1887

Abstract

A Gram-stain-negative, aerobic, non-motile, short-rod bacterium, strain MS2-2, was isolated from mangrove sediment sampled at Jiulong River Estuary, Fujian province, PR China. 16S rRNA gene sequence similarity analysis showed that strain MS2-2 was most closely related to 20V17 (97.41 %) and PrR001 (96.18 %). Phylogenetic trees based on 16S rRNA genes and genome sequences both revealed that strain MS2-2 formed a distinct cluster with 20V17 and PrR001 within family , quite separate from other type species in the genus . The average nucleotide identity value between strain MS2-2 and 20V17 was 78.35 %. Growth of strain MS2-2 was observed at 16–41 ° C (optimum, 34 ° C), pH 3.6–7.5 (pH 6.0) and 0.5–10.0 % (w/v) NaCl (4.0 %). The major cellular fatty acids were summed feature 8 (Cω7 and/or Cω6), C and C. Ubiquinone 10 was the sole quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 67.9 mol%. The combined genotypic and phenotypic data show that strain MS2-2 represents a novel species of a novel genus in the family , for which the name gen. nov., sp. nov. is proposed, with the type strain MS2-2 (=MCCC 1K02682=NBRC 112978). We also propose the reclassification of as comb. nov. and as comb. nov.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003513
2019-08-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/8/2445.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003513&mimeType=html&fmt=ahah

References

  1. Garrity GM, Bell JA, Lilburn T. Rhodobacteraceae fam. nov. In Bergey’s Manual of Systematics of Archaea and Bacteria 2015
    [Google Scholar]
  2. Li J, Huang Z, Lai Q, Liu X, Wang G et al. Oceaniglobus indicus gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from surface seawater. Int J Syst Evol Microbiol 2017; 67:4930–4935 [View Article][PubMed]
    [Google Scholar]
  3. Wang KL, Song ZM, Rong CH, Hao LY, Lai QL et al. Kandeliimicrobium roseum gen. nov., sp. nov., a new member of the family Rhodobacteraceae isolated from mangrove rhizosphere soil. Int J Syst Evol Microbiol 2018; 68:2158–2164 [View Article][PubMed]
    [Google Scholar]
  4. Feng T, Jeong SE, Kim KH, Park HY, Jeon CO et al. 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. Delong EF. Archaea in coastal marine environments. Proc Natl Acad Sci USA 1992; 89:5685–5689 [View Article][PubMed]
    [Google Scholar]
  6. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing 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]
  7. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S et al. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  8. 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]
  9. Rzhetsky A, Nei M. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 1993; 10:1073–1095 [View Article][PubMed]
    [Google Scholar]
  10. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  11. 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]
  12. 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]
  13. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996 [View Article][PubMed]
    [Google Scholar]
  14. 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]
  15. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article][PubMed]
    [Google Scholar]
  16. Yoon SH, Ha SM, 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]
  17. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  18. Jiang L, Xu H, Shao Z, Long M. Defluviimonas indica sp. nov., a marine bacterium isolated from a deep-sea hydrothermal vent environment. Int J Syst Evol Microbiol 2014; 64:2084–2088 [View Article][PubMed]
    [Google Scholar]
  19. Zhang S, Sun C, Xie J, Wei H, Hu Z et al. Defluviimonas pyrenivorans sp. nov., a novel bacterium capable of degrading polycyclic aromatic hydrocarbons. Int J Syst Evol Microbiol 2018; 68:957–961 [View Article][PubMed]
    [Google Scholar]
  20. Foesel BU, Drake HL, Schramm A. Defluviimonas denitrificans gen. nov., sp. nov., and Pararhodobacter aggregans gen. nov., sp. nov., non-phototrophic Rhodobacteraceae from the biofilter of a marine aquaculture. Syst Appl Microbiol 2011; 34:498–502 [View Article][PubMed]
    [Google Scholar]
  21. Collins M. Isoprenoid quinone analysis in bacterial classification and identification. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp. 267–287
    [Google Scholar]
  22. 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]
  23. Cui HL, Gao X, Yang X, Xu XW. Halolamina pelagica gen. nov., sp. nov., a new member of the family Halobacteriaceae . Int J Syst Evol Microbiol 2011; 61:1617–1621 [View Article][PubMed]
    [Google Scholar]
  24. Subhash Y, Tushar L, Sasikala C, Ramana C. 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]
  25. 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][PubMed]
    [Google Scholar]
  26. Helsel LO, Hollis D, Steigerwalt AG, Morey RE, Jordan J et al. Identification of "Haematobacter," a new genus of aerobic Gram-negative rods isolated from clinical specimens, and reclassification of Rhodobacter massiliensis as "Haematobacter massiliensis comb. nov.". J Clin Microbiol 2007; 45:1238–1243 [View Article][PubMed]
    [Google Scholar]
  27. Wang D, Liu H, Zheng S, Wang G. Paenirhodobacter enshiensis gen. nov., sp. nov., a non-photosynthetic bacterium isolated from soil, and emended descriptions of the genera Rhodobacter and Haematobacter . Int J Syst Evol Microbiol 2014; 64:551–558 [View Article][PubMed]
    [Google Scholar]
  28. Imhoff JF, Truper HG, Pfennig N. Rearrangement of the species and genera of the phototrophic "purple nonsulfur bacteria". Int J Syst Bacteriol 1984; 34:340–343 [View Article]
    [Google Scholar]
  29. Srinivas TN, Kumar PA, Sasikala C, Ramana C, Imhoff JF et al. Rhodobacter vinaykumarii sp. nov., a marine phototrophic alphaproteobacterium from tidal waters, and emended description of the genus Rhodobacter . Int J Syst Evol Microbiol 2007; 57:1984–1987 [View Article][PubMed]
    [Google Scholar]
  30. Sorokin DY, Tourova TP, Spiridonova EM, Rainey FA, Muyzer G et al. Thioclava pacifica gen. nov., sp. nov., a novel facultatively autotrophic, marine, sulfur-oxidizing bacterium from a near-shore sulfidic hydrothermal area. Int J Syst Evol Microbiol 2005; 55:1069–1075 [View Article][PubMed]
    [Google Scholar]
  31. Liu Y, Lai Q, Shao Z. Thioclava nitratireducens sp. nov., isolated from surface seawater. Int J Syst Evol Microbiol 2017; 67:2109–2113 [View Article][PubMed]
    [Google Scholar]
  32. Chang R, Bird L, Barr C, Osburn M, Wilbanks E et al. Thioclava electrotropha sp. nov., a versatile electrode and sulfur-oxidizing bacterium from marine sediments. Int J Syst Evol Microbiol 2018; 68:1652–1658 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003513
Loading
/content/journal/ijsem/10.1099/ijsem.0.003513
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
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