sp. nov., isolated from freshwater sediment and reclassification of as comb. nov. Free

Abstract

A polyphasic taxonomic study was carried out on strains CHu50b-3-2 and CHu40b-3-1 isolated from a 67 cm-long sediment core collected from the Daechung Reservoir at a water depth of 17 m, Daejeon, Republic of Korea. The cells of the strains were Gram-stain-negative, non-spore-forming, non-motile and rod-shaped. Comparative 16S rRNA gene sequence studies showed a clear affiliation of two strains with , which showed the highest pairwise sequence similarities to KTce-2 (96.5 %), Gsoil193 (96.3 %), Gsoil 357 (96.1 %), T20R-70 (96.1 %), KCTC 12130 (95.4 %) and YC5194 (95.3 %). The phylogenetic analysis based on 16S rRNA gene sequences showed that the strains formed a clear phylogenetic lineage with the genus . The major fatty acids were identified as summed feature 9 (iso-C 9 and/or C 10-methyl), iso-C, iso-C and iso-C. The respiratory quinone was identified as ubiquinone Q-8. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The genomic DNA G+C content was determined to be 66.8 mol% (genome) for strain CHu50b-3-2 and 66.4 mol% (HPLC) for strain CHu40b-3-1. Based on the combined genotypic and phenotypic data, we propose that strains CHu50b-3-2 and CHu40b-3-1 represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is CHu50b-3-2 (=KCTC 72973=CCTCC AB 2019129). Besides Gsoil 068 formed a phylogenetic group together with strain RIB1-20 (EF626688) that is clearly separated from all other known strains. Based on the phylogenetic relationships together with fatty acid compositions, Gsoil 068 should be reclassified as a member of the genus comb. nov. (type strain Gsoil 068=KCTC 12601=DSM 17927).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004253
2020-06-08
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/6/3878.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004253&mimeType=html&fmt=ahah

References

  1. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article][PubMed]
    [Google Scholar]
  2. Christensen P, Cook FD. Lysobacter, a new genus of nonfruiting, gliding bacteria with a high base ratio. Int J Syst Bacteriol 1978; 28:367–393 [View Article]
    [Google Scholar]
  3. Bae H-S, Im W-T, Lee S-T. Lysobacter concretionis sp. nov., isolated from anaerobic granules in an upflow anaerobic sludge blanket reactor. Int J Syst Evol Microbiol 2005; 55:1155–1161 [View Article][PubMed]
    [Google Scholar]
  4. Romanenko LA, Uchino M, Tanaka N, Frolova GM, Mikhailov VV. Lysobacter spongiicola sp. nov., isolated from a deep-sea sponge. Int J Syst Evol Microbiol 2008; 58:370–374 [View Article][PubMed]
    [Google Scholar]
  5. Fukuda W, Kimura T, Araki S, Miyoshi Y, Atomi H et al. Lysobacter oligotrophicus sp. nov., isolated from an Antarctic freshwater lake in Antarctica. Int J Syst Evol Microbiol 2013; 63:3313–3318 [View Article][PubMed]
    [Google Scholar]
  6. Lin S-Y, Hameed A, Wen C-Z, Liu Y-C, Hsu Y-H et al. Lysobacter lycopersici sp. nov., isolated from tomato plant Solanum lycopersicum . Antonie van Leeuwenhoek 2015; 107:1261–1270 [View Article][PubMed]
    [Google Scholar]
  7. Yang S-Z, Feng G-D, Zhu H-H, Wang Y-H. Lysobacter mobilis sp. nov., isolated from abandoned lead-zinc ore. Int J Syst Evol Microbiol 2015; 65:833–837 [View Article][PubMed]
    [Google Scholar]
  8. Siddiqi MZ, Im W-T. Lysobacter hankyongensis sp. nov., isolated from activated sludge and Lysobacter sediminicola sp. nov., isolated from freshwater sediment. Int J Syst Evol Microbiol 2016; 66:212–218 [View Article][PubMed]
    [Google Scholar]
  9. Lee D, Jang JH, Cha S, Seo T. Lysobacter humi sp. nov., isolated from soil. Int J Syst Evol Microbiol 2017; 67:951–955 [View Article][PubMed]
    [Google Scholar]
  10. Im W-T, Siddiqi MZ, Kim S-Y, Huq MA, Lee JH et al. Lysobacter lacus sp. nov., isolated from from lake sediment. Int J Syst Evol Microbiol 2020 [View Article][PubMed]
    [Google Scholar]
  11. Xu L, Huang X-X, Fan D-L, Sun J-Q. Lysobacter alkalisoli sp. nov., a chitin-degrading strain isolated from saline-alkaline soil. Int J Syst Evol Microbiol 2020; 70:1273–1281 [View Article][PubMed]
    [Google Scholar]
  12. Bai H, Lv H, Deng A, Jiang X, Li X et al. Lysobacter oculi sp. nov., isolated from human Meibomian gland secretions. Antonie van Leeuwenhoek 2020; 113:13–20 [View Article][PubMed]
    [Google Scholar]
  13. Yassin AF, Chen W-M, Hupfer H, Siering C, Kroppenstedt RM et al. Lysobacter defluvii sp. nov., isolated from municipal solid waste. Int J Syst Evol Microbiol 2007; 57:1131–1136 [View Article][PubMed]
    [Google Scholar]
  14. Oh K-H, Kang S-J, Jung Y-T, Oh T-K, Yoon J-H. Lysobacter dokdonensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2011; 61:1089–1093 [View Article][PubMed]
    [Google Scholar]
  15. Luo G, Shi Z, Wang G. Lysobacter arseniciresistens sp. nov., an arsenite-resistant bacterium isolated from iron-mined soil. Int J Syst Evol Microbiol 2012; 62:1659–1665 [View Article][PubMed]
    [Google Scholar]
  16. Jeong SE, Lee HJ, Jeon CO. Lysobacter aestuarii sp. nov., isolated from estuary sediment. Int J Syst Evol Microbiol 2016; 66:1346–1351 [View Article][PubMed]
    [Google Scholar]
  17. Margesin R, Zhang D-C, Albuquerque L, Froufe HJC, Egas C et al. Lysobacter silvestris sp. nov., isolated from alpine forest soil, and reclassification of Luteimonas tolerans as Lysobacter tolerans comb. nov. Int J Syst Evol Microbiol 2018; 68:1571–1577 [View Article][PubMed]
    [Google Scholar]
  18. Tarrand JJ, Gröschel DH, Rapid GDHM. Rapid, modified oxidase test for oxidase-variable bacterial isolates. J Clin Microbiol 1982; 16:772–774 [View Article][PubMed]
    [Google Scholar]
  19. Ren T-T, Jin C-Z, Jin F-J, Li T, Kim C-J et al. Flavihumibacter profundi sp. nov., isolated from eutrophic freshwater sediment. J Microbiol 2018; 56:467–471 [View Article][PubMed]
    [Google Scholar]
  20. Komagata K, Suzuki KI. Lipid and cell wall analysis in bacterial Systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  21. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
    [Google Scholar]
  22. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester, UK: John Wiley & Sons; 1991
    [Google Scholar]
  23. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article][PubMed]
    [Google Scholar]
  24. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucl Acids Symp Ser 1999; 41:95–98
    [Google Scholar]
  25. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
    [Google Scholar]
  26. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  27. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  28. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  29. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  30. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article][PubMed]
    [Google Scholar]
  31. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  32. Tamaoka J, Komagata K. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 1984; 25:125–128 [View Article]
    [Google Scholar]
  33. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
    [Google Scholar]
  34. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  35. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
    [Google Scholar]
  36. Weon H-Y, Kim B-Y, Baek Y-K, Yoo S-H, Kwon S-W et al. Two novel species, Lysobacter daejeonensis sp. nov. and Lysobacter yangpyeongensis sp. nov., isolated from Korean greenhouse soils. Int J Syst Evol Microbiol 2006; 56:947–951 [View Article][PubMed]
    [Google Scholar]
  37. Chhetri G, Kim J, Kim I, Seo T. Lysobacter caseinilyticus, sp. nov., a casein hydrolyzing bacterium isolated from sea water. Antonie van Leeuwenhoek 2019; 112:1349–1356 [View Article][PubMed]
    [Google Scholar]
  38. Kim I, Choi J, Chhetri G, Seo T. Lysobacter helvus sp. nov. and Lysobacter xanthus sp. nov., isolated from Soil in South Korea. Antonie van Leeuwenhoek 2019; 112:1253–1262 [View Article][PubMed]
    [Google Scholar]
  39. Ten LN, Jung H-M, Im W-T, Yoo S-A, Oh H-M et al. Lysobacter panaciterrae sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2009; 59:958–963 [View Article][PubMed]
    [Google Scholar]
  40. Jung H-M, Ten LN, Im W-T, Yoo S-A, Lee S-T. Lysobacter ginsengisoli sp. nov., a novel species isolated from soil in Pocheon Province, South Korea. J Microbiol Biotechnol 2008; 18:1496–1499[PubMed]
    [Google Scholar]
  41. Kim S-J, Ahn J-H, Weon H-Y, Joa J-H, Hong S-B et al. Lysobacter solanacearum sp. nov., isolated from rhizosphere of tomato. Int J Syst Evol Microbiol 2017; 67:1102–1106 [View Article][PubMed]
    [Google Scholar]
  42. Park JH, Kim R, Aslam Z, Jeon CO, Chung YR. Lysobacter capsici sp. nov., with antimicrobial activity, isolated from the rhizosphere of pepper, and emended description of the genus Lysobacter . Int J Syst Evol Microbiol 2008; 58:387–392 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004253
Loading
/content/journal/ijsem/10.1099/ijsem.0.004253
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed