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Abstract

Thirteen isolates of Gram-stain-negative, motile, violet-pigmented bacteria were isolated from marshes along tidal portions of the Potomac and James rivers in Maryland and Virginia, USA, respectively. 16S rRNA gene sequences and fatty acid analysis revealed a high degree of relatedness among the isolates, and genomic sequencing of two isolates, IIBBL 112-1 and IIBBL 274-1 (from the Potomac and James rivers, respectively), revealed highly similar genomic sequences, with a blast-based average nucleotide identity (ANIb) of ca. 98.7 %. Phylogenetic analysis of 16S rRNA gene sequences suggested that the species most highly related to IIBBL 112-1 were Chromobacterium amazonense , Chromobacterium subtsugae and Chromobacterium sphagni . However, deletion of a 25-nucleotide sequence that may have been horizontally acquired by both IIBBL 112-1 and C. amazonense resulted in a substantially different analysis; in the latter case, the species nearest IIBBL 112-1 were Chromobacterium violaceum , Chromobacterium vaccinii and Chromobacterium piscinae . Whole-genome alignments between either IIBBL 112-1 or IIBBL 274-1 and the type strains of C. vaccinii or C. violaceum resulted in ANIb values in the range of ca. 87 %, while alignment with C. amazonense CBMAI 310 resulted in an ANIb of ca. 83 %. Collectively, these data demonstrate that IIBBL 112-1 and IIBBL 274-1 represent a new taxon within the genus Chromobacterium . We propose the name Chromobacterium phragmitis sp. nov. for this taxon; the type strain is IIBBL 112-1 (=NRRL B-67132=JCM 31884).

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2019-06-14
2019-08-25
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References

  1. Martin PA, Gundersen-Rindal D, Blackburn M, Buyer J. Chromobacterium subtsugae sp. nov., a betaproteobacterium toxic to colorado potato beetle and other insect pests. Int J Syst Evol Microbiol 2007;57: 993– 999 [CrossRef] [PubMed]
    [Google Scholar]
  2. Young CC, Arun AB, Lai WA, Chen WM, Chou JH et al. Chromobacterium aquaticum sp. nov., isolated from spring water samples. Int J Syst Evol Microbiol 2008;58: 877– 880 [CrossRef] [PubMed]
    [Google Scholar]
  3. Han XY, Han FS, Segal J. Chromobacterium haemolyticum sp. nov., a strongly haemolytic species. Int J Syst Evol Microbiol 2008;58: 1398– 1403 [CrossRef] [PubMed]
    [Google Scholar]
  4. Kämpfer P, Busse HJ, Scholz HC. Chromobacterium piscinae sp. nov. and Chromobacterium pseudoviolaceum sp. nov., from environmental samples. Int J Syst Evol Microbiol 2009;59: 2486– 2490 [CrossRef] [PubMed]
    [Google Scholar]
  5. Soby SD, Gadagkar SR, Contreras C, Caruso FL. Chromobacterium vaccinii sp. nov., isolated from native and cultivated cranberry (Vaccinium macrocarpon Ait.) bogs and irrigation ponds. Int J Syst Evol Microbiol 2013;63: 1840– 1846 [CrossRef] [PubMed]
    [Google Scholar]
  6. Menezes CB, Tonin MF, Corrêa DB, Parma M, de Melo IS et al. Chromobacterium amazonense sp. nov. isolated from water samples from the Rio Negro, Amazon, Brazil. Antonie Van Leeuwenhoek 2015;107: 1057– 1063 [CrossRef] [PubMed]
    [Google Scholar]
  7. Zhou S, Guo X, Wang H, Kong D, Wang Y et al. Chromobacterium rhizoryzae sp. nov., isolated from rice roots. Int J Syst Evol Microbiol 2016;66: 3890– 3896 [CrossRef] [PubMed]
    [Google Scholar]
  8. Bajaj A, Kumar A, Yadav S, Kaur G, Bala M et al. Isolation and characterization of a novel Gram-negative bacterium Chromobacterium alkanivorans sp. nov., strain IITR-71T degrading halogenated alkanes. Int J Syst Evol Microbiol 2016;66: 5228– 5235 [CrossRef] [PubMed]
    [Google Scholar]
  9. Blackburn MB, Farrar RR, Sparks ME, Kuhar D, Mitchell A et al. Chromobacterium sphagni sp. nov., an insecticidal bacterium isolated from Sphagnum bogs. Int J Syst Evol Microbiol 2017;67: 3417– 3422 [CrossRef] [PubMed]
    [Google Scholar]
  10. Vöing K, Harrison A, Soby SD. Draft genome sequence of Chromobacterium vaccinii, a potential biocontrol agent against mosquito (Aedes aegypti) Larvae. Genome Announc 2015;3: e00477 15 [CrossRef] [PubMed]
    [Google Scholar]
  11. Keeble JR, Cross T. An improved medium for the enumeration of Chromobacterium in soil and water. J Appl Bacteriol 1977;43: 325– 327 [CrossRef]
    [Google Scholar]
  12. Harrison RL, Rowley DL, Mowery JD, Bauchan GR, Burand JP. The Operophtera brumata nucleopolyhedrovirus (OpbuNPV) represents an early, divergent lineage within genus Alphabaculovirus. Viruses 2017;9: 307 [CrossRef] [PubMed]
    [Google Scholar]
  13. Tindall BJ. A comparative study of the lipid composition of halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990;13: 128– 130 [CrossRef]
    [Google Scholar]
  14. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990;66: 199– 202 [CrossRef]
    [Google Scholar]
  15. Kämpfer P, Glaeser SP, Soby SD. Chromobacterium pseudoviolaceum Kämpfer et al. 2009 is a later heterotypic synonym of Chromobacterium violaceum Bergonzini 1880. Int J Syst Evol Microbiol 2018;68: 2967– 2968 [CrossRef] [PubMed]
    [Google Scholar]
  16. Eid J, Fehr A, Gray J, Luong K, Lyle J et al. Real-time DNA sequencing from single polymerase molecules. Science 2009;323: 133– 138 [CrossRef] [PubMed]
    [Google Scholar]
  17. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013;10: 563– 569 [CrossRef] [PubMed]
    [Google Scholar]
  18. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997;25: 4876– 4882 [CrossRef] [PubMed]
    [Google Scholar]
  19. Kumar S, Stecher G, Tamura K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016
    [Google Scholar]
  20. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25: 3389– 3402 [CrossRef] [PubMed]
    [Google Scholar]
  21. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106: 19126– 19131 [CrossRef] [PubMed]
    [Google Scholar]
  22. Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res 2015;43: 6761– 6771 [CrossRef] [PubMed]
    [Google Scholar]
  23. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010;11: 119 [CrossRef] [PubMed]
    [Google Scholar]
  24. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4: 406– 425 [CrossRef] [PubMed]
    [Google Scholar]
  25. Felsenstein J. PHYLIP - phylogeny inference package (Version 3.2). Cladistics 1989;5: 164– 166
    [Google Scholar]
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