1
|
Richards JL, Sheng V, Chung HWY, Liu M, Tsang RHH, McIlroy SE, Baker D. Development of an eDNA‐based survey method for urban fish markets. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- John L. Richards
- Swire Institute of Marine Science, School of Biological Sciences The University of Hong Kong Pokfulam Road Hong Kong SAR
| | - Victoria Sheng
- Swire Institute of Marine Science, School of Biological Sciences The University of Hong Kong Pokfulam Road Hong Kong SAR
| | - Haze Wing Yi Chung
- Swire Institute of Marine Science, School of Biological Sciences The University of Hong Kong Pokfulam Road Hong Kong SAR
| | - Min Liu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences Xiamen University Xiamen Fujian China
| | - Rainbow Hin Hung Tsang
- Swire Institute of Marine Science, School of Biological Sciences The University of Hong Kong Pokfulam Road Hong Kong SAR
| | - Shelby E. McIlroy
- Swire Institute of Marine Science, School of Biological Sciences The University of Hong Kong Pokfulam Road Hong Kong SAR
| | - David Baker
- Swire Institute of Marine Science, School of Biological Sciences The University of Hong Kong Pokfulam Road Hong Kong SAR
| |
Collapse
|
2
|
Sakata MK, Kawata MU, Kurabayashi A, Kurita T, Nakamura M, Shirako T, Kakehashi R, Nishikawa K, Hossman MY, Nishijima T, Kabamoto J, Miya M, Minamoto T. Development and evaluation of PCR primers for environmental DNA (eDNA) metabarcoding of Amphibia. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.76534] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Biodiversity monitoring is important for the conservation of natural ecosystems in general, but particularly for amphibians, whose populations are pronouncedly declining. However, amphibians’ ecological traits (e.g. nocturnal or aquatic) often prevent their precise monitoring. Environmental DNA (eDNA) metabarcoding – analysis of extra-organismal DNA released into the environment – allows the easy and effective monitoring of the biodiversity of aquatic organisms. Here, we developed and tested the utility of original PCR primer sets. First, we conducted in vitro PCR amplification tests with universal primer candidates using total DNA extracted from amphibian tissues. Five primer sets successfully amplified the target DNA fragments (partial 16S rRNA gene fragments of 160–311 bp) from all 16 taxa tested (from the three living amphibian orders Anura, Caudata and Gymnophiona). Next, we investigated the taxonomic resolution retrieved using each primer set. The results revealed that the universal primer set “Amph16S” had the highest resolution amongst the tested sets. Finally, we applied Amph16S to the water samples collected in the field and evaluated its detection capability by comparing the species detected using eDNA and physical survey (capture-based sampling and visual survey) in multiple agricultural ecosystems across Japan (160 sites in 10 areas). The eDNA metabarcoding with Amph16S detected twice as many species as the physical surveys (16 vs. 8 species, respectively), indicating the effectiveness of Amph16S in biodiversity monitoring and ecological research for amphibian communities.
Collapse
|