Integrative taxonomy and population genomics of Aeromonas media and related species

The species Aeromonas media contains bacteria mainly found in aquatic habitats that can be opportunistic pathogens in human and animals. The diversity of strains currently affiliated to the species A. media was explored herein. Forty strains were included in a population study integrating phenotypics, multilocus genetics, genomics, phylogenetics, as well as lifestyle and evolutionary features. Sixteen gene-based multilocus phylogeny delineated three clades. Data from 14 whole genome sequences showed that clades or lineages corresponded to different groups defined by both average nucleotide identity and in silico DNA-DNA hybridization, i.e. to different genomospecies. DL-lactate utilization, cefoxitin susceptibility, nucleotide signatures, ribosomal multi operon diversity and differences in evolution mode distinguished the two main genomospecies, which are proposed as two species: emended Aeromonas media and Aeromonas alphaquinta sp. nov. (type strain LMG 13459T = ATCC 51107T = CIP 74.32T). The third clade was proposed as Aeromonas sp. genomospecies paramedia (reference strain 1086C = CECT 8838 = LMG 28708) awaiting a larger number of strains for species description. Five gene-based multilocus phylogeny suggested that A. alphaquinta sp. nov. is related to the non-validated species ‘Aeromonas rivipollensis’. Integrative data analysis gave a more comprehensive knowledge of the A. media complex of species among aeromonads. Our results mainly suggested different modes of lineage emergence and a speciation process, which could have been influenced by the response to osmotic stress.