Laboratory for Biochemistry and Molecular Biology

Solioz Marc

Contract number

14.Z50.31.0011

Time span of the project

2014-2016

Laboratory's website

Karnachuk Olga Viktorovna

As of 01.11.2022

Number of staff members

scientific publications

Objects of intellectual property

Name of the project: Nanopumps for heavy metals

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.

Scientific results:

We have demonstrated the leading role of sulfate-reducing Desulfovibrio in the formation of hydrogen sulfate in animal farming waste and developed methods of dealing with the small at major animal farming complexes.
Our researchers have developed a strategy for the use of geometric information for isolating a culture of extremophilic organisms into a culture.
We have developed a strategy and isolated Candidates Desulforudis audaxviator into a pure culture from the underground biosphere, which is viewed as a possible example of exoplanetary life.
We have isolated metal-resistant Myxomycetes that participate in biomineralization processes in acid mine drainage.
Approaches have been developed for the use of continuous cultivation for isolating acidophilic microorganisms from acid mine drainage.
New unique extremophiles have been isolated into a pure culture from underground waters.

Implementation of research results:

Conducting large-scale (within the territory of Russia) research of the gut microbiomes of agricultural animals (AA) and dairy products of animal origin, produced with help from civic science tools (volunteering microbiologists). Information on microbial communities and their metagenomes will be used for the targeted isolation of producer strains and creating microbial consortia.
Our researchers have isolated Spirochaeta thermophila into a pure culture with the use of the metagenome (MAG). This organism constitutes an insignificant part in the microbial community of deep water-carrying horizons and cannot be cultivated using traditional methods.
We have established possible consequences of excessive growth of CRP in the human intestine. It is the transition of biologically available iron into poorly soluble crystalline iron sulfides that cause iron deficit in the organism. The loss of iron through the formation of insoluble sulfides can occur in the proximal part of the gastrointestinal tract.
We have demonstrated the leading role of sulfate-reducing Desulfovibrio in the formation of hydrogen sulfate in animal farming waste and developed methods of dealing with the smell in major animal farming complexes.
Our researchers have developed a strategy for the use of genome information for isolating minor components of a community of extremophile microorganisms into a culture.
We have developed a strategy and isolated CandidatusDesulforudisaudaxviator into a pure culture from the underground biosphere, which we view as an example of exoplanetary life.
Our researchers have isolated metal-resistant Myxomycetes that participate in biomineralization in acid mine drainage.
The Laboratory has developed approaches to the use of continuous cultivation for isolating acidophilic microorganisms from acid mine drainage.
We have isolated extremophiles into a pure culture from underground waters.

Education and career development:

The Laboratory has developed and delivered the lecture courses «General microbiology», «Biotechnology», «Environmental microbiology», «Industrial biology» at the Tomsk State University. We are supervising research work of master’s degree and postgraduate students specializing in «Microbiology», «Ecology» and «Plant physiology», 6 Candidate of Sciences dissertations have been prepared and defended, the last of them by Dmitry V. Antsiferov «Isolating sulfate-reducing bacteria promising for forming metal sulfides from acid mine waste and their cultivation» in 2017 in the direction 03.02.03 Microbiology.

Collaborations:

The joint Russian Foundation for Basic Research grant «Diversity and activity of sulfidogenic microorganisms and preventing the formation of hydrogen sulfide on municipal and agricultural waste polygons».

Joint research is conducted in collaboration with:

Faculty of Biology, Lomonosov Moscow State University;
Kurchatov Institute;
Federal Research Center «Fundamentals of Biotechnologies» of the Russian Academy of Sciences;
Foundation «Science and Technology Park of Novosibirsk Akademgorodok»;
Institute of General and Experimental Biology of the Siberian Branch of the Russian Academy of Sciences.

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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 2019, J 13, 1947-1959, doi:10.1038/s41396-019-0402-3 (IF=9.493, Q1)

karnachuk, o.v., lukina, a.p., kadnikov, v.v.,mardanov, a.v., ravin, n.v.

Targeted isolation based on metagenome-assembled genomes reveals a phylogenetically distinct group of thermophilic spirochetes from deep biosphere. Environmental Microbiologythis link is disabled, 23(7), pp. 3585–3598 (2021)

o.v. karnachuk, i.i. rusanov, i. a. panova, m. a. grigoriev, v. s. zyusman, e. a. latygolets, m. k. kadyrbaev, e. v. gruzdev, a. v. beletsky, a. v. mardanov, n. v. pimenov, n. v. ravin

Microbial sulfate reduction by Desulfovibrio is an important source of hydrogen sulfide from a large swine finishing facility //Scientific reports. 2021. Vol. 11, № 1. Art. num. 10720.

kadnikov v.v., mardanov a.v., ivasenko d.a., antsiferov d.v., beletsky a.v., karnachuk o.v., ravin n.v.

(2018) Lignite coal burning seam in the remote Altai Mountains harbors a hydrogen-driven thermophilic microbial community. Sci Rep 8, 6730 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.

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)

i. a. panova, o. p. ikkert, m. r. avakyan, d.s.kopitsyn, a. v. mardanov, n. v. pimenov, v. a. shcherbakova, n. v. ravin, o. v. karnachuk

Desulfosporosinus metallidurans sp. Nov., an acidophilic, metal-resistant sulfate-reducing bacterium from acid mine drainage //International journal of systematic and evolutionary microbiology. 2021. Vol. 71, № 7. Art. num. 4876.

o. v. karnachuk, o. p. ikkert, m.r. avakyan, y. v. knyazev, m. n. volochaev, v. s. zyusman, v. l. panov, v. v. kadnikov a. v. mardanov, n.v. ravin

Desulfovibrio desulfuricans AY5 isolated from a patient with autism spectrum disorder binds iron in low-soluble greigite and pyrite //Microorganisms. 2021. Vol. 9, № 12. Art. num. 2558.

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..

Genomic insights into a new acidophilic, copper-resistant Desulfosporosinus isolate from the oxidized tailings area of an abandoned gold mine. FEMS Microbiol Ecol,2016, 92(8) V 92 № 8 doi.org/10.1093/femsec/fiw111. (IF=4.098, 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)

Hosting organization	Field of studies	City	Invited researcher	Time span of the project
Centre for Integrative Structural Biology (10) National Research Centre «Kurchatov Institute» - (Kurchatov Institute)	Biology	Moscow	Yusupov Marat Russia, France	2024-2028
Laboratory of Revolutionary Trophology A.N. Severtsov Institute of Ecology and Evolution of RAS - (IEE RAS)	Biology	Moscow	Gisbert Enric Casas Spain	2022-2024
Laboratory for Statistical Multi-omics and Bio-informatics Ufa Federal Research Centre of the Russian Academy of Sciences	Biology	Ufa	Prokopenko Inga Anatoliyevna United Kingdom	2021-2023