1887

Abstract

Members of the phylum ‘’ are important heterotrophs involved in cycling organic carbon in aquatic habitats. Their diversity has been studied by molecular methods in both freshwater and marine habitats and many novel genera and species within this phylum have been characterized in recent years. In this study, we examined the diversity of members of the ‘’ that could be readily isolated on solid media from river epilithon and coastal sea water. Most (93 %) of the 55 isolates confirmed as members of the ‘’ and examined by phylogenetic analysis of 16S rRNA gene sequences belonged to the . Furthermore, most (62 %) of these were almost certainly members of the genus and all but one were from river epilithon. Conversely, the sea-water isolates were more widely distributed in clades containing other genera. Some of the isolates were deep-branching within phylogenetic trees and so could not be assigned to putative genera. Two of these deep-branching isolates were characterized by polyphasic taxonomy and are proposed as novel species within two new genera of the family . These are gen. nov., sp. nov. (type strain EP105=NCIMB 14026=DSM 16811) and gen. nov., sp. nov. (type strain SW256=NCIMB 14027=DSM 16809).

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2006-01-01
2024-12-09
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References

  1. Bernardet, J.-F., Segers, P., Vancanneyt, M., Berthe, F., Kersters, K. & Vandamme, P.(1996). Cutting a Gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 46, 128–148.[CrossRef] [Google Scholar]
  2. Bernardet, J.-F., Nakagawa, Y. & Holmes, B.(2002). Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52, 1049–1070.[CrossRef] [Google Scholar]
  3. Böckelmann, U., Manz, W., Neu, T. R. & Szewzyk, U.(2000). Characterization of the microbial community of lotic organic aggregates (‘river snow’) in the Elbe River of Germany by cultivation and molecular methods. FEMS Microbiol Ecol 33, 157–170. [Google Scholar]
  4. Bowman, J. P., McCammon, S. A., Brown, M. V., Nichols, D. S. & McMeekin, T. A.(1997). Diversity and association of psychrophilic bacteria in Antarctic sea ice. Appl Environ Microbiol 63, 3068–3078. [Google Scholar]
  5. Bowman, J. P., McCammon, S. A., Lewis, T., Skerratt, J. H., Brown, J. L., Nichols, D. S. & McMeekin, T. A.(1998).Psychroflexus torquis gen. nov., sp. nov., a psychrophilic species from Antarctic sea ice, and reclassification of Flavobacterium gondwanense ( Dobson et al. 1993 ) as Psychroflexus gondwanense gen. nov., comb. nov. Microbiology 144, 1601–1609.[CrossRef] [Google Scholar]
  6. Bowman, J. P., Nichols, C. M. & Gibson, J. A. E.(2003).Algoriphagus ratkowskyi gen. nov., sp. nov., Brumimicrobium glaciale gen. nov., sp. nov., Cryomorpha ignava gen. nov., sp. nov. and Crocinitomix catalasitica gen. nov., sp. nov., novel flavobacteria isolated from various polar habitats. Int J Syst Evol Microbiol 53, 1343–1355.[CrossRef] [Google Scholar]
  7. Brettar, I., Christen, R. & Höfle, M. G.(2004).Belliella baltica gen. nov., sp. nov., a novel marine bacterium of the CytophagaFlavobacteriumBacteroides group isolated from surface water of the central Baltic Sea. Int J Syst Evol Microbiol 54, 65–70.[CrossRef] [Google Scholar]
  8. Brown, M. V. & Bowman, J. P.(2001). A molecular phylogenetic survey of sea-ice microbial communities (SIMCO). FEMS Microbiol Ecol 35, 267–275.[CrossRef] [Google Scholar]
  9. Burton, N. F., Day, M. J. & Bull, A. T.(1982). Distribution of bacterial plasmids in clean and polluted sites in a South Wales river. Appl Environ Microbiol 44, 1026–1029. [Google Scholar]
  10. Christensen, P. J. & Cook, F. D.(1972). The isolation and enumeration of cytophagas. Can J Microbiol 18, 1933–1939.[CrossRef] [Google Scholar]
  11. Cottrell, M. T. & Kirchman, D. L.(2000a). Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter. Appl Environ Microbiol 66, 1692–1697.[CrossRef] [Google Scholar]
  12. Cottrell, M. T. & Kirchman, D. L.(2000b). Community composition of marine bacterioplankton determined by 16S rRNA gene clone libraries and fluorescence in situ hybridization. Appl Environ Microbiol 66, 5116–5122.[CrossRef] [Google Scholar]
  13. Dawson, R. M. C., Elliot, W. H. & Jones, K. M. (editors)(1969).Data for Biochemical Research. Oxford: Clarendon Press.
  14. De Ley, J., Cattoir, H. & Reynaerts, A.(1970). The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12, 133–142.[CrossRef] [Google Scholar]
  15. Dobson, S. J., Colwell, R. R., McMeekin, T. A. & Franzmann, P. D.(1993). Direct sequencing of the polymerase chain reaction-amplified 16S rRNA gene of Flavobacterium gondwanense sp. nov. and Flavobacterium salegens sp. nov., two new species from a hypersaline Antarctic lake. Int J Syst Bacteriol 43, 77–83.[CrossRef] [Google Scholar]
  16. Flint, K. P.(1985). A note on a selective agar medium for the enumeration of Flavobacterium species in water. J Appl Bacteriol 59, 561–566.[CrossRef] [Google Scholar]
  17. Fry, J. C.(2004). Culture-dependent microbiology. In Microbial Diversity and Bioprospecting, pp. 80–87. Edited by A. T. Bull. Washington, DC: American Society for Microbiology.
  18. Glöckner, F. O., Fuchs, B. M. & Amann, R.(1999). Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl Environ Microbiol 65, 3721–3726. [Google Scholar]
  19. Gosink, J. J., Woese, C. R. & Staley, J. T.(1998).Polaribacter gen. nov., with three new species, P. irgensii sp. nov., P. franzmannii sp. nov. and P. filamentus sp. nov., gas vacuolate polar marine bacteria of the Cytophaga–Flavobacterium–Bacteroides group and reclassification of ‘Flectobacillus glomeratus’ as Polaribacter glomeratus comb. nov. Int J Syst Bacteriol 48, 223–235.[CrossRef] [Google Scholar]
  20. Holmes, B.(1992). The genera Flavobacterium, Sphingobacterium, and Weeksella. In The Prokaryotes, 2nd edn, vol. 4, pp. 3620–3630. Edited by A. Balows, H. G. Trüper, M. Dworkin, W. Harder & K. H. Schleifer. Berlin: Springer.
  21. Humphry, D. R., George, A., Black, G. W. & Cummings, S. P.(2001).Flavobacterium frigidarium sp. nov., an aerobic, psychrophilic, xylanolytic and laminarinolytic bacterium from Antarctica. Int J Syst Evol Microbiol 51, 1235–1243. [Google Scholar]
  22. 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.[CrossRef] [Google Scholar]
  23. Ivanova, E. P., Alexeeva, Y. V., Flavier, S., Wright, J. P., Zhukova, N. V., Gorshkova, N. M., Mikhailov, V. V., Nicolau, D. V. & Christen, R.(2004).Formosa algae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae. Int J Syst Evol Microbiol 54, 705–711.[CrossRef] [Google Scholar]
  24. Johansen, J. E., Nielsen, P. & Sjøholm, C.(1999). Description of Cellulophaga baltica gen. nov., sp. nov. and Cellulophaga fucicola gen. nov., sp. nov. and reclassification of [Cytophaga] lytica to Cellulophaga lytica gen. nov., comb. nov. Int J Syst Bacteriol 49, 1231–1240.[CrossRef] [Google Scholar]
  25. Kämpfer, P., Dreyer, U., Neef, A., Dott, W. & Busse, H.-J.(2003).Chryseobacterium defluvii sp. nov., isolated from wastewater. Int J Syst Evol Microbiol 53, 93–97.[CrossRef] [Google Scholar]
  26. Kim, M. K., Im, W.-T., Shin, Y. K., Lim, J. H., Kim, S.-H., Lee, B. C., Park, M.-Y., Lee, K. Y. & Lee, S.-T.(2004).Kaistella koreensis gen. nov., sp. nov., a novel member of the Chryseobacterium–Bergeyella–Riemerella branch. Int J Syst Evol Microbiol 54, 2319–2324.[CrossRef] [Google Scholar]
  27. Kim, K. K., Bae, H.-S., Schumann, P. & Lee, S.-T.(2005a).Chryseobacterium daecheongense sp. nov., isolated from freshwater lake sediment. Int J Syst Evol Microbiol 55, 133–138.[CrossRef] [Google Scholar]
  28. Kim, K. K., Kim, M. K., Lim, J. H., Park, H. Y. & Lee, S.-T.(2005b). Transfer of Chryseobacterium meningosepticum and Chryseobacterium miricola to Elizabethkingia gen. nov. as Elizabethkingia meningoseptica comb. nov. and Elizabethkingia miricola comb. nov. Int J Syst Evol Microbiol 55, 1287–1293.[CrossRef] [Google Scholar]
  29. Lau, K. W. K., Ng, C. Y. M., Ren, J., Lau, S. C. L., Qian, P.-Y., Wong, P.-K., Lau, T. C. & Wu, M.(2005).Owenweeksia hongkongensis gen. nov., sp. nov., a novel marine bacterium of the phylum ‘Bacteroidetes’. Int J Syst Evol Microbiol 55, 1051–1057.[CrossRef] [Google Scholar]
  30. Mahenthiralingam, E., Urban, T. A. & Goldburg, J. B.(2005). The multifarious, multireplicon Burkholderia cepacia complex. Nat Rev Microbiol 3, 144–156.[CrossRef] [Google Scholar]
  31. Manz, W., Amann, R., Ludwig, W., Vancanneyt, M. & Schleifer, K. H.(1996). Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment. Microbiology 142, 1097–1106.[CrossRef] [Google Scholar]
  32. McCammon, S. A. & Bowman, J. P.(2000). Taxonomy of Antarctic Flavobacterium species: description of Flavobacterium gillisiae sp. nov., Flavobacterium tegetincola sp. nov., and Flavobacterium xanthum sp. nov., nom. rev. and reclassification of [Flavobacterium] salegens as Salegentibacter salegens gen. nov., comb. nov. Int J Syst Evol Microbiol 50, 1055–1063.[CrossRef] [Google Scholar]
  33. McCammon, S. A., Innes, B. H., Bowmann, J. P., Franzmann, P. D., Dobson, S. J., Holloway, P. E., Skerratt, J. H., Nichols, P. D. & Rankin, L. M.(1998).Flavobacterium hibernum sp. nov., a lactose-utilizing bacterium from a freshwater Antarctic lake. Int J Syst Bacteriol 48, 1405–1412.[CrossRef] [Google Scholar]
  34. Nedashkovskaya, O. I., Kim, S. B., Han, S. K. & 7 other authors(2003).Mesonia algae gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm. Int J Syst Evol Microbiol 53, 1967–1971.[CrossRef] [Google Scholar]
  35. Nedashkovskaya, O. I., Kim, S. B., Han, S. K. & 7 other authors(2004a).Maribacter gen. nov., a new member of the family Flavobacteriaceae, isolated from marine habitats, containing the species Maribacter sedimenticola sp. nov., Maribacter aquivivus sp. nov., Maribacter orientalis sp. nov. and Maribacter ulvicola sp. nov. Int J Syst Evol Microbiol 54, 1017–1023.[CrossRef] [Google Scholar]
  36. Nedashkovskaya, O. I., Kim, S. B., Han, S. K., Rhee, M. S., Lysenko, A. M., Falsen, E., Frolova, G. M., Mikhailov, V. V. & Bae, K. S.(2004b).Ulvibacter litoralis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from the green alga Ulva fenestrata. Int J Syst Evol Microbiol 54, 119–123.[CrossRef] [Google Scholar]
  37. Nedashkovskaya, O. I., Kim, S. B., Han, S. K. & 9 other authors(2005a).Winogradskyella thalassocola gen. nov., sp. nov., Winogradskyella epiphytica sp. nov. and Winogradskyella eximia sp. nov., marine bacteria of the family Flavobacteriaceae. Int J Syst Evol Microbiol 55, 49–55.[CrossRef] [Google Scholar]
  38. Nedashkovskaya, O. I., Kim, S. B., Lysenko, A. M., Frolova, G. M., Mikhailov, V. V., Lee, K. H. & Bae, K. S.(2005b). Description of Aquimarina muelleri gen. nov., sp. nov., and proposal of the reclassification of [Cytophaga] latercula Lewin 1969 as Stanierella latercula gen. nov., comb. nov. Int J Syst Evol Microbiol 55, 225–229.[CrossRef] [Google Scholar]
  39. Nikitin, D. I., Strömpl, C., Oranskaya, M. S. & Abraham, W.-R.(2004). Phylogeny of the ring-forming bacterium Arcicella aquatica gen. nov., sp. nov. (ex Nikitin et al. 1994), from a freshwater neuston biofilm. Int J Syst Evol Microbiol 54, 681–684.[CrossRef] [Google Scholar]
  40. O'Sullivan, L. A., Weightman, A. J. & Fry, J. C.(2002). New degenerate CytophagaFlexibacterBacteroides-specific 16S ribosomal DNA-targeted oligonucleotide probes reveal high bacterial diversity in River Taff epilithon. Appl Environ Microbiol 68, 201–210.[CrossRef] [Google Scholar]
  41. O'Sullivan, L. A., Fuller, K. E., Thomas, E. M., Turley, C. M., Fry, J. C. & Weightman, A. J.(2004). Distribution and culturability of the uncultivated ‘AGG58 cluster’ of the Bacteroidetes phylum in aquatic environments. FEMS Microbiol Ecol 47, 359–370.[CrossRef] [Google Scholar]
  42. O'Sullivan, L. A., Rinna, J., Humphreys, G., Weightman, A. J. & Fry, J. C.(2005).Fluviicola taffensis gen. nov., sp. nov., a novel freshwater bacterium of the family Cryomorphaceae in the phylum ‘Bacteroidetes’. Int J Syst Evol Microbiol 55, 2189–2194.[CrossRef] [Google Scholar]
  43. Paster, B. J., Ludwig, W., Weisberg, W. G., Stackebrandt, E., Hespell, R. B., Hahn, C. M., Reichenbach, H., Stetter, K. O. & Woese, C. R.(1985). A phylogenetic grouping of the bacteroides, cytophagas, and certain flavobacteria. Syst Appl Microbiol 6, 34–42.[CrossRef] [Google Scholar]
  44. Reichenbach, H.(1989). Nonphotosynthetic, nonfruiting gliding bacteria. Genus 1. Cytophaga Winogradsky 1929, 577AL, emend. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 3, pp. 2015–2050. Edited by J. Staley, M. P. Bryant, N. Pfennig & J. G. Holt. Baltimore: Williams & Wilkins.
  45. Reichenbach, H.(1992). The order Cytophagales. In The Prokaryotes, 2nd edn, vol. 4, pp. 3631–3687. Edited by A. Balows, H. G. Truper, M. Dworkin, W. Harder & K. H. Schleifer. Berlin: Springer.
  46. Reichenbach, H., Kohl, W., Böttger-Vetter, A. & Achenbach, H.(1980). Flexirubin-type pigments in Flavobacterium. Arch Microbiol 126, 291–293.[CrossRef] [Google Scholar]
  47. Rickard, A. H., Stead, A. T. O'May G. A., Lindsay, S., Banner, M., Handley, P. S. & Gilbert, P.(2005).Adhaeribacter aquaticus gen. nov., sp. nov., a Gram-negative isolate from a potable water biofilm. Int J Syst Evol Microbiol 55, 821–829.[CrossRef] [Google Scholar]
  48. Simon, M., Glöckner, F. O. & Amann, R.(1999). Different community structure and temperature optima of heterotrophic picoplankton in various regions of the Southern Ocean. Aquat Microb Ecol 18, 275–284.[CrossRef] [Google Scholar]
  49. Smibert, R. M. & Krieg, N. R.(1994). Phenotypic characterization. In Methods for General and Molecular Bacteriology, pp. 607–654. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
  50. Sohn, J. H., Lee, J.-H., Yi, H., Chun, J., Bae, K. S., Ahn, T.-Y. & Kim, S.-J.(2004).Kordia algicida gen. nov., sp. nov., an algicidal bacterium isolated from red tide. Int J Syst Evol Microbiol 54, 675–680.[CrossRef] [Google Scholar]
  51. Staples, D. G. & Fry, J. C.(1973). A medium for counting aquatic heterotrophic bacteria in polluted and unpolluted waters. J Appl Bacteriol 36, 179–181.[CrossRef] [Google Scholar]
  52. Suzuki, M. T., Rappé, M. S., Haimberger, Z. W., Winfield, H., Adair, N., Strobel, J. & Giovannoni, S. J.(1997). Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample. Appl Environ Microbiol 63, 983–989. [Google Scholar]
  53. Suzuki, M., Nakagawa, Y., Harayama, S. & Yamamoto, S.(2001). Phylogenetic analysis and taxonomic study of marine Cytophaga-like bacteria: proposal for Tenacibaculum gen. nov. with Tenacibaculum maritimum comb. nov. and Tenacibaculum ovolyticum comb. nov., and description of Tenacibaculum mesophilum sp. nov. and Tenacibaculum amylolyticum sp. nov. Int J Syst Evol Microbiol 51, 1639–1652.[CrossRef] [Google Scholar]
  54. Tenreiro, S., Nobre, M. F., Rainey, F. A., Miguel, C. & da Costa, M. S.(1997).Thermonema rossianum sp. nov., a new thermophilic and slightly halophilic species from saline hot springs in Naples, Italy. Int J Syst Bacteriol 47, 122–126.[CrossRef] [Google Scholar]
  55. Vandamme, P., Bernardet, J.-F., Segers, P., Kersters, K. & Holmes, B.(1994). New perspectives in the classification of the flavobacteria: description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev. Int J Syst Bacteriol 44, 827–831.[CrossRef] [Google Scholar]
  56. Vandamme, P., Pot, B., Gillis, M., De Vos, P. & Swings, J.(1996). Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60, 407–438. [Google Scholar]
  57. Van Trappen, S., Vandecandelaere, I., Mergaert, J. & Swings, J.(2004).Gillisia limnaea gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from a microbial mat in Lake Fryxell, Antarctica. Int J Syst Evol Microbiol 54, 445–448.[CrossRef] [Google Scholar]
  58. Weeks, O. B.(1955).Flavobacterium aquatile (Frankland and Frankland) Bergey et al., type species of the genus Flavobacterium. J Bacteriol 69, 649–658. [Google Scholar]
  59. Woese, C. R., Yang, D., Mandelco, L. & Stetter, K. O.(1990). The Flexibacter-Flavobacter connection. Syst Appl Microbiol 13, 161–165.[CrossRef] [Google Scholar]
  60. Yi, H. & Chun, J.(2004).Hongiella mannitolivorans gen. nov., sp. nov., Hongiella halophila sp. nov. and Hongiella ornithinivorans sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 54, 157–162.[CrossRef] [Google Scholar]
  61. Yi, H., Yoon, H. I. & Chun, J.(2005).Sejongia antarctica gen. nov., sp. nov. and Sejongia jeonii sp. nov., isolated from the Antarctic. Int J Syst Evol Microbiol 55, 409–416.[CrossRef] [Google Scholar]
  62. Young, C.-C., Kämpfer, P., Shen, F.-T., Lai, W.-A. & Arun, A. B.(2005).Chryseobacterium formosense sp. nov., isolated from the rhizosphere of Lactuca sativa L. (garden lettuce). Int J Syst Evol Microbiol 55, 423–426.[CrossRef] [Google Scholar]
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