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METHODS article
Front. Environ. Sci.
Sec. Freshwater Science
Volume 12 - 2024 |
doi: 10.3389/fenvs.2024.1415338
This article is part of the Research Topic Freshwater Biodiversity Crisis: Multidisciplinary Approaches as Tools for Conservation Volume II View all 4 articles
Water filter: A rapid water environmental DNA collector in the field
Provisionally accepted- 1 GeneMind Biosciences Co., Ltd., Shenzhen, China
- 2 Shenzhen Academy of Environmental Sciences, Shenzhen, China
Biological monitoring using environmental DNA (eDNA) technology has expanded from micro-to macro-organisms. In aquatic eDNA studies, large volumes of water need to be filtered rapidly in the field, which requires development of effective eDNA collection devices. Here, we introduce a novel portable eDNA collection system containing a GM dual-channel water filter and a DNA extraction kit adapted to large filter membranes (ø 100 mm). The water filter is powered by a high-capacity lithium battery (9000 mA), which operates two peristaltic pumps and maintains a continuous filtration rate of up to 1 L/min for 5 h in outdoor settings. For sample collection, the optimum conditions are still water and turbidity below 8 nephelometric turbidity units. This allows for the filtration of 10 L of water within 10 min using a 0.22-μm filter. Metagenomic and 12S metabarcoding sequencing showed that the DNA extraction quality and species annotation accuracy of our custom DNA extraction kit, which was tailored for this system, rivaled the performance of established kits. The GM water filter's enrichment mode gave consistent results with vacuum filtration, which greatly reduced the filtration time for large water samples while accurately reproducing species annotations. This innovation streamlines the eDNA collection and annotation process and offers substantial benefits for biodiversity monitoring and conservation efforts.
Keywords: Aquatic ecosystem, eDNA sample collection, metabarcoding, Metagenome, quick filtering environmental DNA
Received: 10 Apr 2024; Accepted: 31 Jul 2024.
Copyright: © 2024 Liu, Wu, Feng, Ju, Wu, Han, Wang, Liao, Zhao, Gao, Zheng, Luo, Gong, Zeng, Lai, Li, Yan and Sun. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Yongfeng Liu, GeneMind Biosciences Co., Ltd., Shenzhen, China
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