Environmental DNA Metabarcoding Effectively Detects Invasive Species, Pests, and Community Changes in Taiwan’s Rice Fields
bioRxiv (Cold Spring Harbor Laboratory)
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 during planting and harvesting, 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 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 analysis as an efficient biomonitoring approach in rice agroecosystems with direct applications for pest, invasive species, and vector surveillance within Taiwan.
Authors 10
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Pritam Banerjee corresponding
National Chung Cheng University · University of California, Berkeley
Affiliation as printed
Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
Department of Environmental Science, Policy, and Management, University of California, University Avenue and Oxford St, Berkeley, CA, 94720, USA
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National Chung Cheng University
Affiliation as printed
Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
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Affiliation as printed
Institute of Environmental Sciences, Leiden University, Leiden, 2333 CC, The Netherlands
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Affiliation as printed
Department of Natural Resources Management, Texas Tech University, Lubbock, Texas, USA
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National Chung Cheng University
Affiliation as printed
Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
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Affiliation as printed
School of Biological Sciences, The University of Hong Kong SAR, China
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National Chung Cheng University
Affiliation as printed
Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
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National Chung Cheng University
Affiliation as printed
Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
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Affiliation as printed
Department of Chemistry, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar, Odisha 751024, India
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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 62102, Taiwan
Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
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