The bacteria of Darwin Harbour: spatial and temporal patterns in a tropical macrotidal estuary subject to urbanisation

Estuaries are renowned for their complex environment and productivity. They are also the focal point of impact between the land and sea and subject to increasing human pressures. Darwin harbour in northern Australia is a macrotidal estuary in the dry-wet tropics subject to increasing urbanisation and shows some localised water degradation due to sewage effluent. Tropical estuaries are poorly studied compared to temperate systems and not much 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 its association with abiotic factors. In particular, we addressed the question whether a human impact signal was discernible in the microbiota beyond the dynamic nature of the estuary. Adopting a single impact–double control study design, we investigated the bacterial community through next-generation sequencing of the 16s ribosomal DNA of water and sediment from tidal control creeks and creeks affected by effluent and urban runoff over two years sampling during neap and spring tides, dry and wet seasons. 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 dry-wet tropics. The neap-tide water microbiota provided the best snapshot in time of the current water conditions while sediment mirrored current and past water conditions. Differences in patterns of the microbiota between different harbour parts reflected the harbour's complex hydrodynamics and bathymetry. Despite these variations, a clear microbial signature was discernible relating to effluent and the composite of nutrients explained most of the microbiota followed by changes in salinity. Microbial signatures not only differed between impacted and control creeks, but also between effluent and urban runoff and between effluents of wastewater treatment plants. Our results confirm the overall good condition of Darwin harbour but show the extent of some hypereutrophic areas. The diversity and high resolution of the microbiota confirm its suitability as a pool of biological indicators to monitor ecosystem health even in this dynamic and complex ecosystem.