1887

Abstract

A Gram-stain-negative, mesophilic bacterial strain, designated SBU1, which degrades polycyclic aromatic hydrocarbons was isolated from the sediments of the mangrove forests of Nayband Bay in the Iranian Persian Gulf during a bioremediation experiment. The 16S rRNA gene sequence of strain SBU1 exhibited highest similarities with P73 (98.52 %) and H 14 (97.05 %). Phylogenetic analysis, based on 16S rRNA gene sequences, demonstrated that strain SBU1 fell within a cluster consisting of the type strains of species of the genus and formed a stable clade with P73 in trees generated with three algorithms. The fatty acid profile of strain SBU1 consisted of the major fatty acids Cω7/ω6 and Cω7 11-methyl. The major compounds in the polar lipid profile were one phosphatidylglycerol and four unidentified phospholipids. The quinone system exclusively comprised ubiquinone (Q-10). The DNA G+C content was 60.4 mol%. A combination of phylogenetic analysis, DNA–DNA hybridization estimation, average nucleotide identity results and differential phenotypic and chemotaxonomic characteristics demonstrated that strain SBU1 could be distinguished from its close relatives. Therefore, strain SBU1 is considered to represent a novel species of the genus for which the name sp. nov. is proposed. The type strain is SBU1 ( = MCCC 1A00672 = DSM 100434).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000961
2016-04-01
2019-12-14
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/4/1875.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000961&mimeType=html&fmt=ahah

References

  1. Auch A. F., von Jan M., Klenk H. P., Göker M.. 2010; Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci2:117–134 [CrossRef][PubMed]
    [Google Scholar]
  2. Baek K., Choi A., Kang I., Cho J. C.. 2014; Celeribacter marinus sp. nov., isolated from coastal seawater. Int J Syst Evol Microbiol64:1323–1327 [CrossRef][PubMed]
    [Google Scholar]
  3. Buchan A., González J. M., Moran M. A.. 2005; Overview of the marine roseobacter lineage. Appl Environ Microbiol71:5665–5677 [CrossRef][PubMed]
    [Google Scholar]
  4. Cao J., Lai Q., Yuan J., Shao Z.. 2015; Genomic and metabolic analysis of fluoranthene degradation pathway in Celeribacter indicus P73T. Sci Rep5:7741 [CrossRef][PubMed]
    [Google Scholar]
  5. Chan J. Z., Halachev M. R., Loman N. J., Constantinidou C., Pallen M. J.. 2012; Defining bacterial species in the genomic era: insights from the genus Acinetobacter. BMC Microbiol12:302 [CrossRef][PubMed]
    [Google Scholar]
  6. Chen Z., Zhang J., Lei X., Lai Q., Yang L., Zhang H., Li Y., Zheng W., Tian Y..other authors 2015; Mameliella phaeodactyli sp. nov., a member of the family Rhodobacteraceae isolated from the marine algae Phaeodactylum tricornutum. Int J Syst Evol Microbiol65:1617–1621 [CrossRef][PubMed]
    [Google Scholar]
  7. Felsenstein J.. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  8. Goris J., Konstantinidis K. T., Klappenbach J. A., Coenye T., Vandamme P., Tiedje J. M.. 2007; DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol57:81–91 [CrossRef][PubMed]
    [Google Scholar]
  9. Hwang C. Y., Cho B. C.. 2008; Ponticoccus litoralis gen. nov., sp. nov., a marine bacterium in the family Rhodobacteraceae. Int J Syst Evol Microbiol58:1332–1338 [CrossRef][PubMed]
    [Google Scholar]
  10. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H., other authors. 2012; Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  11. Kim M., Oh H. S., Park S. C., Chun J.. 2014; Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol64:346–351 [CrossRef][PubMed]
    [Google Scholar]
  12. Konstantinidis K. T., Tiedje J. M.. 2005; Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A102:2567–2572 [CrossRef][PubMed]
    [Google Scholar]
  13. Lai Q., Cao J., Yuan J., Li F., Shao Z.. 2014; Celeribacter indicus sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from deep-sea sediment and reclassification of Huaishuia halophila as Celeribacter halophilus comb. nov. Int J Syst Evol Microbiol64:4160–4167 [CrossRef][PubMed]
    [Google Scholar]
  14. Lenk S., Moraru C., Hahnke S., Arnds J., Richter M., Kube M., Reinhardt R., Brinkhoff T., Harder J., other authors. 2012; Roseobacter clade bacteria are abundant in coastal sediments and encode a novel combination of sulfur oxidation genes. ISME J6:2178–2187 [CrossRef][PubMed]
    [Google Scholar]
  15. Luo R., Liu B., Xie Y., Li Z., Huang W., Yuan J., He G., Chen Y., Pan Q., other authors. 2012; SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience1:18 [CrossRef][PubMed]
    [Google Scholar]
  16. Meier-Kolthoff J. P., Auch A. F., Klenk H.-P., Göker M.. 2013; Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics14:60 [CrossRef][PubMed]
    [Google Scholar]
  17. Richter M., Rosselló-Móra R.. 2009; Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  18. Rzhetsky A., Nei M.. 1992; A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol9:945–967
    [Google Scholar]
  19. Rzhetsky A., Nei M.. 1993; Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol10:1073–1095[PubMed]
    [Google Scholar]
  20. Saitou N., Nei M.. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol4:406–425[PubMed]
    [Google Scholar]
  21. Sasser M.. 1990; Identification of bacteria by gas chromatography of cellular fatty acids MIDI Technical Note 101 Newark, DE: MIDI Inc;
    [Google Scholar]
  22. Shahriari Moghadam M., Ebrahimipour G., Abtahi B., Ghassempour A., Hashtroudi M. S.. 2014; Biodegradation of polycyclic aromatic hydrocarbons by a bacterial consortium enriched from mangrove sediments. J Environ Health Sci Eng12:114 [CrossRef][PubMed]
    [Google Scholar]
  23. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S.. 2013; mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  24. Wang L., Liu Y., Wang Y., Dai X., Zhang X.-H.. 2015; Celeribacter manganoxidans sp. nov., a manganese-oxidizing bacterium isolated from deep-sea sediment of a polymetallic nodule province. Int J Syst Evol Microbiol65:4180–4185 [CrossRef][PubMed]
    [Google Scholar]
  25. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E., other authors. 1987; International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol37:463–464 [CrossRef]
    [Google Scholar]
  26. Zheng Q., Chen C., Yan X. J., Wang Y. N., Zeng Y. H., Hao L. K., He W. H., Jiao N. Z.. 2010; Mameliella alba gen. nov., sp. nov., a marine bacterium of the Roseobacter clade in the order Rhodobacterales. Int J Syst Evol Microbiol60:953–957 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.000961
Loading
/content/journal/ijsem/10.1099/ijsem.0.000961
Loading

Data & Media loading...

Supplements

Supplementary Data

PDF

Most Cited This Month

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