Phylogenomic analysis of Pseudomonas nitroreducens strains FY43 and FY47

Proper identification of strain is essential in understanding the ecology of a bacteria species. The classification of Pseudomonas nitroreducens is still being questioned and revised until now. The novel P. nitroreducens strains FY43 and FY47 used in this study have been reported to show a high level of tolerance to glyphosate. In this study, next-generation sequencing (NGS) and whole genome analysis were used to clarify the delineation of the species. Whole genome analysis showed that P. nitroreducens strains FY43 and FY47 shared high homology to five reference genomes of P. nitroreducens: strain B, Aramco J, NBRC 12694, DF05, and TX01. Phylogenomic and phylogenetic analysis (average nucleotide identity based on BLAST (ANIb), genome-to-genome distance (GGDC) analysis) showed that both P. nitroreducens strains FY43 and FY47 are Pseudomonas nitroreducens members. However, strains DF05 and TX01 were not correctly assigned at the species level for all the analyses. The P. nitroreducens strain DF05 and TX01 should be further investigated for their classification as the correct species classification is the prerequisite for future diversity studies.