Identification of two novel pathovars of Pantoea stewartii subsp. indologenes affecting Allium sp. and millets

Pantoea stewartii subsp. indologenes is a causative agent of leafspot of foxtail millet and pearl millet; however, novel strains were recently identified that are pathogenic on onion. We phenotypically and genotypically characterized seventeen Pantoea stewartii subsp. indologenes strains from onion and other sources (pearl millet, foxtail millet, guar pulse, verbena and corn). Based on the host range evaluation, we propose two pathovars P. stewartii subsp. indologenes pv. cepacicola pv. nov. and P. stewartii subsp. indologenes pv. setariae pv. nov. Pantoea stewartii subsp. indologenes pv. cepacicola pv. nov. causes symptoms on Allium species (leek, onion, chive and Japanese bunching onion) and also on foxtail millet, pearl millet and oat. However, P. stewartii subsp. indologenes pv. setariae pv. nov can only infect the members of Poaceae (foxtail millet, pearl millet and oat). Our study also showed that P. stewartii subsp. indologenes pathovars and P. stewartii subsp. stewartii share high genotypic relatedness and cannot be differentiated by dDDH and ANI values. Although, the newly proposed pathovars are not clearly distinguishable by their fatty acid and methyl esterase profiles, and substrate utilization patterns, a fatty acid (unknown with retention time: 10.9525) and few metabolites (3 methyl glucose, Na butyrate and fusidic acid) can be potentially used to distinguish them. We also report the distribution of previously known pathogenicity (HiVir, hrcC) and virulence (alt) factors of Pantoea sp. in the new pathovars. The impact of these new pathovars in the center rot pathosystem of onion is yet to be determined.