Environmental DNA (eDNA) metabarcoding is increasingly being used to assess community composition in coastal ecosystems. In this study, we chose to examine temporal and spatial changes in the aquatic community of Manly Lagoon – one of the most heavily developed and polluted estuaries in eastern Australia. Based on metabarcoding of the 16S mitochondrial gene (for fish) and the 18S nuclear gene (for macroinvertebrates), we identified seasonal differences in fish and macroinvertebrate community composition as well as species richness, which correlated, in some cases, with environmental parameters (sea surface temperature and freshwater input). Moreover, given the greater taxonomic resolution of fish versus macroinvertebrate assignments, we identified several known migratory fish species of management importance that contributed significantly to the overall patterns observed. Overall, our data support the use of eDNA metabarcoding to track fish assemblages shifting in response to environmental drivers in polluted estuaries with increased sampling and consultation with historical data.

We here provide the raw sequencing data files in fastq format along with an excel spreadsheet listing the sequencing run, assay, sample ID, forward and reverse tags, as well as forward and reverse primers required for demultiplexing and quality filtering ("Sequencing run, assay, sample ID, tags, and primers.xlsx") used in the following paper:

DiBattista, J.D., Riley, I.J., Fowler, A.M., Reader, S., Hay, A., Parkinson, K., and Hobbs, J.-P.A. (in press) The use of environmental DNA to monitor impacted coastal estuaries. Marine Pollution Bulletin. https://doi.org/10.1016/j.marpolbul.2022.113860