Determination of Antimicrobial and Plant Growth Promoting Properties of Actinobacteria Isolated from Sakarya River Sediment

Yıl 2021, Cilt: 11 Sayı: 1, 239 - 256, 15.06.2021

Uğur Çiğdem , Ayten Kumaş Fadime Özdemir Koçak

https://doi.org/10.31466/kfbd.889423

Öz

Actinobacteria with high bioactive compound production potential can produce antibiotics, antitumor agents, factors that promote plant growth and enzymes. Isolation studies from different extreme environments are carried out for the discovery of new bioactive compounds. In this study, isolation of actinobacteria from the sediment of the headwaters of the River Sakarya and screening of their different bioactive metabolites were firstly performed. Gram positive, Gram negative bacteria, yeast and fungi were used in antimicrobial activity assay. The ability to (N) fix nitrogen, to dissolve inorganic phosphate, to produce indole acetic acid (IAA), and caseinase activities of isolates were investigated. As a result of 16S rDNA analysis of 17 actinobacteria isolates, the isolates were defined as Micromonospora sp., (14) as Saccharomonospora sp. (2) and as Cellulomonas sp. (1). In the results obtained, it was revealed that Micromonospora isolates have effective activity against Gram positive, yeast and fungi. 7 of the isolates could produce IAA and 12 of them could fix N and while 2 of the isolates have caseinase activity. The results obtained demostrated that those with high activity in terms of antimicrobial properties will can good pharmaceutical candidates. Isolates that have the potential to stimulate plant growth are also thought to have the potential to be used as biofertilizers in agriculture. In addition, as a result of 16S rDNA sequence analysis, it is possible that 2 Micromonospora sp., Saccharomonospora sp. and Cellulomonas sp. strains are new species.

Anahtar Kelimeler

Actinobacteria , Antimicrobial activity , Plant growth promoting , 16S rDNA analysis

Proje Numarası

2016-01.BŞEÜ.13-01

Sakarya Nehir Sedimentinden İzole Edilen Aktinobakterilerin Antimikrobiyal ve Bitki Gelişim Teşvik Edici Özelliklerinin Belirlenmesi

Öz

Biyoaktif bileşik üretim potansiyeli yüksek olan aktinobakteriler antibiyotik, antitümör ajanı, bitki gelişimini teşvik eden faktörler ve enzimler üretebilmektedirler. Yeni biyoaktif bileşiklerin keşfi için faklı ekstrem ortamlardan izolasyon çalışmaları yapılmaktadır. Bu çalışmada, Sakarya Nehir kaynağının sedimentinden ilk kez aktinobakteri izolasyonu ve bu bakterilerin ürettiği farklı bioaktif metabolitlerin varlığı araştırlmıştır. Antimikrobiyal aktivite deneylerinde Gram pozitif, Gram negatif bakteriler, maya ve funguslar kullanılmıştır. İzolatların azotu (N) fikse edebilme inorganik fosfatı çözebilme yeteneklerine, indol asetik asit (IAA) üretebilme ve kazeinaz aktivitelerine bakılmıştır. 17 aktinobakteri izolatının 16S rDNA analizleri sonucunda, izolatlar Micromonospora sp., (14), Saccharomonospora sp. (2) ve Cellulomonas sp. (1) olarak tanımlanmıştır. Elde edilen sonuçlarda, Micromonospora izolatlarının Gram pozitif bakterilere, maya ve funguslara karşı etkin olduğu belirlenmiştir. 12 izolatın N’u fikse edebildiği, 7 izolatın IAA üretebildiği, 2 izolatın kazeinaz aktivitesine sahip olduğu görülmüştür. Antimikrobiyal özellikleri açısından yüksek aktiviteye sahip olanların iyi birer farmasötik aday olabileceği ve bitki gelişimini teşvik edici potansiyele sahip izolatların da tarım alanında biyogübre olarak kullanım potansiyeline sahip olduğu düşünülmektedir. Ayrıca, 16S rDNA dizi analizleri sonucunda 2 Micromonospora, Saccharomonospora sp. ve Cellulomonas sp. Suşlarının yeni birer tür olması söz konusudur.

Anahtar Kelimeler

Aktinobakteriler , Antimikrobiyal aktivite , Bitki gelişimini teşvik özellikleri , 16S rDNA analizi

Destekleyen Kurum

Bilecik Şeyh Edebali Üniversitesi

Proje Numarası

2016-01.BŞEÜ.13-01

Teşekkür

Bu çalışma Bilecik Şeyh Edebali Üniversitesi BAP tarafından 2016-01.BŞEÜ.13-01.kodlu proje ile desteklenmiştir.

Kaynakça

• Arango, C., Acosta-Gonzalez, A., Parra-Giraldo, C.M., Sánchez-Quitian, Z.A., Kerr, R., and Diaz, L.E., (2018). Characterization of Actinobacterial Communities from Arauca River Sediments (Colombia) Reveals Antimicrobial Potential Presented in Low Abundant Isolates. The Open Microbiology Journal, 12, 181-194.
• Azman, A. S., Othman, I., S Velu, S., Chan, K. G., and Lee, L. H., (2015). Mangrove rare actinobacteria: taxonomy, natural compound, and discovery of bioactivity. Frontiers in Microbiology, 6, 856. Bacteriology", 2nd ed., Vol. 5, Parts A and B.
• Baltz, R., (2007). Antimicrobials from actinomycetes: Back to Future. Microbe. 2, 125-131.
• Barka, E. A., Vatsa, P., Sanchez, L., Gaveau-Vaillant, N., Jacquard, C., Klenk, H.P., Clément, C., Ouhdouch, Y., and van Wezel, G.P., (2016). Taxonomy, Physiology, and Natural Products of Actinobacteria. Microbiology and Molecular Biology Reviews, 80(1), 1–43
• Baskaran, R., Vijayakumar, R., and Mohan, P. M., (2011). Enrichment method for the isolation of bioactive actinomycetes from mangrove sediments of Andaman Islands, India. Malays Journal Microbiology, 7(1), 26-32.
• Berdy, J., (2005). Bioactive microbial metabolites. The Journal of antibiotics, 58(1), 1-26.
• de Souza, R. D., Ambrosini, A., and Passaglia, L. M., (2015). Plant growth-promoting bacteria as inoculants in agricultural soils. Genetics and Molecular Biology, 38(4), 401-419.
• El-Tarabily, K. A., Nassar, A. H., and Sivasithamparam, K., (2008). Promotion of growth of bean (Phaseolus vulgaris L.) in a calcareous soil by a phosphate-solubilizing, rhizosphere-competent isolate of Micromonospora endolithica. Applied soil ecology, 39(2), 161-171.
• Gärtner, A., Wiese, J., and Imhoff, J. F., (2016). Diversity of Micromonospora strains from the deep Mediterranean Sea and their potential to produce bioactive compounds. AIMS Microbiology, 2(2), 205-221.
• Gong, Y., Bai, J. L., Yang, H. T., Zhang, W. D., and Xiong, Y.W. et al., (2018). Phylogenetic diversity and investigation of plant growthpromoting traits of actinobacteria in coastal salt marsh plant rhizospheres from Jiangsu, China. Systematic and Applied Microbiology, 41, 516-527.
• Gordon, S. A., and Weber, R. P., (1951). Colorimetric estimation of indoleacetic acid. Plant Physiology, 26(1), 192.
• Guan, T. W., Lin, Y. J., Ou, M. Y., and Chen, K. B., (2020). Isolation and diversity of sediment bacteria in the hypersaline aiding lake, China. PloS one, 15(7), e0236006.
• Güneş, A., Yıldırım , E., Turan , M., Kotan , R., Ekinci , M., and Argın, S., (2021). Amino Acid and Hormone Content of Plant Growth-Promoting Rhizobacteria Grown in Drought Stress Created by PEG6000. Avrupa Bilim ve Teknoloji Dergisi, 21, 95-112.
• Huang, C. Y., Roessner, U., Eickmeier, I., Genc, Y., Callahan, D. L., Shirley, N., and Bacic, A., et al., (2008). Metabolite profiling reveals distinct changes in carbon and nitrogen metabolism in phosphate-deficient barley plants (Hordeum vulgare L.). Plant and Cell Physiology, 49(5), 691-703.
• Ibrahim, S., (2017). Isolation, identification and antibiosis efficacy of marine thermophilic actinomycetes. Egyptian Journal of Microbiology, 52(1), 113-128.
• Ichiwaki, S., Costa, A. C., Silva, E. G., Rada, L. R., Lima, F. R., Ortíz-Vera, M. P., and Padilla, G., et al., (2017). Genome sequence of Micromonospora sp. NBS 11-29, an antibiotic and hydrolytic enzyme producer, isolated from river sediment in Brazil. Genome announcements, 5(28). e00552-17.
• Jones, K. L., (1949). Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. Journal of Bacteriology, 57,141-145.
• Jose, P. A., and Jha, B., (2017). Intertidal marine sediment harbours Actinobacteria with promising bioactive and biosynthetic potential, Scientific Reports, 7(1), 1-15.
• Jukes T. H., and Cantor C. R., (1969). Evolution of protein molecules, Mammalian Protein Metabolism, in Munro, R.E., ed, Academic Press, New York, pp. 21–132
• Karabi, B., Dipak, P., and Sankar, N. S., (2016). Marine bacteria: a potential tool for antibacterial activity. Journal Applied Environment. Microbiolology, 4, 25–29.
• Kazanas, N., (1968). Proteolytic activity of microorganisms isolated from freshwater fish. Applied Microbiology, 16(1), 128-132.
• Kumar, S., Stecher, G., and Tamura, K., (2016). MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33, 1870-1874.
• Kyeremeh, K., Acquah, K. S., Sazak, A., Houssen, W., Tabudravu, J., Deng, H., and Jaspars, M., (2014). Butremycin, the 3-hydroxyl derivative of ikarugamycin and a protonated aromatic tautomer of 5′-methylthioinosine from a Ghanaian Micromonospora sp. K310. Marine Drugs, 12(2), 999-1012.
• Le, T. C., Yim, C. Y., Park, S., Katila, N., Yang, I., Song, M. C., and Fenical, W., et al., (2017). Lodopyridones B and C from a marine sediment-derived bacterium Saccharomonospora sp. Bioorganic & Medicinal Chemistry Letters, 27(14), 3123-3126.
• Li, D., Chen, Z. J., Luo, X. X., Xia, Z. F., Wan, C. X., and Zhang, L. L., (2016). Saccharomonospora xiaoerkulensis sp. nov., isolated from lake sediment. International Journal of Systematic and Evolutionary Microbiology, 66(12), 5145-5149.
• Liu, W., Shen, X., Liu, C., and Su, Y. C., (2010). Vibrio parahaemolyticus in granulated ark shell clam (Tegillarca granosas): accumulation from water and survival during cold storage and thermal process. International Journal of Food Science & Technology, 45(4), 670-675.
• Ludwig, W., Euzéby, J., Schumann, P., Buss, H.J., Trujillo, M.E., Kämpfer, P. and Whiteman, W.B., (2012). Road map of the phylum Actinobacteria, p 1–28., In Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki KI, Ludwig W, WhitmanWB(ed), Bergey’s manual of systematic bacteriology, vol 5.Springer-Verlag, New York,
• Macagnan, D., Romeiro, R. D. S., de Souza, J. T. and Pomella, A. W. V., (2006). Isolation of actinomycetes and endospore-forming bacteria from the cacao pod surface and their antagonistic activity against the witches’ broom and black pod pathogens, Phytoparasitica, 3:122–132 .
• Nafis, A., Raklami, A., Bechtaoui, N., El Khalloufi, F., El Alaoui, A., Glick, B. R., and Hassani, L., et al. (2019). Actinobacteria from extreme niches in morocco and their plant growth-promoting potentials. Diversity, 11(8), 139.
• Nautiyal, C. S., (1999). An efficient microbiological growth medium for screening phosphate solubilizing microorganisms. FEMS Microbiology Letters, 170(1), 265-270.
• Özcan, K., (2019). Yıldız Gölü Sedimentinden İzole Edilen Aktinobakterilerin Antimikrobiyal ve Enzim Üretim Kapasitelerinin Araştırılması, Karadeniz Fen Bilimleri Dergisi, 9(1), 144-151.
• Özdemir Koçak, F., (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), 391-403.
• Phongsopitanun, W., Kudo, T., Mori, M., Shiomi, K., Pittayakhajonwut, P., Suwanborirux, K., and Tanasupawat, S., (2015). Micromonospora fluostatini sp. nov., isolated from marine sediment. International journal of systematic and evolutionary microbiology, 65(12), 4417-4423.
• Phongsopitanun, W., Kudo, T., Ohkuma, M., Pittayakhajonwut, P., Suwanborirux, K., and Tanasupawat, S., (2016). Micromonospora sediminis sp. nov., isolated from mangrove sediment. International journal of systematic and evolutionary microbiology, 66(8), 3235-3240.
• Pozo, M. I. C., Wieme, A. D., Pérez, S. R., Maury, G. L., Peeters, C., Snauwaert, C., and Vandamme, P. A., et al. (2020). Micromonospora fluminis sp. nov., isolated from mountain river sediment. International Journal of Systematic and Evolutionary Microbiology, 70(12), 6428-6436.
• Ribeiro, I., Girão, M., Alexandrino, D. A., Ribeiro, T., Santos, C., Pereira, F., and Carvalho, M. F., et al. (2020). Diversity and Bioactive Potential of Actinobacteria Isolated from a Coastal Marine Sediment in Northern Portugal. Microorganisms, 8(11), 1691.
• Saitou, N., and Nei, M., (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular biology and evolution, 4(4), 406-425.
• Sathya, A., Vijayabharathi, R., and Gopalakrishnan, S., (2017). Plant growth-promoting actinobacteria: a new strategy for enhancing sustainable production and protection of grain legumes. 3 Biotechnology, 7(2), 1-10.
• Sembiring, L., (2008). Selective İsolation and Characterisation of Streptomyces Associated with the Rhizosphere of the Tropical Legume Paraserianthes falcataria (L)Nielsen, Ph. D.Thesis. University of Newcastle Upon Tyne, UK (2000).
• Seviour, R.J., Kragelund, C., Kong, Y., Eales, K., Nielsen, J.L., and Nielsen, P.H., (2008). Ecophysiology of the Actinobacteria in activated sludge systems. Antonie van Leeuwenhoek, 94,21–33.
• Sivakumar, K., (2008). Actinomycetes. In Centre of Advanced Study in Marine Biology, Annamalai University.
• Tapia-Vázquez, I., Sánchez-Cruz, R., Arroyo-Domínguez, M., Lira-Ruan, V., Sánchez-Reyes, A., del Rayo Sánchez-Carbente, M., and Folch-Mallol, J. L., (2020). Isolation and characterization of psychrophilic and psychrotolerant plant-growth promoting microorganisms from a high-altitude volcano crater in Mexico, Microbiological Research, 232, 126394.
• Trujillo, M.E., Alonso Vega, P., Rodríguez, R., Carro, L., Cerda, E., and Alonso, P., et al., (2010). The genus Micromonospora is widespread in legume root nodules: the example of Lupinus angustifolius. ISME Journal, 4,1265–1281.
• Tseng, M., Chiang, W. P., Liao, H. C., Hsieh, S. Y., and Yuan, G. F., (2018). Saccharomonospora piscinae sp. nov., a novel actinobacterium from fishpond sediment in Taiwan. International Journal of Systematic and Evolutionary Microbiology, 68(5), 1418-1422.
• Veyisoglu, A., Sazak, A., Cetin, D., Guven, K., and Sahin, N., (2013). Saccharomonospora amisosensis sp. nov., isolated from deep marine sediment, International journal of systematic and evolutionary microbiology, 63(10), 3782-3786.
• Veyisoglu, A., Carro, L., Cetin, D., Igual, J. M., Klenk, H. P., and Sahin, N., (2020). Micromonospora orduensis sp. nov., isolated from deep marine sediment, Antonie van Leeuwenhoek, 113(3), 397-405.
• Wang, C., Wang, H., Li, Y., Li, Q., Yan, W., Zhang, Y., and Zhou, Q., et al., (2021). Plant growth promoting rhizobacteria isolation from rhizosphere of submerged macrophytes and their growth promoting effect on Vallisneria natans under high sediment organic matter load, Microbial Biotechnology, 14(2), 726-736.
• Wani, S. P., and Gopalakrishnan, S., (2019). Plant growth-promoting microbes for sustainable agriculture. In Plant Growth Promoting Rhizobacteria (PGPR): Prospects for Sustainable Agriculture, pp. 19-45. Springer, Singapore.
• Williams, D. E., Dalisay, D. S., Chen, J., Polishchuck, E. A., Patrick, B. O., Narula, G., and Andersen, R. J. et al., (2017). Aminorifamycins and sporalactams produced in culture by a Micromonospora sp. isolated from a Northeastern-Pacific marine sediment are potent antibiotics. Organic letters, 19(4), 766-769.
• Williams, J. E., and Cavanaugh, D. C., (1983). Chronic infections in laboratory rodents from inoculation of nonencapsulated plague bacilli (Yersinia pestis), Experientia, 39(4), 408-409.
• Yamamura, H., Hayashi, T., Hamada, M., Kohda, T., Serisawa, Y., Matsuyama-Serisawa, K., and Hayakawa, M., et al., (2019). Cellulomonas algicola sp. nov., an actinobacterium isolated from a freshwater alga, International journal of systematic and evolutionary microbiology, 69(9), 2723-2728.
• Zhang, D. F., Chen, W., He, J., Zhang, X. M., Xiong, Z. J., Sahu, M. K., and Li, W. J. et al., (2013). Saccharomonospora oceani sp. nov. isolated from marine sediments in Little Andaman, India. Antonie van Leeuwenhoek, 103(6), 1377-1384.
• Zothanpuia, A. K., Passari, V. V., Leo, P. C., and Kumar, B., et al., (2018). Bioprospection of actinobacteria derived from freshwater sediments for their potential to produce antimicrobial compounds. Microbiology. Cell Factories, 17, 68.