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Garry M, Farasin J, Drevillon L, Quaiser A, Bouchez C, Le Borgne T, Coffinet S, Dufresne A. Ferriphaselus amnicola strain GF-20, a new iron- and thiosulfate-oxidizing bacterium isolated from a hard rock aquifer. FEMS Microbiol Ecol 2024; 100:fiae047. [PMID: 38573825 PMCID: PMC11044966 DOI: 10.1093/femsec/fiae047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/18/2024] [Accepted: 04/03/2024] [Indexed: 04/06/2024] Open
Abstract
Ferriphaselus amnicola GF-20 is the first Fe-oxidizing bacterium isolated from the continental subsurface. It was isolated from groundwater circulating at 20 m depth in the fractured-rock catchment observatory of Guidel-Ploemeur (France). Strain GF-20 is a neutrophilic, iron- and thiosulfate-oxidizer and grows autotrophically. The strain shows a preference for low oxygen concentrations, which suggests an adaptation to the limiting oxygen conditions of the subsurface. It produces extracellular stalks and dreads when grown with Fe(II) but does not secrete any structure when grown with thiosulfate. Phylogenetic analyses and genome comparisons revealed that strain GF-20 is affiliated with the species F. amnicola and is strikingly similar to F. amnicola strain OYT1, which was isolated from a groundwater seep in Japan. Based on the phenotypic and phylogenetic characteristics, we propose that GF-20 represents a new strain within the species F. amnicola.
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Affiliation(s)
- Mélissa Garry
- Géosciences Rennes, CNRS, Univ Rennes, UMR 6118, Rennes, France
- OSUR, Univ Rennes, UMS 3343, Rennes, France
| | | | - Laetitia Drevillon
- Ecobio—Ecosystèmes, Biodiversité, Evolution, CNRS, Univ Rennes, UMR 6553, Rennes, France
| | - Achim Quaiser
- Ecobio—Ecosystèmes, Biodiversité, Evolution, CNRS, Univ Rennes, UMR 6553, Rennes, France
| | - Camille Bouchez
- Géosciences Rennes, CNRS, Univ Rennes, UMR 6118, Rennes, France
| | | | - Sarah Coffinet
- Ecobio—Ecosystèmes, Biodiversité, Evolution, CNRS, Univ Rennes, UMR 6553, Rennes, France
| | - Alexis Dufresne
- Ecobio—Ecosystèmes, Biodiversité, Evolution, CNRS, Univ Rennes, UMR 6553, Rennes, France
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Hoover RL, Keffer JL, Polson SW, Chan CS. Gallionellaceae pangenomic analysis reveals insight into phylogeny, metabolic flexibility, and iron oxidation mechanisms. mSystems 2023; 8:e0003823. [PMID: 37882557 PMCID: PMC10734462 DOI: 10.1128/msystems.00038-23] [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] [Received: 01/25/2023] [Accepted: 09/20/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Neutrophilic iron-oxidizing bacteria (FeOB) produce copious iron (oxyhydr)oxides that can profoundly influence biogeochemical cycles, notably the fate of carbon and many metals. To fully understand environmental microbial iron oxidation, we need a thorough accounting of iron oxidation mechanisms. In this study, we show the Gallionellaceae FeOB genomes encode both characterized iron oxidases as well as uncharacterized multiheme cytochromes (MHCs). MHCs are predicted to transfer electrons from extracellular substrates and likely confer metabolic capabilities that help Gallionellaceae occupy a range of different iron- and mineral-rich niches. Gallionellaceae appear to specialize in iron oxidation, so it would be advantageous for them to have multiple mechanisms to oxidize various forms of iron, given the many iron minerals on Earth, as well as the physiological and kinetic challenges faced by FeOB. The multiple iron/mineral oxidation mechanisms may help drive the widespread ecological success of Gallionellaceae.
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Affiliation(s)
- Rene L. Hoover
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Jessica L. Keffer
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Shawn W. Polson
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
| | - Clara S. Chan
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
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3
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Li L, Liu Y, Xiao Q, Xiao Z, Meng D, Yang Z, Deng W, Yin H, Liu Z. Dissecting the HGT network of carbon metabolic genes in soil-borne microbiota. Front Microbiol 2023; 14:1173748. [PMID: 37485539 PMCID: PMC10361621 DOI: 10.3389/fmicb.2023.1173748] [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: 02/25/2023] [Accepted: 05/22/2023] [Indexed: 07/25/2023] Open
Abstract
The microbiota inhabiting soil plays a significant role in essential life-supporting element cycles. Here, we investigated the occurrence of horizontal gene transfer (HGT) and established the HGT network of carbon metabolic genes in 764 soil-borne microbiota genomes. Our study sheds light on the crucial role of HGT components in microbiological diversification that could have far-reaching implications in understanding how these microbial communities adapt to changing environments, ultimately impacting agricultural practices. In the overall HGT network of carbon metabolic genes in soil-borne microbiota, a total of 6,770 nodes and 3,812 edges are present. Among these nodes, phyla Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes are predominant. Regarding specific classes, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Bacteroidia, Actinomycetia, Betaproteobacteria, and Clostridia are dominant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) functional assignments of glycosyltransferase (18.5%), glycolysis/gluconeogenesis (8.8%), carbohydrate-related transporter (7.9%), fatty acid biosynthesis (6.5%), benzoate degradation (3.1%) and butanoate metabolism (3.0%) are primarily identified. Glycosyltransferase involved in cell wall biosynthesis, glycosylation, and primary/secondary metabolism (with 363 HGT entries), ranks first overwhelmingly in the list of most frequently identified carbon metabolic HGT enzymes, followed by pimeloyl-ACP methyl ester carboxylesterase, alcohol dehydrogenase, and 3-oxoacyl-ACP reductase. Such HGT events mainly occur in the peripheral functions of the carbon metabolic pathway instead of the core section. The inter-microbe HGT genetic traits in soil-borne microbiota genetic sequences that we recognized, as well as their involvement in the metabolism and regulation processes of carbon organic, suggest a pervasive and substantial effect of HGT on the evolution of microbes.
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Affiliation(s)
- Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yongjun Liu
- Hunan Tobacco Science Institute, Changsha, China
| | - Qinzhi Xiao
- Yongzhou Tobacco Company of Hunan Province, Yongzhou, China
| | - Zhipeng Xiao
- Hengyang Tobacco Company of Hunan Province, Hengyang, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Zhaoyue Yang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Wenqiao Deng
- Changsha Institute of Agricultural Science, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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Tyne RL, Barry PH, Lawson M, Lloyd KG, Giovannelli D, Summers ZM, Ballentine CJ. Identifying and Understanding Microbial Methanogenesis in CO 2 Storage. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37327355 DOI: 10.1021/acs.est.2c08652] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Carbon capture and storage (CCS) is an important component in many national net-zero strategies. Ensuring that CO2 can be safely and economically stored in geological systems is critical. To date, CCS research has focused on the physiochemical behavior of CO2, yet there has been little consideration of the subsurface microbial impact on CO2 storage. However, recent discoveries have shown that microbial processes (e.g., methanogenesis) can be significant. Importantly, methanogenesis may modify the fluid composition and the fluid dynamics within the storage reservoir. Such changes may subsequently reduce the volume of CO2 that can be stored and change the mobility and future trapping systematics of the evolved supercritical fluid. Here, we review the current knowledge of how microbial methanogenesis could impact CO2 storage, including the potential scale of methanogenesis and the range of geologic settings under which this process operates. We find that methanogenesis is possible in all storage target types; however, the kinetics and energetics of methanogenesis will likely be limited by H2 generation. We expect that the bioavailability of H2 (and thus potential of microbial methanogenesis) will be greatest in depleted hydrocarbon fields and least within saline aquifers. We propose that additional integrated monitoring requirements are needed for CO2 storage to trace any biogeochemical processes including baseline, temporal, and spatial studies. Finally, we suggest areas where further research should be targeted in order to fully understand microbial methanogenesis in CO2 storage sites and its potential impact.
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Affiliation(s)
- R L Tyne
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - P H Barry
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | | | - K G Lloyd
- University of Tennessee, Knoxville, Tennessee 37996, United States
| | - D Giovannelli
- University of Naples Federico II, Naples 80138 Italy
| | - Z M Summers
- LanzaTech, Skokie, Illinois 60077, United States
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Hoover RL, Keffer JL, Polson SW, Chan CS. Gallionellaceae pangenomic analysis reveals insight into phylogeny, metabolic flexibility, and iron oxidation mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525709. [PMID: 36747706 PMCID: PMC9900912 DOI: 10.1101/2023.01.26.525709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The iron-oxidizing Gallionellaceae drive a wide variety of biogeochemical cycles through their metabolisms and biominerals. To better understand the environmental impacts of Gallionellaceae, we need to improve our knowledge of their diversity and metabolisms, especially any novel iron oxidation mechanisms. Here, we used a pangenomic analysis of 103 genomes to resolve Gallionellaceae phylogeny and explore the range of genomic potential. Using a concatenated ribosomal protein tree and key gene patterns, we determined Gallionellaceae has four genera, divided into two groups-iron-oxidizing bacteria (FeOB) Gallionella, Sideroxydans, and Ferriphaselus with known iron oxidases (Cyc2, MtoA) and nitrite-oxidizing bacteria (NOB) Candidatus Nitrotoga with nitrite oxidase (Nxr). The FeOB and NOB have similar electron transport chains, including genes for reverse electron transport and carbon fixation. Auxiliary energy metabolisms including S oxidation, denitrification, and organotrophy were scattered throughout the Gallionellaceae FeOB. Within FeOB, we found genes that may represent adaptations for iron oxidation, including a variety of extracellular electron uptake (EEU) mechanisms. FeOB genomes encoded more predicted c-type cytochromes overall, notably more multiheme c-type cytochromes (MHCs) with >10 CXXCH motifs. These include homologs of several predicted outer membrane porin-MHC complexes, including MtoAB and Uet. MHCs are known to efficiently conduct electrons across longer distances and function across a wide range of redox potentials that overlap with mineral redox potentials, which can help expand the range of usable iron substrates. Overall, the results of pangenome analyses suggest that the Gallionellaceae genera Gallionella, Sideroxydans, and Ferriphaselus are primarily iron oxidizers, capable of oxidizing dissolved Fe2+ as well as a range of solid iron or other mineral substrates.
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Affiliation(s)
- Rene L Hoover
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Jessica L Keffer
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Shawn W Polson
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
| | - Clara S Chan
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
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6
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Ranchou-Peyruse M, Guignard M, Haddad PG, Robin S, Boesch F, Lanot M, Carrier H, Dequidt D, Chiquet P, Caumette G, Cézac P, Ranchou-Peyruse A. A deep continental aquifer downhole sampler for microbiological studies. Front Microbiol 2023; 13:1012400. [PMID: 36687568 PMCID: PMC9846368 DOI: 10.3389/fmicb.2022.1012400] [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: 08/05/2022] [Accepted: 12/06/2022] [Indexed: 01/06/2023] Open
Abstract
To be effective, microbiological studies of deep aquifers must be free from surface microbial contaminants and from infrastructures allowing access to formation water (wellheads, well completions). Many microbiological studies are based on water samples obtained after rinsing a well without guaranteeing the absence of contaminants from the biofilm development in the pipes. The protocol described in this paper presents the adaptation, preparation, sterilization and deployment of a commercial downhole sampler (PDSshort, Leutert, Germany) for the microbiological studying of deep aquifers. The ATEX sampler (i.e., explosive atmospheres) can be deployed for geological gas storage (methane, hydrogen). To validate our procedure and confirm the need to use such a device, cell counting and bacterial taxonomic diversity based on high-throughput sequencing for different water samples taken at the wellhead or at depth using the downhole sampler were compared and discussed. The results show that even after extensive rinsing (7 bore volumes), the water collected at the wellhead was not free of microbial contaminants, as shown by beta-diversity analysis. The downhole sampler procedure was the only way to ensure the purity of the formation water samples from the microbiological point of view. In addition, the downhole sampler allowed the formation water and the autochthonous microbial community to be maintained at in situ pressure for laboratory analysis. The prevention of the contamination of the sample and the preservation of its representativeness are key to guaranteeing the best interpretations and understanding of the functioning of the deep biosphere.
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Affiliation(s)
- Magali Ranchou-Peyruse
- E2S-UPPA, CNRS, IPREM, Universite de Pau & Pays Adour, Pau, France
- E2S-UPPA, LaTEP, Universite de Pau & Pays Adour, Pau, France
- Joint Laboratory SEnGA, E2S-UPPA-Teréga, Pau, France
| | - Marion Guignard
- E2S-UPPA, CNRS, IPREM, Universite de Pau & Pays Adour, Pau, France
| | - Perla G Haddad
- E2S-UPPA, LaTEP, Universite de Pau & Pays Adour, Pau, France
| | | | | | | | - Hervé Carrier
- Joint Laboratory SEnGA, E2S-UPPA-Teréga, Pau, France
- E2S-UPPA, CNRS, TOTAL, LFCR, Universite de Pau & Pays Adour, Pau, France
| | - David Dequidt
- STORENGY - Geosciences Department, Bois-Colombes, France
| | - Pierre Chiquet
- Joint Laboratory SEnGA, E2S-UPPA-Teréga, Pau, France
- Teréga, Pau, France
| | - Guilhem Caumette
- Joint Laboratory SEnGA, E2S-UPPA-Teréga, Pau, France
- Teréga, Pau, France
| | - Pierre Cézac
- E2S-UPPA, LaTEP, Universite de Pau & Pays Adour, Pau, France
- Joint Laboratory SEnGA, E2S-UPPA-Teréga, Pau, France
| | - Anthony Ranchou-Peyruse
- E2S-UPPA, CNRS, IPREM, Universite de Pau & Pays Adour, Pau, France
- Joint Laboratory SEnGA, E2S-UPPA-Teréga, Pau, France
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7
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Li S, Feng Q, Liu J, He Y, Shi L, Boyanov MI, O'Loughlin EJ, Kemner KM, Sanford RA, Shao H, He X, Sheng A, Cheng H, Shen C, Tu W, Dong Y. Carbonate Minerals and Dissimilatory Iron-Reducing Organisms Trigger Synergistic Abiotic and Biotic Chain Reactions under Elevated CO 2 Concentration. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:16428-16440. [PMID: 36301735 DOI: 10.1021/acs.est.2c03843] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Increasing CO2 emission has resulted in pressing climate and environmental issues. While abiotic and biotic processes mediating the fate of CO2 have been studied separately, their interactions and combined effects have been poorly understood. To explore this knowledge gap, an iron-reducing organism, Orenia metallireducens, was cultured under 18 conditions that systematically varied in headspace CO2 concentrations, ferric oxide loading, and dolomite (CaMg(CO3)2) availability. The results showed that abiotic and biotic processes interactively mediate CO2 acidification and sequestration through "chain reactions", with pH being the dominant variable. Specifically, dolomite alleviated CO2 stress on microbial activity, possibly via pH control that transforms the inhibitory CO2 to the more benign bicarbonate species. The microbial iron reduction further impacted pH via the competition between proton (H+) consumption during iron reduction and H+ generation from oxidization of the organic substrate. Under Fe(III)-rich conditions, microbial iron reduction increased pH, driving dissolved CO2 to form bicarbonate. Spectroscopic and microscopic analyses showed enhanced formation of siderite (FeCO3) under elevated CO2, supporting its incorporation into solids. The results of these CO2-microbe-mineral experiments provide insights into the synergistic abiotic and biotic processes that alleviate CO2 acidification and favor its sequestration, which can be instructive for practical applications (e.g., acidification remediation, CO2 sequestration, and modeling of carbon flux).
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Affiliation(s)
- Shuyi Li
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan430074, China
| | - Qi Feng
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan430074, China
| | - Juan Liu
- Department of Environmental Engineering, Peking University, Beijing100871, China
| | - Yu He
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan430074, China
| | - Liang Shi
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan430074, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan430074, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, Wuhan430074, China
| | - Maxim I Boyanov
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois60439, United States
- Institute of Chemical Engineering, Bulgarian Academy of Sciences, Sofia1113, Bulgaria
| | - Edward J O'Loughlin
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois60439, United States
| | - Kenneth M Kemner
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois60439, United States
| | - Robert A Sanford
- Department of Geology, University of Illinois Urbana-Champaign, Champaign, Illinois60801, United States
| | - Hongbo Shao
- Illinois State Geological Survey, Champaign, Illinois61820, United States
| | - Xiao He
- Institute of High Energy Physics, Chinese Academy of Sciences, Beijing100049, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Anxu Sheng
- Department of Environmental Engineering, Peking University, Beijing100871, China
| | - Hang Cheng
- Department of Environmental Engineering, Peking University, Beijing100871, China
| | - Chunhua Shen
- Center for Materials Research and Analysis, Wuhan University of Technology, Wuhan430070, China
| | - Wenmao Tu
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan430070, China
| | - Yiran Dong
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan430074, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan430074, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, Wuhan430074, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences (Wuhan), Wuhan430074, China
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, China University of Geosciences (Wuhan), Wuhan430074, China
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8
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Meyer-Dombard DR, Malas J. Advances in Defining Ecosystem Functions of the Terrestrial Subsurface Biosphere. Front Microbiol 2022; 13:891528. [PMID: 35722320 PMCID: PMC9201636 DOI: 10.3389/fmicb.2022.891528] [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: 03/07/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
The subsurface is one of the last remaining 'uncharted territories' of Earth and is now accepted as a biosphere in its own right, at least as critical to Earth systems as the surface biosphere. The terrestrial deep biosphere is connected through a thin veneer of Earth's crust to the surface biosphere, and many subsurface biosphere ecosystems are impacted by surface topography, climate, and near surface groundwater movement and represent a transition zone (at least ephemerally). Delving below this transition zone, we can examine how microbial metabolic functions define a deep terrestrial subsurface. This review provides a survey of the most recent advances in discovering the functional and genomic diversity of the terrestrial subsurface biosphere, how microbes interact with minerals and obtain energy and carbon in the subsurface, and considers adaptations to the presented environmental extremes. We highlight the deepest subsurface studies in deep mines, deep laboratories, and boreholes in crystalline and altered host rock lithologies, with a focus on advances in understanding ecosystem functions in a holistic manner.
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Choi BY, Park J, Ham B, Kirk MF, Kwon MJ. Effect of CO 2 on biogeochemical reactions and microbial community composition in bioreactors with deep groundwater and basalt. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150803. [PMID: 34626629 DOI: 10.1016/j.scitotenv.2021.150803] [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: 07/12/2021] [Revised: 10/01/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
Changes in subsurface microbiology following CO2 injection have the potential to impact carbon trapping in CO2 storage reservoirs. However, much remains to be learned about responses of natural microbial consortia to elevated CO2 in basaltic systems. This study asks: how will microbes from deep (700 m) groundwater change along a gradient in CO2 (0-20 psi) in batch reactor systems containing basalt chips and groundwater amended with lactate? Reactors incubated for 87 days at 23 °C. Results for reactors with low CO2 (0 and 3 psi) differed considerably from those with high CO2 (10 and 20 psi). In reactors with low CO2, pH was >6.5 and lactate started to be used within 24 days. By 40 days, lactate was completely consumed and acetate increased to ~4 mM. As lactate was consumed, sulfate decreased from 0.16 to 0 mM after 40 days. In contrast, in reactors with high CO2, pH was <6.5, lactate and sulfate concentrations varied little and acetate was not produced. Biogeochemical modeling and community analyses indicate that differences between reactors with low and high CO2 reflect tolerances of reactor microbes to CO2 exposure. Communities in the low CO2 reactors carried out syntrophic lactate oxidation coupled with methanogenesis and sulfate reduction. Bacteroidota and Firmicutes became dominant phyla after 24 days and groups capable of sulfate reduction and methanogenesis were detected. In reactors with high CO2, however, biogeochemical activity was insignificant, no groups capable of sulfate reducion or methanogenesis were observed, and the community became less diverse during the incubation. These findings show that the response of microbial consortia can vary sharply along a CO2 gradient, creating significant differences in community composition and biogeochemistry, and that the timescale of basalt weathering is likely not rapid enough to prevent significant stress following a rapid increase in CO2 abundance.
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Affiliation(s)
- Byoung-Young Choi
- Korea Institute of Geoscience and Mineral Resources, Daejeon, South Korea.
| | - Jinyoung Park
- Korea Institute of Geoscience and Mineral Resources, Daejeon, South Korea
| | - Baknoon Ham
- Department of Earth and Environmental Sciences, Korea University, Seoul, South Korea
| | - Matthew F Kirk
- Department of Geology, Kansas State University, Manhattan, KS, United States
| | - Man Jae Kwon
- Department of Earth and Environmental Sciences, Korea University, Seoul, South Korea.
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Evolutionary stasis of a deep subsurface microbial lineage. THE ISME JOURNAL 2021; 15:2830-2842. [PMID: 33824425 PMCID: PMC8443664 DOI: 10.1038/s41396-021-00965-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 02/26/2021] [Accepted: 03/15/2021] [Indexed: 02/01/2023]
Abstract
Sulfate-reducing bacteria Candidatus Desulforudis audaxviator (CDA) were originally discovered in deep fracture fluids accessed via South African gold mines and have since been found in geographically widespread deep subsurface locations. In order to constrain models for subsurface microbial evolution, we compared CDA genomes from Africa, North America and Eurasia using single cell genomics. Unexpectedly, 126 partial single amplified genomes from the three continents, a complete genome from of an isolate from Eurasia, and metagenome-assembled genomes from Africa and Eurasia shared >99.2% average nucleotide identity, low frequency of SNP's, and near-perfectly conserved prophages and CRISPRs. Our analyses reject sample cross-contamination, recent natural dispersal, and unusually strong purifying selection as likely explanations for these unexpected results. We therefore conclude that the analyzed CDA populations underwent only minimal evolution since their physical separation, potentially as far back as the breakup of Pangea between 165 and 55 Ma ago. High-fidelity DNA replication and repair mechanisms are the most plausible explanation for the highly conserved genome of CDA. CDA presents a stark contrast to the current model organisms in microbial evolutionary studies, which often develop adaptive traits over far shorter periods of time.
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Abstract
Iron (Fe) oxidation is one of Earth’s major biogeochemical processes, key to weathering, soil formation, water quality, and corrosion. However, our understanding of microbial contribution is limited by incomplete knowledge of microbial iron oxidation mechanisms, particularly in neutrophilic iron oxidizers. The genomes of many diverse iron oxidizers encode a homolog to an outer membrane cytochrome (Cyc2) shown to oxidize iron in two acidophiles. Phylogenetic analyses show Cyc2 sequences from neutrophiles cluster together, suggesting a common function, though this function has not been verified in these organisms. Therefore, we investigated the iron oxidase function of heterologously expressed Cyc2 from a neutrophilic iron oxidizer Mariprofundus ferrooxydans PV-1. Cyc2PV-1 is capable of oxidizing iron, and its redox potential is 208 ± 20 mV, consistent with the ability to accept electrons from Fe2+ at neutral pH. These results support the hypothesis that Cyc2 functions as an iron oxidase in neutrophilic iron-oxidizing organisms. The results of sequence analysis and modeling reveal that the entire Cyc2 family shares a unique fused cytochrome-porin structure, with a defining consensus motif in the cytochrome region. On the basis of results from structural analyses, we predict that the monoheme cytochrome Cyc2 specifically oxidizes dissolved Fe2+, in contrast to multiheme iron oxidases, which may oxidize solid Fe(II). With our results, there is now functional validation for diverse representatives of Cyc2 sequences. We present a comprehensive Cyc2 phylogenetic tree and offer a roadmap for identifying cyc2/Cyc2 homologs and interpreting their function. The occurrence of cyc2 in many genomes beyond known iron oxidizers presents the possibility that microbial iron oxidation may be a widespread metabolism.
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12
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Nam S, Alday JG, Kim M, Kim H, Kim Y, Park T, Lim HS, Lee BY, Lee YK, Jung JY. The relationships of present vegetation, bacteria, and soil properties with soil organic matter characteristics in moist acidic tundra in Alaska. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 772:145386. [PMID: 33770858 DOI: 10.1016/j.scitotenv.2021.145386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/19/2021] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
Soil organic matter (SOM) is related to vegetation, soil bacteria, and soil properties; however, not many studies link all these parameters simultaneously, particularly in tundra ecosystems vulnerable to climate change. Our aim was to describe the relationships between vegetation, bacteria, soil properties, and SOM composition in moist acidic tundra by integrating physical, chemical, and molecular methods. A total of 70 soil samples were collected at two different depths from 36 spots systematically arranged over an area of about 300 m × 50 m. Pyrolysis-gas chromatography/mass spectrometry and pyrosequencing of the 16S rRNA gene were used to identify the molecular compositions of the SOM and bacterial community, respectively. Vegetation and soil physicochemical properties were also measured. The sampling sites were grouped into three, based on their SOM compositions: Sphagnum moss-derived SOM, lipid-rich materials, and aromatic-rich materials. Our results show that SOM composition is spatially structured and linked to microtopography; however, the vegetation, soil properties, and bacterial community composition did not show overall spatial structuring. Simultaneously, soil properties and bacterial community composition were the main factors explaining SOM compositional variation, while vegetation had a residual effect. Verrucomicrobia and Acidobacteria were related to polysaccharides, and Chloroflexi was linked to aromatic compounds. These relationships were consistent across different hierarchical levels. Our results suggest that SOM composition at a local scale is closely linked with soil factors and the bacterial community. Comprehensive observation of ecosystem components is recommended to understand the in-situ function of bacteria and the fate of SOM in the moist acidic tundra.
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Affiliation(s)
- Sungjin Nam
- Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Josu G Alday
- Joint Research Unit CTFC - AGROTECNIO, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain; Department of Crop and Forest Sciences, University of Lleida, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain
| | - Mincheol Kim
- Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Hyemin Kim
- Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Yongkang Kim
- Department of Statistics, Seoul National University, Seoul 08826, Republic of Korea
| | - Taesung Park
- Department of Statistics, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyoun Soo Lim
- Department of Geological Sciences, Pusan National University, Busan 46241, Republic of Korea
| | - Bang Yong Lee
- Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Yoo Kyung Lee
- Korea Polar Research Institute, Incheon 21990, Republic of Korea.
| | - Ji Young Jung
- Korea Polar Research Institute, Incheon 21990, Republic of Korea.
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13
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Osman JR, Cardon H, Montagnac G, Picard A, Daniel I. Pressure effects on sulfur-oxidizing activity of Thiobacillus thioparus. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:169-175. [PMID: 33421329 PMCID: PMC7986089 DOI: 10.1111/1758-2229.12922] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
Abstract
Carbon capture and storage technologies are crucial for reducing carbon emission from power plants as a response to global climate change. The CarbFix project (Iceland) aims at examining the geochemical response of injected CO2 into subsurface reservoirs. The potential role of the subsurface biosphere has been little investigated up to now. Here, we used Thiobacillus thioparus that became abundant at the CarbFix1 pilot site after injection of CO2 and purified geothermal gases in basaltic aquifer at 400-800 m depth (4-8 MPa). The capacity of T. thioparus to produce sulfate, through oxidation of thiosulfate, was measured by Raman spectroscopy as a function of pressure up to 10 MPa. The results show that the growth and metabolic activity of T. thioparus are influenced by the initial concentration of the electron donor thiosulfate. It grows best at low initial concentration of thiosulfate (here 5 g.l-1 or 31.6 mM) and best oxidizes thiosulfate into sulfate at 0.1 MPa with a yield of 14.7 ± 0.5%. Sulfur oxidation stops at 4.3 ± 0.1 MPa (43 bar). This autotrophic specie can thereby react to CO2 and H2 S injection down to 430 m depth and may contribute to induced biogeochemical cycles during subsurface energy operations.
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Affiliation(s)
- Jorge R. Osman
- Univ Lyon, Université Lyon 1, Ens de Lyon, CNRS, UMR 5276 LGL‐TPEVilleurbanneF‐69622France
| | - Hervé Cardon
- Univ Lyon, Université Lyon 1, Ens de Lyon, CNRS, UMR 5276 LGL‐TPEVilleurbanneF‐69622France
| | - Gilles Montagnac
- Univ Lyon, Université Lyon 1, Ens de Lyon, CNRS, UMR 5276 LGL‐TPEVilleurbanneF‐69622France
| | - Aude Picard
- Univ Lyon, Université Lyon 1, Ens de Lyon, CNRS, UMR 5276 LGL‐TPEVilleurbanneF‐69622France
- School of Life SciencesUniversity of Nevada, Las Vegas, 4505 S. Maryland ParkwayLas VegasNV89154‐4004USA
| | - Isabelle Daniel
- Univ Lyon, Université Lyon 1, Ens de Lyon, CNRS, UMR 5276 LGL‐TPEVilleurbanneF‐69622France
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14
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Orcutt BN, D'Angelo T, Wheat CG, Trembath‐Reichert E. Microbe‐mineral biogeography from multi‐year incubations in oceanic crust at North Pond,
Mid‐Atlantic
Ridge. Environ Microbiol 2021; 23:3923-3936. [DOI: 10.1111/1462-2920.15366] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/16/2020] [Accepted: 12/16/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Beth N. Orcutt
- Bigelow Laboratory for Ocean Sciences East Boothbay ME 04544 USA
- Hanse‐Wissenschaftskolleg Delmenhorst Germany
| | - Timothy D'Angelo
- Bigelow Laboratory for Ocean Sciences East Boothbay ME 04544 USA
| | - C. Geoff Wheat
- Institute of Marine Sciences, College of Fisheries and Ocean Sciences University of Alaska Moss Landing CA 95039 USA
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15
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Bethencourt L, Bochet O, Farasin J, Aquilina L, Borgne TL, Quaiser A, Biget M, Michon-Coudouel S, Labasque T, Dufresne A. Genome reconstruction reveals distinct assemblages of Gallionellaceae in surface and subsurface redox transition zones. FEMS Microbiol Ecol 2020; 96:5800984. [PMID: 32149354 DOI: 10.1093/femsec/fiaa036] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 03/04/2020] [Indexed: 11/15/2022] Open
Abstract
Fe-oxidizing bacteria of the family Gallionellaceae are major players in the Fe biogeochemical cycle in freshwater. These bacteria thrive in redox transition zones where they benefit from both high Fe concentrations and microaerobic conditions. We analysed the Gallionellaceae genomic diversity in an artesian hard-rock aquifer where redox transition zones develop (i) in the subsurface, where ancient, reduced groundwater mixes with recent oxygenated groundwater, and (ii) at the surface, where groundwater reaches the open air. A total of 15 new draft genomes of Gallionellaceae representing to 11 candidate genera were recovered from the two redox transition zones. Sulfur oxidation genes were encoded in most genomes while denitrification genes were much less represented. One genus dominated microbial communities belowground and we propose to name it 'Candidatus Houarnoksidobacter'. The two transition zones were populated by completely different assemblages of Gallionellaceae despite the almost constant upward circulation of groundwater between the two zones. The processes leading to redox transition zones, oxygen diffusion at the surface or groundwater mixing in subsurface, appear to be a major driver of the Gallionellaceae diversity.
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Affiliation(s)
- Lorine Bethencourt
- Univ Rennes, CNRS, ECOBIO - UMR 6553, F-35000 Rennes, France.,Univ Rennes, CNRS, Géosciences Rennes - UMR 6118, F-35000 Rennes, France
| | - Olivier Bochet
- Univ Rennes, CNRS, Géosciences Rennes - UMR 6118, F-35000 Rennes, France
| | - Julien Farasin
- Univ Rennes, CNRS, Géosciences Rennes - UMR 6118, F-35000 Rennes, France
| | - Luc Aquilina
- Univ Rennes, CNRS, Géosciences Rennes - UMR 6118, F-35000 Rennes, France
| | - Tanguy Le Borgne
- Univ Rennes, CNRS, Géosciences Rennes - UMR 6118, F-35000 Rennes, France
| | - Achim Quaiser
- Univ Rennes, CNRS, ECOBIO - UMR 6553, F-35000 Rennes, France
| | - Marine Biget
- Univ Rennes, CNRS, ECOBIO - UMR 6553, F-35000 Rennes, France
| | | | - Thierry Labasque
- Univ Rennes, CNRS, Géosciences Rennes - UMR 6118, F-35000 Rennes, France
| | - Alexis Dufresne
- Univ Rennes, CNRS, ECOBIO - UMR 6553, F-35000 Rennes, France
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16
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Corinne BP, Corentin H, Hélène G, Eric DB, Sébastien T, Isabelle JD, Raphaël P. Analysis of bacterial and archaeal communities associated with Fogo volcanic soils of different ages. FEMS Microbiol Ecol 2020; 96:5848192. [PMID: 32463439 DOI: 10.1093/femsec/fiaa104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/27/2020] [Indexed: 11/13/2022] Open
Abstract
Basaltic rocks play a significant role in CO2 sequestration from the atmosphere during their weathering. Moreover, the primary microorganisms that colonize them, by providing mineral elements and nutrients, are shown to promote growth of diverse heterotrophic communities and plants, therefore positively impacting Earth's long-term climate balance. However, the first steps of microbial colonization and subsequent rock weathering remain poorly understood, especially regarding microbial communities over a chronological sequence. Here, we analyzed the microbial communities inhabiting the soil developed in crevices on lava flows derived from different eruptions on Fogo Island. Investigated soils show typically low carbon and nitrogen content and are relatively similar to one another regarding their phylogenetic composition, and similar to what was recorded in large soil surveys with dominance of Actinobacteria and Proteobacteria. Moreover, our results suggest a stronger effect of the organic carbon than the lava flow age in shaping microbial communities as well as the possibility of exogenous sources of bacteria as important colonizers. Furthermore, archaea reach up to 8.4% of the total microbial community, dominated by the Soil Crenarchaeotic Group, including the ammonium-oxidizer Candidatus Nitrososphaera sp. Therefore, this group might be largely responsible for ammonia oxidation under the environmental conditions found on Fogo.
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Affiliation(s)
- Biderre-Petit Corinne
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Hochart Corentin
- CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Sorbonne Université, F-66650 Banyuls sur Mer, France
| | - Gardon Hélène
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Dugat-Bony Eric
- INRAE, AgroParisTech, UMR SayFood, Université Paris-Saclay, F-78850, Thiverval-Grignon, France
| | - Terrat Sébastien
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Jouan-Dufournel Isabelle
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Paris Raphaël
- CNRS, IRD, OPGC, Laboratoire Magmas et Volcans, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
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17
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Bourges F, Genty D, Perrier F, Lartiges B, Régnier É, François A, Leplat J, Touron S, Bousta F, Massault M, Delmotte M, Dumoulin JP, Girault F, Ramonet M, Chauveau C, Rodrigues P. Hydrogeological control on carbon dioxide input into the atmosphere of the Chauvet-Pont d'Arc cave. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 716:136844. [PMID: 32059316 DOI: 10.1016/j.scitotenv.2020.136844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 06/10/2023]
Abstract
Carbon dioxide (CO2) concentration (CDC) is an essential parameter of underground atmospheres for safety and cave heritage preservation. In the Chauvet cave (South France), a world heritage site hosting unique paintings dated 36,000 years BP, a high-sensitivity monitoring, ongoing since 1997, revealed: 1) two compartments with a spatially uniform CDC, a large volume (A) (40,000 to 80,000 m3) with a mean value of 2.20 ± 0.01% vol. in 2016, and a smaller remote room (B) (2000 m3), with a higher mean value of 3.42 ± 0.01%; 2) large CDC annual variations with peak-to-peak amplitude of 2% and 1.6% in A and B, respectively; 3) long-term changes, with an increase of CDC and of its annual amplitude since 1997, then faster since 2013, reaching a maximum of 4.4% in B in 2017, decreasing afterwards. While a large effect of seasonal ventilation is ruled out, monitoring of seepage at two dripping points indicated that the main control of CDC seasonal reduction was transient infiltration. During periods of water deficit, calculated from surface temperature and rainfall, CDC systematically increased. The carbon isotopic composition of CO2, correlated with water excess, is consistent with a time-varying component of CO2 seeping from above. The CO2 flux, which is the primary driver of CDC in A and B, inferred using box modelling, was found to confirm the relationship between water excess and reduced CO2 flux into A, compatible with a more constant flux into B. A buoyancy-driven horizontal CO2 flow model in the vadose zone, hindered by water infiltration, is proposed. Similarly, pluri-annual and long-term CDC changes can likely be attributed to variations of water excess, but also to increasing vegetation density above the cave. As CDC controls the carbonate geochemistry, an increased variability of CDC raises concern for the preservation of the Chauvet cave paintings.
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Affiliation(s)
- François Bourges
- Géologie Environnement Conseil, 30 rue de la République, F-09200 Saint-Girons, France
| | - Dominique Genty
- Université Paris-Saclay, CEA, CNRS, UVSQ, Laboratoire des Sciences du Climat et de l'Environnement (LSCE/IPSL), Gif-sur-Yvette, France
| | - Frédéric Perrier
- Institut de Physique du Globe de Paris, Université de Paris, 1 rue Jussieu, F-75005 Paris, France.
| | - Bruno Lartiges
- Université de Toulouse III Paul Sabatier, Géosciences Environnement-Toulouse, 14 av. Edouard Belin, F-31400 Toulouse, France
| | - Édouard Régnier
- Université Paris-Saclay, CEA, CNRS, UVSQ, Laboratoire des Sciences du Climat et de l'Environnement (LSCE/IPSL), Gif-sur-Yvette, France
| | - Alexandre François
- Laboratoire de Recherches des Monuments Historiques (CRC, USR3224), Museum national d'Histoire naturelle, Sorbonne Universités, Ministère de la Culture, CRNS, 29 rue de Paris, F-77420 Champs-sur-Marne, France
| | - Johann Leplat
- Laboratoire de Recherches des Monuments Historiques (CRC, USR3224), Museum national d'Histoire naturelle, Sorbonne Universités, Ministère de la Culture, CRNS, 29 rue de Paris, F-77420 Champs-sur-Marne, France
| | - Stéphanie Touron
- Laboratoire de Recherches des Monuments Historiques (CRC, USR3224), Museum national d'Histoire naturelle, Sorbonne Universités, Ministère de la Culture, CRNS, 29 rue de Paris, F-77420 Champs-sur-Marne, France
| | - Faisl Bousta
- Laboratoire de Recherches des Monuments Historiques (CRC, USR3224), Museum national d'Histoire naturelle, Sorbonne Universités, Ministère de la Culture, CRNS, 29 rue de Paris, F-77420 Champs-sur-Marne, France
| | - Marc Massault
- Géosciences Paris-Sud (GEOPS), Université de Paris Saclay, Rue du Belvédère Bâtiment 504, 91400 Orsay, France
| | - Marc Delmotte
- Université Paris-Saclay, CEA, CNRS, UVSQ, Laboratoire des Sciences du Climat et de l'Environnement (LSCE/IPSL), Gif-sur-Yvette, France
| | - Jean-Pascal Dumoulin
- Laboratoire de Mesure du Carbone 14 (LMC14), LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - Frédéric Girault
- Institut de Physique du Globe de Paris, Université de Paris, 1 rue Jussieu, F-75005 Paris, France
| | - Michel Ramonet
- Université Paris-Saclay, CEA, CNRS, UVSQ, Laboratoire des Sciences du Climat et de l'Environnement (LSCE/IPSL), Gif-sur-Yvette, France
| | - Charles Chauveau
- Service de la Conservation de la Grotte Chauvet, Ministère de la Culture, F-07150 Vallon-Pont-d'Arc, France
| | - Paulo Rodrigues
- Service de la Conservation de la Grotte Chauvet, Ministère de la Culture, F-07150 Vallon-Pont-d'Arc, France
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18
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Guðmundsdóttir R, Kreiling AK, Kristjánsson BK, Marteinsson VÞ, Pálsson S. Bacterial diversity in Icelandic cold spring sources and in relation to the groundwater amphipod Crangonyx islandicus. PLoS One 2019; 14:e0222527. [PMID: 31577799 PMCID: PMC6774475 DOI: 10.1371/journal.pone.0222527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/02/2019] [Indexed: 11/18/2022] Open
Abstract
Crangonyx islandicus is a groundwater amphipod endemic to Iceland, considered to have survived the Ice Ages in subglacial refugia. Currently the species is found in spring sources in lava fields along the tectonic plate boundary of the country. The discovery of a groundwater species in this inaccessible habitat indicates a hidden ecosystem possibly based on chemoautotrophic microorganisms as primary producers. To explore this spring ecosystem, we assessed its microbial diversity and analysed whether and how the diversity varied between the amphipods and the spring water, and if was dependent on environmental factors and geological settings. Isolated DNA from spring water and from amphipods was analysed using metabarcoding methods, targeting the 16S rRNA gene. Two genera of bacteria, Halomonas and Shewanella were dominating in the amphipod samples in terms of relative abundance, but not in the groundwater samples where Flavobacterium, Pseudomonas and Alkanindiges among others were dominating. The richness of the bacteria taxa in the microbial community of the groundwater spring sources was shaped by pH level and the beta diversity was shaped by geographic locations.
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Affiliation(s)
| | - Agnes-Katharina Kreiling
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Department of Aquaculture and Fish Biology, Hólar University, Sauðárkrókur, Iceland
| | | | - Viggó Þór Marteinsson
- Matis ohf./Icelandic Food and Biotech R&D, Reykjavík, Iceland
- Faculty of Food Science and Nutrition, University of Iceland, Reykjavík, Iceland
| | - Snæbjörn Pálsson
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
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19
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Onstott T, Ehlmann B, Sapers H, Coleman M, Ivarsson M, Marlow J, Neubeck A, Niles P. Paleo-Rock-Hosted Life on Earth and the Search on Mars: A Review and Strategy for Exploration. ASTROBIOLOGY 2019; 19:1230-1262. [PMID: 31237436 PMCID: PMC6786346 DOI: 10.1089/ast.2018.1960] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 04/25/2019] [Indexed: 05/19/2023]
Abstract
Here we review published studies on the abundance and diversity of terrestrial rock-hosted life, the environments it inhabits, the evolution of its metabolisms, and its fossil biomarkers to provide guidance in the search for life on Mars. Key findings are (1) much terrestrial deep subsurface metabolic activity relies on abiotic energy-yielding fluxes and in situ abiotic and biotic recycling of metabolic waste products rather than on buried organic products of photosynthesis; (2) subsurface microbial cell concentrations are highest at interfaces with pronounced chemical redox gradients or permeability variations and do not correlate with bulk host rock organic carbon; (3) metabolic pathways for chemolithoautotrophic microorganisms evolved earlier in Earth's history than those of surface-dwelling phototrophic microorganisms; (4) the emergence of the former occurred at a time when Mars was habitable, whereas the emergence of the latter occurred at a time when the martian surface was not continually habitable; (5) the terrestrial rock record has biomarkers of subsurface life at least back hundreds of millions of years and likely to 3.45 Ga with several examples of excellent preservation in rock types that are quite different from those preserving the photosphere-supported biosphere. These findings suggest that rock-hosted life would have been more likely to emerge and be preserved in a martian context. Consequently, we outline a Mars exploration strategy that targets subsurface life and scales spatially, focusing initially on identifying rocks with evidence for groundwater flow and low-temperature mineralization, then identifying redox and permeability interfaces preserved within rock outcrops, and finally focusing on finding minerals associated with redox reactions and associated traces of carbon and diagnostic chemical and isotopic biosignatures. Using this strategy on Earth yields ancient rock-hosted life, preserved in the fossil record and confirmable via a suite of morphologic, organic, mineralogical, and isotopic fingerprints at micrometer scale. We expect an emphasis on rock-hosted life and this scale-dependent strategy to be crucial in the search for life on Mars.
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Affiliation(s)
- T.C. Onstott
- Department of Geosciences, Princeton University, Princeton, New Jersey, USA
- Address correspondence to: T.C. Onstott, Department of Geosciences, Princeton University,, Princeton, NJ 008544
| | - B.L. Ehlmann
- Division of Geological & Planetary Sciences, California Institute of Technology, Pasadena, California, USA
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- B.L. Ehlmann, Division of Geological & Planetary Sciences, California Institute of Technology, Pasadena, CA 91125
| | - H. Sapers
- Division of Geological & Planetary Sciences, California Institute of Technology, Pasadena, California, USA
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
| | - M. Coleman
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- NASA Astrobiology Institute, Pasadena, California, USA
| | - M. Ivarsson
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - J.J. Marlow
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - A. Neubeck
- Department of Earth Sciences, Uppsala University, Uppsala, Sweden
| | - P. Niles
- Astromaterials Research and Exploration Science Division, NASA Johnson Space Center, Houston, Texas, USA
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20
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Hamilton-Brehm SD, Stewart LE, Zavarin M, Caldwell M, Lawson PA, Onstott TC, Grzymski J, Neveux I, Lollar BS, Russell CE, Moser DP. Thermoanaerosceptrum fracticalcis gen. nov. sp. nov., a Novel Fumarate-Fermenting Microorganism From a Deep Fractured Carbonate Aquifer of the US Great Basin. Front Microbiol 2019; 10:2224. [PMID: 31611860 PMCID: PMC6776889 DOI: 10.3389/fmicb.2019.02224] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/11/2019] [Indexed: 12/16/2022] Open
Abstract
Deep fractured rock ecosystems across most of North America have not been studied extensively. However, the US Great Basin, in particular the Nevada National Security Site (NNSS, formerly the Nevada Test Site), has hosted a number of influential subsurface investigations over the years. This investigation focuses on resident microbiota recovered from a hydrogeologically confined aquifer in fractured Paleozoic carbonate rocks at 863 - 923 meters below land surface. Analysis of the microorganisms living in this oligotrophic environment provides a perspective into microbial metabolic strategies required to endure prolonged hydrogeological isolation deep underground. Here we present a microbiological and physicochemical characterization of a deep continental carbonate ecosystem and describe a bacterial genus isolated from the ecosystem. Strain DRI-13T is a strictly anaerobic, moderately thermophilic, fumarate-respiring member of the phylum Firmicutes. This bacterium grows optimally at 55°C and pH 8.0, can tolerate a concentration of 100 mM NaCl, and appears to obligately metabolize fumarate to acetate and succinate. Culture-independent 16S rRNA gene sequencing indicates a global subsurface distribution, while the closest cultured relatives of DRI-13T are Pelotomaculum thermopropionicum (90.0% similarity) and Desulfotomaculum gibsoniae (88.0% similarity). The predominant fatty acid profile is iso-C15 : 0, C15 : 0, C16 : 0 and C14 : 0. The percentage of the straight-chain fatty acid C15 : 0 is a defining characteristic not present in the other closely related species. The genome is estimated to be 3,649,665 bp, composed of 87.3% coding regions with an overall average of 45.1% G + C content. Strain DRI-13T represents a novel genus of subsurface bacterium isolated from a previously uncharacterized rock-hosted geothermal habitat. The characterization of the bacterium combined with the sequenced genome provides insights into metabolism strategies of the deep subsurface biosphere. Based on our characterization analysis we propose the name Thermoanaerosceptrum fracticalcis (DRI-13T = DSM 100382T = ATCC TSD-12T).
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Affiliation(s)
- Scott D. Hamilton-Brehm
- Division of Earth and Ecosystems Sciences, Desert Research Institute, Las Vegas, NV, United States
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL, United States
| | | | - Mavrik Zavarin
- Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Matt Caldwell
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Paul A. Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Tullis C. Onstott
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Joseph Grzymski
- Division of Earth and Ecosystems Sciences, Desert Research Institute, Las Vegas, NV, United States
| | - Iva Neveux
- Division of Earth and Ecosystems Sciences, Desert Research Institute, Las Vegas, NV, United States
| | | | - Charles E. Russell
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, United States
| | - Duane P. Moser
- Division of Earth and Ecosystems Sciences, Desert Research Institute, Las Vegas, NV, United States
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, United States
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21
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Schmitt-Kopplin P, Hemmler D, Moritz F, Gougeon RD, Lucio M, Meringer M, Müller C, Harir M, Hertkorn N. Systems chemical analytics: introduction to the challenges of chemical complexity analysis. Faraday Discuss 2019; 218:9-28. [DOI: 10.1039/c9fd00078j] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We present concepts of complexity, and complex chemistry in systems subjected to biotic and abiotic transformations, and introduce analytical possibilities to disentangle chemical complexity into its elementary parts as a global integrated approach termed systems chemical analytics.
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Affiliation(s)
- Philippe Schmitt-Kopplin
- HelmholtzZentrum Muenchen
- German Research Center for Environmental Health
- Department of Environmental Sciences
- D-85764 Neuherberg
- Germany
| | - Daniel Hemmler
- HelmholtzZentrum Muenchen
- German Research Center for Environmental Health
- Department of Environmental Sciences
- D-85764 Neuherberg
- Germany
| | - Franco Moritz
- HelmholtzZentrum Muenchen
- German Research Center for Environmental Health
- Department of Environmental Sciences
- D-85764 Neuherberg
- Germany
| | - Régis D. Gougeon
- UMR PAM Université de Bourgogne/AgroSup Dijon
- Institut Universitaire de la Vigne et du Vin
- Dijon
- France
| | - Marianna Lucio
- HelmholtzZentrum Muenchen
- German Research Center for Environmental Health
- Department of Environmental Sciences
- D-85764 Neuherberg
- Germany
| | - Markus Meringer
- German Aerospace Center (DLR)
- Earth Observation Center (EOC)
- 82234 Oberpfaffenhofen-Wessling
- Germany
| | - Constanze Müller
- HelmholtzZentrum Muenchen
- German Research Center for Environmental Health
- Department of Environmental Sciences
- D-85764 Neuherberg
- Germany
| | - Mourad Harir
- HelmholtzZentrum Muenchen
- German Research Center for Environmental Health
- Department of Environmental Sciences
- D-85764 Neuherberg
- Germany
| | - Norbert Hertkorn
- HelmholtzZentrum Muenchen
- German Research Center for Environmental Health
- Department of Environmental Sciences
- D-85764 Neuherberg
- Germany
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22
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Jones RM, Goordial JM, Orcutt BN. Low Energy Subsurface Environments as Extraterrestrial Analogs. Front Microbiol 2018; 9:1605. [PMID: 30072971 PMCID: PMC6058055 DOI: 10.3389/fmicb.2018.01605] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/27/2018] [Indexed: 11/13/2022] Open
Abstract
Earth's subsurface is often isolated from phototrophic energy sources and characterized by chemotrophic modes of life. These environments are often oligotrophic and limited in electron donors or electron acceptors, and include continental crust, subseafloor oceanic crust, and marine sediment as well as subglacial lakes and the subsurface of polar desert soils. These low energy subsurface environments are therefore uniquely positioned for examining minimum energetic requirements and adaptations for chemotrophic life. Current targets for astrobiology investigations of extant life are planetary bodies with largely inhospitable surfaces, such as Mars, Europa, and Enceladus. Subsurface environments on Earth thus serve as analogs to explore possibilities of subsurface life on extraterrestrial bodies. The purpose of this review is to provide an overview of subsurface environments as potential analogs, and the features of microbial communities existing in these low energy environments, with particular emphasis on how they inform the study of energetic limits required for life. The thermodynamic energetic calculations presented here suggest that free energy yields of reactions and energy density of some metabolic redox reactions on Mars, Europa, Enceladus, and Titan could be comparable to analog environments in Earth's low energy subsurface habitats.
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Affiliation(s)
| | | | - Beth N. Orcutt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
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23
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Gíslason SR, Sigurdardóttir H, Aradóttir ES, Oelkers EH. A brief history of CarbFix: Challenges and victories of the project’s pilot phase. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.egypro.2018.07.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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24
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Miller QRS, Schaef HT, Kaszuba JP, Qiu L, Bowden ME, McGrail BP. Tunable Manipulation of Mineral Carbonation Kinetics in Nanoscale Water Films via Citrate Additives. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:7138-7148. [PMID: 29874053 DOI: 10.1021/acs.est.8b00438] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We explored the influence of a model organic ligand on mineral carbonation in nanoscale interfacial water films by conducting five time-resolved in situ X-ray diffraction (XRD) experiments at 50 °C. Forsterite was exposed to water-saturated supercritical carbon dioxide (90 bar) that had been equilibrated with 0-0.5 m citrate (C6H5O7-3) solutions. The experimental results demonstrated that greater concentrations of citrate in the nanoscale interfacial water film promoted the precipitation of magnesite (MgCO3) relative to nesquehonite (MgCO3·3H2O). At the highest concentrations tested, magnesite nucleation and growth were inhibited, lowering the carbonation rate constant from 9.1 × 10-6 to 3.6 × 10-6 s-1. These impacts of citrate were due to partial dehydration of Mg2+(aq) and the adsorption of citrate onto nuclei and magnesite surfaces. This type of information may be used to predict and tailor subsurface mineralization rates and pathways.
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Affiliation(s)
- Quin R S Miller
- Department of Geology and Geophysics , University of Wyoming , 1000 E. University Avenue , Laramie , Wyoming 82071 , United States
| | - Herbert T Schaef
- Physical and Computational Sciences Directorate , Pacific Northwest National Laboratory , P.O. Box 999, MS K8-98, Richland , Washington 99352 , United States
| | - John P Kaszuba
- Department of Geology and Geophysics , University of Wyoming , 1000 E. University Avenue , Laramie , Wyoming 82071 , United States
- School of Energy Resources , University of Wyoming , 1000 E. University Avenue , Laramie , Wyoming 82071 , United States
| | - Lin Qiu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Pudong Xinqu, Shanghai , China 201203
| | - Mark E Bowden
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , P.O. Box 999, MS K8-98, Richland , Washington 99352 , United States
| | - Bernard P McGrail
- Energy and Environment Directorate , Pacific Northwest National Laboratory , P.O. Box 999, MS K8-98, Richland , Washington 99352 , United States
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