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. 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
  2. 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
  3. 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
  4. 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. Published 14th March 2017.
  5. 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
  6. 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
  7. Slobodkina G.B., Kolganova T.V., Kopitsyn D.S., Viryasov M.B., Bonch-Osmolovskaya E.A., Slobodkin A.I. (2016) Dissulfurirhabdus thermomarina gen. nov., sp. nov. a thermophilic, autotrophic, sulfite-reducing and disproportionating deltaproteobacterium isolated from a shallow-sea hydrothermal vent // International Journal of Systematic and Evolutionary Microbiology. V. 66. P. 2515-2519. doi:10.1099/ijsem.0.001083
  8. Mardanov A.V., Beletsky A.V., Kadnikov V.V., Slobodkin A.I., Ravin N.V. (2016) Genome analysis of Thermosulfurimonas dismutans, the first thermophilic sulfur-disproportionating bacterium of the phylum Thermodesulfobacteria. Front. Microbiol. 7:950. doi: 10.3389/fmicb.2016.00950
  9. Slobodkin A.I., Slobodkina G.B., Panteleeva A.N., Chernyh N.A., Novikov A.A., Bonch-Osmolovskaya E.A. (2016) Dissulfurimicrobium hydrothermale gen. nov., sp. nov., a thermophilic, autotrophic, sulfur-disproportionating deltaproteobacterium isolated from a hydrothermal pond of Uzon Caldera, Kamchatka // International Journal of Systematic and Evolutionary Microbiology. V. 66. P. 1022-1026. doi 10.1099/ijsem.0.000828
  10. Slobodkina G.B., Baslerov R.V., Novikov A.A., Viryasov M.B., Bonch-Osmolovskaya E.A., Slobodkin A.I. (2016) Inmirania thermothiophila gen. nov., sp. nov., a thermophilic, facultatively autotrophic, sulfur-oxidizing gammaproteobacterium isolated from shallow-sea hydrothermal vent // International Journal of Systematic and Evolutionary Microbiology. V. 66. P. 701-706. doi:10.1099/ijsem.0.000773
  11. Slobodkina G.B., Panteleeva A.N., Beskorovaynaya D.A., Bonch-Osmolovskaya E.A., Slobodkin A.I. (2016) Thermostilla marina gen. nov., sp. nov., a novel thermophilic facultatively anaerobic planctomycete isolated from a shallow submarine hydrothermal vent // International Journal of Systematic and Evolutionary Microbiology. V. 66. P. 663-668. doi:10.1099/ijsem.0.000767
  12. Slobodkin A., Gavrilov S., Ionov V., Iliyin V. (2015) Spore-Forming Thermophilic Bacterium within Artificial Meteorite Survives Entry into the Earth’s Atmosphere on FOTON-M4 Satellite Landing Module. // PLoS ONE 10(7): e0132611. doi:10.1371/journal.pone.0132611
  13. Slobodkina G.B., Kovaleva O.L., Miroshnichenko M.L., Slobodkin A.I., Kolganova T.V., Novikov A.A., van Heerden E., Bonch-Osmolovskaya E.A. (2015) Thermogutta terrifontis gen. nov., sp. nov. and Thermogutta hypogea sp. nov., thermophilic anaerobic representatives of the phylum Planctomycetes // International Journal of Systematic and Evolutionary Microbiology. V. 65. P. 760-765. doi:10.1099/ijs.0.000009
  14. Slobodkina G.B., Lebedinsky A.V., Chernych N.A., Bonch-Osmolovskaya E.A., Slobodkin A.I. (2015) Pyrobaculum ferrireducens sp.nov., a novel hyperthermophilic Fe(III), selenate and arsenate-reducing crenarchaeon isolated from a hot spring // International Journal of Systematic and Evolutionary Microbiology.V. 65. P. 851-856. doi:10.1099/ijs.0.000027
  15. Mardanov A., Slododkina G., Slobodkin A., Beletsky A., Gavrilov S., Kublanov I., Bonch-Osmolovskaya E., Skryabin K., Ravin N. (2015) The genome of Geoglobus acetivotans: Fe(III) reduction, acetate utilization, autotrophic growth and degradation of aromatic compounds in a hyperthermophilic archaeon // Applied Environmental Microbiology. V. 81. P. 1003-1012. doi:10.1128/AEM.02705-14