RT Journal Article SR Electronic T1 Ecological and phenotypic differentiation in sympatric populations of aquatic Stenotrophomonas uncovered by evolutionary species delimitation JF bioRxiv FD Cold Spring Harbor Laboratory SP 138990 DO 10.1101/138990 A1 Luz Edith Ochoa-Sánchez A1 Pablo Vinuesa YR 2017 UL http://biorxiv.org/content/early/2017/05/17/138990.abstract AB The genus Stenotrophomonas (Gammaproteobacteria) has a broad environmental distribution. S. maltophilia is its best known species because it is a globally emerging multidrug-resistant (MDR) opportunistic nosocomial pathogen. Members of this species are known to display high genetic, ecological and phenotypic diversity, forming the so-called S. maltophilia complex (Smc). Heterogeneous resistance and virulence phenotypes have been reported for environmental Smc isolates of diverse ecological origin. We hypothesized that failure to properly delimit species borders within the Smc has precluded the identification of significant species-phenotype associations, particularly for environmental isolates. Here we used state-of-the-art phylogenetic and population genetics methods to challenge this hypothesis based on the multilocus dataset available for the genus at pubmlst.org. It was extended with sequences from complete and draft genome sequences to assemble a comprehensive set of reference sequences comprising representatives of all validly described Stenotrophomonas species. This framework was used to analyze 108 environmental isolates obtained in this study from the sediment and water column of four rivers and streams in Central Mexico, affected by contrasting levels of anthropogenic pollution, with the aim of identifying genetically cohesive lineages in this collection. We used the multispecies coalescent, coupled with Bayes factor analysis, together with population genetic structure analyses, recombination and gene flow estimates between sequence clusters, to delimit species borders, revealing that the Smc contains at least 5 significantly differentiated lineages. Only the lineage defined as S. maltophilia ¿ was found to be intrinsically MDR, all its members expressing metallo-β-lactamases, whereas the other four were not MDR. We also obtained isolates of S. acidaminiphila, S. humi and S. terrae that were significantly more susceptible to antibiotics than Smsl. We demonstrate that the sympatric lineages recovered display significantly differentiated habitat preferences, antibiotic resistance profiles and beta-lactamase expression phenotypes, as shown by diverse multivariate analyses and robust univariate statistical tests. We discuss our data in light of current models of bacterial speciation, which fit these data well, stressing the implications of species delimitation in ecological, evolutionary and clinical research.