1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 12

sp. nov., a marine bacterium isolated from a tidal flat and reclassification of , and comb. nov., comb. nov. and comb. nov. No Access

Abstract

A yellow-coloured bacterium, designated strain JGD-16, was isolated from a tidal flat in Janggu-do, Garorim Bay, Taean-gun, Chungcheongbuk-do, Republic of Korea. Cells were Gram-stain-negative, aerobic, non-flagellated and short ovoid to coccoid-shaped. Growth was observed at 10–37 °C (optimum, 30 °C), pH 6.0–9.0 (pH 8.0) and with 1–5% (w/v) NaCl (2%). Results of 16S rRNA gene sequence analysis indicated that strain JGD-16 was closely related to LY02 (97.1 %), O30 (96.3 %), JPCCMB0017 (95.8 %), JCS350 (95.7 %) and BPTF-M16 (95.3%). Phylogenomic analysis using the maximum-likelihood algorithm showed that strain JGD-16 formed a clade with the genus . The genomic DNA G+C content was 57.8 mol%. The predominant respiratory quinone was ubiquinone-10. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, a sphingoglycolipid, an unidentified glycolipid and an unidentified lipid. The major fatty acids were C 7 (31.5 %) and C 6 (19.6 %). On the basis of its phylogenomic, physiological and chemotaxonomical characteristics, strain JGD-16 represents a novel species within the genus , for which the name JGD-16sp. nov. is proposed. The type strain is JGD-16 (=KCTC 72632=KACC 21405=JCM 33750). We also propose the reclassification of as comb. nov., as comb. nov. and as comb. nov.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Altererythrobacter , Erythrobacteraceae , marine bacteria and tidal flats
Funding
This study was supported by the:
  • korea university grant
    • Principle Award Recipient: DongjunKim
  • ministry of oceans and fisheries (Award 20210427 and 20170325)
    • Principle Award Recipient: DongjunKim
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005134
2021-12-07
2024-04-24
Loading full text...

Full text loading...

References

  1. Shiba T, Simidu U. Erythrobacter longus gen. nov., sp. nov., an aerobic bacterium which contains bacteriochlorophyll a. Int J Syst Evol Microbiol 1982; 32:211–217 [View Article]
     [Google Scholar]
  2. Yurkov V, Stackebrandt E, Holmes A, Fuerst JA, Hugenholtz P et al. Phylogenetic positions of novel aerobic, bacteriochlorophyll a-containing bacteria and description of Roseococcus thiosulfatophilus gen. nov., sp. nov., Erythromicrobium ramosum gen. nov., sp. nov., and Erythrobacter litoralis sp. nov. Int J Syst Evol Microbiol 1994; 44:427–434 [View Article]
     [Google Scholar]
  3. Fuerst JA, Hawkins JA, Holmes A, Sly LI, Moore CJ et al. Porphyrobacter neustonensis gen. nov., sp. nov., an aerobic bacteriochlorophyll-synthesizing budding bacterium from fresh water. Int J Syst Evol Microbiol 1993; 43:125–134 [View Article]
     [Google Scholar]
  4. Lee K-B, Liu C-T, Anzai Y, Kim H, Aono T et al. The hierarchical system of the ‘Alphaproteobacteria’: description of Hyphomonadaceae fam nov, Xanthobacteraceae fam nov and Erythrobacteraceae fam nov. Int J Syst Evol 2005; 55:1907–1919
     [Google Scholar]
  5. Kwon KK, Woo J-H, Yang S-H, Kang J-H, Kang SG et al. Altererythrobacter epoxidivorans gen. nov., sp. nov., an epoxide hydrolase-active, mesophilic marine bacterium isolated from cold-seep sediment, and reclassification of Erythrobacter luteolus Yoon et al. 2005 as Altererythrobacter luteolus comb. nov. Int J Syst Evol Microbiol 2007; 57:2207–2211 [View Article] [PubMed]
     [Google Scholar]
  6. Liu Y-H, Fang B-Z, Dong Z-Y, Li L, Mohamad OAA et al. Croceibacterium gen. nov., with description of Croceibacterium ferulae sp. nov., an endophytic bacterium isolated from Ferula sinkiangensis K. M. Shen and reclassification of Porphyrobacter mercurialis as Croceibacterium mercuriale comb. nov. Int J Syst Evol Microbiol 2019; 69:2547–2554 [View Article] [PubMed]
     [Google Scholar]
  7. Xu X-W, Wu Y-H, Wang C-S, Wang X-G, Oren A et al. Croceicoccus marinus gen. nov., sp. nov., a yellow-pigmented bacterium from deep-sea sediment, and emended description of the family Erythrobacteraceae. Int J Syst Evol Microbiol 2009; 59:2247–2253 [View Article] [PubMed]
     [Google Scholar]
  8. Feng X-M, Mo Y-X, Han L, Nogi Y, Zhu Y-H et al. Qipengyuania sediminis gen. nov., sp. nov., a member of the family Erythrobacteraceae isolated from subterrestrial sediment. Int J Syst Evol Microbiol 2015; 65:3658–3665 [View Article] [PubMed]
     [Google Scholar]
  9. Xu L, Sun C, Fang C, Oren A, Xu X-W. Genomic-based taxonomic classification of the family Erythrobacteraceae. Int J Syst Evol Microbiol 2020; 70:4470–4495 [View Article] [PubMed]
     [Google Scholar]
  10. Yoon J-H, Kang KH, Yeo S-H, Oh T-K. Erythrobacter luteolus sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2005; 55:1167–1170 [View Article] [PubMed]
     [Google Scholar]
  11. Parte AC. LPSN--list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014; 42:D613–6 [View Article] [PubMed]
     [Google Scholar]
  12. Xue X, Zhang K, Cai F, Dai J, Wang Y et al. Altererythrobacter xinjiangensis sp. nov., isolated from desert sand, and emended description of the genus Altererythrobacter. Int J Syst Evol Microbiol 2012; 62:28–32 [View Article] [PubMed]
     [Google Scholar]
  13. Dahal RH, Kim J. Altererythrobacter fulvus sp. nov., a novel alkalitolerant alphaproteobacterium isolated from forest soil. Int J Syst Evol Microbiol 2018; 68:1502–1508 [View Article] [PubMed]
     [Google Scholar]
  14. Yan Z-F, Lin P, Won K-H, Yang J-E, Li C-T et al. Altererythrobacter deserti sp. nov., isolated from desert soil. Int J Syst Evol Microbiol 2017; 67:3806–3811 [View Article] [PubMed]
     [Google Scholar]
  15. Lee DW, Lee H, Kwon B-O, Khim JS, Yim UH et al. Biosurfactant-assisted bioremediation of crude oil by indigenous bacteria isolated from Taean beach sediment. Environ Pollut 2018; 241:254–264 [PubMed]
     [Google Scholar]
  16. Lee DW, Lee H, Lee AH, Kwon B-O, Khim JS et al. Microbial community composition and PAHs removal potential of indigenous bacteria in oil contaminated sediment of Taean coast, Korea. Environ Pollut 2018; 234:503–512 [PubMed]
     [Google Scholar]
  17. Hopwood DA, Bibb M, Chater K, Kieser T, Bruton C et al. Genetic manipulation of Streptomyces–A laboratory manual; 1985
  18. Lane D. 16S/23S rRNA sequencing In Nucleic Acid Techniques in Bacterial Systematics Chichester, UK: John Wiley & Sons; 1991
     [Google Scholar]
  19. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. troducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article] [PubMed]
     [Google Scholar]
  20. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article] [PubMed]
     [Google Scholar]
  21. 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]
  22. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  23. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
     [Google Scholar]
  24. 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]
  25. Paradis E, Claude J, Strimmer K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 2004; 20:289–290 [View Article] [PubMed]
     [Google Scholar]
  26. Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 2019; 20:1–14
     [Google Scholar]
  27. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
     [Google Scholar]
  28. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552 [View Article] [PubMed]
     [Google Scholar]
  29. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
     [Google Scholar]
  30. Claus D. A standardized Gram staining procedure. World J Microbiol Biotechnol 1992; 8:451–452 [View Article]
     [Google Scholar]
  31. Bernardet J-F, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [PubMed]
     [Google Scholar]
  32. Phillips RW, Wiegel J, Berry CJ, Fliermans C, Peacock AD et al. Kineococcus radiotolerans sp. nov., a radiation-resistant, gram-positive bacterium. Int J Syst Evol Microbiol 2002; 52:933–938 [View Article] [PubMed]
     [Google Scholar]
  33. Yoo Y, Lee DW, Lee H, Kwon B-O, Khim JS et al. Gemmobacter lutimaris sp. nov., a marine bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 2019; 69:1676–1681 [View Article] [PubMed]
     [Google Scholar]
  34. Yoo Y, Lee H, Kwon B-O, Khim JS, Baek S et al. Marinobacter halodurans sp. nov., a halophilic bacterium isolated from sediment of a salt flat. Int J Syst Evol Microbiol 2020; 70:6294–6300 [View Article] [PubMed]
     [Google Scholar]
  35. Collins M. Analysis of isoprenoid quinones. Methods Microbiol 1985; 18:329–366
     [Google Scholar]
  36. Kroppenstedt R. Fatty acid and menaquinone analysis of actinomycetes and related organisms. Soc Appl Bacteriol Technical Series 1985173–199
     [Google Scholar]
  37. 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 [View Article]
     [Google Scholar]
  38. Kates M. Techniques of lipidology. In Laboratory Techniques in Biochemistry and Molecular Biotechniques in Biochemistry and Molecular Biology vol. 3 Elsevier; 1972
     [Google Scholar]
  39. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI technical note 101. Newark, DE: MIDI inc; 1990
     [Google Scholar]
  40. Qin D, Ma C, Hu A, Zhang F, Hu H et al. Altererythrobacter estronivorus sp. nov., an estrogen-degrading strain isolated from Yundang Lagoon of Xiamen City in China. Curr Microbiol 2016; 72:634–640 [View Article] [PubMed]
     [Google Scholar]
  41. Azpiazu-Muniozguren M, Martinez-Ballesteros I, Gamboa J, Seoane S, Alonso R et al. Altererythrobacter muriae sp. nov., isolated from hypersaline Añana Salt Valley spring water, a continental thalassohaline-type solar saltern. Int J Syst Evol Microbiol 2019; 71:004734 [View Article]
     [Google Scholar]
  42. Lei X, Li Y, Chen Z, Zheng W, Lai Q et al. Altererythrobacter xiamenensis sp. nov., an algicidal bacterium isolated from red tide seawater. Int J Syst Evol Microbiol 2014; 64:631–637 [View Article] [PubMed]
     [Google Scholar]
  43. Matsumoto M, Iwama D, Arakaki A, Tanaka A, Tanaka T et al. Altererythrobacter ishigakiensis sp. nov., an astaxanthin-producing bacterium isolated from a marine sediment. Int J Syst Evol Microbiol 2011; 61:2956–2961 [View Article] [PubMed]
     [Google Scholar]
  44. Park S, Park J-M, Oh T-K, Yoon J-H. Altererythrobacter insulae sp. nov., a lipolytic bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 2019; 69:1009–1015 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005134
Loading
Altererythrobacter lutimaris sp. nov., a marine bacterium isolated from a tidal flat and reclassification of Altererythrobacter deserti, Altererythrobacter estronivorus and Altererythrobacter muriae as Tsuneonella deserti comb. nov., Croceicoccus estronivorus comb. nov. and Alteripontixanthobacter muriae comb. nov.
Int J Syst Evol Microbiol 71, 005134 (2021); https://doi.org/10.1099/ijsem.0.005134
/content/journal/ijsem/10.1099/ijsem.0.005134
/content/journal/ijsem/10.1099/ijsem.0.005134
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