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Abstract

Two sequenced nodulation regions of lupin Bradyrhizobium sp. WM9 carried the majority of genes involved in the Nod factor production. The nod region I harbored: nolA, nodD, nodA, nodB, nodC, nodS, nodI, nodJ, nolO, nodZ, fixR, nifA, fixA, nodM, nolK and noeL. This gene arrangement resembled that found in the nodulation region of Bradyrhizobium japonicum USDA110, however strain WM9 harbored only one nodD gene copy, while the nodM, nolK and noeL genes had no counterparts in the 410 kb symbiotic region of strain USDA110. Region II harbored nolL and nodW, but lacked an nodV gene. Both regions carried ORFs that lacked similarity to the published USDA110 sequences, though they had homologues in symbiotic regions of Rhizobium etli, Sinorhizobium sp. NGR234 and Mesorhizobium loti. These differences in gene content, as well as a low average sequence identity (70%) of symbiotic genes with respect to B. japonicum USDA110 were in contrast with the phylogenetic relationship of USDA110 and WM9 revealed by the analysis of 16S rDNA and dnaK sequences. This most likely reflected an early divergence of symbiotic loci, and possible co-speciation with distinct legumes. During this process the loss of a noel gene and the acquisition of a nolL gene could be regarded as an adaptation towards these legumes that responded to Nod factors carrying 4-O-acetylfucose rather than 2-O-methylfucose. This explained various responses of lupins and serradella plants to infection by mutants in nodZ and nolL genes, knowing that serradella is a stringent legume while lupins are more promiscuous legumes.

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.

“…The ad hoc Committee for the Re-evaluation of the Species Definition in Bacteriology (Stackebrandt et al, 2002;Gevers et al, 2005) suggested the sequence analysis of a set of protein-encoding genes as alternative phylogenetic markers, or multilocus sequence analysis (MLSA). Several recent studies have confirmed that sequences from housekeeping genes can be used for identification at the species level (Wertz et al, 2003;Zeigler, 2003), for evolutionary population genetics and in taxonomy (Stepkowski et al, 2003;Vinuesa et al, 2005a,b;Bailly et al, 2006). The analysis of a small number of carefully selected gene sequences may equal or even surpass the precision of DNA-DNA hybridization for the quantification of genome relatedness and this approach thus has the potential to replace cumbersome DNA-DNA hybridizations (Zeigler, 2003, Martens et al, 2008.…”

Mesorhizobium ciceri biovar biserrulae, a novel biovar nodulating the pasture legume Biserrula pelecinus L.

“…The Mediterranean basin is the centre of origin of this monospecific genus (Allen & Allen, 1981). B. pelecinus forms a highly specific nitrogen-fixing symbiotic association with bacteria that have been classified within the genus Mesorhizobium (Howieson et al, 1995; Nandasena et al, 2001 Nandasena et al, , 2004 The locus dnaK encodes a highly conserved chaperone protein with multiple cellular functions, and this gene has proven to be a useful diagnostic tool for root-nodule bacteria (Stepkowski et al, 2003;Eardly et al, 2005). A 300 bp intragenic fragment from the variable region of dnaK was amplified and sequenced using the primers TSdnaK2 and TSdnaK3 (Stepkowski et al, 2003 and WSM1540) differed by only 1 or 2 bp.…”

“…B. pelecinus forms a highly specific nitrogen-fixing symbiotic association with bacteria that have been classified within the genus Mesorhizobium (Howieson et al, 1995; Nandasena et al, 2001 Nandasena et al, , 2004 The locus dnaK encodes a highly conserved chaperone protein with multiple cellular functions, and this gene has proven to be a useful diagnostic tool for root-nodule bacteria (Stepkowski et al, 2003;Eardly et al, 2005). A 300 bp intragenic fragment from the variable region of dnaK was amplified and sequenced using the primers TSdnaK2 and TSdnaK3 (Stepkowski et al, 2003 and WSM1540) differed by only 1 or 2 bp. These Biserrula mesorhizobia had >99.3 % sequence similarity to M. ciceri and <91.9 % sequence similarity to M. loti and, as a consequence, all 14 Biserrula mesorhizobia given in Table 1 clustered with M. ciceri when a phylogenetic tree was developed (not shown) using the available partial dnaK sequences of type strains of root-nodule bacteria.…”

“…The locus dnaK encodes a highly conserved chaperone protein with multiple cellular functions, and this gene has proven to be a useful diagnostic tool for root-nodule bacteria (Stepkowski et al, 2003;Eardly et al, 2005). A 300 bp intragenic fragment from the variable region of dnaK was amplified and sequenced using the primers TSdnaK2 and TSdnaK3 (Stepkowski et al, 2003).…”

“…A 300 bp intragenic fragment from the variable region of dnaK was amplified and sequenced using the primers TSdnaK2 and TSdnaK3 (Stepkowski et al, 2003). Ten strains, WSM1283, WSM1448, WSM1449, WSM1493, WSM1497,…”