• Study of functional and species diversity of hydrocarbon-oxidizing actinobacteria of anthropogenically disturbed biocenoses using metagenomics and bioinformatics methods.
• Scientific grounds for intensification of remediation processes in oil-contaminated ecosystems using Rhodococcus biosurfactants and immobilized rhodococcal cells with functionalized surfaces.
• Development of environmentally friendly technologies for synthesis of desired bioactive products, transformation of organic compounds, and biodegradation of persistent toxic xenobiotics using the bioresources of the Collection of alkanotrophic microorganisms.
Based on the theoretical and experimental studies and genome sequencing of actinobacteria of ecologically significant taxa, the following was identified: universal reactions involved in the neutralization of highly hazardous mineral and organic eco-pollutants, including the production of enzymes with broad substrate specificity; over-synthesis of protective substances; increased affinity of the cell surface to hydrophobic damaging agents; morphometric distortions (e.g., the average size of vegetative cells, the relative area and relief of the cell surface, etc.) and changes in the integral physicochemical parameters of cells (zeta potential, lipid content, etc.) [Microorganisms. 2022. 10(6): 1101; Microbiology Resource Announcements. 2022: e01070-22; State registration certificate No. 2018619759 of the computer software].
The results of the study of mechanisms of resistance formation and compensatory reactions to the negative effects of pollutants in actinobacteria were used in the developments for bioremediation of biotopes contaminated with persistent ecotoxicants, and biotransformation of complex hydrophobic compounds in order to obtain bioactive metabolites [Microbiology. 2022. 91(4): 419−432; Scientific Reports. 2019. 9: 9159; PLoS One. 2021. 16(11): e0260032; Catalysts. 2022. 12(11): 1352; Pharmaceuticals. 2022.15(8): 964; Frontiers in Microbiology. 2022. 13: 967127, 2-23. 14: 1275553. RF Patents 2656145, 2707536, 2762007,2784816].
As a result of whole genome sequencing, the genomes of 110 strains of Dietzia spp., Gordonia spp. and Rhodococcus spp. were obtained and key genes of biodegradation and biotransformation of complex organic compounds were identified [Catalysts. 2022.12:1352; Microbiology Resource Announcements. 2022: e01070-22; Molecules. 2023. 28: 2393].
The adhesion mechanisms of rhodococci to petroleum hydrocarbons are investigated. The physiological role of Rhodococcus biosurfactants in the process of bacterial adhesion and film formation has been confirmed. The developed temperature model of bacterial adhesion kinetics was used to prove the expediency and effectiveness of using glycolipid biosurfactants to create a strong cellular monolayer of actinobacteria with high catalytic activity on the surface of the carrier [Catalysts. 2019. 19(3): 236; Scientific Reports. 12: 21559. Doctoral thesis defense Krivoruchko A.V., 09.12.2022].
New results have been obtained in the study of polyfunctional biosurfactants synthesized by non-pathogenic actinobacteria of the genus Rhodococcus and their potential for ecobiotechnology and medicine. [Biology of Rhodococcus. 2019. 16. 231−270; Applied Biochemistry and Microbiology. 2020. 56. 245–255]. Based on Rhodococcus biosurfactants, biopreparations were obtained to clean up ecosystems contaminated with petroleum products and salts of heavy metals [Applied Sciences. 2020. 10: 831; International Biodeterioration & Biodegradation. 2021. 164: 105308]. The possibility of using Rhodococcus biosurfactants to reduce the phytotoxicity of soil contaminated with petroleum products and heavy metal salts is shown [Microbiology. 2019. 88(2): 191–199; Biology of Rhodococcus, Microbiol. Monogr. Springer. 2019. 16: 271–298. RF Patent 2798871].
Efficient biocatalytic systems for the transformation of complex hydrophobic compounds have been developed and patented [Catalysts. 2019. 9: 236; 2022. 12(11): 1352; Molecules. 2019. 24: 4121; 2020. 25: 5526; Scientific Reports. 2019. 9: 9159; Pharmaceuticals. 2022. 15: 964, 2023. 16: 872; Microbiology. 2023. 92(2): 304‒314. RF Patents 2707536, 2762007, 2784816, 2796679, 2803338, 2810501. Doctoral thesis defense Cheremnykh K.M., 01.01.2019; Tyumina E.A., 20.12.2019; Luchnikova N.A., 15.12.2023 and Krivoruchko A.V., 09.12.2021].
Rhodococci fixed on modified sawdust and in polyvinyl alcohol cryogel are used in bioremediation of oil-contaminated soil and in the processes of contaminated water purification in a bioreactor [International Biodeterioration & Biodegradation. 2021. 164: 105308].
A technology for treating the oilfield wastewater in a bioreactor has been developed [Russian Journal of Biomechanics. 2019. 23: 48–57; Journal of Environmental Chemical Engineering. 2017. 5: 1252–1260; Biology of Rhodococcus, Microbiol. Monogr. Springer. 2019. 16: 231–270; International Biodeterioration & Biodegradation. 2021. 164: 105308].
Large-scale priority studies are being carried out on the bioconversion of pharmaceutical pollutants — a new kind of emerging pollutants [Microbiology. 2020. 89(2): 148‒163; Scientific Reports. 2019. 9: 9159; PLoS ONE. 2021. 16(11): e0260032; Frontiers in Microbiology. 2022. 13: 967127; RF Patents 2707536, 2762007 and 2803338]. The prospects of practical utilization of biocatalytic systems based on Rhodococcus for the biodegradation of widely used nonsteroidal anti-inflammatory drugs (NSAIDs), particularly ibuprofen, ketoprofen, meloxicam, and naproxen, have been revealed through experimental and theoretical studies.
Priority data on the dynamics of morphofunctional and nanomechanical rearrangements of Rhodococcus cells influenced by metal nanoparticles were obtained. [Nanomaterials. 2022. 12: 951; Heliyon. 2022. 8: e11632]. It has been first shown that nickel nanoparticles increase the efficiency of the purification process of jet fuel-contaminated water in a bioreactor with immobilized rhodococci. [International Biodeterioration & Biodegradation. 2021. 164: 105308; Nanomaterials. 2022. 12(6): 951]. Using the example of biosynthesis of gold nanoparticles, it has been determined that rhodococci are capable of reducing metals from ions [International Journal of Molecular Sciences. 2022. 23: 12939].
The Regional Specialized Collection of Alkanotrophic Microorganisms operates at the subdivision (collection acronym is IEGM, UNU/CKP 73559/480868, http://www.iegmcol.ru). The IEGM Collection aims at meeting the challenges of biotechnology and studying and maintaining the hydrocarbon- and xenobiotic-degrading cultures. The collection gene pool comprises 3500 pure identified non-pathogenic strains isolated from samples of soil, surface and stratal water, snow, air, and core of contrasting ecological and geographical regions. The IEGM Collection is registered with the World Federation for Culture Collections (WFCC, http://www.wfcc.nig.ac.jp/index.html) and the European Culture Collections’ Organization (ECCO, http://www.eccosite.org), and included in the World Data Centre for Microorganisms (WCDM #768, http://wdcm.nig.ac.jp). It possesses computerized database and skilled personnel experienced in polyphasic taxonomy methods. There have been published the Index and Catalog of strains (1994, 2002, 2006, 2010, 2014, 2018, and 2022). Integrated databases and a website of the collection have been established. Biological information about the cultures of the publicly available holdings of the IEGM Collection is included in the Global Catalog of Microorganisms (Global Catalog of Microorganisms, GCM, http://gcm.wfcc.info) and Consolidated Database of collections of the Russian National Node (VKM-UNIQEM-IEGM).
The results of the research were presented at Russian and international scientific conferences, including three (I‒III) Russian Microbiological Congresses (Pushchino, 2017, Saransk, 2019, and Pskov, 2021); XXXVIII Annual Conference of the European Culture Collections’ Organization (ECCO 2019); Congresses of European Microbiologists, namely FEMS 2019 (Glasgow, UK), FEMS 2022 (Belgrade, Serbia), etc. Additionally, the research outcomes were presented at the 63rd International Fair of Technology and Technical Achievements, May, 2019 (Belgrade, Serbia); IV International Salon of Inventions ISIF 2019, September, 2019 (Istanbul, Turkey); and 75 International Technical Fairs, 2019 (Plovdiv, Bulgaria).
The laboratory staff is involved in teaching activities. On the basis of the laboratory, special lecture courses are delivered: Systematics of Microorganisms, Petroleum Microbiology, Technogenic Ecosystems and Environmental Risk, and Molecular Basis of Life. Additionally, practical classes are provided for students of the Microbiology and Immunology Department of Perm State National Research University. The research results are incorporated in lectures, while the collection strains are employed in laboratory classes in the academic discipline Big Practical Classes in Microbiology.
The laboratory staff actively engage in teaching activities. Specialized lecture courses are conducted at the laboratory, including “Microorganism Systematics”, “Biological Safety in Biotechnology”, “Microbial Biotechnologies”, “Petroleum Microbiology”, “Technologies for Remediation of Polluted Ecosystems in the Arctic and Subarctic”, “Technogenic Ecosystems and Environmental Risk”, “Microbiology and Virology”, and “Molecular Basis of Life”. Practical sessions are also held with students from the Department of Microbiology and Immunology at Perm State National Research University.
The results of scientific research conducted by the laboratory are incorporated into lecture courses. Collection strains are utilized in laboratory sessions for the educational discipline “Microbiology Practical Training”. Educational materials, including textbooks, have been developed and published, such as “Biodiversity and Systematics of Microorganisms”, Perm, 2019 (304 pp.), and a “Workbook for Laboratory Practical Sessions” for students studying in the field of “Biology” (Microbiology profile), Perm, 2022 (100 pp.).
