Metagenomics for the bioassessment of waterbodies using mesocosm experiments

Water bodies and their resident biodiversity are at risk from contaminants, disease agents, biological invasions, and abiotic stressors. In the European Union, the Water Framework Directive (WFD) is designed to provide the means to assess, monitor and manage water bodies in order to ensure safety, economic, and natural resource sustainability.

Traditionally, kick sampling is applied to retrieve representative samples of macroinvertebrate diversity. Species are identified using morphological methods of identification. The river is then given a qualitative score based on biodiversity, and physicochemical factors. This methodology is often time consuming, labour intensive, and requires expert identification of macroinvertebrates.
There is the need for conventional approaches to be supplemented with new technologies. Here, we propose to explore new approaches for the assessment of water bodies, which benefit from the latest developments in (eco)metagenomics, bioinformatic and chemical biology. Recent molecular advances, including the use of environmental DNA (eDNA) extracted from the water column, provide the ability to derive presence, absence of a species from a water sample without needing to directly interact with it. These novel high through-put technologies could enable us to track and describe focal species as well as the wider food web within which they are embedded.

The aim of the project is to use eDNA and metagenomic approaches with the mesocosms available at Imperial College to determine the effects of chemical stressors on freshwater ecosystems. Mesocosm-based approaches are increasingly recognized as spanning the critical gap between field observations and lab experiments, by offering realistic levels of biocomplexity, whilst also affording a degree of control and replication of experimental conditions. Through the assembly of artificial communities in mesocosms and extraction of eDNA, metabarcoding can recover presence and abundance of key species, employing cutting-edge molecular computational methods to better exploit metagenomic data and derive maximum value. As well as the mesocosms, microcosms may be constructed and used to assess the microbial communities within the mesocosms. It is an aim of this project to develop these techniques as an alternative to the lengthy and costly methodology currently provided by the WFD.

In particular there is an interest in how anthropogenically derived chemicals impact the food webs of freshwater environments. Particular chemicals of interest are ammonia from waste waters, and surfactants from household products. Ammonia was chosen as there is strong evidence in literature that increases in ammonia lead to damage to gill structures, fatal to many species. Furthermore, pollution of ammonia often leads to eutrophication and depletion of dissolved oxygen. Surfactants are also of interest as they are common at home and in industry, as soaps, laundry detergents, and enhanced oil production. Surfactants are a broad class of chemicals that could be disruptive to the ecosystem as they interfere with cell membranes, solubilize proteins, and cause cell lysis. Due to these reasons microbes are likely to be influenced by surfactants, this may have an impact the rates of key biogeochemical cycles that are mediated by microbes in the mesocosms