Emended description of the genus Phyllobacterium and description of four novel species associated with plant roots: Phyllobacterium bourgognense sp. nov., Phyllobacterium ifriqiyense sp. nov., Phyllobacterium leguminum sp. nov. and Phyllobacterium brassicacearum sp. nov.

References

1. Abraham W. R., Strompl C., Meyer H. 8 other authors 1999; Phylogeny and polyphasic taxonomy of Caulobacter species. Proposal of Maricaulis gen. nov. with Maricaulis maris (Poindexter) comb. nov. as the type species, and emended description of the genera Brevundimonas and Caulobacter . Int J Syst Bacteriol 49:1053–1073 [CrossRef]
   [Google Scholar]
2. Alavi M., Miller T., Erlandson K., Schneider R., Belas R. 2001; Bacterial community associated with Pfiesteria -like dinoflagellate cultures. Environ Microbiol 3:380–396 [CrossRef]
   [Google Scholar]
3. Bernaerts M. J., De Ley J. 1963; A biochemical test for crown gall bacteria. Nature 197:406–407
   [Google Scholar]
4. Bertrand H., Nalin R., Bally R., Cleyet-Marel J.-C. 2001; Isolation and identification of the most efficient plant growth-promoting bacteria associated with canola ( Brassica napus . Biol Fertil Soils 33:152–156 [CrossRef]
   [Google Scholar]
5. Catara V., Sutra L., Morineau A., Achouak W., Christen R., Gardan L. 2002; Phenotypic and genomic evidence for the revision of Pseudomonas corrugata and proposal of Pseudomonas mediterranea sp. nov. Int J Syst Evol Microbiol 52:1749–1758 [CrossRef]
   [Google Scholar]
6. Chanway C. P., Shishido M., Holl F. B. 1994; Root-endophytic and rhizosphere plant growth-promoting rhizobacteria for conifer seedlings. In Improving Plant Productivity with Rhizosphere Bacteria pp  72–74 Edited by Ryder M. H. Glen Osmond, Australia: CSIRO Division of Soils;
   [Google Scholar]
7. Chen W. P., Kuo T. T. 1993; A simple and rapid method for the preparation of gram-negative bacterial genomic DNA. Nucleic Acids Res 21:2260 [CrossRef]
   [Google Scholar]
8. Cleenwerck I., Vandemeulebroecke K., Janssens D., Swings J. 2002; Re-examination of the genus Acetobacter , with descriptions of Acetobacter cerevisiae sp. nov. and Acetobacter malorum sp. nov. Int J Syst Evol Microbiol 52:1551–1558 [CrossRef]
   [Google Scholar]
9. Crosa J. H., Brenner D. J., Falkow S. 1973; Use of a single-strand specific nuclease for analysis of bacterial and plasmid deoxyribonucleic acid homo- and heteroduplexes. J Bacteriol 115:904–911
   [Google Scholar]
10. de Lajudie P., Willems A., Pot B. 7 other authors 1994; Polyphasic taxonomy of rhizobia: emendation of the genus Sinorhizobium and description of Sinorhizobium meliloti comb. nov., Sinorhizobium saheli sp. nov., and Sinorhizobium teranga sp. nov. Int J Syst Bacteriol 44:715–733 [CrossRef]
    [Google Scholar]
11. Descamps P., Véron M. 1981; Une méthode de choix des caractères d'identification basée sur le théorème de Bayes et la mesure de l'information. Ann Inst Pasteur Microbiol 132B:157–170 (in French
    [Google Scholar]
12. Don R. H., Cox P. T., Wainwright B. J., Baker K., Mattick J. S. 1991; ‘Touchdown’ PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res 19:4008 [CrossRef]
    [Google Scholar]
13. Elo S., Maunuksela L., Salkinoja-Salonen M., Smolander A., Haahtela K. 2000; Humus bacteria of Norway spruce stands: plant growth promoting properties and birch, red fescue and alder colonizing capacity. FEMS Microbiol Ecol 31:143–152 [CrossRef]
    [Google Scholar]
14. Gaunt M. W., Turner S. L., Rigottier-Gois L., Lloyd-Macgilp S. A., Young J. P. W. 2001; Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia. Int J Syst Evol Microbiol 51:2037–2048 [CrossRef]
    [Google Scholar]
15. Gevers D., Cohan F. M., Lawrence J. G. 8 other authors 2005; Re-evaluating prokaryotic species. Nat Rev Microbiol 3:733–739 [CrossRef]
    [Google Scholar]
16. Gillis M., De Ley J. 1980; Intra- and intergeneric similarities of the ribosomal ribonucleic acid cistrons of Acetobacter and Gluconobacter . Int J Syst Bacteriol 30:7–27 [CrossRef]
    [Google Scholar]
17. Gillis M., Van T. V., Bardin R. &7 other authors; 1995; Polyphasic taxonomy in the genus Burkholderia leading to an emended description of the genus and proposition of Burkholderia vietnamiensis sp. nov. for N₂-fixing isolates from rice in Vietnam. Int J Syst Bacteriol 45:274–289 [CrossRef]
    [Google Scholar]
18. Gonzalez-Bashan L. E., Lebsky V. K., Hernandez J. P., Bustillos J. J., Bashan Y. 2000; Changes in the metabolism of the microalga Chlorella vulgaris when coimmobilized in alginate with the nitrogen-fixing Phyllobacterium myrsinacearum . Can J Microbiol 46:653–659 [CrossRef]
    [Google Scholar]
19. Grimont P. A. D., Popoff M. Y., Grimont F., Coynault C., Lemelin M. 1980; Reproducibility and correlation study of three deoxyribonucleic acid hybridization procedures. Curr Microbiol 4:325–330 [CrossRef]
    [Google Scholar]
20. Hallmann J., Kloepper J. W., Rodriguez-Kabana R. 1997; Application of the Scholander pressure bomb to studies on endophytic bacteria of plants. Can J Microbiol 43:411–416 [CrossRef]
    [Google Scholar]
21. 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
    [Google Scholar]
22. Jurado V., Laiz L., Gonzalez J. M., Hernandez-Marine M., Valens M., Saiz-Jimenez C. 2005; Phyllobacterium catacumbae sp. nov., a member of the order ‘ Rhizobiales ’ isolated from Roman catacombs. Int J Syst Evol Microbiol 55:1487–1490 [CrossRef]
    [Google Scholar]
23. Knösel D. H. 1962; Prüfung von Bakterien auf Fähigkeit zür Sternbildung. Zentralbl Bakteriol Parasitenkd Infektionskr Hyg 116:79–100 (in German
    [Google Scholar]
24. Knösel D. H. 1984; Genus IV. Phyllobacterium ( ex Knösel 1962) nom. rev. In Bergey's Manual of Systematic Bacteriology vol 1 pp  254–256 Edited by Krieg N. R., Holt J. G. Baltimore: Williams & Wilkins;
    [Google Scholar]
25. Kovacs N. 1956; Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 178:703
    [Google Scholar]
26. Lambert B., Joos H., Dierickx S., Vantomme R., Swings J., Kersters K., van Montagu M. 1990; Identification and plant interaction of a Phyllobacterium sp., a predominant rhizobacterium of young sugar beet plants. Appl Environ Microbiol 56:1093–1102
    [Google Scholar]
27. Larcher M., Muller B., Mantelin S., Rapior S., Cleyet-Marel J.-C. 2003; Early modifications of Brassica napus root system architecture induced by a plant growth-promoting Phyllobacterium strain. New Phytol 160:119–125 [CrossRef]
    [Google Scholar]
28. Lilley A. K., Fry J. C., Bailey M. J., Day M. J. 1996; Comparison of aerobic heterotrophic taxa isolated from four root domains of mature sugar beet ( Beta vulgaris . FEMS Microbiol Ecol 21:231–242 [CrossRef]
    [Google Scholar]
29. Mantelin S., Desbrosses G., Larcher M., Tranbarger T. J., Cleyet-Marel J.-C., Touraine B. 2006; Nitrate-dependent control of root architecture and N nutrition are altered by a plant growth-promoting Phyllobacterium sp. Planta 223:591–603 [CrossRef]
    [Google Scholar]
30. Marmur J., Doty P. 1962; Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5:109–118 [CrossRef]
    [Google Scholar]
31. Martínez J., Martínez L., Rosenblueth M., Silva J., Martínez-Romero E. 2004; How are gene sequence analyses modifying bacterial taxonomy? The case of Klebsiella . Int Microbiol 7:261–268
    [Google Scholar]
32. McInroy J. A., Kloepper J. W. 1995; Survey of indigenous bacterial endophytes from cotton and sweet corn. Plant Soil 173:337–342 [CrossRef]
    [Google Scholar]
33. Mergaert J., Boley A., Cnockaert M. C., Muller W. R., Swings J. 2001; Identity and potential functions of heterotrophic bacterial isolates from a continuous-upflow fixed-bed reactor for denitrification of drinking water with bacterial polyester as source of carbon and electron donor. Syst Appl Microbiol 24:303–310 [CrossRef]
    [Google Scholar]
34. Mergaert J., Cnockaert M. C., Swings J. 2002; Phyllobacterium myrsinacearum (subjective synonym Phyllobacterium rubiacearum ) emend. Int J Syst Evol Microbiol 52:1821–1823 [CrossRef]
    [Google Scholar]
35. Nicholas K. B., Nicholas H. B. Jr, Deerfield D. W. II 1997; GeneDoc: analysis and visualization of genetic variation. EMBNEW News 4:14 http://www.psc.edu/biomed/genedoc/
    [Google Scholar]
36. Nour S. M., Cleyet-Marel J.-C., Beck D., Effosse A., Fernandez M. P. 1994; Genotypic and phenotypic diversity of Rhizobium isolated from chickpea ( Cicer arietinum L.). Can J Microbiol 40:345–354 [CrossRef]
    [Google Scholar]
37. Oger P. M., Mansouri H., Nesme X., Dessaux Y. 2004; Engineering root exudation of Lotus toward the production of two novel carbon compounds leads to the selection of distinct microbial populations in the rhizosphere. Microb Ecol 47:96–103 [CrossRef]
    [Google Scholar]
38. Owen R. J., Lapage S. P. 1976; The thermal denaturation of partly purified bacterial deoxyribonucleic acid and its taxonomic implications. J Appl Bacteriol 41:335–340 [CrossRef]
    [Google Scholar]
39. Pitcher D. G., Saunders N. A., Owen R. J. 1989; Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 8:151–156 [CrossRef]
    [Google Scholar]
40. Posada D., Crandall K. A. 1998; modeltest: testing the model of DNA substitution. Bioinformatics 14:817–818 [CrossRef]
    [Google Scholar]
41. Rasolomampianina R., Bailly X., Fetiarison R. 8 other authors 2005; Nitrogen-fixing nodules from rose wood legume trees ( Dalbergia spp.) endemic to Madagascar host seven different genera belonging to α - and β -Proteobacteria. Mol Ecol 14:4135–4146 [CrossRef]
    [Google Scholar]
42. Rojas A., Holguin G., Glick B. R., Bashan Y. 2001; Synergism between Phyllobacterium sp. (N₂-fixer) and Bacillus licheniformis (P-solubilizer), both from a semiarid mangrove rhizosphere. FEMS Microbiol Ecol 35:181–187 [CrossRef]
    [Google Scholar]
43. Sands D. C. 1990; Physiological criteria – determinative tests. In Methods in Phytobacteriology pp  133–143 Edited by Klement Z., Rudolph K., Sands D. C. Budapest: Akadémiai Kiadó;
    [Google Scholar]
44. Sneath P. H. A., Sokal R. R. 1973 Numerical Taxonomy. The Principles and Practice of Numerical Classification San Francisco: W. H. Freeman;
    [Google Scholar]
45. Sturz A. V., Christie B. R., Matheson B. G., Nowak J. 1997; Biodiversity of endophytic bacteria which colonize red clover nodules, roots, stems and foliage and their influence on host growth. Biol Fertil Soils 25:13–19 [CrossRef]
    [Google Scholar]
46. Sturz A. V., Christie B. R., Matheson B. G. 1998; Associations of bacterial endophyte populations from red clover and potato crops with potential for beneficial allelopathy. Can J Microbiol 44:162–167 [CrossRef]
    [Google Scholar]
47. Suslow T. V., Schroth M. N., Isaka M. 1982; Application of a rapid method for Gram differentiation of plant pathogenic and saprophytic bacteria without staining. Phytopathology 72:917–918 [CrossRef]
    [Google Scholar]
48. Swofford D. L. 1998 paup – phylogenetic analysis using parsimony and other methods Sunderland, MA: Sinauer Associates;
    [Google Scholar]
49. Sy A., Giraud E., Jourand P. 8 other authors 2001; Methylotrophic Methylobacterium bacteria nodulate and fix nitrogen in symbiosis with legumes. J Bacteriol 183:214–220 [CrossRef]
    [Google Scholar]
50. 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]
    [Google Scholar]
51. Turner S. L., Young J. P. W. 2000; The glutamine synthetases of rhizobia: phylogenetics and evolutionary implications. Mol Biol Evol 17:309–319 [CrossRef]
    [Google Scholar]
52. Valverde A., Velazquez E., Fernandez-Santos F., Vizcaino N., Rivas R., Mateos P. F., Martinez-Molina E., Igual J. M., Willems A. 2005; Phyllobacterium trifolii sp. nov., nodulating Trifolium and Lupinus in Spanish soils. Int J Syst Evol Microbiol 55:1985–1989 [CrossRef]
    [Google Scholar]
53. Vandamme P., Pot B., Gillis M., de Vos P., Kersters K., Swings J. 1996; Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438
    [Google Scholar]
54. van Veen R. J. M., den Dulk-Ras H., Bisseling T., Schilperoort R. A., Hooykaas P. J. J. 1988; Crown gall tumor and root nodule formation by the bacterium Phyllobacterium myrsinacearum after the introduction of an Agrobacterium Ti plasmid or a Rhizobium Sym plasmid. Mol Plant Microbe Interact 1:231–234 [CrossRef]
    [Google Scholar]
55. Vincent J. M. 1970; A Manual for the Practical Study of the Root-Nodule Bacteria . IBP Handbook no: 15 Oxford: Blackwell Scientific;
    [Google Scholar]
56. Von Faber F. C. 1912; Das erbliche Zusammenleben von Bakterien und tropischen Pflanzen. Jahrb Wiss Bot 51:285–375 (in German
    [Google Scholar]
57. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J. 1991; 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703
    [Google Scholar]
58. Willems A., Collins M. D. 1993; Phylogenetic analysis of rhizobia and agrobacteria based on 16S rRNA gene sequences. Int J Syst Bacteriol 43:305–313 [CrossRef]
    [Google Scholar]
59. Young J. P. W., Haukka K. 1996; Diversity and phylogeny of rhizobia. New Phytol 133:87–94 [CrossRef]
    [Google Scholar]
60. Zimmermann A. 1902; Uber Bakterienknoten in den Blättern einiger Rubiaceen. Jahrb Wiss Bot 37:1–11 (in German
    [Google Scholar]