Opportunistic bacteria of grapevine crown galls are equipped with the genomic repertoire for opine utilization.

Young grapevines (Vitis vinifera) suffer and eventually can die from the crown gall (CG) disease caused by the plant pathogen Allorhizobium vitis (Rhizobiaceae). Virulent members of A. vitis harbour a tumor-inducing (Ti) plasmid and induce formation of crown galls (CGs) due to the oncogenes encoded on the transfer-DNA (T-DNA). Expression of oncogenes in transformed host cells induce unregulated cell proliferation, metabolic and physiological changes. The CG produces opines uncommon to plants, which provide an important nutrient source for A. vitis harbouring opine catabolism enzymes. CGs host a distinct bacterial community and the mechanisms establishing a CG-specific bacterial community are currently unknown. Thus, we were interested in whether genes homologous to those of the Ti-plasmid coexist in the genomes of the microbial species coexisting in CGs. We isolated eight bacterial strains from grapevine CGs, sequenced their genomes and tested their virulence and opine utilization ability in bioassays. In addition, the eight genome sequences were compared to 34 published bacterial genomes, including closely related plant associated bacteria not from CGs. Homologous genes for virulence and opine anabolism were only present in the virulent Rhizobiaceae. By contrast, homologs of the opine catabolism genes were present in all strains including the non-virulent members of the Rhizobiaceae and non-Rhizobiaceae. Gene neighbourhood and sequence identity of the opine degradation cluster of virulent and non-virulent strains together with the results of the opine utilization assay support the important role of opine utilization for co-colonization in CGs, thereby shaping the CG community.