Article

A common genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria.

The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.
PLoS ONE (Impact Factor: 3.53). 02/2008; 3(7):e2567. DOI: 10.1371/journal.pone.0002567
Source: PubMed Central

ABSTRACT This work centres on the genomic comparisons of two closely-related nitrogen-fixing symbiotic bacteria, Rhizobium leguminosarum biovar viciae 3841 and Rhizobium etli CFN42. These strains maintain a stable genomic core that is also common to other rhizobia species plus a very variable and significant accessory component. The chromosomes are highly syntenic, whereas plasmids are related by fewer syntenic blocks and have mosaic structures. The pairs of plasmids p42f-pRL12, p42e-pRL11 and p42b-pRL9 as well large parts of p42c with pRL10 are shown to be similar, whereas the symbiotic plasmids (p42d and pRL10) are structurally unrelated and seem to follow distinct evolutionary paths. Even though purifying selection is acting on the whole genome, the accessory component is evolving more rapidly. This component is constituted largely for proteins for transport of diverse metabolites and elements of external origin. The present analysis allows us to conclude that a heterogeneous and quickly diversifying group of plasmids co-exists in a common genomic framework.

0 Bookmarks
 · 
178 Views
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Symbiosis genes (nod and nif) involved in nodulation and nitrogen fixation in legumes are plasmid-borne in Rhizobium. Rhizobial symbiotic variants (symbiovars) with distinct host specificity would depend on the type of symbiosis plasmid. In Rhizobium etli or in Rhizobium phaseoli, symbiovar phaseoli strains have the capacity to form nodules in Phaseolus vulgaris while symbiovar mimosae confers a broad host range including different mimosa trees.
    BMC Genomics 07/2014; 15(1):575. DOI:10.1186/1471-2164-15-575 · 4.04 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Genomics has provided data for defining bacterial-species limits from estimates of gene conservation, synteny, average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH). Phylogenomic analyses that allowed a more accurate definition of rhizobial relationships showed two major superclades within the family Rhizobiaceae that corresponded to the Rhizobium/Agrobacterium and Shinella/Ensifer groups. Within the Rhizobium/Agrobacterium group, four highly-supported clades were evident that could correspond to distinct genera. The Shinella/Ensifer group encompassed not only the genera Shinella and Ensifer but also a separate clade containing the type strain of R. giardinii. Ensifer adhaerens (Casida AT) was an outlier within its group, separated from the rest of the Ensifer (formerly Sinorhizobium) strains. The phylogenomic analysis presented provided support for the revival of Allorhizobium as a bona fide genus within the Rhizobiaceae, the distinctiveness of Agrobacterium and the recently proposed Neorhizobium genus, and suggested that R. giardinii may be transferred to a novel genus. ANI reference values are becoming the gold standard in rhizobial taxonomy and are being used to recognize novel rhizobial lineages and species that seem to be biologically coherent, as shown in this study.
    Systematic and Applied Microbiology 12/2014; DOI:10.1016/j.syapm.2014.12.002 · 3.31 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Legumes form a large group of plants that constitute the third largest family of angiosperms, including near 20,000 species and 750 genera. Most of them have the ability to establish symbioses with diazotrophic bacteria, collectively known as rhizobia, which induce root nodules where biological nitrogen fixation takes place, conferring legumes a relevant ecological advantage. This group of bacteria that for many years was thought to be formed by a scarce number of genera and species within alpha proteobacteria, shows nowadays an important genetic diversity including species phylogenetically divergent both in core and symbiotic genes sequences. Together with rhizobia, other endophytic bacteria are present in legume nodules coexisting with rhizobial strains and their ecological role remains unknown in most cases, but they likely have an effect in plant health, plant growth or even in the rhizobia-legume symbiosis. In this review we present an overview of the associations of bacteria with legumes, the current available knowledge on the phylogenetic diversity of both rhizobia and endophytic bacteria inhabiting root nodules, and the symbiotic features used to define symbiovars in rhizobia.
    Critical Reviews in Plant Sciences 06/2015; 34. DOI:10.1080/07352689.2014.897899 · 5.29 Impact Factor

Full-text (4 Sources)

Download
92 Downloads
Available from
Jun 3, 2014