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Volume 65, Issue Pt_9

sp. nov., isolated from soft coastal sediments Free

Abstract

A novel purple sulfur bacterium, strain AX1YPE, was isolated from marine sediments sampled at 47 m depth in Callao Bay, Perú. Strain AX1YPE grew anaerobically, synthesizing bacteriochlorophyll and carotenoid pigments of the spirilloxanthin series. Cells were Gram-stain-negative rods and actively motile by a polar flagellum. Strain AX1YPE was able to grow photolithoautotrophically with sulfide and thiosulfate as electron donors. This new phototrophic organism utilized ammonium salt, N, urea and glutamate as nitrogen sources. Strain AX1YPE had a DNA base composition of 63.9 mol% G+C. Analysis of the 16S rRNA gene sequence indicated that strain AX1YPE clusters in a separate branch within the genus of the family Strain AX1YPE showed 16S rRNA gene sequence similarities of 98.2 % with DSM 180 and DSM 1376, 98.1 % with JA144, 97.3 % with DSM 18713 and 96.8 % with DSM 173. DNA–DNA hybridization values to the type strains of its closest relatives, and , were 59 and 64 %, respectively. The predominant fatty acid of strain AX1YPE was Cω;7 and it notably possessed C as a minor component. PCR-based molecular typing (Box A1R and randomly amplified polymorphic DNA) produced a unique banding pattern for strain AX1YPE in comparison with the type strains of and . Based on data from this polyphasic taxonomic study, which also includes average nucleotide identity comparison of five concatenated housekeeping genes, strain AX1YPE is considered to represent a novel species of the genus for which the name sp. nov. is proposed. The type strain is AX1YPE ( = DSM 21881 = KCTC 15448).

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2015-09-01
2024-04-20
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References

  1. Anil Kumar P., Srinivas T.N.R., Sasikala Ch., Ramana ChV. ( 2008;). Allochromatium renukae sp. nov. Int J Syst Evol Microbiol 58 404–407 [View Article] [PubMed] .
     [Google Scholar]
  2. De Ley J., Cattoir H., Reynaerts A. ( 1970;). The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12 133–142 [View Article] [PubMed] .
     [Google Scholar]
  3. 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 [View Article] [PubMed] .
     [Google Scholar]
  4. Guindon S., Gascuel O. ( 2003;). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52 696–704 [View Article] [PubMed] .
     [Google Scholar]
  5. Imhoff J.F., Caumette P. ( 2004;). Recommended standards for the description of new species of anoxygenic phototrophic bacteria. Int J Syst Evol Microbiol 54 1415–1421 [View Article] [PubMed] .
     [Google Scholar]
  6. Imhoff J.F., Süling J., Petri R. ( 1998;). Phylogenetic relationships among the Chromatiaceae, their taxonomic reclassification and description of the new genera Allochromatium, Halochromatium, Isochromatium, Marichromatium, Thiococcus, Thiohalocapsa and Thermochromatium . Int J Syst Bacteriol 48 1129–1143 [View Article] [PubMed] .
     [Google Scholar]
  7. 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 Microbiol 64 346–351 [View Article] [PubMed] .
     [Google Scholar]
  8. Konstantinidis K.T., Ramette A., Tiedje J.M. ( 2006;). The bacterial species definition in the genomic era. Phil Trans R Soc B 361 1929–1940 [View Article].
     [Google Scholar]
  9. Marmur J. ( 1961;). A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3 208–218 [View Article].
     [Google Scholar]
  10. Marmur J., Doty P. ( 1962;). Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5 109–118 [View Article] [PubMed] .
     [Google Scholar]
  11. Muyzer G., de Waal E.C., Uitterlinden A.G. ( 1993;). Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59 695–700 [PubMed].
     [Google Scholar]
  12. Pfennig N., Trüper H.G. ( 1981;). Isolation of members of the families Chromatiaceae and Chlorobiaceae. . In The Prokaryotes, pp. 279–289. Edited by Starr M. P., Stolp H., Trüper H. G., Balows A., Schlegel H. G. Berlin: Springer;. [CrossRef]
    [Google Scholar]
  13. Pfennig N., Trüper H.G. ( 1992;). The family Chromatiaceae. . In The Prokaryotes, pp. 3200–3221. Edited by Balows A., Trüper H. G., Dworkin M., Harder W., Schleifer K. H. Berlin: Springer;. [CrossRef]
    [Google Scholar]
  14. 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 [View Article] [PubMed] .
     [Google Scholar]
  15. Serrano W., Amann R., Fischer U. ( 2009;). A new moderately thermophilic and high sulfide tolerant biotype of Marichromatium gracile, isolated from tidal sediments of the German Wadden Sea: Marichromatium gracile biotype thermosulfidiphilum . Syst Appl Microbiol 32 1–7 [View Article] [PubMed] .
     [Google Scholar]
  16. Serrano W., Amann R., Rosselló-Móra R., Herbert R.A., Fischer U. ( 2011;). The genus Allochromatium (Chromatiales Chromatiaceae) revisited: a study on its intragenic structure based on multilocus sequence analysis (MLSA) and DNA-DNA hybridization (DDH). Syst Appl Microbiol 34 590–594 [View Article] [PubMed] .
     [Google Scholar]
  17. Srinivas T.N.R., Anil Kumar P., Sucharitha K., Sasikala Ch., Ramana ChV. ( 2009;). Allochromatium phaeobacterium sp. nov. Int J Syst Evol Microbiol 59 750–753 [View Article] [PubMed] .
     [Google Scholar]
  18. 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 [View Article] [PubMed] .
     [Google Scholar]
  19. 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 Bacteriol 37 463–464 [View Article].
     [Google Scholar]
  20. Weissgerber T., Zigann R., Bruce D., Chang Y.-J., Detter J.C., Han C., Hauser L., Jeffries C.D., Land M., other authors. ( 2011;). Complete genome sequence of Allochromatium vinosum DSM 180T . Stand Genomic Sci 5 311–330 [View Article] [PubMed] .
     [Google Scholar]
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Allochromatium humboldtianum sp. nov., isolated from soft coastal sediments
Int J Syst Evol Microbiol 65, 2980 (2015); https://doi.org/10.1099/ijs.0.000364
/content/journal/ijsem/10.1099/ijs.0.000364
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