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Lokal Endemik Bitki Rizosferinden İzole Edilen Aktinobakterilerin Tanımlanması ve Antimikrobiyal Aktivitesi

Year 2021, Volume: 31 Issue: 4, 876 - 885, 31.12.2021
https://doi.org/10.29133/yyutbd.957756

Abstract

Patojenlerin direncinin artmasıyla birlikte yeni antimikrobiyal bileşik arayışı hız kazanmaktadır. Bu çalışmada, Türkiye'deki üç yerel endemik bitkinin rizosfer topraklarından izole edilen 11 lokal Aktinobakteri izolatının farklı patojen bakterilere ve Candida albicans'a karşı antimikrobiyal potansiyeli değerlendirilmiştir. In vitro antimikrobiyal aktivite, modifiye Bennett's ve Tryptic Soy Broth (TSB) besiyerinde üretilen izolatların organik özütleri kullanılarak disk difüzyon agar yöntemiyle araştırılmıştır. Sekiz izolatın patojenlere karşı kayda değer antimikrobiyal aktiviteye sahip olduğu belirlenmiştir. Biyoaktif metabolitlerin üretimi üzerine iki farklı kültür ortamının incelenmesi sonucu, modifiye Bennett ortamında daha yüksek antimikrobiyal aktivitenin elde edildiği bulunmuştur. Ayrıca kısmi 16S rDNA dizi analizleri ile bu lokal suşların 10'unun Streptomyces ve birinin de Promicromonospora cinsine ait olduğu tespit edilmiştir.

Supporting Institution

TÜBİTAK, DİCLE ÜNİVERSİTESİ

Project Number

TÜBİTAK-107T502, DUBAP-09-FF-45

References

  • Abou-Zeid, A., El-Diwany, A. I. & Salem, H. M. (1980). Utilisation of molasses as a natural medium for production of magnamycin by Streptomyces halsted II. Agricultural Wastes, 2, 23-30.
  • Barakate, M., Ouhdouch, Y., Oufdou, K. & Beaulieu, C. (2002). Characterization of rhizospheric soil streptomycetes from Moroccan habitats and their antimicrobial activities. World Journal of Microbiology and Biotechnology, 18, 49–54.
  • Basilio, A., Gonzales, I., Vicente, M. F., Gorrochategui, J., Cabello, A., Gonzales, A. & Genilloud, O. (2003). Patterns of antimicrobial activities from soil actinomycetes isolated under different conditions of pH and salinity. Journal of Applied Microbiology, 95, 814–823.
  • Berdy, J. (2005). Bioactive microbial metabolites. The Journal of Antibiotics,  58, 1-26.
  • Bills, G. F., Platas, G., Fillola, A., Jiménez, M. R., Collado, J., Vicente, F., Serrano, J. M., Gonzalez, A., Zimmermann, J. B., Tormo, J. R. & Peláez, F. (2008). Enhancement of antibiotic and secondary metabolite detection from filamentous fungi by growth on nutritional arrays. Journal of Applied Microbiology, 104, 1644-1658.
  • Bush, K., Courvalin, P., Dantas, G., Davies, J., Eisenstein, B., Huovinen, P., Jacoby, G. A., Kishony, R., Kreiswirth, B. R., Kutter, E., Lerner, S. A., Levy, S., Lewis, K., Lomovskaya, O., Miller, J. H., Mobashery, S., Piddock, L. J. V., Projan, S., Thomas, C. M., Thomasz, A., Tulkens, P. M., Walsh, T. R., Watson, J. D., Witkowski, J., Witte, W., Wright, G., Yeh, P. & Zgurskaya, H. I. (2011). Tackling antibiotic resistance. Nature Reviews Microbiology, 9, 894-896.
  • Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32,1792-1797.
  • Fiedurek, J., Gromada, A. & Jamroz, J. (1996). Effect of medium components and metabolic inhibitors on β‐galactosidase production and secretion by Penicillium notatum 1. Journal of Basic Microbiology, 36, 27-32.
  • Fguira, L. F. B., Fotso, S., Ameur-Mehdi, R. B., Mellouli, L. & Laatsch, H. (2005). Purification and structure elucidation of antifungal and antibacterial activities of newly isolated Streptomyces sp. strain US80. Research in Microbiology, 156,341-347.
  • Hwang, K. S., Kim, H. U., Charusanti, P., Palsson, B. Ø. & Lee, S. Y. (2014). Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites. Biotechnology Advances, 32, 255-268.
  • Johnson, J. S., Spakowicz, D. J., Hong, B. Y., Petersen, L. M., Demkowicz, P., Chen, L., Leopold, S. R., Hanson, B. M., Agresta, H. O., Gerstein, M., Sodergren, E. & Weinstock, G. M. (2019). Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nature Communications, 10:1-11.
  • Kalyani, B. S., Krishna, P. & Sreenivasulu, K. (2019). Screening and identification of novel isolate Streptomyces sp., NLKPB45 from Nellore costal region for its biomedical applications. Saudi Journal of Biological Sciences, 26, 1655-1660.
  • Kämpfer, P. & Labeda, D. (2006). International committee on systematics of prokaryotes; Subcommittee on the taxonomy of the Streptomycetaceae. International Journal of Systematic and Evolutionary Microbiology, 56, 495.
  • Kataoka, M., Ueda, K., Kudo, T., Seki, T. & Yoshida, T. (1997). Application of the variable region in 16S rDNA to create an index for rapid species identification in the genus Streptomyces. FEMS Microbiology Letters, 151, 249–255.
  • Kim, M., Oh, H. S., Park, S. C. & Chun, J. (2014). Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. International Journal of Systematic and Evolutionary Microbiology, 64, 346-351.
  • Ling, L., Schneider, T., Peoples, A., Spoering, A. L., Engels, I., Conlon, B. P., Mueller, A., Schaberle, T. F., Hughes, D. E., Epstein, S., Jones, M., Lazarides, L., Steadman, V. A., Cohen, D. R., Felix, C. R., Fetterman, K. A., Millet, W. P., Nitti, A. G., Zullo, A. M., Chen, C. A new antibiotic kills pathogens without detectable resistance Lewis, K. (2015). A new antibiotic kills pathogens without detectable resistance. Nature, 517, 455–459.
  • Meier-Kolthoff, J. P., Auch, A. F., Klenk, H. P. & Göker, M. (2013). Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics, 14, 60.
  • National Committee for Clinical Lab. Standards (NCCLS). (2002). Performance standards for antimicrobial disk susceptibility test: approved standard 6th ed, M2-A6.
  • Nett, M., Ikeda, H. & Moore, B. S. (2009). Genomic basis for natural product biosynthetic diversity in the actinomycetes. Natural Product Reports, 26, 1362-1384.
  • Nouioui, I., Carro, L., García-López, M., Meier-Kolthoff, J. P., Woyke, T., Kyrpides, N. C., Pukall, R., Klenk, H. P., Goodfellow, M. & Göker, M. (2018). Genome-based taxonomic classification of the phylum Actinobacteria. Frontiers in Microbiology, 9:2007.
  • Ouhdouch, Y., Barakate, M. & Finance, C. (2001). Actinomycetes of Moroccan habitats: Isolation and screening for antifungal activities. The European Journal of Soil Biology, 37, 69-74.
  • Qin, S., Jiang, J. H., Klenk, H. P., Zhu, W. Y., Zhao, G. Z., Zhao, L. X., Tang, S. K., Xu, L. H. & Li, W. J. (2012). Promicromonospora xylanilytica sp. nov., an endophytic actinomycete isolated from surface-sterilized leaves of the medicinal plant Maytenus austroyunnanensis. International Journal of Systematic and Evolutionary Microbiology, 62, 84-89.
  • Qin, Z., Munnoch, J. T., Devine, R., Holmes, N. A., Seipke, R. F., Wilkinson, K. A., Wilkinson, B. & Hutchings, M. I. (2017). Formicamycins, antibacterial polyketides produced by Streptomyces formicae isolated from African Tetraponera plant-ants. Chemical Science, 8, 3218-3227.
  • Riahi, K., Hosni, K., Raies, A. & Oliveira, R. (2019). Unique secondary metabolites of a Streptomyces strain isolated from extreme salty wetland show antioxidant and antibacterial activities. Journal of Applied Microbiology, 127, 1727-1740.
  • Saadoun, I. & Gharaibeh, R. (2003). The Streptomyces flora of Badia region of Jordan and its potential as a source of antibiotics active against antibiotic-resistant bacteria. Journal of Arid Environments, 53, 365–371.
  • Sahin, N. (2005). Antimicrobial activity of Streptomyces species against mushroom blotch disease pathogen. Journal of Basic Microbiology, 45, 64–71.
  • Schein, C. H. (2020). Repurposing approved drugs on the pathway to novel therapies. Medicinal Research Reviews, 40, 586-605.
  • Stackebrandt, E. & Goebel, B. M. (1994). Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. The International Journal of Systematic and Evolutionary Microbiology, 44, 846-849.
  • Stackebrandt, E. & Ebers, J. (2006). Taxonomic parameters revisited: Tarnished gold standards. Microbiology Today, 33, 152-155.
  • Stamatakis, A. (2014). RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30, 1312-1313.
  • Tindall, B. J., Rosselló-Móra, R., Busse, H. J., Ludwig, W. & Kämpfer, P. (2010). Notes on the characterization of prokaryote strains for taxonomic purposes. The International Journal of Systematic and Evolutionary Microbiology, 60, 249-266.
  • VanderMolen, K. M., Raja, H. A., El-Elimat, T. & Oberlies, N. H. (2013). Evaluation of culture media for the production of secondary metabolites in a natural products screening program. AMB Express, 3, 1-7.
  • Wang, Z. X., Qin, S., Xu, L. H., Chen, H. P., Sun, H., Huang, R., Li, Z. H., Feng, T. & Liu, J. K. (2018). Xylanilyticolides A–C, three new compounds from cultures of the actinomycete Promicromonospora xylanilytica YIM 61515. Natural Products and Bioprospecting, 8, 91-95.
  • WHO. (2014). Antimicrobial Resistance: Global Report on Surveillance. Geneva, Switzerland.
  • Wolfe, A. J. (2005). The Acetate Switch. Microbiology and Molecular Biology Reviews, 69, 12-50.
  • Yilmaz, E. I., Yavuz, M. & Kizil, M. (2008). Molecular characterization of rhizospheric soil streptomycetes isolated from indigenous Turkish plants and their antimicrobial activity. World Journal of Microbiology and Biotechnology, 24, 1461-1470.
  • Zipperer, A., Konnerth, M. C., Laux, C., Berscheid, A., Janek, D., Weidenmaier, C., Burian, M., Schilling, N. A., Slavetinsky, C., Marschal, M., Willmann, M., Kalbacher, H., Schittek, B., Brötz-Oesterhelt, H., Grond, S., Peschel, A. & Krismer, B. (2016). Human commensals producing a novel antibiotic impair pathogen colonization. Nature, 535, 511–516.

Identification and Antimicrobial Activity of Actinobacteria Isolated from Rhizosphere of the Local Endemic Plants

Year 2021, Volume: 31 Issue: 4, 876 - 885, 31.12.2021
https://doi.org/10.29133/yyutbd.957756

Abstract

The search for novel antimicrobial compounds from the environment has been gaining momentum with the increase in resistance of pathogens. In the present study, the antimicrobial potential of 11 local isolates of Actinobacteria which were isolated from rhizosphere soils of the three local endemic plants in Turkey was evaluated against different pathogenic bacteria and Candida albicans. Antimicrobial activity was investigated by the disk diffusion agar method using the organic extracts obtained from the isolates grown in the modified Bennett's medium and Tryptic Soy Broth (TSB). Eight isolates were revealed to show remarkable antimicrobial activity against to pathogens. Study of the production of bioactive metabolites in two different culture media indicated that the higher antimicrobial activity was observed in modified Bennett's medium when compared to TSB. Also, partial 16S rDNA sequence analyses revealed that 10 of these local isolates belong to member of Streptomyces and one of them to member Promicromonospora genera.

Project Number

TÜBİTAK-107T502, DUBAP-09-FF-45

References

  • Abou-Zeid, A., El-Diwany, A. I. & Salem, H. M. (1980). Utilisation of molasses as a natural medium for production of magnamycin by Streptomyces halsted II. Agricultural Wastes, 2, 23-30.
  • Barakate, M., Ouhdouch, Y., Oufdou, K. & Beaulieu, C. (2002). Characterization of rhizospheric soil streptomycetes from Moroccan habitats and their antimicrobial activities. World Journal of Microbiology and Biotechnology, 18, 49–54.
  • Basilio, A., Gonzales, I., Vicente, M. F., Gorrochategui, J., Cabello, A., Gonzales, A. & Genilloud, O. (2003). Patterns of antimicrobial activities from soil actinomycetes isolated under different conditions of pH and salinity. Journal of Applied Microbiology, 95, 814–823.
  • Berdy, J. (2005). Bioactive microbial metabolites. The Journal of Antibiotics,  58, 1-26.
  • Bills, G. F., Platas, G., Fillola, A., Jiménez, M. R., Collado, J., Vicente, F., Serrano, J. M., Gonzalez, A., Zimmermann, J. B., Tormo, J. R. & Peláez, F. (2008). Enhancement of antibiotic and secondary metabolite detection from filamentous fungi by growth on nutritional arrays. Journal of Applied Microbiology, 104, 1644-1658.
  • Bush, K., Courvalin, P., Dantas, G., Davies, J., Eisenstein, B., Huovinen, P., Jacoby, G. A., Kishony, R., Kreiswirth, B. R., Kutter, E., Lerner, S. A., Levy, S., Lewis, K., Lomovskaya, O., Miller, J. H., Mobashery, S., Piddock, L. J. V., Projan, S., Thomas, C. M., Thomasz, A., Tulkens, P. M., Walsh, T. R., Watson, J. D., Witkowski, J., Witte, W., Wright, G., Yeh, P. & Zgurskaya, H. I. (2011). Tackling antibiotic resistance. Nature Reviews Microbiology, 9, 894-896.
  • Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32,1792-1797.
  • Fiedurek, J., Gromada, A. & Jamroz, J. (1996). Effect of medium components and metabolic inhibitors on β‐galactosidase production and secretion by Penicillium notatum 1. Journal of Basic Microbiology, 36, 27-32.
  • Fguira, L. F. B., Fotso, S., Ameur-Mehdi, R. B., Mellouli, L. & Laatsch, H. (2005). Purification and structure elucidation of antifungal and antibacterial activities of newly isolated Streptomyces sp. strain US80. Research in Microbiology, 156,341-347.
  • Hwang, K. S., Kim, H. U., Charusanti, P., Palsson, B. Ø. & Lee, S. Y. (2014). Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites. Biotechnology Advances, 32, 255-268.
  • Johnson, J. S., Spakowicz, D. J., Hong, B. Y., Petersen, L. M., Demkowicz, P., Chen, L., Leopold, S. R., Hanson, B. M., Agresta, H. O., Gerstein, M., Sodergren, E. & Weinstock, G. M. (2019). Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nature Communications, 10:1-11.
  • Kalyani, B. S., Krishna, P. & Sreenivasulu, K. (2019). Screening and identification of novel isolate Streptomyces sp., NLKPB45 from Nellore costal region for its biomedical applications. Saudi Journal of Biological Sciences, 26, 1655-1660.
  • Kämpfer, P. & Labeda, D. (2006). International committee on systematics of prokaryotes; Subcommittee on the taxonomy of the Streptomycetaceae. International Journal of Systematic and Evolutionary Microbiology, 56, 495.
  • Kataoka, M., Ueda, K., Kudo, T., Seki, T. & Yoshida, T. (1997). Application of the variable region in 16S rDNA to create an index for rapid species identification in the genus Streptomyces. FEMS Microbiology Letters, 151, 249–255.
  • Kim, M., Oh, H. S., Park, S. C. & Chun, J. (2014). Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. International Journal of Systematic and Evolutionary Microbiology, 64, 346-351.
  • Ling, L., Schneider, T., Peoples, A., Spoering, A. L., Engels, I., Conlon, B. P., Mueller, A., Schaberle, T. F., Hughes, D. E., Epstein, S., Jones, M., Lazarides, L., Steadman, V. A., Cohen, D. R., Felix, C. R., Fetterman, K. A., Millet, W. P., Nitti, A. G., Zullo, A. M., Chen, C. A new antibiotic kills pathogens without detectable resistance Lewis, K. (2015). A new antibiotic kills pathogens without detectable resistance. Nature, 517, 455–459.
  • Meier-Kolthoff, J. P., Auch, A. F., Klenk, H. P. & Göker, M. (2013). Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics, 14, 60.
  • National Committee for Clinical Lab. Standards (NCCLS). (2002). Performance standards for antimicrobial disk susceptibility test: approved standard 6th ed, M2-A6.
  • Nett, M., Ikeda, H. & Moore, B. S. (2009). Genomic basis for natural product biosynthetic diversity in the actinomycetes. Natural Product Reports, 26, 1362-1384.
  • Nouioui, I., Carro, L., García-López, M., Meier-Kolthoff, J. P., Woyke, T., Kyrpides, N. C., Pukall, R., Klenk, H. P., Goodfellow, M. & Göker, M. (2018). Genome-based taxonomic classification of the phylum Actinobacteria. Frontiers in Microbiology, 9:2007.
  • Ouhdouch, Y., Barakate, M. & Finance, C. (2001). Actinomycetes of Moroccan habitats: Isolation and screening for antifungal activities. The European Journal of Soil Biology, 37, 69-74.
  • Qin, S., Jiang, J. H., Klenk, H. P., Zhu, W. Y., Zhao, G. Z., Zhao, L. X., Tang, S. K., Xu, L. H. & Li, W. J. (2012). Promicromonospora xylanilytica sp. nov., an endophytic actinomycete isolated from surface-sterilized leaves of the medicinal plant Maytenus austroyunnanensis. International Journal of Systematic and Evolutionary Microbiology, 62, 84-89.
  • Qin, Z., Munnoch, J. T., Devine, R., Holmes, N. A., Seipke, R. F., Wilkinson, K. A., Wilkinson, B. & Hutchings, M. I. (2017). Formicamycins, antibacterial polyketides produced by Streptomyces formicae isolated from African Tetraponera plant-ants. Chemical Science, 8, 3218-3227.
  • Riahi, K., Hosni, K., Raies, A. & Oliveira, R. (2019). Unique secondary metabolites of a Streptomyces strain isolated from extreme salty wetland show antioxidant and antibacterial activities. Journal of Applied Microbiology, 127, 1727-1740.
  • Saadoun, I. & Gharaibeh, R. (2003). The Streptomyces flora of Badia region of Jordan and its potential as a source of antibiotics active against antibiotic-resistant bacteria. Journal of Arid Environments, 53, 365–371.
  • Sahin, N. (2005). Antimicrobial activity of Streptomyces species against mushroom blotch disease pathogen. Journal of Basic Microbiology, 45, 64–71.
  • Schein, C. H. (2020). Repurposing approved drugs on the pathway to novel therapies. Medicinal Research Reviews, 40, 586-605.
  • Stackebrandt, E. & Goebel, B. M. (1994). Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. The International Journal of Systematic and Evolutionary Microbiology, 44, 846-849.
  • Stackebrandt, E. & Ebers, J. (2006). Taxonomic parameters revisited: Tarnished gold standards. Microbiology Today, 33, 152-155.
  • Stamatakis, A. (2014). RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30, 1312-1313.
  • Tindall, B. J., Rosselló-Móra, R., Busse, H. J., Ludwig, W. & Kämpfer, P. (2010). Notes on the characterization of prokaryote strains for taxonomic purposes. The International Journal of Systematic and Evolutionary Microbiology, 60, 249-266.
  • VanderMolen, K. M., Raja, H. A., El-Elimat, T. & Oberlies, N. H. (2013). Evaluation of culture media for the production of secondary metabolites in a natural products screening program. AMB Express, 3, 1-7.
  • Wang, Z. X., Qin, S., Xu, L. H., Chen, H. P., Sun, H., Huang, R., Li, Z. H., Feng, T. & Liu, J. K. (2018). Xylanilyticolides A–C, three new compounds from cultures of the actinomycete Promicromonospora xylanilytica YIM 61515. Natural Products and Bioprospecting, 8, 91-95.
  • WHO. (2014). Antimicrobial Resistance: Global Report on Surveillance. Geneva, Switzerland.
  • Wolfe, A. J. (2005). The Acetate Switch. Microbiology and Molecular Biology Reviews, 69, 12-50.
  • Yilmaz, E. I., Yavuz, M. & Kizil, M. (2008). Molecular characterization of rhizospheric soil streptomycetes isolated from indigenous Turkish plants and their antimicrobial activity. World Journal of Microbiology and Biotechnology, 24, 1461-1470.
  • Zipperer, A., Konnerth, M. C., Laux, C., Berscheid, A., Janek, D., Weidenmaier, C., Burian, M., Schilling, N. A., Slavetinsky, C., Marschal, M., Willmann, M., Kalbacher, H., Schittek, B., Brötz-Oesterhelt, H., Grond, S., Peschel, A. & Krismer, B. (2016). Human commensals producing a novel antibiotic impair pathogen colonization. Nature, 535, 511–516.
There are 37 citations in total.

Details

Primary Language English
Subjects Agricultural, Veterinary and Food Sciences, Soil Sciences and Ecology
Journal Section Articles
Authors

Süleyman Özakın 0000-0001-9536-9852

Bilgin Taşkın 0000-0002-9772-7438

Ebru İnce Bostancı 0000-0002-9048-5798

Project Number TÜBİTAK-107T502, DUBAP-09-FF-45
Publication Date December 31, 2021
Acceptance Date November 22, 2021
Published in Issue Year 2021 Volume: 31 Issue: 4

Cite

APA Özakın, S., Taşkın, B., & İnce Bostancı, E. (2021). Identification and Antimicrobial Activity of Actinobacteria Isolated from Rhizosphere of the Local Endemic Plants. Yuzuncu Yıl University Journal of Agricultural Sciences, 31(4), 876-885. https://doi.org/10.29133/yyutbd.957756
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Yuzuncu Yil University Journal of Agricultural Sciences by Van Yuzuncu Yil University Faculty of Agriculture is licensed under a Creative Commons Attribution 4.0 International License.