Phenotypic tests in Rhizobium species description: An opinion and (a sympatric speciation) hypothesis

Systematic and Applied Microbiology

Volumn 36, Issue 3, 2013, Pages 145-147

  Ormeño Orrillo, Ernesto ^a   Martínez Romero, Esperanza ^a  

^a INSTITUTO DE CIENCIAS FÍSICAS   (Mexico)

Author keywords

Catabolism; Legume nodule bacteria; Rhizobium speciation; Rhizosphere

Indexed keywords

ARTICLE; BACTERIAL GENOME; CATABOLISM; GENE FUNCTION; GENOME ANALYSIS; NONHUMAN; PHENOTYPE; PLASMID; PRIORITY JOURNAL; RHIZOBIUM; TAXONOMY;

BACTERIAL TYPING TECHNIQUES; BIOLOGICAL EVOLUTION; PHENOTYPE; PLANT ROOT NODULATION; RHIZOBIUM;

RHIZOBIUM;

EID: 84876324945     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2012.11.009     Document Type: Article

References (56)

1. Aserse A.A., Räsänen L.A., Assefa F., Hailemariam A., Lindström K. Phylogeny and genetic diversity of native rhizobia nodulating common bean (Phaseolus vulgaris L.) in Ethiopia. Syst. Appl. Microbiol. 2012, 35:120-131.
2. Baldani J.I., Weaver R.W., Hynes M.F., Eardly B.D. Utilization of carbon substrates, electrophoretic enzyme patterns, and symbiotic performance of plasmid-cured clover rhizobia. Appl. Environ. Microbiol. 1992, 58:2308-2314.
3. Blount Z.D., Barrick J.E., Davidson C.J., Lenski R.E. Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 2012, 489:513-518.
4. Blount Z.D., Borland C.Z., Lenski R.E. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:7899-7906.
5. Boivin C., Barran L.R., Malpica C.A., Rosenberg C. Genetic analysis of a region of the Rhizobium meliloti pSym plasmid specifying catabolism of trigonelline, a secondary metabolite present in legumes. J. Bacteriol. 1991, 173:2809-2817.
6. Boivin C., Camut S., Malpica C.A., Truchet G., Rosenberg C. Rhizobium meliloti genes encoding catabolism of trigonelline are induced under symbiotic conditions. Plant Cell 1990, 2:1157-1170.
7. Borthakur D., Soedarjo M. Isolation and characterization of a DNA fragment containing genes for mimosine degradation from Rhizobium sp. strain TAL1145. Highlights of Nitrogen Fixation Research 1999, 91-95. Kluwer/Plenum, New York. E. Martinez, G. Hernández (Eds.).
8. Cabrera-Valladares N., Martínez A., Piñero S., Lagunas V.H., Tinoco R., De Anda R., Vazquez-Duhalt R., Bolívar F., Gosset G. Expression of the melA gene from Rhizobium etli CFN42 in Escherichia coli and characterization of the encoded tyrosinase. Enzyme Microb. Technol. 2006, 38:772-779.
9. Cesco S., Neumann G., Tomasi N., Pinton R., Weisskopf L. Release of plant-borne flavonoids into the rhizosphere and their role in plant nutrition. Plant Soil 2010, 329:1-25.
10. Chen W.X., Yan G.H., Li J.L. Numerical taxonomic study of fast-growing soybean rhizobia and a proposal that Rhizobium fredii be assigned to Sinorhizobium gen. nov. Int. J. Syst. Bacteriol. 1988, 38:392-397.
11. Ding H., Yip C.B., Geddes B.A., Oresnik I.J., Hynes M.F. Glycerol utilization by Rhizobium leguminosarum requires an ABC transporter and affects competition for nodulation. Microbiology 2012, 158:1369-1378.
12. Ferrer J.L., Austin M.B., Stewart C., Noel J.P. Structure and function of enzymes involved in the biosynthesis of phenylpropanoids. Plant Physiol. Biochem. 2008, 46:356-370.
13. Frassinetti S., Setti L., Corti A., Farrinelli P., Montevecchi P., Vallini G. Biodegradation of dibenzothiophene by a nodulating isolate of Rhizobium meliloti. Can. J. Microbiol. 1998, 44:289-297.
14. Glick B.R. Teamwork in phytoremediation. Nat. Biotechnol. 2004, 22:526-527.
15. Goldmann A., Boivin C., Fleury V., Message B., Lecoeur L., Maille M., Tepfer D. Betaine use by rhizosphere bacteria: genes essential for trigonelline, stachydrine, and carnitine catabolism in Rhizobium meliloti are located on pSym in the symbiotic region. Mol. Plant Microbe Interact. 1991, 4:571-578.
16. González-Paredes Y., Alarcón A., Ferrera-Cerrato R., Almaraz J.J., Martínez-Romero E., Cruz-Sánchez J.S., Mendoza-López M.R., Ormeño-Orrillo E. Tolerance growth and degradation of phenanthrene and benzo[a]pyrene by Rhizobium tropici CIAT 899 in liquid culture medium. Appl. Soil Ecol. 2013, 63:105-111.
17. Guntli D., Heeb M., Moenne-Loccoz Y., Defago G. Contribution of calystegine catabolic plasmid to competitive colonization of the rhizosphere of calystegine-producing plants by Sinorhizobium meliloti Rm41. Mol. Ecol. 1999, 8:855-863.
18. Gutiérrez-Zamora M.L., Martínez-Romero E. Natural endophytic association between Rhizobium etli and maize (Zea mays L.). J. Biotechnol. 2001, 91:117-126.
19. Harrison P.W., Lower R.P.J., Kim N.K.D., Young J.P.W. Introducing the bacterial chromid: not a chromosome, not a plasmid. Trends Microbiol. 2010, 18:141-148.
20. Hosie A.H., Allaway D., Galloway C.S., Dunsby H.A., Poole P.S. Rhizobium leguminosarum has a second general amino acid permease with unusually broad substrate specificity and high similarity to branched-chain amino acid transporters (Bra/LIV) of the ABC family. J. Bacteriol. 2002, 184:4071-4080.
21. Hynes M.F., Brucksch K., Priefer U. Melanin production encoded by a cryptic plasmid in a Rhizobium leguminosarum strain. Arch. Microbiol. 1988, 150:326-332.
22. Juhasz A.L., Britz M.L., Stanley G.A. Degradation of fluoranthene, pyrene, benz[a]anthracene and dibenz[a,h]anthracene by Burkholderia cepacia. J. Appl. Microbiol. 1997, 83:189-198.
23. Keum Y.S., Seo J.S., Hu Y., Li Q.J. Degradation pathways of phenanthrene by Sinorhizobium sp. C4. Appl. Microbiol. Biotechnol. 2006, 71:935-941.
24. Knee E.M., Gong F.C., Gao M., Teplitski M., Jones A.R., Foxworthy A., Mort A.J., Bauer W.D. Root mucilage from pea and its utilization by rhizosphere bacteria as a sole carbon source. Mol. Plant Microbe Interact. 2001, 14:775-784.
25. Kontchou C.Y., Blondeau R. Biodegradation of soil humic acids by Streptomyces viridosporus. Can. J. Microbiol. 1992, 38:203-208.
26. Kuiper I., Bloemberg G.V., Noreen S., Thomas-Oates J.E., Lugtenberg B.J.J. Increased uptake of putrescine in the rhizosphere inhibits competitive root colonization by Pseudomonas fluorescens strain WCS365. Mol. Plant Microbe Interact. 2001, 14:1096-1104.
27. Leyva A., Palacios J.M., Mozo T., Ruiz-Argüeso T. Cloning and characterization of hydrogen uptake genes from Rhizobium leguminosarum. J. Bacteriol. 1987, 169:4929-4934.
28. López-Guerrero M.G., Ormeño-Orrillo E., Acosta J.L., Mendoza-Vargas A., Rogel M.A., Ramírez M.A., Rosenblueth M., Martínez-Romero J., Martínez-Romero E. Rhizobial extrachromosomal replicon variability, stability and expression in natural niches. Plasmid 2012, 68:149-158.
29. López-Guerrero, M.G., Ramírez, M.A., Martínez-Romero, E. Rhizobial genetic repertoire to inhabit legume and non-legume rhizospheres. In: De Bruijn, F.J. (Ed.), Molecular Microbial Ecology of the Rhizosphere, Wiley-Blackwell, in press.
30. Martínez-Romero E., Segovia L., Mercante F.M., Franco A.A., Graham P., Pardo M.A. Rhizobium tropici, a novel species nodulating Phaseolus vulgaris L. beans and Leucaena sp. trees. Int. J. Syst. Bacteriol. 1991, 41:417-426.
31. Mauchline T.H., Fowler J.E., East A.K., Sartor A.L., Zaheer R., Hosie A.H., Poole P.S., Finan T.M. Mapping the Sinorhizobium meliloti 1021 solute-binding protein-dependent transportome. Proc. Natl. Acad. Sci. U. S. A. 2006, 103:17933-17938.
32. Mercado-Blanco J., García F., Fernandez-Lopez M., Olivares J. Melanin production by Rhizobium meliloti GR4 is linked to nonsymbiotic plasmid pRmeGR4b: cloning, sequencing, and expression of the tyrosinase gene mepA. J. Bacteriol. 1993, 175:5403-5410.
33. Murphy P.J., Saint C.P. Rhizopines in the legume-Rhizobium symbiosis. Molecular signals in plant-microbe communication 1992, 377-390. CRC Press, Boca Raton, FL. D.P.S. Verma (Ed.).
34. Nogales J., Domínguez-Ferreras A., Amaya-Gómez C.V., van Dillewijn P., Cuéllar V., Sanjuán J., Olivares J., Soto M.J. Transcriptome profiling of a Sinorhizobium meliloti fadD mutant reveals the role of rhizobactin 1021 biosynthesis and regulation genes in the control of swarming. BMC Genomics 2010, 11:157.
35. Ormeño-Orrillo E., Menna P., Almeida L.G.P., Ollero F.J., Nicolás M.F., Pains Rodrigues E., Shigueyoshi Nakatani A., Silva Batista J.S., Oliveira Chueire L.M., Souza R.C., Ribeiro Vasconcelos A.T., Megías M., Hungria M., Martínez-Romero E. Genomic basis of broad host range and environmental adaptability of Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 which are used in inoculants for common bean (Phaseolus vulgaris L.). BMC Genomics 2012, 13:735.
36. Oresnik I.J., Pacarynuk L.A., O'Brien Sh.A.P., Yost Ch.K., Hynes M.F. Plasmid-encoded catabolic genes in Rhizobium leguminosarum bv. trifolii: evidence for a plant-inducible rhamnose locus involved in competition for nodulation. Mol. Plant Microbe Interact. 1998, 11:1175-1185.
37. Pham T.T., Tu Y., Sylvestre M. Remarkable ability of Pandoraea pnomenusa B356 biphenyl dioxygenase to metabolize simple flavonoids. Appl. Environ. Microbiol. 2012, 78:3560-3570.
38. Poonthrigpun S., Pattaragulwanit K., Paengthai S., Kriangkripipat T., Juntongjin K., Thaniyavarn S., Petsom A., Pinphanichakarn P. Novel intermediates of acenaphthylene degradation by Rhizobium sp. strain CU-A1: evidence for naphthalene-1,8-dicarboxylic acid metabolism. Appl. Environ. Microbiol. 2006, 72:6034-6039.
39. Ramachandran V.K., East A.K., Karunakaran R., Downie J.A., Poole P.S. Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics. Genome Biol. 2011, 12:R106.
40. Ramírez-Bahena M.H., García-Fraile P., Peix A., Valverde A., Rivas R., Igual J.M., Mateos P.F., Martínez-Molina E., Velázquez E. Revision of the taxonomic status of the species Rhizobium leguminosarum (Frank 1879) Frank 1889AL, Rhizobium phaseoli Dangeard 1926AL and Rhizobium trifolii Dangeard 1926AL. R. trifolii is a later synonym of R. leguminosarum. Reclassification of the strain R. leguminosarum DSM 30132 (=NCIMB 11478) as Rhizobium pisi sp. nov. Int. J. Syst. Evol. Microbiol. 2008, 58:2484-2490.
41. Ramírez-Puebla S.T., Servín L.E., Jiménez-Marín B., Bolaños L.M., Rosenblueth M., Martínez J., Rogel M.A., Ormeño-Orrillo E., Martínez-Romero E. Gut and root microbiota commonalities. Appl. Environ. Microbiol. 2013, 79:2-9.
42. Rao J.R., Cooper J.E. Rhizobia catabolize nod gene-inducing flavonoids via C-ring fission mechanisms. J. Bacteriol. 1994, 176:5409-5413.
43. Ribeiro R.A., Rogel M.A., López-López A., Ormeño-Orrillo E., Barcellos F.G., Martínez J., Thompson F.L., Martínez-Romero E., Hungria M. Reclassification of Rhizobium tropici type A strains as Rhizobium leucaenae sp. nov. Int. J. Syst. Evol. Microbiol. 2012, 62:1179-1184.
44. Robleto E.A., Kmiecik K., Oplinger E.S., Nienhuis J., Triplett E.W. Trifolitoxin production increases nodulation competitiveness of Rhizobium etli CE3 under agricultural conditions. Appl. Environ. Microbiol. 1998, 64:2630-2633.
45. Rosenblueth M., Hynes M.F., Martínez-Romero E. Rhizobium tropici teu genes involved in specific uptake of Phaseolus vulgaris bean-exudate compounds. Mol. Gen. Genet. 1998, 258:587-598.
46. Shaw L.J., Morris P., Hooker J.E. Perception and modification of plant flavonoid signals by rhizosphere microorganisms. Environ. Microbiol. 2006, 8:1867-1880.
47. Soedarjo M., Hemscheidt T.K., Borthakur D. Mimosine, a toxin present in leguminous trees (Leucaena spp.), induces a mimosine-degrading enzyme activity in some Rhizobium strains. Appl. Environ. Microbiol. 1994, 60:4268-4272.
48. Suominen L., Jussila M.M., Mäkeläinen K., Romantschuk M., Lindström K. Evaluation of the Galega-Rhizobium galegae system for the bioremediation of oil-contaminated soil. Environ. Pollut. 2000, 107:239-244.
49. Tepfer D., Goldmann A., Pamboukdjian N., Maille M., Lepingle A., Chevalier D., Dénarié J., Rosenberg C. A plasmid of Rhizobium meliloti 41 encodes catabolism of two compounds from root exudate of Calystegium sepium. J. Bacteriol. 1988, 170:1153-1161.
50. Treves D.S., Manning S., Adams J. Repeated evolution of an acetate-crossfeeding polymorphism in long-term populations of Escherichia coli. Mol. Biol. Evol. 1998, 15:789-797.
51. van Dillewijn P., Soto M.J., Villadas P.J., Toro N. Construction and environmental release of a Sinorhizobium meliloti strain genetically modified to be more competitive for alfalfa nodulation. Appl. Environ. Microbiol. 2001, 67:3860-3865.
52. van Dillewijn P., Villadas P.J., Toro N. Effect of a Sinorhizobium meliloti strain with a modified putA gene on the rhizosphere microbial community of alfalfa. Appl. Environ. Microbiol. 2002, 68:4201-4208.
53. Van Egeraat A.W.S.M. The possible role of homoserine in the development of Rhizobium leguminosarum in the rhizosphere of pea seedlings. Plant Soil 1975, 42:381-386.
54. Vílchez S., Molina L., Ramos C., Ramos J.L. Proline catabolism by Pseudomonas putida: cloning, characterization, and expression of the put genes in the presence of root exudates. J. Bacteriol. 2000, 182:91-99.
55. Yost C.K., Rath A.M., Noel T.C., Hynes M.F. Characterization of genes involved in erythritol catabolism in Rhizobium leguminosarum bv. viciae. Microbiology 2006, 152:2061-2074.
56. Zhang X.S., Cheng H.P. Identification of Sinorhizobium meliloti early symbiotic genes by use of a positive functional screen. Appl. Environ. Microbiol. 2006, 72:2738-2748.