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Dai J, Li XG, Zhang WJ, Wu LF. Tepidibacter hydrothermalis sp. nov., a novel anaerobic bacterium isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2023; 73. [PMID: 37921840 DOI: 10.1099/ijsem.0.006151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Abstract
A novel anaerobic heterotrophic bacterium, designated strain SWIR-1T, was isolated from a deep-sea hydrothermal vent field sample collected from the Southwest Indian Ridge at a depth of 2700 m. Phylogenetic analysis indicated that strain SWIR-1T belongs to the genus Tepidibacter, and the most closely related species are Tepidibacter mesophilus B1T (99.1 % 16S rRNA gene sequence similarity), Tepidibacter formicigenes DV1184T (94.6 %) and Tepidibacter thalassicus SC562T (93.9 %). Strain SWIR-1T shares 77.3-87.2 % average nucleotide identity and 21.5-35.7 % digital DNA-DNA hybridization values with the three type strains of Tepidibacter species. Cells of strain SWIR-1T were Gram-stain-positive, motile, short straight rods. Endospores were observed in stationary-phase cells when grown on Thermococcales rich medium. Strain SWIR-1T grew at 15-45 °C (optimum, 30°C), at pH 5.5-8.0 (optimum, pH 7.0) and with 1.0-6.0 % (w/v) NaCl (optimum, 2.0 %). Substrates utilized by strain SWIR-1T included complex proteinaceous, chitin, starch, lactose, maltose, fructose, galactose, glucose, rhamnose, arabinose, ribose, alanine, glycine and glycerol. The major fermentation products from glucose were acetate, lactate, H2 and CO2. Elemental sulphur, sulphate, thiosulphate, sulphite, fumarate, nitrate, nitrite and FeCl3 are not used as terminal electron acceptors. The main cellular fatty acids consisted of iso-C15 : 0 (28.4 %), C15 : 1 iso F (15.4 %) and C16 : 0 (9.8 %). The major polar lipids were phospholipids and glycolipids. No respiratory quinones were detected. Genomic comparison revealed a distinctive blended gene cluster comprising hyb-tat-hyp genes, which play a crucial role in the synthesis, maturation, activation and export of NiFe-hydrogenase. Based on the phylogenetic analysis, genomic, physiologic and chemotaxonomic characteristics, strain SWIR-1T is considered to represent a novel species within the genus Tepidibacter, for which the name Tepidibacter hydrothermalis sp. nov. is proposed. The type strain is strain SWIR-1T (=DSM 113848T=MCCC 1K07078T).
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Affiliation(s)
- Jie Dai
- Aix Marseille Univ, CNRS, LCB, IMM, IM2B, Marseille, France
| | - Xue-Gong Li
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/ CAS, Sanya, PR China
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
- Institution of Deep-sea Life Sciences, IDSSE-BGI, Hainan Deep-sea Technology Laboratory, Sanya, Hainan, PR China
| | - Wei-Jia Zhang
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/ CAS, Sanya, PR China
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
- Institution of Deep-sea Life Sciences, IDSSE-BGI, Hainan Deep-sea Technology Laboratory, Sanya, Hainan, PR China
| | - Long-Fei Wu
- Aix Marseille Univ, CNRS, LCB, IMM, IM2B, Marseille, France
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/ CAS, Sanya, PR China
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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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Cario A, Oliver GC, Rogers KL. Characterizing the Piezosphere: The Effects of Decompression on Microbial Growth Dynamics. Front Microbiol 2022; 13:867340. [PMID: 35663870 PMCID: PMC9157427 DOI: 10.3389/fmicb.2022.867340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/20/2022] [Indexed: 12/04/2022] Open
Abstract
The extent to which the full diversity of the subsurface microbiome can be captured via cultivation is likely hindered by the inevitable loss of cellular viability from decompression during sampling, enrichment, and isolation. Furthermore, the pressure tolerance of previously isolated strains that span surface and subsurface ecosystems can shed light into microbial activity and pressure adaptation in these transition zones. However, assessments of the effects of elevated pressure on the physiology of piezotolerant and piezosensitive species may be biased by high-pressure enrichment techniques. Here, we compared two high-pressure cultivation techniques-one that requires decompression of the whole cultures during sampling and one that employs the previously described isobaric PUSH devices-to explore the effects of repeated decompression during incubations performed to characterize isolates from deep environments. Two model sulfate-reducing prokaryotes were used to test the effects of decompression/repressurization cycles on growth rates, cell yields, and pressure tolerance. The mesophilic bacterium Desulfovibrio salexigens was cultivated from 0.1 to 50 MPa, and the hyperthermophilic archaeon Archaeoglobus fulgidus was tested from 0.1 to 98 MPa. For both cultivation methods, D. salexigens showed exponential growth up to 20 MPa, but faster growth rates were observed for isobaric cultivation. Furthermore, at 30 MPa minor growth was observed in D. salexigens cultures only for isobaric conditions. Isobaric conditions also extended exponential growth of A. fulgidus to 60 MPa, compared to 50 MPa when cultures were decompressed during subsampling. For both strains, growth rates and cell yields decreased with increasing pressures, and the most pronounced effects of decompression were observed at the higher end of the pressure ranges. These results highlight that repeated decompression can have a significant negative impact on cell viability, suggesting that decompression tolerance may depend on habitat depth. Furthermore, sampling, enrichment, and cultivation in isobaric devices is critical not only to explore the portion of the deep biosphere that is sensitive to decompression, but also to better characterize the pressure limits and growth characteristics of piezotolerant and piezosensitive species that span surface and subsurface ecosystems.
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Affiliation(s)
- Anaïs Cario
- Department of Earth and Environmental Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Gina C. Oliver
- Department of Earth and Environmental Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Karyn L. Rogers
- Department of Earth and Environmental Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
- Rensselaer Astrobiology Research and Education Center, Rensselaer Polytechnic Institute, Troy, NY, United States
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