A Gram-negative, flagellated, heterotrophic, catalase-negative, rod-shaped bacterium previously identified as an earthworm symbiont was isolated from nephridia of the earthworm . Comparisons of 16S rRNA gene sequences indicated its relatedness to the betaproteobacterial genus and the novel isolates shared 92–94 % sequence similarity with recognized species of this genus. Gene sequence phylogenies revealed that the group of earthworm symbionts formed a cohesive and independent clade. The DNA G+C content was 67.0±0.2 mol%. Major fatty acids were C, C 7 and C cyclo. While capable of growing in fully aerated media, all isolates favoured low oxygen concentrations and all required biotin or a mix of amino acids in order to grow on defined mineral media. Based on phylogenies inferred from three housekeeping gene sequences (, and ), DNA–DNA hybridization values, the unique ecology and the distinct physiology of the novel strains, the new genus gen. nov. is proposed for the earthworm nephridial symbionts. The name sp. nov. is proposed for the type species with strain EF01-2 (=ATCC BAA-1489=DSM 19286) as the type strain of the type species.


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  1. Adl, S. M., Simpson, A. G. B., Farmer, M. A., Andersen, R. A., Anderson, O. R., Barta, J. R., Bowser, S. S., Brugerolle, G., Fensome, R. A. & other authors(2005). The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Eukaryot Microbiol 52, 399–451.[CrossRef] [Google Scholar]
  2. Ballinger, M. L., Blanchette, A. R., Krause, T. L., Smyers, M. E., Fishman, H. M. & Bittner, G. D.(1997). Delaminating myelin membranes help seal the cut ends of severed earthworm giant axons. J Neurobiol 33, 945–960.[CrossRef] [Google Scholar]
  3. Barton, B. M., Harding, G. P. & Zuccarelli, A. J.(1995). A general method for detecting and sizing large plasmids. Anal Biochem 226, 235–240.[CrossRef] [Google Scholar]
  4. Bousfield, I. J., Smith, G. L., Dando, T. R. & Hobbs, G.(1983). Numerical analysis of total fatty acid profiles in the identification of coryneform, nocardioform and some other bacteria. J Gen Microbiol 129, 375–394. [Google Scholar]
  5. Cole, J. R., Chai, B., Marsh, T. L., Farris, R. J., Wang, Q., Kulam, S. A., Chandra, S., McGarrell, D. M., Schmidt, T. M. & other authors(2003). The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31, 442–443.[CrossRef] [Google Scholar]
  6. Davidson, S. K. & Stahl, D. A.(2006). Transmission of nephridial bacteria of the earthworm Eisenia fetida. Appl Environ Microbiol 72, 769–775.[CrossRef] [Google Scholar]
  7. Ezaki, T., Hashimoto, Y. & Yabuuchi, E.(1989). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Evol Microbiol 39, 224–229. [Google Scholar]
  8. Felsenstein, J.(1989).phylip - phylogeny inference package (version 3.2). Cladistics 5, 164–166. [Google Scholar]
  9. Fuchs, G.(1999). Biosynthesis of Building Blocks. In Biology of the Prokaryotes, pp. 127–134. Edited by J. W. Lengeler, G. Drews & H. G. Schlegel. Stuttgart: Thieme.
  10. Fuchs, G. & Kröger, A.(1999). Growth and Nutrition. In Biology of the Prokaryotes, pp. 88–109. Edited by J. W. Lengeler, G. Drews & H. G. Schlegel. Stuttgart: Thieme.
  11. Gardan, L., Dauga, C., Prior, P., Gillis, M. & Saddler, G. S.(2000).Acidovorax anthurii sp. nov., a new phytopathogenic bacterium which causes bacterial leaf-spot of anthurium. Int J Syst Evol Microbiol 50, 235–246.[CrossRef] [Google Scholar]
  12. Gardan, L., Stead, D. E., Dauga, C. & Gillis, M.(2003).Acidovorax valerianellae sp. nov., a novel pathogen of lamb's lettuce [Valerianella locusta (L.) Laterr.]. Int J Syst Evol Microbiol 53, 795–800.[CrossRef] [Google Scholar]
  13. Grogan, D. W. & Cronan, J. E.(1997). Cyclopropane ring formation in membrane lipids of bacteria. Microbiol Mol Biol Rev 61, 429–441. [Google Scholar]
  14. Guckert, J. B., Hood, M. A. & White, D. C.(1986). Phospholipid ester-linked fatty acid profile changes during nutrient deprivation of Vibrio cholerae: increases in the trans/cis ratio and proportions of cyclopropyl fatty acids. Appl Environ Microbiol 52, 794–801. [Google Scholar]
  15. Heylen, K., Lebbe, L. & De Vos, P.(2008).Acidovorax caeni sp. nov., a denitrifying species with genetically diverse isolates from activated sludge. Int J Syst Evol Microbiol 58, 73–77.[CrossRef] [Google Scholar]
  16. Hoshino, T., Terahara, T., Tsuneda, S., Hirata, A. & Inamori, Y.(2005). Molecular analysis of microbial population transition associated with the start of denitrification in a wastewater treatment process. J Appl Microbiol 99, 1165–1175.[CrossRef] [Google Scholar]
  17. Knop, J.(1926). Bakterien und Bakteroiden bei Oligochäten. Z Morph Ökol Tiere 6, 588–624 (in German).[CrossRef] [Google Scholar]
  18. Könneke, M. & Widdel, F.(2003). Effect of growth temperature on cellular fatty acids in sulphate-reducing bacteria. Environ Microbiol 5, 1064–1070.[CrossRef] [Google Scholar]
  19. Konstantinidis, K. T. & Tiedje, J. M.(2005a). Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 102, 2567–2572.[CrossRef] [Google Scholar]
  20. Konstantinidis, K. T. & Tiedje, J. M.(2005b). Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187, 6258–6264.[CrossRef] [Google Scholar]
  21. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, Buchner, A., Lai, T., Steppi, S. & other authors(2004).arb: a software environment for sequence data. Nucleic Acids Res 32, 1363–1371.[CrossRef] [Google Scholar]
  22. Manefield, M., Griffiths, R. I., Leigh, M. B., Fisher, R. & Whiteley, A. S.(2005). Functional and compositional comparison of two activated sludge communities remediating coking effluent. Environ Microbiol 7, 715–722.[CrossRef] [Google Scholar]
  23. Marmur, J.(1963). A procedure for the isolation of deoxyribonucleic acid from microorganisms. Methods Enzymol 6, 726–738. [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 Evol Microbiol 39, 159–167. [Google Scholar]
  25. 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. [Google Scholar]
  26. Ramsay, J. A.(1949). The site of formation of hypotonic urine in the nephridium of Lumbricus. J Exp Biol 26, 65–75. [Google Scholar]
  27. Schramm, A., Davidson, S. K., Dodsworth, J. A., Drake, H. L., Stahl, D. A. & Dubilier, N.(2003).Acidovorax-like symbionts in the nephridia of earthworms. Environ Microbiol 5, 804–809.[CrossRef] [Google Scholar]
  28. Schulze, R., Spring, S., Amann, R., Huber, I., Ludwig, W., Schleifer, K.-H. & Kämpfer, P.(1999). Genotypic diversity of Acidovorax strains isolated from activated sludge and description of Acidovorax defluvii sp. nov. Syst Appl Microbiol 22, 205–214.[CrossRef] [Google Scholar]
  29. Schweitzer, B., Huber, I., Amann, R., Ludwig, W. & Simon, M.(2001).α- and β-proteobacteria control the consumption and release of amino acids on Lake Snow aggregates. Appl Environ Microbiol 67, 632–645.[CrossRef] [Google Scholar]
  30. Scott, D. A. & Musgrave, A. J.(1971). Aspects of fine structure of symbiotes and related host tissues in nephridia of Allolobophora caliginosa typica (Annelida - Lumbricidae). J Invertebr Pathol 18, 51–60.[CrossRef] [Google Scholar]
  31. 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: ASM Press.
  32. Sonnenburg, J. L., Xu, J., Leip, D. D., Chen, C.-H., Westover, B. P., Weatherford, J., Buhler, J. D. & Gordon, J. I.(2005). Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science 307, 1955–1959.[CrossRef] [Google Scholar]
  33. Stackebrandt, E. & Goebel, B. M.(1994). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 44, 846–849. [Google Scholar]
  34. Stackebrandt, E., Frederiksen, W., Garrity, G. M., Grimont, P., Kampfer, P., Maiden, M., Nesme, X., Rossello-Mora, R., Swings, J. & other authors(2002). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52, 1043–1047.[CrossRef] [Google Scholar]
  35. Thompson, J. D., Higgins, D. G. & Gibson, T. J.(1994).clustalw: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–4680.[CrossRef] [Google Scholar]
  36. Willems, A., Falsen, E., Pot, B., Jantzen, E., Hoste, B., Vandamme, P., Gillis, M., Kersters, K. & De Ley, J.(1990).Acidovorax, a new genus for Pseudomonas facilis, Pseudomonas delafieldii, E. Falsen (EF) Group 13, EF Group 16, and several clinical isolates, with the species Acidovorax facilis comb. nov., Acidovorax delafieldii comb. nov., and Acidovorax temperans sp. nov. Int J Syst Evol Microbiol 40, 384–398. [Google Scholar]
  37. Willems, A., Goor, M., Thielemans, S., Gillis, M., Kersters, K. & De Ley, J. (1992). Transfer of several phytopathogenic Pseudomonas species to Acidovorax as Acidovorax avenae subsp. avenae subsp. nov., comb. nov., Acidovorax avenae subsp. citrulli, Acidovorax avenae subsp. cattleyae, and Acidovorax konjaci. Int J Syst Evol Microbiol 42, 107–119. [Google Scholar]
  38. Willems, A., Doignon-Bourcier, F., Goris, J., Coopman, R., de Lajudie, P., De Vos, P. & Gillis, M.(2001). DNA-DNA hybridization study of Bradyrhizobium strains. Int J Syst Evol Microbiol 51, 1315–1322. [Google Scholar]

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Vitamin requirements for growth on defined medium. [ PDF] 153 KB


Siderophore production assayed through the CAS method. [ PDF] 54 KB


Details of soil DNA surveys and siderophore production and uptake. [ PDF] 77 KB


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