ABSTRACT
This study reports the multilocus sequence analysis (MLSA) of nine house-keeping gene fragments (atpD, dnaK, glnA, glnB, gltA, gyrB, recA, rpoB and thrC) on a collection of 38 Bradyrhizobium isolated from Aeschynomene species in Senegal, which had previously been characterised by several phenotypic and genotypic techniques, allowing a comparative analysis of MLSA resolution power for species delineation in this genus. The nifH locus was also studied to compare house-keeping and symbiotic gene phylogenies and obtain insights into the unusual symbiotic properties of these Aeschynomene symbionts. Phylogenetic analyses (maximum likelihood, Bayesian) of concatenated nine loci produced a well-resolved phylogeny of the strain collection separating photosynthetic bradyrhizobial strains (PB) from non-photosynthetic bradyrhizobial (NPB) ones. The PB clade was interpreted as the remains an expanding ancient species that presently shows high diversification, giving rise to potential new species. B. denitrificans LMG8443 and BTAi1 strains formed a sub-clade that was identified as recently emerging new species. Congruence analyses (by Shimodaira-Hasegawa (S-H) tests) identified three gene-fragments (dnaK, glnB and recA) that should be preferred for MLSA analyses in Bradyrhizobium genus. The nine loci or nifH phylogenies were not correlated with the unusual symbiotic properties of PB (nod-dependent/nod-independent). Advantages and drawbacks of MLSA for species delineation in Bradyrhizobium are discussed.
Subject(s)
Bacterial Proteins/genetics , Bradyrhizobium/classification , Bradyrhizobium/genetics , Fabaceae/microbiology , Phylogeny , Sequence Analysis, DNA/methods , Bacterial Typing Techniques , Bradyrhizobium/isolation & purification , DNA, Bacterial/analysis , Nitrogen Fixation/genetics , Oxidoreductases/genetics , Photosynthesis , Senegal , Species SpecificityABSTRACT
AIMS: Genista saharae, indigenous of Sahara, is a spontaneous shrub that plays an important ecological role for the preservation and fertility of poor and eroded soils. This legume has not been examined for its root nodule bacteria. The taxonomic diversity of bacteria from root nodules of G. saharae growing in the infra-arid region of Tunisia was investigated. METHODS AND RESULTS: A total of 28 bacterial strains isolated from root nodules of G. saharae grown in Tunisian soil were characterized using a polyphasic approach including phenotypic characteristics, PCR-RFLP of 16S rDNA and 16S rRNA gene sequencing. It was found that new isolates are diverse and affiliated to Ensifer (75%), Rhizobium (10%) and Phyllobacterium (15%). The Phyllobacterium isolates lacked the capacity for nodule formation on this plant. CONCLUSIONS: Genista saharae formed nodules with diverse rhizobia in Tunisian soils. Furthermore, our results support the presence of non-nodulating commensal strains (Phyllobacterium) in legumes nodule. SIGNIFICANCE AND IMPACT OF THE STUDY: This study is the first report on the characterization of G. saharae microsymbionts in Tunisia.
