Molecular Diet Analysis of Asian Clams for Supplementary Biodiversity Monitoring: A Case Study of Nakdong River Estuary
Environmental DNA (eDNA) extracted from the gut contents of filter feeders can be used to identify biodiversity in aquatic ecosystems. In this study, we used eDNA from the gut contents of the Asian clam <i>Corbicula fluminea</i> to examine biodiversity within estuarine ecosystem. Field s...
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MDPI AG
2023-09-01
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| author | Kanghui Kim Gea-Jae Joo Kwang-Seuk Jeong Jeong-Soo Gim Yerim Lee Donghyun Hong Hyunbin Jo |
| author_facet | Kanghui Kim Gea-Jae Joo Kwang-Seuk Jeong Jeong-Soo Gim Yerim Lee Donghyun Hong Hyunbin Jo |
| author_sort | Kanghui Kim |
| collection | DOAJ |
| description | Environmental DNA (eDNA) extracted from the gut contents of filter feeders can be used to identify biodiversity in aquatic ecosystems. In this study, we used eDNA from the gut contents of the Asian clam <i>Corbicula fluminea</i> to examine biodiversity within estuarine ecosystem. Field sampling was conducted at three points in the Nakdong River Estuary, which is characterised by closed estuarine features resulting from the presence of an estuarine barrage. The collected <i>C. fluminea</i> samples were dissected to separate the gut contents, and the extracted eDNA was amplified using 18S V9 primer targeting all eukaryote-derived DNA. The amplified DNA was sequenced using a next-generation sequencing (NGS) technique, and a BLASTn search was performed based on the National Centre for Biotechnology Information (NCBI) database for taxa identification. We obtained 23 unique operational taxonomic units (OTUs), including fish (approximately 8.70%), copepods (approximately 17.39%), and green algae (approximately 21.74%), representing a wide range of habitats. Furthermore, 8 out of the 20 families were identified through comparisons with reference data from conventional field surveys, and the OTUs of elusive migratory fish were detected. The results support the application of <i>C. fluminea</i> as an eDNA sampler for supplementary biodiversity monitoring. |
| first_indexed | 2024-03-10T23:01:09Z |
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| issn | 2079-7737 |
| language | English |
| last_indexed | 2024-03-10T23:01:09Z |
| publishDate | 2023-09-01 |
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| spelling | doaj.art-27fb8964f7864c90b57ace2428f24ff52023-11-19T09:39:03ZengMDPI AGBiology2079-77372023-09-01129124510.3390/biology12091245Molecular Diet Analysis of Asian Clams for Supplementary Biodiversity Monitoring: A Case Study of Nakdong River EstuaryKanghui Kim0Gea-Jae Joo1Kwang-Seuk Jeong2Jeong-Soo Gim3Yerim Lee4Donghyun Hong5Hyunbin Jo6Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of KoreaDepartment of Integrated Biological Science, Pusan National University, Busan 46241, Republic of KoreaDepartment of Nursing Science, Busan Health University, Busan 49318, Republic of KoreaDepartment of Integrated Biological Science, Pusan National University, Busan 46241, Republic of KoreaDepartment of Integrated Biological Science, Pusan National University, Busan 46241, Republic of KoreaDepartment of Integrated Biological Science, Pusan National University, Busan 46241, Republic of KoreaDepartment of Integrated Biological Science, Pusan National University, Busan 46241, Republic of KoreaEnvironmental DNA (eDNA) extracted from the gut contents of filter feeders can be used to identify biodiversity in aquatic ecosystems. In this study, we used eDNA from the gut contents of the Asian clam <i>Corbicula fluminea</i> to examine biodiversity within estuarine ecosystem. Field sampling was conducted at three points in the Nakdong River Estuary, which is characterised by closed estuarine features resulting from the presence of an estuarine barrage. The collected <i>C. fluminea</i> samples were dissected to separate the gut contents, and the extracted eDNA was amplified using 18S V9 primer targeting all eukaryote-derived DNA. The amplified DNA was sequenced using a next-generation sequencing (NGS) technique, and a BLASTn search was performed based on the National Centre for Biotechnology Information (NCBI) database for taxa identification. We obtained 23 unique operational taxonomic units (OTUs), including fish (approximately 8.70%), copepods (approximately 17.39%), and green algae (approximately 21.74%), representing a wide range of habitats. Furthermore, 8 out of the 20 families were identified through comparisons with reference data from conventional field surveys, and the OTUs of elusive migratory fish were detected. The results support the application of <i>C. fluminea</i> as an eDNA sampler for supplementary biodiversity monitoring.https://www.mdpi.com/2079-7737/12/9/1245<i>Corbicula fluminea</i>eDNA metabarcodingconventional field surveynext-generation sequencing18S V9 |
| spellingShingle | Kanghui Kim Gea-Jae Joo Kwang-Seuk Jeong Jeong-Soo Gim Yerim Lee Donghyun Hong Hyunbin Jo Molecular Diet Analysis of Asian Clams for Supplementary Biodiversity Monitoring: A Case Study of Nakdong River Estuary Biology <i>Corbicula fluminea</i> eDNA metabarcoding conventional field survey next-generation sequencing 18S V9 |
| title | Molecular Diet Analysis of Asian Clams for Supplementary Biodiversity Monitoring: A Case Study of Nakdong River Estuary |
| title_full | Molecular Diet Analysis of Asian Clams for Supplementary Biodiversity Monitoring: A Case Study of Nakdong River Estuary |
| title_fullStr | Molecular Diet Analysis of Asian Clams for Supplementary Biodiversity Monitoring: A Case Study of Nakdong River Estuary |
| title_full_unstemmed | Molecular Diet Analysis of Asian Clams for Supplementary Biodiversity Monitoring: A Case Study of Nakdong River Estuary |
| title_short | Molecular Diet Analysis of Asian Clams for Supplementary Biodiversity Monitoring: A Case Study of Nakdong River Estuary |
| title_sort | molecular diet analysis of asian clams for supplementary biodiversity monitoring a case study of nakdong river estuary |
| topic | <i>Corbicula fluminea</i> eDNA metabarcoding conventional field survey next-generation sequencing 18S V9 |
| url | https://www.mdpi.com/2079-7737/12/9/1245 |
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