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Resistance, resilience, and functional redundancy of freshwater microbial communities facing multiple agricultural stressors in a mesocosm experiment

Freshwater biodiversity is threatened by fertilizers and pesticides from agricultural sources. Microbial communities can be resistant (i.e., community composition stays largely the same) or resilient (i.e., composition changes but then returns to its initial state) to these contaminants. Even after changes in composition, communities may continue to support ecosystem processes due to functional redundancy, in which different taxa carry out the same process, such that the process is maintained even after some taxa are lost. To test the extent of resistance, resilience, and functional redundancy in aquatic bacterial communities (bacterioplankton) faced with agricultural stressors, we exposed freshwater mesocosms to two commonly used pesticides: the herbicide Roundup (glyphosate) and the neonicotinoid insecticide imidacloprid, alone or in combination, and in high or low nutrient backgrounds. Over the 42-day experiment, we tracked bacterial density with flow cytometry, functional composition with Biolog EcoPlates, and taxonomic diversity with culture-independent 16S rRNA gene amplicon sequencing. We show that only glyphosate, but not imidacloprid or nutrients, measurably changed community structure. Despite this change, metabolic capabilities were maintained, suggesting functional redundancy. We further show that communities are resilient at broad, but not fine phylogenetic levels: the precise amplicon sequence variants (ASVs) driven below the limit of detection by glyphosate stress do not return, but tend to be replaced by relatives within the same genus. Together, our results show that bacterioplankton are broadly resistant, resilient, and redundant faced with severe agricultural stressors on weekly time scales, but that high doses of glyphosate can have longer-lasting effects on fine-scale diversity.