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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. Microb Ecol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Karnachuk OV, Rusanov II, Panova IA, Kadnikov VV, Avakyan MR, Ikkert OP, Lukina AP, Beletsky AV, Mardanov AV, Knyazev YV, Volochaev MN, Pimenov NV, Ravin NV. The low-temperature germinating spores of the thermophilic Desulfofundulus contribute to an extremely high sulfate reduction in burning coal seams. Front Microbiol 2023; 14:1204102. [PMID: 37779687 PMCID: PMC10540450 DOI: 10.3389/fmicb.2023.1204102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/31/2023] [Indexed: 10/03/2023] Open
Abstract
Burning coal seams, characterized by massive carbon monoxide (CO) emissions, the presence of secondary sulfates, and high temperatures, represent suitable environments for thermophilic sulfate reduction. The diversity and activity of dissimilatory sulfate reducers in these environments remain unexplored. In this study, using metagenomic approaches, in situ activity measurements with a radioactive tracer, and cultivation we have shown that members of the genus Desulfofundulus are responsible for the extremely high sulfate reduction rate (SRR) in burning lignite seams in the Altai Mountains. The maximum SRR reached 564 ± 21.9 nmol S cm-3 day-1 at 60°C and was of the same order of magnitude for both thermophilic (60°C) and mesophilic (23°C) incubations. The 16S rRNA profiles and the search for dsr gene sequences in the metagenome revealed members of the genus Desulfofundulus as the main sulfate reducers. The thermophilic Desulfofundulus sp. strain Al36 isolated in pure culture, did not grow at temperatures below 50°C, but produced spores that germinated into metabolically active cells at 20 and 15°C. Vegetative cells germinating from spores produced up to 0.738 ± 0.026 mM H2S at 20°C and up to 0.629 ± 0.007 mM H2S at 15°C when CO was used as the sole electron donor. The Al36 strain maintains significant production of H2S from sulfate over a wide temperature range from 15°C to 65°C, which is important in variable temperature biotopes such as lignite burning seams. Burning coal seams producing CO are ubiquitous throughout the world, and biogenic H2S may represent an overlooked significant flux to the atmosphere. The thermophilic spore outgrowth and their metabolic activity at temperatures below the growth minimum may be important for other spore-forming bacteria of environmental, industrial and clinical importance.
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Affiliation(s)
- Olga V. Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Igor I. Rusanov
- Institute of Microbiology, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Inna A. Panova
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Vitaly V. Kadnikov
- Institute of Bioengineering, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Marat R. Avakyan
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Olga P. Ikkert
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Anastasia P. Lukina
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | | | | | - Nikolai V. Pimenov
- Institute of Microbiology, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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Karnachuk OV, Beletsky AV, Rakitin AL, Ikkert OP, Avakyan MR, Zyusman VS, Napilov A, Mardanov AV, Ravin NV. Antibiotic-Resistant Desulfovibrio Produces H2S from Supplements for Animal Farming. Microorganisms 2023; 11:microorganisms11040838. [PMID: 37110261 PMCID: PMC10146906 DOI: 10.3390/microorganisms11040838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Sulphate-reducing bacteria, primarily Desulfovibrio, are responsible for the active generation of H2S in swine production waste. The model species for sulphate reduction studies, Desulfovibrio vulgaris strain L2, was previously isolated from swine manure characterized by high rates of dissimilatory sulphate reduction. The source of electron acceptors in low-sulphate swine waste for the high rate of H2S formation remains uncertain. Here, we demonstrate the ability of the L2 strain to use common animal farming supplements including L-lysine-sulphate, gypsum and gypsum plasterboards as electron acceptors for H2S production. Genome sequencing of strain L2 revealed the presence of two megaplasmids and predicted resistance to various antimicrobials and mercury, which was confirmed in physiological experiments. Most of antibiotic resistance genes (ARG) are carried by two class 1 integrons located on the chromosome and on the plasmid pDsulf-L2-2. These ARGs, predicted to confer resistance to beta-lactams, aminoglycosides, lincosamides, sulphonamides, chloramphenicol and tetracycline, were probably laterally acquired from various Gammaproteobacteria and Firmicutes. Resistance to mercury is likely enabled by two mer operons also located on the chromosome and on pDsulf-L2-2 and acquired via horizontal gene transfer. The second megaplasmid, pDsulf-L2-1, encoded nitrogenase, catalase and type III secretion system suggesting close contact of the strain with intestinal cells in the swine gut. The location of ARGs on mobile elements allows us to consider D. vulgaris strain L2 as a possible vector transferring antimicrobials resistance determinants between the gut microbiote and microbial communities in environmental biotopes.
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Karnachuk OV, Panova IA, Panov VL, Ikkert OP, Kadnikov VV, Rusanov II, Avakyan MR, Glukhova LB, Lukina AP, Rakitin AV, Begmatov S, Beletsky AV, Pimenov NV, Ravin NV. Active Sulfate-Reducing Bacterial Community in the Camel Gut. Microorganisms 2023; 11:microorganisms11020401. [PMID: 36838366 PMCID: PMC9963290 DOI: 10.3390/microorganisms11020401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/18/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
The diversity and activity of sulfate-reducing bacteria (SRB) in the camel gut remains largely unexplored. An abundant SRB community has been previously revealed in the feces of Bactrian camels (Camelus bactrianus). This study aims to combine the 16S rRNA gene profiling, sulfate reduction rate (SRR) measurement with a radioactive tracer, and targeted cultivation to shed light on SRB activity in the camel gut. Fresh feces of 55 domestic Bactrian camels grazing freely on semi-arid mountain pastures in the Kosh-Agach district of the Russian Altai area were analyzed. Feces were sampled in early winter at an ambient temperature of -15 °C, which prevented possible contamination. SRR values measured with a radioactive tracer in feces were relatively high and ranged from 0.018 to 0.168 nmol S cm-3 day-1. The 16S rRNA gene profiles revealed the presence of Gram-negative Desulfovibrionaceae and spore-forming Desulfotomaculaceae. Targeted isolation allowed us to obtain four pure culture isolates belonging to Desulfovibrio and Desulforamulus. An active SRB community may affect the iron and copper availability in the camel intestine due to metal ions precipitation in the form of sparingly soluble sulfides. The copper-iron sulfide, chalcopyrite (CuFeS2), was detected by X-ray diffraction in 36 out of 55 analyzed camel feces. In semi-arid areas, gypsum, like other evaporite sulfates, can be used as a solid-phase electron acceptor for sulfate reduction in the camel gastrointestinal tract.
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Affiliation(s)
- Olga V. Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
- Correspondence:
| | - Inna A. Panova
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Vasilii L. Panov
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Olga P. Ikkert
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Vitaly V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, 119071 Moscow, Russia
| | - Igor I. Rusanov
- Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Marat R. Avakyan
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Lubov B. Glukhova
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Anastasia P. Lukina
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Anatolii V. Rakitin
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Shahjahon Begmatov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, 119071 Moscow, Russia
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, 119071 Moscow, 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, 119071 Moscow, Russia
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Panova IA, Ikkert O, Avakyan MR, Kopitsyn DS, Mardanov AV, Pimenov NV, Shcherbakova VA, Ravin NV, Karnachuk OV. Desulfosporosinus metallidurans sp. nov., an acidophilic, metal-resistant sulfate-reducing bacterium from acid mine drainage. Int J Syst Evol Microbiol 2021; 71. [PMID: 34255623 DOI: 10.1099/ijsem.0.004876] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, spore-forming, acidophilic and metal-resistant sulfate-reducing bacterium, strain OLT, was isolated from a microbial mat in a tailing dam at a gold ore mining site. Cells were slightly curved immotile rods, 0.5 µm in diameter and 2.0-3.0 µm long. Cells were stained Gram-negative, despite the Gram-positive cell structure revealed by electron microscopy of ultrathin layers. OLT grew at pH 4.0-7.0 with an optimum at 5.5. OLT utilised H2, lactate, pyruvate, malate, formate, propionate, ethanol, glycerol, glucose, fructose, sucrose, peptone and tryptone as electron donors for sulfate reduction. Sulfate, sulfite, thiosulfate, nitrate and fumarate were used as electron acceptors in the presence of lactate. Elemental sulfur, iron (III), and arsenate did not serve as electron acceptors. The major cellular fatty acids were C16:1ω7c (39.0 %) and C16 : 0 (12.1 %). The draft genome of OLT was 5.29 Mb in size and contained 4909 protein-coding genes. The 16S rRNA gene sequence placed OLT within the phylum Firmicutes, class Clostridia, family Peptococcaceae, genus Desulfosporosinus. Desulfosporosinus nitroreducens 59.4BT was the closest relative with 97.6 % sequence similarity. On the basis of phenotypic and phylogenetic characteristics, strain OLT represents a novel species within the genus Desulfosporosinus, for which we propose the name Desulfosporosinus metallidurans sp. nov. with the type strain OLT (=DSM 104464T=VKM В-3021T).
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Affiliation(s)
- Inna A Panova
- Laboratory of Molecular Biology and Biochemistry, Tomsk State University, Tomsk 634050, Russia
| | - Olga Ikkert
- Laboratory of Molecular Biology and Biochemistry, Tomsk State University, Tomsk 634050, Russia
| | - Marat R Avakyan
- Laboratory of Molecular Biology and Biochemistry, Tomsk State University, Tomsk 634050, Russia
| | | | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Nikolai V Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Viktoria A Shcherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research, Russian Academy of Sciences", Pushchino, Moscow region 142290, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Olga V Karnachuk
- Laboratory of Molecular Biology and Biochemistry, Tomsk State University, Tomsk 634050, Russia
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Bukhtiyarova PA, Antsiferov DV, Brasseur G, Avakyan MR, Frank YA, Ikkert OP, Pimenov NV, Tuovinen OH, Karnachuk OV. Isolation, characterization, and genome insights into an anaerobic sulfidogenic Tissierella bacterium from Cu-bearing coins. Anaerobe 2019; 56:66-77. [PMID: 30776428 DOI: 10.1016/j.anaerobe.2019.02.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 01/27/2019] [Accepted: 02/14/2019] [Indexed: 01/19/2023]
Abstract
Recent reports on antimicrobial effects of metallic Cu prompted this study of anaerobic microbial communities on copper surfaces. Widely circulating copper-containing coinage was used as a potential source for microorganisms that had had human contact and were tolerant to copper. This study reports on the isolation, characterization, and genome of an anaerobic sulfidogenic Tissierella sp. P1from copper-containing brass coinage. Dissimilatory (bi)sulfite reductase dsrAB present in strain P1 genome and the visible absorbance around 630 nm in the cells suggested the presence of a desulfoviridin-type protein. However, the sulfate reduction rate measurements with 35SO42- did not confirm the dissimilatory sulfate reduction by the strain. The P1 genome lacks APS reductase, sulfate adenylyltransferase, DsrC, and DsrMK necessary for dissimilatory sulfate reduction. The isolate produced up to 0.79 mM H2S during growth, possibly due to cysteine synthase (CysK) and/or cysteine desulfhydrase (CdsH) activities, encoded in the genome. The strain can tolerate up to 2.4 mM Cu2+(150 mg/l) in liquid medium, shows affinity to metallic copper, and can survive on copper-containing coins up to three days under ambient air and dry conditions. The genome sequence of strain P1 contained cutC, encoding a copper resistance protein, which distinguishes it from all other Tissierella strains with published genomes.
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Affiliation(s)
- Polina A Bukhtiyarova
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Dmitry V Antsiferov
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Gael Brasseur
- Laboratoire de Chimie Bactérienne, CNRS, Mediterranean Institute of Microbiology, Marseille, France
| | - Marat R Avakyan
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Yulia A Frank
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Olga P Ikkert
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Nikolay V Pimenov
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Olli H Tuovinen
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
| | - Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia.
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Glukhova LB, Frank YA, Danilova EV, Avakyan MR, Banks D, Tuovinen OH, Karnachuk OV. Isolation, Characterization, and Metal Response of Novel, Acid-Tolerant Penicillium spp. from Extremely Metal-Rich Waters at a Mining Site in Transbaikal (Siberia, Russia). Microb Ecol 2018; 76:911-924. [PMID: 29663040 DOI: 10.1007/s00248-018-1186-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/06/2018] [Indexed: 06/08/2023]
Abstract
The role of fungi in metal cycling in acidic environments has been little explored to date. In this study, two acid-tolerant and metal-resistant Penicillium isolates, strains ShG4B and ShG4C, were isolated from a mine site in the Transbaikal area of Siberia (Russia). Waters at the mine site were characterized by extremely high metal concentrations: up to 18 g l-1 Fe and > 2 g l-1 each of Cu, Zn, Al, and As. Both isolates were identified as Penicillium spp. by phylogenetic analyses and they grew well in Czapek medium acidified to pH 2.5. Resistance to Cu, Cd, Ni, Co, and arsenate was in the range of 1-10 g l-1. Further experiments with Penicillium strain ShG4C demonstrated that growth in Cu-containing media was accompanied by the precipitation of Cu-oxalate (moolooite) and the formation of extracellular vesicles enriched in Cu on the mycelia. Vesicles were greatly reduced in size in Cd-containing media and were not formed in the presence of Ni or Co. Cd-oxalate was detected as a crystalline solid phase in Cd-exposed mycelia. Hydrated Ni-sulfate (retgersite) and Co-sulfate (bieberite) were detected in mycelia grown in the presence of Ni and Co, respectively. The results demonstrated that acid-tolerant and metal-resistant Penicillium constitute a component in extremophilic microbiomes, contributing to organic matter breakdown and formation of secondary solid phases at pH ranges found in acid rock drainage.
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Affiliation(s)
- Lubov B Glukhova
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Lenin Ave. 36, Tomsk, Russia, 634050
| | - Yulia A Frank
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Lenin Ave. 36, Tomsk, Russia, 634050
| | - Ehrzena V Danilova
- Institute of General and Experimental Biology, Russian Academy of Sciences, Sakhyanovoy St. 6, Ulan-Ude, Russia, 670047
| | - Marat R Avakyan
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Lenin Ave. 36, Tomsk, Russia, 634050
| | - David Banks
- School of Engineering, Systems Power & Energy, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
- Holymoor Consultancy Ltd., 360 Ashgate Road, Chesterfield, Derbyshire, S40 4BW, UK
| | - Olli H Tuovinen
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
| | - Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Lenin Ave. 36, Tomsk, Russia, 634050.
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Kovaliova A, Kadnikov VV, Antsiferov DV, Beletsky AV, Danilova EV, Avakyan MR, Mardanov AV, Karnachuk OV. Genome sequence of the acid-tolerant Desulfovibrio sp. DV isolated from the sediments of a Pb-Zn mine tailings dam in the Chita region, Russia. Genom Data 2017; 11:125-127. [PMID: 28217441 PMCID: PMC5300300 DOI: 10.1016/j.gdata.2017.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 01/25/2017] [Indexed: 11/29/2022]
Abstract
Here we report the draft genome sequence of the acid-tolerant Desulfovibrio sp. DV isolated from the sediments of a Pb-Zn mine tailings dam in the Chita region, Russia. The draft genome has a size of 4.9 Mb and encodes multiple K+-transporters and proton-consuming decarboxylases. The phylogenetic analysis based on concatenated ribosomal proteins revealed that strain DV clusters together with the acid-tolerant Desulfovibrio sp. TomC and Desulfovibrio magneticus. The draft genome sequence and annotation have been deposited at GenBank under the accession number MLBG00000000.
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Affiliation(s)
- Anastasiia Kovaliova
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Vitaly V Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Dmitrii V Antsiferov
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Ehrzena V Danilova
- Institute of General and Experimental Biology, Siberian Branch Russian Academy of Sciences, 670047 Ulan-Ude, Buryatia, Russia
| | - Marat R Avakyan
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
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Frank YA, Kadnikov VV, Lukina AP, Banks D, Beletsky AV, Mardanov AV, Sen'kina EI, Avakyan MR, Karnachuk OV, Ravin NV. Characterization and Genome Analysis of the First Facultatively Alkaliphilic Thermodesulfovibrio Isolated from the Deep Terrestrial Subsurface. Front Microbiol 2016; 7:2000. [PMID: 28066337 PMCID: PMC5165239 DOI: 10.3389/fmicb.2016.02000] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 11/29/2016] [Indexed: 11/16/2022] Open
Abstract
Members of the genus Thermodesulfovibrio belong to the Nitrospirae phylum and all isolates characterized to date are neutrophiles. They have been isolated from terrestrial hot springs and thermophilic methanogenic anaerobic sludges. Their molecular signatures have, however, also been detected in deep subsurface. The purpose of this study was to characterize and analyze the genome of a newly isolated, facultatively alkaliphilic Thermodesulfovibrio from a 2 km deep aquifer system in Western Siberia, Russia. The new isolate, designated N1, grows optimally at pH 8.5 and at 65°C. It is able to reduce sulfate, thiosulfate or sulfite with a limited range of electron donors, such as formate, pyruvate, and lactate. Analysis of the 1.93 Mb draft genome of strain N1 revealed that it contains a set of genes for dissimilatory sulfate reduction, including sulfate adenyltransferase, adenosine-5′-phosphosulfate reductase AprAB, membrane-bound electron transfer complex QmoABC, dissimilatory sulfite reductase DsrABC, and sulfite reductase-associated electron transfer complex DsrMKJOP. Hydrogen turnover is enabled by soluble cytoplasmic, membrane-linked, and soluble periplasmic hydrogenases. The use of thiosulfate as an electron acceptor is enabled by a membrane-linked molybdopterin oxidoreductase. The N1 requirement for organic carbon sources corresponds to the lack of the autotrophic C1-fixation pathways. Comparative analysis of the genomes of Thermodesulfovibrio (T. yellowstonii, T. islandicus, T. àggregans, T. thiophilus, and strain N1) revealed a low overall genetic diversity and several adaptive traits. Consistent with an alkaliphilic lifestyle, a multisubunit Na+/H+ antiporter of the Mnh family is encoded in the Thermodesulfovibrio strain N1 genome. Nitrogenase genes were found in T. yellowstonii, T. aggregans, and T. islandicus, nitrate reductase in T. islandicus, and cellulose synthetase in T. aggregans and strain N1. Overall, our results provide genomic insights into metabolism of the Thermodesulfovibrio lineage in microbial communities of the deep subsurface biosphere.
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Affiliation(s)
- Yulia A Frank
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University Tomsk, Russia
| | - Vitaly V Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Anastasia P Lukina
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University Tomsk, Russia
| | - David Banks
- Systems, Power and Energy, School of Engineering, Glasgow UniversityGlasgow, UK; Holymoor Consultancy Ltd.Chesterfield, UK
| | - Alexey V Beletsky
- 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
| | - Elena I Sen'kina
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University Tomsk, Russia
| | - Marat R Avakyan
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University Tomsk, 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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Mardanov AV, Panova IA, Beletsky AV, Avakyan MR, Kadnikov VV, Antsiferov DV, Banks D, Frank YA, Pimenov NV, Ravin NV, Karnachuk OV. Genomic insights into a new acidophilic, copper-resistantDesulfosporosinusisolate from the oxidized tailings area of an abandoned gold mine. FEMS Microbiol Ecol 2016; 92:fiw111. [DOI: 10.1093/femsec/fiw111] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2016] [Indexed: 11/15/2022] Open
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Karnachuk OV, Kurganskaya IA, Avakyan MR, Frank YA, Ikkert OP, Filenko RA, Danilovac EV, Pimenov NV. [An Acidophilic Desulfosporosinus Isolated from the Oxidized Mining Wastes in the Transbaikal Area]. Mikrobiologiia 2015; 84:595-605. [PMID: 27169248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Dissimilatory sulfate reduction plays an important role in removal of dissolved metals from acidic mine waters. Although this process was convincingly shown to occur in acidic waste of metal recovery, few isolates of acid-tolerant sulfate rducers are known. We isolated a new acidophilic sulfidogen, strain BG, from the oxidized acidic waste of the Bom-Gorkhon tungsten deposit, Transbaikalia, Russia. Phylogenetic analysis of its 16S rRNA gene sequence made it possible to identify it as a member of the genus Desulfosporosinus. Unlike other known acidophilic sulfate reducers of this genus, strain BG was tolerant to high copper concentrations (up to 5 g/L), could grow on organic acids at low ambient pH, and formed crystalline copper sulfides (covellite and chalcopyrite). Molecular analysis of the phenotypes predominating in oxidized waste and in enrichment cultures confirmed the presence of various Desulfosporosinus strains.
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Karnachuk OV, Gavrilov SN, Avakyan MR, Podosokorskaya OA, Frank YA, Bonch-Osmolovskaya EA, Kublanov IB. [Diversity of Cuproproteins and Copper Homeostasis Systems in Melioribacter roseus, a Facultatively Anaerobic Thermophilic Member of a New Phylum Ignavibacteriae]. Mikrobiologiia 2015; 84:165-174. [PMID: 26263622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The genome of Melioribacter roseus, one of two members of the recently described phylum Ignavibacteriae, was searched for the genes encoding proteins associated with copper transport or containing copper as cofactors, and the effect of Cu2+ concentration in the medium on M. roseus growth was investigated. Genomic analysis revealed a variety of copper-containing oxidoreductases in this facultative anaerobe. Three ATPases responsible for copper transport were identified. One of them (MROS_1511) was.probably involved in assembly of the copper-containing cytochrome c oxidase, while two others (MROS_0327 and MROS_0791) probably carried out a detoxification function. The presence of several copper-containing oxidoreductases and copper homeostasis systems in M. roseus is in agreement with the previously hypothesized origin of the phylum Ignavibacteriae from an aerobic ancestor common with those of Bacteroidetes and Chlorobi.
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Karnachuk OV, Mardanov AV, Avakyan MR, Kadnikov VV, Vlasova M, Beletsky AV, Gerasimchuk AL, Ravin NV. Draft genome sequence of the first acid-tolerant sulfate-reducing deltaproteobacterium Desulfovibrio sp. TomC having potential for minewater treatment. FEMS Microbiol Lett 2015; 362:fnv007. [DOI: 10.1093/femsle/fnv007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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