We use cookies.
By using the site, you agree to our Privacy Policy.

Laboratory of Biochemistry and Molecular Biology

Invited researcher Marc Walter Solioz
Contract number
14.Z50.31.0011
Time span of the project
2014-2016
Head of the laboratory

As of 15.02.2021

12
Number of staff members
65
scientific publications
10
Objects of intellectual property
General information

Name of the project: Nanopumps for heavy metals

Strategy for Scientific and Technological Development Priority Level: г


Goals and objectives

Research directions: Isolating new microorganisms – prokaryotes and eukaryotes, study of mechanisms of resistivity against heavy metals and applications of tolerant forms in biotechnologies.

Project objective:

  • Creation of the laboratory for biochemistry and molecular biology that will specialize in determining functions of heavy metal ion pumps and other proteins involved in homeostasis of heavy metals as well as development of new technologies of nanodiscs to investigate functions of ion pumps.
  • Development of technologies for expression, purification and research of new proteins on a wide scale
  • Development of nanodisc technologies and their applications to membrane ion pumps.
  • Decoding genomes of new sulfate reducing bacteria and analysis of mechanisms of resistivity against heavy metals.

The practical value of the study

  1. We have demonstrated the leading role of sulfate-reducing Desulfovibrio in the formation of hydrogen sulfide in cattle farming waste and developed methods of suppression of smell in major cattle-breeding complexes (Karnachuk et al., 2021, Scientific Reports, in press).
  2. A strategy has been developed for the use of genome information to isolate a culture of minor components of a community of extremophile micro-organisms. (Karnachuk et al., 2020). Karnachuk, O.V., Lukina, A.P., Kadnikov, V.V., Sherbakova, V.A., Beletsky, A.V., Mardanov, A.V. and Ravin, N.V. (2020), Targeted isolation based on metagenome‐assembled genomes reveals a phylogenetically distinct group of thermophilic spirochetes from deep biosphere. Environ Microbiol. doi:10.1111/1462-2920.15218 (IF=4.933, Q1).
  3. Our team have developed a strategy and isolated Candidatus Desulforudis audaxviator into a pure culture from underground biosphere (Karnachuk et al., 2019) viewed as a possible representative of life on exoplanets. Karnachuk O.V., Frank Y.A., Lukina A.P., Kadnikov V.V., Beletsky A.V., Mardanov A.V., Ravin N.V. Domestication of previously uncultivated Candidatus Desulforudis audaxviator from a deep aquifer in Siberia sheds light on its physiology and evolution. ISME J 13, 1947-1959 (2019) doi:10.1038/s41396-019-0402-3 (IF=9.493, Q1).
  4. We have isolated metal-resistant micro-micellas participating in processes of biomineralisation in acid mine drainage (Glukhova et al., 2018). Glukhova L.B., Frank Y.A., Danilova E.V., Avakyan M.R., Banks D., Tuovinen O.H., Karnachuk O.V. 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 Nov;76(4):911-924. doi: 10.1007/s00248-018-1186-0. (IF=3.611, Q1).
  5. New approaches have been developed for the use of continuous cultivation to isolate acidophilic micro-organisms from acid mine drainage (Antsiferov et al., 2017). Antsiferov DV, Fyodorova TS, Kovalyova AA, Lukina A, Frank YA, Avakyan MR, Banks D, Tuovinen OH, Karnachuk OV. Selection for novel, acid-tolerant Desulfovibrio spp. from a closed Transbaikal mine site in a temporal pH-gradient bioreactor. Antonie Van Leeuwenhoek. 017 Dec;110(12):1669-1679. doi: 10.1007/s10482-017-0917-4.
  6. Our researcher have isolated new unique extremophile cultures from underground waters into a pure culture (Frank et al., 2016). Frank Y.A., Kadnikov V.V., Lukina A.P., Banks D., Beletsky A.V., Mardanov A.V., Sen’kina E.I., Avakyan M.R., Karnachuk O.V., Ravin N.V. Characterization and Genome Analysis of the First Facultatively Alkaliphilic Thermodesulfovibrio Isolated from the Deep Terrestrial Subsurface. Front Microbiol. 2016; 7: 2000. doi: 10.3389/fmicb.2016.02000 (IF=4.259, Q1).

Education and career development:

Our Laboratory has developed and has been delivered the lecture courses «General micro-biology», «Bio-technology», «Ecological micro-biology», «Industrial biology» at the Tomsk State University. The Laboratory supervises the scientific work of undergraduate and postgraduate students majoring in Micro-biology, Ecology, and Plant physiology, 6 Candidate of Science dissertations have been defended, the last of which in 2017 was defended by D. B. Antsiferov «Isolation of sulfate-reducing bacteria promising for the formation of metal sulfides and their cultivation ».

Collaborations:

Joint research with the Federal Research Centre «Bio-technologies» of the Russian Academy of Sciences.

A joint project funded by the Russian Foundation for Basic Research called «‎The diversity and the activity of sulfidogenic micro-organisms and the prevention of the formation of hydrogen sulfide in municipal and agricultural waste landfills»‎.

Hide Show full
Karnachuk, O.V., Lukina, A.P., Kadnikov, V.V., Sherbakova, V.A., Beletsky, A.V., Mardanov, A.V. and Ravin, N.V. (2020)
Targeted isolation based on metagenome‐assembled genomes reveals a phylogenetically distinct group of thermophilic spirochetes from deep biosphere. Environ Microbiol. doi:10.1111/1462-2920.15218 (IF=4.933, Q1)
Kadnikov VV, Mardanov AV, Beletsky AV, Karnachuk OV and Ravin NV (2020)
Microbial Life in the Deep Subsurface Aquifer Illuminated by Metagenomics. Front. Microbiol. 11:572252. doi: 10.3389/fmicb.2020.572252 (IF=4.235, Q1)
Karnachuk O.V., Frank Y.A., Lukina A.P., Kadnikov V.V., Beletsky A.V., Mardanov A.V., Ravin N.V.
Domestication of previously uncultivated Candidatus Desulforudis audaxviator from a deep aquifer in Siberia sheds light on its physiology and evolution. ISME J 13, 1947-1959 (2019) doi:10.1038/s41396-019-0402-3 (IF=9.493, Q1)
Kadnikov V.V., Mardanov A.V., Beletsky A.V., Rakitin A.L., Frank Y.A., Karnachuk O.V., Ravin N.V.
Phylogeny and physiology of candidate phylum BRC1 inferred from the first complete metagenome-assembled genome obtained from deep subsurface aquifer. Syst Appl Microbiol. 2019 Jan;42(1):67-76. doi: 10.1016/j.syapm.2018.08.013. (IF=3.283, Q1)
Kadnikov V.V., Mardanov A.V., Ivasenko D.A., Antsiferov D.V., Beletsky A.V., Karnachuk O.V., Ravin N.V.
Lignite coal burning seam in the remote Altai Mountains harbors a hydrogen-driven thermophilic microbial community. Sci Rep 8, 6730 (2018) doi:10.1038/s41598-018-25146-9 (IF=4.011, Q1)
Glukhova L.B., Frank Y.A., Danilova E.V., Avakyan M.R., Banks D., Tuovinen O.H., Karnachuk O.V.
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 Nov;76(4):911-924. doi: 10.1007/s00248-018-1186-0. (IF=3.611, Q1)
Kadnikov V.V., Mardanov A.V., Beletsky A.V., Banks D., Pimenov N.V., Frank Y.A., Karnachuk O.V., Ravin N.V.
A metagenomic window into the 2-km-deep terrestrial subsurface aquifer revealed multiple pathways of organic matter decomposition. FEMS Microbiol Ecol. 2018 Oct 1;94(10). doi: 10.1093/femsec/fiy152. (IF=4.098, Q1)
Mardanov A.V., Panova I.A., Beletsky A.V., Avakyan M.R., Kadnikov V.V., Antsiferov D.V., Banks D., Frank Y.A., Pimenov N.V., Ravin N.V., Karnachuk O.V. (2016)
Genomic insights into a new acidophilic, copper-resistant Desulfosporosinus isolate from the oxidized tailings area of an abandoned gold mine. FEMS Microbiol Ecol 92(8) V 92 № 8 doi.org/10.1093/femsec/fiw111. (IF=4.098, Q1)
Frank Y.A., Kadnikov V.V., Lukina A.P., Banks D., Beletsky A.V., Mardanov A.V., Sen’kina E.I., Avakyan M.R., Karnachuk O.V., Ravin N.V.
Characterization and Genome Analysis of the First Facultatively Alkaliphilic Thermodesulfovibrio Isolated from the Deep Terrestrial Subsurface. Front Microbiol. 2016; 7: 2000. doi: 10.3389/fmicb.2016.02000 (IF=4.259, Q1)
Frank Y.A., Kadnikov V.V., Gavrilov S.N., Banks D., Gerasimchuk A., Podosokorskaya O.A., Merkel A.Yu., Chernyh N.A., Mardanov A., Ravin N., Karnachuk O.V., Bonch-Osmolovskyaya E.A.
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. doi:10.3389/fmicb.2016.02101. (IF=4.165 Q1)
Other laboratories and scientists
Hosting organization
Field of studies
City
Invited researcher
Time span of the project
Research Laboratory «‎Regulatory Genomics»

Kazan (Volga region) Federal University

Biology and biochemistry

Kazan

Yoshihide Hayashizaki

Japan

2021-2023

Laboratory of Statistical Multi-omics and Bio-informatics

Ufa Federal Research Centre of the Russian Academy of Sciences

Biology and biochemistry

Ufa

Inga Anatoliyevna Prokopenko

United Kingdom

2021-2023

Research and manufacturing biotechnology complex for conducting works in study, preservation and practical application of cultivated cells and organs of higher plants and microalgae

Timiryazev Institute of plant physiology of the Russian Academy of Sciences

Biology and biochemistry

Moscow

Keeyoeup Paek

Korea

2019-2021