Korean Journal of Environmental Biology (환경생물)

Korean Society of Environmental Biology (한국환경생물학회)
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A report of 44 unrecorded bacterial species isolated from Nakdong River in Korea

  • Ju-Hyung Jeon (Microbial Research Department, Nakdonggang National Institute of Biological Resources) ;
  • Sanghwa Park (Microbial Research Department, Nakdonggang National Institute of Biological Resources) ;
  • Ja Young Cho (Microbial Research Department, Nakdonggang National Institute of Biological Resources) ;
  • Soo-Yeong Lee (Microbial Research Department, Nakdonggang National Institute of Biological Resources) ;
  • Seoni Hwang (Microbial Research Department, Nakdonggang National Institute of Biological Resources) ;
  • Jun Sung Kim (Microbial Research Department, Nakdonggang National Institute of Biological Resources) ;
  • Eui-Jin Kim (Microbial Research Department, Nakdonggang National Institute of Biological Resources) ;
  • Ji Young Jung (Microbial Research Department, Nakdonggang National Institute of Biological Resources)
  • Received : 2023.07.31
  • Accepted : 2023.09.20
  • Published : 2023.09.30
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Abstract

This study investigated unrecorded freshwater bacterial species in Korea. Water and sediment samples were collected from the Nakdong River basin from 2020-2022. Bacterial isolates obtained through the conventional culture method with commercial media were subjected to 16S rRNA gene sequencing to identify unrecorded bacterial species. Results of 16S rRNA gene sequencing of the bacterial isolates revealed that a total of 44 bacterial isolates shared 16S rRNA gene sequence similarities of more than 98.65%, with validly published bacterial species not reported in Korea yet. These isolates were phylogenetically assigned to 4 phyla, 7 classes, 21 orders, 33 families, and 42 genera. A total of 2, 6, 12, and 24 species belonged to phyla Bacillota, Bacteroidota, Actinomycetota, and Pseudomonadota, respectively. Here, we provide details of these 44 unrecorded bacterial species, including Gram staining, colony and cellular morphologies, biochemical properties, and phylogenetic position.

Keywords

Acknowledgement

This work was supported by a Nakdonggang National Institute of Biological Resources grant (project no. NNIBR202301103) funded by the Ministry of Environment, Republic of Korea.

References

  1. Arora-Williams K, SW Olesen, BP Scandella, K Delwiche, SJ Spencer, EM Myers and SP Preheim. 2018. Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake. Microbiome 6:165. https://doi.org/10.1186/s40168-018-0556-7
  2. Boukid F and M Castellari. 2022. Algae as nutritional and functional food sources. Foods 12:122. https://doi.org/10.3390/foods12010122
  3. Chantarasiri A. 2021. Diversity and activity of aquatic cellulolytic bacteria isolated from sedimentary water in the littoral zone of Tonle Sap Lake, Cambodia. Water 13:1797. https://doi.org/10.3390/w13131797
  4. Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376. https://doi.org/10.1007/BF01734359
  5. 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
  6. Fitch WM. 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20:406-416. https://doi.org/10.1093/sysbio/20.4.406
  7. Ghai R, CM Mizuno, A Picazo, A Camacho and F Rodriguez-Valera. 2014. Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing. Mol. Ecol. 23:6073-6090. https://doi.org/10.1111/mec.12985
  8. Graffius S, JFG Garzon, M Zehl, P Pjevac, R Kirkegaard, M Flieder, A Loy, T Rattei, A Ostrovsky and SB Zotchev. 2023. Secondary metabolite production potential in a microbiome of the freshwater sponge Spongilla lacustris. Microbiol. Spectr. 11:e0435322. https://doi.org/10.1128/spectrum.04353-22
  9. Grossart HP, R Massana, KD McMahon and DA Walsh. 2019. Linking metagenomics to aquatic microbial ecology and biogeochemical cycles. Limnol. Oceanogr. 65:S2-S20. https://doi.org/10.1002/lno.11382
  10. Henson MW, VC Lanclos, BC Faircloth and JC Thrash. 2018. Cultivation and genomics of the first freshwater SAR11(LD12) isolate. ISME J. 12:1846-1860. https://doi.org/10.1038/s41396-018-0092-2
  11. Jung JY, MH Lee, YH Nam, HK Kang, YJ Jeon, S Park, JH Han and H Kim. 2023. Solitalea lacus sp. nov., isolated from pond sediment. Int. J. Syst. Evol. Microbiol. 73:005743. https://doi.org/10.1099/ijsem.0.005743
  12. Kim H, S Park, KJ Yim, JY Cho and EJ Kim. 2022. A report of 31 unrecorded bacterial species isolated from freshwater. Korean J. Environ. Biol. 40:442-454. https://doi.org/10.11626/KJEB.2022.40.4.442
  13. 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
  14. Linz AM, S He, SLR Stevens, K Anantharaman, RR Rohwer, RR Malmstrom, S Bertilsson and KD McMahon. 2018. Freshwater carbon and nutrient cycles revealed through reconstructed population genomes. PeerJ 10:e6075. https://doi.org/10.7717/peerj.6075
  15. Mabinya LV, S Cosa, U Nwodo and AI Okoh. 2012. Studies on bioflocculant production by Arthrobacter sp. Raats, a freshwater bacteria isolated from Tyume River, South Africa. Int. J. Mol. Sci. 13:1054-1065. https://doi.org/10.3390/ijms13011054
  16. 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
  17. Suhadolnik MLS, APC Salgado, LLS Scholte, L Bleicher, PS Costa, MP Reis, MF Dias, MP Avila, FAR Barbosa, E Chartone-Souza and AMA Nascimento. 2017. Novel arsenic-transforming bacteria and the diversity of their arsenic-related genes and enzymes arising from arsenic-polluted freshwater sediment. Sci. Rep. 7:11231. https://doi.org/10.1038/s41598-017-11548-8
  18. Tamura K, G Stecher and S Kumar. 2021. MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol. Biol. Evol. 38:3022-3027. https://doi.org/10.1093/molbev/msab120
  19. Thompson JD, DG Higgins and TJ Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680. https://doi.org/10.1093/nar/22.22.4673
  20. Tran PQ, SC Bachand, PB McIntyre, BM Kraemer, Y Vadeboncoeur, IA Kimirei, R Tamatamah, KD McMahon and K Anantharaman. 2021. Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika. ISME J. 15:1971-1986. https://doi.org/10.1038/s41396-021-00898-x
  21. 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
  22. Zak D, M Hupfer, A Cabezas, G Jurasinski, J Audet, A Kleeberg, R McInnes, SM Kristiansen, RJ Petersen, H Liu and T Goldhammer. 2021. Sulphate in freshwater ecosystems: A review of sources, biogeochemical cycles, ecotoxicological effects and bioremediation. Earth-Sci. Rev. 212:103446. https://doi.org/10.1016/j.earscirev.2020.103446
  23. Zhao A, Y Lu, Q Li, T Li and J Zhao. 2023. Metagenomics reveals the diversity and role of surface-water microbes in biogeochemical cycles in lakes at different terrain ladders. Front. Environ. Sci. 11:1121775. https://doi.org/10.3389/fenvs.2023.1121775