Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia.

Abstract

The current classification of the rhizobia (root-nodule symbionts) assigns them to six genera. It is strongly influenced by the small subunit (16S, SSU) rRNA molecular phylogeny, but such single-gene phylogenies may not reflect the evolution of the genome as a whole. To test this, parts of the atpD and recA genes have been sequenced for 25 type strains within the α-Proteobacteria, representing species in Rhizobium, Sinorhizobium, Mesorhizobium, Bradyrhizobium, Azorhizobium, Agrobacterium, Phyllobacterium, Mycoplana and Brevundimonas. The current genera Sinorhizobium and Mesorhizobium are well supported by these genes, each forming a distinct phylogenetic clade with unequivocal bootstrap support. There is good support for a Rhizobium clade that includes Agrobacterium tumefaciens, and the very close relationship between Agrobacterium rhizogenes and Rhizobium tropici is confirmed. There is evidence for recombination within the genera Mesorhizobium and Sinorhizobium, but the congruence of the phylogenies at higher levels indicates that the genera are genetically isolated. rRNA provides a reliable distinction between genera, but genetic relationships within a genus may be disturbed by recombination. Rhizobium, Sinorhizobium, Mesorhizobium, recA, atpD Keywords : INTRODUCTIONThe rhizobia are root-nodulating bacteria responsible for a significant part of the global fixation of nitrogen. The ability of rhizobia to nodulate plants and reduce N # is conferred by genes that are plasmid-borne in many species (Pueppke, 1996), and the lateral transfer The atpD and recA sequences and details of the SimPlot analyses are available as supplementary material in IJSEM Online (http :// ijs.sgmjournals.org/ ).Abbreviations : HKY85, Hasegawa-Kishino-Yano model ; K2P, Kimura's two-parameter model ; SSU, small subunit rRNA.The EMBL accession numbers for the sequences reported in this study are AJ294386-AJ294409 (atpD) and AJ294363-AJ294385 (recA). of these genes is the most likely explanation for their occurrence within several distinct clades of subgroup 2 of the α-Proteobacteria (Dobert et al., 1994 ; Kaijalainen & Lindstro$ m, 1989 ;Lindstro$ m et al., 1995 ;Young, 1998 ;Young & Johnston, 1989). The phylogeny of the nodulation genes is quite different from that of the small subunit rRNA (SSU or 16S rRNA) genes in these bacteria. As in other bacterial groups, the SSU phylogeny has had a major influence on our current perception of evolutionary relationships among rhizobia ( Willems & Collins, 1993 ;Young, 1996 ;Young et al., 1991). More than 20 species have been described, and they are classified into the genera Rhizobium, Sinorhizobium, Allorhizobium, Mesorhizobium, Bradyrhizobium and Azorhizobium as well as ' Methylobacterium nodulans ' (de Lajudie et al., 1994' (de Lajudie et al., , 1998b Dreyfus et al., 1988 ; Jarvis et al., 1997 ; Jordan, 1982 ;Sy et al., 2001 M. W. Gaunt and others ing much slower growth on laboratory media (Dreyfus et al., 1988 ; Fred et al., 1932 ; Jordan, 1982). They are also fairly distant in the SSU p...

Bifidobacterium lactisDSM 10140: Identification of theatp(atpBEFHAGDC) Operon and Analysis of Its Genetic Structure, Characteristics, and Phylogeny

“…The genes of the atp operon, especially the atpD gene, have all of the prerequisites to be suitable phylogenetic markers, such as very high genetic stability and a wide distribution (22,23). This operon has already been used to infer phylogeny in the genera Salmonella (6) and Rhizobium (13). This alternative molecular marker might corroborate and help complete the evolutionary history of various LAB species.…”

Multilocus sequence analysis of root nodule isolates from Lotus arabicus (Senegal), Lotus creticus, Argyrolobium uniflorum and Medicago sativa (Tunisia) and description of Ensifer numidicus sp. nov. and Ensifer garamanticus sp. nov.

“…Previously, six of them had been partially characterized by ARDRA, SDS-PAGE and 16S rRNA gene sequencing (Zakhia et al, 2004). Genes for MLSA were chosen according to previous taxonomic and phylogenetic studies: recA (recombinase A) and atpD (ATP synthase beta subunit) were used in a phylogenetic study of the genera Agrobacterium and Rhizobium (Gaunt et al, 2001); glnA (glutamine synthase) was used by Turner & Young (2000) and gltA (citrate synthase) was used by Hernandez-Lucas et al (2004). In a study evaluating the taxonomic potential of ten housekeeping genes, Martens et al (2007Martens et al ( , 2008 found these genes and additionally thrC (threonine synthase) useful for identification and for the inference of phylogenetic relationships of species of the genus Ensifer.…”

Rhizobium populi sp. nov., an endophytic bacterium isolated from Populus euphratica

“…Isoprenoid quinones were isolated using the methods of Minnikin et al (1984) and separated by HPLC (Kroppenstedt, 1982). The DNA G+C content of strain K-38 T was 63.5 mol%, well within the range reported for other species of the genus Rhizobium (57-66 mol%; Young et al, 2001). The predominant isoprenoid quinone of strain K-38 T was Q-10, in line with all members of the family Rhizobiaceae (Bibi et al, 2012;Ramana et al, 2013;Turdahon et al, 2013).…”

“…To further clarify the taxonomic status of strain K-38 T , two housekeeping genes, ATP synthase b (atpD) and DNA recombinase A (recA), were amplified with the corresponding protocols and primer pairs, atpD273F and atpD771R, recA6F and recA555R, respectively (Gaunt et al, 2001). Phylogenetic trees based on atpD and recA genes were reconstructed using the MEGA 4.0 software.…”