Clavibacter vidaverae sp. nov., Clavibacter rahimiani sp. nov. and Clavibacter davisi sp. nov.: corynebacterial plant pathogens isolated from small-grain cereals.

Abstract

During 2020-2024, 25 Gram-positive actinobacterial strains were isolated from small-grain cereals in Iran. Colony morphology, phenotypic characteristics and multilocus sequence analyses showed that the strains belonged to the coryneform genus Clavibacter (family Microbacteriaceae). The Clavibacter strains isolated from small-grain cereals in Iran were distributed within five distinct phylogenetic clades. Two of those clades included Clavibacter tessellarius and Clavibacter zhangzhiyongii, while the other three groups of Clavibacter strains were taxonomically undetermined and phylogenetically distinct from all validly described species in the genus. Whole-genome sequence-based indices, i.e. average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH), showed that the latter three phylogenetic clades differed from all validly described Clavibacter species, with ANI/dDDH values <94% and <70%, respectively. Analyses of KEGG pathways and pathogenicity-associated genes revealed substantial differences among the five Clavibacter groups associated with small-grain cereals. All Clavibacter strains were capable of infecting their hosts of isolation, i.e. wheat, barley and oat. Thus, based on both phenotypic features, i.e. differences in colony morphology, biolog microbial identification microplate data and polar lipid repertoires, as well as DNA similarity indices, the three clades could represent three new species within Clavibacter. In this study, we provide formal species descriptions for three Clavibacter clades isolated from small-grain cereals. These three species include Clavibacter vidaverae sp. nov. (type strain Sh2088ᵀ=CFBP 9070ᵀ=ICMP 24732ᵀ), Clavibacter rahimiani sp. nov. (type strain Sh2141ᵀ=CFBP 9069ᵀ=ICMP 24735ᵀ) and Clavibacter davisi sp. nov. (type strain Sh2036ᵀ=CFBP 9071ᵀ=ICMP 24729ᵀ).