Characterization of a novel clade of Xanthomonas isolated from rice leaves in Mali and proposal of Xanthomonas maliensis sp. nov.

Abstract

Four bacterial strains, designated M89, M92, M97(T), and M106, were isolated in a previous study from surface-sterilized leaves of rice (Oryza sativa) or murainagrass (Ischaemum rugosum) at three sites in Mali, Africa. Here they were examined by a polyphasic taxonomic approach and analysis of a whole-genome sequence. Phylogenetic analyses based on 16S rRNA sequence and multilocus sequence analysis of seven genes showed that these four strains formed a distinct lineage representing a novel species within the genus Xanthomonas. This was supported by whole-genome average nucleotide identity values calculated from comparisons of strain M97(T) with established Xanthomonas species. The strains can be differentiated from the known Xanthomonas species on the basis of their fatty acid and carbohydrate utilization profiles. Population growth studies on rice confirmed that these bacteria multiply in rice leaves without causing symptoms. Identification of this novel species can be accomplished by using diagnostic primer sets or by gyrB gene sequence analysis. We propose to classify these rice- and grass-associated bacteria as Xanthomonas maliensis sp. nov. with strain M97(T) = CFBP7942(T) = LMG27592(T) as the type strain.

Comparative genomics of a cannabis pathogen reveals insight into the evolution of pathogenicity in Xanthomonas

“…Interestingly, there are xanthomonads that possess hrpG and hrpX but not the Hrp Type III secretion system nor any type III effectors, such as the cannabis pathogen, the new X. maliensis clade (Triplett et al, 2015), and a recently sequenced strain of X. arboricola (Ignatov et al, 2015). This could be taken as evidence that the Hrp system was either (1) acquired later or (2) got lost in some lineages.…”

Using Ecology, Physiology, and Genomics to Understand Host Specificity in Xanthomonas

“…Heterogeneous populations of yellow-pigmented nonpathogenic strains from different plants and identified as Xanthomonas by various serological, protein profile, or sequence-based methods could not be assigned to existing pathovars, including those grouping strains from the same host species (42,95,131,133). These strains do not cluster with the pathogenic strains of the host from which they were isolated.…”

“…Interestingly, it was noticed that most of these strains belong to the Xanthomonas arboricola species (95). Some represent new separate lineages in known species (42,47) and others form new clades such as the Xanthomonas maliensis species proposed to group the nonpathogenic strains isolated from disinfected rice leaves (131). These observations indicate that pathogenic and nonpathogenic Xanthomonas may evolve in sympatry, as they do with the other members of the natural microbiota.…”

“…Indeed, strains identified as Xanthomonas were isolated from symptomless plant tissues of rice, apple, and weeds sampled in bean fields and failed to induce symptoms on the host of isolation or any other plants (3,36,89). More recently, many nonpathogenic look-alikes of Xanthomonas pathogens have been reported from symptomatic or asymptomatic host tissues such as walnut buds, citrus or rice leaves, and bean seeds (21,42,52,105,131). These various reports demonstrate that both the diversity of Xanthomonas and the diversity of hosts of Xanthomonas have been underestimated.…”

“…Nonpathogenic strains of Xanthomonas devoid of T3SSs and T3Es (or featuring a very restricted number of T3E genes) were isolated from several ecosystems (42,70,131). An emerging picture of the acquisition of pathogenicity in strains of Xanthomonas involves as a first step the acquisition of master regulators, such as HrpG and HrpX, and key CWDEs (70).…”