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 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 coastal waterways that vary
greatly in tropical regions. To address this knowledge gap, we used
environmental DNA (eDNA) metabarcoding to examine 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 elevated during the sampled wet season with
the influx of freshwater and agricultural run-off. Fish taxa richness
significantly decreased in all three estuaries (F = 164.73, P =
<0.001), along with pronounced changes in community composition (F
= 46.68, P = 0.001) associated with environmental variables (largely
salinity: 27.48% contribution to total variance). 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.
Among the four sampled locations, variation in fish community composition
was more pronounced within the wet season (F = 2.5, P = 0.001). Notably,
variation in the wet season was significantly correlated with agricultural
contaminants (phosphorus: 6.25%, pesticides: 5.22%) alongside
environmental variables (salinity: 5.61%, DOC: 5.57%). Historically
contaminated and relatively unimpacted estuaries each demonstrated
distinct fish communities, reflecting their associated catchment use. Our
findings emphasise that while seasonal effects play a key role in shaping
the community structure of fish in this region, agricultural contaminants
are also important contributors in estuarine systems.