title: 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.).
abstract: BACKGROUND
  Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 are α-Proteobacteria that establish nitrogen-fixing symbioses with a range of legume hosts. These strains are broadly used in commercial inoculants for application to common bean (Phaseolus vulgaris) in South America and Africa. Both strains display intrinsic resistance to several abiotic stressful conditions such as low soil pH and high temperatures, which are common in tropical environments, and to several antimicrobials, including pesticides. The genetic determinants of these interesting characteristics remain largely unknown.
  
  
  RESULTS
  Genome sequencing revealed that CIAT 899 and PRF 81 share a highly-conserved symbiotic plasmid (pSym) that is present also in Rhizobium leucaenae CFN 299, a rhizobium displaying a similar host range. This pSym seems to have arisen by a co-integration event between two replicons. Remarkably, three distinct nodA genes were found in the pSym, a characteristic that may contribute to the broad host range of these rhizobia. Genes for biosynthesis and modulation of plant-hormone levels were also identified in the pSym. Analysis of genes involved in stress response showed that CIAT 899 and PRF 81 are well equipped to cope with low pH, high temperatures and also with oxidative and osmotic stresses. Interestingly, the genomes of CIAT 899 and PRF 81 had large numbers of genes encoding drug-efflux systems, which may explain their high resistance to antimicrobials. Genome analysis also revealed a wide array of traits that may allow these strains to be successful rhizosphere colonizers, including surface polysaccharides, uptake transporters and catabolic enzymes for nutrients, diverse iron-acquisition systems, cell wall-degrading enzymes, type I and IV pili, and novel T1SS and T5SS secreted adhesins.
  
  
  CONCLUSIONS
  Availability of the complete genome sequences of CIAT 899 and PRF 81 may be exploited in further efforts to understand the interaction of tropical rhizobia with common bean and other legume hosts.
authors.affiliation: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico. eormeno.orrillo@gmail.com
authors.forename: Ernesto
authors.initials: E
authors.lastname: Ormeño-Orrillo
authors.forename: Pâmela
authors.initials: P
authors.lastname: Menna
authors.forename: Luiz Gonzaga P
authors.initials: LG
authors.lastname: Almeida
authors.forename: Francisco Javier
authors.initials: FJ
authors.lastname: Ollero
authors.forename: Marisa Fabiana
authors.initials: MF
authors.lastname: Nicolás
authors.forename: Elisete
authors.initials: E
authors.lastname: Pains Rodrigues
authors.forename: Andre
authors.initials: A
authors.lastname: Shigueyoshi Nakatani
authors.forename: Jesiane Stefânia
authors.initials: JS
authors.lastname: Silva Batista
authors.forename: Ligia Maria
authors.initials: LM
authors.lastname: Oliveira Chueire
authors.forename: Rangel Celso
authors.initials: RC
authors.lastname: Souza
authors.forename: Ana Tereza
authors.initials: AT
authors.lastname: Ribeiro Vasconcelos
authors.forename: Manuel
authors.initials: M
authors.lastname: Megías
authors.forename: Mariangela
authors.initials: M
authors.lastname: Hungria
authors.forename: Esperanza
authors.initials: E
authors.lastname: Martínez-Romero
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D059827:Agricultural Inoculants / Q000166:cytology / Q000235:genetics* / Q000378:metabolism / Q000502:physiology; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001692:Biological Transport / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D024881:Drug Resistance, Bacterial / Q000235:genetics; D004777:Environment; D018745:Genome, Plant / Q000235:genetics; D023281:Genomics; D006863:Hydrogen-Ion Concentration; D006864:Hydrogenase / Q000235:genetics; D007501:Iron / Q000378:metabolism; D008670:Metals / Q000494:pharmacology; D005810:Multigene Family / Q000235:genetics; D009586:Nitrogen Fixation / Q000235:genetics; D015538:Nitrosation / Q000235:genetics; D009997:Osmotic Pressure; D018384:Oxidative Stress / Q000235:genetics; D027805:Phaseolus / Q000382:microbiology* / Q000502:physiology; D010802:Phylogeny; D010937:Plant Growth Regulators / Q000096:biosynthesis; D055170:Plant Root Nodulation / Q000235:genetics; D010957:Plasmids / Q000235:genetics; D011134:Polysaccharides / Q000235:genetics; D042162:Rhizobium tropici / Q000166:cytology / Q000235:genetics* / Q000378:metabolism / Q000502:physiology*; D013045:Species Specificity; D013312:Stress, Physiological / Q000235:genetics; D013559:Symbiosis / Q000235:genetics; D013696:Temperature
chemical_list: D000900:Anti-Bacterial Agents; D008670:Metals; D010937:Plant Growth Regulators; D011134:Polysaccharides; D007501:Iron; D006864:Hydrogenase