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Bhendarkar M, Rodriguez-Ezpeleta N. Exploring uncharted territory: new frontiers in environmental DNA for tropical fisheries management. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:617. [PMID: 38874640 DOI: 10.1007/s10661-024-12788-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
Tropical ecosystems host a significant share of global fish diversity contributing substantially to the global fisheries sector. Yet their sustainable management is challenging due to their complexity, diverse life history traits of tropical fishes, and varied fishing techniques involved. Traditional monitoring techniques are often costly, labour-intensive, and/or difficult to apply in inaccessible sites. These limitations call for the adoption of innovative, sensitive, and cost-effective monitoring solutions, especially in a scenario of climate change. Environmental DNA (eDNA) emerges as a potential game changer for biodiversity monitoring and conservation, especially in aquatic ecosystems. However, its utility in tropical settings remains underexplored, primarily due to a series of challenges, including the need for a comprehensive barcode reference library, an understanding of eDNA behaviour in tropical aquatic environments, standardized procedures, and supportive biomonitoring policies. Despite these challenges, the potential of eDNA for sensitive species detection across varied habitats is evident, and its global use is accelerating in biodiversity conservation efforts. This review takes an in-depth look at the current state and prospects of eDNA-based monitoring in tropical fisheries management research. Additionally, a SWOT analysis is used to underscore the opportunities and threats, with the aim of bridging the knowledge gaps and guiding the more extensive and effective use of eDNA-based monitoring in tropical fisheries management. Although the discussion applies worldwide, some specific experiences and insights from Indian tropical fisheries are shared to illustrate the practical application and challenges of employing eDNA in a tropical context.
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Affiliation(s)
- Mukesh Bhendarkar
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), 48395, Sukarrieta, Bizkaia, Spain.
- ICAR-National Institute of Abiotic Stress Management, Baramati, 413 115, Maharashtra, India.
| | - Naiara Rodriguez-Ezpeleta
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), 48395, Sukarrieta, Bizkaia, Spain
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Yoshitake K, Yanagisawa K, Sugimoto Y, Nakamura H, Mizusawa N, Miya M, Hamasaki K, Kobayashi T, Watabe S, Nishikiori K, Asakawa S. Pilot study of a comprehensive resource estimation method from environmental DNA using universal D-loop amplification primers. Funct Integr Genomics 2023; 23:96. [PMID: 36947319 PMCID: PMC10033627 DOI: 10.1007/s10142-023-01013-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/23/2023]
Abstract
Many studies have investigated the ability of environmental DNA (eDNA) to identify the species. However, when individual species are to be identified, accurate estimation of their abundance using traditional eDNA analyses is still difficult. We previously developed a novel analytical method called HaCeD-Seq (haplotype count from eDNA by sequencing), which focuses on the mitochondrial D-loop sequence for eels and tuna. In this study, universal D-loop primers were designed to enable the comprehensive detection of multiple fish species by a single sequence. To sequence the full-length D-loop with high accuracy, we performed nanopore sequencing with unique molecular identifiers (UMI). In addition, to determine the D-loop reference sequence, whole genome sequencing was performed with thin coverage, and complete mitochondrial genomes were determined. We developed a UMI-based Nanopore D-loop sequencing analysis pipeline and released it as open-source software. We detected 5 out of 15 species (33%) and 10 haplotypes out of 35 individuals (29%) among the detected species. This study demonstrates the possibility of comprehensively obtaining information related to population size from eDNA. In the future, this method can be used to improve the accuracy of fish resource estimation, which is currently highly dependent on fishing catches.
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Affiliation(s)
- Kazutoshi Yoshitake
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, 113-8657, Tokyo, Japan
| | - Kyohei Yanagisawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, 113-8657, Tokyo, Japan
| | - Yuma Sugimoto
- Tokyo Sea Life Park, 6-2-3 Rinkai-cho, Edogawa-ku, 134-8587, Tokyo, Japan
| | - Hiroshi Nakamura
- Tokyo Sea Life Park, 6-2-3 Rinkai-cho, Edogawa-ku, 134-8587, Tokyo, Japan
| | - Nanami Mizusawa
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Kanagawa, 252-0373, Sagamihara, Japan
| | - Masaki Miya
- Department of Collection Management, Natural History Museum and Institute, Chiba, 260-8682, Japan
| | - Koji Hamasaki
- Department of Marine Ecosystem Science, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takanori Kobayashi
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Kanagawa, 252-0373, Sagamihara, Japan
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Kanagawa, 252-0373, Sagamihara, Japan
| | - Kazuomi Nishikiori
- Tokyo Sea Life Park, 6-2-3 Rinkai-cho, Edogawa-ku, 134-8587, Tokyo, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, 113-8657, Tokyo, Japan.
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Huang S, Yoshitake K, Watabe S, Asakawa S. Environmental DNA study on aquatic ecosystem monitoring and management: Recent advances and prospects. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 323:116310. [PMID: 36261997 DOI: 10.1016/j.jenvman.2022.116310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Environmental DNA (eDNA) is organismal DNA that can be detected in the environment and is derived from cellular material of organisms shed into aquatic or terrestrial environments. It can be sampled and monitored using molecular methods, which is important for the early detection of invasive and native species as well as the discovery of rare and cryptic species. While few reviews have summarized the latest findings on eDNA for most aquatic animal categories in the aquatic ecosystem, especially for aquatic eDNA processing and application. In the present review, we first performed a bibliometric network analysis of eDNA studies on aquatic animals. Subsequently, we summarized the abiotic and biotic factors affecting aquatic eDNA occurrence. We also systematically discussed the relevant experiments and analyses of aquatic eDNA from various aquatic organisms, including fish, molluscans, crustaceans, amphibians, and reptiles. Subsequently, we discussed the major achievements of eDNA application in studies on the aquatic ecosystem and environment. The application of eDNA will provide an entirely new paradigm for biodiversity conservation, environment monitoring, and aquatic species management at a global scale.
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Affiliation(s)
- Songqian Huang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 200120, China; Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, 113-8657, Japan.
| | - Kazutoshi Yoshitake
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University, Minami-ku, Sagamihara, Kanagawa, 252-0313, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, 113-8657, Japan.
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