Multilocus sequence analysis of Ensifer and related taxa

Abstract

Multilocus sequence analysis (MLSA) was performed on representatives of Ensifer (including species previously assigned to the genus Sinorhizobium) and related taxa. Neighbour-joining (NJ), maximum-parsimony (MP) and maximum-likelihood (ML) phylogenies of dnaK, gltA, glnA, recA, thrC and 16S rRNA genes were compared. The data confirm that the potential for discrimination of Ensifer species is greater using MLSA of housekeeping genes than 16S rRNA genes. In incongruence-length difference tests, the 16S rRNA gene was found to be significantly incongruent with the other genes, indicating that this gene should not be used as a single indicator of relatedness in this group. Significant congruence was detected for dnaK, glnA and thrC. Analyses of concatenated sequences of dnaK, glnA and thrC genes yielded very similar NJ, MP and ML trees, with high bootstrap support. In addition, analysis of a concatenation of all six genes essentially produced the same result, levelling out potentially conflicting phylogenetic signals. This new evidence supports the proposal to unite Ensifer and Sinorhizobium in a single genus. Support for an alternative solution preserving the two genera is less strong. In view of the opinions expressed by the Judicial Commission, the name of the genus should be Ensifer, as proposed by Young [Young, J. M. (2003). Int J Syst Evol Microbiol 53, 2107-2110]. Data obtained previously and these new data indicate that Ensifer adhaerens and 'Sinorhizobium morelense' are not heterotypic synonyms, but represent separate species. However, transfer to the genus Ensifer is not possible at present because the species name is the subject of a pending Request for an Opinion, which would affect whether a novel species in the genus Ensifer or a new combination based on a basonym would be created.

Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates

“…The relative divergence of the reference strain WSM 419 from the population Population genomics of Sinorhizobium medicae X Bailly et al we sampled was greatest for the chromosome and least for pSMED1 and pSMED2, as estimated by the K ST statistic (Table 4). The low genetic divergence on the chromosome between S. medicae WSM 419 and the population we sampled (0.0029 substitutions per bp), compared with the genetic divergence of around 0.1 substitutions per bp described between S. medicae and S. meliloti isolates based on multilocus sequence typing data (Bailly et al, 2006;van Berkum et al, 2006;Martens et al, 2007), confirms our initial assumption that our isolates were all S. medicae. We investigated the degree to which the phylogenetic signal was consistent across the genome by means of a PCA.…”

“…meliloti and S. medicae are closely related species that form a tight phylogenetic clade together with Sinorhizobium arboris (Martens et al, 2007). The genomes of S. meliloti 1021 and S. medicae WSM 419 share similar architectures.…”

Horizontal Gene Transfer and Homologous Recombination Drive the Evolution of the Nitrogen-Fixing Symbionts of Medicago Species

“…meliloti (1,14,31,54). Moreover, phylogenies based on a sample of housekeeping genes suggest that S. meliloti and S. medicae are not sister species (28). Most of the topologies obtained indeed suggest that S. medicae might be the first emerging taxon within a clade including S. medicae and S. meliloti but also another species, Sinorhizobium arboris (28), suggesting a rather ancient speciation event leading to the first two species.…”

Characterization of Rhizobium naphthalenivorans sp. nov. with special emphasis on aromatic compound degradation and multilocus sequence analysis of housekeeping genes

“…MLSA-based phylogenetic analyses were preformed by studying sequence information on the housekeeping genes that encode ATP synthase beta subunit (atpD), heat-shock protein Hsp70 (dnaK), glutamine synthetase II (glnII), DNA gyrase subunit B (gyrB), and recombinase A protein (recA) as well as on 16S rRNA genes and the ITS region. PCR amplifi cations of atpD, dnaK, glnII, gyrB, and recA genes were performed using specifi c primer sets of atpD255F/ atpD782R, dnaK1466F/dnaK1777R, glnII12f/glnII689r, gyrB343F/gyrB1043R, and recA41F/recA649R, respectively, under optimized PCR conditions as reported (Martens et al, 2007(Martens et al, , 2008Vinuesa et al, 2005). The ITS sequences were amplifi ed with a primer set of 1492f (Lane, 1991) and LS117r (Okamura et al, 2009) as described.…”

“…These levels of similarity correspond to the threshold of grouping bacterial strains as a genetically single species (Stackebrandt and Ebers, 2006). To get a more comprehensive understanding of the taxonomic position of our isolates, therefore, we performed the MLSA of housekeeping genes and the ITS region, which has been successfully made for phylogenetic studies on Rhizobium species and related alphaproteobacteria (Martens et al, 2007;Menna et al, 2009;Okamura et al, 2009;Tan et al, 2001;Willems et al, 2001). In this study, the MLSA analysis of the atpD, dnaK, gluII, gyrB, and recA genes and the ITS region has revealed that our isolates represent a distinct lineage within the genus Rhizobium with R. selenitireducens as their phylogenetic neighbor.…”