Journal of Species Research

The National Institute of Biological Resources (국립생물자원관)
권호 표지
DOI QR코드

DOI QR Code

A report of 37 unrecorded anaerobic bacterial species isolated from the Geum River in South Korea

  • Lee, Changsu (Microbiology and Functionality Research Group, World Institute of Kimchi) ;
  • Kim, Joon Yong (Microbiology and Functionality Research Group, World Institute of Kimchi) ;
  • Kim, Yeon Bee (Microbiology and Functionality Research Group, World Institute of Kimchi) ;
  • Kim, Juseok (Microbiology and Functionality Research Group, World Institute of Kimchi) ;
  • Ahn, Seung Woo (Microbiology and Functionality Research Group, World Institute of Kimchi) ;
  • Song, Hye Seon (Microbiology and Functionality Research Group, World Institute of Kimchi) ;
  • Roh, Seong Woon (Microbiology and Functionality Research Group, World Institute of Kimchi)
  • Received : 2020.02.03
  • Accepted : 2020.04.01
  • Published : 2020.05.31
Download PDF
⟨ Previous Next ⟩

Abstract

A total of 37 anaerobic bacteria strains within the classes Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Bacteroidia, Flavobacteriia, Bacilli, Clostridia, and Fusobacteriia were isolated from freshwater and sediment of the Geum River in Korea. The unreported species were related with Rhizobium and Oleomonas of the class Alphaproteobacteria; Acidovorax, Pseudogulbenkiania, and Aromatoleum of the class Betaproteobacteria; Tolumonas, Aeromonas, Cronobacter, Lonsdalea, and Phytobacter of the class Gammaproteobacteria; Bacteroides, Dysgonomonas, Macellibacteroides, and Parabacteroides of the class Bacteroidia; Flavobacterium of the class Flavobacteriia; Bacillus and Paenibacillus of the class Bacilli; Clostridium, Clostridioides, Paraclostridium, Romboutsia, Sporacetigenium, and Terrisporobacter of the class Clostridia; and Cetobacterium and Ilyobacter of the class Fusobacteriia. A total of 37 strains, with >98.7% 16S rRNA gene sequence similarity with validly published bacterial species, but not reported in Korea, were determined to be unrecorded anaerobic bacterial species in Korea.

Keywords

References

  1. Brady, C.L., I. Cleenwerck, S. Denman, S.N. Venter, P. Rodriguez-Palenzuela, T.A. Coutinho and P. De Vos. 2012. Proposal to reclassify Brenneria quercina (Hildebrand and Schroth 1967) Hauben et al. 1999 into a new genus, Lonsdalea gen. nov., as Lonsdalea quercina comb. nov., descriptions of Lonsdalea quercina subsp. quercina comb. nov., Lonsdalea quercina subsp. iberica subsp. nov. and Lonsdalea quercina subsp. britannica subsp. nov., emendation of the description of the genus Brenneria, reclassification of Dickeya dieffenbachiae as Dickeya dadantii subsp. dieffenbachiae comb. nov., and emendation of the description of Dickeya dadantii. International Journal of Systematic and Evolutionary Microbiology 62(7):1592-1602. https://doi.org/10.1099/ijs.0.035055-0
  2. Broda, D., D. Saul, P. Lawson, R. Bell and D. Musgrave. 2000. Clostridium gasigenes sp. nov., a psychrophile causing spoilage of vacuum-packed meat. International Journal of Systematic and Evolutionary Microbiology 50(1):107-118. https://doi.org/10.1099/00207713-50-1-107
  3. Buck, M. and C. Hamilton. 2011. The Nagoya Protocol on access to genetic resources and the fair and equitable sharing of benefits arising from their utilization to the Convention on Biological Diversity. Review of European Community & International Environmental Law 20(1):47-61. https://doi.org/10.1111/j.1467-9388.2011.00703.x
  4. Chen, S., L. Song and X. Dong. 2006. Sporacetigenium mesophilum gen. nov., sp. nov., isolated from an anaerobic digester treating municipal solid waste and sewage. International Journal of Systematic and Evolutionary Microbiology 56(4):721-725. https://doi.org/10.1099/ijs.0.63686-0
  5. Chertkov, O., A. Copeland, S. Lucas, A. Lapidus, K.W. Berry, J.C. Detter, T.G. Del Rio, N. Hammon, E. Dalin and H. Tice. 2011. Complete genome sequence of Tolumonas auensis type strain (TA $4^T$). Standards in Genomic Sciences 5(1):112. https://doi.org/10.4056/sigs.2184986
  6. Cirne, D.G., O.D. Delgado, S. Marichamy and B. Mattiasson. 2006. Clostridium lundense sp. nov., a novel anaerobic lipolytic bacterium isolated from bovine rumen. International Journal of Systematic and Evolutionary Microbiology 56(3):625-628. https://doi.org/10.1099/ijs.0.63730-0
  7. Collins, M., P. Lawson, A. Willems, J. Cordoba, J. Fernandez-Garayzabal, P. Garcia, J. Cai, H. Hippe and J. Farrow. 1994. The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. International Journal of Systematic and Evolutionary Microbiology 44(4):812-826.
  8. Du, J. and T.-H. Yi. 2016. Flavobacterium tyrosinilyticum sp. nov., isolated from the rhizosphere of wild strawberry. International Journal of Systematic and Evolutionary Microbiology 66(7):2629-2634. https://doi.org/10.1099/ijsem.0.001104
  9. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17(6):368-376. https://doi.org/10.1007/BF01734359
  10. Finegold, S.M., M.-L. Vaisanen, D.R. Molitoris, T.J. Tomzynski, Y. Song, C. Liu, M.D. Collins and P.A. Lawson. 2003. Cetobacterium somerae sp. nov. from human feces and emended description of the genus Cetobacterium. Systematic and Applied Microbiology 26(2):177-181. https://doi.org/10.1078/072320203322346010
  11. Fitch, W.M. 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Biology 20(4):406-416. https://doi.org/10.1093/sysbio/20.4.406
  12. Grim, C.J., M.L. Kotewicz, K.A. Power, G. Gopinath, A.A. Franco, K.G. Jarvis, Q.Q. Yan, S.A. Jackson, V. Sathyamoorthy and L. Hu. 2013. Pan-genome analysis of the emerging foodborne pathogen Cronobacter spp. suggests a species-level bidirectional divergence driven by niche adaptation. BMC Genomics 14(1):366. https://doi.org/10.1186/1471-2164-14-366
  13. Hong, Y.-Y., Y.-C. Ma, Y.-G. Zhou, F. Gao, H.-C. Liu and S.-F. Chen. 2009. Paenibacillus sonchi sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Sonchus oleraceus. International Journal of Systematic and Evolutionary Microbiology 59(11):2656-2661. https://doi.org/10.1099/ijs.0.009308-0
  14. Inglett, K., H. Bae, H. Aldrich, K. Hatfield and A. Ogram. 2011. Clostridium chromiireducens sp. nov., isolated from Cr (VI)-contaminated soil. International Journal of Systematic and Evolutionary Microbiology 61(11):2626-2631. https://doi.org/10.1099/ijs.0.024554-0
  15. Jabari, L., H. Gannoun, J.-L. Cayol, A. Hedi, M. Sakamoto, E. Falsen, M. Ohkuma, M. Hamdi, G. Fauque and B. Ollivier. 2012. Macellibacteroides fermentans gen. nov., sp. nov., a member of the family Porphyromonadaceae isolated from an upflow anaerobic filter treating abattoir wastewaters. International Journal of Systematic and Evolutionary Microbiology 62(10):2522-2527. https://doi.org/10.1099/ijs.0.032508-0
  16. Kim, J., J.Y. Kim, H.S. Song, I.-T. Cha, S.W. Roh and S.H. Lee. 2019. Paracoccus jeotgali sp. nov., isolated from Korean salted and fermented shrimp. Journal of Microbiology 57(6):444-449. https://doi.org/10.1007/s12275-019-8704-8
  17. Kodama, Y., T. Shimoyama and K. Watanabe. 2012. Dysgonomonas oryzarvi sp. nov., isolated from a microbial fuel cell. International Journal of Systematic and Evolutionary Microbiology 62(12):3055-3059. https://doi.org/10.1099/ijs.0.039040-0
  18. Krieger, C.J., H.R. Beller, M. Reinhard and A.M. Spormann. 1999. Initial reactions in anaerobic oxidation of m-xylene by the denitrifying bacterium Azoarcus sp. strain T. Journal of Bacteriology 181(20):6403-6410. https://doi.org/10.1128/JB.181.20.6403-6410.1999
  19. Kumar, S., G. Stecher and K. Tamura. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33(7):1870-1874. https://doi.org/10.1093/molbev/msw054
  20. Marti, E. and J.L. Balcazar. 2015. Aeromonas rivipollensis sp. nov., a novel species isolated from aquatic samples. Journal of Basic Microbiology 55(12):1435-1439. https://doi.org/10.1002/jobm.201500264
  21. Mishra, A.K., J.-C. Lagier, C. Robert, D. Raoult and P.-E. Fournier. 2012. Non-contiguous finished genome sequence and description of Clostridium senegalense sp. nov. Standards in Genomic Sciences 6(3):386. https://doi.org/10.4056/sigs.2766062
  22. National species list of Korea. 2019. National Institute of Biological Resources, online at http://www.kbr.go.kr, accessed on 1 April 2020.
  23. O'Neal, L., A.J. Obregon-Tito, R.Y. Tito, A.T. Ozga, S.I. Polo, C.M. Lewis Jr and P.A. Lawson. 2015. Clostridium amazonense sp. nov. an obliqately anaerobic bacterium isolated from a remote Amazonian community in Peru. Anaerobe 35:33-37. https://doi.org/10.1016/j.anaerobe.2015.06.005
  24. Ruan, Z., Y. Wang, C. Zhang, J. Song, Y. Zhai, Y. Zhuang, H. Wang, X. Chen, Y. Li and B. Zhao. 2014. Clostridium huakuii sp. nov., an anaerobic, acetogenic bacterium isolated from methanogenic consortia. International Journal of Systematic and Evolutionary Microbiology 64(12):4027-4032. https://doi.org/10.1099/ijs.0.062711-0
  25. Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4(4):406-425.
  26. Sheu, S.-Y., H.-W. Huang, C.-C. Young and W.-M. Chen. 2015. Rhizobium alvei sp. nov., isolated from a freshwater river. International Journal of Systematic and Evolutionary Microbiology 65(2):472-478. https://doi.org/10.1099/ijs.0.065706-0
  27. Stackebrandt, E., I. Kramer, J. Swiderski and H. Hippe. 1999. Phylogenetic basis for a taxonomic dissection of the genus Clostridium. FEMS Immunology & Medical Microbiology 24(3):253-258. https://doi.org/10.1111/j.1574-695X.1999.tb01291.x
  28. Tan, H.-Q., T.-T. Li, C. Zhu, X.-Q. Zhang, M. Wu and X.-F. Zhu. 2012. Parabacteroides chartae sp. nov., an obligately anaerobic species from wastewater of a paper mill. International Journal of Systematic and Evolutionary Microbiology 62(11):2613-2617. https://doi.org/10.1099/ijs.0.038000-0
  29. Thompson, J.D., D.G. Higgins and T.J. 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 Research 22(22):4673-4680. https://doi.org/10.1093/nar/22.22.4673
  30. Tushar, L., T.S. Jyothsna, C. Sasikala and C. Ramana. 2015. Draft genome sequence of antimicrobial-producing Clostridium sp. JC272, isolated from marine sediment. Genome Announc. 3(3):e00650-15.
  31. Wang, Y., J. Song, Y. Zhai, C. Zhang, J. Gerritsen, H. Wang, X. Chen, Y. Li, B. Zhao and B. Zhao. 2015. Romboutsia sedimentorum sp. nov., isolated from an alkaline-saline lake sediment and emended description of the genus Romboutsia. International Journal of Systematic and Evolutionary Microbiology 65(4):1193-1198. https://doi.org/10.1099/ijs.0.000079
  32. Yoon, S.-H., S.-M. 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. International Journal of Systematic and Evolutionary Microbiology 67(5):1613. https://doi.org/10.1099/ijsem.0.001755
  33. Zhang, G.X., G.X. Peng, E.T. Wang, H. Yan, Q.H. Yuan, W. Zhang, X. Lou, H. Wu and Z.Y. Tan. 2008. Diverse endophytic nitrogen-fixing bacteria isolated from wild rice Oryza rufipogon and description of Phytobacter diazotrophicus gen. nov. sp. nov. Archives of Microbiology 189(5):431-439. https://doi.org/10.1007/s00203-007-0333-7
  34. Zhang, Y.Z., W.F. Chen, M. Li, X.H. Sui, H.-C. Liu, X.X. Zhang and W.X. Chen. 2012. Bacillus endoradicis sp. nov., an endophytic bacterium isolated from soybean root. International Journal of Systematic and Evolutionary Microbiology 62(2):359-363. https://doi.org/10.1099/ijs.0.028936-0