Rapid and Efficient Identification of Agrobacterium Species by recA Allele Analysis

Abstract

The analysis of housekeeping recA gene sequences from 138 strains from 13 species or genomic species of Agrobacterium, nine being biovar 1 genomospecies, and the others Agrobacterium larrymoorei, Agrobacterium rubi, Agrobacterium sp. NCPPB 1650, and Agrobacterium vitis and one "former" Agrobacterium species, Rhizobium rhizogenes, led to the identification of 50 different recA alleles and to a clear delineation of the 14 species or genomospecies entirely consistent with that obtained by amplified fragment length polymorphism (AFLP) analysis. The relevance of a recA sequencing approach for epidemiological analyses was next assessed on agrobacterial Tunisian isolates. All Tunisian isolates were found to belong to the Agrobacterium tumefaciens/biovar 1 species complex by both biochemical tests and rrs sequencing. recA sequence analysis further permitted their unambiguous assignment to A. tumefaciens genomospecies G4, G6, G7, and G8 in total agreement with the results of an AFLP-based analysis. At subspecific level, several Tunisian recA alleles were novel, indicating the power and accuracy of recA-based typing for studies of Agrobacterium spp.

Phylogenetic Analysis and Polyphasic Characterization of Clavibacter michiganensis Strains Isolated from Tomato Seeds Reveal that Nonpathogenic Strains Are Distinct from C. michiganensis subsp. michiganensis

“…The advantage of MLSA is that phylogenetic relationships of large sets of strains can be analyzed with better portability than any previous genotyping technique such as DNA/DNA hybridization, amplified fragment length polymorphism (AFLP), or repetitive sequence-based PCR (rep-PCR). It has also proven valuable for assessing phylogenetic relationships within complex species such as Stenotrophomonas maltophilia (36), Agrobacterium tumefaciens species complex (4,12), and Ralstonia solanacearum (11). The MLSA scheme we designed is based on six housekeeping genes routinely used for phylogenetic studies of Gram-positive bacteria belonging to Microbacterium, Aureobacterium (63), Lactobacillus (59), and Gram-negative bacteria (20,58,80,82).…”

Analysis of Hydroxycinnamic Acid Degradation in Agrobacterium fabrum Reveals a Coenzyme A-Dependent, Beta-Oxidative Deacetylation Pathway

“…We recently showed that Agrobacterium fabrum, a species of the Agrobacterium tumefaciens species complex (20)(21)(22), has several species-specific regions in the genome, including the SpG8-1b region containing 15 different genes named atu1409 to atu1423. This region confers on A. fabrum the ability to degrade FA, since a mutant with the region deleted was no longer able to degrade the compound (23).…”

Reconciliation of Sequence Data and Updated Annotation of the Genome of Agrobacterium tumefaciens C58, and Distribution of a Linear Chromosome in the Genus Agrobacterium

“…S1 in the supplemental material). It is important to note in considering this analysis that strong evidence supports the reclassification of biovar II strains as Rhizobium (6,10,(16)(17)(18)(19). Our survey data indicate that linear chromosomes are unique to biovar I strains (see Table S5 in the supplemental material) (14,20).…”

“…have traditionally been subdivided into three different groups, called biovars, based on differences in physiology and host range. Biovar I can be further subdivided into genomovars, with C58 belonging to genomovar 8 (6)(7)(8)(9)(10).…”