Abstract
Carriage of resistance genes can underpin bacterial survival, and by spreading these genes between species, mobile genetic elements (MGEs) can potentially protect diversity within microbial communities. The spread of MGEs could be affected by environmental factors such as selection for resistance, and biological factors such as plasmid host range, with consequences for individual species and for community structure. Here we cultured a focal bacterial strain, Pseudomonas fluorescens SBW25, embedded within a soil microbial community, with and without mercury selection, and with and without mercury resistance plasmids (pQBR57 or pQBR103), to investigate the effects of selection and resistance gene introduction on (1) the focal species; (2) the community as a whole; (3) the spread of the introduced mer resistance operon. We found that P. fluorescens SBW25 only escaped competitive exclusion by other members of community under mercury selection, even when it did not begin with a mercury resistance plasmid, due to its propensity to acquire resistance from the community by horizontal gene transfer. Mercury pollution had a significant effect on community structure, decreasing alpha diversity within communities while increasing beta diversity between communities, a pattern that was not affected by the introduction of mercury resistance plasmids by P. fluorescens SBW25. Nevertheless, the introduced merA gene spread to a phylogenetically diverse set of recipients over the 5 weeks of the experiment, as assessed by epicPCR. Our data demonstrates how the effects of MGEs can be experimentally assessed for individual lineages, the wider community, and for the spread of adaptive traits.
Highlights
Many of the traits that make bacteria economically, ecologically, or clinically important are encoded by accessory genes carried by mobile genetic elements (MGEs) (Hall et al, 2017a)
A negative effect of mercury pollution at high levels (64 μg/g) on the density of P. fluorescens SBW25 over time was detected in the plasmid-free treatment [linear mixed effects model (LMM), likelihood ratio test (LRT) plasmid:mercury:timepoint interaction, χ2 = 9.91, p = 0.007], but these populations persisted at levels ∼10% of those of plasmid bearers
By taking an experimental evolution approach to study entire microbial communities, we show how community structure responds to an environmental change, in this case mercury pollution, and, how MGEs play a critical role by transferring adaptive genes among lineages
Summary
Many of the traits that make bacteria economically, ecologically, or clinically important are encoded by accessory genes carried by mobile genetic elements (MGEs) (Hall et al, 2017a). Conjugative MGEs, i.e., those with genes that produce a channel (the conjugative pilus) through which the MGE can be copied between neighboring bacteria (Garcillán-Barcia and de la Cruz, 2013; Cury et al, 2017), are important for the spread of traits in bacterial communities. This is because of the efficiency with which conjugative MGEs can transmit large accessory gene cargos between individuals, including those of different species (Halary et al, 2010; Klümper et al, 2015). Probiotic treatments, designed to introduce new traits such as phytoprotection or detoxification of pollutants into microbial communities ( known as “bioaugmentation”), could benefit from a consideration of the mobility of the genes encoding the introduced function (Garbisu et al, 2017)
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