Laboratory of Diversity and Ecology of Extremophilic Microorganisms

Alexander I. Slobodkin
Dr.Sci. (Biology)
Head of Laboratory
INMI, room 411
Телефон +7 (499) 135-73-75
E-Mail  aslobodkin@hotmail.com

Keywords
extremophilic microorganisms, thermophilic bacteria, hyperthermophilic archaea, anaerobes, alkaliphiles, lithoautotrophic microorganisms, new types of metabolism, microbial communities, deep-sea hydrothermal vents, deep continental biosphere, space microbiology


Research topics

  • Biological diversity of extremophilic microorganisms
  • Isolation and description of novel extremophilic bacteria and archaea
  • Exploration and characterization of new types of catabolism
  • Microbial processes of sulfur and nitrogen cycles in extreme environments
  • Microbial metal reduction
  • Autotrophic extremophilic microorganisms


Research methods
Isolation, cultivation and characterization of new thermophilic prokaryotes, including anaerobes, gasotrophic microorganisms and inorganic electron acceptor-reducing microorganisms.

Characterization of new isolates:

  • Cell morphology and growth – light phase-contrast microscopy, fluorescent microscopy
  • Metabolism – HPLC, gas chromatography, spectrophotometry
  • Genosystematic – determination of phylogenetic position based on the results of sequencing of complete genomes and 16S rRNA genes

Characterization of microbial communities:

  • Isolation of DNA and RNA from natural communities and enrichment cultures
  • preparation of libraries for high-throughput sequencing
  • analysis of the taxonomic diversity of microbial communities based on high-throughput sequencing of 16S rRNA gene amplicons development and application of PCR primers and probes

Bioinformatics techniques:

  • analysis of complete genomes of pure cultures
  • assembling and analysis of metagenome assembled l genomes (MAGs)
  • comparative genomics and metabolism reconstruction


Short history
Laboratory is organized in February 2017 by dividing Laboratory of Hyperthermophilic Microbial Communities (Head Prof. Elizaveta Bonch-Osmolovskaya) in two laboratories within the Department of Extremophiles Biology.

 

Selected publications:

  1. Khomyakova M.A., Merkel A.Y., Kopitsyn D.S., Slobodkin A.I. (2022) Pelovirga terrestris gen. nov., sp. nov., anaerobic, alkaliphilic, fumarate-, arsenate-, Fe(III)- and sulfur-reducing bacterium isolated from a terrestrial mud volcano // Systematic and Applied Microbiology 45 (2022) 126304. https://doi.org/10.1016/j.syapm.2022.126304
  2. Khomyakova M., Merkel A., Novikov A., Klyukina A., Slobodkin A. (2021) Alkalibacter mobilis sp. nov., an anaerobic bacterium isolated from a coastal lake // Int. J. Syst. Evol. Microbiol. 2021; 71:005174 DOI 10.1099/ijsem.0.005174
  3. Frolova A.A., Merkel A.Y., Kuchierskaya A.A., Bonch-Osmolovskaya E.A., Slobodkin A.I. (2021) Pseudodesulfovibrio alkaliphilus, sp. nov., an alkaliphilic sulfate-reducing bacterium isolated from a terrestrial mud volcano // Antonie van Leeuwenhoek (2021) 114:1387–1397. https://doi.org/10.1007/s10482-021-01608-5
  4. Khomyakova M.A., Merkel A.Y., Slobodkin A.I. (2021) Perlabentimonas gracilis gen. nov., sp. nov., a gliding aerotolerant anaerobe of the order Bacteroidales, isolated from a terrestrial mud volcano // Systematic and Applied Microbiology 44 (2021) 126245. https://doi.org/10.1016/j.syapm.2021.126245
  5. Merkel A.Y., Chernyh N.A., Pimenov N.V., Bonch-Osmolovskaya E.A., Slobodkin A.I. (2021) Diversity and metabolic potential of the terrestrial mud volcano microbial community with a high abundance of archaea mediating the anaerobic oxidation of methane. // Life 2021, 11, 953. https://doi.org/10.3390/life11090953
  6. Slobodkina G., Allioux M., Merkel A., Cambon-Bonavita M.-A., Alain K., Jebbar M. and Slobodkin A. (2021) Physiological and genomic characterization of a hyperthermophilic archaeon Archaeoglobus neptunius sp. nov. isolated from a deep-sea hydrothermal vent warrants the reclassification of the genus Archaeoglobus // Front. Microbiol. 12:679245. doi: 10.3389/fmicb.2021.679245
  7. Frolova A., Merkel A.Yu.,· Novikov A. A., Bonch‑Osmolovskaya E. A., Slobodkin A. I. (2021) Anaerotalea alkaliphila gen. nov., sp. nov., an alkaliphilic, anaerobic, fermentative bacterium isolated from a terrestrial mud volcano // Extremophiles (2021) 25:301–309. https://doi.org/10.1007/s00792-021-01229-w
  8. Slobodkina G., Allioux M., Merkel A., Alain K, Jebbar M., Slobodkin A. (2020) Genome analysis of Thermosulfuriphilus ammonigenes ST65T, an anaerobic thermophilic chemolithoautotrophic bacterium isolated from a deep-sea hydrothermal vent // Marine Genomics 54 (2020) 100786. https://doi.org/10.1016/j.margen.2020.100786
  9. Khomyakova M.A., Merkel A.Y., Petrova D.A., Bonch-Osmolovskaya E.A., Slobodkin A.I. (2020) Alkalibaculum sporogenes sp. nov., isolated from a terrestrial mud volcano and emended description of the genus Alkalibaculum. Int. J. Syst. Evol. Microbiol. V. 70. P. 4914–4919. DOI 10.1099/ijsem.0.004361
  10. Khomyakova M.A., Merkel A.Y., Kopitsyn D.S., Bonch-Osmolovskaya E.A., Slobodkin A.I. (2020) Calorimonas adulescens gen. nov., sp. nov., an anaerobic thermophilic bacterium utilizing methoxylated benzoates // Int. J. Syst. Evol. Microbiol. V. 70. P. 2066-2071. https://doi.org/10.1099/ijsem.0.004019
  11. Ratnikova N.M., Slobodkin A.I., Merkel A.Y., Kopitsyn D.S., Kevbrin V.V., Bonch-Osmolovskaya E.A., Slobodkina G.B. (2020) Sulfurimonas crateris sp. nov., a facultative anaerobic sulfur-oxidizing chemolithoautotrophic bacterium isolated from a terrestrial mud volcano // Int. J. Syst. Evol. Microbiol. V. 70. P. 487-492. doi: 10.1099/ijsem.0.003779
  12. Slobodkina G.B., Merkel A.Y., Novikov A.A., Bonch‑Osmolovskaya E. A., Slobodkin A. I. (2020) Pelomicrobium methylotrophicum gen. nov., sp. nov. a moderately thermophilic, facultatively anaerobic, lithoautotrophic and methylotrophic bacterium isolated from a terrestrial mud volcano // Extremophiles. V. 24. P. 177-185. doi: 10.1007/s00792-019-01145-0
  13. Slobodkin A., Slobodkina G., Allioux M., Alain K., Jebbar M., Shadrin V., Kublanov I., Toshchakov S., Bonch-Osmolovskaya E. (2019) Genomic insights into the carbon and energy metabolism of a thermophilic deep-sea bacterium Deferribacter autotrophicus revealed new metabolic traits in the phylum Deferribacteres // Genes. 10, 849. doi:10.3390/genes10110849
  14. Slobodkina G. “Thermodesulfitimonas” in Bergey’s Manual of Systematics of Archaea and Bacteria, ed W.B. Whitman, John Wiley: Chichester. DOI: 10.1002/9781118960608.gbm01661
  15. Slobodkina G.B., Baslerov R.V., Kostryukova N.K., Bonch-Osmolovskaya E.A., Slobodkin A.I. (2018) Tepidibaculum saccharolyticum gen. nov., sp. nov. a moderately thermophilic, anaerobic, spore-forming bacterium isolated from a terrestrial hot spring // Extremophiles. V. 22. P. 761-768. doi: 10.1007/s00792-018-1036-5
  16. Slobodkina G.B., Reysenbach A.-L., Kolganova T.V., Novikov A.A, Bonch-Osmolovskaya E.A., Slobodkin A.I. (2017) Thermosulfuriphilus ammonigenes gen. nov., sp. nov., a thermophilic, chemolithoautotrophic bacterium capable of respiratory ammonification of nitrate with elemental sulfur // International Journal of Systematic and Evolutionary Microbiology. V. 67. P. 3474-3479. doi: 10.1099/ijsem.0.002142
  17. Slobodkina G.B., Baslerov R.V., Novikov A.A, Bonch-Osmolovskaya E.A., Slobodkin A.I. (2017) Thermodesulfitimonas autotrophica gen. nov., sp. nov. a thermophilic, obligate sulfite-reducing bacterium isolated from a terrestrial hot spring // International Journal of Systematic and Evolutionary Microbiology. V. 67. P. 301-305. doi: 10.1099/ijsem.0.001619
  18. Slobodkin A. (2017) “Tepidimicrobium” in Bergey’s Manual of Systematics of Archaea and Bacteria, ed W.B. Whitman, John Wiley: Chichester. DOI: 10.1002/9781118960608.gbm01399.
  19. Merkel A.Yu., Pimenov N.V,.·Rusanov I.I.,·Slobodkin A.I.,·Slobodkina G.B. Tarnovetckii I.Yu., Frolov E.N., Dubin A.V.,·Perevalova A.A., Bonch‑Osmolovskaya E.A. (2017) Microbial diversity and autotrophic activity in Kamchatka hot springs // Extremophiles V. 21 P.307–317. DOI 10.1007/s00792-016-0903-1
  20. Slobodkina G.B., Mardanov A.V., Ravin N.V., Frolova A.A., Chernyh N.A., Bonch-Osmolovskaya E.A., Slobodkin A.I. (2017) Respiratory ammonification of nitrate coupled to anaerobic oxidation of elemental sulfur in deep-sea autotrophic thermophilic bacteria // Front. Microbiol. 8:87. doi: 10.3389/fmicb.2017.00087
  21. Slobodkina G. “Caloribacterium” in Bergey’s Manual of Systematics of Archaea and Bacteria, ed W.B. Whitman, John Wiley: Chichester. DOI: 10.1002/9781118960608.gbm01453