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, lithoautotrophic microorganisms, new types of metabolism, microbial communities, deep-sea hydrothermal vents, deep continental biosphere, space microbiology

Research topics

  • Biological diversity of extremophilic microorganisms
  • Functional diversity of thermophilic prokaryotes
  • Phylogenetic diversity of thermophilic prokaryotes
  • Exploration and characterization of new types of catabolism in extremophilic microorganisms
  • Reduction of inorganic electron acceptors by prokaryotes
  • Microbial metal reduction
  • Microbial disproportionation of sulfur compounds
  • Dissimilatory nitrate ammonification by prokaryotes
  • Autotrophic CO2 fixation in extremophilic microorganisms
  • Ecology of extremophilic microorganisms

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

Techniques of characterization of new isolates:

  • Cell morphology and growth – light phase-contrast microscopy, fluorescent microscopy
  • Metabolism – HPLC, gas chromatography, spectrophotometry
  • Genosystematic – G+C content, DNA-DNA hybridization

Techniques of characterization of microbial communities:

  • Isolation of DNA and RNA from natural communities and enrichment cultures
  • DGGE of 16S rRNA and functional genes

Bioinformatics techniques:

  • Phylogenetic analysis based on 16S rRNA genes
  • Analysis of functional genes
  • Development of PCR primers and probes for analysis of microbial
  • Analysis of complete genomes of new isolates

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. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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.
  9. 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
  10. 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
  11. 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