Zoogloea oleivorans sp. nov., a floc-forming, petroleum hydrocarbon-degrading bacterium isolated from biofilm

References

1. Cashion P., Holder-Franklin M. A., McCully J., Franklin M. ( 1977 ). A rapid method for the base ratio determination of bacterial DNA. . Anal Biochem 81, 461–466. [View Article] [PubMed]
   [Google Scholar]
2. Claus D. ( 1992 ). A standardized Gram staining procedure. . World J Microbiol Biotechnol 8, 451–452. [View Article] [PubMed]
   [Google Scholar]
3. Cowan S. T., Steel K. J. ( 1974 ). Manual of Identification of Medical Bacteria. Cambridge:: University Press;.
   [Google Scholar]
4. Crabtree K., McCoy E. ( 1967 ). Zoogloea ramigera Itzigsohn, identification and description. . Int J Syst Bacteriol 17, 1–10. [View Article]
   [Google Scholar]
5. 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]
6. Dugan P. R., Stoner D. L., Pickrum H. M. ( 1992 ). The genus Zoogloea . . In The Prokaryotes, , 2nd edn., pp. 3952–3964. Edited by Balows A., Trüper H. G., Dworkin M., Harder W., Schleifer K.-H. . New York:: Springer;. [View Article]
   [Google Scholar]
7. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368–376. [View Article] [PubMed]
   [Google Scholar]
8. Hugh R., Leifson E. ( 1953 ). The taxonomic significance of fermentative versus oxidative metabolism of carbohydrates by various gram negative bacteria. . J Bacteriol 66, 24–26.[PubMed]
   [Google Scholar]
9. Huß V. A. R., Festl H., Schleifer K. H. ( 1983 ). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. . Syst Appl Microbiol 4, 184–192. [View Article] [PubMed]
   [Google Scholar]
10. Jechalke S., Franchini A. G., Bastida F., Bombach P., Rosell M., Seifert J., von Bergen M., Vogt C., Richnow H. H. ( 2013 ). Analysis of structure, function, and activity of a benzene-degrading microbial community. . FEMS Microbiol Ecol 85, 14–26. [View Article] [PubMed]
    [Google Scholar]
11. 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. [View Article] [PubMed]
    [Google Scholar]
12. 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. [View Article] [PubMed]
    [Google Scholar]
13. Lane D. J. ( 1991 ). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–175 . Edited by Stackebrandt E. , Goodfellow M. . Chichester:: Wiley;.
    [Google Scholar]
14. 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. [View Article]
    [Google Scholar]
15. Mohn W. W., Wilson A. E., Bicho P., Moore E. R. B. ( 1999 ). Physiological and phylogenetic diversity of bacteria growing on resin acids. . Syst Appl Microbiol 22, 68–78. [View Article] [PubMed]
    [Google Scholar]
16. Pastorella G., Gazzola G., Guadarrama S., Marsili E. ( 2012 ). Biofilms: applications in bioremediation. . In Microbial Biofilms, pp. 73–98. Edited by Lear G., Lewis G. D. . Norwich:: Caister Academic Press;.
    [Google Scholar]
17. Poly F., Monrozier L. J., Bally R. ( 2001 ). Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil. . Res Microbiol 152, 95–103. [View Article] [PubMed]
    [Google Scholar]
18. 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]
19. Shao Y., Chung B. S., Lee S. S., Park W., Lee S. S., Jeon C. O. ( 2009 ). Zoogloea caeni sp. nov., a floc-forming bacterium isolated from activated sludge. . Int J Syst Evol Microbiol 59, 526–530. [View Article] [PubMed]
    [Google Scholar]
20. 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]
21. Szabó I., Szoboszlay S., Kriszt B., Háhn J., Harkai P., Baka E., Táncsics A., Kaszab E., Privler Z., Kukolya J. ( 2011 ). Olivibacter oleidegradans sp. nov., a hydrocarbon-degrading bacterium isolated from a biofilter clean-up facility on a hydrocarbon-contaminated site. . Int J Syst Evol Microbiol 61, 2861–2865. [View Article] [PubMed]
    [Google Scholar]
22. Szoboszlay S., Atzél B., Kukolya J., Tóth E. M., Márialigeti K., Schumann P., Kriszt B. ( 2008 ). Chryseobacterium hungaricum sp. nov., isolated from hydrocarbon-contaminated soil. . Int J Syst Evol Microbiol 58, 2748–2754. [View Article] [PubMed]
    [Google Scholar]
23. Tamaoka J., Komagata K. ( 1984 ). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. . FEMS Microbiol Lett 25, 125–128. [View Article]
    [Google Scholar]
24. 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. [View Article] [PubMed]
    [Google Scholar]
25. Táncsics A., Szoboszlay S., Szabó I., Farkas M., Kovács B., Kukolya J., Mayer Z., Kriszt B. ( 2012 ). Quantification of subfamily I.2.C catechol 2,3-dioxygenase mRNA transcripts in groundwater samples of an oxygen-limited BTEX-contaminated site. . Environ Sci Technol 46, 232–240. [View Article] [PubMed]
    [Google Scholar]
26. Táncsics A., Farkas M., Szoboszlay S., Szabó I., Kukolya J., Vajna B., Kovács B., Benedek T., Kriszt B. ( 2013 ). One-year monitoring of meta-cleavage dioxygenase gene expression and microbial community dynamics reveals the relevance of subfamily I.2.C extradiol dioxygenases in hypoxic, BTEX-contaminated groundwater. . Syst Appl Microbiol 36, 339–350. [View Article] [PubMed]
    [Google Scholar]
27. Tarrand J. J., Gröschel D. H. ( 1982 ). Rapid, modified oxidase test for oxidase-variable bacterial isolates. . J Clin Microbiol 16, 772–774.[PubMed]
    [Google Scholar]
28. Unz R. F. ( 1984 ). Genus IV. Zoogloea Itzigsohn 1868, 30^AL . . In Bergey’s Manual of Systematic Bacteriology, vol. 1, pp. 214–219. Edited by Krieg N. R., Holt J. G. . Baltimore:: Williams & Wilkins;.
    [Google Scholar]
29. 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]
30. Weissbrodt D. G., Neu T. R., Kuhlicke U., Rappaz Y., Holliger C. ( 2013 ). Assessment of bacterial and structural dynamics in aerobic granular biofilms. . Front Microbiol 4, 175. [View Article] [PubMed]
    [Google Scholar]
31. Xie C. H., Yokota A. ( 2006 ). Zoogloea oryzae sp. nov., a nitrogen-fixing bacterium isolated from rice paddy soil, and reclassification of the strain ATCC 19623 as Crabtreella saccharophila gen. nov., sp. nov.. Int J Syst Evol Microbiol 56, 619–624. [View Article] [PubMed]
    [Google Scholar]
32. Zhao Y., Huang J., Zhao H., Yang H. ( 2013 ). Microbial community and N removal of aerobic granular sludge at high COD and N loading rates. . Bioresour Technol 143, 439–446. [View Article] [PubMed]
    [Google Scholar]