Liken ve Orkide Bitkisinden İzole Edilen Aktinobakterilerin Biyoaktivite Özellikleri

Yıl 2023, Cilt: 13 Sayı: 1&2, 43 - 58, 31.12.2023

Hilal Ateş Hilal Ay

https://doi.org/10.37094/adyujsci.1221660

Öz

Aktinobakteriler için seçici bir izolasyon prosedürü kullanılarak bir liken ve orkide türünden toplam 10 aktinobakteri izole edilmiştir. İzolatların antimikrobiyal aktiviteleri Aspergillus niger ATCC 16404, Candida albicans ATCC 10231, Enterococcus faecalis ATCC 29212, Bacillus subtilis ATCC 6633, Escherichia coli ATCC 25922, Klebsiella pneumoniae ATCC 700603, Pseudomonas aeruginosa ATCC 27853, Salmonella enterica ATCC 13311, Staphylococcus aureus ATCC 29213 ve Listeria monocytogenes NCTC 5348 patojenlerine karşı değerlendirilmiştir. On izolattan sekizi, en az bir patojene karşı antimikrobiyal aktivite göstermiştir. İzolatları moleküler olarak tanımlamak amacıyla 16S rRNA gen dizi analizi yapılmıştır. 16S rRNA geni karşılaştırmalı analizleri bütün izolatların Streptomyces cinsi üyesi olduklarını ve %98,9 – 100 gen dizi benzerliği taşıdıklarını göstermiştir. İzolatların Streptomyces cinsi içerisindeki filogenetik ilişkileri maksimum olabilirlik ve maksimum sıkılık filogenetik ağaçları ile ortaya çıkarılmıştır. Sonuçlar, likenler ve bitki dokuları gibi henüz çalışılmamış çevresel habitatların önemli biyoaktivite özelliklerine sahip yeni aktinobakteriler için potansiyel bir kaynak olabileceğini göstermektedir.

Anahtar Kelimeler

16S rRNA Geni, Aktinobakteriler, Antimikrobiyal Aktivite, Liken, Orkide Yumrusu

Bioactivity Features of Novel Actinobacteria Isolated from Lichen and Orchid Plant

Öz

A total of 10 actinobacterial strains were isolated from a lichen and an orchid species by employing a selective isolation procedure for actinobacteria. Antimicrobial activities of the isolates were evaluated against Aspergillus niger ATCC 16404, Candida albicans ATCC 10231, Enterococcus faecalis ATCC 29212, Bacillus subtilis ATCC 6633, Escherichia coli ATCC 25922, Klebsiella pneumoniae A TCC 700603, Pseudomonas aeruginosa A TCC 27853, Salmonella enterica ATCC 13311, Staphylococcus aureus ATCC 29213 and Listeria monocytogenes NCTC 5348. Out of the 10 isolates, eight showed antimicrobial activity against at least one pathogen. For molecular identification of the strains, 16S rRNA gene sequence analysis was performed. The pairwise comparison of the 16S rRNA gene sequences of the strains with the databases showed that the strains are members of the genus Streptomyces by sharing 98.9 – 100% gene sequence similarities. Phylogenetic relationships of the strains within the genus Streptomyces were revealed by maximum likelihood and maximum parsimony phylogenetic trees. The results revealed that unexplored environmental habitats like lichens and plant tissues may represent a potential reservoir for novel actinobacteria with promising bioactivity features.

Anahtar Kelimeler

16S rRNA Gene, Actinobacteria, Antimicrobial Activity, Lichen, Orchid Tuber

Kaynakça

• Payne, D.J., Gwynn, M.N., Holmes, D.J., Pompliano, D.L., Drugs for bad bugs: confronting the challenges of antibacterial discovery, Nature reviews Drug discovery, 6(1), 29- 40, 2007.
• Olano, C., Méndez, C., Salas, J.A., Molecular insights on the biosynthesis of antitumour compounds by actinomycetes, Microbial Biotechnology, 4(2), 144-164, 2011.
• Manivasagan, P., Kang, K.H., Sivakumar, K., Li-Chan, E.C., Oh, H.M., Kim, S.K., Marine actinobacteria: an important source of bioactive natural products, Environmental toxicology and pharmacology, 38(1), 172-188, 2014.
• Barka, E.A., Vatsa, P., Sanchez, L., Gaveau-Vaillant, N., Jacquard, C., Klenk, H.P., Clément, C., Ouhdouch, Y., van Wezel, G.P., Taxonomy, physiology, and natural products of Actinobacteria, Microbiology and Molecular Biology Reviews, 80(1), 1-43, 2016.
• Lee, L.H., Goh, B.H., Chan, K.G., Actinobacteria: Prolific producers of bioactive metabolites, Frontiers Media SA, 1612, 2020.
• Kumar, N., Singh, R.K., Mishra, S., Singh, A., Pachouri, U.C., Isolation and screening of soil Actinomycetes as source of antibiotics active against bacteria, International Journal of Microbiology Research, 2(2), 12, 2010.
• Manivasagan, P., Venkatesan, J., Sivakumar, K., Kim, S.K., Pharmaceutically active secondary metabolites of marine actinobacteria, Microbiological research, 169(4), 262-278, 2014.
• Ay, H., Nouioui, I., del Carmen Montero-Calasanz, M., Carro, L., Klenk, H.P., Goodfellow, M., Igual, J.M., Çetin, D., Şahin, N., Işık, K., Actinomadura alkaliterrae sp. nov., isolated from an alkaline soil, Antonie van Leeuwenhoek, 110(6), 787-794, 2017.
• Khan, S.T., Tamura, T., Takagi, M., Shin-Ya, K., Streptomyces tateyamensis sp. nov., Streptomyces marinus sp. nov. and Streptomyces haliclonae sp. nov., isolated from the marine sponge Haliclona sp., International journal of systematic and evolutionary microbiology, 60(12), 2775-2779, 2010.
• Xiao, J., Luo, Y., Xu, J., Xie, S., Xu, J., Modestobacter marinus sp. nov., a psychrotolerant actinobacterium from deep-sea sediment, and emended description of the genus Modestobacter, International journal of systematic and evolutionary microbiology, 61(7), 1710- 1714, 2011.
• Duan, Y.Y., Ming, H., Dong, L., Yin, Y.R., Zhang, Y., Zhou, E.M., Liu, L., Nie, G.X., Li, W.J., Streptomyces calidiresistens sp. nov., isolated from a hot spring sediment, Antonie van Leeuwenhoek, 106(2), 189-196, 2014.
• Wang, Z., Tian, J., Li, X., Gan, L., He, L., Chu, Y., Tian, Y., Streptomyces dioscori sp. nov., a Novel Endophytic Actinobacterium Isolated from Bulbil of Dioscorea bulbifera L., Current microbiology, 75(10), 1384-1390, 2018.
• Parrot, D., Legrave, N., Delmail, D., Grube, M., Suzuki, M., Tomasi, S., Review– Lichen-associated bacteria as a hot spot of chemodiversity: focus on uncialamycin, a promising compound for future medicinal applications, Planta Medica, 82(13), 1143-1152, 2016.
• Lutzoni, F., Miadlikowska, J., Lichens. Current Biology, 19(13), R502-R503, 2009.
• Asplund, J., Wardle, D.A., How lichens impact on terrestrial community and ecosystem properties, Biological Reviews, 92(3), 1720-1738, 2017.
• Boustie, J., Tomasi, S., Grube, M., Bioactive lichen metabolites: alpine habitats as an untapped source, Phytochemistry Reviews, 10(3), 287-307, 2011.
• Calcott, M.J., Ackerley, D.F., Knight, A., Keyzers, R.A., Owen, J.G., Secondary metabolism in the lichen symbiosis, Chemical Society Reviews, 47(5), 1730-1760, 2018.
• Muggia, L., Vancurova, L., Škaloud, P., Peksa, O., Wedin, M., Grube, M., The symbiotic playground of lichen thalli–a highly flexible photobiont association in rock-inhabiting lichens, FEMS Microbiology Ecology, 85(2), 313-323, 2013.
• Liu, C., Jiang, Y., Wang, X., Chen, D., Chen, X., Wang, L., Han, L., Huang, X., Jiang, C., Diversity, antimicrobial activity, and biosynthetic potential of cultivable actinomycetes associated with lichen symbiosis, Microbial ecology, 74(3), 570-584, 2017.
• Grube, M., Cernava, T., Soh, J., Fuchs, S., Aschenbrenner, I., Lassek, C., Wegner, U., Becher, D., Riedel, K., Sensen, C.W., Berg, G., Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics, The ISME journal, 9(2), 412-424, 2015.
• Liu, Y.H., Guo, J.W., Salam, N., Li, L., Zhang, Y.G., Han, J., Mohamad, O.A., Li, W.J., Culturable endophytic bacteria associated with medicinal plant Ferula songorica: molecular phylogeny, distribution and screening for industrially important traits, 3 Biotech, 6(2), 1-9, 2016.
• Li, J., Zhao, G.Z., Chen, H.H., Wang, H.B., Qin, S., Zhu, W.Y., Xu, L.H., Jiang, C.L., Li, W.J., Antitumour and antimicrobial activities of endophytic streptomycetes from pharmaceutical plants in rainforest, Letters in applied microbiology, 47(6), 574-580, 2008.
• Golinska, P., Wypij, M., Agarkar, G., Rathod, D., Dahm, H., Rai, M., Endophytic actinobacteria of medicinal plants: diversity and bioactivity, Antonie Van Leeuwenhoek, 108(2), 267-289, 2015.
• Reasoner, D.J., Geldreich, E.E., A new medium for the enumeration and subculture of bacteria from potable water, Applied and environmental microbiology, 49(1), 1-7, 1985.
• Weyland, H., Actinomycetes in North Sea and Atlantic ocean sediments, Nature, 223(5208), 858-858, 1969.
• Hamaki, T., Suzuki, M., Fudou, R., Jojima, Y., Kajiura, T., Tabuchi, A., Sen, K., Shibai, H., Isolation of novel bacteria and actinomycetes using soil-extract agar medium, Journal of bioscience and bioengineering, 99(5), 485-492, 2005.
• Shirling, E.T., Gottlieb, D., Methods for characterization of Streptomyces species, International journal of systematic bacteriology, 16(3), 313-340, 1966.
• Jones, K.L., Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic, Journal of bacteriology, 57(2), 141-145, 1949.
• Sankar Ganesh, P., Rai Vittal, R., In vitro antibiofilm activity of Murraya koenigii essential oil extracted using supercritical fluid CO2 method against Pseudomonas aeruginosa PAO1, Natural Product Research, 29(24), 2295-2298, 2015.
• Chun, J., Goodfellow, M., A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences, International Journal of Systematic and Evolutionary Microbiology, 45(2), 240-245, 1995.
• Yoon, S.H., Ha, S.M., Kwon, S., Lim, J., Kim, Y., Seo, H., Chun, J., Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies, International journal of systematic and evolutionary microbiology, 67(5), 1613, 2017.
• Meier-Kolthoff, J.P., Carbasse, J.S., Peinado-Olarte, R.L., Göker, M., TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes, Nucleic acids research, 50(D1), D801-D807, 2022.
• Ay, H., Genomic insight into a novel actinobacterium, Actinomadura rubrisoli sp. nov., reveals high potential for bioactive metabolites, Antonie van Leeuwenhoek, 114(2), 195- 208, 2021.
• Meier-Kolthoff, J.P., Hahnke, R.L., Petersen, J., Scheuner, C., Michael, V., Fiebig, A., Rohde, C., Rohde, M., Fartmann, B., Goodwin, L.A., Chertkov, O., Reddy, T., Pati, A., Ivanova, N.N, Markowitz, V., Kyrpides, N.C., Woyke, T., Göker M., Klenk, H.P., Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy, Standards in Genomic Sciences, 9(2), 2014.
• Edgar, R.C., MUSCLE: a multiple sequence alignment method with reduced time and space complexit, BMC bioinformatics, 5(1), 1-19, 2004.
• Stamatakis, A., RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, 30(9), 1312-1313, 2014.
• Goloboff, P.A., Farris, J.S., Nixon, K.C., TNT, a free program for phylogenetic analysis, Cladistics, 24(5), 774-786, 2008.
• Pattengale, N.D., Alipour, M., Bininda-Emonds, O.R., Moret, B.M., Stamatakis, A., How many bootstrap replicates are necessary? in Annual International Conference on Research in Computational Molecular Biology, pp.184-200, 2009.
• Swofford, D.L., PAUP: phylogenetic analysis using parsimony, version 4.0 b10, Sinauer Associates, Sunderland, MA, 2002.
• Koch, E., Löffler, I., Partial characterization of the antimicrobial activity of Streptomyces antimycoticus FZB53, Journal of Phytopathology, 157(4), 235-242, 2009.
• Motohashi, K., Sue, M., Furihata, K., Ito, S., Seto, H., Terpenoids produced by actinomycetes: Napyradiomycins from Streptomyces antimycoticus NT17, Journal of natural products, 71(4), 595-601, 2008.
• Benouagueni, S., Ranque, S., Kirane, D.G., A non-polyenic antifungal produced by a Streptomyces yatensis strain isolated from Mellah Lake in El Kala, North-East of Algeria, Journal de Mycologie Medicale, 25(1), 2-10, 2015.
• Park, E.J., Jang, H.J., Park, C.S., Lee, S.J., Lee, S., Kim, K.H., Yun, B.S., Lee, S.W., Rho, M.C., Evaluation of Nematicidal Activity of Streptomyces yatensis KRA-28 against Meloidogyne incognita, Journal of Microbiolog and Biotechnology, 30(5), 700-707, 2020.
• Kumar, Y., Goodfellow, M., Reclassification of Streptomyces hygroscopicus strains as Streptomyces aldersoniae sp. nov., Streptomyces angustmyceticus sp. nov., comb. nov., Streptomyces ascomycinicus sp. nov., Streptomyces decoyicus sp. nov., comb. nov., Streptomyces milbemycinicus sp. nov. and Streptomyces wellingtoniae sp. nov., International journal of systematic and evolutionary microbiology, 60(4), 769-775, 2010.
• Tokura, K., Torı, K., Yoshımura, Y., Okabe, K., Otsuka, H., Matsushıta, K., Inagakı, F., Mıyazawa, T., The structure of siomycin-D1, peptide antibiotic isolated from Streptomyces sioyaensis, The Journal of Antibiotics, 33(12), 1563-1567, 1980.
• Alvariño, R., Alonso, E., Lacret, R., Oves-Costales, D., Genilloud, O., Reyes, F., Alfonso, A., Botana, L.M., Caniferolide A, a macrolide from Streptomyces caniferus, attenuates neuroinflammation, oxidative stress, amyloid-beta, and tau pathology in vitro, Molecular Pharmaceutics, 16(4), 1456-1466, 2019.
• zkumar Sahu, M., Murugan, M., Sivakumar, K., Thangaradjou, T., Kannan, L., Occurrence and distribution of actinomycetes in marine environs and their antagonistic activity against bacteria that is pathogenic to shrimps, Israeli Journal of Aquaculture-Bamidgeh, 59(3), 155-161, 2007.
• Selbmann, L., Zucconi, L., Ruisi, S., Grube, M., Cardinale, M., Onofri, S., Culturable bacteria associated with Antarctic lichens: affiliation and psychrotolerance, Polar biology, 33, 71-83, 2010.
• Davies, J., Wang, H., Taylor, T., Warabi, K., Huang, X.H., Andersen, R.J., Uncialamycin, a new enediyne antibiotic, Organic letters, 7(23), 5233-5236, 2005.
• Williams, D.E., Davies, J., Patrick, B.O., Bottriell, H., Tarling, T., Roberge, M., Andersen, R.J., Cladoniamides A−G, tryptophan-derived alkaloids produced in culture by Streptomyces uncialis, Organic letters, 10(16), 3501-3504, 2008.
• Parrot, D., Antony-Babu, S., Intertaglia, L., Grube, M., Tomasi, S., Suzuki, M.T., Littoral lichens as a novel source of potentially bioactive Actinobacteria, Scientific Reports, 5(1), 15839, 2015.
• Herrera, H., Fuentes, A., Soto, J., Valadares, R., Arriagada, C., Orchid-associated bacteria and their plant growth promotion capabilities, In Orchids phytochemistry, biology and horticulture: fundamentals and applications, 175-200, 2022.
• Alibrandi, P., Schnell, S., Perotto, S., Cardinale, M., Diversity and structure of the endophytic bacterial communities associated with three terrestrial orchid species as revealed by 16S rRNA gene metabarcoding, Frontiers in Microbiology, 11, 604964, 2020.
• Saikia, J., Mazumdar, R., Thakur, D., Phylogenetic affiliation of endophytic actinobacteria associated with selected orchid species and their role in growth promotion and suppression of phytopathogens, Frontiers in Plant Science, 13, 1058867, 2022.
• Chater, K.F., Streptomyces inside-out: a new perspective on the bacteria that provide us with antibiotics, Philosophical Transactions of the Royal Society B: Biological Sciences, 361(1469), 761-768, 2006.
• Bull, A.T., Stach, J.E., Marine actinobacteria: new opportunities for natural product search and discovery, Trends in microbiology, 15(11), 491-499, 2007.
• Sharma, S. B., Gupta, R., Drug development from natural resource: a systematic approach, Mini reviews in medicinal chemistry, 15(1), 52-57, 2015.