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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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Kochetkova TV, Podosokorskaya OA, Elcheninov AG, Kublanov IV. Diversity of Thermophilic Prokaryotes Inhabiting Russian Natural Hot Springs. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722010064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Lavrentyeva EV, Banzaraktsaeva TG, Radnagurueva AA, Buryukhaev SP, Dambaev VB, Baturina OA, Kozyreva LP, Barkhutova DD. Microbial Community of Umkhei Thermal Lake (Baikal Rift Zone) in the Groundwater Discharge Zone. CONTEMP PROBL ECOL+ 2020. [DOI: 10.1134/s1995425519060088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Jones RM, Goordial JM, Orcutt BN. Low Energy Subsurface Environments as Extraterrestrial Analogs. Front Microbiol 2018; 9:1605. [PMID: 30072971 PMCID: PMC6058055 DOI: 10.3389/fmicb.2018.01605] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/27/2018] [Indexed: 11/13/2022] Open
Abstract
Earth's subsurface is often isolated from phototrophic energy sources and characterized by chemotrophic modes of life. These environments are often oligotrophic and limited in electron donors or electron acceptors, and include continental crust, subseafloor oceanic crust, and marine sediment as well as subglacial lakes and the subsurface of polar desert soils. These low energy subsurface environments are therefore uniquely positioned for examining minimum energetic requirements and adaptations for chemotrophic life. Current targets for astrobiology investigations of extant life are planetary bodies with largely inhospitable surfaces, such as Mars, Europa, and Enceladus. Subsurface environments on Earth thus serve as analogs to explore possibilities of subsurface life on extraterrestrial bodies. The purpose of this review is to provide an overview of subsurface environments as potential analogs, and the features of microbial communities existing in these low energy environments, with particular emphasis on how they inform the study of energetic limits required for life. The thermodynamic energetic calculations presented here suggest that free energy yields of reactions and energy density of some metabolic redox reactions on Mars, Europa, Enceladus, and Titan could be comparable to analog environments in Earth's low energy subsurface habitats.
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Affiliation(s)
| | | | - Beth N. Orcutt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
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Frank YA, Kadnikov VV, Gavrilov SN, Banks D, Gerasimchuk AL, Podosokorskaya OA, Merkel AY, Chernyh NA, Mardanov AV, Ravin NV, Karnachuk OV, Bonch-Osmolovskaya EA. Stable and Variable Parts of Microbial Community in Siberian Deep Subsurface Thermal Aquifer System Revealed in a Long-Term Monitoring Study. Front Microbiol 2016; 7:2101. [PMID: 28082967 PMCID: PMC5187383 DOI: 10.3389/fmicb.2016.02101] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 12/12/2016] [Indexed: 11/13/2022] Open
Abstract
The goal of this work was to study the diversity of microorganisms inhabiting a deep subsurface aquifer system in order to understand their functional roles and interspecies relations formed in the course of buried organic matter degradation. A microbial community of a deep subsurface thermal aquifer in the Tomsk Region, Western Siberia was monitored over the course of 5 years via a 2.7 km deep borehole 3P, drilled down to a Palaeozoic basement. The borehole water discharges with a temperature of ca. 50°C. Its chemical composition varies, but it steadily contains acetate, propionate, and traces of hydrocarbons and gives rise to microbial mats along the surface flow. Community analysis by PCR-DGGE 16S rRNA genes profiling, repeatedly performed within 5 years, revealed several dominating phylotypes consistently found in the borehole water, and highly variable diversity of prokaryotes, brought to the surface with the borehole outflow. The major planktonic components of the microbial community were Desulfovirgula thermocuniculi and Methanothermobacter spp. The composition of the minor part of the community was unstable, and molecular analysis did not reveal any regularity in its variations, except some predominance of uncultured Firmicutes. Batch cultures with complex organic substrates inoculated with water samples were set in order to enrich prokaryotes from the variable part of the community. PCR-DGGE analysis of these enrichments yielded uncultured Firmicutes, Chloroflexi, and Ignavibacteriae. A continuous-flow microaerophilic enrichment culture with a water sample amended with acetate contained Hydrogenophilus thermoluteolus, which was previously detected in the microbial mat developing at the outflow of the borehole. Cultivation results allowed us to assume that variable components of the 3P well community are hydrolytic organotrophs, degrading buried biopolymers, while the constant planktonic components of the community degrade dissolved fermentation products to methane and CO2, possibly via interspecies hydrogen transfer. Occasional washout of minor community components capable of oxygen respiration leads to the development of microbial mats at the outflow of the borehole where residual dissolved fermentation products are aerobically oxidized. Long-term community analysis with the combination of molecular and cultivation techniques allowed us to characterize stable and variable parts of the community and propose their environmental roles.
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Affiliation(s)
- Yulia A. Frank
- Department of Plant Physiology and Biotechnology, Tomsk State UniversityTomsk, Russia
| | - Vitaly V. Kadnikov
- Federal Research Centre (FRC) Biotechnology, Institute of BioengineeringMoscow, Russia
| | - Sergey N. Gavrilov
- Federal Research Centre (FRC) Biotechnology, Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences (RAS)Moscow, Russia
| | - David Banks
- Glasgow and Holymoor Consultancy Ltd., Glasgow UniversityChesterfield, UK
| | - Anna L. Gerasimchuk
- Department of Plant Physiology and Biotechnology, Tomsk State UniversityTomsk, Russia
| | - Olga A. Podosokorskaya
- Federal Research Centre (FRC) Biotechnology, Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences (RAS)Moscow, Russia
| | - Alexander Y. Merkel
- Federal Research Centre (FRC) Biotechnology, Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences (RAS)Moscow, Russia
| | - Nikolai A. Chernyh
- Federal Research Centre (FRC) Biotechnology, Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences (RAS)Moscow, Russia
| | - Andrey V. Mardanov
- Federal Research Centre (FRC) Biotechnology, Institute of BioengineeringMoscow, Russia
| | - Nikolai V. Ravin
- Federal Research Centre (FRC) Biotechnology, Institute of BioengineeringMoscow, Russia
| | - Olga V. Karnachuk
- Department of Plant Physiology and Biotechnology, Tomsk State UniversityTomsk, Russia
| | - Elizaveta A. Bonch-Osmolovskaya
- Federal Research Centre (FRC) Biotechnology, Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences (RAS)Moscow, Russia
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Podosokorskaya OA, Merkel AY, Heerden EV, Cason ED, Kopitsyn DS, Vasilieva M, Bonch-Osmolovskaya EA, Kublanov IV. Sporosalibacterium tautonense sp. nov., a thermotolerant, halophilic, hydrolytic bacterium isolated from a gold mine, and emended description of the genus Sporosalibacterium. Int J Syst Evol Microbiol 2016; 67:1457-1461. [PMID: 27974092 DOI: 10.1099/ijsem.0.001737] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel strictly anaerobic, thermotolerant, moderately halophilic, organotrophic bacterium, strain MRo-4T, was isolated from a sample of a microbial mat, developed under the flow of subsurface water in TauTona gold mine, South Africa. Cells of the novel isolate stained Gram-positive and were motile, spore-forming rods, 0.2-0.3 µm in width and 5-20 µm in length. Strain MRo-4T grew at 25-50 °C, at pH 7.0-8.8 and at an NaCl concentration of 5-100 g l-1. The isolate was able to ferment yeast extract, peptone and mono-, oligo- and polysaccharides, including cellulose and chitin. Elemental sulfur, thiosulfate, sulfate, sulfite, nitrate, nitrite, fumarate and arsenate were not reduced. The major fatty acids were iso-C15 : 0, iso-C15 : 0 dimethyl acetyl and anteiso-C15 : 0. The G+C content of the DNA was 32.9 mol%. Phylogenetic analysis of 16S rRNA gene sequences of strain MRo-4T and its nearest relatives showed its affiliation to the genus Sporosalibacterium. Sporosalibacteriumfaouarense SOL3f37T, the only valid published representative of the genus, appeared to be its closest relative (96.8 % 16S rRNA gene sequence similarity). However, strains MRo-4T and S. faouarense SOL3f37T differed in temperature, pH and salinity ranges for growth, requirement for yeast extract and substrate profiles. Based on the phylogenetic analysis and physiological properties of the novel isolate, we propose a novel species, Sporosalibacterium tautonense sp. nov. The type strain is MRo-4T (=DSM 28179T=VKM B-2948T).
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Affiliation(s)
- Olga A Podosokorskaya
- Research Center for Biotechnology, Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russia
| | - Alexander Y Merkel
- Research Center for Biotechnology, Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russia
| | - Esta van Heerden
- TIA-UFS SAENSE Platform, University of the Free State, Bloemfontein, South Africa
| | - Errol D Cason
- TIA-UFS SAENSE Platform, University of the Free State, Bloemfontein, South Africa
| | | | - Maria Vasilieva
- Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | | | - Ilya V Kublanov
- Research Center for Biotechnology, Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russia
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Molecular Mechanisms Contributing to the Growth and Physiology of an Extremophile Cultured with Dielectric Heating. Appl Environ Microbiol 2016; 82:6233-6246. [PMID: 27520819 DOI: 10.1128/aem.02020-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 08/08/2016] [Indexed: 11/20/2022] Open
Abstract
The effect of microwave frequency electromagnetic fields on living microorganisms is an active and highly contested area of research. One of the major drawbacks to using mesophilic organisms to study microwave radiation effects is the unavoidable heating of the organism, which has limited the scale (<5 ml) and duration (<1 h) of experiments. However, the negative effects of heating a mesophile can be mitigated by employing thermophiles (organisms able to grow at temperatures of >60°C). This study identified changes in global gene expression profiles during the growth of Thermus scotoductus SA-01 at 65°C using dielectric (2.45 GHz, i.e., microwave) heating. RNA sequencing was performed on cultures at 8, 14, and 24 h after inoculation to determine the molecular mechanisms contributing to long-term cellular growth and survival under microwave heating conditions. Over the course of growth, genes associated with amino acid metabolism, carbohydrate metabolism, and defense mechanisms were upregulated; the number of repressed genes with unknown function increased; and at all time points, transposases were upregulated. Genes involved in cell wall biogenesis and elongation were also upregulated, consistent with the distinct elongated cell morphology observed after 24 h using microwave heating. Analysis of the global differential gene expression data enabled the identification of molecular processes specific to the response of T. scotoductus SA-01 to dielectric heating during growth. IMPORTANCE The residual heating of living organisms in the microwave region of the electromagnetic spectrum has complicated the identification of radiation-only effects using microorganisms for 50 years. A majority of the previous experiments used either mature cells or short exposure times with low-energy high-frequency radiation. Using global differential gene expression data, we identified molecular processes unique to dielectric heating using Thermus scotoductus SA-01 cultured over 30 h in a commercial microwave digestor. Genes associated with amino acid metabolism, carbohydrate metabolism, and defense mechanisms were upregulated; the number of repressed genes with unknown function increased; and at all time points, transposases were upregulated. These findings serve as a platform for future studies with mesophiles in order to better understand the response of microorganisms to microwave radiation.
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Xia W, Dong H, Zheng C, Cui Q, He P, Tang Y. Hydrocarbon degradation by a newly isolated thermophilic Anoxybacillus sp. with bioemulsifier production and new alkB genes. RSC Adv 2015. [DOI: 10.1039/c5ra17137g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this work, a new thermophilic bacterial strain was isolated and identified asAnoxybacillussp. WJ-4. This strain of WJ-4 can degrade a wide range of hydrocarbons, and production of an oligosaccharide–lipid–peptide bioemulsifier was detected.
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Affiliation(s)
- Wenjie Xia
- Power Environmental Energy Research Institute
- Covina
- USA
- Institute of Porous Flow & Fluid Mechanics
- Chinese Academy of Sciences
| | - Hao Dong
- State Key Laboratory of Heavy Oil Processing
- China University of Petroleum
- Beijing 102249
- PR China
| | - Chenggang Zheng
- Petroleum Exploration and Production Research Institute
- SINOPEC
- PR China
| | - Qingfeng Cui
- Institute of Porous Flow & Fluid Mechanics
- Chinese Academy of Sciences
- Langfang 065007
- PR China
| | - Panqing He
- Power Environmental Energy Research Institute
- Covina
- USA
| | - Yongchun Tang
- Power Environmental Energy Research Institute
- Covina
- USA
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