PS 12-104 - Ecological and evolutionary changes in freshwater bacterioplankton after severe stress induced by a glyphosate-based herbicide

Background/Question/Methods

Glyphosate-based herbicides (GBH) are the most used herbicides worldwide, raising concerns about their impact on biodiversity. Freshwater resources close to application areas are often contaminated by traces of glyphosate which may affect microbial communities at the base of aquatic food webs. Here, we tested the effect of a GBH on the composition of bacterioplankton communities over time and on the genetic diversity within populations. We hypothesized that community composition would change due to selection for glyphosate-resistant species and that within-species diversity would be purged due to selective sweeps. To test these hypotheses, we treated 1000L freshwater mesocosms with the GBH Roundup at different concentrations in two nutrient backgrounds. Over 57 days, GBH pulses of 0.3 and 15 mg/L were applied twice, followed by one pulse of 40 mg/L. Water samples were filtered at 11 timepoints for DNA extraction and shotgun metagenomic sequencing. Abundances of genomes were calculated based on metagenomic reads recruitment. Treatment effect on community composition was estimated through principal response curves (PRCs). To assess intra-specific genetic diversity we selected 31 genomes with low or high responsiveness to GBH pulses and inferred single-nucleotide variants (SNVs) of the 14 genomes with coverage >5X at different treatments or time points.

Results/Conclusions

PRCs revealed that high doses of glyphosate (15 mg/L) resulted in long-lasting changes in bacterioplankton composition at the species level, favoring a few glyphosate-resistant genomes, mainly from the phylum Proteobacteria. When genomes were grouped by their phylogenetic affiliation (phylum/class), we observed a recovery 20-30 days after the 15 mg/L glyphosate pulse, showing that community resilience occurred only at higher phylogenetic scales. Only two low-responsive species had sufficient metagenomic read coverage to allow SNV inference after the GBH pulses: a genome identified to family level as Verrucomicrobiaceae had low intraspecific diversity kept after the three GBH pulses and a Streptomycetaceae genome had high intraspecific diversity throughout the experiment. Similarly, among the 12 high-responsive species, most maintained SNV diversity after GBH pulses, except for a genome of Alphaproteobacteria, in which some alleles were fixed after the 40 mg/L glyphosate pulse in loci where there was allelic variation before, consistent with a genome-wide selective purge of diversity. Together, our results show that dramatic changes in community composition are not necessarily accompanied by evolutionary change and that standing diversity within bacterial species can be maintained or purged in the face of stressors, it will depend on the species.