A metagenomic and metabolomic approach in unraveling the reactivity of modeled multi-species freshwater biofilms exposed to emerging pollutants

Abstract

Freshwater biofilms are vital components in aquatic environments known for their multiple ecological and environmental functions. Unfortunately, freshwater environments are increasingly influenced by emerging pollutants that are not fully assessed of their ecotoxicological effects. Freshwater biofilms are also exposed to those emerging pollutants, and their reactivity to such compounds is still not fully elucidated. The thesis first studied the level of pollutants in freshwater biofilms sampled from streams in Hong Kong, which was necessary to understand the ecological significance of freshwater biofilms and their roles in response to emerging pollutants. Biofilm samples were found to have a higher accumulation of specific compounds than their corresponding bulk water. Meanwhile, the study also revealed different microbial profiles and structural morphologies based on the extent of pollution exposures and absorption. However, the dynamics of freshwater are impacted by extrinsic factors. Hence the necessity of employing a standardized and controlled biofilm model to study the changes attributed to the exposure of selected emerging pollutants. Two separate studies were further investigated by surveying specific chemical and physical emerging pollutants with a modelled multispecies biofilms. Erythromycin was selected as a chemical pollutant model as it is a widely used antibiotic in the agriculture industry. In this study, a distinct phenotypic change was observed in biofilms exposed to erythromycin, as characterized by the specific presence of elongated cells, which was justified by increased levels of cell wall biogenesis. Nevertheless, the study identified Verrucomicrobia, Bacteroidetes, and Betaproteobacteri as potential biomarkers to be determined following erythromycin exposure, as revealed by their gene abundance shifts and corresponding metabolism pathways. An untargeted metabolomics study demonstrated that lipid metabolism was critical upon exposure. Silver nanoparticles (AgNP) were selected as model physical emerging pollutant due to their wide applications and increasing prevalence in freshwater environments. Similar to findings under erythromycin exposure, no considerable diversity differences were observed when freshwater biofilms are exposed to AgNPs. However, Armatimonadota, Bacteroidota, Planctomycetota and Verruccomicrobiota showed significant gene abundance shifts, which implied their roles in response to AgNP exposure. Untargeted metabolomics revealed that Glycerophospholipids metabolism was the key pathway. Those studies have presented a unique picture of freshwater multispecies’ reactivity upon emerging pollutants exposure and also shed light on water treatment studies.