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 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 = <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.

Influence of Human Activities on Broad-Scale Estuarine-Marine Habitats Using Omics-Based Approaches Applied to Marine Sediments.

Rapid urban expansion and increased human activities have led to the progressive deterioration of many marine ecosystems. The diverse microbial communities that inhabit these ecosystems are believed to influence large-scale geochemical processes and, as such, analyzing their composition and functional metabolism can be a means to assessing an ecosystem's resilience to physical and chemical perturbations, or at the very least provide baseline information and insight into future research needs. Here we show the utilization of organic and inorganic contaminant screening coupled with metabolomics and bacterial 16S rRNA gene sequencing to assess the microbial community structure of marine sediments and their functional metabolic output. The sediments collected from Moreton Bay (Queensland, Australia) contained low levels of organic and inorganic contaminants, typically below guideline levels. The sequencing dataset suggest that sulfur and nitrite reduction, dehalogenation, ammonia oxidation, and xylan degradation were the major metabolic functions. The community metabolites suggest a level of functional homogeneity down the 40-cm core depth sampled, with sediment habitat identified as a significant driver for metabolic differences. The communities present in river and sandy channel samples were found to be the most active, with the river habitats likely to be dominated by photoheterotrophs that utilized carbohydrates, fatty acids and alcohols as well as reduce nitrates to release atmospheric nitrogen and oxidize sulfur. Bioturbated mud habitats showed overlapping faunal activity between riverine and sandy ecosystems. Nitrogen-fixing bacteria and lignin-degrading bacteria were most abundant in the sandy channel and bioturbated mud, respectively. The use of omics-based approaches provide greater insight into the functional metabolism of these impacted habitats, extending beyond discrete monitoring to encompassing whole community profiling that represents true phenotypical outputs. Ongoing omics-based monitoring that focuses on more targeted pathway analyses is recommended in order to quantify the flux changes within these systems and establish variations from these baseline measurements.