Mesorhizobial strains nodulating Anagyris latifolia and Lotus berthelotii in Tamadaya ravine (Tenerife, Canary Islands) are two symbiovars of the same species, Mesorhizobium tamadayense sp. nov.

Systematic and Applied Microbiology

Volumn 35, Issue 5, 2012, Pages 334-341

  Ramírez Bahena, Martha Helena ^a,c   Hernández, Mariano ^b   Peix, álvaro ^a,c   Velázquez, Encarna ^c   León Barrios, Milagros ^b  

^a INSTITUTO DE RECURSOS NATURALES Y AGROBIOLOGÍA DE SALAMANCA   (Spain)

^b UNIVERSIDAD DE LA LAGUNA   (Spain)

^c UNIVERSITY OF SALAMANCA   (Spain)

Author keywords

Anagyris latifolia; Bayesian phylogeny; Canary Islands; Lotus berthelotii; Mesorhizobium; MLSA

Indexed keywords

BACTERIAL RNA; RIBOSOME RNA; RNA 16S;

ANAGYRIS LATIFOLIA; ARTICLE; ATPD GENE; DNA DNA HYBRIDIZATION; DNAK GENE; GENETIC SIMILARITY; GLNII GENE; HOUSEKEEPING GENE; LEGUME; LOTUS BERTHELOTII; MESORHIZOBIUM; MESORHIZOBIUM TAMADAYENSE; MULTILOCUS SEQUENCE TYPING; NODULATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PRIORITY JOURNAL; RECA GENE; RRS GENE; TAXONOMIC IDENTIFICATION;

BAYES THEOREM; DNA, BACTERIAL; FABACEAE; LOTUS; MESORHIZOBIUM; MOLECULAR SEQUENCE DATA; MULTILOCUS SEQUENCE TYPING; PHENOTYPE; PHYLOGENY; ROOT NODULES, PLANT; SPAIN;

ANAGYRIS; LOTUS BERTHELOTII; MESORHIZOBIUM;

EID: 84864306748     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2012.05.003     Document Type: Article

References (58)

1. Akaike H. A new look at the statistical model identification. IEEE Trans. Auto. Control 1974, 19:716-723.
2. Barker F.K., Lutzoni F.M. The utility of the incongruence length difference test. Syst. Biol. 2002, 51:625-637.
3. Chen W., Zhu W., Bontemps C., Young J.P.W., Wei G. Mesorhizobium alhagi sp. nov., isolated from root nodules of the wild legume Alhagi sparsifolia. Int. J. Syst. Evol. Microbiol. 2009, 60:958-962.
4. Chen W.M., Zhu W.F., Bontemps C., Young J.P.W., Wei G.H. Mesorhizobium camelthorni sp. nov., isolated from Alhagi sparsifolia. Int. J. Syst. Evol. Microbiol. 2011, 61:574-579.
5. Chun J., Goodfellow M. A phylogenetic analysis of the genus Nocardia with 16S rRNA sequences. Int. J. Syst. Bacteriol. 1995, 45:240-245.
6. Chun J., Lee J.H., Jung Y., Kim M., Kim S., Kim B.K., Lim Y.W. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. J. Syst. Evol. Microbiol. 2007, 57:2259-2261.
7. Darlu P., Lecointre G. When does the incongruence length difference test fail?. Mol. Biol. Evol. 2002, 19:432-437.
8. Degefu T., Wolde-meskela E., Frostegarda A. Multilocus sequence analyses reveal several unnamed Mesorhizobium genospecies nodulating Acacia species and Sesbania sesban in southern regions of Ethiopia. Syst. Appl. Microbiol. 2011, 34:226-236.
9. Donate-Correa J., León-Barrios M., Hernández M., Pérez-Galdona R., del Arco-Aguilar M. Different Mesorhizobium species sharing the same symbiotic genes nodulate the shrub legume Anagyris latifolia. Syst. Appl. Microbiol. 2007, 30:615-623.
10. Dowton M., Austin A.D. Increased incongruence does not necessarily indicate increased phylogenetic accuracy-the behavior of the ILD test in mixed-model analyses. Syst. Biol. 2002, 51:19-31.
11. Eardly B., Nour S.M., van Berkum P., Selander K. Rhizobial 16S rRNA and dnaK genes: Mosaicism and the uncertain phylogenetic placement of Rhizobium galegae. Appl. Environ. Microbiol. 2005, 71:1328-1335.
12. Ezaki T., Hashimoto Y., Yabuchi E. Fluorometric 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. Bacteriol. 1989, 39:224-229.
13. Gaunt M.W., Turner S.L., Rigottier-Gois L., Lloyd-Macgilp S., Young J.P. Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia. Int. J. Syst. Evol. Microbiol. 2001, 51:2037-2048.
14. Ghosh W., Roy P. Mesorhizobium thiogangeticum sp. nov., a novel sulfur-oxidizing chemolithoautotroph from rhizosphere soil of an Indian tropical leguminous plant. Int. J. Syst. Evol. Microbiol. 2006, 56:91-97.
15. Guan S.H., Chen W.F., Wang E.T., Lu Y.L., Yan X.R., Zhang X.X., Chen W.X. Mesorhizobium caraganae sp. nov., a novel rhizobial species nodulated with Caragana spp. in China. Int. J. Syst. Evol. Microbiol. 2008, 58:2646-2653.
16. Han T.X., Han L.L., Wu L.J., Chen W.F., Sui X.H., Gu J.G., Wang E.T., Chen W.X. Mesorhizobium gobiense sp. nov. and Mesorhizobium tarimense sp. nov., isolated from wild legumes growing in desert soils of Xinjiang, China. Int. J. Syst. Evol. Microbiol. 2008, 58:2610-2618.
17. Hansen A., Sunding P. Flora of Macaronesica, checklist of vascular plants. Sommerfeltia 1993, 17:1-295.
18. Jarabo-Lorenzo A., Velázquez E., Pérez-Galdona R., Vega M.C., Martínez-Molina E., Mateos P., Vinuesa P., Martínez-Romero E., León-Barrios M. Restriction fragment length polymorphism analysis of PCR-amplified 16S rDNA and low molecular weight RNA profiling in the characterisation of rhizobial isolates from shrubby legumes endemic to the Canary Islands. Syst. Appl. Microbiol. 2000, 23:418-425.
19. Jobb, G. (2011) TREEFINDER version of March 2011. Munich, Germany.
20. Konstantinidis K.T., Ramette A., Tiedje J.M. Toward a more robust assessment of intraspecies diversity using fewer genetic markers. Appl. Environ. Microbiol. 2006, 72:7286-7293.
21. León-Barrios M., Gutiérrez-Navarro A., Pérez-Galdona R., Corzo J. Characterization of Canary Island isolates of Bradyrhizobium sp. (Chamaecytisus). Soil Biol. Biochem. 1991, 23:487-489.
22. Lee M.S.Y. Uninformative characters and apparent conflict between molecules and morphology. Mol. Biol. Evol. 2001, 18:676-680.
23. Lorite M.J., Donate-Correa J., del Arco-Aguilar M., Pérez-Galdona R., Sanjuán J., León-Barrios M. Lotus endemic the Canary Islands are nodulated by diverse and novel rhizobial species and symbiotypes. Syst. Appl. Microbiol. 2010, 33:282-290.
24. Lu Y.L., Chen W.F., Wang E.T., Han L.L., Zhang X., Chen W.X., Han S.Z. Mesorhizobium shangrilense sp. nov., isolated from root nodules of Caragana spp. grown in Yunnan Province of China. Int. J. Syst. Evol. Microbiol. 2009, 59:3012-3018.
25. Mandel M., Mamur J. Use of ultraviolet absorbance temperature profile for determining the guanine plus cytosine content of DNA. Methods Enzymol. 1968, 12:195-206.
26. Martens M., Delaere M., Coopman R., De Vos P., Gillis M., Willems A. Multilocus sequence analysis of Ensifer and related taxa. Int. J. Syst. Evol. Microbiol. 2007, 57:489-503.
27. Martin D., Rybicki E. RDP: detection of recombination amongst aligned sequences. Bioinformatics 2000, 16:562-563.
28. Martens M., Dawyndt P., Coopman R., Gillis M., De Vos P., Willems A. Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium). Int. J. Syst. Evol. Microbiol. 2008, 58:200-214.
29. Maynard-Smith J., Smith N.H., O'Rourke M., Spratt B.G. How clonal are bacteria?. Proc. Natl. Acad. Sci. U.S.A. 1993, 90:4384-4388.
30. Merabet C., Martens M., Mahdhi M., Zakhia F., Sy A., LeRoux C., Domergue O., Coopman R., Bekki A., Mars M., Willems A., de Lajudie P. Multilocus sequence analysis of root nodule isolates from Lotus arabicus (Senegal), L. creticus, Argyrolobium uniflorum and Medicago sativa (Tunisia) and description of Ensifer numidicus sp. nov. and Ensifer garamanticus sp. nov. Int. J. Syst. Evol. Microbiol. 2010, 60:664-674.
31. Moreno, J.C. coord. (2008) Lista Roja 2008 de la flora vascular española. Dirección General de Medio Natural y Política Forestal (Ministerio de Medio Ambiente y Medio Rural y Marino, y Sociedad Española de Biología de la Conservación de Plantas), Madrid, 86 pp.
32. Nandasena K., O'Hara G., Tiwari R., Willems A., Howieson J. Mesorhizobium australicum sp. nov. and Mesorhizobium opportunistum sp. nov. from Biserrula pelecinus L. in Australia. Int. J. Syst. Evol. Microbiol. 2009, 59:2140-2147.
33. Nylander J.A. MrModeltest v2. 3 Program Distributed by the Author 2004, Evolutionary Biology Centre, Uppsala University.
34. Posada D., Buckley T.R. Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests. Syst. Biol. 2004, 53:793-808.
35. Posada D., Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
36. Posada D., Crandall K. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc. Natl. Acad. Sci. U.S.A. 2001, 98:13757-13762.
37. Rambaut, A., Drummond, A.J. (2007) Tracer v1.4. Available from . http://beast.bio.ed.ac.uk/Tracer.
38. Reyes-Betancort A., Santos-Guerra A., Guma I., Hamphries C.J., Carine M.C. Diversity, rarity and evolution and conservation of the Canary Island endemic Flora. Anales del Jardín Botánico de Madrid 2008, 65:25-45.
39. Rivas R., Martensa M., de Lajudie P., Willems A. Multilocus sequence analysis of the genus Bradyrhizobium. Syst. Appl. Microbiol. 2009, 32:101-110.
40. Rogel M., Ormeño-Orrillo E., Martinez-Romero E. Symbiovars in rhizobia reflect bacterial adaptation to legumes. Syst. Appl. Microbiol. 2011, 34:96-104.
41. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
42. Salminen M.O., Carr J.K., Burke D.S., McCutcham F.E. Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning. AIDS Res. Hum. Retroviruses 1995, 11:1423-1425.
43. Sawyer S. Statistical tests for detecting gene conversion. Mol. Biol. Evol. 1998, 6:526-538.
44. Stackebrandt E., Frederiksen W., Garrity G.M., Grimont P.A.D., Kämpfer P., Maiden M.C.J., Nesme X., Rosselló-Mora R., Swings J., Trüper H.G., Vauterin L., Ward A.C., Whitman W.B. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Microbiol. 2002, 52:1043-1047.
45. Stepkowski T., Czaplinska M., Miedzinska K., Moulin L. The variable part of the dnak gene as an alternative marker for phylogenetic studies of rhizobia and related alpha proteobacteria. Syst. Appl. Microbiol. 2003, 26:483-494.
46. *and Other Methods). Version 4 2002, Sinauer Associates, Sunderland, MA.
47. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance and maximum parsimony. Methods Mol. Biol. Evol. 2011, 28:2731-2739.
48. Thompson J., Higgins D., Gibson T. CLUSTALW: improving sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22:4673-4680.
49. Turner S.L., Young J.P.W. The glutamine synthetases of rhizobia: phylogenetics and evolutionary implications. Mol. Biol. Evol. 2000, 17:309-319.
50. van Berkum P., Terefework Z., Paulin L., Suomalainen S., Lindstrom K., Eardly B. Discordant phylogenies within the rrs loci of rhizobia. J. Bacteriol. 2003, 185:2988-2998.
51. Vidal C., Chantreuil C., Berge O., Mauré L., Escarré J., Bena G., Brunel B., Cleyet-Marel J.C. Mesorhizobium metallidurans sp. nov., a metal resistant symbiont of Anthyllis vulneraria growing on metallicolous soil in Languedoc, France. Int. J. Syst. Evol. Microbiol. 2009, 59:850-855.
52. Vincent J.M. A manual for the practical study of root-nodule bacteria. Int. Biological programme Handbook 1970, Blackwell Scientific Publications, Oxford, pp. 73-97.
53. Vinuesa P., León-Barrios M., Silva C., Willems A., Jarabo-Lorenzo A., Pérez-Galdona R., Werner D., Martínez-Romero E. Bradyrhizobium canariense sp. nov., an acid-tolerant endosymbiont that nodulates endemic genistoid legumes (Papilionoideae: Genisteae) from the Canary Islands, along with Bradyrhizobium japonicum bv. genistearum, Bradyrhizobium genospecies alpha and Bradyrhizobium genospecies beta. Int. J. Syst. Evol. Microbiol. 2005, 55:569-575.
54. Vinuesa P., Silva C., Lorite M., Izaguirre-Mayoral M., Bedmar E., Martinez-Romero E. Molecular systematics of rhizobia based on maximum likelihood and Bayesian phylogenies inferred from rrs, atpD, recA and nifH sequences, and their use in the classification of Sesbania microsymbionts from Venezuelan wetlands. Syst. Appl. Microbiol. 2005, 28:702-716.
55. Wang F.Q., Wang E.T., Liu J., Chen Q., Sui X.H., Chen W.F., Chen W.X. Mesorhizobium albiziae sp. nov., a novel bacterium that nodulates Albizia kalkora in a subtropical region of China. Int. J. Syst. Evol. Microbiol. 2007, 55:1192-1199.
56. Wayne L.G., Brenner D.J., Colwell R.R., Grimont P.A., Kandler O., Krichevsky M.I., Moore L.H., Moore W.E., Murray R.G., Stackebrandt E., Starr M.P., Trüper H.G. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 1987, 37:463-464.
57. Willems A., Doignon-Bourcier F., Goris J., Coopman R., De Lajudie P., Gillis M. DNA-DNA hybridization study of Bradyrhizobium strains. Int. J. Syst. Evol. Microbiol. 2001, 51:1315-1322.
58. Zhou P.F., Chen W.M., Wei G.H. Mesorhizobium robiniae sp. nov., a novel species isolated from root nodule of Robinia pseudoacacia in China. Int. J. Syst. Evol. Microbiol. 2009, 60:2552-2556.