1887

Abstract

A Gram-stain-negative, strictly aerobic, light-beige, rod-shaped, motile bacterium with peritrichous flagella that cleaves dimethylsulfoniopropionate (DMSP), designated strain LZD062, was isolated from bottom seawater of the East China Sea. The isolate required sea salts for growth and grew optimally at pH 8.0 and 28 °C and in the presence of 2 % (w/v) NaCl. The major fatty acid (>10 %) was summed feature 8 (Cω7 and/or Cω6) and the major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, one unidentified aminolipid and one unidentified glycolipid. Ubiquinone Q-10 was the only quinone detected. Phylogenetic analyses based on 16S rRNA and gene sequences placed LZD062 within the genus of the family in the class . The most closely related type strain was, in both cases, JCM 20689 ( = IAM 12618 = DSM 5890), which gave sequence similarities of 97.7 % in the 16S rRNA gene and 90.4 % in the gene. Genome relatedness between strain LZD062 and JCM 20689 was computed using both genome-to-genome distance analysis and average nucleotide identity, giving values of 22.10 ± 2.35 and 79.55 %, respectively. The genomic DNA G+C content calculated from the genome sequence was 50.1 mol%. On the basis of our polyphasic analyses, strain LZD062 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is LZD062 ( = MCCC 1K00254 = JCM 30117 = DSM 28886). Emended descriptions of the genus and are also proposed.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000805
2016-02-01
2019-12-06
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/2/874.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000805&mimeType=html&fmt=ahah

References

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J.. ( 1990;). Basic local alignment search tool. J Mol Biol 215: 403–410 [CrossRef] [PubMed].
    [Google Scholar]
  2. Auch A. F., von Jan M., Klenk H. P., Göker M.. ( 2010a;). Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2: 117–134 [CrossRef] [PubMed].
    [Google Scholar]
  3. Auch A. F., Klenk H. P., Göker M.. ( 2010b;). Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2: 142–148 [CrossRef] [PubMed].
    [Google Scholar]
  4. Beveridge T. J., Lawrence J. R., Murray R. G. E. ( 2007;). Sampling and staining for light microscopy. . In Methods for General and Molecular Microbiology, 3rd edn.., pp. 19–33. Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G., Schmidt T. M., Snyder L. R.. Washington, DC: American Society for Microbiology;.
    [Google Scholar]
  5. Biebl H., Tindall B. J., Pukall R., Lünsdorf H., Allgaier M., Wagner-Döbler I.. ( 2006;). Hoeflea phototrophica sp. nov., a novel marine aerobic alphaproteobacterium that forms bacteriochlorophyll a. Int J Syst Evol Microbiol 56: 821–826 [CrossRef] [PubMed].
    [Google Scholar]
  6. Bradford M. M.. ( 1976;). A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72: 248–254 [CrossRef] [PubMed].
    [Google Scholar]
  7. Curson A. R. J, Rogers R., Todd J. D., Brearley C. A., Johnston A. W. B. ( 2008;). Molecular genetic analysis of a dimethylsulfoniopropionate lyase that liberates the climate-changing gas dimethylsulfide in several marine α-proteobacteria and Rhodobacter sphaeroides. Environ Microbiol 10: 757–767 [CrossRef] [PubMed].
    [Google Scholar]
  8. Dong X.-Z., Cai M.-Y.. (editors) ( 2001;). Determinative Manual for Routine Bacteriology Beijing: (English translation) Scientific Press;.
    [Google Scholar]
  9. Felsenstein J.. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368–376 [CrossRef] [PubMed].
    [Google Scholar]
  10. Fitch W. M.. ( 1971;). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20: 406–416 [CrossRef].
    [Google Scholar]
  11. Flores-Félix J. D., Carro L., Velázquez E., Valverde Á., Cerda-Castillo E., García-Fraile P., Rivas R.. ( 2013;). Phyllobacterium endophyticum sp. nov., isolated from nodules of Phaseolus vulgaris. Int J Syst Evol Microbiol 63: 821–826 [CrossRef] [PubMed].
    [Google Scholar]
  12. 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 Microbiol 57: 81–91 [CrossRef] [PubMed].
    [Google Scholar]
  13. Hsu S. C., Lockwood J. L.. ( 1975;). Powdered chitin agar as a selective medium for enumeration of actinomycetes in water and soil. Appl Microbiol 29: 422–426 [PubMed].
    [Google Scholar]
  14. Jung Y.-T., Park S., Lee J.-S., Oh T.-K., Yoon J.-H.. ( 2012;). Pseudahrensia aquimaris gen. nov., sp. nov., isolated from seawater. Int J Syst Evol Microbiol 62: 2056–2061 [CrossRef] [PubMed].
    [Google Scholar]
  15. 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 Microbiol 62: 716–721 [CrossRef] [PubMed].
    [Google Scholar]
  16. Kimura M.. ( 1980;). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111–120 [CrossRef] [PubMed].
    [Google Scholar]
  17. Komagata K., Suzuki K.. ( 1987;). Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19: 161–207 [CrossRef].
    [Google Scholar]
  18. Lyman J., Fleming R. H.. ( 1940;). Composition of seawater. J Mar Res 3: 134–146.
    [Google Scholar]
  19. 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 Bioinformatics 14: 60 [CrossRef] [PubMed].
    [Google Scholar]
  20. Mergaert J., Swings J.. ( 2005;). Family IV. Phyllobacteriaceae fam. nov. . In Bergey's Manual of Systematic Bacteriologyvol. 2C, 2nd edn.., p. 393. Edited by Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M.. New York: Springer;.
    [Google Scholar]
  21. Mergaert J., Swings J.. ( 2006;). Phyllobacteriaceae fam. nov. In List of new names and new combinations previously effectively, but not validly, published, Validation List no. 107. Int J Syst Evol Microbiol 56: 1–6 [CrossRef] [PubMed].
    [Google Scholar]
  22. Minnikin D. E., O'Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. H.. ( 1984;). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2: 233–241 [CrossRef].
    [Google Scholar]
  23. Montero-Calasanz M. C., Göker M., Rohde M., Spröer C., Schumann P., Busse H.-J., Schmid M., Tindall B. J., Klenk H.-P., Camacho M.. ( 2013;). Chryseobacterium hispalense sp. nov., a plant-growth-promoting bacterium isolated from a rainwater pond in an olive plant nursery, and emended descriptions of Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium. Int J Syst Evol Microbiol 63: 4386–4395 [CrossRef] [PubMed].
    [Google Scholar]
  24. Peix A., Rivas R., Trujillo M. E., Vancanneyt M., Velázquez E., Willems A.. ( 2005;). Reclassification of Agrobacterium ferrugineum LMG 128 as Hoeflea marina gen. nov., sp. nov. Int J Syst Evol Microbiol 55: 1163–1166 [CrossRef] [PubMed].
    [Google Scholar]
  25. Raina J. B., Tapiolas D., Willis B. L., Bourne D. G.. ( 2009;). Coral-associated bacteria and their role in the biogeochemical cycling of sulfur. Appl Environ Microbiol 75: 3492–3501 [CrossRef] [PubMed].
    [Google Scholar]
  26. Richter M., Rosselló-Móra R.. ( 2009;). Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106: 19126–19131 [CrossRef] [PubMed].
    [Google Scholar]
  27. Rosselló-Mora R., Amann R.. ( 2001;). The species concept for prokaryotes. FEMS Microbiol Rev 25: 39–67 [CrossRef] [PubMed].
    [Google Scholar]
  28. Rüger H.-J., Höfle M. G.. ( 1992;). Marine star-shaped-aggregate-forming bacteria: Agrobacterium atlanticum sp. nov.; Agrobacterium meteori sp. nov.; Agrobacterium ferrugineum sp. nov., nom. rev.; Agrobacterium gelatinovorum sp. nov., nom. rev.; and Agrobacterium stellulatum sp. nov., nom. rev. Int J Syst Bacteriol 42: 133–143 [CrossRef] [PubMed].
    [Google Scholar]
  29. Saitou N., Nei M.. ( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406–425 [PubMed].
    [Google Scholar]
  30. Sánchez M., Ramírez-Bahena M. H., Peix A., Lorite M. J., Sanjuán J., Velázquez E., Monza J.. ( 2014;). Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus. Int J Syst Evol Microbiol 64: 781–786 [CrossRef] [PubMed].
    [Google Scholar]
  31. Sasser M.. ( 1990;). Identification of bacteria by gas chromatography of cellular fatty acids MIDI Technical Note 101 Newark, DE: MIDI Inc;.
    [Google Scholar]
  32. Sievert S., Kiene R., Schulz-Vogt H.. ( 2007;). The sulfur cycle. Oceanography (Wash DC) 20: 117–123 [CrossRef].
    [Google Scholar]
  33. Stefels J., Steinke M., Turner S., Malin G., Belviso S.. ( 2007;). Environmental constraints on the production and removal of the climatically active gas dimethylsulphide (DMS) and implications for ecosystem modelling. Biogeochemistry 83: 245–275 [CrossRef].
    [Google Scholar]
  34. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S.. ( 2011;). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731–2739 [CrossRef] [PubMed].
    [Google Scholar]
  35. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G.. ( 1997;). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876–4882 [CrossRef] [PubMed].
    [Google Scholar]
  36. Tindall B. J., Sikorski J., Smibert R. M., Krieg N. R.. ( 2007;). Phenotypic characterization and the principles of comparative systematics. . In Methods for General and Molecular Microbiology, 3rd edn.., pp. 330–393. Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G., Schmidt T. M., Snyder L. R.. Washington, DC:: American Society for Microbiology;. [CrossRef]
    [Google Scholar]
  37. Todd J. D., Rogers R., Li Y. G., Wexler M., Bond P. L., Sun L., Curson A. R., Malin G., Steinke M., Johnston A. W.. ( 2007;). Structural and regulatory genes required to make the gas dimethyl sulfide in bacteria. Science 315: 666–669 [CrossRef] [PubMed].
    [Google Scholar]
  38. Uchino Y., Hirata A., Yokota A., Sugiyama J.. ( 1998;). Reclassification of marine Agrobacterium species: proposals of Stappia stellulata gen. nov., comb. nov., Stappia aggregata sp. nov., nom. rev., Ruegeria atlantica gen. nov., comb. nov., Ruegeria gelatinovora comb. nov., Ruegeria algicola comb. nov., and Ahrensia kieliense gen. nov., sp. nov., nom. rev. J Gen Appl Microbiol 44: 201–210 [CrossRef] [PubMed].
    [Google Scholar]
  39. Vallina S. M., Simó R.. ( 2007;). Strong relationship between DMS and the solar radiation dose over the global surface ocean. Science 315: 506–508 [CrossRef] [PubMed].
    [Google Scholar]
  40. Xie C.-H., Yokota A.. ( 2003;). Phylogenetic analyses of Lampropedia hyalina based on the 16S rRNA gene sequence. J Gen Appl Microbiol 49: 345–349 [CrossRef] [PubMed].
    [Google Scholar]
  41. Xu H.-Y., Chen L.-P., Fu S.-Z., Fan H.-X., Zhou Y.-G., Liu S.-J., Liu Z.-P.. ( 2009;). Zhangella mobilis gen. nov., sp. nov., a new member of the family Hyphomicrobiaceae isolated from coastal seawater. Int J Syst Evol Microbiol 59: 2297–2301 [CrossRef] [PubMed].
    [Google Scholar]
  42. Zhang H.-H., Yang G.-P., Zhu T.. ( 2008;). Distribution and cycling of dimethylsulfide (DMS) and dimethylsulfoniopropionate (DMSP) in the sea-surface microlayer of the Yellow Sea, China, in spring. Cont Shelf Res 28: 2417–2427 [CrossRef].
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.000805
Loading
/content/journal/ijsem/10.1099/ijsem.0.000805
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