Use of streptomyces for biocontrol of pests and virus mitigation in tomatoes in arid zones

The “greening” of crop production technologies is fundamental to the modern concept of phytosanitary optimization of agroecosystems. Environmentally friendly plant protection products based on actinobacteria, with their novel mechanisms of action and high physiological and biochemical potential, are of particular interest. While soil streptomyces are technologically scalable, have long shelf lives, and are field-friendly, their effectiveness can vary due to limited knowledge of the properties of introduced actinobacteria. This study is the first to establish the in vivo biological effectiveness of Streptomyces carpaticus RCAM04697 for biocontrol of insect pests and reduction of phytovirus damage in open-field tomatoes in the Astrakhan Region. The study aimed to investigate the virucidal and antifungal properties of S. carpaticus RCAM04697 suspensions and extracts, and to evaluate their impact on tomato yields under arid conditions. The S. carpaticus RCAM04697 strain was isolated from brown semi-desert soils of the Astrakhan Region. Field trials demonstrated that treatment of tomato plants with a seven-day culture suspension of S. carpaticus RCAM04697 exhibited high virucidal activity against three phytovirus isolates: cucumber mosaic virus (75.3%), tomato mosaic virus (69.1%), and tomato bronzing virus (82.5%). Maximum antifungal activity was also observed with S. carpaticus RCAM04697 suspension on day 14 after the third treatment, reaching 87.5% against A. crassivora, 86.9% against A. gossypii, and 86.6% against A. fabae, indicating a sustained antagonistic effect. Bacterization of the open field tomatoes with the S. carpaticus RCAM04697 strain resulted in a 2.9-fold yield increase compared to the control. These findings suggest that S. carpaticus RCAM04697 possesses significant potential for developing biological products with virucidal, antifungal, and phytoregulatory properties for open-field tomato protection.

1. Tumanyan A.F., Thanh Deep H.T. Agrotechnics of tomato cultivation in the arid zone. Nauchno-agronomicheskiy zhurnal. 2010;(2(87)):40-43. (In Russ.)

2. Bairambekov Sh.B., Korneva O.G., Dubrovin N.K., Polyakova E.V. To engage more fully the phytosanitary potential of the irrigated agrocenoses of vegetable and melon crops and potato. Plant Protection and Quarantine. 2017:27-32. (In Russ.)

3. Levitin M.M. Microorganisms and global climate change. Agricultural Biology. 2015;(5):119-125. (In Russ.) https://doi.org/10.15389/agrobiology.2015.5.641rus

4. Bataeva Yu.V., Grigoryan L.N., Kurashov E.A., Krylova Yu.V. et al. Study of metabolites of Streptomyces carpaticus RCAM04697 for the creation of environmentally friendly plant protection products. Theoretical and Applied Ecology. 2021;(3):172-178. (In Russ.) https://doi.org/10.25750/1995-4301-2021-3-172-178

5. Ivanov A.L. Scientific agriculture of Russia: results and prospects. Zemledelie. 2014;(3):25-29. (In Russ.)

6. Shirokikh I.G., Lyskova I.V., Nazarova Ya.I., Gradoboeva T.P. et al. Local strains of actinobacteria protect peas (Pisum sativum L.) from harmful infections. Theoretical and Applied Ecology. 2022;(2):173-182. (In Russ.) https://doi.org/10.25750/1995-4301-2022-2-173-182

7. Grigoryan L.N., Bataeva Yu.V., Novichenko O.V., Shaheen M. et al. Study of the effect of suspension and extracts Streptomyces carpaticus RCAM04697 strain on safety and quality indicators of tomato. II International Conference “Sustainable Development: Agriculture, Veterinary Medicine and Ecology”. AIP Conference Proceedings. 2023;(3011):225-234. https://doi.org/10.1063/5.0162340

8. Chebotar V.K., Shcherbakov A.V., Shcherbakova E.N., Maslennikova S.N. et al. Biodiversity of endophytic bacteria as a promising biotechnological resource. Agricultural Biology. 2015;(50(5)):648-654. (In Russ.) https://doi.org/10.15389/agrobiology.2015.5.648rus

9. Mnif I., Ghribi D. Review lipopeptides biosurfactants: Mean classes and new insights for industrial, biomedical and environmental applications. Biopolymers. 2015;104(3):129-147. https://doi.org/10.1002/bip.22630

10. Olfa K.-F., Saoussen B.K., Mouna D., Amel K. et al. Improvement of antifungal metabolites production by Bacillus subtilis V 26 for biocontrol of tomato postharvest disease. Biological Control. 2016;95:73-82. https://doi.org/10.1016/j.biocontrol.2016.01.005

11. Grigoryan L.N., Bataeva Yu.V., Andreeva E.D., Zakar’yaeva D.Kh. et al. Study of the component structure of the metabolites of bacteria Nocardiopsis umidischolae in the search for eco-friendly plant protection agents. Russian Journal of General Chemistry. 2020;90(13):2531-2541. https://doi.org/10.1134/S1070363220130010

12. Shirokikh I.G., Shirokikh A.A., Ashikhmina T.Ya. Assessing the antagonistic potential and antibiotic resistance of actinomycetes isolated from two zheltozems of southeastern China. Pochvovedenie. 2018;51(7):859-867. (In Russ.) https://doi.org/10.1134/S0032180X18070122

13. Grigoryan L.N., Bataeva Yu.V. Ecological features and biotechnological possibilities of soil actinobacteria (review). Theoretical and Applied Ecology. 2023;(2):6-19. (In Russ.) https://doi.org/10.25750/1995-4301-2023-2-006-019

14. Bataeva Yu.V., Grigoryan L.N., Bogun A.G., Kislichkina A.A. et al. Biological Activity and Composition of Metabolites of Potential Agricultural Application from Streptomyces carpaticus K-11 RCAM04697 (SCPM-O-B-9993). Microbiology. 2023;92(3):459-467. https://doi.org/10.1134/S0026261723600155

15. Nazarova Ya.I., Shirokikh I.G., Bakulina A.V., Baranova E.N. et al. Identification of two strains of streptomycetes from the rhizosphere and in vitro study of their colonizing activity. Theoretical and Applied Ecology. 2019;(3):72-79. (In Russ.) https://doi.org/10.25750/1995-4301-2019-3-072-079

16. Čihák M., Kameník Z., Šmídová K., Bergman N. et al. Secondary metabolites produced during the germination of Streptomyces coelicolor. Frontiers in Microbiology. 2017;8:2495. https://doi.org/10.3389/fmicb.2017.02495

17. Wink J., Mohammadipanah F. Biology and biotechnology of Actinobacteria. Ed. Journal Hamedi. 2017:395-408. https://doi.org/10.1007/978-3-319-60339-1

18. Vurukonda S.S.K.P., Giovanardi D., Stefani E. Plant growth promoting and biocontrol activity of Streptomyces spp. as endophytes. International Journal of Molecular Sciences. 2018;19(4):952-961. https://doi.org/10.3390/ijms19040952

19. Tarkka M., Hampp R. Secondary metabolites of soil streptomycetes in biotic interactions. Secondary Metabolites in Soil Ecology. 2008:107-126.

20. Trenozhnikova L.P., Balgimbaeva A.S., Sultanbekova G.D., Galimbaeva R.Sh. Antifungal activity against pathogens of cereals and characterization of antibiotics of Streptomyces sp. strain K-541 isolated from extreme ecosystems in Kazakhstan. Agricultural Biology. 2018;53(1):96-102. (In Russ.) https://doi.org/10.15389/agrobiology.2018.1.96rus

21. Ceylan O., Okmen G., Ugur A. Isolation of soil Streptomyces as source antibiotics active against antibioticresistant bacteria. EurAsian Journal of BioSciences. 2008;2:73-82.

22. Bataeva Yu.V., Delegan Ya.A., Bogun A.G., Shishkina L.А. et al. Whole Genome Analysis and Assessment of the Metabolic Potential of Streptomyces carpaticus SCPM-OB-9993, a Promising Phytostimulant and Antiviral Agent. Biology. 2024;13(6):388. https://doi.org/10.3390/biology13060388

23. Cohen M.F., Mazzola M. Resident Bacteria, Nitric Oxide Emission and Particle Size Modulate the Effect of Brassica napus Seed Meal on Disease Incited by Rhizoctonia solani and Pythium spp. Plant and Soil. 2006;286(12):75-86. https://doi.org/10.1007/s11104-006-9027-1

24. Wellington B., Figueiredo J.E.F. Efficacy and Dose – Response Relationship in Biocontrol in Fusarium Disease in Maize by Streptomyces spp. European Journal of Plant Pathology. 2008;120(3):311-316 https://doi.org/10.1007/s10658-007-9220-y

25. Chater K.F., Biro S., Lee K.J., Palner T. et al. The Complex Extracellular Biology of Streptomyces. FEMS Microbiology Reviews. 2010;34:171-198. https://doi.org/10.1111/j.1574-6976.2009.00206.x

26. Sharma М. Actinomycetes: Source, Identification, and Their Applications. International Journal of Current Microbiology and Applied Sciences. 2014;3(2):801-832. https://doi.org/10.20546/ijcmas.2017.602.089

27. Ulloa-Ogaz A.L., Muñoz-Castellanos L.N., NevárezMoorillón G.V. Biocontrol of Phytopathogens: Antibiotic Production as Mechanism of Control. The Battle against Microbial Pathogens: Basic Science, Technological Advances and Educational Programs. 2015:305-309.

28. Li Y., Kong L., Shen J., Wang Q. et al. Characterization of the Positive SARP Family Regulator PieR for Improving Piericidin A1 Production in Streptomyces piomogeues var. hangzhouwanensis. Synthetic and Systems Biotechnology. 2019;4(1):16-24. https://doi.org/10.1016/j.synbio.2018.12.002

29. Williamson N.P., Brian E.M., Wellington H. Molecular Detection of Bacterial and Streptomycete Chitinases in the Environment. Antonie van Leeuwenhoek. 2000;78.3(4):315-321. https://doi.org/10.1023/a:1010225909148

30. Efimenko T.A., Malanicheva I.A., Vasil’eva B.F., Glukhova A.A. et al. Antibiotic Activity of Bacterial Endobionts of Basidiomycete Fruit Bodies. Microbiology. 2016;5:740-747. https://doi.org/10.1134/S0026261716060084

31. Sergeeva O.V., Dolzhenko T.V. Biological efficacy of aversectin C against sucking pests. Izvestiya Saint-Petersburg State Agrarian University. 2018;(2(51)):89-94. (In Russ.)

32. Patent 2695157 C1 (Russian Federation): IPC C12N1/20, A01N63/02, C12R1/465. Strain of Streptomyces carpaticus for protection against insect pests, fungal, viral diseases and stimulation of tomato growth. Grigoryan L.N., Bataeva Yu.V., Shlyakhov V.A., Dzerzhinskaya I.S., 2019. (In Russ.)

33. Gnutova R.V. Modern tendencies in taxonomy and nomenclature of viruses. Uspekhi sovremennoi biologii. 2011;(131(6)):563-577. (In Russ.)

34. Tolkach V.F., Gnutova R.V. Harmfulness of cucumber mosaic virus for vegetable and ornamental crops. Plant Protection and Quarantine. 2011;(7):24-26. (In Russ.)

35. Gnutova R.V. The current state of viruses studying in vegetable crops of the Far East. Izvestiya of Timiryazev Agricultural Academy. 2013;(5):321-340. (In Russ.)

36. Turaeva S.M., Kurbanova E.R., Mamarozikov U.B., Xidirova N.K. et al. Biological efficiency of the extract of Haplophyllum perforatum against Tuta absoluta and its influence on the physiological properties of tomato plants. Agricultural Biology. 2022;(57(1)):183-1192. (In Russ.) https://doi.org/10.15389/agrobiology.2022.1.183rus

37. Sheshegova T.K., Shchekleina L.M. Phytopathogenic biota in the conditions of climate warming (review). Theoretical and Applied Ecology. 2022:(2):6-13. https://doi.org/10.25750/1995-4301-2022-3-006-013

38. Schrey S.D., Tarkka M.T. Friends and Foes: Streptomycetes as Modulators of Plant Disease and Symbiosis. Antonie Van Leeuwenhoek. 2008;94(1):11-19. https://doi.org/10.1007/s10482-008-9241-3

39. Kruglov Yu.V., Lisina T.O. Bacillus megaterium 501 RIF introduced into the soil: factors affecting the rate of survival, sporulation and decomposition of the herbicide prometryn. Agricultural Biology. 2014;(5):107-111. https://doi.org/10.15389/agrobiology.2014.5.107rus

40. Shirokikh I.G., Lyskova I.V., Nazarova Ya.I., Gradoboeva T.P. et al. Local strains of actinobacteria protect peas (Pisum sativum L.) from harmful infections. Theoretical andApplied Ecology. 2022;(2):173-182. (In Russ.) https://doi.org/10.25750/1995-4301-2022-2-173-182

41. Grigoryan L.N., Bataeva Yu.V., Shlyakhov V.A., Magzanova D.K. et al. Phytotoxicity and insectoacaricidal activity of actinomycetes isolated from saline soils of arid territory. South of Russia: Ecology, Development. 2020;(15(2)):103-112. (In Russ.) https://doi.org/10.18470/1992-1098-2020-2-103-112

42. Gauze G.F., Preobrazhenskaya T.P., Sveshnikova M.A., Terekhova L.P. et al. Determinant of actinomycetes. Genera Streptomyces, Streptoverticilium, Chainia. Moscow, Russia: Nauka, 1983:248. (In Russ.)

43. Boikova I.V., Pavlushin V.A. The application of metabolites generated by actinomycetes against greenhouse whitefly, aphids, thrips and spider mite. Information bulletin EPRS IOBC. 2002;(33):102-113. (In Russ.)

44. Govorov D.N., Zhivykh A.V., Shabelnikova A.A., Nikulin A.N. et al. An overview of the phytosanitary status of agricultural crops in the Russian Federation in 2023 and a forecast of the development of harmful objects in 2024: a mongraph. Moscow, Russia: Plant Protection and Quarantine, 2023:1459. (In Russ.)

45. Alexandrov S.O., Shantasov A.M., Khudyakova E.A., Belyalov R.M. Agrochemical characteristics of soils in the Astrakhan region. Astrakhan, Russia: GTsAS Astrakhanskiy, 2020:68. (In Russ.)

46. Dospekhov B.A. Methodology of field experience (with the basics of statistical processing of research results): a textbook. 6th ed. Moscow, Russia: Al’yans, 2011:350. (In Russ.)

47. Soroka S.V., Blotskaya Zh.V., Vabishevich V.V. Viruses and viral diseases of agricultural crops. Nesvizh, Belarus: Nesvizhskaya ukrupnennaya tipografiya, 2009:39. (In Russ.)

48. Tsyplenkov A.E., Parshin V.G. Study of pathogenicity of cucumber mosaic virus isolates. Biological methods of plant protection from viral and bacterial diseases: proceedings. Leningrad, USSR: VIZR, 1988:49. (In Russ.)

49. Kiray Z., Klement Z., Shoymoshi F., Veresh Y. Methods of phytopathology. Moscow, USSR: Kolos, 1974:343. (In Russ.)

50. Zorina E.A., Fominykh T.S., Novikova I.I. Influence of strain Bacillus subtilis M-22, producer of biopesticide Gamair, on tomato mosaic virus infection development. Plant Protection News. 2016;(2(88)):50-55. (In Russ.)

51. State catalog of pesticides and agrochemicals approved for use on the territory of the Russian Federation. Moscow, Russia, 2023:368. (In Russ.)

52. Gibbs A., Harrison B. Fundamentals of plant virology. Moscow, USSR: Mir, 1978:430. (In Russ.)

53. Pavlovskaya N.E., Solokhina I.Yu., Lushnikov A.V. The creation of test systems for the identification of phytopathogens a solid-phase enzyme immunoassay. Biologiya v selskom khozyaystve. 2015;(4(9)):7-11. (In Russ.)

54. Pavlovskaya N.E., Gneusheva I.A., Solokhina I.Yu. Practical recommendations on the use of methods of pre-visual diagnosis of viral diseases of vegetable products. Moscow, Russia, 2017:40. (In Russ.)

55. Dolzhenko V.I., Laptiev A.B., Burkova L.A., Dolzhenko O.V. et al. Guidelines for registration tests of pesticides in terms of biological efficacy. Moscow, Russia, 2018:61. (In Russ.)

56. Voronina E.G., Gindina G.M., Novikova I.I., Mukamolova T.Y. Method of testing mycoafidine T in laboratory, field and industrial conditions. Leningrad, USSR: VIZR, 1988:9-13. (In Russ.)

57. Henderson C.F., Tilton E.W. Tests with acaricides against the brow wheat mite. Journal of Economic Entomology. 1955:48.

58. Dolzhenko V.I., Sukhoruchenko G.I., Burkova L.A., Laptev A.B. et al. Guidelines for registration tests of insecticides, acaricides, molluscicides and rodenticides in agriculture. Moscow, Russia: Rosinformagrotech, 2022:508. (In Russ.)

59. Urbach V.Y. Statistical analysis in biological and medical research. Moscow, USSR: Meditsina, 1975:297. (In Russ.)

60. Marzieh E.-Z., Roohallah S.R., Mika T.Т. Actinobacteria as effective biocontrol agents against plant pathogens, an overview on their role in eliciting plant defense. Microorganisms. 2022;10(9):1739. https://doi.org/10.3390/microorganisms10091739

61. Gaber A.A., Saleh M.M., Ahmed A. Induction of plant resistance against Tobacco Mosaic Virus using the biocontrol agent Streptomyces cellulosae isolate Actino 48. Agronomy. 2020;10:1620. https://doi.org/10.3390/agronomy10111620

62. Ara I., Bukhari N.A., Aref N.M., Shinwari M.M.A. et al. Antiviral activities of streptomycetes against tobacco mosaic virus (TMV) in Datura plant: Evaluation of different organic compounds in their metabolites. African Journal of Biotechnology. 2012;11:2130-2138. https://doi.org/10.5897/AJB11.3388

63. Chen J., Liu H., Xia Z., Zhao X. et al. Purification and structural analysis of the effective anti-TMV compound ε-poly-L-lysine produced by Streptomyces ahygroscopicus. Molecules. 2019;24:1156. https://doi.org/10.3390/molecules24061156

64. Li Y., Guo Q., Li Y., Sun Y., Xue Q., Lai H. Streptomyces pactum Act12 controls tomato yellow leaf curl virus disease and alters rhizosphere microbial communities. Biology and Fertility of Soils. 2019;55:149-169. https://doi.org/10.1007/s00374-019-01339-w

65. Abdel-Moneim M.G. Induction of systemic acquired resistance in cucumber plant against Cucumber Mosaic Cucumovirus by local Streptomyces strains. Plant Pathology Journal. 2006;5:343-349. https://doi.org/10.3923/ppj.2006.343.349

66. Shafie R.M., Hamed A.H., El-Sharkawy H.H.A. Inducing systemic resistance against Сucumber Mosaic Cucumovirus using Streptomyces spp. Egyptian Journal of Phytopathology. 2016;44:127-142. https://doi.org/10.21608/ejp.2016.91931

67. Cushnie T.P., Cushnie B., Lamb A.J. Alkaloids: an overview of their antibacterial, antibiotic-enhancing and antivirulence activities. International Journal of Antimicrobial Agents. 2014;44(5):377-386. https://doi.org/10.1016/j.ijantimicag.2014.06.001

68. Chowański S., Adamski Z., Marciniak P., Rosiński G. et al. A Review of bioinsecticidal activity of solanaceae alkaloids. Toxins. 2016;8:60. https://doi.org/10.3390/toxins8030060

69. Benslama O. Bioinsecticidal activity of actinomycete secondary metabolites against the acetylcholinesterase of the legume’s insect pest Acyrthosiphon pisum: a computational study. Journal of Genetic Engineering and Biotechnology. 2022;20:158. https://doi.org/10.1186/s43141-022-00442-0

70. Raveh A., Delekta P.C., Dobry C.J., Peng W. et al. Discovery of potent broad spectrum antivirals derived from marine actinobacteria. PLoS One. 2013;5.8(12):82318. https://doi.org/10.1371/journal.pone.0082318