Unveiling pesticide effects and antibiotic resistance in freshwater microorganisms through genomics.

Abstract

A large proportion of the rivers worldwide are impacted by human activities and pollution. Freshwater microorganisms, including bacteria, algae, and fungi are crucial for nutrient cycling and primary production. Chemical pollution can alter aquatic microorganisms at both cellular and community-levels, sometimes leading to acclimation or adaptation responses. Antibiotic resistance is the mechanism by which bacteria increase their tolerance towards antibiotic exposure. The rapid increase of antibiotic resistance in pathogenic bacteria during the last decades has become a major global health problem. River sediments, can act as reservoirs of ARGs that persist and spread in the environment. The four papers in this thesis investigate how freshwater microorganisms respond and acclimate to pesticides at both cellular and community levels and explore the presence and characteristics of ARGs in a high-flow Scandinavian river. Altogether, this thesis combines single-organism and community approaches in laboratory and field settings, integrating metagenomics, transcriptomic, phenotypic, and chemical profiling tools. Paper I showed that the green alga Raphidocelis subcapitata acclimated within four weeks to toxic but environmental levels of the herbicide diflufenican. This acclimation was accompanied by fitness trade-offs. Acclimated cells were smaller and overexpressed stress-related genes, such as genes related to DNA repair and replication, and cellular division. Paper II demonstrated that aquatic biofilms exposed to environmental levels of the fungicide tebuconazole exhibited a reduction in fungal biomass, while algae and bacteria were unaffected. As a response to tebuconazole, the fungal community composition shifted. Moreover, biofilms also partly degraded tebuconazole, releasing unknown transformation products, suggesting a potential acclimation or adaptation mechanism. In paper III, a field ecotoxicological assessment was performed using periphyton. A reduction in algal species richness was observed, accompanied by changes in community composition in periphyton of agricultural streams, compared to non-agricultural streams. Agricultural streams had a higher pesticide mixture toxic pressure, and green algae (Chlorophyta), decreased in relative abundance in the agricultural streams, while opportunistic cyanobacteria (Cyanobacteriota) increased, likely replacing them. Paper IV characterized the sediment resistome of the Göta Älv river and examined the potential influence of WWTP effluents as sources of antimicrobials and ARGs. ARGs were found to accumulate downstream, with distinct resistome composition and taxonomic diversity compared to the upstream sites. Overall, this thesis investigates how human activities influence freshwater microorganisms using high-throughput molecular methods. The studies reveal molecular mechanisms, cellular responses, community shifts, and ecologically or clinically relevant genes in freshwater microbial communities resulting from pesticide exposure as well as agricultural and urban activities.