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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 9

sp. nov., a member of the isolated from the marine red algae sp. No Access

Abstract

A Gram-negative, pale yellow-pigmented, non-flagellated, motile, rod-shaped and aerobic bacterium, designated strain PG104, was isolated from red algae sp. collected from the coastal area of Pohang, Republic of Korea. Growth of strain PG104 was observed at 15–35 °C (optimum, 30 °C), pH 6.0–10.0 (optimum, pH 7.5–8.0) and in the presence of 0–8.0 % (w/v) NaCl (optimum, 5.0 %). The predominant fatty acids included C, C, 11-methyl C 7 and summed feature 8 (C 7 and/or C 6) and the major respiratory quinone was Q-10. Polar lipids included phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified lipid and one unidentified aminolipid. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain PG104 formed a phylogenetic lineage with members of the genus and exhibited 16S rRNA gene sequence similarities of 97.1 and 96.6 % to W402 and JA744, respectively. The complete genome of strain PG104 consisted of a single circular chromosome of approximately 2.8 Mbp with five plasmids. Based on polyphasic taxonomic data, strain PG104 represents a novel species in the genus , for which the name sp. nov. is proposed. The type strain of is PG104 (=KCTC 82230=JCM 34380).

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Keyword(s): Falsirhodobacter algicola , Grateloupia sp. , new taxa , PG104 and Rhodobacteraceae
© 2023 The Authors
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/content/journal/ijsem/10.1099/ijsem.0.006056
2023-09-26
2024-05-08
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References

  1. Subhash Y, Tushar L, Sasikala C, Ramana CV. Falsirhodobacter halotolerans gen. nov., sp. nov., isolated from dry soils of a solar saltern. Int J Syst Evol Microbiol 2013; 63:2132–2137 [View Article] [PubMed]
     [Google Scholar]
  2. Wang L, Zhou Z, Wu G, Chen M, Lin M et al. Falsirhodobacter deserti sp. nov., isolated from sandy soil. Int J Syst Evol Microbiol 2015; 65:650–655 [View Article]
     [Google Scholar]
  3. Tanaka Y, Tamaki H, Matsuzawa H, Nigaya M, Mori K et al. Microbial community analysis in the roots of aquatic plants and isolation of novel microbes including an organism of the candidate phylum OP10. Microbes Environ 2012; 27:149–157 [View Article] [PubMed]
     [Google Scholar]
  4. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics New York: Wiley; 1991 pp 115–175
     [Google Scholar]
  5. Lee I, Kim YO, 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]
  6. 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]
  7. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  8. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
     [Google Scholar]
  9. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
     [Google Scholar]
  10. Nawrocki EP, Eddy SR. Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Comput Biol 2007; 3:e56 [View Article] [PubMed]
     [Google Scholar]
  11. Kim M, Oh HS, Park SC, 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]
  12. Kwon YM, Patra AK, Chung D, Yang Y. Complete genome sequence of Falsirhodobacter sp. Pg104, an alginate-degrading marine bacterium. Korean J Microbiol 2020; 56:327–330
     [Google Scholar]
  13. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365 [View Article] [PubMed]
     [Google Scholar]
  14. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [View Article] [PubMed]
     [Google Scholar]
  15. Lombard V, Bernard T, Rancurel C, Brumer H, Coutinho PM et al. A hierarchical classification of polysaccharide lyases for glycogenomics. Biochem J 2010; 432:437–444 [View Article] [PubMed]
     [Google Scholar]
  16. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
     [Google Scholar]
  17. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  18. Osterås M, Boncompagni E, Vincent N, Poggi MC, Le Rudulier D. Presence of a gene encoding choline sulfatase in Sinorhizobium meliloti bet operon: choline-O-sulfate is metabolized into glycine betaine. Proc Natl Acad Sci 1998; 95:11394–11399 [View Article] [PubMed]
     [Google Scholar]
  19. Gerdes K, Christensen SK, Løbner-Olesen A. Prokaryotic toxin-antitoxin stress response loci. Nat Rev Microbiol 2005; 3:371–382 [View Article] [PubMed]
     [Google Scholar]
  20. Mori T, Takahashi M, Tanaka R, Miyake H, Shibata T et al. Falsirhodobacter sp. alg1 harbors single homologs of endo and exo-type alginate lyases efficient for alginate depolymerization. PLoS One 2016; 11:e0155537 [View Article] [PubMed]
     [Google Scholar]
  21. Teramoto M, Takaichi S, Inomata Y, Ikenaga H, Misawa N. Structural and functional analysis of a lycopene beta-monocyclase gene isolated from a unique marine bacterium that produces myxol. FEBS Lett 2003; 545:120–126 [View Article] [PubMed]
     [Google Scholar]
  22. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kämpfer P et al. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 2002; 52:1043–1047 [View Article]
     [Google Scholar]
  23. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  24. Wang H, Sha X, Li R, Li Y, Khaleque HN et al. Comparative genome analysis provides molecular evidence for reclassification of the photosynthetic bacterium Rhodobacter sphaeroides EBL0706 as a strain of Luteovulum azotoformans. Microorganisms 2021; 9:1754 [View Article]
     [Google Scholar]
  25. Sheu C, Li ZH, Sheu SY, Yang CC, Chen WM. Tabrizicola oligotrophica sp. nov. and Rhodobacter tardus sp. nov., two new species of bacteria belonging to the family Rhodobacteraceae. Int J Syst Evol Microbiol 2020; 70:6266–6283 [View Article]
     [Google Scholar]
  26. Conrad JC, Gibiansky ML, Jin F, Gordon VD, Motto DA et al. Flagella and pili-mediated near-surface single-cell motility mechanisms in P. aeruginosa. Biophys J 2011; 100:1608–1616 [View Article] [PubMed]
     [Google Scholar]
  27. 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 [View Article] [PubMed]
     [Google Scholar]
  28. Kwon YM, Yang S-H, Kwon KK, Kim S-J. Nonlabens antarcticus sp. nov., a psychrophilic bacterium isolated from glacier ice, and emended descriptions of Nonlabens marinus Park et al. 2012 and Nonlabens agnitus Yi and Chun 2012. Int J Syst Evol Microbiol 2014; 64:400–405 [View Article] [PubMed]
     [Google Scholar]
  29. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P. ed Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  30. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note vol 101 Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  31. 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]
  32. Collins MD. Isoprenoid quinone analysis in bacterial classification and identification. In Goodfellow M, Minnikin DE. eds Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 267–287
     [Google Scholar]
  33. Blatt A, Lohr M. Extraction and analysis of carotenoids from Escherichia coli in color complementation assays. Bio Protoc 2017; 7:e2179 [View Article] [PubMed]
     [Google Scholar]
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Falsirhodobacter algicola sp. nov., a member of the Rhodobacteraceae isolated from the marine red algae Grateloupia sp.
Int J Syst Evol Microbiol 73, 006056 (2023); https://doi.org/10.1099/ijsem.0.006056
/content/journal/ijsem/10.1099/ijsem.0.006056
/content/journal/ijsem/10.1099/ijsem.0.006056
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