Korean Journal of Environmental Biology (환경생물)

Korean Society of Environmental Biology (한국환경생물학회)
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A report on 22 unrecorded Actinomycetota species isolated from freshwater environments in the Republic of Korea

  • Soo-Yeong Lee (Biological Resources Research Department, Nakdonggang National Institute of Biological Resources (NNIBR)) ;
  • Jaeduk Goh (Biological Resources Research Department, Nakdonggang National Institute of Biological Resources (NNIBR)) ;
  • Ahyoung Choi (Biological Resources Research Department, Nakdonggang National Institute of Biological Resources (NNIBR))
  • Received : 2024.07.12
  • Accepted : 2024.09.10
  • Published : 2024.09.30
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Abstract

Freshwater environments are rich ecosystems that support diverse microbial communities, including members of the phylum Actinomycetota critical for nutrient cycling, organic matter decomposition, and water quality maintenance. Actinomycetota known to produce numerous bioactive secondary metabolites are valuable in biotechnology, medicine, and agriculture. Despite their significance, the diversity and distribution of Actinomycetota in freshwater habitats, especially in the Republic of Korea, are underexplored. This study aimed to report the isolation and characterization of 22 previously unrecorded bacterial species of Actinomycetota from various freshwater environments in Korea. Using standard dilution plating techniques on six different culture media, 22 bacterial strains were isolated, incubated, and characterized based on colony and cellular morphologies, Gram staining, and biochemical properties. Genomic DNA was extracted and the 16S rRNA gene was sequenced to determine species identity using the EzBioCloud service with a cutoff of 98.7% sequence similarity for classification as unreported species. These strains were phylogenetically diverse, belonging to two classes, ten orders, and eighteen genera. This study enhances our understanding of bacterial diversity in freshwater ecosystems and underscores the importance of exploring microbial diversity in underexplored habitats, potentially leading to discovery of novel bioactive compounds. Findings of this study contribute valuable insights into ecological roles and biotechnological potential of Actinomycetota in freshwater environments.

Keywords

Acknowledgement

This study was supported by a grant from the Nakdonggang National Institute of Biological Resources (NNIBR), funded by the Ministry of Environment (MOE) of the Republic of Korea (NNIBR20241103).

References

  1. Bae KS, MS Kim, JH Lee, JW Kang, DI Kim, JH Lee and CN Seong. 2016. Korean indigenous bacterial species with valid names belonging to the phylum Actinobacteria. J. Microbiol. 54:789-795. https://doi.org/10.1007/s12275-016-6446-4
  2. Behera S and S Das. 2023. Potential and prospects of Actinobacteria in the bioremediation of environmental pollutants: Cellular mechanisms and genetic regulations. Microbiol. Res. 273: 127399. https://doi.org/10.1016/j.micres.2023.127399
  3. Berdy J. 2005. Bioactive microbial metabolites. J. Antibiot. 58:1-26. https://doi.org/10.1038/ja.2005.1
  4. Blin K, S Shaw, SA Kautsar, MH Medema and T Weber. 2021. The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes. Nucleic Acids Res. 49:D639-D643. https://doi.org/10.1093/nar/gkaa978
  5. Bockelmann U, W Manz, TR Neu and U Szewzyk. 2000. Characterization of the microbial community of lotic organic aggregates ('river snow') in the Elbe River of Germany by cultivation and molecular methods. FEMS Microbiol. Ecol. 33:157-170. https://doi.org/10.1016/S0168-6496(00)00056-8
  6. Bruna P, K Nunez-Montero, MJ Contreras, K Leal, M Garcia, M Abanto and L Barrientos. 2024. Biosynthetic gene clusters with biotechnological applications in novel Antarctic isolates from Actinomycetota. Appl. Microbiol. Biotechnol. 108:325. https://doi.org/10.1007/s00253-024-13154-x
  7. Chen J, L Xu, Y Zhou and B Han. 2021. Natural products from Actinomycetes associated with marine organisms. Mar. Drugs 19:629. https://doi.org/10.3390/md19110629
  8. Comba S, S Menendez-Bravo, A Arabolaza and H Gramajo. 2013. Identification and physiological characterization of phosphatidic acid phosphatase enzymes involved in triacylglycerol biosynthesis in Streptomyces coelicolor. Microb. Cell Fact. 12:9. https://doi.org/10.1186/1475-2859-12-9
  9. Donald L, A Pipite, R Subramani, J Owen, RA Keyzers and T Taufa. 2022. Streptomyces: Still the biggest producer of new natural secondary metabolites, a current perspective. Microbiol. Res. 13:418-465. https://doi.org/10.3390/microbiolres13030031
  10. Felsenstein J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
  11. Ferreira V, A Elosegi, SD Tiegs, D von Schiller and R Young. 2020. Organic matter decomposition and ecosystem metabolism as tools to assess the functional integrity of streams and rivers -A systematic review. Water 12:3523. https://doi.org/10.3390/w12123523
  12. Gao B and RS Gupta. 2012. Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria. Microbiol. Mol. Biol. Rev. 76:66-112. https://doi.org/10.1128/mmbr.05011-11
  13. Goodfellow M and ST Williams. 1983. Ecology of Actinomycetes. Annu. Rev. Microbiol. 37:189-216. https://doi.org/10.1146/annurev.mi.37.100183.001201
  14. Heo CS, JS Kang, JH Kwon, CV Anh and HJ Shin. 2023. Pyrrole-containing alkaloids from a marine-derived actinobacterium Streptomyces zhaozhouensis and their antimicrobial and cytotoxic activities. Mar. Drugs 21:167. https://doi.org/10.3390/md21030167
  15. Jeon YS, K Lee, SC Park, BS Kim, YJ Cho, SM Ha and J Chun. 2014. EzEditor: a versatile sequence alignment editor for both rRNA-and protein-coding genes. Int. J. Syst. Evol. Microbiol. 64:689-691. https://doi.org/10.1099/ijs.0.059360-0
  16. Kim S, MR Islam, I Kang and JC Cho. 2021. Cultivation of dominant freshwater bacterioplankton lineages using a high-throughput dilution-to-extinction culturing approach over a 1-year period. Front. Microbiol. 12:700637. https://doi.org/10.3389/fmicb.2021.700637
  17. Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120. https://doi.org/10.1007/BF01731581
  18. Kumar S, G Stecher and K Tamura. 2016. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33:1870-1874. https://doi.org/10.1093/molbev/msw054
  19. Larkin MA, G Blackshields, NP Brown, R Chenna, PA McGettigan, H McWilliam, F Valentin, IM Wallace, A Wilm, R Lopez, JD Thompson, TJ Gibson and DG Higgins. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948. https://doi.org/10.1093/bioinformatics/btm404
  20. Lee HJ, SI Han and KS Whang. 2016. Phylogenetic characteristics of actinobacterial population in bamboo (Sasa borealis) soil. Korean J. Microbiol. 52:59-64. https://doi.org/10.7845/kjm.2016.6006
  21. Lipko IA and OI Belykh. 2021. Environmental features of freshwater planktonic Actinobacteria. Contemp. Probl. Ecol. 14:158-170. https://doi.org/10.1134/S1995425521020074
  22. Ngamcharungchit C, N Chaimusik, W Panbangred, J Euanorasetr and B Intra. 2023. Bioactive metabolites from terrestrial and marine Actinomycetes. Molecules 28:5915. https://doi.org/10.3390/molecules28155915
  23. Oren A and GM Garrity. 2021. Valid publication of the names of forty-two phyla of prokaryotes. Int. J. Syst. Evol. Microbiol. 71:005056. https://doi.org/10.1099/ijsem.0.005056
  24. Saitou N and M Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
  25. Servin JA, CW Herbold, RG Skophammer and JA Lake. 2008. Evidence excluding the root of the tree of life from the actinobacteria. Mol. Biol. Evol. 25:1-4. https://doi.org/10.1093/molbev/msm249
  26. Slemc L, S Pikl, H Petkovic and M Avbelj. 2021. Molecular biology methods in Streptomyces rimosus, a producer of oxytetracycline. pp. 303-330. In: Antimicrobial Therapies (Barreiro C and JL Barredo, eds.). Methods in Molecular Biology. Vol. 2296. Humana. New York, USA. https://doi.org/10.1007/978-1-0716-1358-0_18
  27. Weisburg WG, SM Barns, DA Pelletier and DJ Lane. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173:697-703. https://doi.org/10.1128/jb.173.2.697-703.1991
  28. Wu J, Z Peng, TW Guan, H Yang and X Tian. 2021. Diversity of actinobacteria in sediments of Qaidam Lake and Qinghai Lake, China. Arch. Microbiol. 203:2875-2885. https://doi.org/10.1007/s00203-021-02277-8
  29. Yoon SH, SM Ha, S Kwon, J Lim, Y Kim, H Seo and J Chun. 2017. Introducing EzBioCloud: A taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int. J. Syst. Evol. Microbiol. 67:1613-1617. https://doi.org/10.1099/ijsem.0.001755