Biodiversity of Actinobacteria from Kula Geopark in Türkiye

Abstract

Investigating the microbial diversity of Actinobacteria inhabiting the soils of the Kula-Salihli Geopark and identifying species at the genus level using 16S rRNA gene sequences are the primary goals of this work. In the literature review of this geopark located within the borders of Manisa province, no study on actinobacterial biodiversity was found. In this study, 10 different selective isolation media were used to investigate the biodiversity of Actinobacteria in the Geopark. A total of 469 Actinobacteria strains were isolated using the dilution-plate method. From these 469 strains, 34 strains were selected based on their colony morphology and pigmentation characteristics. The isolates performed phylogenetic analysis based on sequencing of the 16S ribosomal RNA gene region. The isolates were found to belong to nine different genera, including Actinomadura, Amycolatopsis, Kribbella, Micromonospora, Nocardia, Nonomuraea, Pseudonocardia, Saccharothrix and Streptomyces, according to the results of phylogenetic analysis. Five isolates have been identified as novel species as a consequence of our current study.

Keywords

• Actinobacteria
• Geopark soil
• 16S rRNA gene
• Biodiversity

References

1. Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C, Klenk HP, Meier-Kolthoff JP, Clément C, Ouhdouch Y, van Wezel GP. 2016. Taxonomy, physiology, and natural products of Actinobacteria. Microbiol Mol Biol Rev, 80(1): 1-43.
2. Buchholz-Cleven BEE, Rattunde B, Straub KL. 1997. Screening for genetic diversity of isolates of anaerobic Fe(II)-oxidizing bacteria using DGGE and whole-cell hybridization. Syst Appl Microbiol, 20(2): 301-309.
3. Chun J, Goodfellow MA. 1995. Phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol, 45(2): 240-245.
4. Faddetta T, Polito G, Abbate L, Alibrandi P, Zerbo M, Caldiero C, Reina C, Puccio G, Vaccaro E, Abenavoli MR, Cavalieri V, Mercati F, Piccionello AP, Gallo G. 2023. Bioactive metabolite survey of Actinobacteria showing plant growth promoting traits to develop novel biofertilizers. Metabolites, 13(3): 374.
5. Felsenstein J. 1985. Phylogenies and the comparative method. Am Nat, 125(1): 1-15.
6. Hayakawa M, Nonomura H. 1987. Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. J Ferment Technol, 65(5): 501-509.
7. Hickey RJ, Tresner HD. 1952. A cobalt-containing medium for sporulation of Streptomyces species. J Bacteriol, 64(6): 891.
8. Hui MLY, Tan LTH, Letchumanan V, He YW, Fang CM, Chan KG, Law JWF, Lee LH. 2021. The extremophilic actinobacteria: From microbes to medicine. Antibiotics, 10(6): 682.

9. Jiang Y, Li Q, Chen X. 2016. Isolation and cultivation methods of actinobactera. In: Dhanasekaran D, editor. Actinobacteria–basics and biotechnological application, IntechOpen, London, UK, pp: 39-57.
10. Jukes TH, Cantor CR. 1969. Evolution of protein molecules. Mammal Prot Metabol, 3(24): 21-132.
11. Kelly KL. 1964. Color-name charts illustrated with centroid colors. Inter-Society Color Council-National Bureau of Standards, Supplement to NBS Circ. 533, Standard sample No. 2106, Chicago, US.
12. Kuester E, Williams ST. 1964. Selection of media for isolation of streptomycetes. Nature, 202: 928-929.
13. Kumar A, Gupta R, Shrivastava B, Khasa YP, Kuhad RC. 2012. Xylanase production from an alkalophilic actinomycete isolate Streptomyces sp. RCK-2010, its characterization and application in saccharification of second generation biomass. J Mol Catal B Enzym, 74(3-4): 170-177.
14. Lane DJ. 1991. 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M. Nucleic acid techniques in bacterial systematics, Wiley, New York, US, pp: 115-175.
15. Mawang CI, Azman AS, Fuad ASM, Ahamad M. 2021. Actinobacteria: An eco-friendly and promising technology for the bioaugmentation of contaminants. Biotechnol Rep, 32: e00679.
16. Meena B, Anburajan L, Vinithkumar NV, Kirubagaran R, Dharani G. 2019. Biodiversity and antibacterial potential of cultivable halophilic actinobacteria from the deep sea sediments of active volcanic Barren Island. Microb Pathog, 132: 129-136.
17. Miao V, Davies J. 2010. Actinobacteria: the good, the bad, and the ugly. Antonie Van Leeuwenhoek, 98: 143-150.
18. Penkhrue W, Sujarit K, Kudo T, Ohkuma M, Masaki K, Aizawa T, Pathom-Aree W, Khanongnuch C, Lumyong S. 2018. Amycolatopsis oliviviridis sp. nov., a novel polylactic acid-bioplastic-degrading actinomycete isolated from paddy soil. Int J Syst Evol Microbiol, 68(5): 1448-1454.
19. Reasoner DJ, Geldreich EE. 1985. A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol, 49(1): 1-7.
20. Riquelme C, Rigal F, Hathaway JJ, Northup DE, Spilde MN, Borges PAV, Gabriel R, Amorim IR, Dapkevicius MDLNE. 2015. Cave microbial community composition in oceanic islands: disentangling the effect of different colored mats in diversity patterns of Azorean lava caves. FEMS Microbiol Ecol, 91(12): fiv141.
21. Sadoway T, Rule D, Watson K, Moote P, Soliman LC, Azad N, Donkor K, Cheeptham N, Horne D. 2013. Cure from the cave: volcanic cave actinomycetes and their potential in drug discovery. Int J Speleol, 42(1): 5.
22. Saini A, Aggarwal NK, Sharma A, Yadav A. 2015. Actinomycetes: a source of lignocellulolytic enzymes. Enzyme Res, 2015: 279381. https://doi.org/10.1155/2015/279381.
23. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for. Mol Biol Evol, 4(4): 406-425.
24. Sanglier, JJ, Whitehead, D, Saddler, GS, Ferguson, EV and Goodfellow, M. 1992. Pyrolysis mass spectrometry as a method for the classification, identification and selection of actinomycetes. Gene, 115(1-2): 235-242.
25. Saricaoglu S, Saygin H, Topkara AR, Gencbay T, Guven K, Cetin D, Sahin N, Isik K. 2020. Nonomuraea basaltis sp. nov., a siderophore-producing actinobacteria isolated from surface soil of basaltic parent material. Arch Microbiol, 202: 1535-1543.
26. Shirling EB, Gottlieb D. 1966. Methods for characterization of Streptomyces species. Int J Syst Bacteriol, 16(3): 313-340.
27. Songsumanus A, Kuncharoen N, Kudo T, Yuki M, Ohkuma M, Igarashi Y, Tanasupawat S. 2021. Actinomadura decatromicini sp. nov., isolated from mountain soil in Thailand. J Antibiot, 74(1): 51-58.
28. Sottorff I, Wiese J, Imhoff JF. 2019. High diversity and novelty of Actinobacteria isolated from the coastal zone of the geographically remote young volcanic Easter Island, Chile. Int Microbiol, 22(3): 377-390.
29. Tamura K, Stecher G, Kumar S. 2021. MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol, 38(7): 3022-3027.
30. Tan GYA, Ward AC, Goodfellow M. 2006. Exploration of Amycolatopsis diversity in soil using genus-specific primers and novel selective media. Syst Appl Microbiol. 29(7): 557-569.
31. Tiwari K, Gupta, RK. 2012. Rare actinomycetes: a potential storehouse for novel antibiotics. Crit Rev Biotechnol, 32(2): 108-132.
32. UNESCO. 2024. List of UNESCO Global Geoparks and Regional Networks. URL: https://www.unesco.org/en/iggp/geoparks (accessed date: March 1, 2024).
33. Weisburg WG, Barns SM, Pelletier DA. 1991. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol, 173(2): 697-703.
34. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J. 2017. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol, 67(5): 1613-1617.