Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation

Abstract

323 words). 27 Background: In bacteria, pan-genomes are the result of the evolutionary "tug of 28 war" between selection and horizontal gene transfer (HGT). High rates of HGT 29 increase the genetic pool and the effective population size, resulting in open pan-30 genomes. In contrast, selective pressures can lead to local adaptation by purging 31 the variation introduced by HGT, resulting in closed pan-genomes and clonal 32 lineages. In this study, we explored both hypotheses elucidating the pan-genome 33 of Vibrionaceae isolates after a perturbation event in the endangered oasis of 34 Cuatro Ciénegas Basin (CCB), Mexico, and looking for signals of adaptation to the 35 environments in their genomes.36Results: We obtained 42 genomes of Vibrionaceae distributed in six lineages, two 37 of them did not showed any close reference strain in databases. Five of the 38 lineages showed closed pan-genomes and were associated to either water or 39 sediment environment; their high effective population size (Ne) estimates suggest 40 that these lineages are not from a recent origin. The only clade with an open pan-41 genome was found in both environments and was formed by ten genetic groups 42 with low Ne, suggesting a recent origin. The recombination and mutation estimators 43 (r/m) ranged from 0.0052 to 2.7249, which are similar to oceanic Vibrionaceae 44 estimations; however, we identified 367 gene families with signals of positive 45 selection, most of them found in the core genome; suggesting that despite 46 recombination, natural selection moves the Vibrionaceae CCB lineages to local 47 adaptation purging the genomes and keeping closed pan-genome patterns. 48 Moreover, we identify 598 SNPs associated with an unstructured environment; 49 some of the genes under this SNPs were related to sodium transport. 50 Conclusions: Different lines of evidence suggest that the sampled Vibrionaceae, 51 are part of the rare biosphere usually living under famine conditions. Two of these 52 lineages were reported by the first time. Most Vibrionaceae lineages of CCB are 53 adapted to their microhabitats rather than to the sampled environments. This 54 pattern of adaptation agrees with the association of closed pan-genomes and local 55 adaptation. 56 57 3Comparative genomics analyses have shown a wide range of genomic 78 variation within bacteria from different phylogenetic groups [1][2][3]. This variation 79 range has been explained in part by the wide ecological niche occupied by different 80 bacterial groups [4][5][6][7][8]. Bacterial genomes, in contrast to eukaryotic genomes, 81 usually maintain constant genome sizes [9, 10], suggesting that while horizontal 82 gene transfer (HGT) increases the genome size by adding new genes, selection 83 maintains the genome size by removing deleterious, non-functional or non-useful 84 genes [11][12][13]. Therefore, bacteria can present very different genomic 85 compositions even within a species, with HGT creating a flexible genome and 86 natural selection purging or maintaining it [10, 14]. 87...

Fast eco-evolutionary changes in bacterial genomes after anthropogenic perturbation

“…This in turn could explain the increase in the size of the gene pool in 2015 due to the incorporation of exogenous DNA. However, r/m decreased significantly, suggesting that although recombination increased, it occurred between a less diverse gene pool, which coincides with the loss of diversity observed and that closer bacterial lineages tend to recombine more frequently [94, 95]. Phosphorylation is a key mechanism involved in signal transduction as a response to environmental stimuli such as nitrogen deprivation, phosphorous availability, osmolarity and chemotaxis molecules [71].…”