Environmental DNA maps estuarine regionalisation, zonation, and water quality impacts

High throughput metabarcoding sequencing of environmental DNA was applied to analyse estuarine biota, along a latitudinal gradient across three regions, estuarine zones, and water quality types. A total of 4757 detections, in 36 biota groupings were observed. The majority in seven key groups: bacteria (23%), plants (13%), fungi (9%), fish (8%), ciliates (6%), insects (6%), and crustaceans (4%). Despite high sample variability, differences were observed in detected biota between region, estuary, estuary zone, and water quality types. Water quality pressures differed in each region; however, at sites with the poorest water quality (highest nutrients, and turbidity), differentiation of detected biota was observed. Biota groups that best characterised these differences comprised primarily lower order groups, bacteria, cryptomonads, and ciliates, photosynthetic groups including green algae, dinoflagellates, diatoms, and one higher order group, crustaceans. Typically, lower diversity and number of total detections were observed at the sites with more impacted water quality, this was to the greatest extent in the most human influenced Central region, at mid-estuary sites. However, this trend was not observed for all biota groups, with higher aggregated counts and diversity detected for bacteria, plants, and archaea at more impacted sites. These data set a baseline across regions and estuaries, subject to a range of water quality impacts. Further study is necessary to establish eDNA as an indicator of estuarine condition, to better characterise the influences of other relevant drivers, both natural and human influenced, and change associated with management interventions.