Comparison of Environmental DNA Metabarcoding and Underwater Visual Census for Assessing Macrobenthic Diversity
The rapid advancement of environmental DNA (eDNA) technology has transformed ecological research, particularly in aquatic ecosystems. However, the optimal sampling matrix (e.g., water or sediment) and the potential for eDNA to replace or complement traditional underwater visual census (UVC) remain u...
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MDPI AG
2025-07-01
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| author | Zifeng Zhan Weiwei Huo Shangwei Xie Wandong Chen Xinming Liu Kuidong Xu Yanli Lei |
| author_facet | Zifeng Zhan Weiwei Huo Shangwei Xie Wandong Chen Xinming Liu Kuidong Xu Yanli Lei |
| author_sort | Zifeng Zhan |
| collection | DOAJ |
| description | The rapid advancement of environmental DNA (eDNA) technology has transformed ecological research, particularly in aquatic ecosystems. However, the optimal sampling matrix (e.g., water or sediment) and the potential for eDNA to replace or complement traditional underwater visual census (UVC) remain unclear. Here, we integrate water eDNA, sediment eDNA, and UVC approaches to systematically compare the diversity of benthic macrofauna in the subtidal zones of the Nanji Islands, China. Our results show that sediment eDNA samples exhibited the highest species richness, while UVC had the lowest. Each method revealed distinct species profiles, with relatively few shared taxa at the order level and below. Environmental eDNA showed significant advantages in detecting key phyla such as Annelida and Arthropoda. In contrast, traditional UVC was crucial for identifying certain taxa, such as Bryozoa, which were undetectable by eDNA methods. The low overlap in species detected by these methods underscores their complementary nature, highlighting the necessity of integrating multiple approaches to achieve a more comprehensive and accurate biodiversity assessment. Future research should focus on refining eDNA techniques, such as developing more universal primers, to further enhance their applicability in biodiversity monitoring. |
| format | Article |
| id | doaj-art-171fed76310e4c6690e7c168eb6fcdb2 |
| institution | Kabale University |
| issn | 2079-7737 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | MDPI AG |
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| series | Biology |
| spelling | doaj-art-171fed76310e4c6690e7c168eb6fcdb22025-08-20T03:32:24ZengMDPI AGBiology2079-77372025-07-0114782110.3390/biology14070821Comparison of Environmental DNA Metabarcoding and Underwater Visual Census for Assessing Macrobenthic DiversityZifeng Zhan0Weiwei Huo1Shangwei Xie2Wandong Chen3Xinming Liu4Kuidong Xu5Yanli Lei6Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, ChinaLaboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, ChinaNanji Islands National Marine Nature Reserve Administration, Wenzhou 325400, ChinaNanji Islands National Marine Nature Reserve Administration, Wenzhou 325400, ChinaInstitutes of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, ChinaLaboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, ChinaLaboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, ChinaThe rapid advancement of environmental DNA (eDNA) technology has transformed ecological research, particularly in aquatic ecosystems. However, the optimal sampling matrix (e.g., water or sediment) and the potential for eDNA to replace or complement traditional underwater visual census (UVC) remain unclear. Here, we integrate water eDNA, sediment eDNA, and UVC approaches to systematically compare the diversity of benthic macrofauna in the subtidal zones of the Nanji Islands, China. Our results show that sediment eDNA samples exhibited the highest species richness, while UVC had the lowest. Each method revealed distinct species profiles, with relatively few shared taxa at the order level and below. Environmental eDNA showed significant advantages in detecting key phyla such as Annelida and Arthropoda. In contrast, traditional UVC was crucial for identifying certain taxa, such as Bryozoa, which were undetectable by eDNA methods. The low overlap in species detected by these methods underscores their complementary nature, highlighting the necessity of integrating multiple approaches to achieve a more comprehensive and accurate biodiversity assessment. Future research should focus on refining eDNA techniques, such as developing more universal primers, to further enhance their applicability in biodiversity monitoring.https://www.mdpi.com/2079-7737/14/7/821eDNAspecies detection efficiencymarine protected areasubtidal zonebiodiversity assessment |
| spellingShingle | Zifeng Zhan Weiwei Huo Shangwei Xie Wandong Chen Xinming Liu Kuidong Xu Yanli Lei Comparison of Environmental DNA Metabarcoding and Underwater Visual Census for Assessing Macrobenthic Diversity Biology eDNA species detection efficiency marine protected area subtidal zone biodiversity assessment |
| title | Comparison of Environmental DNA Metabarcoding and Underwater Visual Census for Assessing Macrobenthic Diversity |
| title_full | Comparison of Environmental DNA Metabarcoding and Underwater Visual Census for Assessing Macrobenthic Diversity |
| title_fullStr | Comparison of Environmental DNA Metabarcoding and Underwater Visual Census for Assessing Macrobenthic Diversity |
| title_full_unstemmed | Comparison of Environmental DNA Metabarcoding and Underwater Visual Census for Assessing Macrobenthic Diversity |
| title_short | Comparison of Environmental DNA Metabarcoding and Underwater Visual Census for Assessing Macrobenthic Diversity |
| title_sort | comparison of environmental dna metabarcoding and underwater visual census for assessing macrobenthic diversity |
| topic | eDNA species detection efficiency marine protected area subtidal zone biodiversity assessment |
| url | https://www.mdpi.com/2079-7737/14/7/821 |
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