Metabarcoding of benthic eukaryote communities predicts the ecological condition of estuaries

•We used metabarcoding to examine the benthic eukaryote composition of five estuaries.•Biotic richness (based on MOTUs) was greater in the most impacted estuary.•Similarities among estuaries reflected their environmental condition.•Composition was strongly correlated with nutrients, turbidity and pH.•Metabarcoding can provide fast, comprehensive and ecologically informative data.

DNA-derived measurements of biological composition have the potential to produce data covering all of life, and provide a tantalizing proposition for researchers and managers. We used metabarcoding to compare benthic eukaryote composition from five estuaries of varying condition. In contrast to traditional studies, we found biotic richness was greatest in the most disturbed estuary, with this being due to the large volume of extraneous material (i.e. run-off from aquaculture, agriculture and other catchment activities) being deposited in the system. In addition, we found strong correlations between composition and a number of environmental variables, including nutrients, pH and turbidity. A wide range of taxa responded to these environmental gradients, providing new insights into their sensitivities to natural and anthropogenic stressors. Metabarcoding has the capacity to bolster current monitoring techniques, enabling the decisions regarding ecological condition to be based on a more holistic view of biodiversity.