Darwin Harbour is a macrotidal estuary in the Australian wet-dry tropics, subject to increasing urbanisation, with some localised water quality degradation due to treated sewage effluent. Tropical estuaries are poorly studied compared to temperate systems and little is known about the microbial community-level response to nutrient load.
The aim of this study was to analyse the spatial and temporal patterns of the bacterial community across Darwin Harbour and to examine their association with abiotic factors. In particular, we sought to determine if a human impact signal was discernible in the microbiota.
Adopting a single impact–double control design, we investigated the bacterial community in water and sediment from reference creeks and from others affected by effluent and urban runoff. Samples were taken over two years during neap and spring tides, in the dry and wet seasons. We analysed the 16S rDNA MiSeq data using the QIIME open reference pipeline and used various statistical methods including PERMANOVA, constrained ordinations, spatial eigenvector models and variance partitioning to differentiate spatial, salinity and nutrient-related factors.
We found that temporal drivers, namely seasonal and tidal-related effects, had the largest impact upon the water microbiota reflecting the macrotidal nature of the estuary and its location in the wet-dry tropics. The neap-tide water microbiota provided the clearest discrimination of current nutrient loads, while the sediment microbiota mirrored current and past water conditions. Differences in patterns of the microbiota between different parts of the harbour reflected the harbour's complex hydrodynamics and bathymetry. Despite these variations, a clear microbial signature was discernible relating to effluent, and nutrients explained most of the variation in the microbiota followed by salinity. Microbial signatures not only differed between impacted and reference creeks, but also between effluent and urban runoff, and between the different wastewater treatment plants.
Overall, our results confirm that the water quality of Darwin Harbour is good but they also reveal the extent of some eutrophic areas.