Ultra-sensitive detection of ecologically rare fish from eDNA samples based on the RPA-CRISPR/Cas12a technology
Summary: Environmental DNA (eDNA) research holds great promise for improving biodiversity science and conservation efforts by enabling worldwide species censuses in near real-time. Current eDNA methods face challenges in detecting low-abundance ecologically important species. In this study, we used...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2023-09-01
|
| Series: | iScience |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004223015961 |
| _version_ | 1827866290493063168 |
|---|---|
| author | Xing-Yi Wei Li Liu Huan Hu Huang-Jie Jia Ling-Kang Bu De-Sheng Pei |
| author_facet | Xing-Yi Wei Li Liu Huan Hu Huang-Jie Jia Ling-Kang Bu De-Sheng Pei |
| author_sort | Xing-Yi Wei |
| collection | DOAJ |
| description | Summary: Environmental DNA (eDNA) research holds great promise for improving biodiversity science and conservation efforts by enabling worldwide species censuses in near real-time. Current eDNA methods face challenges in detecting low-abundance ecologically important species. In this study, we used isothermal recombinase polymerase amplification (RPA)-CRISPR/Cas detection to test Ctenopharyngodon idella. RPA-CRISPR-Cas12a detected 6.0 eDNA copies/μL within 35 min. Ecologically rare species were identified in the Three Gorges Reservoir Area (TGRA) using functional distinctiveness and geographical restrictiveness, with seven fish species (9%) classified as potentially ecologically rare including three species in this investigation. RPA-CRISPR/Cas12a-FQ outperformed high-throughput sequencing (HTS) and qPCR in detecting low-abundance eDNA (AUC = 0.883∗∗). A significant linear correlation (R2 = 0.682∗∗) between RPA-CRISPR/Cas12a-FQ and HTS quantification suggests its potential for predicting species abundance and enhancing eDNA-based fish biodiversity monitoring. This study highlights the value of RPA-CRISPR/Cas12a-FQ as a tool for advancing eDNA research and conservation efforts. |
| first_indexed | 2024-03-12T15:01:51Z |
| format | Article |
| id | doaj.art-c4d2f5f5fcda4433a745e92a62df0c79 |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-03-12T15:01:51Z |
| publishDate | 2023-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-c4d2f5f5fcda4433a745e92a62df0c792023-08-14T04:07:49ZengElsevieriScience2589-00422023-09-01269107519Ultra-sensitive detection of ecologically rare fish from eDNA samples based on the RPA-CRISPR/Cas12a technologyXing-Yi Wei0Li Liu1Huan Hu2Huang-Jie Jia3Ling-Kang Bu4De-Sheng Pei5Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China; Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing 400714, ChinaChongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing 400714, ChinaKey Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China; Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing 400714, ChinaChongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing 400714, ChinaChongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing 400714, ChinaSchool of Public Health, Chongqing Medical University, Chongqing 400016, China; Corresponding authorSummary: Environmental DNA (eDNA) research holds great promise for improving biodiversity science and conservation efforts by enabling worldwide species censuses in near real-time. Current eDNA methods face challenges in detecting low-abundance ecologically important species. In this study, we used isothermal recombinase polymerase amplification (RPA)-CRISPR/Cas detection to test Ctenopharyngodon idella. RPA-CRISPR-Cas12a detected 6.0 eDNA copies/μL within 35 min. Ecologically rare species were identified in the Three Gorges Reservoir Area (TGRA) using functional distinctiveness and geographical restrictiveness, with seven fish species (9%) classified as potentially ecologically rare including three species in this investigation. RPA-CRISPR/Cas12a-FQ outperformed high-throughput sequencing (HTS) and qPCR in detecting low-abundance eDNA (AUC = 0.883∗∗). A significant linear correlation (R2 = 0.682∗∗) between RPA-CRISPR/Cas12a-FQ and HTS quantification suggests its potential for predicting species abundance and enhancing eDNA-based fish biodiversity monitoring. This study highlights the value of RPA-CRISPR/Cas12a-FQ as a tool for advancing eDNA research and conservation efforts.http://www.sciencedirect.com/science/article/pii/S2589004223015961EcologyBiological sciencesMolecular biology |
| spellingShingle | Xing-Yi Wei Li Liu Huan Hu Huang-Jie Jia Ling-Kang Bu De-Sheng Pei Ultra-sensitive detection of ecologically rare fish from eDNA samples based on the RPA-CRISPR/Cas12a technology iScience Ecology Biological sciences Molecular biology |
| title | Ultra-sensitive detection of ecologically rare fish from eDNA samples based on the RPA-CRISPR/Cas12a technology |
| title_full | Ultra-sensitive detection of ecologically rare fish from eDNA samples based on the RPA-CRISPR/Cas12a technology |
| title_fullStr | Ultra-sensitive detection of ecologically rare fish from eDNA samples based on the RPA-CRISPR/Cas12a technology |
| title_full_unstemmed | Ultra-sensitive detection of ecologically rare fish from eDNA samples based on the RPA-CRISPR/Cas12a technology |
| title_short | Ultra-sensitive detection of ecologically rare fish from eDNA samples based on the RPA-CRISPR/Cas12a technology |
| title_sort | ultra sensitive detection of ecologically rare fish from edna samples based on the rpa crispr cas12a technology |
| topic | Ecology Biological sciences Molecular biology |
| url | http://www.sciencedirect.com/science/article/pii/S2589004223015961 |
| work_keys_str_mv | AT xingyiwei ultrasensitivedetectionofecologicallyrarefishfromednasamplesbasedontherpacrisprcas12atechnology AT liliu ultrasensitivedetectionofecologicallyrarefishfromednasamplesbasedontherpacrisprcas12atechnology AT huanhu ultrasensitivedetectionofecologicallyrarefishfromednasamplesbasedontherpacrisprcas12atechnology AT huangjiejia ultrasensitivedetectionofecologicallyrarefishfromednasamplesbasedontherpacrisprcas12atechnology AT lingkangbu ultrasensitivedetectionofecologicallyrarefishfromednasamplesbasedontherpacrisprcas12atechnology AT deshengpei ultrasensitivedetectionofecologicallyrarefishfromednasamplesbasedontherpacrisprcas12atechnology |