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.Microsoft Excel, Microsoft Word, NotepadFunding provided by: H2020 Marie Skłodowska-Curie ActionsCrossref Funder Registry ID: http://dx.doi.org/10.13039/100010665Award Number: MSCA-GF 750570This dataset comprises eDNA and chemical data obtained from water samples collected at four locations in Queensland, Australia in 2018 and again in 2020. Three of the locations are estuaries, and the fourth is the Mackay Harbour. 10 sites were selected at each estuary, at approximately 1 km intervals from the mouth of the river going upstream, and four sites were selected in the harbour. For chemical analyses, water samples were collected from each site following Queensland Government protocols. Nutrient analyses were carried out by the Chemistry Centre of the Department of Environment and Science, Queensland Government. Total and dissolved organic carbon were measured using a non-dispersive infrared sensor (NDIS). Total Kjeldahl values for nitrogen and phosphorus were measured through low-level atomic absorption (AA) analysis. Pesticide analyses were conducted by the Queensland Government Forensic and Scientific Services through direct injection using Liquid Chromatography with tandem mass spectrometry (LC-MS-MS). Chemical analysis results may be found in Sheet-1 and Sheet-2. For eDNA analyses, three 2 L water samples were collected at each site. Samples were filtered at the field laboratory within 16 hours of collection and stored frozen in liquid nitrogen. Further processing took place in the eDNA and Biomonitoring Lab of Macquarie University. This included eDNA extraction using Qiagen PowerWater kits (Qiagen, Netherlands), DNA amplication via PCR using two fish-specific primer sets targeting teleost and elasmobranch fishes respectively, and pooling and purification of amplified samples. Final products were sequenced at the Ramaciotti Centre for Genomics, University of New South Wales. Sequencing results were processed through the Greenfield Hybrid Analysis Pipeline (GHAP), with operational taxonomic units matched to the MitoFish reference database for taxonomic assignment with the cutoff of 0.8 or higher match similarity. Prior to statistical analyses, datasets were cleaned based on contamination from positive controls, replicates were combined, low abundance reads (