1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 10

gen. nov., sp. nov., a new member of the family isolated from a tidal mudflat Free

Abstract

A strictly aerobic, Gram-stain-negative, non-motile, ovoid- and rod-shaped bacterium, designated strain GH1-50, was isolated from a tidal mudflat sample collected from Dongmak seashore on Gangwha Island, Republic of Korea. The organism showed growth at 20–40 °C (optimum, 30 °C), pH 7–8 (optimum, pH 7) and 2–6  % (w/v) NaCl (optimum, 5 %). The genes were present but bacteriochlorophyll a was not detected. The major isoprenoid quinone was Q-10. The polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol, an unidentified aminolipid and five unidentified lipids. The predominant cellular fatty acids were C 7c, C 7c 11-methyl and C. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that the isolate belonged to the family and was loosely associated with members of the recognized genera. The closest relative was the type strain of (96.8 % similarity) followed by (96.4 %). Other members of the family shared 16S rRNA gene similarity values below 96.0 % to the novel isolate. The DNA G+C content calculated from the draft genome sequence was 64.0 %. The average amino acid identity, average nucleotide identity and digital DNA–DNA hybridization values between genome sequences of strain GH1-50 and all the type strains of the recognized taxa compared were <70.0, <84.1 and <20.5 %, respectively. Based on data obtained by a polyphasic approach, strain GH1-50 (=KCTC 72224=NBRC 113929) represents a novel species of a new genus in the family , for which the name gen. nov., sp. nov. is proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Kansaoukella pontilimi , new genus , polyphasic approach , Rhodobacteraceae and tidal mudflat
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004401
2020-08-27
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/10/5235.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004401&mimeType=html&fmt=ahah

References

  1. Garrity GM, Bell JA, Lilburn T. Family I. Rhodobacteraceae fam. nov. In Brenner DJ, Krieg NR, Staley JT, Garrity GM. (editors) Bergey's Manual of Systematic Bacteriology vol 2 (The Proteobacteria), part C (The Alpha-, Beta-, Delta-, and Epsilonproteobacteria, 2nd ed. New York: Springer; 2005 p 161
     [Google Scholar]
  2. Selje N, Simon M, Brinkhoff T. A newly discovered Roseobacter cluster in temperate and polar oceans. Nature 2004; 427:445–448 [View Article][PubMed]
     [Google Scholar]
  3. Brinkhoff T, Giebel H-A, Simon M. Diversity, ecology, and genomics of the Roseobacter clade: a short overview. Arch Microbiol 2008; 189:531–539 [View Article][PubMed]
     [Google Scholar]
  4. Feng T, Jeong SE, Kim KH, Park HY, Jeon CO. Aestuariicoccus marinus gen. nov., sp. nov., isolated from sea-tidal flat sediment. Int J Syst Evol Microbiol 2018; 68:260–265 [View Article][PubMed]
     [Google Scholar]
  5. Park S, Won S-M, Kim H, Park D-S, Yoon J-H. Aestuariivita boseongensis gen. nov., sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2014; 64:2969–2974 [View Article][PubMed]
     [Google Scholar]
  6. Park S, Park J-M, Lee K-C, Bae KS, Yoon J-H. Boseongicola aestuarii gen. nov., sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2014; 64:2618–2624 [View Article][PubMed]
     [Google Scholar]
  7. Kim JM, Jung JY, Chae HB, Park W, Jeon CO. Hwanghaeicola aestuarii gen. nov., sp. nov., a moderately halophilic bacterium isolated from a tidal flat of the Yellow Sea. Int J Syst Evol Microbiol 2010; 60:2877–2881 [View Article][PubMed]
     [Google Scholar]
  8. Park S, Yoon SY, Ha M-J, Yoon J-H. Jindonia aestuariivivens gen. nov., sp. nov., isolated from a tidal flat on the south-western sea in Republic of Korea. J Microbiol 2017; 55:421–427 [View Article][PubMed]
     [Google Scholar]
  9. Park S, Park J-M, Kang C-H, Kim S-G, Yoon J-H. Pseudoseohaeicola caenipelagi gen. nov., sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2015; 65:1819–1824 [View Article][PubMed]
     [Google Scholar]
  10. Lee SD. Maribius pontilimi sp. nov., isolated from a tidal mudflat. Int J Syst Evol Microbiol 2018; 68:353–357 [View Article][PubMed]
     [Google Scholar]
  11. Lee SD. Altererythrobacter lutipelagi sp. nov., isolated from a tidal mudflat, and emended description of the genus Altererythrobacter . Int J Syst Evol Microbiol 2019; 69:1980–1985 [View Article][PubMed]
     [Google Scholar]
  12. Lee SD. Sneathiella limimaris sp. nov., a marine alphaproteobacterium isolated from a tidal mudflat and emended description of the genus Sneathiella . Int J Syst Evol Microbiol 2019; 69:1993–1997 [View Article][PubMed]
     [Google Scholar]
  13. 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]
  14. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 24:4876–4882
     [Google Scholar]
  15. 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]
  16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  17. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416
     [Google Scholar]
  18. Phylip FJ. (Phylogeny Inference Package) version 3.6a. Distributed by the author Seattle, USA: Department of Genome Sciences, University of Washington; 2002
  19. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. editor Mammalian Protein Metabolism New York: Academic Press; 1969 pp 21–132
     [Google Scholar]
  20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  21. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article][PubMed]
     [Google Scholar]
  22. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article][PubMed]
     [Google Scholar]
  23. 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]
  24. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–668
     [Google Scholar]
  25. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 2014; 9:111–118
     [Google Scholar]
  26. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
     [Google Scholar]
  27. Wirth JS, Whitman WB. Phylogenomic analyses of a clade within the Roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera. Int J Syst Evol Microbiol 2018; 68:2393–2411 [View Article][PubMed]
     [Google Scholar]
  28. Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Bell ME et al. Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. Int J Syst Evol Microbiol 2020 [View Article][PubMed]
     [Google Scholar]
  29. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
     [Google Scholar]
  30. Pfeifer F. Gas vesicles of archaea and bacteria. In Shively JM. editor Complex Intracellular Structures in Prokaryotes Verlag Berlin Heidelberg: Springer; 2006 pp 116–140
     [Google Scholar]
  31. Allgaier M, Uphoff H, Felske A, Wagner-Döbler I. Aerobic anoxygenic photosynthesis in Roseobacter clade bacteria from diverse marine habitats. Appl Environ Microbiol 2003; 69:5051–5059 [View Article][PubMed]
     [Google Scholar]
  32. Biebl H, Wagner-Döbler I. Growth and bacteriochlorophyll a formation in taxonomically diverse aerobic anoxygenic phototrophic bacteria in chemostat culture: influence of light regimen and starvation. Process Biochem 2006; 41:2153–2159
     [Google Scholar]
  33. Biebl H, Tindall BJ, Pukall R, Lünsdorf H, Allgaier M et al. Hoeflea phototrophica sp. nov., a novel marine aerobic alphaproteobacterium that forms bacteriochlorophyll a. Int J Syst Evol Microbiol 2006; 56:821–826 [View Article][PubMed]
     [Google Scholar]
  34. Zhang Y, Xu Y, Fang W, Wang X, Fang Z et al. Pseudoruegeria marinistellae sp. nov., isolated from an unidentified starfish in Sanya, China. Antonie van Leeuwenhoek 2017; 110:187–194 [View Article][PubMed]
     [Google Scholar]
  35. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241
     [Google Scholar]
  36. Kroppenstedt RM. Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 173–199
     [Google Scholar]
  37. Minnikin DE, Patal PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–107
     [Google Scholar]
  38. Lee K, Choo Y-J, Giovannoni SJ, Cho J-C. Maritimibacter alkaliphilus gen. nov., sp. nov., a genome-sequenced marine bacterium of the Roseobacter clade in the order Rhodobacterales . Int J Syst Evol Microbiol 2007; 57:1653–1658 [View Article][PubMed]
     [Google Scholar]
  39. Zhong Z-P, Liu Y, Zhou Y-G, Liu H-C, Wang F et al. Maritimibacter lacisalsi sp. nov., isolated from a salt lake, and emended description of the genus Maritimibacter Lee et al. 2007. Int J Syst Evol Microbiol 2015; 65:3462–3468 [View Article][PubMed]
     [Google Scholar]
  40. Lai PY, Miao L, Lee OO, Liu L-L, Zhou X-J et al. Profundibacterium mesophilum gen. nov., sp. nov., a novel member in the family Rhodobacteraceae isolated from deep-sea sediment in the Red Sea, Saudi Arabia. Int J Syst Evol Microbiol 2013; 63:1007–1012 [View Article][PubMed]
     [Google Scholar]
  41. Yoon J-H, Lee S-Y, Kang S-J, Lee C-H, Oh T-K. Pseudoruegeria aquimaris gen. nov., sp. nov., isolated from seawater of the East Sea in Korea. Int J Syst Evol Microbiol 2007; 57:542–547 [View Article][PubMed]
     [Google Scholar]
  42. Jung Y-T, Kim B-H, Oh T-K, Yoon J-H. Pseudoruegeria lutimaris sp. nov., isolated from a tidal flat sediment, and emended description of the genus Pseudoruegeria . Int J Syst Evol Microbiol 2010; 60:1177–1181 [View Article][PubMed]
     [Google Scholar]
  43. Hyun D-W, Shin N-R, Kim M-S, Kim PS, Kim JY et al. Pseudoruegeria haliotis sp. nov., isolated from the gut of the abalone Haliotis discus hannai. Int J Syst Evol Microbiol 2013; 63:4626–4632 [View Article][PubMed]
     [Google Scholar]
  44. Park S, Jung Y-T, Won S-M, Yoon J-H. Pseudoruegeria sabulilitoris sp. nov., isolated from seashore sand. Int J Syst Evol Microbiol 2014; 64:3276–3281 [View Article][PubMed]
     [Google Scholar]
  45. Cha I-T, Park I, Lee H-W, Lee H, Park J-M et al. Pseudoruegeria aestuarii sp. nov., of the family Rhodobacteraceae, isolated from a tidal flat. Int J Syst Evol Microbiol 2016; 66:3125–3131 [View Article][PubMed]
     [Google Scholar]
  46. Park S, Park J-M, Yoon J-H. Pseudoruegeria insulae sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2018; 68:3587–3592 [View Article][PubMed]
     [Google Scholar]
  47. Harwati TU, Kasai Y, Kodama Y, Susilaningsih D, Watanabe K. Tropicimonas isoalkanivorans gen. nov., sp. nov., a branched-alkane-degrading bacterium isolated from Semarang Port in Indonesia. Int J Syst Evol Microbiol 2009; 59:388–391 [View Article][PubMed]
     [Google Scholar]
  48. Oh K-H, Choi W-C, Jung Y-T, Kang S-J, Oh T-K et al. Tropicimonas aquimaris sp. nov., isolated from seawater, and emended description of the genus Tropicimonas Harwati et al. 2009. Int J Syst Evol Microbiol 2012; 62:688–692 [View Article][PubMed]
     [Google Scholar]
  49. Shin N-R, Roh SW, Kim M-S, Yun B, Whon TW et al. Tropicimonas sediminicola sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2012; 62:2424–2429 [View Article][PubMed]
     [Google Scholar]
  50. Oh M, Kim J-H, Kim W. Tropicimonas arenosa sp. nov., isolated from marine sand. Int J Syst Evol Microbiol 2016; 66:5514–5518 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004401
Loading
Kangsaoukella pontilimi gen. nov., sp. nov., a new member of the family Rhodobacteraceae isolated from a tidal mudflat
Int J Syst Evol Microbiol 70, 5235 (2020); https://doi.org/10.1099/ijsem.0.004401
/content/journal/ijsem/10.1099/ijsem.0.004401
/content/journal/ijsem/10.1099/ijsem.0.004401
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error