesis occurs at La Crouen.
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
Leprich DJ, Flood BE, Schroedl PR, Ricci E, Marlow JJ, Girguis PR, Bailey JV. Sulfur bacteria promote dissolution of authigenic carbonates at marine methane seeps. ISME JOURNAL 2021; 15:2043-2056. [PMID: 33574572 PMCID: PMC8245480 DOI: 10.1038/s41396-021-00903-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 12/21/2020] [Accepted: 01/20/2021] [Indexed: 01/04/2023]
Abstract
Carbonate rocks at marine methane seeps are commonly colonized by sulfur-oxidizing bacteria that co-occur with etch pits that suggest active dissolution. We show that sulfur-oxidizing bacteria are abundant on the surface of an exemplar seep carbonate collected from Del Mar East Methane Seep Field, USA. We then used bioreactors containing aragonite mineral coupons that simulate certain seep conditions to investigate plausible in situ rates of carbonate dissolution associated with sulfur-oxidizing bacteria. Bioreactors inoculated with a sulfur-oxidizing bacterial strain, Celeribacter baekdonensis LH4, growing on aragonite coupons induced dissolution rates in sulfidic, heterotrophic, and abiotic conditions of 1773.97 (±324.35), 152.81 (±123.27), and 272.99 (±249.96) μmol CaCO3 • cm−2 • yr−1, respectively. Steep gradients in pH were also measured within carbonate-attached biofilms using pH-sensitive fluorophores. Together, these results show that the production of acidic microenvironments in biofilms of sulfur-oxidizing bacteria are capable of dissolving carbonate rocks, even under well-buffered marine conditions. Our results support the hypothesis that authigenic carbonate rock dissolution driven by lithotrophic sulfur-oxidation constitutes a previously unknown carbon flux from the rock reservoir to the ocean and atmosphere.
Collapse
Affiliation(s)
- Dalton J Leprich
- Department of Earth and Environmental Sciences, University of Minnesota Twin-Cities, Minneapolis, MN, 55455, USA.
| | - Beverly E Flood
- Department of Earth and Environmental Sciences, University of Minnesota Twin-Cities, Minneapolis, MN, 55455, USA
| | - Peter R Schroedl
- Department of Earth and Environmental Sciences, University of Minnesota Twin-Cities, Minneapolis, MN, 55455, USA
| | - Elizabeth Ricci
- Department of Earth and Environmental Sciences, University of Minnesota Twin-Cities, Minneapolis, MN, 55455, USA
| | - Jeffery J Marlow
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Jake V Bailey
- Department of Earth and Environmental Sciences, University of Minnesota Twin-Cities, Minneapolis, MN, 55455, USA.
| |
Collapse
|
32
|
Molecular Evidence for an Active Microbial Methane Cycle in Subsurface Serpentinite-Hosted Groundwaters in the Samail Ophiolite, Oman. Appl Environ Microbiol 2021; 87:AEM.02068-20. [PMID: 33127818 DOI: 10.1128/aem.02068-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/20/2020] [Indexed: 01/04/2023] Open
Abstract
Serpentinization can generate highly reduced fluids replete with hydrogen (H2) and methane (CH4), potent reductants capable of driving microbial methanogenesis and methanotrophy, respectively. However, CH4 in serpentinized waters is thought to be primarily abiogenic, raising key questions about the relative importance of methanogens and methanotrophs in the production and consumption of CH4 in these systems. Herein, we apply molecular approaches to examine the functional capability and activity of microbial CH4 cycling in serpentinization-impacted subsurface waters intersecting multiple rock and water types within the Samail Ophiolite of Oman. Abundant 16S rRNA genes and transcripts affiliated with the methanogenic genus Methanobacterium were recovered from the most alkaline (pH, >10), H2- and CH4-rich subsurface waters. Additionally, 16S rRNA genes and transcripts associated with the aerobic methanotrophic genus Methylococcus were detected in wells that spanned varied fluid geochemistry. Metagenomic sequencing yielded genes encoding homologs of proteins involved in the hydrogenotrophic pathway of microbial CH4 production and in microbial CH4 oxidation. Transcripts of several key genes encoding methanogenesis/methanotrophy enzymes were identified, predominantly in communities from the most hyperalkaline waters. These results indicate active methanogenic and methanotrophic populations in waters with hyperalkaline pH in the Samail Ophiolite, thereby supporting a role for biological CH4 cycling in aquifers that undergo low-temperature serpentinization.IMPORTANCE Serpentinization of ultramafic rock can generate conditions favorable for microbial methane (CH4) cycling, including the abiotic production of hydrogen (H2) and possibly CH4 Systems of low-temperature serpentinization are geobiological targets due to their potential to harbor microbial life and ubiquity throughout Earth's history. Biomass in fracture waters collected from the Samail Ophiolite of Oman, a system undergoing modern serpentinization, yielded DNA and RNA signatures indicative of active microbial methanogenesis and methanotrophy. Intriguingly, transcripts for proteins involved in methanogenesis were most abundant in the most highly reacted waters that have hyperalkaline pH and elevated concentrations of H2 and CH4 These findings suggest active biological methane cycling in serpentinite-hosted aquifers, even under extreme conditions of high pH and carbon limitation. These observations underscore the potential for microbial activity to influence the isotopic composition of CH4 in these systems, which is information that could help in identifying biosignatures of microbial activity on other planets.
Collapse
|
33
|
Postec A, Quéméneur M, Lecoeuvre A, Chabert N, Joseph M, Erauso G. Alkaliphilus serpentinus sp. nov. and Alkaliphilus pronyensis sp. nov., two novel anaerobic alkaliphilic species isolated from the serpentinite-hosted Prony Bay Hydrothermal Field (New Caledonia). Syst Appl Microbiol 2020; 44:126175. [PMID: 33422701 DOI: 10.1016/j.syapm.2020.126175] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 11/26/2022]
Abstract
Two novel anaerobic alkaliphilic strains, designated as LacTT and LacVT, were isolated from the Prony Bay Hydrothermal Field (PBHF, New Caledonia). Cells were motile, Gram-positive, terminal endospore-forming rods, displaying a straight to curved morphology during the exponential phase. Strains LacTT and LacVT were mesophilic (optimum 30°C), moderately alkaliphilic (optimum pH 8.2 and 8.7, respectively) and halotolerant (optimum 2% and 2.5% NaCl, respectively). Both strains were able to ferment yeast extract, peptone and casamino acids, but only strain LacTT could use sugars (glucose, maltose and sucrose). Both strains disproportionated crotonate into acetate and butyrate. Phylogenetic analysis revealed that strains LacTT and LacVT shared 96.4% 16S rRNA gene sequence identity and were most closely related to A. peptidifermentans Z-7036, A. namsaraevii X-07-2 and A. hydrothermalis FatMR1 (95.7%-96.3%). Their genome size was of 3.29Mb for strain LacTT and 3.06Mb for strain LacVT with a G+C content of 36.0 and 33.9mol%, respectively. The ANI value between both strains was 73.2 %. Finally, strains LacTT (=DSM 100337=JCM 30643) and LacVT (=DSM 100017=JCM 30644) are proposed as two novel species of the genus Alkaliphilus, order Clostridiales, phylum Firmicutes, Alkaliphilus serpentinus sp. nov. and Alkaliphilus pronyensis sp. nov., respectively. The genomes of the three Alkaliphilus species isolated from PBHF were consistently detected in the PBHF chimney metagenomes, although at very low abundance, but not significantly in the metagenomes of other serpentinizing systems (marine or terrestrial) worldwide, suggesting they represent indigenous members of the PBHF microbial ecosystem.
Collapse
Affiliation(s)
- Anne Postec
- AixMarseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France.
| | - Marianne Quéméneur
- AixMarseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Aurélien Lecoeuvre
- Université de Paris, Institut de Physique du Globe de Paris, CNRS UMR 7154, Paris, France
| | - Nicolas Chabert
- AixMarseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Manon Joseph
- AixMarseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Gaël Erauso
- AixMarseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| |
Collapse
|
34
|
Lecoeuvre A, Ménez B, Cannat M, Chavagnac V, Gérard E. Microbial ecology of the newly discovered serpentinite-hosted Old City hydrothermal field (southwest Indian ridge). ISME JOURNAL 2020; 15:818-832. [PMID: 33139872 PMCID: PMC8027613 DOI: 10.1038/s41396-020-00816-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 10/13/2020] [Accepted: 10/19/2020] [Indexed: 01/06/2023]
Abstract
Lost City (mid-Atlantic ridge) is a unique oceanic hydrothermal field where carbonate-brucite chimneys are colonized by a single phylotype of archaeal Methanosarcinales, as well as sulfur- and methane-metabolizing bacteria. So far, only one submarine analog of Lost City has been characterized, the Prony Bay hydrothermal field (New Caledonia), which nonetheless shows more microbiological similarities with ecosystems associated with continental ophiolites. This study presents the microbial ecology of the ‘Lost City’-type Old City hydrothermal field, recently discovered along the southwest Indian ridge. Five carbonate-brucite chimneys were sampled and subjected to mineralogical and geochemical analyses, microimaging, as well as 16S rRNA-encoding gene and metagenomic sequencing. Dominant taxa and metabolisms vary between chimneys, in conjunction with the predicted redox state, while potential formate- and CO-metabolizing microorganisms as well as sulfur-metabolizing bacteria are always abundant. We hypothesize that the variable environmental conditions resulting from the slow and diffuse hydrothermal fluid discharge that currently characterizes Old City could lead to different microbial populations between chimneys that utilize CO and formate differently as carbon or electron sources. Old City discovery and this first description of its microbial ecology opens up attractive perspectives for understanding environmental factors shaping communities and metabolisms in oceanic serpentinite-hosted ecosystems.
Collapse
Affiliation(s)
- Aurélien Lecoeuvre
- Université de Paris, Institut de physique du globe de Paris, CNRS UMR 7154, Paris, France.
| | - Bénédicte Ménez
- Université de Paris, Institut de physique du globe de Paris, CNRS UMR 7154, Paris, France
| | - Mathilde Cannat
- Université de Paris, Institut de physique du globe de Paris, CNRS UMR 7154, Paris, France
| | - Valérie Chavagnac
- Université de Toulouse, Géosciences Environnement Toulouse, CNRS UMR 5563, Toulouse, France
| | - Emmanuelle Gérard
- Université de Paris, Institut de physique du globe de Paris, CNRS UMR 7154, Paris, France
| |
Collapse
|
35
|
Seyler L, Kujawinski EB, Azua-Bustos A, Lee MD, Marlow J, Perl SM, Cleaves II HJ. Metabolomics as an Emerging Tool in the Search for Astrobiologically Relevant Biomarkers. ASTROBIOLOGY 2020; 20:1251-1261. [PMID: 32551936 PMCID: PMC7116171 DOI: 10.1089/ast.2019.2135] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
It is now routinely possible to sequence and recover microbial genomes from environmental samples. To the degree it is feasible to assign transcriptional and translational functions to these genomes, it should be possible, in principle, to largely understand the complete molecular inputs and outputs of a microbial community. However, gene-based tools alone are presently insufficient to describe the full suite of chemical reactions and small molecules that compose a living cell. Metabolomic tools have developed quickly and now enable rapid detection and identification of small molecules within biological and environmental samples. The convergence of these technologies will soon facilitate the detection of novel enzymatic activities, novel organisms, and potentially extraterrestrial life-forms on solar system bodies. This review explores the methodological problems and scientific opportunities facing researchers who hope to apply metabolomic methods in astrobiology-related fields, and how present challenges might be overcome.
Collapse
Affiliation(s)
- Lauren Seyler
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Address correspondence to: Lauren Seyler, Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, 86 Water Street, Woods Hole, MA 02543, USA
| | - Elizabeth B. Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Armando Azua-Bustos
- Department of Planetology and Habitability, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago, Chile
| | - Michael D. Lee
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Exobiology Branch, NASA Ames Research Center, Moffett Field, California, USA
| | - Jeffrey Marlow
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Scott M. Perl
- Geological and Planetary Sciences, California Institute of Technology/NASA Jet Propulsion Laboratory, Pasadena, California, USA
- Mineral Sciences, Los Angeles Natural History Museum, Los Angeles, California, USA
| | - Henderson James Cleaves II
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- School of Natural Sciences, Institute for Advanced Study, Princeton, New Jersey, USA
- Geographical Research Laboratory, Carnegie Institution of Washington
| |
Collapse
|
36
|
Seto M, Iwasa Y. Microbial material cycling, energetic constraints and ecosystem expansion in subsurface ecosystems. Proc Biol Sci 2020; 287:20200610. [PMID: 33043868 PMCID: PMC7423649 DOI: 10.1098/rspb.2020.0610] [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] [Indexed: 01/21/2023] Open
Abstract
To harvest energy from chemical reactions, microbes engage in diverse catabolic interactions that drive material cycles in the environment. Here, we consider a simple mathematical model for cycling reactions between alternative forms of an element (A and Ae), where reaction 1 converts A to Ae and reaction 2 converts Ae to A. There are two types of microbes: type 1 microbes harness reaction 1, and type 2 microbes harness reaction 2. Each type receives its own catabolic resources from the other type and provides the other type with the by-products as the catabolic resources. Analyses of the model show that each type increases its steady-state abundance in the presence of the other type. The flux of material flow becomes faster in the presence of microbes. By coupling two catabolic reactions, types 1 and 2 can also expand their realized niches through the abundant resource premium, the effect of relative quantities of products and reactants on the available chemical energy, which is especially important for microbes under strong energetic limitations. The plausibility of mutually beneficial interactions is controlled by the available chemical energy (Gibbs energy) of the system. We conclude that mutualistic catabolic interactions can be an important factor that enables microbes in subsurface ecosystems to increase ecosystem productivity and expand the ecosystem.
Collapse
Affiliation(s)
- Mayumi Seto
- Department of Chemistry, Biology, and Environmental Sciences, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
| | - Yoh Iwasa
- Department of Bioscience, School of Science and Technology, Kwansei Gakuin University, Gakuen 2-1, Sanda-shi, Hyogo 669-1337, Japan
| |
Collapse
|
37
|
Newman SA, Lincoln SA, O'Reilly S, Liu X, Shock EL, Kelemen PB, Summons RE. Lipid Biomarker Record of the Serpentinite-Hosted Ecosystem of the Samail Ophiolite, Oman and Implications for the Search for Biosignatures on Mars. ASTROBIOLOGY 2020; 20:830-845. [PMID: 32648829 DOI: 10.1089/ast.2019.2066] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Serpentinization is a weathering process in which ultramafic rocks react with water, generating a range of products, including serpentine and other minerals, in addition to H2 and low-molecular-weight hydrocarbons that are capable of sustaining microbial life. Lipid biomarker analyses of serpentinite-hosted ecosystems hold promise as tools for investigating microbial activity in ancient Earth environments and other terrestrial planets such as Mars because lipids have the potential for longer term preservation relative to DNA, proteins, and other more labile organic molecules. Here, we report the first lipid biomarker record of microbial activity in the mantle section of the Samail Ophiolite, in the Sultanate of Oman, a site undergoing active serpentinization. We detected isoprenoidal (archaeal) and branched (bacterial) glycerol dialkyl glycerol tetraether (GDGT) lipids, including those with 0-3 cyclopentane moieties, and crenarchaeol, an isoprenoidal GDGT containing four cyclopentane and one cyclohexane moieties, as well as monoether lipids and fatty acids indicative of sulfate-reducing bacteria. Comparison of our geochemical data and 16S rRNA data from the Samail Ophiolite with those from other serpentinite-hosted sites identifies the existence of a common core serpentinization microbiome. In light of these findings, we also discuss the preservation potential of serpentinite lipid biomarker assemblages on Earth and Mars. Continuing investigations of the Samail Ophiolite and other terrestrial analogues will enhance our understanding of microbial habitability and diversity in serpentinite-hosted environments on Earth and elsewhere in the Solar System.
Collapse
Affiliation(s)
- Sharon A Newman
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California
| | - Sara A Lincoln
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Geosciences, The Pennsylvania State University, University Park, Pennsylvania
| | - Shane O'Reilly
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
- School of Earth Sciences, University College Dublin, Belfield, Ireland
| | - Xiaolei Liu
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
- School of Geology and Geophysics, University of Oklahoma, Norman, Oklahoma
| | - Everett L Shock
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona
| | - Peter B Kelemen
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York
| | - Roger E Summons
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
| |
Collapse
|
38
|
Jin D, Zhang F, Shi Y, Kong X, Xie Y, Du X, Li Y, Zhang R. Diversity of bacteria and archaea in the groundwater contaminated by chlorinated solvents undergoing natural attenuation. ENVIRONMENTAL RESEARCH 2020; 185:109457. [PMID: 32247910 DOI: 10.1016/j.envres.2020.109457] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 03/27/2020] [Accepted: 03/27/2020] [Indexed: 06/11/2023]
Abstract
Chlorinated solvents (CS)-contaminated groundwater poses serious risks to the environment and public health. Microorganisms play a vital role in efficient remediation of CS. In this study, the microbial community (bacterial and archaeal) composition of three CS-contaminated groundwater wells located at an abandoned chemical factory which covers three orders of magnitude in concentration (0.02-16.15 mg/L) were investigated via 16S rRNA gene high-throughput sequencing. The results indicated that Proteobacteria and Thaumarchaeota were the most abundant bacterial and archaeal groups at the phylum level in groundwater, respectively. The major bacterial genera (Flavobacterium sp., Mycobacterium sp. and unclassified Parcubacteria taxa, etc.) and archaeal genera (Thaumarchaeota Group C3, Miscellaneous Crenarchaeotic Group and Miscellaneous Euryarchaeotic Group, etc.) might be involved in the dechlorination processes. In addition, Pearson's correlation analyses showed that alpha diversity of the bacterial community was not significantly correlated with CS concentration, while alpha diversity of archaeal community greatly decreased with the increased contamination of CS. Moreover, partial Mantel test indicated that oxidation-reduction potential, dissolved oxygen, temperature and methane concentration were major drivers of bacterial and archaeal community composition, whereas CS concentration had no significant impact, indicating that both indigenous bacterial and archaeal community compositions are capable of withstanding elevated CS contamination. This study improves our understanding of how the natural microbial community responds to high CS-contaminated groundwater.
Collapse
Affiliation(s)
- Decai Jin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fengsong Zhang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yi Shi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Xiao Kong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunfeng Xie
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Xiaoming Du
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Yanxia Li
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Ruiyong Zhang
- Federal Institute for Geosciences and Natural Resources (BGR), Hannover, 30655, Germany
| |
Collapse
|
39
|
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.
Collapse
|
40
|
Sabuda MC, Brazelton WJ, Putman LI, McCollom TM, Hoehler TM, Kubo MDY, Cardace D, Schrenk MO. A dynamic microbial sulfur cycle in a serpentinizing continental ophiolite. Environ Microbiol 2020; 22:2329-2345. [PMID: 32249550 DOI: 10.1111/1462-2920.15006] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 03/19/2020] [Accepted: 03/30/2020] [Indexed: 12/11/2022]
Abstract
Serpentinization is the hydration and oxidation of ultramafic rock, which occurs as oceanic lithosphere is emplaced onto continental margins (ophiolites), and along the seafloor as faulting exposes this mantle-derived material to circulating hydrothermal fluids. This process leads to distinctive fluid chemistries as molecular hydrogen (H2 ) and hydroxyl ions (OH- ) are produced and reduced carbon compounds are mobilized. Serpentinizing ophiolites also serve as a vector to transport sulfur compounds from the seafloor onto the continents. We investigated hyperalkaline, sulfur-rich, brackish groundwater in a serpentinizing continental ophiolite to elucidate the role of sulfur compounds in fuelling in situ microbial activities. Here we illustrate that key sulfur-cycling taxa, including Dethiobacter, Desulfitispora and 'Desulforudis', persist throughout this extreme environment. Biologically catalysed redox reactions involving sulfate, sulfide and intermediate sulfur compounds are thermodynamically favourable in the groundwater, which indicates they may be vital to sustaining life in these characteristically oxidant- and energy-limited systems. Furthermore, metagenomic and metatranscriptomic analyses reveal a complex network involving sulfate reduction, sulfide oxidation and thiosulfate reactions. Our findings highlight the importance of the complete inorganic sulfur cycle in serpentinizing fluids and suggest sulfur biogeochemistry provides a key link between terrestrial serpentinizing ecosystems and their submarine heritage.
Collapse
Affiliation(s)
- Mary C Sabuda
- Department of Earth and Environmental Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Lindsay I Putman
- Department of Earth and Environmental Sciences, Michigan State University, East Lansing, MI, 48824, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - Tom M McCollom
- Laboratory for Atmospheric and Space Physics, UCB 600, University of Colorado-Boulder, Boulder, CO, 80309, USA
| | - Tori M Hoehler
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Michael D Y Kubo
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, 94035, USA.,SETI Institute, Mountain View, CA, 94043, USA
| | - Dawn Cardace
- Department of Geosciences, University of Rhode Island, Kingston, RI, 02881, USA
| | - Matthew O Schrenk
- Department of Earth and Environmental Sciences, Michigan State University, East Lansing, MI, 48824, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| |
Collapse
|
41
|
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.
Collapse
|
42
|
Lang SQ, Brazelton WJ. Habitability of the marine serpentinite subsurface: a case study of the Lost City hydrothermal field. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020; 378:20180429. [PMID: 31902336 PMCID: PMC7015304 DOI: 10.1098/rsta.2018.0429] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
The Lost City hydrothermal field is a dramatic example of the biological potential of serpentinization. Microbial life is prevalent throughout the Lost City chimneys, powered by the hydrogen gas and organic molecules produced by serpentinization and its associated geochemical reactions. Microbial life in the serpentinite subsurface below the Lost City chimneys, however, is unlikely to be as dense or active. The marine serpentinite subsurface poses serious challenges for microbial activity, including low porosities, the combination of stressors of elevated temperature, high pH and a lack of bioavailable ∑CO2. A better understanding of the biological opportunities and challenges in serpentinizing systems would provide important insights into the total habitable volume of Earth's crust and for the potential of the origin and persistence of life in Earth's subsurface environments. Furthermore, the limitations to life in serpentinizing subsurface environments on Earth have significant implications for the habitability of subsurface environments on ocean worlds such as Europa and Enceladus. Here, we review the requirements and limitations of life in serpentinizing systems, informed by our research at the Lost City and the underwater mountain on which it resides, the Atlantis Massif. This article is part of a discussion meeting issue 'Serpentinite in the Earth System'.
Collapse
Affiliation(s)
- Susan Q. Lang
- School of the Earth, Ocean, and Environment, University of South Carolina, Columbia, SC 29208, USA
| | | |
Collapse
|
43
|
Magnuson E, Mykytczuk NC, Pellerin A, Goordial J, Twine SM, Wing B, Foote SJ, Fulton K, Whyte LG. Thiomicrorhabdus
streamers and sulfur cycling in perennial hypersaline cold springs in the Canadian high Arctic. Environ Microbiol 2020; 23:3384-3400. [DOI: 10.1111/1462-2920.14916] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 12/10/2019] [Accepted: 01/08/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Elisse Magnuson
- Natural Resource Sciences McGill University Montreal QC Canada
| | | | - Andre Pellerin
- Centre for Geomicrobiology Aarhus University Aarhus Denmark
| | - Jacqueline Goordial
- Natural Resource Sciences McGill University Montreal QC Canada
- School of Environmental Sciences University of Guelph Guelph, ON Canada
| | - Susan M. Twine
- Institute for Biological Sciences National Research Council Ottawa Ontario
| | - Boswell Wing
- Earth and Planetary Sciences McGill University Montreal QC Canada
| | - Simon J. Foote
- Institute for Biological Sciences National Research Council Ottawa Ontario
| | - Kelly Fulton
- Institute for Biological Sciences National Research Council Ottawa Ontario
| | - Lyle G. Whyte
- Natural Resource Sciences McGill University Montreal QC Canada
| |
Collapse
|
44
|
Taubner RS, Olsson-Francis K, Vance SD, Ramkissoon NK, Postberg F, de Vera JP, Antunes A, Camprubi Casas E, Sekine Y, Noack L, Barge L, Goodman J, Jebbar M, Journaux B, Karatekin Ö, Klenner F, Rabbow E, Rettberg P, Rückriemen-Bez T, Saur J, Shibuya T, Soderlund KM. Experimental and Simulation Efforts in the Astrobiological Exploration of Exooceans. SPACE SCIENCE REVIEWS 2020; 216:9. [PMID: 32025060 PMCID: PMC6977147 DOI: 10.1007/s11214-020-0635-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/06/2020] [Indexed: 05/05/2023]
Abstract
The icy satellites of Jupiter and Saturn are perhaps the most promising places in the Solar System regarding habitability. However, the potential habitable environments are hidden underneath km-thick ice shells. The discovery of Enceladus' plume by the Cassini mission has provided vital clues in our understanding of the processes occurring within the interior of exooceans. To interpret these data and to help configure instruments for future missions, controlled laboratory experiments and simulations are needed. This review aims to bring together studies and experimental designs from various scientific fields currently investigating the icy moons, including planetary sciences, chemistry, (micro-)biology, geology, glaciology, etc. This chapter provides an overview of successful in situ, in silico, and in vitro experiments, which explore different regions of interest on icy moons, i.e. a potential plume, surface, icy shell, water and brines, hydrothermal vents, and the rocky core.
Collapse
Affiliation(s)
- Ruth-Sophie Taubner
- Archaea Biology and Ecogenomics Division, University of Vienna, Vienna, Austria
| | | | | | | | | | | | - André Antunes
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology, Macau SAR, China
| | | | | | - Lena Noack
- Freie Universität Berlin, Berlin, Germany
| | | | | | | | | | | | | | - Elke Rabbow
- German Aerospace Center (DLR), Cologne, Germany
| | | | | | | | - Takazo Shibuya
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | | |
Collapse
|
45
|
Galambos D, Anderson RE, Reveillaud J, Huber JA. Genome-resolved metagenomics and metatranscriptomics reveal niche differentiation in functionally redundant microbial communities at deep-sea hydrothermal vents. Environ Microbiol 2019; 21:4395-4410. [PMID: 31573126 PMCID: PMC6899741 DOI: 10.1111/1462-2920.14806] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/12/2019] [Accepted: 09/13/2019] [Indexed: 12/11/2022]
Abstract
The structure and function of microbial communities inhabiting the subseafloor near hydrothermal systems are influenced by fluid geochemistry, geologic setting and fluid flux between vent sites, as well as biological interactions. Here, we used genome-resolved metagenomics and metatranscriptomics to examine patterns of gene abundance and expression and assess potential niche differentiation in microbial communities in venting fluids from hydrothermal vent sites at the Mid-Cayman Rise. We observed similar patterns in gene and transcript abundance between two geochemically distinct vent fields at the community level but found that each vent site harbours a distinct microbial community with differing transcript abundances for individual microbial populations. Through an analysis of metabolic pathways in 64 metagenome-assembled genomes (MAGs), we show that MAG transcript abundance can be tied to differences in metabolic pathways and to potential metabolic interactions between microbial populations, allowing for niche-partitioning and divergence in both population distribution and activity. Our results illustrate that most microbial populations have a restricted distribution within the seafloor, and that the activity of those microbial populations is tied to both genome content and abiotic factors.
Collapse
Affiliation(s)
- David Galambos
- Biology DepartmentCarleton CollegeNorthfieldMinnesotaUSA
| | | | | | - Julie A. Huber
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| |
Collapse
|
46
|
Preiner M, Xavier JC, Vieira ADN, Kleinermanns K, Allen JF, Martin WF. Catalysts, autocatalysis and the origin of metabolism. Interface Focus 2019; 9:20190072. [PMID: 31641438 PMCID: PMC6802133 DOI: 10.1098/rsfs.2019.0072] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/30/2019] [Indexed: 12/24/2022] Open
Abstract
If life on Earth started out in geochemical environments like hydrothermal vents, then it started out from gasses like CO2, N2 and H2. Anaerobic autotrophs still live from these gasses today, and they still inhabit the Earth's crust. In the search for connections between abiotic processes in ancient geological systems and biotic processes in biological systems, it becomes evident that chemical activation (catalysis) of these gasses and a constant source of energy are key. The H2–CO2 redox reaction provides a constant source of energy and anabolic inputs, because the equilibrium lies on the side of reduced carbon compounds. Identifying geochemical catalysts that activate these gasses en route to nitrogenous organic compounds and small autocatalytic networks will be an important step towards understanding prebiotic chemistry that operates only on the basis of chemical energy, without input from solar radiation. So, if life arose in the dark depths of hydrothermal vents, then understanding reactions and catalysts that operate under such conditions is crucial for understanding origins.
Collapse
Affiliation(s)
- Martina Preiner
- Institute for Molecular Evolution, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Joana C Xavier
- Institute for Molecular Evolution, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | | | - Karl Kleinermanns
- Institute for Physical Chemistry, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - John F Allen
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - William F Martin
- Institute for Molecular Evolution, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| |
Collapse
|
47
|
Bhattarai S, Cassarini C, Lens PNL. Physiology and Distribution of Archaeal Methanotrophs That Couple Anaerobic Oxidation of Methane with Sulfate Reduction. Microbiol Mol Biol Rev 2019; 83:e00074-18. [PMID: 31366606 PMCID: PMC6710461 DOI: 10.1128/mmbr.00074-18] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In marine anaerobic environments, methane is oxidized where sulfate-rich seawater meets biogenic or thermogenic methane. In those niches, a few phylogenetically distinct microbial types, i.e., anaerobic methanotrophs (ANME), are able to grow through anaerobic oxidation of methane (AOM). Due to the relevance of methane in the global carbon cycle, ANME have drawn the attention of a broad scientific community for 4 decades. This review presents and discusses the microbiology and physiology of ANME up to the recent discoveries, revealing novel physiological types of anaerobic methane oxidizers which challenge the view of obligate syntrophy for AOM. An overview of the drivers shaping the distribution of ANME in different marine habitats, from cold seep sediments to hydrothermal vents, is given. Multivariate analyses of the abundance of ANME in various habitats identify a distribution of distinct ANME types driven by the mode of methane transport. Intriguingly, ANME have not yet been cultivated in pure culture, despite intense attempts. Further advances in understanding this microbial process are hampered by insufficient amounts of enriched cultures. This review discusses the advantages, limitations, and potential improvements for ANME laboratory-based cultivation systems.
Collapse
Affiliation(s)
- S Bhattarai
- UNESCO-IHE, Institute for Water Education, Delft, The Netherlands
| | - C Cassarini
- UNESCO-IHE, Institute for Water Education, Delft, The Netherlands
- National University of Ireland Galway, Galway, Ireland
| | - P N L Lens
- UNESCO-IHE, Institute for Water Education, Delft, The Netherlands
- National University of Ireland Galway, Galway, Ireland
| |
Collapse
|
48
|
Eickenbusch P, Takai K, Sissman O, Suzuki S, Menzies C, Sakai S, Sansjofre P, Tasumi E, Bernasconi SM, Glombitza C, Jørgensen BB, Morono Y, Lever MA. Origin of Short-Chain Organic Acids in Serpentinite Mud Volcanoes of the Mariana Convergent Margin. Front Microbiol 2019; 10:1729. [PMID: 31404165 PMCID: PMC6677109 DOI: 10.3389/fmicb.2019.01729] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 07/12/2019] [Indexed: 11/17/2022] Open
Abstract
Serpentinitic systems are potential habitats for microbial life due to frequently high concentrations of microbial energy substrates, such as hydrogen (H2), methane (CH4), and short-chain organic acids (SCOAs). Yet, many serpentinitic systems are also physiologically challenging environments due to highly alkaline conditions (pH > 10) and elevated temperatures (>80°C). To elucidate the possibility of microbial life in deep serpentinitic crustal environments, International Ocean Discovery Program (IODP) Expedition 366 drilled into the Yinazao, Fantangisña, and Asùt Tesoru serpentinite mud volcanoes on the Mariana Forearc. These mud volcanoes differ in temperature (80, 150, 250°C, respectively) of the underlying subducting slab, and in the porewater pH (11.0, 11.2, 12.5, respectively) of the serpentinite mud. Increases in formate and acetate concentrations across the three mud volcanoes, which are positively correlated with temperature in the subducting slab and coincide with strong increases in H2 concentrations, indicate a serpentinization-related origin. Thermodynamic calculations suggest that formate is produced by equilibrium reactions with dissolved inorganic carbon (DIC) + H2, and that equilibration continues during fluid ascent at temperatures below 80°C. By contrast, the mechanism(s) of acetate production are not clear. Besides formate, acetate, and H2 data, we present concentrations of other SCOAs, methane, carbon monoxide, and sulfate, δ13C-data on bulk carbon pools, and microbial cell counts. Even though calculations indicate a wide range of microbial catabolic reactions to be thermodynamically favorable, concentration profiles of potential energy substrates, and very low cell numbers suggest that microbial life is scarce or absent. We discuss the potential roles of temperature, pH, pressure, and dispersal in limiting the occurrence of microbial life in deep serpentinitic environments.
Collapse
Affiliation(s)
- Philip Eickenbusch
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zurich, Switzerland
| | - Ken Takai
- SUGAR Program, Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science Technology, Yokosuka, Japan
| | | | - Shino Suzuki
- Geomicrobiology Research Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, Kochi, Japan
| | - Catriona Menzies
- Ocean and Earth Science, National Oceanography Centre, University of Southampton, Southampton, United Kingdom.,Department of Geology and Petroleum Geology, University of Aberdeen, Aberdeen, United Kingdom
| | - Sanae Sakai
- SUGAR Program, Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science Technology, Yokosuka, Japan
| | - Pierre Sansjofre
- Laboratoire Géosciences Océan UMR 6538, Université de Bretagne Occidentale, Brest, France
| | - Eiji Tasumi
- SUGAR Program, Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science Technology, Yokosuka, Japan
| | | | - Clemens Glombitza
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zurich, Switzerland.,NASA Ames Research Center, Moffett Field, CA, United States
| | - Bo Barker Jørgensen
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Yuki Morono
- Geomicrobiology Research Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, Kochi, Japan
| | - Mark Alexander Lever
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zurich, Switzerland
| |
Collapse
|
49
|
Quéméneur M, Erauso G, Frouin E, Zeghal E, Vandecasteele C, Ollivier B, Tamburini C, Garel M, Ménez B, Postec A. Hydrostatic Pressure Helps to Cultivate an Original Anaerobic Bacterium From the Atlantis Massif Subseafloor (IODP Expedition 357): Petrocella atlantisensis gen. nov. sp. nov. Front Microbiol 2019; 10:1497. [PMID: 31379757 PMCID: PMC6647913 DOI: 10.3389/fmicb.2019.01497] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/14/2019] [Indexed: 01/03/2023] Open
Abstract
Rock-hosted subseafloor habitats are very challenging for life, and current knowledge about microorganisms inhabiting such lithic environments is still limited. This study explored the cultivable microbial diversity in anaerobic enrichment cultures from cores recovered during the International Ocean Discovery Program (IODP) Expedition 357 from the Atlantis Massif (Mid-Atlantic Ridge, 30°N). 16S rRNA gene survey of enrichment cultures grown at 10–25°C and pH 8.5 showed that Firmicutes and Proteobacteria were generally dominant. However, cultivable microbial diversity significantly differed depending on incubation at atmospheric pressure (0.1 MPa), or hydrostatic pressures (HP) mimicking the in situ pressure conditions (8.2 or 14.0 MPa). An original, strictly anaerobic bacterium designated 70B-AT was isolated from core M0070C-3R1 (1150 meter below sea level; 3.5 m below seafloor) only from cultures performed at 14.0 MPa. This strain named Petrocella atlantisensis is a novel species of a new genus within the newly described family Vallitaleaceae (order Clostridiales, phylum Firmicutes). It is a mesophilic, moderately halotolerant and piezophilic chemoorganotroph, able to grow by fermentation of carbohydrates and proteinaceous compounds. Its 3.5 Mb genome contains numerous genes for ABC transporters of sugars and amino acids, and pathways for fermentation of mono- and di-saccharides and amino acids were identified. Genes encoding multimeric [FeFe] hydrogenases and a Rnf complex form the basis to explain hydrogen and energy production in strain 70B-AT. This study outlines the importance of using hydrostatic pressure in culture experiments for isolation and characterization of autochthonous piezophilic microorganisms from subseafloor rocks.
Collapse
Affiliation(s)
- Marianne Quéméneur
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France
| | - Gaël Erauso
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France
| | - Eléonore Frouin
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France
| | - Emna Zeghal
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France
| | | | - Bernard Ollivier
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France
| | - Christian Tamburini
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France
| | - Marc Garel
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France
| | - Bénédicte Ménez
- Université de Paris, Institut de Physique du Globe de Paris, CNRS UMR 7154, Paris, France
| | - Anne Postec
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France
| |
Collapse
|
50
|
Klasek SA, Torres ME, Loher M, Bohrmann G, Pape T, Colwell FS. Deep-Sourced Fluids From a Convergent Margin Host Distinct Subseafloor Microbial Communities That Change Upon Mud Flow Expulsion. Front Microbiol 2019; 10:1436. [PMID: 31281306 PMCID: PMC6596357 DOI: 10.3389/fmicb.2019.01436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/07/2019] [Indexed: 11/13/2022] Open
Abstract
Submarine mud volcanoes (MVs) along continental margins emit mud breccia and globally significant amounts of hydrocarbon-rich fluids from the subsurface, and host distinct chemosynthetic communities of microbes and macrofauna. Venere MV lies at 1,600 m water depth in the Ionian Sea offshore Italy and is located in a forearc basin of the Calabrian accretionary prism. Porewaters of recently extruded mud breccia flowing from its west summit are considerably fresher than seawater (10 PSU), high in Li+ and B (up to 300 and 8,000 μM, respectively), and strongly depleted in K+ (<1 mM) at depths as shallow as 20 cm below seafloor. These properties document upward transport of fluids sourced from >3 km below seafloor. 16S rRNA gene and metagenomic sequencing were used to characterize microbial community composition and gene content within deep-sourced mud breccia flow deposits as they become exposed to seawater along a downslope transect of Venere MV. Summit samples showed consistency in microbial community composition. However, beta-diversity increased markedly in communities from downslope cores, which were dominated by methyl- and methanotrophic genera of Gammaproteobacteria. Methane, sulfate, and chloride concentrations were minor but significant contributors to variation in community composition. Metagenomic analyses revealed differences in relative abundances of predicted protein categories between Venere MV and other subsurface microbial communities, characterizing MVs as windows into distinct deep biosphere habitats.
Collapse
Affiliation(s)
- Scott A Klasek
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, United States
| | - Marta E Torres
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
| | - Markus Loher
- MARUM - Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Gerhard Bohrmann
- MARUM - Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Thomas Pape
- MARUM - Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Frederick S Colwell
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, United States.,College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
| |
Collapse
|