Optimal Environmental DNA Sampling Strategy for Comprehensively Assessing Biodiversity in Rice Paddy Fields

This is the authors' abstract. We don't add key points for this paper.

Irrigated paddy fields provide alternative habitats for aquatic species amid degrading natural wetland habitats. Paddy field biodiversity depends on surrounding landscapes and agricultural practices, and biodiversity surveys are important in understanding it. However, its assessment is often time‐consuming and depends on specialist skills. To overcome these limitations, we used environmental DNA (eDNA) metabarcoding of paddy water samples to detect species diversity of insects, fishes, and birds, and assessed the optimal sampling effort and sampling design. From each of seven paddy fields, we collected samples at each of eight positions. eDNA metabarcoding detected 118 insect, 14 fish, and 6 bird operational taxonomic units, most of them aquatic. Resampling analyzes suggested that four sampling replicates can recover all detectable operational taxonomic units of fishes and birds with > 50% probability, but the species accumulation curves suggested greater insect diversity than we detected, attributable to insufficient reference data. Samples collected near inlets included eDNA from irrigation channels, so inlets should be avoided in assessing biodiversity in paddy fields. Pooled samples could detect abundant species, but the samples detected fewer species than the total species diversity detected from eight sampling replications. Our findings are applicable to most paddies in Japan because the research was conducted in Japanese standard rectangular paddies. Moreover, given the prevalence of small agricultural fields in many Asian countries, our findings will promote the use of eDNA in biodiversity monitoring in paddy fields.