Environmental DNA Metabarcoding Effectively Detects Invasive Species, Pests, and Community Changes in Taiwan's Rice Fields

Ecology and Evolution, vol. 16, pp. e73339

Abstract

ABSTRACT 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 rice fields during planting and harvesting time, employing eDNA metabarcoding (COI) to detect diverse taxonomic groups. We assigned 77 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 status affected overall diversity, with higher species richness during planting compared to harvesting. No significant differences were observed between native/non‐native taxa and 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 analysis as an efficient biomonitoring approach in rice agroecosystems with direct applications for pest, invasive species, and vector surveillance within Taiwan.

Authors 10

1. Pritam Banerjee corresponding

   National Chung Cheng University · University of California, Berkeley

   Affiliation as printed

   Department of Earth and Environmental Sciences National Chung Cheng University Chiayi County Taiwan

   Department of Environmental Science, Policy, and Management University of California Berkeley California USA

2. Gobinda Dey

   National Chung Cheng University

   Affiliation as printed

   Department of Earth and Environmental Sciences National Chung Cheng University Chiayi County Taiwan

3. Kathryn A. Stewart Aachen Institute of Environmental Sciences (CML) Leiden University Leiden The Netherlands

   Leiden University

   Affiliation as printed

   Institute of Environmental Sciences Leiden University Leiden the Netherlands

4. Matthew A. Barnes

   Texas Tech University

   Affiliation as printed

   Department of Natural Resources Management Texas Tech University Lubbock Texas USA

5. Md. Taharia

   National Chung Cheng University

   Affiliation as printed

   Department of Earth and Environmental Sciences National Chung Cheng University Chiayi County Taiwan

6. Mathew Seymour

   University of Hong Kong

   Affiliation as printed

   School of Biological Sciences The University of Hong Kong SAR Hong Kong SAR China

7. Chin-Wen Wang

   National Chung Cheng University

   Affiliation as printed

   Department of Earth and Environmental Sciences National Chung Cheng University Chiayi County Taiwan

8. Raju Kumar Sharma

   National Chung Cheng University

   Affiliation as printed

   Department of Earth and Environmental Sciences National Chung Cheng University Chiayi County Taiwan

9. Jyoti Prakash Maity

   KIIT University

   Affiliation as printed

   Department of Chemistry, School of Applied Sciences KIIT Deemed to be University Bhubaneswar Odisha India

10. Chien‐Yen Chen corresponding

    National Chung Cheng University

    Affiliation as printed

    Center for Nano Bio‐Detection, Center for Innovative Research on Aging Society, AIM‐HI National Chung Cheng University Chiayi Taiwan

    Department of Earth and Environmental Sciences National Chung Cheng University Chiayi County Taiwan

    PhD in Doctoral Program in Science, Technology, Environment, and Mathematics, National Chung Cheng University Chiayi Taiwan