title: Nitrogen-fixing rhizobial strains isolated from common bean seeds: phylogeny, physiology, and genome analysis.
abstract: Rhizobial bacteria are commonly found in soil but also establish symbiotic relationships with legumes, inhabiting the root nodules, where they fix nitrogen. Endophytic rhizobia have also been reported in the roots and stems of legumes and other plants. We isolated several rhizobial strains from the nodules of noninoculated bean plants and looked for their provenance in the interiors of the seeds. Nine isolates were obtained, covering most known bean symbiont species, which belong to the Rhizobium and Sinorhizobium groups. The strains showed several large plasmids, except for a Sinorhizobium americanum isolate. Two strains, one Rhizobium phaseoli and one S. americanum strain, were thoroughly characterized. Optimal symbiotic performance was observed for both of these strains. The S. americanum strain showed biotin prototrophy when subcultured, as well as high pyruvate dehydrogenase (PDH) activity, both of which are key factors in maintaining optimal growth. The R. phaseoli strain was a biotin auxotroph, did not grow when subcultured, accumulated a large amount of poly-β-hydroxybutyrate, and exhibited low PDH activity. The physiology and genomes of these strains showed features that may have resulted from their lifestyle inside the seeds: stress sensitivity, a ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) complex, a homocitrate synthase (usually present only in free-living diazotrophs), a hydrogenase uptake cluster, and the presence of prophages. We propose that colonization by rhizobia and their presence in Phaseolus seeds may be part of a persistence mechanism that helps to retain and disperse rhizobial strains.
authors.affiliation: Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National University of Mexico, Chamilpa, Cuernavaca, Morelos, Mexico.
authors.forename: Yolanda
authors.initials: Y
authors.lastname: Mora
authors.affiliation: Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National University of Mexico, Chamilpa, Cuernavaca, Morelos, Mexico.
authors.forename: Rafael
authors.initials: R
authors.lastname: Díaz
authors.affiliation: Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National University of Mexico, Chamilpa, Cuernavaca, Morelos, Mexico.
authors.forename: Carmen
authors.initials: C
authors.lastname: Vargas-Lagunas
authors.affiliation: Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National University of Mexico, Chamilpa, Cuernavaca, Morelos, Mexico.
authors.forename: Humberto
authors.initials: H
authors.lastname: Peralta
authors.affiliation: Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National University of Mexico, Chamilpa, Cuernavaca, Morelos, Mexico.
authors.forename: Gabriela
authors.initials: G
authors.lastname: Guerrero
authors.affiliation: Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National University of Mexico, Chamilpa, Cuernavaca, Morelos, Mexico.
authors.forename: Alejandro
authors.initials: A
authors.lastname: Aguilar
authors.affiliation: Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National University of Mexico, Chamilpa, Cuernavaca, Morelos, Mexico.
authors.forename: Sergio
authors.initials: S
authors.lastname: Encarnación
authors.affiliation: Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National University of Mexico, Chamilpa, Cuernavaca, Morelos, Mexico.
authors.forename: Lourdes
authors.initials: L
authors.lastname: Girard
authors.affiliation: Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National University of Mexico, Chamilpa, Cuernavaca, Morelos, Mexico mora@ccg.unam.mx.
authors.forename: Jaime
authors.initials: J
authors.lastname: Mora
mesh_terms: D008969:Molecular Sequence Data; D009586:Nitrogen Fixation; D010088:Oxidoreductases / Q000235:genetics; D027805:Phaseolus / Q000382:microbiology*; D012231:Rhizobium / Q000145:classification* / Q000302:isolation & purification / Q000378:metabolism* / Q000502:physiology; D017422:Sequence Analysis, DNA; D020579:Sinorhizobium / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D013559:Symbiosis
chemical_list: D010088:Oxidoreductases; C029130:nitrogenase reductase