Methods-NYC/NJ fish eDNA Project
Link to NYC/NJ Fish eDNA home page
Download pdf NYC/NJ aquatic eDNA protocol (updated April 4, 2017)
Annotated references
Ficetola GF, Miaud C, Pompanon F, Taberlet P (2008) Species detection using environment DNA from water samples. Biol Lett 4:423-425 (open access link)
First demonstration of aquatic vertebrate eDNA detection; 15 mL water samples; ethanol ppt, spin, then extract DNA
Thomsen PF, Kielgast J, Iversen LL, Moller PR, Rasmussen M, Willerslev E (2012) Detection of diverse marine fish fauna using environmental DNA from seawater samples. PLOS ONE 7:e41732 (open access link)
Near shore marine fish along a pier; eDNA analysis equally or more effective than traditional methods; mostly used species-specific mtDNA primers; 30 x 50 mL samples pooled, then filtered 500 mL onto 47 mm diameter 0.45-µm pore size nylon filters (Osmonics, Penang, Malaysia); bead beating then Qiagen DNeasy
Thomasen PF, Kielgast J, Iversen LL, Wiuf C, Rasmussen M, Gilbert MTP, Orlando L, Willerslev E (2012) Monitoring endangered freshwater biodiversity using environmental DNA. Mol Ecol 21: 2565-2573 (link to abstract)
Detected endangered freshwater fish, frog, newt, river otter, and insects using species-specific qPCRs, also did 454 sequencing to confirm qPCR results; 3 x 15 mL samples per site, followed same ethanol ppt protocol as Ficetola 2008
Foote AD, Thomsen PF, Sveegaard S, Wahlberg M, Kielgast J, Kyhn LA, Salling AB, Galatius A, Orlando, Gilbert MTP (2012) Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals. PLOS ONE 7:e41781 (open access link)
Tested for dolphin DNA; 3/3 samples positive in or near captive dolphin pen; 1/8 samples positive near pen; 1/8 positive in open water sites where dolphins were nearby according to acoustic monitoring; also detected long-finned pilot whale; 3 x 15 mL each site; ethanol ppt, Qiagen extraction;
Kelly RP, Port JA, Yamahara KM, Crowder LB (2014) Using environmental DNA to census marine fish in a large mesocosm. PLOS ONE 9:e86175 (open access link)
Aquatic eDNA detection applied to 4.5 million liter Monterey Bay Aquarium; 12s RNA primers amplifying 106 bp fragment detected all bony fish, needed other primers for cartilaginous fish and turtles; 1 L samples vacuum filtered onto 0.22-µm Durapore membrane filters (Millipore, MA, USA); Qiagen extraction