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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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Mateos G, Martínez-Bonilla A, Martínez JM, Amils R. Vitamin B 12 Auxotrophy in Isolates from the Deep Subsurface of the Iberian Pyrite Belt. Genes (Basel) 2023; 14:1339. [PMID: 37510244 PMCID: PMC10378866 DOI: 10.3390/genes14071339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Vitamin B12 is an enzymatic cofactor that is essential for both eukaryotes and prokaryotes. The development of life in extreme environments depends on cofactors such as vitamin B12 as well. The genomes of twelve microorganisms isolated from the deep subsurface of the Iberian Pyrite Belt have been analyzed in search of enzymatic activities that require vitamin B12 or are involved in its synthesis and import. Results have revealed that vitamin B12 is needed by these microorganisms for several essential enzymes such as ribonucleotide reductase, methionine synthase and epoxyqueosine reductase. Isolate Desulfosporosinus sp. DEEP is the only analyzed genome that holds a set core of proteins that could lead to the production of vitamin B12. The rest are dependent on obtaining it from the subsurface oligotrophic environment in which they grow. Sought proteins involved in the import of vitamin B12 are not widespread in the sample. The dependence found in the genomes of these microorganisms is supported by the production of vitamin B12 by microorganisms such as Desulfosporosinus sp. DEEP, showing that the operation of deep subsurface biogeochemical cycles is dependent on cofactors such as vitamin B12.
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Affiliation(s)
- Guillermo Mateos
- Centro de Biología Molecular Severo Ochoa (CBMSO), Calle Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Adrián Martínez-Bonilla
- Centro de Biología Molecular Severo Ochoa (CBMSO), Calle Nicolás Cabrera 1, 28049 Madrid, Spain
| | - José M Martínez
- Centro de Biología Molecular Severo Ochoa (CBMSO), Calle Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Ricardo Amils
- Centro de Biología Molecular Severo Ochoa (CBMSO), Calle Nicolás Cabrera 1, 28049 Madrid, Spain
- Centro de Astrobiología (CAB-INTA), 28850 Torrejón de Ardoz, Spain
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3
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Gonzalez JM, Aranda B. Microbial Growth under Limiting Conditions-Future Perspectives. Microorganisms 2023; 11:1641. [PMID: 37512814 PMCID: PMC10383181 DOI: 10.3390/microorganisms11071641] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/02/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Microorganisms rule the functioning of our planet and each one of the individual macroscopic living creature. Nevertheless, microbial activity and growth status have always been challenging tasks to determine both in situ and in vivo. Microbial activity is generally related to growth, and the growth rate is a result of the availability of nutrients under adequate or adverse conditions faced by microbial cells in a changing environment. Most studies on microorganisms have been carried out under optimum or near-optimum growth conditions, but scarce information is available about microorganisms at slow-growing states (i.e., near-zero growth and maintenance metabolism). This study aims to better understand microorganisms under growth-limiting conditions. This is expected to provide new perspectives on the functions and relevance of the microbial world. This is because (i) microorganisms in nature frequently face conditions of severe growth limitation, (ii) microorganisms activate singular pathways (mostly genes remaining to be functionally annotated), resulting in a broad range of secondary metabolites, and (iii) the response of microorganisms to slow-growth conditions remains to be understood, including persistence strategies, gene expression, and cell differentiation both within clonal populations and due to the complexity of the environment.
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Affiliation(s)
- Juan M Gonzalez
- Instituto de Recursos Naturales y Agrobiología de Sevilla, Consejo Superior de Investigaciones Científicas, IRNAS-CSIC, E-41012 Sevilla, Spain
| | - Beatriz Aranda
- Instituto de Recursos Naturales y Agrobiología de Sevilla, Consejo Superior de Investigaciones Científicas, IRNAS-CSIC, E-41012 Sevilla, Spain
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He LX, He LY, Gao FZ, Zhang M, Chen J, Jia WL, Ye P, Jia YW, Hong B, Liu SS, Liu YS, Zhao JL, Ying GG. Mariculture affects antibiotic resistome and microbiome in the coastal environment. JOURNAL OF HAZARDOUS MATERIALS 2023; 452:131208. [PMID: 36966625 DOI: 10.1016/j.jhazmat.2023.131208] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 02/23/2023] [Accepted: 03/12/2023] [Indexed: 05/03/2023]
Abstract
Antibiotics are increasingly used and released into the marine environment due to the rapid development of mariculture, resulting in spread of antibiotic resistance. The pollution, distribution, and characteristics of antibiotics, antibiotic resistance genes (ARGs) and microbiomes have been investigated in this study. Results showed that 20 antibiotics were detected in Chinese coastal environment, with predominance of erythromycin-H2O, enrofloxacin and oxytetracycline. In coastal mariculture sites, antibiotic concentrations were significantly higher than in control sites, and more types of antibiotics were detected in the South than in the North of China. Residues of enrofloxacin, ciprofloxacin and sulfadiazine posed high resistance selection risks. β-Lactam, multi-drug and tetracycline resistance genes were frequently detected with significantly higher abundance in the mariculture sites. Of the 262 detected ARGs, 10, 26, and 19 were ranked as high-risk, current-risk, future-risk, respectively. The main bacterial phyla were Proteobacteria and Bacteroidetes, of which 25 genera were zoonotic pathogens, with Arcobacter and Vibrio in particular ranking in the top10. Opportunistic pathogens were more widely distributed in the northern mariculture sites. Phyla of Proteobacteria and Bacteroidetes were the potential hosts of high-risk ARGs, while the conditional pathogens were associated with future-risk ARGs, indicating a potential threat to human health.
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Affiliation(s)
- Lu-Xi He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Liang-Ying He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China.
| | - Fang-Zhou Gao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Min Zhang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; Guangdong Provincial Engineering Technology Research Center for Life and Health of River & Lake, Pearl River Hydraulic Research Institute, Pearl River Water Resources Commission of the Ministry of Water Resources, Guangzhou 510611, China
| | - Jun Chen
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; Guangdong Provincial Engineering Technology Research Center for Life and Health of River & Lake, Pearl River Hydraulic Research Institute, Pearl River Water Resources Commission of the Ministry of Water Resources, Guangzhou 510611, China
| | - Wei-Li Jia
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Pu Ye
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Yu-Wei Jia
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Bai Hong
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Si-Si Liu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - You-Sheng Liu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Jian-Liang Zhao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China.
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Hallsworth JE, Udaondo Z, Pedrós‐Alió C, Höfer J, Benison KC, Lloyd KG, Cordero RJB, de Campos CBL, Yakimov MM, Amils R. Scientific novelty beyond the experiment. Microb Biotechnol 2023; 16:1131-1173. [PMID: 36786388 PMCID: PMC10221578 DOI: 10.1111/1751-7915.14222] [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: 10/20/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 02/15/2023] Open
Abstract
Practical experiments drive important scientific discoveries in biology, but theory-based research studies also contribute novel-sometimes paradigm-changing-findings. Here, we appraise the roles of theory-based approaches focusing on the experiment-dominated wet-biology research areas of microbial growth and survival, cell physiology, host-pathogen interactions, and competitive or symbiotic interactions. Additional examples relate to analyses of genome-sequence data, climate change and planetary health, habitability, and astrobiology. We assess the importance of thought at each step of the research process; the roles of natural philosophy, and inconsistencies in logic and language, as drivers of scientific progress; the value of thought experiments; the use and limitations of artificial intelligence technologies, including their potential for interdisciplinary and transdisciplinary research; and other instances when theory is the most-direct and most-scientifically robust route to scientific novelty including the development of techniques for practical experimentation or fieldwork. We highlight the intrinsic need for human engagement in scientific innovation, an issue pertinent to the ongoing controversy over papers authored using/authored by artificial intelligence (such as the large language model/chatbot ChatGPT). Other issues discussed are the way in which aspects of language can bias thinking towards the spatial rather than the temporal (and how this biased thinking can lead to skewed scientific terminology); receptivity to research that is non-mainstream; and the importance of theory-based science in education and epistemology. Whereas we briefly highlight classic works (those by Oakes Ames, Francis H.C. Crick and James D. Watson, Charles R. Darwin, Albert Einstein, James E. Lovelock, Lynn Margulis, Gilbert Ryle, Erwin R.J.A. Schrödinger, Alan M. Turing, and others), the focus is on microbiology studies that are more-recent, discussing these in the context of the scientific process and the types of scientific novelty that they represent. These include several studies carried out during the 2020 to 2022 lockdowns of the COVID-19 pandemic when access to research laboratories was disallowed (or limited). We interviewed the authors of some of the featured microbiology-related papers and-although we ourselves are involved in laboratory experiments and practical fieldwork-also drew from our own research experiences showing that such studies can not only produce new scientific findings but can also transcend barriers between disciplines, act counter to scientific reductionism, integrate biological data across different timescales and levels of complexity, and circumvent constraints imposed by practical techniques. In relation to urgent research needs, we believe that climate change and other global challenges may require approaches beyond the experiment.
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Affiliation(s)
- John E. Hallsworth
- Institute for Global Food Security, School of Biological SciencesQueen's University BelfastBelfastUK
| | - Zulema Udaondo
- Department of Biomedical InformaticsUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Carlos Pedrós‐Alió
- Department of Systems BiologyCentro Nacional de Biotecnología (CSIC)MadridSpain
| | - Juan Höfer
- Escuela de Ciencias del MarPontificia Universidad Católica de ValparaísoValparaísoChile
| | - Kathleen C. Benison
- Department of Geology and GeographyWest Virginia UniversityMorgantownWest VirginiaUSA
| | - Karen G. Lloyd
- Microbiology DepartmentUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Radamés J. B. Cordero
- Department of Molecular Microbiology and ImmunologyJohns Hopkins Bloomberg School of Public HealthBaltimoreMarylandUSA
| | - Claudia B. L. de Campos
- Institute of Science and TechnologyUniversidade Federal de Sao Paulo (UNIFESP)São José dos CamposSPBrazil
| | | | - Ricardo Amils
- Department of Molecular Biology, Centro de Biología Molecular Severo Ochoa (CSIC‐UAM)Nicolás Cabrera n° 1, Universidad Autónoma de MadridMadridSpain
- Department of Planetology and HabitabilityCentro de Astrobiología (INTA‐CSIC)Torrejón de ArdozSpain
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6
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Berera A, Brener DJ, Cockell CS. Detecting Microbiology in the Upper Atmosphere: Relative-Velocity Filtered Sampling. ASTROBIOLOGY 2023; 23:469-475. [PMID: 36800170 DOI: 10.1089/ast.2022.0045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The purpose of this article is to reopen from a practical perspective the question of the extent in altitude of Earth's biosphere. We make a number of different suggestions for how searches for biological material could be conducted in the mesosphere and lower thermosphere, colloquially referred to as the "ignore-osphere" because it has been generally ignored in the meteorological community compared to other regions. Relatively recent technological advances such as CubeSats in very low Earth orbit or more standard approaches such as the rocket-borne MAGIC meteoric smoke particle sampler are shown as potentially viable for sampling biological material in the ignore-osphere. The issue of contamination is discussed, and a potential solution to the problem is proposed by means of a new detector design that filters for particles based on their size and relative velocity to the detector.
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Affiliation(s)
- Arjun Berera
- The Higgs Centre for Theoretical Physics, University of Edinburgh, Edinburgh, UK
| | - Daniel J Brener
- The Higgs Centre for Theoretical Physics, University of Edinburgh, Edinburgh, UK
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Nuppunen-Puputti M, Kietäväinen R, Kukkonen I, Bomberg M. Implications of a short carbon pulse on biofilm formation on mica schist in microcosms with deep crystalline bedrock groundwater. Front Microbiol 2023; 14:1054084. [PMID: 36819068 PMCID: PMC9932282 DOI: 10.3389/fmicb.2023.1054084] [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: 09/26/2022] [Accepted: 01/06/2023] [Indexed: 02/05/2023] Open
Abstract
Microbial life in the deep subsurface occupies rock surfaces as attached communities and biofilms. Previously, epilithic Fennoscandian deep subsurface bacterial communities were shown to host genetic potential, especially for heterotrophy and sulfur cycling. Acetate, methane, and methanol link multiple biogeochemical pathways and thus represent an important carbon and energy source for microorganisms in the deep subsurface. In this study, we examined further how a short pulse of low-molecular-weight carbon compounds impacts the formation and structure of sessile microbial communities on mica schist surfaces over an incubation period of ∼3.5 years in microcosms containing deep subsurface groundwater from the depth of 500 m, from Outokumpu, Finland. The marker gene copy counts in the water and rock phases were estimated with qPCR, which showed that bacteria dominated the mica schist communities with a relatively high proportion of epilithic sulfate-reducing bacteria in all microcosms. The dominant bacterial phyla in the microcosms were Proteobacteria, Firmicutes, and Actinobacteria, whereas most fungal genera belonged to Ascomycota and Basidiomycota. Dissimilarities between planktic and sessile rock surface microbial communities were observed, and the supplied carbon substrates led to variations in the bacterial community composition.
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Affiliation(s)
- Maija Nuppunen-Puputti
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland,*Correspondence: Maija Nuppunen-Puputti,
| | | | - 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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Amils R, Escudero C, Oggerin M, Puente Sánchez F, Arce Rodríguez A, Fernández Remolar D, Rodríguez N, García Villadangos M, Sanz JL, Briones C, Sánchez-Román M, Gómez F, Leandro T, Moreno-Paz M, Prieto-Ballesteros O, Molina A, Tornos F, Sánchez-Andrea I, Timmis K, Pieper DH, Parro V. Coupled C, H, N, S and Fe biogeochemical cycles operating in the continental deep subsurface of the Iberian Pyrite Belt. Environ Microbiol 2023; 25:428-453. [PMID: 36453153 PMCID: PMC10107794 DOI: 10.1111/1462-2920.16291] [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: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022]
Abstract
Microbial activity is a major contributor to the biogeochemical cycles that make up the life support system of planet Earth. A 613 m deep geomicrobiological perforation and a systematic multi-analytical characterization revealed an unexpected diversity associated with the rock matrix microbiome that operates in the subsurface of the Iberian Pyrite Belt (IPB). Members of 1 class and 16 genera were deemed the most representative microorganisms of the IPB deep subsurface and selected for a deeper analysis. The use of fluorescence in situ hybridization allowed not only the identification of microorganisms but also the detection of novel activities in the subsurface such as anaerobic ammonium oxidation (ANAMMOX) and anaerobic methane oxidation, the co-occurrence of microorganisms able to maintain complementary metabolic activities and the existence of biofilms. The use of enrichment cultures sensed the presence of five different complementary metabolic activities along the length of the borehole and isolated 29 bacterial species. Genomic analysis of nine isolates identified the genes involved in the complete operation of the light-independent coupled C, H, N, S and Fe biogeochemical cycles. This study revealed the importance of nitrate reduction microorganisms in the oxidation of iron in the anoxic conditions existing in the subsurface of the IPB.
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Affiliation(s)
- Ricardo Amils
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Spain
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Cristina Escudero
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Spain
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Monike Oggerin
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Spain
| | | | - Alejandro Arce Rodríguez
- Institute of Microbiology, Technical University Braunschweig, Germany
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Nuria Rodríguez
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Spain
| | | | - José Luis Sanz
- Department of Molecular Biology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Carlos Briones
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Spain
| | | | - Felipe Gómez
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Spain
| | - Tania Leandro
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | | | | | - Antonio Molina
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Spain
| | - Fernando Tornos
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Spain
| | | | - Kenneth Timmis
- Institute of Microbiology, Technical University Braunschweig, Germany
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Victor Parro
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Spain
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Rempfert KR, Nothaft DB, Kraus EA, Asamoto CK, Evans RD, Spear JR, Matter JM, Kopf SH, Templeton AS. Subsurface biogeochemical cycling of nitrogen in the actively serpentinizing Samail Ophiolite, Oman. Front Microbiol 2023; 14:1139633. [PMID: 37152731 PMCID: PMC10160414 DOI: 10.3389/fmicb.2023.1139633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/15/2023] [Indexed: 05/09/2023] Open
Abstract
Nitrogen (N) is an essential element for life. N compounds such as ammonium ( NH 4 + ) may act as electron donors, while nitrate ( NO 3 - ) and nitrite ( NO 2 - ) may serve as electron acceptors to support energy metabolism. However, little is known regarding the availability and forms of N in subsurface ecosystems, particularly in serpentinite-hosted settings where hydrogen (H2) generated through water-rock reactions promotes habitable conditions for microbial life. Here, we analyzed N and oxygen (O) isotope composition to investigate the source, abundance, and cycling of N species within the Samail Ophiolite of Oman. The dominant dissolved N species was dependent on the fluid type, with Mg2+- HCO 3 - type fluids comprised mostly of NO 3 - , and Ca2+-OH- fluids comprised primarily of ammonia (NH3). We infer that fixed N is introduced to the serpentinite aquifer as NO 3 - . High concentrations of NO 3 - (>100 μM) with a relict meteoric oxygen isotopic composition (δ18O ~ 22‰, Δ17O ~ 6‰) were observed in shallow aquifer fluids, indicative of NO 3 - sourced from atmospheric deposition (rainwater NO 3 - : δ18O of 53.7‰, Δ17O of 16.8‰) mixed with NO 3 - produced in situ through nitrification (estimated endmember δ18O and Δ17O of ~0‰). Conversely, highly reacted hyperalkaline fluids had high concentrations of NH3 (>100 μM) with little NO 3 - detectable. We interpret that NH3 in hyperalkaline fluids is a product of NO 3 - reduction. The proportionality of the O and N isotope fractionation (18ε / 15ε) measured in Samail Ophiolite NO 3 - was close to unity (18ε / 15ε ~ 1), which is consistent with dissimilatory NO 3 - reduction with a membrane-bound reductase (NarG); however, abiotic reduction processes may also be occurring. The presence of genes commonly involved in N reduction processes (narG, napA, nrfA) in the metagenomes of biomass sourced from aquifer fluids supports potential biological involvement in the consumption of NO 3 - . Production of NH 4 + as the end-product of NO 3 - reduction via dissimilatory nitrate reduction to ammonium (DNRA) could retain N in the subsurface and fuel nitrification in the oxygenated near surface. Elevated bioavailable N in all sampled fluids indicates that N is not likely limiting as a nutrient in serpentinites of the Samail Ophiolite.
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Affiliation(s)
- Kaitlin R. Rempfert
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
- *Correspondence: Kaitlin R. Rempfert
| | - Daniel B. Nothaft
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - Emily A. Kraus
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
| | - Ciara K. Asamoto
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - R. Dave Evans
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - John R. Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
- Quantitative Biosciences and Engineering, Colorado School of Mines, Golden, CO, United States
| | - Juerg M. Matter
- National Oceanography Centre, University of Southampton, Southampton, United Kingdom
| | - Sebastian H. Kopf
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - Alexis S. Templeton
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
- Alexis S. Templeton
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10
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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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11
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Shewanella sp. T2.3D-1.1 a Novel Microorganism Sustaining the Iron Cycle in the Deep Subsurface of the Iberian Pyrite Belt. Microorganisms 2022; 10:microorganisms10081585. [PMID: 36014003 PMCID: PMC9415397 DOI: 10.3390/microorganisms10081585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
The Iberian Pyrite Belt (IPB) is one of the largest deposits of sulphidic minerals on Earth. Río Tinto raises from its core, presenting low a pH and high metal concentration. Several drilling cores were extracted from the IPB’s subsurface, and strain T2.3D-1.1 was isolated from a core at 121.8 m depth. We aimed to characterize this subterranean microorganism, revealing its phylogenomic affiliation (Average Nucleotide Identity, digital DNA-DNA Hybridization) and inferring its physiology through genome annotation, backed with physiological experiments to explore its relationship with the Fe biogeochemical cycle. Results determined that the isolate belongs to the Shewanella putrefaciens (with ANI 99.25 with S. putrefaciens CN-32). Its genome harbours the necessary genes, including omcA mtrCAB, to perform the Extracellular Electron Transfer (EET) and reduce acceptors such as Fe3+, napAB to reduce NO3− to NO2−, hydAB to produce H2 and genes sirA, phsABC and ttrABC to reduce SO32−, S2O32− and S4O62−, respectively. A full CRISPR-Cas 1F type system was found as well. S. putrefaciens T2.3D-1.1 can reduce Fe3+ and promote the oxidation of Fe2+ in the presence of NO3− under anaerobic conditions. Production of H2 has been observed under anaerobic conditions with lactate or pyruvate as the electron donor and fumarate as the electron acceptor. Besides Fe3+ and NO3−, the isolate also grows with Dimethyl Sulfoxide and Trimethyl N-oxide, S4O62− and S2O32− as electron acceptors. It tolerates different concentrations of heavy metals such as 7.5 mM of Pb, 5 mM of Cr and Cu and 1 mM of Cd, Co, Ni and Zn. This array of traits suggests that S. putrefaciens T2.3D-1.1 could have an important role within the Iberian Pyrite Belt subsurface participating in the iron cycle, through the dissolution of iron minerals and therefore contributing to generate the extreme conditions detected in the Río Tinto basin.
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12
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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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13
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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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14
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Sanz JL, Rodriguez N, Escudero C, Carrizo D, Amils R. Biological production of H 2 , CH 4 and CO 2 in the deep subsurface of the Iberian Pyrite Belt. Environ Microbiol 2021; 23:3913-3922. [PMID: 33973338 DOI: 10.1111/1462-2920.15561] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/29/2021] [Accepted: 05/01/2021] [Indexed: 11/26/2022]
Abstract
Most of the terrestrial deep subsurfaces are oligotrophic environments in which some gases, mainly H2 , CH4 and CO2 , play an important role as energy and/or carbon sources. In this work, we assessed their biotic and abiotic origin in samples from subsurface hard-rock cores of the Iberian Pyrite Belt (IPB) at three different depths (414, 497 and 520 m). One set of samples was sterilized (abiotic control) and all samples were incubated under anaerobic conditions. Our results showed that H2 , CH4 and CO2 remained low and constant in the sterilized controls while their levels were 4, 4.1 and 2.5 times higher respectively, in the unsterilized samples compared to the abiotic controls. The δ13 CCH4 -values measured in the samples (range -31.2 to -43.0 ‰) reveals carbon isotopic signatures that are within the range for biological methane production. Possible microorganisms responsible for the biotic production of the gases were assessed by CARD-FISH. The analysis of sequenced genomes of detected microorganisms within the subsurface of the IPB allowed to identify possible metabolic activities involved in H2 (Rhodoplanes, Shewanella and Desulfosporosinus), CH4 (Methanobacteriales) and CO2 production. The obtained results suggest that part of the H2 , CH4 and CO2 detected in the deep subsurface has a biological origin.
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Affiliation(s)
- Jose L Sanz
- Molecular Biology Department, Universidad Autónoma de Madrid, Madrid, Spain
| | - Nuria Rodriguez
- Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, 28850, Spain
| | - Cristina Escudero
- Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, 28850, Spain.,Centro de Biología Molecular Severo Ochoa (UAM-CSIC), Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Daniel Carrizo
- Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, 28850, Spain
| | - Ricardo Amils
- Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, 28850, Spain.,Centro de Biología Molecular Severo Ochoa (UAM-CSIC), Universidad Autónoma de Madrid, Madrid, 28049, Spain
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15
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Dai X, Wang Y, Luo L, Pfiffner SM, Li G, Dong Z, Xu Z, Dong H, Huang L. Detection of the deep biosphere in metamorphic rocks from the Chinese continental scientific drilling. GEOBIOLOGY 2021; 19:278-291. [PMID: 33559972 DOI: 10.1111/gbi.12430] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 01/17/2021] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
It is generally accepted that there is a vast, well-populated biosphere in the subsurface, but the depth limit of the terrestrial biosphere has yet to be determined, largely because of the lack of access to the subsurface. Here as part of the Chinese Continental Scientific Drilling (CCSD) project in eastern China, we acquired continuous rock cores and endeavored to probe the depth limit of the biosphere and the depth-dependent distribution of microorganisms at a geologically unique site, that is, a convergent plate boundary. Microbiological analyses of ultra-high-pressure metamorphic rock cores taken from the ground surface to 5,158-meter reveal that microbial distribution was continuous up to a depth of ~4,850 m, where temperature was estimated to be ~137°C. The metabolic state of these organisms at such great depth remains to be determined. Microbial abundance, ranging from 103 to 108 cells/g, was also related to porosity, but not to the depth and rock composition. In addition, microbial diversity systematically decreased with depth. Our results support the notion that temperature is a key factor in determining the lower limit of the biosphere in the continental subsurface.
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Affiliation(s)
- Xin Dai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuanliang Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Liqiang Luo
- National Research Center for Geoanalysis, Chinese Academy of Geological Sciences, Beijing, China
| | - Susan M Pfiffner
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA
| | - Guangyu Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhiyang Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhiqin Xu
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing, China
| | - Hailiang Dong
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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16
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Shah AP, Archana G. Evaluation of bacterial strains isolated from Late Quaternary alluvial sediments spanning ~ 28 m in depth for heavy metal tolerance and Cr(VI) removal ability. Int Microbiol 2021; 24:385-398. [PMID: 33783650 DOI: 10.1007/s10123-021-00174-0] [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: 07/08/2020] [Revised: 01/21/2021] [Accepted: 03/17/2021] [Indexed: 11/27/2022]
Abstract
Microbial heavy metal tolerance in subsurface samples is indicative of long-term ecotoxicological impact of metals and could also reflect metal contamination of groundwater. However, the heavy metal tolerance characteristics of microbes isolated from subsurface river sediment profiles are still obscure. In the present study, determination of heavy metal tolerance of bacterial strains isolated from two Late Quaternary sediment profiles (~ 28 m and ~25 m deep) located at the Mahi river basin, Western India, was carried out. Identification of bacterial isolates by the 16S rRNA gene sequencing revealed that bacterial isolates affiliated with phyla Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes were dominant in both sediment profiles. Heavy metal tolerance of bacterial strains as determined by plate diffusion assay revealed order of metal tolerance as follows: Hg(II)<Cd(II)< Ni(II)<Cu(II)=Cr(VI). Chromate removal study in liquid medium suggested that bacterial strains procured from subsurface possessed the ability to remove Cr(VI) with varied magnitude. A packed bed column experiment indicated that bacterial strains obtained from the subsurface have the potential for Cr(VI) removal from different particle size consistencies of the sediments.
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Affiliation(s)
- Abhi P Shah
- Department of Microbiology and Biotechnology Centre, The Maharaja Sayajirao University of Baroda, Vadodara, 390 002, India
| | - G Archana
- Department of Microbiology and Biotechnology Centre, The Maharaja Sayajirao University of Baroda, Vadodara, 390 002, India.
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17
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Escudero C, Del Campo A, Ares JR, Sánchez C, Martínez JM, Gómez F, Amils R. Visualizing Microorganism-Mineral Interaction in the Iberian Pyrite Belt Subsurface: The Acidovorax Case. Front Microbiol 2020; 11:572104. [PMID: 33324359 PMCID: PMC7726209 DOI: 10.3389/fmicb.2020.572104] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/20/2020] [Indexed: 11/18/2022] Open
Abstract
Despite being considered an extreme environment, several studies have shown that life in the deep subsurface is abundant and diverse. Microorganisms inhabiting these systems live within the rock pores and, therefore, the geochemical and geohydrological characteristics of this matrix may influence the distribution of underground biodiversity. In this study, correlative fluorescence and Raman microscopy (Raman-FISH) was used to analyze the mineralogy associated with the presence of members of the genus Acidovorax, an iron oxidizing microorganisms, in native rock samples of the Iberian Pyrite Belt subsurface. Our results suggest a strong correlation between the presence of Acidovorax genus and pyrite, suggesting that the mineral might greatly influence its subsurface distribution.
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Affiliation(s)
- Cristina Escudero
- Centro de Biología Molecular Severo Ochoa (CBMSO, CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain.,Departamento de Planetología y Habitabilidad, Centro de Astrobiología (CAB, INTA-CSIC), Madrid, Spain
| | - Adolfo Del Campo
- Departamento de Electrocerámica, Instituto de Cerámica y Vidrio, CSIC, Madrid, Spain
| | - Jose R Ares
- Departamento de Física de Materiales, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Carlos Sánchez
- Departamento de Física de Materiales, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Jose M Martínez
- Centro de Biología Molecular Severo Ochoa (CBMSO, CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Felipe Gómez
- Departamento de Planetología y Habitabilidad, Centro de Astrobiología (CAB, INTA-CSIC), Madrid, Spain
| | - Ricardo Amils
- Centro de Biología Molecular Severo Ochoa (CBMSO, CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain.,Departamento de Planetología y Habitabilidad, Centro de Astrobiología (CAB, INTA-CSIC), Madrid, Spain
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18
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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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19
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Purkamo L, Kietäväinen R, Nuppunen-Puputti M, Bomberg M, Cousins C. Ultradeep Microbial Communities at 4.4 km within Crystalline Bedrock: Implications for Habitability in a Planetary Context. Life (Basel) 2020; 10:E2. [PMID: 31947979 PMCID: PMC7175195 DOI: 10.3390/life10010002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/31/2019] [Accepted: 01/01/2020] [Indexed: 01/06/2023] Open
Abstract
The deep bedrock surroundings are an analog for extraterrestrial habitats for life. In this study, we investigated microbial life within anoxic ultradeep boreholes in Precambrian bedrock, including the adaptation to environmental conditions and lifestyle of these organisms. Samples were collected from Pyhäsalmi mine environment in central Finland and from geothermal drilling wells in Otaniemi, Espoo, in southern Finland. Microbial communities inhabiting the up to 4.4 km deep bedrock were characterized with phylogenetic marker gene (16S rRNA genes and fungal ITS region) amplicon and DNA and cDNA metagenomic sequencing. Functional marker genes (dsrB, mcrA, narG) were quantified with qPCR. Results showed that although crystalline bedrock provides very limited substrates for life, the microbial communities are diverse. Gammaproteobacterial phylotypes were most dominant in both studied sites. Alkanindiges -affiliating OTU was dominating in Pyhäsalmi fluids, while different depths of Otaniemi samples were dominated by Pseudomonas. One of the most common OTUs detected from Otaniemi could only be classified to phylum level, highlighting the uncharacterized nature of the deep biosphere in bedrock. Chemoheterotrophy, fermentation and nitrogen cycling are potentially significant metabolisms in these ultradeep environments. To conclude, this study provides information on microbial ecology of low biomass, carbon-depleted and energy-deprived deep subsurface environment. This information is useful in the prospect of finding life in other planetary bodies.
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Affiliation(s)
- Lotta Purkamo
- School of Earth and Environmental Sciences, University of St Andrews, St Andrews KY16 9AL, UK
- Geological Survey of Finland, 02151 Espoo, Finland
| | - Riikka Kietäväinen
- Geological Survey of Finland, 02151 Espoo, Finland
- Department of Geosciences and Geography, University of Helsinki, 00014 Helsinki, Finland
| | | | - Malin Bomberg
- VTT Technical Research Centre of Finland, 02044 VTT, Finland
| | - Claire Cousins
- School of Earth and Environmental Sciences, University of St Andrews, St Andrews KY16 9AL, UK
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Tamaki H. Cultivation Renaissance in the Post-Metagenomics Era: Combining the New and Old. Microbes Environ 2019; 34:117-120. [PMID: 31243255 PMCID: PMC6594738 DOI: 10.1264/jsme2.me3402rh] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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21
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Gregory SP, Barnett MJ, Field LP, Milodowski AE. Subsurface Microbial Hydrogen Cycling: Natural Occurrence and Implications for Industry. Microorganisms 2019; 7:E53. [PMID: 30769950 PMCID: PMC6407114 DOI: 10.3390/microorganisms7020053] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/01/2019] [Accepted: 02/03/2019] [Indexed: 12/21/2022] Open
Abstract
Hydrogen is a key energy source for subsurface microbial processes, particularly in subsurface environments with limited alternative electron donors, and environments that are not well connected to the surface. In addition to consumption of hydrogen, microbial processes such as fermentation and nitrogen fixation produce hydrogen. Hydrogen is also produced by a number of abiotic processes including radiolysis, serpentinization, graphitization, and cataclasis of silicate minerals. Both biotic and abiotically generated hydrogen may become available for consumption by microorganisms, but biotic production and consumption are usually tightly coupled. Understanding the microbiology of hydrogen cycling is relevant to subsurface engineered environments where hydrogen-cycling microorganisms are implicated in gas consumption and production and corrosion in a number of industries including carbon capture and storage, energy gas storage, and radioactive waste disposal. The same hydrogen-cycling microorganisms and processes are important in natural sites with elevated hydrogen and can provide insights into early life on Earth and life on other planets. This review draws together what is known about microbiology in natural environments with elevated hydrogen, and highlights where similar microbial populations could be of relevance to subsurface industry.
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Affiliation(s)
- Simon P Gregory
- British Geological Survey, Environmental Science Centre, Keyworth, Nottingham NG12 5GG, UK.
| | - Megan J Barnett
- British Geological Survey, Environmental Science Centre, Keyworth, Nottingham NG12 5GG, UK.
| | - Lorraine P Field
- British Geological Survey, Environmental Science Centre, Keyworth, Nottingham NG12 5GG, UK.
| | - Antoni E Milodowski
- British Geological Survey, Environmental Science Centre, Keyworth, Nottingham NG12 5GG, UK.
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