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Collection of cultures of agricultural microorganisms (ARCAM)
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Laboratory of biodiversity of agricultural microorganisms №10

KARLOV DENIS SERGEEVICH

Head of the Laboratory, Senior Researcher, PhD

Contact phone number: +7 812 476 28 02

E-mail: ds.karlov@arriam.ru

The main task of the laboratory is to study the biodiversity of genetic resources of endosymbionts of cultivated and wild legumes, promising for practical use. To date, a unique collection of bacterial economically valuable strains has been created, which have a wide potential for use in various soil and climatic conditions of Russia. To expand the collection fund, laboratory staff participate in organizing and conducting research expeditions to various regions of the Russian Federation (Altai, Buryatia, Baikal Region, Kamchatka, Caucasus), including hard to rich and remote areas of the Arctic (Northern Yakutia, Chukotka, Putorana plateau).

THE MAIN AREAS OF RESEARCH

1. Arctic bean-rhizobial systems

A unique collection of cold-resistant Arctic bacterial strains has been created and continues to be replenished, promising as effective microsymbionts of cultivated (Vicia, Lathyrus, Trifolium) and wild-growing (Astragalus, Oxytropis, Hedysarum) legumes with the potential to be used in the formation of highly productive perennial pasture and hay phytocenoses in the northern regions of Russia. The ability of a promising wild plant of Oxytropis adamsiana to form an effective symbiosis with Mesorhizobium strains has been shown, which will allow in the future to use this species as a component of grass mixtures in the creation of perennial pasture and hay phytocenoses in the Arctic territories.

2. Relict legume-rhizobial systems

A unique collection of microsymbionts of relict legumes growing in the Baikal region, Altai and Kamchatka peninsula has been created and is being actively studied. The phenomenon of rhizobial synergy was discovered, which is expressed in the ability of strains with different taxonomic positions and complementary sets of symbiotic genes to simultaneously be present in nodules and increase the efficiency of symbiosis with joint inoculation (the rate of nodule formation, the total number of nodules, nitrogen-fixing activity and plant biomass). It has also been shown that strains isolated from relict symbiotic systems can possess a wide range of host plants, including highly specific species of cultivated plants alfalfa (Medicago sativa) and clover (Trifolium pratense). The results obtained suggest that symbiotic systems of relict plants are formed with the participation of representatives of various rhizobial taxa, which can be co-microsymbionts and jointly participate in increasing the efficiency of symbiosis with a wide range of host plants, including agricultural crops.

3. Symbiosis of Cyamopsis tetragonoloba (guar) with rhizobial strains

Cyamopsis tetragonoloba (L.) Taub. is an annual leguminous crop with a high protein content. It is grown as a vegetable crop and can be consumed as food and animal feed. Guar is a nitrogen—fixing plant and serves as a good precursor in crop rotation. Guar gum is of particular value (it is used as a natural thickener and emulsifier in the food, medical, textile and pulp and paper industries, in the production of cosmetics, explosives, as well as as a surfactant with high viscosity in the coal and oil and gas industries). Currently, the issue of creating conditions for guar cultivation in the southern regions of the Russian Federation is acute. One of these conditions is the study of microsymbionts of this culture, including the selection of promising inoculant strains. As a result of evaluating the effectiveness of 30 guar microsymbiont strains in vegetation experiments, 2 strains (Bradyrhizobium archetypum RCAM05275 and Ensifer aridi RCAM05276) were selected, which significantly increased the symbiotic parameters: plant biomass by 70% and the total nitrogen content in them by 1.4 times.




Staff

Grants

  1. Grant from St. Petersburg in the field of scientific and scientific-technical activities "Creation of a biological resource center for useful microorganisms for agricultural purposes on the basis of a unique automated cryopreservation facility", 2010
  2. Grant CNR- Short Term Mobility Program 2011 «Study of the interactions between rhizosphere microorganisms and plant species growing on sandy soils» (CNR-ISPAAM, Italy), 2011 г.
  3. State contract No. 16.518.11.7095 "Conducting research in the field of long-term conservation and certification of genetic resources of agricultural microorganisms on the basis of a unique low-temperature automated storage station for biological samples of the Departmental collection of useful microorganisms for agricultural purposes of the Russian Agricultural Academy", 2011-2012.
  4. RFBR grant 12-04-01501-a "Study of the mechanisms of integration of components and phytoremediation potential of a heavy metal-resistant legume-bacterial symbiotic system", 2012
  5. Grant of St. Petersburg in the field of scientific and technical activities "Genetic, physiological and functional characteristics of bacteria living in the soils of St. Petersburg and utilizing the phytohormone abscisic acid", 2012
  6. RFBR grant 13-04-01655-a "Utilization of the phytohormone of abscisic acid by symbiotrophic bacteria: a new mechanism of plant-microbial interactions", 2013 – 2015
  7. RFBR grant 13-04-90833-mol_rf_nr "Study of the taxonomic position and symbiotic properties of nodule bacteria – microsymbionts of the relict legume plant Vavilovia formosa", 2013
  8. RNF Grant 14-16-00137 "Studying the role of root exometabolites in the ecochemical mechanisms of adaptation of symbiotic plant-microbial systems to toxic metals", 2014 – 2016
  9. Agreement No. 14.604.21.0024 with the Ministry of Education and Science "Integration of the latest achievements of genomics and metagenomics into the technology of production of microbial preparations", 2014 – 2015
  10. RNF grant No. 16-16-00080 "Study of the formation of the specificity of plant-microbial interaction using relict legumes and its relationship with the productivity of symbiosis", 2016-2018.
  11. RNF Grant No.20-76-10042 "Study of genetic resources of beneficial soil microorganisms of the Arctic regions of Russia in connection with climate change and prospects for expanding the range of agricultural land to the North", 2020-2025.
  12. RNF Grant No. 21-16-00084 "Study of the taxonomic structure of guar microsymbionts (Cyamopsis tetragonoloba (L.) Taub.) and molecular genetic mechanisms of interaction of symbiotic partners", 2021-2023.
  13. Agreement with the Ministry of Education and Science on the grant in the form of subsidy No. 075-15-2021-1055 dated 09/28/2021. "Mobilization of genetic resources of microorganisms based on the Departmental collection of useful microorganisms for agricultural Purposes (VKSM) at the Federal State Budgetary Budgetary Institution VNIISHM using the network principle of organization", 2021-2023.

Publications

  1. Gogoleva N.E., Nikolaichik Y.A., Ismailov T.T., Gorshkov V.Y., Safronova V.I., Belimov A.A., Gogolev Y. Complete genome sequence of the abscisic acid-utilizing strain Novosphingobium sp. P6W. 3 Biotech., 2019, 9(3):94. doi: 10.1007/s13205-019-1625-8.
  2. Safronova V., Belimov A., Sazanova A., Chirak E., Kuznetsova I., Andronov E., Pinaev A., Tsyganova A., Seliverstova E., Kitaeva A., Tsyganov V., Tikhonovich I. Two Broad Host Range Rhizobial Strains Isolated from Relict Legumes Have Various Complementary Effects on Symbiotic Parameters of Co-inoculated Plants. Front Microbiol. 2019, 10:514, doi: 10.3389/fmicb.2019.00514.
  3. Sazanova A.L., Safronova V.I., Kuznetsova I.G., Karlov D.S., Belimov A.A., Andronov E.E, Chirak E.R., Popova J.P., Verkhozina A.V., Willems A., Tikhonovich I.A. Bosea caraganae sp. nov. a new species of slow-growing bacteria isolated from root nodules of the relict species Caragana jubata (Pall.) Poir. originating from Mongolia. Int J Syst Evol Microbiol. 2019, 69(9):2687-2695.  doi: 10.1099/ijsem.0.003509.
  4. Belimov A.A., Zinovkina N.Y., Safronova V.I., Litvinsky V.A., Nosikov V.V., Zavalin A.A., Tikhonovich I.A. Rhizobial ACC deaminase contributes to efficient symbiosis with pea (Pisum sativum L.) under single and combined cadmium and water deficit stress. Environmental and Experimental Botany, 2019, 167: 103859. doi: 10.1016/j.envexpbot.2019.10385.
  5. Yamada K., Koroleva A., Laughlin M., Oksanen N., Akhgari A., Safronova V., Yakovleva E., Kolodyaznaya V., Buldakova T., Metsä-Ketelä M. Characterization and overproduction of cell-associated cholesterol oxidase ChoD from Streptomyces lavendulae YAKB-15.Scientific Reports,2019, 9: 11850. doi: 10.1038/s41598-019-48132-1.
  6. Kimeklis A., Chirak E., Kuznetsova I., Sazanova A., Safronova V., Belimov A., Onishchuk O., Kurchak O., Aksenova T., Pinaev A., Andronov E., Provorov N. Rhizobia Isolated from the Relict Legume Vavilovia formosa Represent a Genetically Specific Group within Rhizobium leguminosarum bv. viciae. Genes, 2019, 10, 991; doi:10.3390/genes10120991.
  7. Chirak E., Kimeklis A., Karasev E., Kopat V., Safronova V., Belimov A., Aksenova T., Kabilov M., Provorov N., Andronov E. Search for ancestral features in genomes of Rhizobium leguminosarum bv. viciae strains isolated from the relict legume Vavilovia formosa. Genes 2019, 10, 990; doi:10.3390/genes10120990.
  8. Kuzikova, I., Rybalchenko, O., Kurashov, E., Krylova Y., Safronova V., Medvedeva N. Defense Responses of the Marine-Derived Fungus Аspergillus tubingensis to Alkylphenols Stress. Water Air Soil Pollut2020, 231, 271. https://doi.org/10.1007/s11270-020-04639-2
  9. Safronova VI, Guro PV, Sazanova AL, Kuznetsova IG, Belimov AA, Yakubov VV, Chirak ER, Afonin AМ, Gogolev YV, Andronov EE, Tikhonovich IA. Rhizobial Microsymbionts of Kamchatka Oxytropis Species Possess Genes of the Type III and VI Secretion Systems, Which Can Affect the Development of Symbiosis. Mol Plant Microbe Interact. 2020, 33(10):1232-1241. doi: 10.1094/MPMI-05-20-0114-R.
  10. Belimov, A., Dodd, I., Safronova, V., and Dietz, K. Leaf nutrient homeostasis and maintenance of photosynthesis integrity contribute to adaptation of the pea mutant SGECd t to cadmium. Biologia Plantarum, 2020, 64:447-453. doi: 10.32615/bp.2020.061.
  11. Belimov, A., Shaposhnikov, A., Azarova, T.S., Makarova, N.M., Safronova, V., Litvinskiy, V., Nosikov, V.V., Zavalin, A.A., and Tikhonovich, I. Microbial Consortium of PGPR, Rhizobia and Arbuscular Mycorrhizal Fungus Makes Pea Mutant SGECdt Comparable with Indian Mustard in Cadmium Tolerance and Accumulation. Plants, 2020, 9(8): 975. doi: 10.3390/plants9080975.
  12. Belimov, A.A.; Shaposhnikov, A.I.; Syrova, D.S.; Kichko, A.A.; Guro, P.V.; Yuzikhin, O.S.; Azarova, T.S.; Sazanova, A.L.; Sekste, E.A.; Litvinskiy, V.A.; Nosikov, V.V.; Zavalin, A.A.; Andronov, E.E.; Safronova, V.I. The Role of Symbiotic Microorganisms, Nutrient Uptake and Rhizosphere Bacterial Community in Response of Pea (Pisum sativumL.) Genotypes to Elevated Al Concentrations in Soil. Plants,2020,9, 1801. https://doi.org/10.3390/PLANTS9121801
  13. Karlov D., Sazanova A., Kuznetsova I., Tikhomirova N., Popova Z., Osledkin Y., Demidov N., Belimov A., Safronova V. Rhizobial isolates in active layer samples of permafrost soil of Spitsbergen, Arctic. Biological communications, 2021, 66 (1): 73 – 82. https://doi.org/10.21638/spbu03.2021.109.
  14. Safronova V, Sazanova A, Kuznetsova I, Belimov A, Guro P, Karlov D, Yuzikhin O, Chirak E, Verkhozina A, Afonin A, Andronov E, Tikhonovich I. Increasing the Legume–Rhizobia Symbiotic Efficiency Due to the Synergy between Commercial Strains and Strains Isolated from Relict Symbiotic Systems. Agronomy. 2021; 11(7):1398. https://doi.org/10.3390/agronomy11071398.
  15. Yuzikhin OS, Gogoleva NE, Shaposhnikov AI, Konnova TA, Osipova EV, Syrova DS, Ermakova EA, Shevchenko VP, Nagaev IY, Shevchenko KV, Myasoedov NF, Safronova VI, Shavarda AL, Nizhnikov AA, Belimov AA, Gogolev YV. Rhizosphere Bacterium Rhodococcus sp. P1Y Metabolizes Abscisic Acid to Form Dehydrovomifoliol. Biomolecules. 2021; 11(3):345. doi: 10.3390/biom11030345.
  16. Ульянич П.С., Белимов А.А., Кузнецова И.Г., Сазанова А.Л., Юзихин О.С., Лактионов Ю.В., Карлов Д.С., Вишнякова М.А.,Сафронова В.И. Эффективность азотфиксирующего симбиоза гуара (Cyamopsistetragonoloba) со штаммами Bradyrhizobiumretamae RCAM05275 и Ensiferaridi RCAM05276 в вегетационном опыте. Сельскохозяйственная биология, 2022, т. 57, №3, с. 555-565. doi: 10.15389/agrobiology.2022.3.555rus.
  17. Karlov, D., Sazanova, A., Guro, P., Kuznetsova, I., Verkhozina, A., Belimov, A., and Safronova, V. 2022. Genetic diversity of rhizobial strains isolated from the relict legumes Gueldenstaedtia monophylla and G. verna growing in the republics of Altai and Buryatia (Russia). Bio. Comm. 67(3): 141–151. https://doi.org/10.21638/spbu03.2022.301
  18. Зайцева Т.Б., Сафронова В.И., Медведева Н.Г. StreptomycesgeldanamycininusZ374 – новый штамм с биоцидной активностью в отношении цианобактерий. Теорeтическая и прикладная экология, 2022. № 1, с.159 – 166.doi: 10.25750/1995-4301-2022-1-159-166.
  19. Martynenko, E.; Arkhipova, T.; Safronova, V.; Seldimirova, O.; Galin, I.; Akhtyamova, Z.; Veselov, D.; Ivanov, R.; Kudoyarova, G. Effects of Phytohormone-Producing Rhizobacteria on Casparian Band Formation, Ion Homeostasis and Salt Tolerance of Durum Wheat. Biomolecules 2022, 12, 230. https://doi.org/10.3390/biom12020230.
  20. Brazhnikova YV, Shaposhnikov AI, Sazanova AL, Belimov AA, Mukasheva TD, Ignatova LV. Phosphate Mobilization by Culturable Fungi and Their Capacity to Increase Soil P Availability and Promote Barley Growth. Curr Microbiol. 2022; 79(8):240. doi: 10.1007/s00284-022-02926-1.
  21. Belimov AA, Shaposhnikov AI, Azarova TS, Syrova DS, Kitaeva AB, Ulyanich PS, Yuzikhin OS, Sekste EA, Safronova VI, Vishnyakova MA, Tsyganov VE, Tikhonovich II. Rhizobacteria Mitigate the Negative Effect of Aluminum on Pea Growth by Immobilizing the Toxicant and Modulating Root Exudation. Plants. 2022; 11(18):2416. https://doi.org/10.3390/plants11182416.
  22. Sazanova A, Safronova V, Belimov A, Gogolev Y, Chirak E, Karlov D, Kuznetsova I, Kuzmina L, Tikhonovich I. Complete Genome Sequence of Rhizobium sp. Strain RCAM05350 from Shulgan-Tash Karst Cave. Microbiol Resour Announc. 2022, 11(10):e0056922. doi: 10.1128/mra.00569-22.
  23. Kichko A.A., Gladkov, G.V., Ulyanich P.S., Safronova V.I., Pinaev A.G., Sekste E.A., Belimov A.A., Andronov E.E. Water stress, cadmium and plant genotype modulate rhizosphere microbiome of Pisum sativum L. Plants 2022, 11(22), 3013; https://doi.org/10.3390/plants11223013.
  24. Yuzikhin O.S., Shaposhnikov A.I., Konnova T.A., Syrova D.S., Hamo H., Ermekkaliev T.S.; Shevchenko V.P., Shevchenko K.V., Gogoleva N.E., Nizhnikov A.A., Safronova V.I., Kamnev A.A., Belimov A.A., Gogolev Y.V. Isolation and Characterization of 1-Hydroxy-2,6,6-trimethyl-4-oxo-2-cyclohexene-1-acetic acid, a metabolite in bacterial transformation of abscisic acid. Biomolecules, 2022, 12, 1508. doi:10.3390/biom12101508.
  25. Belimov A.A., Ulianich P.S., Syrova D.S., Shaposhnikov A.I., Safronova V.I., Dodd I.C. Modulation of tomato root architecture and root hair traits by Pseudomonas brassicacearum and Variovorax paradoxus containing 1-aminocyclopropane-1-carboxylate deaminase. Biologia Plantarum, 2022, 66. 228-239. doi:10.32615/bp.2022.025.
  26. Sazanova A, Belimov A, Gogolev Y, Chirak E, Afonin A, Karlov D, Kuznetsova I, Guro P, Kuzmina L, Safronova V. Complete Genome Sequences of Massilia sp. Strains B-10 and H-1, Isolated from the Water in the Shulgan-Tash Cave. Microbiol Resour Announc. 2023 Jan 12:e0116022. doi: 10.1128/mra.01160-22.
  27. Дзюбенко Е.А., Сафронова В.И., Вишнякова М.А. Селекция гуара в Российской Федерации в связи с перспективой производства отечественной камеди (обзор). Сельскохозяйственная биология, 2023, том 58, № 1, с. 43-59. doi: 10.15389/agrobiology.2023.1.43rus.

  28. Safronova, V.; Sazanova, A.; Belimov, A.; Guro, P.; Kuznetsova, I.; Karlov, D.; Chirak, E.; Yuzikhin, O.; Verkhozina, A.; Afonin, A.; et al. Synergy between Rhizobial Co-Microsymbionts Leads to an Increase in the Efficiency of Plant–Microbe Interactions. Microorganisms 2023, 11, 1206. https://doi.org/10.3390/microorganisms11051206

  29. Boykova I, Yuzikhin O, Novikova I, Ulianich P, Eliseev I, Shaposhnikov A, Yakimov A, Belimov A. Strain Streptomyces sp. P-56 Produces Nonactin and Possesses Insecticidal, Acaricidal, Antimicrobial and Plant Growth-Promoting Traits. Microorganisms. 2023, 11(3):764. https://doi.org/10.3390/microorganisms11030764

  30. Belimov, A.A.; Shaposhnikov, A.I.; Azarova, T.S.; Yuzikhin, O.S.; Sekste, E.A.; Safronova, V.I.; Tikhonovich, I.A. Aluminum-Immobilizing Rhizobacteria Modulate Root Exudation and Nutrient Uptake and Increase Aluminum Tolerance of Pea Mutant E107 (brz). Plants 2023, 12, 2334. https://doi.org/10.3390/plants12122334

  31. Guro P, Ulianich P, Shaposhnikov A, Yuzikhin O, Karlov D, Sazanova A, Safronova V, Belimov A. Draft Genome Sequence of the Bacterium Cupriavidus sp. Strain D39, Inhabiting the Rhizosphere of Pea Plants (Pisum sativum L.). Microbiol Resour Announc. 2023, 12(4):e0135422. https://doi.org/10.1128/mra.01354-22

  32. Guro P, Ulianich P, Belimov A, Sazanova A, Kuznetsova I, Vishnyakova M, Safronova V. Draft Genome Sequence of Guar (Cyamopsis tetragonoloba L.) Microsymbiont Rhizobium sp. Strain RCAM05973. Microbiol Resour Announc. 2023, 12(6):e0007123. https://doi.org/10.1128/mra.00071-23

  33. Guro P, Karaevskaya E, Kuznetsova I, Karlov D, Sazanova A, Safronova V. Complete Genome Sequence of Glutamicibacter sp. Strain M10, Isolated from an Arctic Permafrost Sample. Microbiol Resour Announc. 2023, 12(2):e0112022. https://doi.org/10.1128/mra.01120-22

  34. Guro P, Karlov D, Kuznetsova I, Sazanova A, Alekhina I, Belimov A, Safronova V. Whole-Genome Sequence of Rhizobacterium Sphingomonas sp. Strain 7/4-4, Isolated from the Root Nodule of Astragalus tugarinovii Basil Growing in the Russian Arctic. Microbiol Resour Announc. 2023:e0014123. https://doi.org/10.1128/mra.00141-23

  35. Guro P, Karaevskaya E, Karlov D, Kuznetsova I, Sazanova A, Safronova V. Complete Genome Sequence of Rhodopseudomonas sp. Strain P2A-2r, Isolated from Arctic Soil. Microbiol Resour Announc. 2023, 12(3):e0001323. https://doi.org/10.1128/mra.00013-23

  36. Guro P, Karlov D, Kuznetsova I, Sazanova A, Belimov A, Safronova V. Draft Genome Sequence of Rhizobium sp. Strain 32-5/1, Isolated from Vicia cracca L. Root Nodules in the Russian Arctic. Microbiol Resour Announc. 2023:e0028723. https://doi.org/10.1128/mra.00287-23

  37. Karlov D.S., Guro P.V., Sazanova А.L. I.G. Kuznetsova, N.Yu. Tikhomirova, N.N. Laschinsky, Pavlov I.S., Belimov А.А., Safronova V.I. Study of the genetic diversity and symbiotic efficiency of microsymbionts isolated from Lathyrus palustris L. and Vicia cracca L. growing in Arctic Yakutia. Sel'skokhozyaistvennaya Biologiya [Agricultural Biology], 2023, Vol. 58, № 3, p. 403-415. https://doi.org/10.15389/agrobiology.2023.3.403eng

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