Phyllobacterium meliloti sp. nov. a novel non-symbiotic bacterium isolated from root nodules of Melilotus albus (white sweet clover) grown in Canada

Abstract

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 T1293T as representative of a novel species and present the first complete closed genome sequence of a bacterial strain (T1018) representing the species P. pellucidum. Phylogenetic analysis of genome sequences as well as analysis of 53 core genes placed novel strain T1293T in a highly supported cluster of strains distinct from named Phyllobacterium species with P. myrsinacearum and P. calauticae as closest relatives. The highest average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of genome sequences of T1293T 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 T1293T has a size of 5074034 bp with a DNA G+C content of 55 mol% and possesses three plasmids with sizes of 397619 bp, 476847 bp and 519835 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. Further analysis revealed that T1293T, like other Phyllobacterium species, possesses key genes encoding an enzyme complex implicated in the degradation of glyphosate, a widely used broad-spectrum herbicide that has negative consequences for many microorganisms including the human gut microbiome. A novel prophage (size [~] 41.5 kb) was also detected in the genome of T1293T. Data for multiple phenotypic tests complemented the sequence-based characterization of strain T1293T. The data presented support the description of a new species and the name Phyllobacterium meliloti sp. nov. is proposed with T1293T = LMG32641T = HAMBI 3765T as the species type strain.