Biodiversity of Actinobacteria Isolated from Marmara and Avşa Islands in Türkiye

Öz

The main purpose of this study is to investigate the microbial diversity of Actinobacteria, living in soils in the “Marmara” and “Avşa” Islands and to identify species at genus level based on 16S rRNA gene sequences. These islands are located in the southwest of the Sea of Marmara and in the literature review, no Actinobacteria biodiversity studies related to Marmara and Avşa Islands were found. Such unexplored ecological habitats are potentially rich source for discovery sources of novel species and bioactive molecule. Actinobacteria play an important role in many natural phenomena such as nitrogen fixation, roles of these prokaryotic microorganisms. In this article, we focused on the presence and the diversity of Actinobacteria on the Islands by examining multiple sampling sites and using different selective isolation media. A total of 400 culturable Actinobacteria were isolated using ten different isolation media by dilution-plating method. Among the 400 isolates, 112 isolates were selected according to their morphology in different culture media. The isolates were characterized on the basis of 16S ribosomal RNA gene sequencing and phylogenetic analysis. The results showed a high level of actinobacterial diversity with 16 different genera. These genera obtained as a result of phylogenetic analyzes are Streptomyces, Nonomuraea, Nocardia, Actinomadura, Micromonospora, Kribbella, Mycolicibacterium, Microbispora, Saccharopolyspora, Jiangella, Rhodococcus, Actinopolymorpha, Geodermatophilus, Dactylosporangium, Pseudonocardia and Nocardioides. Many isolates are identified as new species by our current research. Findings from this study showed that the soil of Marmara and Avşa Islands can be a good source of isolation for Actinobacteria.

Anahtar Kelimeler

• Actinobacteria
• Isolation
• 16S rRNA gene
• Island soil
• Biodiversity

Kaynakça

1. Altschul SF, Gish W, Miller W. 1990. Basic local alignment search tool. J Mol Biol, 215: 403-410.
2. Amin A, Ahmed I, Khalid N, Osman G, Khan IU, Xiao M, Li WJ. 2017. Streptomyces caldifontis sp. nov., isolated from a hot water spring of Tatta Pani, Kotli, Pakistan. Antonie van Leeuwenhoek, 110(1): 77-86.
3. Barabote RD, Xie G, Leu DH, Normand P, Necsulea A, Daubin V, Me´digue C, Adney WS, Xu XC, Lapidus A, Parales RE, Detter C, Pujic P, Bruce D, Lavire C, Challacombe JF, Brettin TS, Berry AM. 2009. Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations. Genome Res, 19: 1033-1043.
4. 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.
5. Chaouch FC, Bouras N, Mokrane S, Zitouni A, Schumann P, Spröer C, Sabaou N, Klenk HP. 2016. Streptosporangium becharense sp. nov., an actinobacterium isolated from desert soil. International Journal of Systematic and Evolutionary Microbiology, 64(7): 2484-2490.
6. Chun J, Goodfellow MA. 1995. Phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol, 45(2): 240–245.
7. Corretto E, Antonielli L, Sessitsch A, Compant S, Gorfer M, Kuffner M, Brader G. 2016. Agromyces aureus sp. nov., isolated from the rhizosphere of Salix caprea L. grown in a heavy-metal-contaminated soil. Int J Syst Evol Microbiol, 66(9): 3749-3754.
8. Deng S, Chang X, Zhang Y, Ren L, Jiang F, Qu Z, Peng F. 2015. Nocardioides antarcticus sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol, 65(8): 2615-2621.

9. El-Tarabily KA, Hardy GESJ, Sivasithamparam K, Kurtböke ID. 1996. Microbiological differences between limed and unlimed soils and their relationship with cavity spot disease of carrots (Daucus carota L.) caused by Pythium coloratum in Western Australia. Plant and Soil, 183(2): 279-290.
10. El-Tarabily KA, Sivasithamparam K. 2006. Non-streptomycete actinomycetes as biocontrol agents of soil-borne fungal plant pathogens and as plant growth promoters. Soil Biology and Biochemistry, 38(7): 1505-1520.
11. Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17(6): 368-376.
12. Felsenstein J. 1985. Confidence limits on phylogeny: an approach using the bootstrap. Evolution, 39: 783-791.
13. Fitch WM. 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Biol, 20(4): 406-416.
14. Goodfellow M, Williams ST. 1983. Ecology of actinomycetes. Annu Rev Microbiol, 37: 189-216.
15. Groth I, Vettermann R, Schuetze B, Schumann P, Sáiz-Jiménez C. 1999. Actinomycetes in karstic caves of northern Spain (Altamira and Tito Bustillo). Journal of Microbiological Methods, 36(1-2): 115-122.
16. Hasegawa S, Meguro A, Shimizu M, Nishimura T, Kunoh H. 2006. Endophytic Actinomycetes and their interactions with host plants. Actinomycetologica, 20(2): 72-81.
17. Huang X, Zhou S, Huang D, Chen J, Zhu W. 2016. Streptomyces spongiicola sp. nov., an Actinomycete derived from marine sponge. Int J Syst Evol Microbiol, 66(2): 738-743.
18. Jukes TH, Cantor CR. 1969. Evolution of protein molecules. In: Munro HN, editor. Mammalian Protein Metabolism., Academic Press, New York, USA, pp: 21-132.
19. Kämpfer P, Glaeser SP, Busse HJ, Abdelmohsen UR, Ahmed S, Hentschel U. 2015. Actinokineospora spheciospongiae sp. nov., isolated from the marine sponge Spheciospongia vagabunda. Int J Syst Evol Microbiol, 65(3): 879-884.
20. 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.
21. Kim M, Oh HS, Park SC, Chun J. 2014. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64: 346–351.
22. Koçak FÖ. 2019. "Identification of Streptomyces strains isolated from Humulus lupulus rhizosphere and determination of plant growth promotion potential of selected strains," Turkish Journal of Biology, 43(6):5.
23. Kurane R, Suzuki T, Fukuoka S. 1984. Purification and some properties of a phthalate ester hydrolyzing enzyme from Nocardia erythropolis. Applied Microbiology and Biotechnology, 20(6): 378-383.
24. Kurtboke I. 2000. Australian actinomycetes: An unexhausted source for biotechnological applications. Actinomycetologica, 14(2): 43-53.
25. Kurtböke DI, Neller RJ, Bellgard SE. 2007. Mesophilic actinomycetes in the natural and reconstructed Antonie van Leeuwenhoek, 77(3-4): 399-405.
26. Küster E. 1968. Taxonomy of soil Actinomycetes and Related organisms. In: Ecology of soil bacteria, Liverpool University Press, Liverpool, pp: 322-336.
27. Küster E, Williams ST. 1964. Selection of media for isolation of streptomycetes. Nature, 202: 928-929.
28. Lazzarini A, Cavaletti L, Toppo G, Marinelli F. 2000. Rare genera of actinomycetes as potential producers of new antibiotics. Antonie van Leeuwenhoek, 78(3-4): 399-405.
29. Lane DJ. 1991. 16S/23S rRNA sequencing. In Stackebrandt, E, Goodfellow M. Nucleic acid techniques in bacterial systematics, Wiley, New York, pp: 115-175.
30. Lim CP, Hoon KC, Cheah YK. 2017. Actinobacteria from Greenwich Island and Dee Island: Isolation, diversity and distribution. Life Sciences, Medicine and Biomedicine, 1-1.
31. Mincer TJ, Jensen PR, Kauffman CA, Fenical W. 2002. Widespread and persistent populations of a majör new marine actinomycete taxon in ocean sediments. Appl Environ Microbiol, 68: 5005-5011.
32. Montero-Calasanz MDC, Hofner B, Göker M, Rohde M, Spröer C, Hezbri K, Klenk H. P. 2014. Geodermatophilus poikilotrophi sp. nov., amultitolerant actinomycete isolated from dolomitic marble. BioMed Research International, 1-11.
33. Phongsopitanun W, Kudo T, Mori M, Shiomi K, Pittayakhajonwut P, Suwanborirux K, Tanasupawat S. 2015. Micromonospora fluostatini sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol, 65(12): 4417-4423.
34. Phongsopitanuna W, Sripreechasakb P, Sangvichienc E, Tanasupawat S. 2021. Diversity, antimicrobial activity, and susceptibility of culturable soil actinobacteria isolated from Sichang Island. ScienceAsia, 47: 673-681.
35. Piao CY, Zheng WW, Li Y, Liu CX, Jin LY, Song W, Yan K, Wang XJ, Xiang WS. 2017. Two new species ofthe genus Streptomyces: Streptomyces camponoti sp. nov. and Streptomyces cuticulae sp. nov., isolated from the cuticle of Camponotus japonicus Mayr. Arch Microbiol, 199: 963-970.
36. Prescott LM, Harley JP, Klein DA. 2002. Microbial taxonomy. In: Microbiology, The McGraw-Hill Companies, Inc. Boston, USA. 5th ed., pp: 421-449.
37. 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.
38. Röttig A, Atasayar E, Meier-Kolthoff JP, Spröer C, Schumann P, Schauer J, Steinbüchel A. 2017. Streptomyces jeddahensis sp. nov., an oleaginous bacterium isolated from desert soil. Int J Syst Evol Microbiol, 67(6): 1676-1682.
39. Saitou N, Nei M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4:406-425.
40. Saygin H, Ay H, Guven K, Cetin D, Sahin N. 2019. Desertiactinospora gelatinilytica gen. nov., sp. nov., a new member of the family Streptosporangiaceae isolated from the Karakum Desert. Antonie van Leeuwenhoek, 112(3):409-423.
41. Sarıcaoğlu S, Işık K, Veyisoglu A, Saygın H, Çetin D, Güven K, Sproeer C, Klenk H, Şahin N. 2014. Streptomyces burgazadensis sp nov., isolated from soil. Int J Syst Evol Microbiol, 64: 4043-4048.
42. Shirling EB, Gottlieb D. 1966. Methods for characterisation of Streptomyces species. International Journal of Systematic Bacteriology, 16(3): 313-340.
43. Siddharth S, Vittal RR, Wink J, Steinert M. 2020. Diversity and Bioactive Potential of Actinobacteria from Unexplored Regions of Western Ghats, India. Microorganisms, 8(2): 225.
44. Sujarit K, Kudo T, Ohkuma M, Pathom-Aree W, Lumyong S. 2016. Streptomyces palmae sp. nov., isolated from oil palm (Elaeis guineensis) rhizosphere soil. Int J Syst Evol Microbiol, 66(10): 3983-3988.
45. Taechowison Tanaka YT, Omura S. 1993. Agroactive compounds of microbial origin. Annu Rev Microbiol, 47: 57-87.
46. Také A, Inahashi Y, Ōmura S, Takahashi Y, Matsumoto A. 2018. Streptomyces boninensis sp. nov., isolated from soil from a limestone cave in the Ogasawara Islands. Int J Syst Evol Microbiol, 68(5): 1795-1799.
47. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGAX: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30(12): 2725-2729.
48. Tan GYA, Ward AC, Goodfellow M. 2006. Exploration of Amycolatopsis diversity in soil using genus-specific primers and novel selective media. Syst Appl Microbial, 29: 557-569.
49. Tanasupawat S, Phongsopitanun W, Suwanborirux K, Ohkuma M, Kudo T. 2016. Streptomyces actinomycinicus sp. nov., isolated from soil of a peat swamp forest. Int J Syst Evol Microbiol, 66(1): 290-295.
50. Thawai C, Rungjindamai N, Klanbu TK, Tanasupawa TS. 2017. Nocardia xestospongiae sp. nov., isolated from a marine sponge in the Andaman Sea. International Journal of Systematic and Evolutionary Microbiology, 67(5):1451-1456.
51. Tiwari K, Gupta RK. 2012. Rare actinomycetes: a potential storehouse for novel antibiotics. Crit Rev Biotechnol, 32(2): 108–132.
52. Trujillo ME, Idris H, Riesco R, Nouioui I, Igual JM, Bull AT, Goodfellow M. 2017. Pseudonocardia nigra sp. nov., isolated from Atacama Desert rock. International journal of systematic and evolutionary microbiology, 67(8): 2980-2985.
53. Vickers JC, Williams ST, Ross GW. 1984. A taxonomic approach to selective isolation of streptomycetes from soil. In: Ortiz-Ortiz L, Bojalil LF, Yakoleff V (eds) Bio- logical, biochemical and biomedical aspects of actinomycetes. Academic Press, London, 553-561.
54. Ventura M, Canchaya C, Tauch A, Chandra G, Fitzgerald GF, Chater KF, van Sinderen D. 2007. Genomics of Actinobacteria: Tracing the evolutionary history of an ancient phylum. Microbiol Mol Biol Rev, 71:495-548.
55. Veyisoglu A, Carro L, Cetin D, Guven K, Spröer C, Pötter G, Goodfellow M. 2016. Micromonospora profundi sp. nov., isolated from deep marine sediment. Int J Syst Evol Microbiol, 66(11): 4735-4743.
56. Wang HF, Zhang YG, Chen JY, Hozzein WN, Li L, Wadaan MA, Li WJ. 2014. Nesterenkonia rhizosphaerae sp. nov., an alkaliphilic actinobacterium isolated from rhizosphere soil in a saline-alkaline desert. Int J Syst Evol Microbiol, 64(12): 4021-4026.
57. Waksman, SA. 1967. The Actinomycetes. A summary of current knowledge. The Actinomycetes. A summary of current knowledge, 286.
58. Weisburg WG, Barns SM, Pelletier DA, et al. 1991. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol, 173(2): 697–703.
59. Williams ST, Goodfellow M, Alderson G, Wellington EMH, Sneath PHA, Sackin MJ. 1983. Numerical classification of Streptomyces and related genera. Microbiology, 129:6, 1743-1813.
60. Wink J, Schumann P, Atasayar E, Klenk HP, Zaburannyi N, Westermann M, Kämpfer P. 2017. ‘Streptomyces caelicus’, an antibiotic-producing species of the genus Streptomyces, and Streptomyces canchipurensis Li et al. 2015 are later heterotypic synonyms of Streptomyces muensis Ningthoujam et al. 2014. International Journal of Systematic and Evolutionary Microbiology, 67(3): 548-556.
61. Yoon SH, Ha SM, Kwon S. 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.
62. Zhang YQ, Chen J, Liu HY, Zhang YQ, Li, WJ, Yu LY. 2011. Geodermatophilus ruber sp. nov., isolated from rhizosphere soil of a medicinal plant. International Journal of Systematic and Evolutionary Microbiology, 61(1): 190-193.
63. Zothanpuia Passari AK, Chandra P, Leo VV. 2017. Production of potent antimicrobial compounds from Streptomyces cyaneofuscatus associated with freshwater sediment. Front Microbiol, 8:68.
64. ZoBell CE. 1941. Studies on marine bacteria. I. The cultural requirements of heterotrophic aerobes. Journal of Marine Resources, 4: 41-75.