Environmental DNA highlights the influence of salinity and agricultural run-off on coastal fish assemblages in the Great Barrier Reef region

Agricultural run-off in Australia's Mackay-Whitsunday region is a major source of nutrient and pesticide pollution to the coastal and inshore ecosystems of the Great Barrier Reef. While the effects of run-off are well documented for the region's coral and seagrass habitats, the ecological impacts on estuaries, the direct recipients of run-off, are less known. This is particularly true for fish communities, which are shaped by the physico-chemical properties of the coastal waterways that vary greatly in tropical regions. To address this knowledge gap, we used environmental DNA (eDNA) metabarcoding to examine teleost and elasmobranch fish assemblages at four locations (three estuaries and a harbour) subjected to varying levels of agricultural run-off during a wet and dry season. Pesticide and nutrient concentrations were markedly lower during the sampled dry season. With the influx of freshwater and agricultural run-off during the wet season, teleost and elasmobranch taxa richness significantly decreased in all three estuaries, along with pronounced changes in fish community composition which were largely associated with environmental variables (particularly salinity). In contrast, the nearby Mackay Harbour exhibited a far more stable community structure, with no marked changes in fish assemblages observed between the sampled seasons. Within the wet season, differing compositions of fish communities were observed among the four sampled locations, with this variation being significantly correlated with environmental variables (salinity, chlorophyll, DOC) and contaminants from agricultural run-off, i.e., nutrients (nitrogen and phosphorus) and pesticides. Historically contaminated and relatively unimpacted estuaries each demonstrated distinct fish communities, reflecting their associated catchment use. Our findings emphasise that while seasonal effects (e.g., changes in salinity) play a key role in shaping the community structure of estuarine fish in this region, agricultural contaminants (nutrients and pesticides) are also important contributors in some systems.