Environmental DNA as a tool for detecting ocean outfall impacts and environmental gradients in coastal ecosystems

As pressures on coastal ecosystems intensify, there is a growing need for sensitive, scalable tools to detect early signs of ecological change. Environmental DNA (eDNA) metabarcoding has emerged as a powerful approach for marine biomonitoring, providing a non-invasive, high-resolution alternative to traditional methods. This study applied eDNA metabarcoding to assess potential impacts of effluent discharge from the Belmont Wastewater Treatment Works (WWTW) ocean outfall in New South Wales, Australia. Benthic infauna were sampled from sandy sediments at ∼25 m depth along north-east and south-west transects extending up to 2 km from the outfall. Eukaryotic (18S rDNA) and prokaryotic (16S rDNA) communities were sequenced and compared with data from concurrent morpho-taxonomic surveys. No clear evidence of ecological disturbance from effluent discharge was detected using eDNA, consistent with morpho-taxonomic results. Nevertheless, eDNA identified a broader range of taxa, revealing distinct spatial structuring in community composition, particularly along the southern transect where richness correlated with sediment grain size. This spatial pattern was not evident in the morpho-taxonomic dataset, highlighting the greater sensitivity of molecular methods to habitat-driven gradients. A weak but significant correlation between eDNA read counts and morpho-taxonomic abundance supported the use of metabarcoding data as a proxy for relative abundance. These findings demonstrate that eDNA metabarcoding complements traditional biomonitoring, offering enhanced sensitivity to environmental gradients even in the absence of detectable anthropogenic impact, and extends the reach of conventional surveys by capturing otherwise undetectable taxa.