1887

Abstract

Two Gram-staining-negative, aerobic, rod-shaped, non-spore-forming bacterial strains that are motile by a monopolar flagellum, designated CC-AMH-11 and CC-AMHZ-5, were isolated from droppings of a seashore bird off the coast of Hualien, Taiwan. The strains showed 99.7 % mutual pairwise 16S rRNA gene sequence similarity, while exhibiting <96.2 % sequence similarity to strains of other species of the genus (95.7–95.9 % similarity with type species, Pseudomonas aeruginosa LMG 1242T), and formed a distinct co-phyletic lineage in the phylogenetic trees. The common major fatty acids (>5 % of the total) were Cω7 and/or Cω6 (summed feature 8), Cω6 and/or Cω7 (summed feature 3), C and C. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylserine, an unidentified lipid and an unidentified phospholipid were detected as common polar lipids. The DNA G+C contents of strains CC-AMH-11 and CC-AMHZ-5 were 61.1 and 61.6 mol%, respectively. The common major respiratory quinone was ubiquinone 9 (Q-9), and the predominant polyamine was putrescine. The DNA–DNA hybridization obtained between the two strains was 79.0 % (reciprocal value 89.4 % using CC-AMHZ-5 DNA as the probe). The very high 16S rRNA gene sequence similarity and DNA–DNA relatedness and the poorly distinguishable phenotypic features witnessed between CC-AMH-11 and CC-AMHZ-5 suggested unambiguously that they are two distinct strains of a single genomic species. However, the strains also showed several genotypic and phenotypic characteristics that distinguished them from other closely related species of . Thus, the strains are proposed to represent a novel species of , for which the name sp. nov. is proposed. The type strain is CC-AMH-11 ( = JCM 19513 = BCRC 80696); a second strain of the same species is CC-AMHZ-5 ( = JCM 19512 = BCRC 80697). In addition, emended descriptions of the species , and are also proposed.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.060319-0
2014-07-01
2020-01-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/7/2330.html?itemId=/content/journal/ijsem/10.1099/ijs.0.060319-0&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. Anzai Y., Kim H., Park J.-Y., Wakabayashi H., Oyaizu H.. ( 2000;). Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. . Int J Syst Evol Microbiol 50:, 1563–1589. [CrossRef][PubMed]
    [Google Scholar]
  3. Busse H., El-Banna T., Auling G.. ( 1989;). Evaluation of different approaches for identification of xenobiotic-degrading pseudomonads. . Appl Environ Microbiol 55:, 1578–1583.[PubMed]
    [Google Scholar]
  4. Collins M. D.. ( 1985;). Analysis of isoprenoid quinones. . Methods Microbiol 18:, 329–366. [CrossRef]
    [Google Scholar]
  5. Embley T. M., Wait R.. ( 1994;). Structural lipids of eubacteria. . In Chemical Methods in Prokaryotic Systematics, pp. 121–161. Edited by Goodfellow M., O’Donnell A. G... Chichester:: Wiley;.
    [Google Scholar]
  6. Espírito Santo C., Lin Y., Hao X., Wei G., Rensing C., Grass G.. ( 2012;). Draft genome sequence of Pseudomonas psychrotolerans L19, isolated from copper alloy coins. . J Bacteriol 194:, 1623–1624. [CrossRef][PubMed]
    [Google Scholar]
  7. Felsenstein J.. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17:, 368–376. [CrossRef][PubMed]
    [Google Scholar]
  8. Felsenstein J.. ( 1985;). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39:, 783–791. [CrossRef]
    [Google Scholar]
  9. Feng Z., Zhang J., Huang X., Zhang J., Chen M., Li S.. ( 2012;). Pseudomonas zeshuii sp. nov., isolated from herbicide-contaminated soil. . Int J Syst Evol Microbiol 62:, 2608–2612. [CrossRef][PubMed]
    [Google Scholar]
  10. Fitch W. M.. ( 1971;). Towards defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20:, 406–416. [CrossRef]
    [Google Scholar]
  11. Fox G. E., Wisotzkey J. D., Jurtshuk P. Jr. ( 1992;). How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. . Int J Syst Bacteriol 42:, 166–170. [CrossRef][PubMed]
    [Google Scholar]
  12. GCG ( 1995;). Wisconsin Package Version 8.1 Program Manual. Madison, WI:: Computer Group;.
    [Google Scholar]
  13. Hameed A., Shahina M., Lin S.-Y., Cho J. C., Lai W.-A., Young C.-C.. ( 2013;). Kordia aquimaris sp. nov., a zeaxanthin-producing member of the family Flavobacteriaceae isolated from surface seawater, and emended description of the genus Kordia. . Int J Syst Evol Microbiol 63:, 4790–4796. [CrossRef][PubMed]
    [Google Scholar]
  14. Hameed A., Shahina M., Lin S.-Y., Lai W.-A., Hsu Y.-H., Liu Y.-C., Young C.-C.. ( 2014;). Aquibacter zeaxanthinifaciens gen. nov., sp. nov., a zeaxanthin-producing bacterium of the family Flavobacteriaceae isolated from surface seawater, and emended descriptions of the genera Aestuariibaculum and Gaetbulibacter. . Int J Syst Evol Microbiol 64:, 138–145. [CrossRef][PubMed]
    [Google Scholar]
  15. Hauser E., Kämpfer P., Busse H.-J.. ( 2004;). Pseudomonas psychrotolerans sp. nov.. Int J Syst Evol Microbiol 54:, 1633–1637. [CrossRef][PubMed]
    [Google Scholar]
  16. Heiner C. R., Hunkapiller K. L., Chen S. M., Glass J. I., Chen E. Y.. ( 1998;). Sequencing multimegabase-template DNA with BigDye terminator chemistry. . Genome Res 8:, 557–561.[PubMed]
    [Google Scholar]
  17. Kämpfer P., Kroppenstedt R. M.. ( 1996;). Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. . Can J Microbiol 42:, 989–1005. [CrossRef]
    [Google Scholar]
  18. 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]
  19. 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]
  20. Lang E., Burghartz M., Spring S., Swiderski J., Spröer C.. ( 2010;). Pseudomonas benzenivorans sp. nov. and Pseudomonas saponiphila sp. nov., represented by xenobiotics degrading type strains. . Curr Microbiol 60:, 85–91. [CrossRef][PubMed]
    [Google Scholar]
  21. Lin S.-Y., Hameed A., Liu Y.-C., Hsu Y.-H., Lai W.-A., Chen W.-M., Shen F.-T., Young C.-C.. ( 2013a;). Pseudomonas sagittaria sp. nov., a siderophore-producing bacterium isolated from oil-contaminated soil. . Int J Syst Evol Microbiol 63:, 2410–2417. [CrossRef][PubMed]
    [Google Scholar]
  22. Lin S.-Y., Hameed A., Liu Y.-C., Hsu Y.-H., Lai W.-A., Young C.-C.. ( 2013b;). Pseudomonas formosensis sp. nov., a gamma-proteobacteria isolated from food-waste compost in Taiwan. . Int J Syst Evol Microbiol 63:, 3168–3174. [CrossRef][PubMed]
    [Google Scholar]
  23. Liu Y.-C., Young L.-S., Lin S.-Y., Hameed A., Hsu Y.-H., Lai W.-A., Shen F.-T., Young C.-C.. ( 2013;). Pseudomonas guguanensis sp. nov., a gammaproteobacterium isolated from a hot spring. . Int J Syst Evol Microbiol 63:, 4591–4598. [CrossRef][PubMed]
    [Google Scholar]
  24. Mesbah M., Premachandran U., Whitman W. B.. ( 1989;). Precise measurement of the G + C content of deoxyribonucleic acid by high-performance liquid chromatography. . Int J Syst Bacteriol 39:, 159–167. [CrossRef]
    [Google Scholar]
  25. Migula W.. ( 1894;). Über ein neues System der Bakterien. . Arb Bakteriol Inst Karlsruhe 1:, 235–238 (in German).
    [Google Scholar]
  26. 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]
  27. 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]
  28. Murray R. G. E., Doetsch R. N., Robinow C. F.. ( 1994;). Determinative and cytological light microscopy. . In Methods for General and Molecular Bacteriology, pp. 21–41. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R... Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  29. Oyaizu H., Komagata K.. ( 1983;). Grouping of Pseudomonas species on the basis of cellular fatty acid composition and the quinone system with special reference to the existence of 3-hydroxy fatty acids. . J Gen Appl Microbiol 29:, 17–40. [CrossRef]
    [Google Scholar]
  30. Palleroni N. J.. ( 1984;). Genus I. Pseudomonas Migula 1894. . In Bergey’s Manual of Systematic Bacteriology, vol. 1, pp. 141–199. Edited by Krieg N. R., Holt J. G... Baltimore:: Williams & Wilkins;.
    [Google Scholar]
  31. Park Y. D., Yi H., Baik K. S., Seong C. N., Bae K. S., Moon E. Y., Chun J.. ( 2006;). Pseudomonas segetis sp. nov., isolated from soil. . Int J Syst Evol Microbiol 56:, 2593–2595. [CrossRef][PubMed]
    [Google Scholar]
  32. Pascual J., Lucena T., Ruvira M. A., Giordano A., Gambacorta A., Garay E., Arahal D. R., Pujalte M. J., Macián M. C.. ( 2012;). Pseudomonas litoralis sp. nov., isolated from Mediterranean seawater. . Int J Syst Evol Microbiol 62:, 438–444. [CrossRef][PubMed]
    [Google Scholar]
  33. 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]
  34. Sasser M.. ( 1990;). Identification of bacteria by gas chromatography of cellular fatty acids. . USFCC Newsl 20:, 16.
    [Google Scholar]
  35. Scherer P., Kneifel H.. ( 1983;). Distribution of polyamines in methanogenic bacteria. . J Bacteriol 154:, 1315–1322.[PubMed]
    [Google Scholar]
  36. Shahina M., Hameed A., Lin S.-Y., Hsu Y.-H., Liu Y.-C., Cheng I.-C., Lee M.-R., Lai W.-A., Lee R.-J., Young C.-C.. ( 2013;). Sphingomicrobium astaxanthinifaciens sp. nov., an astaxanthin-producing glycolipid-rich bacterium isolated from surface seawater and emended description of the genus Sphingomicrobium. . Int J Syst Evol Microbiol 63:, 3415–3422. [CrossRef][PubMed]
    [Google Scholar]
  37. Smibert R. M., Krieg N. R.. ( 1994;). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607–654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R... Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  38. Sneath P. H. A., Stevens M., Sackin M. J.. ( 1981;). Numerical taxonomy of Pseudomonas based on published records of substrate utilization. . Antonie van Leeuwenhoek 47:, 423–448. [CrossRef][PubMed]
    [Google Scholar]
  39. Stanier R. Y., Palleroni N. J., Doudoroff M.. ( 1966;). The aerobic pseudomonads: a taxonomic study. . J Gen Microbiol 43:, 159–271. [CrossRef][PubMed]
    [Google Scholar]
  40. Stover C. K., Pham X. Q., Erwin A. L., Mizoguchi S. D., Warrener P., Hickey M. J., Brinkman F. S., Hufnagle W. O., Kowalik D. J.. & other authors ( 2000;). Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. . Nature 406:, 959–964. [CrossRef][PubMed]
    [Google Scholar]
  41. 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]
  42. 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]
  43. Tindall B. J., Rosselló-Móra R., Busse H.-J., Ludwig W., Kämpfer P.. ( 2010;). Notes on the characterization of prokaryote strains for taxonomic purposes. . Int J Syst Evol Microbiol 60:, 249–266. [CrossRef][PubMed]
    [Google Scholar]
  44. Watts D., MacBeath J. R.. ( 2001;). Automated fluorescent DNA sequencing on the ABI PRISM 310 Genetic Analyzer. . Methods Mol Biol 167:, 153–170.[PubMed]
    [Google Scholar]
  45. Weon H. Y., Kim B. Y., Yoo S. H., Baek Y. K., Lee S. Y., Kwon S. W., Go S. J., Stackebrandt E.. ( 2006;). Pseudomonas pohangensis sp. nov., isolated from seashore sand in Korea. . Int J Syst Evol Microbiol 56:, 2153–2156. [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.060319-0
Loading
/content/journal/ijsem/10.1099/ijs.0.060319-0
Loading

Data & Media loading...

Supplements

Supplementary material 

PDF

Most cited articles

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