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Beaver RC, Neufeld JD. Microbial ecology of the deep terrestrial subsurface. THE ISME JOURNAL 2024; 18:wrae091. [PMID: 38780093 PMCID: PMC11170664 DOI: 10.1093/ismejo/wrae091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 03/04/2024] [Accepted: 05/22/2024] [Indexed: 05/25/2024]
Abstract
The terrestrial subsurface hosts microbial communities that, collectively, are predicted to comprise as many microbial cells as global surface soils. Although initially thought to be associated with deposited organic matter, deep subsurface microbial communities are supported by chemolithoautotrophic primary production, with hydrogen serving as an important source of electrons. Despite recent progress, relatively little is known about the deep terrestrial subsurface compared to more commonly studied environments. Understanding the composition of deep terrestrial subsurface microbial communities and the factors that influence them is of importance because of human-associated activities including long-term storage of used nuclear fuel, carbon capture, and storage of hydrogen for use as an energy vector. In addition to identifying deep subsurface microorganisms, recent research focuses on identifying the roles of microorganisms in subsurface communities, as well as elucidating myriad interactions-syntrophic, episymbiotic, and viral-that occur among community members. In recent years, entirely new groups of microorganisms (i.e. candidate phyla radiation bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoloarchaeota, Nanoarchaeota archaea) have been discovered in deep terrestrial subsurface environments, suggesting that much remains unknown about this biosphere. This review explores the historical context for deep terrestrial subsurface microbial ecology and highlights recent discoveries that shape current ecological understanding of this poorly explored microbial habitat. Additionally, we highlight the need for multifaceted experimental approaches to observe phenomena such as cryptic cycles, complex interactions, and episymbiosis, which may not be apparent when using single approaches in isolation, but are nonetheless critical to advancing our understanding of this deep biosphere.
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Affiliation(s)
- Rachel C Beaver
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
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2
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Karnachuk OV, Panova IA, Rusanov II, Schetinina L, Lepokurova OY, Domrocheva EV, Kadnikov VV, Avakyan MR, Lukina AP, Glukhova LB, Pimenov NV, Ravin NV. Coexistence of Psychrophilic, Mesophilic, and Thermophilic Sulfate-Reducing Bacteria in a Deep Subsurface Aquifer Associated with Coal-Bed Methane Production. MICROBIAL ECOLOGY 2023; 86:1934-1946. [PMID: 36821051 DOI: 10.1007/s00248-023-02196-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/11/2023] [Indexed: 06/18/2023]
Abstract
The microbial community of subsurface environments remains understudied due to limited access to deep strata and aquifers. Coal-bed methane (CBM) production is associated with a large number of wells pumping water out of coal seams. CBM wells provide access to deep biotopes associated with coal-bed water. Temperature is one of the key constraints for the distribution and activity of subsurface microorganisms, including sulfate-reducing prokaryotes (SRP). The 16S rRNA gene amplicon sequencing coupled with in situ sulfate reduction rate (SRR) measurements with a radioactive tracer and cultivation at various temperatures revealed that the SRP community of the coal bed water of the Kuzbass coal basin is characterized by an overlapping mesophilic-psychrophilic boundary. The genus Desulfovibrio comprised a significant share of the SRP community. The D. psychrotolerans strain 1203, which has a growth optimum below 20 °C, dominated the cultivated SRP. SRR in coal bed water varied from 0.154 ± 0.07 to 2.04 ± 0.048 nmol S cm-3 day-1. Despite the ambient water temperature of ~ 10-20 °C, an active thermophilic SRP community occurred in the fracture water, which reduced sulfate with the rate of 0.159 ± 0.023 to 0.198 ± 0.007 nmol S cm-3 day-1 at 55 °C. A novel moderately thermophilic "Desulforudis audaxviator"-clade SRP has been isolated in pure culture from the coal-bed water.
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Affiliation(s)
- Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, 634050, Russia.
| | - Inna A Panova
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, 634050, Russia
| | - Igor I Rusanov
- Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Lilia Schetinina
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, 634050, Russia
| | - Olesya Y Lepokurova
- Tomsk Branch of the Trofimuk Institute of Petroleum Geology and Geophysics in the Siberian Branch of the Russian Academy of Sciences, Akademicheskiy 4, 634055, Tomsk, Russia
| | - Evgenia V Domrocheva
- Tomsk Branch of the Trofimuk Institute of Petroleum Geology and Geophysics in the Siberian Branch of the Russian Academy of Sciences, Akademicheskiy 4, 634055, Tomsk, Russia
| | - Vitaly V Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, Bld. 33‑2, Moscow, Russia, 119071
| | - Marat R Avakyan
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, 634050, Russia
| | - Anstasia P Lukina
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, 634050, Russia
| | - Liubov B Glukhova
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, 634050, Russia
| | - Nikolai V Pimenov
- Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, Bld. 33‑2, Moscow, Russia, 119071
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3
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Bornemann TLV, Esser SP, Stach TL, Burg T, Probst AJ. uBin: A manual refining tool for genomes from metagenomes. Environ Microbiol 2023; 25:1077-1083. [PMID: 36764661 DOI: 10.1111/1462-2920.16351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023]
Abstract
Resolving bacterial and archaeal genomes from metagenomes has revolutionized our understanding of Earth's biomes yet producing high-quality genomes from assembled fragments has been an ever-standing problem. While automated binning software and their combination produce prokaryotic bins in high throughput, their manual refinement has been slow, sometimes difficult or missing entirely facilitating error propagation in public databases. Here, we present uBin, a GUI-based, standalone bin refiner that runs on all major operating platforms and was additionally designed for educational purposes. When applied to the public CAMI dataset, refinement of bins using GC content, coverage and taxonomy was able to improve 78.9% of bins by decreasing their contamination. We also applied the bin refiner as a standalone binner to public metagenomes from the International Space Station and demonstrate the recovery of near-complete genomes, whose replication indices indicate the active proliferation of microbes in Earth's lower orbit. uBin is an easy to instal software for bin refinement, binning of simple metagenomes and communication of metagenomic results to other scientists and in classrooms. The software and its helper scripts are open source and available under https://github.com/ProbstLab/uBin.
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Affiliation(s)
- Till L V Bornemann
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Germany
| | - Sarah P Esser
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Germany
| | - Tom L Stach
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Germany
| | - Tim Burg
- Independent Researcher, Im Acker 59, Koblenz, Germany
| | - Alexander J Probst
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Germany
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Germany
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4
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Lossouarn J, Nesbø CL, Bienvenu N, Geslin C. Plasmid pMO1 from Marinitoga okinawensis, first non-cryptic plasmid reported within Thermotogota. Res Microbiol 2023; 174:104044. [PMID: 36805054 DOI: 10.1016/j.resmic.2023.104044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/19/2023]
Abstract
Mobile genetic elements (MGEs), such as viruses and plasmids, drive the evolution and adaptation of their cellular hosts from all three domains of life. This includes microorganisms thriving in the most extreme environments, like deep-sea hydrothermal vents. However, our knowledge about MGEs still remains relatively sparse in these abyssal ecosystems. Here we report the isolation, sequencing, assembly, and functional annotation of pMO1, a 28.2 kbp plasmid associated with the reference strain Marinitoga okinawensis. Carrying restriction/modification and chemotaxis protein-encoding genes, pMO1 likely affects its host's phenotype and represents the first non-cryptic plasmid described among the phylum Thermotogota.
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Affiliation(s)
- Julien Lossouarn
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.
| | - Camilla L Nesbø
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada; Biozone, Department of Chemical Engineering and Applied Chemistry and BioZone, University of Toronto, 200 College Street, Toronto, Ontario, Canada, M5S 3E5.
| | - Nadège Bienvenu
- Univ Brest, Ifremer, CNRS, Unité Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France.
| | - Claire Geslin
- Univ Brest, Ifremer, CNRS, Unité Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France. mailto:
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5
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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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Mandal S, Bose H, Ramesh K, Sahu RP, Saha A, Sar P, Kazy SK. Depth wide distribution and metabolic potential of chemolithoautotrophic microorganisms reactivated from deep continental granitic crust underneath the Deccan Traps at Koyna, India. Front Microbiol 2022; 13:1018940. [PMID: 36504802 PMCID: PMC9731672 DOI: 10.3389/fmicb.2022.1018940] [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: 08/14/2022] [Accepted: 11/01/2022] [Indexed: 11/25/2022] Open
Abstract
Characterization of inorganic carbon (C) utilizing microorganisms from deep crystalline rocks is of major scientific interest owing to their crucial role in global carbon and other elemental cycles. In this study we investigate the microbial populations from the deep [up to 2,908 meters below surface (mbs)] granitic rocks within the Koyna seismogenic zone, reactivated (enriched) under anaerobic, high temperature (50°C), chemolithoautotrophic conditions. Subsurface rock samples from six different depths (1,679-2,908 mbs) are incubated (180 days) with CO2 (+H2) or HCO3 - as the sole C source. Estimation of total protein, ATP, utilization of NO3 - and SO4 2- and 16S rRNA gene qPCR suggests considerable microbial growth within the chemolithotrophic conditions. We note a better response of rock hosted community towards CO2 (+H2) over HCO3 -. 16S rRNA gene amplicon sequencing shows a depth-wide distribution of diverse chemolithotrophic (and a few fermentative) Bacteria and Archaea. Comamonas, Burkholderia-Caballeronia-Paraburkholderia, Ralstonia, Klebsiella, unclassified Burkholderiaceae and Enterobacteriaceae are reactivated as dominant organisms from the enrichments of the deeper rocks (2335-2,908 mbs) with both CO2 and HCO3 -. For the rock samples from shallower depths, organisms of varied taxa are enriched under CO2 (+H2) and HCO3 -. Pseudomonas, Rhodanobacter, Methyloversatilis, and Thaumarchaeota are major CO2 (+H2) utilizers, while Nocardioides, Sphingomonas, Aeromonas, respond towards HCO3 -. H2 oxidizing Cupriavidus, Hydrogenophilus, Hydrogenophaga, CO2 fixing Cyanobacteria Rhodobacter, Clostridium, Desulfovibrio and methanogenic archaea are also enriched. Enriched chemolithoautotrophic members show good correlation with CO2, CH4 and H2 concentrations of the native rock environments, while the organisms from upper horizons correlate more to NO3 -, SO4 2- , Fe and TIC levels of the rocks. Co-occurrence networks suggest close interaction between chemolithoautotrophic and chemoorganotrophic/fermentative organisms. Carbon fixing 3-HP and DC/HB cycles, hydrogen, sulfur oxidation, CH4 and acetate metabolisms are predicted in the enriched communities. Our study elucidates the presence of live, C and H2 utilizing Bacteria and Archaea in deep subsurface granitic rocks, which are enriched successfully. Significant impact of depth and geochemical controls on relative distribution of various chemolithotrophic species enriched and their C and H2 metabolism are highlighted. These endolithic microorganisms show great potential for answering the fundamental questions of deep life and their exploitation in CO2 capture and conversion to useful products.
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Affiliation(s)
- Sunanda Mandal
- Environmental Microbiology and Biotechnology Laboratory, Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, India
| | - Himadri Bose
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, India
| | - Kheerthana Ramesh
- Environmental Microbiology and Biotechnology Laboratory, Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, India
| | - Rajendra Prasad Sahu
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, India
| | - Anumeha Saha
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, India
| | - Pinaki Sar
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, India
| | - Sufia Khannam Kazy
- Environmental Microbiology and Biotechnology Laboratory, Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, India,*Correspondence: Sufia Khannam Kazy,
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Nuppunen-Puputti M, Kietäväinen R, Raulio M, Soro A, Purkamo L, Kukkonen I, Bomberg M. Epilithic Microbial Community Functionality in Deep Oligotrophic Continental Bedrock. Front Microbiol 2022; 13:826048. [PMID: 35300483 PMCID: PMC8921683 DOI: 10.3389/fmicb.2022.826048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/12/2022] [Indexed: 01/03/2023] Open
Abstract
The deep terrestrial biosphere hosts vast sessile rock surface communities and biofilms, but thus far, mostly planktic communities have been studied. We enriched deep subsurface microbial communities on mica schist in microcosms containing bedrock groundwater from the depth of 500 m from Outokumpu, Finland. The biofilms were visualized using scanning electron microscopy, revealing numerous different microbial cell morphologies and attachment strategies on the mica schist surface, e.g., bacteria with outer membrane vesicle-like structures, hair-like extracellular extensions, and long tubular cell structures expanding over hundreds of micrometers over mica schist surfaces. Bacterial communities were analyzed with amplicon sequencing showing that Pseudomonas, Desulfosporosinus, Hydrogenophaga, and Brevundimonas genera dominated communities after 8–40 months of incubation. A total of 21 metagenome assembled genomes from sessile rock surface metagenomes identified genes involved in biofilm formation, as well as a wide variety of metabolic traits indicating a high degree of environmental adaptivity to oligotrophic environment and potential for shifting between multiple energy or carbon sources. In addition, we detected ubiquitous organic carbon oxidation and capacity for arsenate and selenate reduction within our rocky MAGs. Our results agree with the previously suggested interaction between the deep subsurface microbial communities and the rock surfaces, and that this interaction could be crucial for sustaining life in the harsh anoxic and oligotrophic deep subsurface of crystalline bedrock environment.
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Affiliation(s)
| | | | - Mari Raulio
- European Chemicals Agency (ECHA), Helsinki, Finland
| | - Aino Soro
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | | | - Ilmo Kukkonen
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Malin Bomberg
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
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Oren A, Garrity GM. CANDIDATUS LIST No. 3. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2022; 72. [PMID: 35100104 DOI: 10.1099/ijsem.0.005186] [Citation(s) in RCA: 251] [Impact Index Per Article: 125.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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9
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OUP accepted manuscript. FEMS Microbiol Ecol 2022; 98:6577122. [DOI: 10.1093/femsec/fiac054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/07/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
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10
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Sahu RP, Kazy SK, Bose H, Mandal S, Dutta A, Saha A, Roy S, Dutta Gupta S, Mukherjee A, Sar P. Microbial diversity and function in crystalline basement beneath the Deccan Traps explored in a 3 km borehole at Koyna, western India. Environ Microbiol 2021; 24:2837-2853. [PMID: 34897962 DOI: 10.1111/1462-2920.15867] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/29/2021] [Accepted: 12/05/2021] [Indexed: 12/20/2022]
Abstract
Deep terrestrial subsurface represents a huge repository of global prokaryotic biomass. Given its vastness and importance, microbial life within the deep subsurface continental crust remains under-represented in global studies. We characterize the microbial communities of deep, extreme and oligotrophic realm hosted by crystalline Archaean granitic rocks underneath the Deccan Traps, through sampling via 3000 m deep scientific borehole at Koyna, India through metagenomics, amplicon sequencing and cultivation-based analyses. Gene sequences 16S rRNA (7.37 × 106 ) show considerable bacterial diversity and the existence of a core microbiome (5724 operational taxonomic units conserved out of a total 118,064 OTUs) across the depths. Relative abundance of different taxa of core microbiome varies with depth in response to prevailing lithology and geochemistry. Co-occurrence network analysis and cultivation attempt to elucidate close interactions among autotrophic and organotrophic bacteria. Shotgun metagenomics reveals a major role of autotrophic carbon fixation via the Wood-Ljungdahl pathway and genes responsible for energy and carbon metabolism. Deeper analysis suggests the existence of an 'acetate switch', coordinating biosynthesis and cellular homeostasis. We conclude that the microbial life in the nutrient- and energy-limited deep granitic crust is constrained by the depth and managed by a few core members via a close interplay between autotrophy and organotrophy.
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Affiliation(s)
- Rajendra Prasad Sahu
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Sufia K Kazy
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India
| | - Himadri Bose
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Sunanda Mandal
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India
| | - Avishek Dutta
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Anumeha Saha
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Sukanta Roy
- Ministry of Earth Sciences, Borehole Geophysics Research Laboratory, Karad, MH, 415114, India
| | - Srimanti Dutta Gupta
- School of Environmental Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Abhijit Mukherjee
- School of Environmental Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India.,Department of Geology and Geophysics, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Pinaki Sar
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
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11
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Ranchou-Peyruse M, Guignard M, Casteran F, Abadie M, Defois C, Peyret P, Dequidt D, Caumette G, Chiquet P, Cézac P, Ranchou-Peyruse A. Microbial Diversity Under the Influence of Natural Gas Storage in a Deep Aquifer. Front Microbiol 2021; 12:688929. [PMID: 34721313 PMCID: PMC8549729 DOI: 10.3389/fmicb.2021.688929] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 09/08/2021] [Indexed: 11/30/2022] Open
Abstract
Deep aquifers (up to 2km deep) contain massive volumes of water harboring large and diverse microbial communities at high pressure. Aquifers are home to microbial ecosystems that participate in physicochemical balances. These microorganisms can positively or negatively interfere with subsurface (i) energy storage (CH4 and H2), (ii) CO2 sequestration; and (iii) resource (water, rare metals) exploitation. The aquifer studied here (720m deep, 37°C, 88bar) is naturally oligotrophic, with a total organic carbon content of <1mg.L-1 and a phosphate content of 0.02mg.L-1. The influence of natural gas storage locally generates different pressures and formation water displacements, but it also releases organic molecules such as monoaromatic hydrocarbons at the gas/water interface. The hydrocarbon biodegradation ability of the indigenous microbial community was evaluated in this work. The in situ microbial community was dominated by sulfate-reducing (e.g., Sva0485 lineage, Thermodesulfovibriona, Desulfotomaculum, Desulfomonile, and Desulfovibrio), fermentative (e.g., Peptococcaceae SCADC1_2_3, Anaerolineae lineage and Pelotomaculum), and homoacetogenic bacteria ("Candidatus Acetothermia") with a few archaeal representatives (e.g., Methanomassiliicoccaceae, Methanobacteriaceae, and members of the Bathyarcheia class), suggesting a role of H2 in microenvironment functioning. Monoaromatic hydrocarbon biodegradation is carried out by sulfate reducers and favored by concentrated biomass and slightly acidic conditions, which suggests that biodegradation should preferably occur in biofilms present on the surfaces of aquifer rock, rather than by planktonic bacteria. A simplified bacterial community, which was able to degrade monoaromatic hydrocarbons at atmospheric pressure over several months, was selected for incubation experiments at in situ pressure (i.e., 90bar). These showed that the abundance of various bacterial genera was altered, while taxonomic diversity was mostly unchanged. The candidate phylum Acetothermia was characteristic of the community incubated at 90bar. This work suggests that even if pressures on the order of 90bar do not seem to select for obligate piezophilic organisms, modifications of the thermodynamic equilibria could favor different microbial assemblages from those observed at atmospheric pressure.
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Affiliation(s)
- Magali Ranchou-Peyruse
- IPREM, Institut des Sciences Analytiques et de Physico-Chimie pour l’Environnement et les Matériaux, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
- Laboratoire de thermique, énergétique et procédés IPRA, EA1932, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, France
| | - Marion Guignard
- IPREM, Institut des Sciences Analytiques et de Physico-Chimie pour l’Environnement et les Matériaux, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
| | - Franck Casteran
- Laboratoire de thermique, énergétique et procédés IPRA, EA1932, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
| | - Maïder Abadie
- IPREM, Institut des Sciences Analytiques et de Physico-Chimie pour l’Environnement et les Matériaux, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
| | - Clémence Defois
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - Pierre Peyret
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - David Dequidt
- STORENGY – Geosciences Department, Bois-Colombes, France
| | - Guilhem Caumette
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, France
- Teréga, Pau, France
| | - Pierre Chiquet
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, France
- Teréga, Pau, France
| | - Pierre Cézac
- Laboratoire de thermique, énergétique et procédés IPRA, EA1932, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, France
| | - Anthony Ranchou-Peyruse
- IPREM, Institut des Sciences Analytiques et de Physico-Chimie pour l’Environnement et les Matériaux, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, France
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12
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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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13
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Abstract
In recent years, the tree of life has expanded substantially. Despite this, many abundant yet uncultivated microbial groups remain to be explored. Sumerlaeota is a mysterious, putative phylum-level lineage distributed globally but rarely reported. As such, their physiology, ecology, and evolutionary history remain unknown. The 16S rRNA gene survey reveals that Sumerlaeota is frequently detected in diverse environments globally, especially cold arid desert soils and deep-sea basin surface sediments, where it is one dominant microbial group. Here, we retrieved four Sumerlaeota metagenome-assembled genomes (MAGs) from two hot springs and one saline lake. Including another 12 publicly available MAGs, they represent six of the nine putative Sumerlaeota subgroups/orders, as indicated by 16S rRNA gene-based phylogeny. These elusive organisms likely obtain carbon mainly through utilization of refractory organics (e.g., chitin and cellulose) and proteinaceous compounds, suggesting that Sumerlaeota act as scavengers in nature. The presence of key bidirectional enzymes involved in acetate and hydrogen metabolisms in these MAGs suggests that they are acetogenic bacteria capable of both the production and consumption of hydrogen. The capabilities of dissimilatory nitrate and sulfate reduction, nitrogen fixation, phosphate solubilization, and organic phosphorus mineralization may confer these heterotrophs great advantages to thrive under diverse harsh conditions. Ancestral state reconstruction indicated that Sumerlaeota originated from chemotrophic and facultatively anaerobic ancestors, and their smaller and variably sized genomes evolved along dynamic pathways from a sizeable common ancestor (2,342 genes), leading to their physiological divergence. Notably, large gene gain and larger loss events occurred at the branch to the last common ancestor of the order subgroup 1, likely due to niche expansion and population size effects.
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14
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He C, Liu T, Ou H, Yuan S, Hu Z, Wang W. Coupling granular activated carbon and exogenous hydrogen to enhance anaerobic digestion of phenol via predominant syntrophic acetate oxidation and hydrogenotrophic methanogenesis pathway. BIORESOURCE TECHNOLOGY 2021; 323:124576. [PMID: 33401163 DOI: 10.1016/j.biortech.2020.124576] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/12/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
Anaerobic digestion is a promising biological method for treating phenol-containing wastewater. However, the low methane yield of phenol due to the biological toxicity limits its potential application. This study presents a novel method to enhance the conversion rate of phenol to methane by coupling of granular activated carbon and exogenous hydrogen (GAC/H2). The cumulative methane production in the GAC/H2, H2, GAC, and control groups were 408.2 ± 16.2, 336.5 ± 5.7, 287.2 ± 26. 2, and 258.1 ± 8.6 mL CH4/g COD, respectively. Compared with the control group, the hydrogenotrophic methanogenic activity and electron transfer activity of GAC/H2 group were increased by 403.9 and 367.4%, respectively. The results of the 16SrRNA analysis indicated GAC enhanced the relative abundances of Syntrophus and Syntrophorhabdus, and hydrogen promoted the relative abundances of Cryptanaerobacter, Aminicenantes, and Methanobacterium. Therefore, the coupling of GAC and exogenous hydrogen promoted a dominate SAO-HM pathway to convert phenol to methane.
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Affiliation(s)
- Chunhua He
- Department of Municipal Engineering, School of Civil Engineering, Hefei University of Technology, Hefei 230009, China; Anhui Provincial Engineering Laboratory for Rural Water Environment and Resources, Hefei 230009, China
| | - Tingxia Liu
- Department of Municipal Engineering, School of Civil Engineering, Hefei University of Technology, Hefei 230009, China; Anhui Provincial Engineering Laboratory for Rural Water Environment and Resources, Hefei 230009, China
| | - Hua Ou
- Department of Municipal Engineering, School of Civil Engineering, Hefei University of Technology, Hefei 230009, China; Anhui Provincial Engineering Laboratory for Rural Water Environment and Resources, Hefei 230009, China
| | - Shoujun Yuan
- Department of Municipal Engineering, School of Civil Engineering, Hefei University of Technology, Hefei 230009, China; Anhui Provincial Engineering Laboratory for Rural Water Environment and Resources, Hefei 230009, China
| | - Zhenhu Hu
- Department of Municipal Engineering, School of Civil Engineering, Hefei University of Technology, Hefei 230009, China; Anhui Provincial Engineering Laboratory for Rural Water Environment and Resources, Hefei 230009, China
| | - Wei Wang
- Department of Municipal Engineering, School of Civil Engineering, Hefei University of Technology, Hefei 230009, China; Anhui Provincial Engineering Laboratory for Rural Water Environment and Resources, Hefei 230009, China.
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15
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Karnachuk OV, Lukina AP, Kadnikov VV, Sherbakova VA, Beletsky AV, Mardanov AV, Ravin NV. Targeted isolation based on metagenome‐assembled genomes reveals a phylogenetically distinct group of thermophilic spirochetes from deep biosphere. Environ Microbiol 2020; 23:3585-3598. [DOI: 10.1111/1462-2920.15218] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/18/2020] [Accepted: 08/27/2020] [Indexed: 12/22/2022]
Affiliation(s)
| | | | - Vitaly V. Kadnikov
- Institute of Bioengineering Research Center of Biotechnology of the Russian Academy of Sciences Moscow 119071 Russia
| | - Viktoria A. Sherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms Federal Research Center ‘Pushchino Scientific Center for Biological Research, Russian Academy of Sciences’ Pushchino Moscow 142290 Russia
| | - Alexey V. Beletsky
- Institute of Bioengineering Research Center of Biotechnology of the Russian Academy of Sciences Moscow 119071 Russia
| | - Andrey V. Mardanov
- Institute of Bioengineering Research Center of Biotechnology of the Russian Academy of Sciences Moscow 119071 Russia
| | - Nikolai V. Ravin
- Institute of Bioengineering Research Center of Biotechnology of the Russian Academy of Sciences Moscow 119071 Russia
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16
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Kadnikov VV, Mardanov AV, Beletsky AV, Karnachuk OV, Ravin NV. Microbial Life in the Deep Subsurface Aquifer Illuminated by Metagenomics. Front Microbiol 2020; 11:572252. [PMID: 33013807 PMCID: PMC7509429 DOI: 10.3389/fmicb.2020.572252] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 08/13/2020] [Indexed: 01/08/2023] Open
Abstract
To get insights into microbial diversity and biogeochemical processes in the terrestrial deep subsurface aquifer, we sequenced the metagenome of artesian water collected at a 2.8 km deep oil exploration borehole 5P in Western Siberia, Russia. We obtained 71 metagenome-assembled genomes (MAGs), altogether comprising 93% of the metagenome. Methanogenic archaea accounted for about 20% of the community and mostly belonged to hydrogenotrophic Methanobacteriaceae; acetoclastic and methylotrophic lineages were less abundant. ANME archaea were not found. The most numerous bacteria were the Firmicutes, Ignavibacteriae, Deltaproteobacteria, Chloroflexi, and Armatimonadetes. Most of the community was composed of anaerobic heterotrophs. Only six MAGs belonged to sulfate reducers. These MAGs accounted for 5% of the metagenome and were assigned to the Firmicutes, Deltaproteobacteria, Candidatus Kapabacteria, and Nitrospirae. Organotrophic bacteria carrying cytochrome c oxidase genes and presumably capable of aerobic respiration mostly belonged to the Chloroflexi, Ignavibacteriae, and Armatimonadetes. They accounted for 13% of the community. The first complete closed genomes were obtained for members of the Ignavibacteriae SJA-28 lineage and the candidate phylum Kapabacteria. Metabolic reconstruction of the SJA-28 bacterium, designated Candidatus Tepidiaquacella proteinivora, predicted that it is an anaerobe growing on proteinaceous substrates by fermentation or anaerobic respiration. The Ca. Kapabacteria genome contained both the sulfate reduction pathway and cytochrome c oxidase. Presumably, the availability of buried organic matter of Mesozoic marine sediments, long-term recharge of the aquifer with meteoric waters and its spatial heterogeneity provided the conditions for the development of microbial communities, taxonomically and functionally more diverse than those found in oligotrophic underground ecosystems.
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Affiliation(s)
- Vitaly V Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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17
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Kadnikov VV, Mardanov AV, Beletsky AV, Karnachuk OV, Ravin NV. Genome Analysis of a Member of the Uncultured Phylum Riflebacteria Revealed Pathways of Organotrophic Metabolism and Dissimilatory Iron Reduction. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720030078] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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18
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Kadnikov VV, Mardanov AV, Beletsky AV, Frank YA, Karnachuk OV, Ravin NV. Complete Genome Sequence of an Uncultured Bacterium of the Candidate Phylum Bipolaricaulota. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719040064] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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19
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Domestication of previously uncultivated Candidatus Desulforudis audaxviator from a deep aquifer in Siberia sheds light on its physiology and evolution. ISME JOURNAL 2019; 13:1947-1959. [PMID: 30899075 DOI: 10.1038/s41396-019-0402-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 02/07/2019] [Accepted: 02/28/2019] [Indexed: 11/09/2022]
Abstract
An enigmatic uncultured member of Firmicutes, Candidatus Desulforudis audaxviator (CDA), is known by its genome retrieved from the deep gold mine in South Africa, where it formed a single-species ecosystem fuelled by hydrogen from water radiolysis. It was believed that in situ conditions CDA relied on scarce energy supply and did not divide for hundreds to thousand years. We have isolated CDA strain BYF from a 2-km-deep aquifer in Western Siberia and obtained a laboratory culture growing with a doubling time of 28.5 h. BYF uses not only H2 but also various organic electron donors for sulfate respiration. Growth required elemental iron, and ferrous iron did not substitute for it. A complex intracellular organization included gas vesicles, internal membranes, and electron-dense structures enriched in phosphorus, iron, and calcium. Genome comparison of BYF with the South African CDA revealed minimal differences mostly related to mobile elements and prophage insertions. Two genomes harbored <800 single-nucleotide polymorphisms and had nearly identical CRISPR loci. We suggest that spores with the gas vesicles may facilitate global distribution of CDA followed by colonization of suitable subsurface environments. Alternatively, a slow evolution rate in the deep subsurface could result in high genetic similarity of CDA populations at two sites spatially separated for hundreds of millions of years.
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Phylogeny and physiology of candidate phylum BRC1 inferred from the first complete metagenome-assembled genome obtained from deep subsurface aquifer. Syst Appl Microbiol 2019; 42:67-76. [DOI: 10.1016/j.syapm.2018.08.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/21/2018] [Accepted: 08/29/2018] [Indexed: 11/24/2022]
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21
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Genome of the candidate phylum Aminicenantes bacterium from a deep subsurface thermal aquifer revealed its fermentative saccharolytic lifestyle. Extremophiles 2019; 23:189-200. [DOI: 10.1007/s00792-018-01073-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/17/2018] [Indexed: 10/27/2022]
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22
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Stott M, Lueders T. Editorial: Deep life, kia ora! FEMS Microbiol Ecol 2018; 94:5101342. [DOI: 10.1093/femsec/fiy176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 09/03/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Matthew Stott
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Tillmann Lueders
- Institute of Groundwater Ecology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
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