Rhizobium tumorigenes sp. nov., a novel plant tumorigenic bacterium isolated from cane gall tumors on thornless blackberry

Abstract

Four plant tumorigenic strains 932, 1019, 1078T and 1081 isolated from cane gall tumors on thornless blackberry (Rubus sp.) were characterized. They shared low sequence identity with related Rhizobium spp. based on comparisons of 16S rRNA gene (≤98%) and housekeeping genes atpD, recA and rpoB (<90%). Phylogenetic analysis indicated that the strains studied represent a novel species within the genus Rhizobium, with Rhizobium tubonense CCBAU 85046T as their closest relative. Furthermore, obtained average nucleotide identity (ANI) and in silico DNA–DNA hybridization (DDH) values calculated for whole-genome sequences of strain 1078T and related Rhizobium spp. confirmed the authenticity of the novel species. The ANI-Blast (ANIb), ANI-MUMmer (ANIm) and in silico DDH values between strain 1078T and most closely related R. tubonense CCBAU 85046T were 76.17%, 84.11% and 21.3%, respectively. The novel species can be distinguished from R. tubonense based on phenotypic and chemotaxonomic properties. Here, we demonstrated that four strains studied represent a novel species of the genus Rhizobium, for which the name Rhizobium tumorigenes sp. nov. is proposed (type strain 1078T = DSM 104880T = CFBP 8567T). R. tumorigenes is a new plant tumorigenic species carrying the tumor-inducing (Ti) plasmid.

Complete genomic sequence and phylogenomics analysis of Agrobacterium strain AB2/73: a new Rhizobium species with a unique mega-Ti plasmid

“…Its genome shares only 83.3% ANI and 25% dDDH with the two fully sequenced R. rhizogenes strains, K84 [24] and LBA9402 [25]. Neither does AB2/73 belong to the recently described species Rhizobium tumorigenes [6] with which it shares only 79.3% ANI and 20.9% % dDDH. The genome shows more similarity to that of Rhizobium tropici strain CIAT899 (89.8% ANI, dDDH 38.6%), that of Rhizobium sp.…”

“…These very different bacteria may nevertheless contain virtually identical Ti plasmids. More recently, four new tumorigenic strains isolated from blackberry galls were found to belong to the genus Rhizobium, but differ from R. rhizogenes and were given the species name Rhizobium tumorigenes [6].…”

Agrobacterium pusense, a new plant tumour‐inducing pathogen isolated from Lawson cypress

“…NCHU2750, a potential nitrogen-fixing mutualist, leads to its pathogenicity on several plants in different families (Haryono et al, 2018). Rhizobium tumorigenes, a newly reported tumour-inducing species of Rhizobium, has also been identified as the causal agent of cane galls on thornless blackberry (Kuzmanović et al, 2018 (Bega, 1964). Crown gall disease has been reported from different plant families including economically important fruit-producing species and grape, ornamental and landscape plants (Jeon et al, 2008).…”

“…Some species of Agrobacterium, Allorhizobium and Rhizobium in the family Rhizobiaceae cause crown and stem gall in a broad range of the dicotyledonous plant species (Abdallah et al, 2020;Kuzmanović et al, 2018;Wu et al, 2019). These plant pathogens are competent soil inhabitants, can adhere to soil particles and may survive for years in the absence of susceptible hosts (Krimi et al, 2002).…”

History and current taxonomic status of genus Agrobacterium

“…later validated in IJSEM [33]. The old species A. rhizogenes was maintained as Rhizobium rhizogenes in the genus Rhizobium, which currently also contains the new species Rhizobium tumorigenes able to induce plant tumours [27]. Mousavi et al [31] did not considered the species Agrobacterium fabrum isolated from tumours of various plants [29] because it was not officially proposed, although the complete genome of its type strain C58 was the first obtained for a member of the genus Agrobacterium and it was sequenced twice independently due to the importance of this strain for plant genetic engineering [16,54].…”