DOI: 10.5061/dryad.ttdz08m16
title: Environmental DNA highlights the influence of salinity and agricultural run-off on coastal fish assemblages in the Great Barrier Reef region

description: 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 =
 &lt;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.
description: This 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. Samples were collected at different depths to
 establish a profile along the water column and measurements were averaged
 for each location. All samples for nutrient and pesticide analyses were
 placed on ice in the field and immediately refrigerated (pesticides) or
 frozen (nutrients) upon returning to the field laboratory until analysis.
 Nutrient analyses were carried out by the Chemistry Centre of the
 Department of Environment and Science, Queensland Government (Queensland,
 Australia), a NATA (National Association of Testing Authorities)
 accredited laboratory. Chlorophyll a concentrations were determined by
 spectrophotometric procedures. Dissolved organic carbon was measured using
 an automated carbon analyser. Total Kjeldahl values for nitrogen and
 phosphorus were measured via catalysed acidic block digestion with
 colorimetric segmented flow analyser finish. Targeted pesticide analyses
 were conducted by the Queensland Government Forensic and Scientific
 Services (Queensland, Australia) and a NATA accredited library through
 direct injection using Liquid Chromatography with tandem mass spectrometry
 (LC-MS-MS). Water samples were filtered through a 0.2 mm membrane prior to
 LC-MS-MS, and the concentrations measured were of soluble pesticides (see
 Supplementary Material Table S2 for limits of reporting). Chemical
 analysis results may be found in Supplementary-Workbook-1_Env-Data-2018
 and Supplementary-Workbook-2_Env-Data-2020. 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 (&lt;0.0001 proportion for each sample) were removed,
 and all the read counts were converted into presence-absence. The
 presence-absence OTU table may be found in
 Supplementary-Workbook-3_Datasets-Tele01-Elas02.
description: Microsoft Excel, Microsoft Word, Notepad, R
description: # Environmental DNA reveals associations between fish assemblages and
 seasonal changes in salinity and agricultural run-off in the Great Barrier
 Reef region ## Description
 of the data and file structure
 "Supplementary-Workbook-1_Env-Data-2018.xlsx" and
 "Supplementary-Workbook-2_Env-Data-2020.xlsx" are Microsoft
 Excel workbooks for the sampled dry season (2018) and wet season (2020)
 respectively that contain measurements of chemical and physico-chemical
 parameters from the sites and locations sampled within this study. These
 measurements were obtained via chemical analysis of water samples from
 each study site.
 "Supplementary-Workbook-3_Datasets-Tele01-Elas02.xlsx" is also
 an Excel workbook, containing OTU (operational taxonomic unit) tables of
 the occurrences of the different species detected at each sampled site in
 this study for two datasets - Tele01 (obtained using the Tele01 primer
 set) and Elas02 (obtained using the Elas02 primer set). The first tab of
 this spreadsheet has a key for abbreviations and colour codes used in the
 two datasets. These data were obtained from environmental DNA
 metabarcoding of water samples collected from the study sites.
 "Supplementary-Material_Parikh-et-al-2024.docx" is a Microsoft
 Word document containing figures, tables and text which support the main
 article. "Elas_AmpliconPipeline_log.txt" and
 "Tele_AmpliconPipeline_log.txt" are text files that contain a
 log of the bionformatics processing carried out on DNA sequencing results,
 to match sequences back to sampled sites and to species reference
 databases. Parikh-et-al-2024_Stats.R is an R script file which can be
 opened in a text editor or R and contains the R code used to perform
 statistical analyses for this paper. ## Sharing/Access information The
 listed data is currently available only via this platform, however, please
 reach out to the author at for
 any data requests.