Journal
FISHERIES SCIENCE
Volume 86, Issue 6, Pages 939-970Publisher
SPRINGER JAPAN KK
DOI: 10.1007/s12562-020-01461-x
Keywords
eDNA; Fish community; Biodiversity monitoring; Ecosystem-based fishery management; Ecosystem conservation
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Funding
- Japan Science and Technology Agency (JST) [JPMJCR13A2]
- Canon Foundation
- Environment Research and Technology Development Fund of the Ministry of the Environment, Japan [4-1602]
- Japan Society for the Promotion of Science KAKENHI [JP19H03291]
- Ministry of Education, Culture, Sports, Science and Technology
- Ocean Resource Use Promotion Technology Development Program [JPMXD0618068274]
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We reviewed the current methodology and practices of the DNA metabarcoding approach using a universal PCR primer pair MiFish, which co-amplifies a short fragment of fish DNA (approx. 170 bp from the mitochondrial 12S rRNA gene) across a wide variety of taxa. This method has mostly been applied to biodiversity monitoring using environmental DNA (eDNA) shed from fish and, coupled with next-generation sequencing technologies, has enabled massively parallel sequencing of several hundred eDNA samples simultaneously. Since the publication of its technical outline in 2015, this method has been widely used in various aquatic environments in and around the six continents, and MiFish primers have demonstrably outperformed other competing primers. Here, we outline the technical progress in this method over the last 5 years and highlight some case studies on marine, freshwater, and estuarine fish communities. Additionally, we discuss various applications of MiFish metabarcoding to non-fish organisms, single-species detection systems, quantitative biodiversity monitoring, and bulk DNA samples other than eDNA. By recognizing the MiFish eDNA metabarcoding strengths and limitations, we argue that this method is useful for ecosystem conservation strategies and the sustainable use of fishery resources in ecosystem-based fishery management through continuous biodiversity monitoring at multiple sites.
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