Unveiling structure of tropical estuarine communities through eDNA and implications for biomonitoring

Tropical estuaries are hyper-diverse ecosystems, hosting essential habitats for freshwater, euryhaline and marine life. Understanding how biological communities are distributed in these systems has long been a challenge because of their inherent dynamic nature, and the diversity of interacting natural pressures and anthropogenic stressors they are subjected to. In this study, we used environmental DNA (eDNA) metabarcoding to examine the structure of multi-taxonomic communities in estuarine ecosystems (diatoms, crustacean, fish and eukaryote as a whole) and their relationships with environmental drivers in three differentially impacted locations facing the Great Barrier Reef in Central Queensland (Australia). We first demonstrated that eDNA signals from sediment and water matrices provide complementary information, and that both should be monitored for a more holistic understanding of community trajectories in anthropogenically-impacted aquatic environments. We also observed that, indepe..., This dataset comprises environmental DNA datasets (both raw and filtered datasets along with associated scripts) and physico-chemical data obtained from water and sediment collected in three different estuaries from Queensland, Australia in 2018. 10 sites were selected at each estuary, at approximately 1 km intervals from the mouth of the river going upstream.
Environmental parameters of the water column (including salinity, pH, dissolved oxygen, turbidity, chlorophyll-a and temperature) were measured using a calibrated EXO2 YSI multiparameter sonde (YSI, Yellow Springs, OH, USA). Standard sampling protocols from the Queensland Government Department of Environment and Science were followed for determining contaminant (nutrient and pesticide) concentrations in the water column. Analysis of nutrients in water was carried out by the DES Chemistry Centre laboratory. Total and dissolved organic carbon were measured using a non-dispersive infrared sensor (NDIS). Total Kjeldahl values for nitr..., # Unveiling structure of tropical estuarine communities through eDNA and implications for biomonitoring

Dataset DOI: [10.5061/dryad.qnk98sfvp](10.5061/dryad.qnk98sfvp)

## Description of the data and file structure

### Description of the data

This dataset contains environmental DNA metabarcoding data use to describe the composition and structure of estuarine communities from Queensland, australia. Four taxonomic groups have been targeted (diatoms, crustacean, fish and eukaryote). Environmental data and metadata, raw and filtered as well as scripts to filter the sequencing data and run statistical analyses described in Pansu et al. (2025 Environmental DNA) are provided.

Multiple folders in this repository have been deposited:

* '*Raw data*' contains the raw paired-end sequencing data (fastq files) generated by Illumina sequencing along with the scripts and associated files to conduct the first steps of the bioinformatic analysis. These scripts (to run under Linux) required the OBI...,