Taxonomic characterization and secondary metabolite production of newly isolated Streptomyces sp. MC12

Year 2024, Volume: 11 Issue: 4, 740 - 750

Mustafa Oskay

https://doi.org/10.21448/ijsm.1481362

Abstract

An actinobacterium newly isolated from soil during a screening study was identified as Streptomyces sp. MC12 (GenBank accession number: PP757795) based on 16S rRNA analysis. For secondary metabolite production, fermentation was carried out in ISP 2 broth at 30°C, pH 7.3, for seven days under shaking conditions at 180 rpm. As a result of fermentation studies, the antagonistic effect of the crude extract, obtained through ethyl acetate extraction, against various microorganisms was determined. The MIC values of the extract against Staphylococcus aureus and Escherichia coli were 101.3 µg/mL and 153.6 µg/mL, respectively. It was also found to exhibit strong antifungal activity against Penicillium spp. Streptomyces sp. MC12, which displays both antifungal and antibacterial properties, is considered a potential secondary metabolite producer for future studies, particularly in pharmacology and the biocontrol of fungal pathogens.

Keywords

Fermentation, Identification, Secondary metabolite, Streptomyces sp., 16S rRNA sequencing

Project Number

Project number: 2015-075

References

• Al Farraj, D.A., Varghese, R., Vágvölgyi, C., Elshikh, M.S., Alokda, A.M., & Mahmoud, A.H. (2020). Antibiotics production in optimized culture condition using low cost substrates from Streptomyces sp. AS4 isolated from mangrove soil sediment. Journal of King Saud University-Science, 32(2), 1528-1535. https://doi.org/10.1016/j.jksus.2019.12.008
• Anderson, A.S., & Wellington, E.M. (2001). The taxonomy of Streptomyces and related genera. International Journal of Systematic and Evolutionary Microbiology, 51(3), 797-814. https://doi.org/10.1099/00207713-51-3-797
• Almuhayawi, M.S., Mohamed, M.S., Abdel-Mawgoud, M., Selim, S., Al Jaouni, S.K., & AbdElgawad, H. (2021). Bioactive potential of several actinobacteria isolated from microbiologically barely explored desert habitat, Saudi Arabia. Biology, 10(3), 235. https://doi.org/10.3390/biology10030235
• Ateş, H., & Ay, H. (2023). Bioactivity Features of Novel Actinobacteria Isolated from Lichen and Orchid Plant. Adıyaman University Journal of Science, 13(1&2), 43 58. https://doi.org/10.37094/adyujsci.1221660
• Ay, H. (2020). Phylogeny of plant growth-promoting actinobacteria isolated from legume nodules in Turkey. Yuzuncu Yil University Journal of Agricultural Sciences, 30(3), 611-619. https://doi.org/10.29133/yyutbd.705227
• Balagurunathan, R., Radhakrishnan, M., Shanmugasundaram, T., Gopikrishnan, V., & Jerrine, J. (2020). Sample collection, isolation, and diversity of Actinobacteria. Protocols in Actinobacterial Research, 1-24. Springer Protocols Handbooks. Springer, New York. https://doi.org/10.1007/978-1-0716-0728-2_1
• Barka, E.A., Vatsa, P., Sanchez, L., Gaveau-Vaillant, N., Jacquard, C., Klenk, H.P., & van Wezel, G.P. (2016). Taxonomy, physiology, and natural products of Actinobacteria. Microbiology and Molecular Biology Reviews, 80(1), 1 43. https://doi.org/10.1128/mmbr.00019-15
• Bayraktar, B., & Işık, K. (2024) Biodiversity of Actinobacteria from Kula Geopark in Türkiye. Black Sea Journal of Engineering and Science, 7(3), 31 32. https://doi.org/10.34248/bsengineering.1459935
• Chakraborty, B., Kumar, R.S., Almansour, A.I., Gunasekaran, P., & Nayaka, S. (2022). Bioprospection and secondary metabolites profiling of marine Streptomyces levis strain KS46. Saudi Journal of Biological Sciences, 29, 667 679. https://doi.org/10.1016/j.sjbs.2021.11.055
• Chinnathambi, A., Salmen, S.H., Al-Garadi, M.A., Wainwright, M., & Alharbi, S.A. (2023). Marine Actinomycetes: An Endless Source of Potentially Therapeutic Novel Secondary Metabolites and Other Bioactive Compounds. Journal of King Saud University-Science, 35, 102931. https://doi.org/10.1016/j.jksus.2023.102931
• Clinical and Laboratory Standards Institute (CLSI), (2003). Methods for Dilution Antimicrobial Susceptibility Test for Bacteria that Grow Aerobically; Approved Standard M7-A6, 6th edition. National Committee for Clinical Laboratory Standards, Wayne, Philadelphia.
• Clinical and Laboratory Standards Institute (CLSI), (2006). Performance Standards for Antimicrobial Susceptibility Testing, 16th Informational Supplement M100-S16. National Committee for Clinical Laboratory Standards, Wayne, Philadelphia.
• Cuozzo, S., de LeBlanc, A.D.M., LeBlanc, J.G., Hoffmann, N., & Tortella, G.R. (2023). Streptomyces genus as a source of probiotics and its potential for its use in health. Microbiological Research, 266, 127248. https://doi.org/10.1016/j.micres.2022.127248
• Demain, A.L. (1998). Microbial natural products: alive and well in 1998. Nature Biotechnology, 16(1), 3-4. https://doi.org/10.1038/nbt0198-3
• Djebaili, R., Pellegrini, M., Ercole, C., Farda, B., Kitouni, M., & Del Gallo, M. (2021). Biocontrol of soil-borne pathogens of Solanum lycopersicum L. and Daucus carota L. by plant growth-promoting actinomycetes: In vitro and in planta antagonistic activity. Pathogens, 10(10), 1305. https://doi.org/10.3390/pathogens10101305
• Donald, L., Pipite, A., Subramani, R., Owen, J., Keyzers, R.A., & Taufa, T. (2022). Streptomyces: Still the biggest producer of new natural secondary metabolites, a current perspective. Microbiology Research, 13(3), 418 465. https://doi.org/10.3390/microbiolres13030031
• Durham, S. (2005). Detectives search for antimicrobial-resistant organisms. Agricultural Research, 53(3), 18-20.
• Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39(4), 783-791. https://doi.org/10.2307/2408678
• Gauba, A., & Rahman, K.M. (2023). Evaluation of antibiotic resistance mechanisms in Gram-negative bacteria. Antibiotics, 12(11), 1590. https://doi.org/10.3390/antibiotics12111590
• Hazarika, S.N., & Thakur, D. (2020). Actinobacteria. In Beneficial Microbes in Agro-Ecology (pp. 443-476). Academic Press. https://doi.org/10.1016/B978-0-12-823414-3.00021-6
• Hui, M.L.Y., Tan, L.T.H., Letchumanan, V., He, Y.W., Fang, C.M., Chan, K.G., Law, J.W.F., & Lee, L.H. (2021). The extremophilic actinobacteria: from microbes to medicine. Antibiotics, 10(6), 682. https://doi.org/10.3390/antibiotics10060682
• Jose, P.A., Maharshi, A., & Jha, B. (2021). Actinobacteria in natural products research: Progress and prospects. Microbiological Research, 246, 126708. https://doi.org/10.1016/j.micres.2021.126708
• Jukes, T.H., & Cantor, C.R. (1969). Evolution of protein molecules. Mammalian Protein Metabolism, 3(24), 21-132. https://doi.org/10.1016/B978-1-4832-3211-9.50009-7
• Karagoz, K., Dadasoglu, F., Alaylar, B., & Kotan, R. (2024). Evaluation of molecular typing methods for some scab-causing Streptomyces strains from Turkey. World Journal of Microbiology and Biotechnology, 40(4), 122. https://doi.org/10.1007/s11274-024-03914-2
• Kum, E., & İnce, E. (2021). Genome-guided investigation of secondary metabolites produced by a potential new strain Streptomyces BA2 isolated from an endemic plant rhizosphere in Turkey. Archives of Microbiology, 203(5), 2431-2438. https://doi.org/10.1007/s00203-021-02210-z
• Lane, D.J. (1991). 16S/23S rRNA sequencing. Nucleic acid techniques in bacterial systematics. Chichester: Wiley, 125-175.
• Marzoug, A.N., Ayari, A., Khaldi, F., Guehria, I., & Gheid, A. (2023). Effect of Peganum harmala L. extract supplemented ISP2 medium on growth and production of secondary metabolites of Streptomyces ayarius S115. Electronic Journal of Biotechnology, 64, 34-41. https://doi.org/10.1016/j.ejbt.2022.12.006
• Mazumdar, R., Dutta, P.P., Saikia, J., Borah, J.C., & Thakur, D. (2023). Streptomyces sp. strain PBR11, a forest-derived soil actinomycetia with antimicrobial potential. Microbiology Spectrum, 11(2), e03489-22. https://doi.org/10.1128/spectrum.03489-22
• Meena, B., Anburajan, L., Johnthini, M.A., Vinithkumar, N.V., & Dharani, G. (2023). Exploration of mangrove-associated actinobacteria from South Andaman Islands, India. Systems Microbiology and Biomanufacturing, 3(4),702 718. https://doi.org/10.1007/s43393-022-00134-3
• Mehling, A., Wehmeier, U.F., & Piepersberg, W. (1995). Nucleotide sequences of streptomycete 16S ribosomal DNA: towards a specific identification system for streptomycetes using PCR. Microbiology, 141, 2139 2147. https://doi.org/10.1099/13500872-141-9-2139
• Mirsonbol, S.Z., Issazadeh, K., Zarrabi, S., & Mirpour, M. (2023). Evaluation of antimicrobial activity of Streptomyces pactum isolated from paddy soils and identification of bioactive volatile compounds by GC-MS analysis. World Journal of Microbiology and Biotechnology, 39(2), 63. https://doi.org/10.1007/s11274-022-03508-w
• Nazari, M.T., Schommer, V.A., Braun, J.C.A., dos Santos, L.F., Lopes, S.T., Simon, V., Machado, B.S., Ferrari, V., Maria Colla, L., & Piccin, J.S. (2023). Using Streptomyces spp. as plant growth promoters and biocontrol agents. Rhizosphere, 100741. https://doi.org/10.1016/j.rhisph.2023.100741
• Oskay, M. (2009). Antifungal and antibacterial compounds from Streptomyces strains. African Journal of Biotechnology, 8(13), 3007-3017.
• Oskay, M. (2011). Effects of some environmental conditions on biomass and antimicrobial metabolite production by Streptomyces sp., KGG32. International Journal of Agriculture and Biology, 13(3), 317-324.
• Perez, C., Pauli, M., & Bazerque, P. (1990). An antibiotic assay by the agar well diffusion method. Acta Biologiae et Medicinae Experimentalis, 15, 113-115.
• Peris-Vicente, J., Peris-García, E., Albiol-Chiva, J., Durgbanshi, A., Ochoa-Aranda, E., Carda-Broch, S., Bose, D., & Esteve-Romero, J. (2022). Liquid chromatography, a valuable tool in the determination of antibiotics in biological, food and environmental samples. Microchemical Journal, 177, 107309. https://doi.org/10.1016/j.microc.2022.107309
• Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology Evolution, 4, 406 425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
• Salehghamari, E., Moradi, M., Sardabi, M., Etesami, S.A., Hassani, G. H., Hosseini, M., & Amoozegar, M.A. (2023). Diversity of actinomycete and their metabolites isolated from Howz Soltan Lake, Iran. Archives of Microbiology, 205(1), 24. https://doi.org/10.1007/s00203-022-03364-0
• Salwan, R., & Sharma, V. (2020). Molecular and biotechnological aspects of secondary metabolites in actinobacteria. Microbiological Research, 231, 126374. https://doi.org/10.1016/j.micres.2019.126374
• Sapkota, A., Thapa, A., Budhathoki, A., Sainju, M., Shrestha, P., & Aryal, S. (2020). Isolation, characterization, and screening of antimicrobial‐producing Actinomycetes from soil samples. International Journal of Microbiology, 2020(1), 2716584. https://doi.org/10.1155/2020/2716584
• Seçkin, H., Özdemir, K., Önalan, Ş., Ertaş, M., & Öğün, E. (2023). Aras Nehrinin Belirli Noktalarından Alınan Sediment Örneklerinden Streptomyces Bakterilerinin İzolasyonu Teşhisi ve Moleküler Karakterizasyonu. Journal of Anatolian Environmental and Animal Sciences, 8(1), 132-139. https://doi.org/10.35229/jaes.1228752
• Selim, M.S.M., Abdelhamid, S.A., & Mohamed, S.S. (2021). Secondary metabolites and biodiversity of actinomycetes. Journal of Genetic Engineering and Biotechnology, 19(1), 72. https://doi.org/10.1186/s43141-021-00156-9
• Sharma, P., & Thakur, D. (2020). Antimicrobial biosynthetic potential and diversity of culturable soil actinobacteria from forest ecosystems of Northeast India. Scientific Reports, 10(1), 4104. https://doi.org/10.1038/s41598-020-60968-6
• Shirling, E.T., & Gottlieb, D. (1966). Methods for characterization of Streptomyces species. International Journal of Systematic and Evolutionary Microbiology, 16(3), 313-340.
• Talpur, M.K.A., Qazi, M.A., Phulpoto, A.H., Maitlo, M.A., Phulpoto, I.A., Syed, F.H., & Kanhar, N.A. (2020). Bioprospecting actinobacterial diversity antagonistic to multidrug-resistant bacteria from untapped soil resources of Kotdiji, Pakistan. Biologia, 75(1), 129-138. https://doi.org/10.2478/s11756-019-00315-x
• Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA11: Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution, 38(7), 3022 3027. https://doi.org/10.1093/molbev/msab120
• Topkara, A.R., & Işık, K. (2023). Biodiversity of Actinobacteria Isolated from Marmara and Avşa Islands in Türkiye. Black Sea Journal of Engineering and Science, 6(4), 502-521. https://doi.org/10.34248/bsengineering.1355194
• Tüfekci, E.F., Uzun, Ü., Ertunga, N.S., Biber, A., Hıdıroğlu, İ.A., Tekkılıç, İ., Altay, B., & Kılıç, A.O. (2023). Investigation of antimicrobial activities and 16S rRNA sequences of Actinomycetes isolated from Karst Caves in the Eastern Black Sea Region of Türkiye. Kahramanmaraş Sütçü İmam Üniversitesi Tarım ve Doğa Dergisi, 26(6), 1277-1290. https://doi.org/10.18016/ksutarimdoga.vi.1226184
• Wassenaar, T.M. (2005). Use of antimicrobial agents in veterinary medicine and implications for human health. Critical Reviews in Microbiology, 31(3), 155 169. https://doi.org/10.1080/10408410591005110
• Watve, M.G., Tickoo, R., Jog, M.M., & Bhole, B.D. (2001). How many antibiotics are produced by the genus Streptomyces? Archives of Microbiology, 176, 386 390. https://doi.org/10.1007/s002030100345
• Zhu, H., Hu, L., Rozhkova, T., Wang, X., & Li, C. (2023). Spectrophotometric analysis of bioactive metabolites and fermentation optimisation of Streptomyces sp. HU2014 with antifungal potential against Rhizoctonia solani. Biotechnology and Biotechnological Equipment, 37(1), 231-242. https://doi.org/10.1080/13102818.2023.2178822