Characterization of Phyllobacterium spp. isolated from root nodules of Melilotus albus (white sweet clover) grown in Canada and description of Phyllobacterium meliloti sp. nov.

Two novel bacterial strains isolated from root nodules of white sweet clover (Melilotus albus) plants grown at a Canadian site were previously characterized and placed in the genus Phyllobacterium. Here, we present phylogenomic and phenotypic data to support the description of strain T1293^T as representative of a novel species and present the first complete closed genome sequence of a bacterial strain (T1018) representing the species 'Phyllobacterium pellucidum'. Phylogenetic analysis of genome sequences, as well as analysis of 53 core genes, placed novel strain T1293^T in a highly supported cluster of strains distinct from named Phyllobacterium species with Phyllobacterium myrsinacearum and Phyllobacterium calauticae as closest relatives. The highest average nucleotide identity and digital DNA-DNA hybridization values of genome sequences of T1293^T compared to closest species type strains (84.1 and 26.5%, respectively) are well below the threshold values for bacterial species circumscription. The genome of strain T1293^T has a size of 5,074,034 bp with a DNA G+C content of 55.1 mol% and possesses three plasmids with sizes of 397,619 bp, 476,847 bp and 519,835 bp. Detected in the genome were type III and type VI secretion system genes, implicated in plant-microbe and microbe-microbe interactions, but key nodulation, nitrogen-fixation and photosystem genes were not detected. A novel prophage (size ~41.5 kb) was also detected in the genome of T1293^T. Tests using defined culture media revealed that novel strains T1293^T and T1018 were highly resistant to, and able to metabolize glyphosate, a widely used herbicide that has negative consequences for the environment and human health. Data for multiple morphological, physiological, biochemical and plant tests complemented the sequence-based data. The data presented support the description of a new species, and the name Phyllobacterium meliloti sp. nov. is proposed with T1293^T=LMG 32641^T=HAMBI 3765^T as the species type strain.