Data from: Environmental DNA metabarcoding effectively detects invasive species, pests, and community changes in Taiwan’s rice fields

Rice fields represent man-made semi-aquatic wetlands primed for invasive
pests. Monitoring rice field biodiversity using conventional methods,
however, is time-consuming and laborious. Environmental DNA (eDNA) methods
can provide a fast and effective means to monitor rice field communities
and inform management decisions. Our study provides proof-of-concept of
rice field eDNA biodiversity assessments, with a focus on native and
non-native pests across cultivation phases. We collected eDNA samples from
locations in southern Taiwan during planting and harvesting, employing
eDNA metabarcoding (COI) to detect diverse taxonomic groups. We assigned
78 ASVs across all sites to animal taxa, 34 of which were identified to
species. Overall, 18 species were designated as native or non-native (83.3
% and 16.6 %, respectively), including three major rice pests, Chilo
suppressalis (native), Coptotermes formosanus (native), and Pomacea
canaliculata (non-native). Cultivation affected overall diversity, with
higher species richness during planting compared to harvesting. No
significant differences were observed between native and non-native taxa
between cultivation phases. Altogether, we detected a complex environment
across trophic levels comprised of both native and non-native agricultural
pests using limited sampling effort, demonstrating eDNA as an efficient
biomonitoring approach in rice agroecosystems with direct applications for
pest, invasive species, and vector surveillance within Taiwan.