Environmental DNA(eDNA)originates from cellular material shed by organisms into aquatic or terrestrial environments and can be sampled and monitored using metabarcoding technology,which is revolutionizing fish biodive...Environmental DNA(eDNA)originates from cellular material shed by organisms into aquatic or terrestrial environments and can be sampled and monitored using metabarcoding technology,which is revolutionizing fish biodiversity monitoring.Several reviews concerning fish eDNA have focused on standard sampling methods and its applications,though a systematic review focused on marker genes,databases,and bioinformatic pipelines has not yet been published.Here,we present a comprehensive literature review of studies applying metabarcoding technology to fish eDNA for the purpose of fish biodiversity monitoring.We systematically provide the available universal primers used to amplify barcoding sequences from fish eDNA,and then discuss reference barcoding databases,relevant bioinformatic analyses,as well as developed pipelines.The performances of universal primers and their relevant reference databases are summarized.Combined use of multiple primer pairs targeted for more than one gene marker(e.g.,12S,16S,Cytb,COI),and use of both local and public databases are recommended as approaches to improve the sensitivity and reliability of fish eDNA analyses.We also compare the effectiveness of eDNA metabarcoding to traditional approaches for monitoring fish biodiversity and highlight challenges and future perspectives associated with this new tool.Ultimately,we advocate for greater incorporation of eDNA analysis into fish biodiversity assessments to assist environmental managers.展开更多
We surveyed the distribution, composition and diversity of freshwater fish in Hong Kong, China from 2002 to 2004. Sites surveyed were mainly streams, marshes and estuaries. There are ponds for aquaculture and reservoi...We surveyed the distribution, composition and diversity of freshwater fish in Hong Kong, China from 2002 to 2004. Sites surveyed were mainly streams, marshes and estuaries. There are ponds for aquaculture and reservoirs in Hong Kong but no large natural water bodies. From the 220 sites surveyed, 114 species of 37 families were found. Gobiidae (with 24 species) and Cyprinidae (21 species) were the dominant families. This survey has increased the number of freshwater fish species recorded in Hong Kong to 167. Among these, 71 (42.5%) are primary freshwater fish, 44 are brackish and 46 are vagrants. The remaining 6 species are diadromous. In Hong Kong, freshwater fish are conserved by a combination of measures. About 38% of Hong Kong’s land area is designated as country parks and/or special areas, and is managed for nature conservation and educational purposes. In addition, another 5% of land area is zoned for conservation in the statutory land use zoning system to protect them from development and incompatible land uses. Major development projects have to go through the statutory environmental impact assessment process to ensure that they will not have adverse impact as far as practicable. There are conservation action plans for important species. For example, captive-bred individuals of the endemic Hong Kong Paradise Fish Macropodus hongkongensis have been released to suitable and secure sites inside country parks and their populations are regularly monitored. Other measures such as wetland creation, restoration and enhancement programmes are also implemented for freshwater fish conservation.展开更多
基金supported by the grant from the Graduate Student Research Innovation Project of Chongqing(CYB20093)。
文摘Environmental DNA(eDNA)originates from cellular material shed by organisms into aquatic or terrestrial environments and can be sampled and monitored using metabarcoding technology,which is revolutionizing fish biodiversity monitoring.Several reviews concerning fish eDNA have focused on standard sampling methods and its applications,though a systematic review focused on marker genes,databases,and bioinformatic pipelines has not yet been published.Here,we present a comprehensive literature review of studies applying metabarcoding technology to fish eDNA for the purpose of fish biodiversity monitoring.We systematically provide the available universal primers used to amplify barcoding sequences from fish eDNA,and then discuss reference barcoding databases,relevant bioinformatic analyses,as well as developed pipelines.The performances of universal primers and their relevant reference databases are summarized.Combined use of multiple primer pairs targeted for more than one gene marker(e.g.,12S,16S,Cytb,COI),and use of both local and public databases are recommended as approaches to improve the sensitivity and reliability of fish eDNA analyses.We also compare the effectiveness of eDNA metabarcoding to traditional approaches for monitoring fish biodiversity and highlight challenges and future perspectives associated with this new tool.Ultimately,we advocate for greater incorporation of eDNA analysis into fish biodiversity assessments to assist environmental managers.
基金the comprehensive ecological baseline survey programme of the Department of Agriculture ,Fisheries and Conservation
文摘We surveyed the distribution, composition and diversity of freshwater fish in Hong Kong, China from 2002 to 2004. Sites surveyed were mainly streams, marshes and estuaries. There are ponds for aquaculture and reservoirs in Hong Kong but no large natural water bodies. From the 220 sites surveyed, 114 species of 37 families were found. Gobiidae (with 24 species) and Cyprinidae (21 species) were the dominant families. This survey has increased the number of freshwater fish species recorded in Hong Kong to 167. Among these, 71 (42.5%) are primary freshwater fish, 44 are brackish and 46 are vagrants. The remaining 6 species are diadromous. In Hong Kong, freshwater fish are conserved by a combination of measures. About 38% of Hong Kong’s land area is designated as country parks and/or special areas, and is managed for nature conservation and educational purposes. In addition, another 5% of land area is zoned for conservation in the statutory land use zoning system to protect them from development and incompatible land uses. Major development projects have to go through the statutory environmental impact assessment process to ensure that they will not have adverse impact as far as practicable. There are conservation action plans for important species. For example, captive-bred individuals of the endemic Hong Kong Paradise Fish Macropodus hongkongensis have been released to suitable and secure sites inside country parks and their populations are regularly monitored. Other measures such as wetland creation, restoration and enhancement programmes are also implemented for freshwater fish conservation.
