eDNA metabarcoding reveals shifts in sediment eukaryote communities in a metal contaminated estuary

Metal contamination is a global issue impacting biodiversity in urbanised estuaries. Traditional methods to assess biodiversity are time consuming, costly and often exclude small or cryptic organisms due to difficulties with morphological identification. Metabarcoding approaches have been increasingly recognised for their utility in monitoring, however studies have focused on freshwater and marine systems despite the ecological significance of estuaries. We targeted estuarine eukaryote communities within the sediments of Australia's largest urbanised estuary, where a history of industrial activity has resulted in a metal contamination gradient. We identified specific eukaryote families with significant correlations with bioavailable metal concentrations, indicating sensitivity or tolerance to specific metals. While polychaete families Terebellidae and Syllidae demonstrated tolerance to the contamination gradient, members of the meio- and microfaunal communities including diatoms, dinoflagellates and nematodes displayed sensitivities. These may have high value as indicators but are frequently missed in traditional surveys due to sampling limitations.

Legacy metal contamination is reflected in the fish gut microbiome in an urbanised estuary

Estuaries are critical habitats subject to a range of stressors requiring effective management. Microbes are gaining recognition as effective environmental indicators, however, the response of host associated communities to stressors remains poorly understood. We examined microbial communities from seawater, sediments and the estuarine fish Pelates sexlineatus, in Australia's largest urbanised estuary, and hypothesised that anthropogenic contamination would be reflected in the microbiology of these sample types. The human faecal markers Lachno3 and HF183 were not detected, indicating negligible influence of sewage, but a gradient in copy numbers of the class 1 integron (intI-1), which is often used as a marker for anthropogenic contamination, was observed in sediments and positively correlated with metal concentrations. While seawater communities were not strongly driven by metal contamination, shifts in the diversity and composition of the fish gut microbiome were observed, with statistical links to levels of metal contamination (F_{2, 21} = 1.536, p < 0.01). Within the fish gut microbiome, we further report increased relative abundance of amplicon sequence variants (ASVs; single inferred DNA sequences obtained in sequencing) identified as metal resistant and potentially pathogenic genera, as well as those that may have roles in inflammation. These results demonstrate that microbial communities from distinct habitats within estuarine systems have unique response to stressors, and alterations of the fish gut microbiome may have implications for the adaptation of estuarine fish to legacy metal contamination.