Determining freshwater biofilms' functional and community shifts caused by extrinsic factors : a meta-omics study on multispecies biofilms sampled from environmental and simulated irrigation water distribution systems

Abstract

Biofilms are ubiquitous throughout aquatic environments, known for their influence on water quality for drinking and irrigation purposes. These biofilms are thought to play an essential role in organic matter decomposition, nutrient dynamics, biogeochemical cycling, and pollutants dissemination, such as antibiotic resistance genes (ARGs). Advances in high-throughput sequencing technologies have enabled extensive investigations of environmental biofilms and yielded significant breakthroughs in biofilm meta-omics. However, very little has been done in understanding biofilms formed within Irrigation Water Distribution Systems (IWDS), which can negatively impact produce safety. With a growing population, agricultural productivity is expected to increase, which would also mean intensifying freshwater withdrawals for irrigation purposes. Hence, produce safety is a rising concern in managing irrigation water quality in distribution systems colonized by unregulated biofilms. The work described in this thesis focuses on understanding biofilms in environmental freshwater, and simulated IWDS engineered systems to gain fundamental insights on the direct impacts of anthropogenic activities towards these biofilms.

It is already established that the environment is polluted with a wide range of emerging chemical pollutants, which include antibiotics. These antibiotic can lead to the establishment of antibiotic resistant genes among microorganisms associated with biofilms. However, there is a lack of comprehensive studies describing the diversity of ARGs, their abundance, transferability, and hosts within freshwater biofilms at a large scale. An investigation was carried out by applying a metagenomics approach to delineate the ARGs distribution patterns in freshwater biofilms at a cross-continental scale. Main results revealed that certain ARGs could potentially serve as representative biomarkers to indicate high pollution area in freshwater environments.

Furthermore, there is an existing knowledge gap on the reactivity of these freshwater biofilms towards pollutants, which has primarily been caused by challenges faced when extracting nucleic acids from environmental biofilm samples. The third chapter demonstrates that different extraction methods could impact the functional analyses and data interpretations of freshwater biofilms.

The importance of lab-based biofilm models is to obtain a controlled fundamental understanding of biofilm responses towards various pollutants. Finding the proper environmental conditions of the biofilm model is crucial for all following experiments. A protocol has been established for developing and maintaining the biofilm reactor. In Chapter 4, the impacts of carbon supplementation facilitated increases in biofilm turnover rates, however to the alteration of biofilm community structure and the expected biofilm phenotype.

Finally, the experimental biofilm setup was used to assess the impact of erythromycin on a simulated freshwater biofilm model. Metatranscriptomic analysis revealed that following erythromycin exposure at subinhibitory levels, significant changes in the biofilm structure, active microbiome and functional attributes were observed.

Overall, this thesis provides important insights into freshwater and IWDS biofilm studies at the field scale and lab-scale, thereby providing a fundamental understanding of selected pollutants' dynamic and mechanistic action on a complex consortium of microorganisms. The findings presented in this thesis constitutes an initial step in generating data to improve IWDS management and freshwater quality monitoring and assessment.