Assessment of the genetic and phenotypic diversity among rhizogenicAgrobacteriumbiovar 1 strains infecting solanaceous and cucurbit crops

Abstract

Rhizogenic Agrobacterium biovar 1 strains have been found to cause extensive root proliferation on hydroponically grown Cucurbitaceae and Solanaceae crops, resulting in substantial economic losses. As these agrobacteria live under similar ecological conditions, infecting a limited number of crops, it may be hypothesized that genetic and phenotypic variation among such strains is relatively low. In this study we assessed the phenotypic diversity as well as the phylogenetic and evolutionary relationships of several rhizogenic Agrobacterium biovar 1 strains from cucurbit and solanaceous crops. A collection of 41 isolates was subjected to a number of phenotypic assays and characterized by MLSA targeting four housekeeping genes (16S rRNA gene, recA, rpoB and trpE) and two loci from the root-inducing Ri-plasmid (part of rolB and virD2). Besides phenotypic variation, remarkable genotypic diversity was observed, especially for some chromosomal loci such as trpE. In contrast, genetic diversity was lower for the plasmid-borne loci, indicating that the studied chromosomal housekeeping genes and Ri-plasmid-borne loci might not exhibit the same evolutionary history. Furthermore, phylogenetic and network analyses and several recombination tests suggested that recombination could be contributing in some extent to the evolutionary dynamics of rhizogenic Agrobacterium populations. Finally, a genomospecies-level identification analysis revealed that at least four genomospecies may occur on cucurbit and tomato crops (G1, G3, G8 and G9). Together, this study gives a first glimpse at the genetic and phenotypic diversity within this economically important plant pathogenic bacterium.

Potential for Biocontrol of Hairy Root Disease by a Paenibacillus Clade

“…After 24 h of incubation, the diameter of the inhibition visible zones surrounding spotted colonies was recorded using a digital caliper (Tyc et al, 2014; Bosmans et al, 2016b). Experiments were performed for one rhizogenic Agrobacterium biovar 1 strain (ST15.13/097, isolated from tomato; Bosmans et al, 2015), and were independently repeated twice (no replicates within the same experiment).…”

“…Antagonistic effects were observed as a clear zone of inhibition where growth of the tested bacterium was inhibited (+). −, no inhibition zone observed .b AD, NIOO culture collection, Wageningen, The Netherlands; LMG, Laboratory of Microbiology, Ghent University, Ghent, Belgium; MAFF, NIAS Genebank (National Institute of Agrobiological Sciences), Ibaraki, Japan; NCPPB, National Collection of Plant Pathogenic Bacteria, York, UK; EMI, EPU, EHE, and ST, PME&BIM culture collection, Sint-Katelijne Waver, Belgium .c Agrobacterium biovar 1 strains isolated from Cucurbitaceae (melon, cucumber) and Solanaceae (tomato crops; for more information, see Bosmans et al, 2015) are indicated by green and red circles, respectively .…”

“…c Agrobacterium biovar 1 strains isolated from Cucurbitaceae (melon, cucumber) and Solanaceae (tomato crops; for more information, see Bosmans et al, 2015) are indicated by green and red circles, respectively .…”

“…For all strains with antagonistic activity the 16S ribosomal RNA (rRNA) genes were partially amplified and sequenced as described by Bosmans et al (2015). Obtained sequences were individually trimmed for quality, using a minimum Phred score of 20, and, in cases of ambiguous base calls, manually edited based on the obtained electropherograms.…”

“…Once plants are infected, HRD cannot be controlled by curative means. Instead, preventative actions should be taken, such as preventing, and/or removing Agrobacterium containing biofilms that are often associated with the disease in the greenhouse irrigation system (Danhorn and Fuqua, 2007; Bosmans et al, 2015). However, to effectively prevent the disease generally high concentrations of chemical disinfectants are required, including levels that may be phytotoxic (Bosmans et al, 2016c).…”