Ecological forensic testing: Using multiple primers for eDNA detection of marine vertebrates in an estuarine lagoon subject to anthropogenic influences

• Published in: Gene Vol. 928; p. 148720
• Main Authors: Chiquillo, Kelcie L., Wong, Juliet M., Eirin-Lopez, Jose M.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 30.11.2024
• Subjects: aquatic ecosystems; Biodiversity; Biscayne Bay; DNA barcoding; ecosystem management; environmental DNA; Environmental Stress; estuaries; fish; Florida; forensic sciences; genes; humans; Metabarcoding; Monitoring; pollution; risk; species; species diversity; traffic; Trichechus manatus; Urbanization; Vertebrates; Florida; mM; Metabarcoding; DI; Biscayne Bay; HABs; Biodiversity; L; Niskin; BSA; R; UF ICBR; kb; NCBI; BLASTN; eDNA; Monitoring; MIDORI2; UV; km; ASV; rRNA; Environmental Stress; Vertebrates; Chordates; IUCN; DNA; Urbanization; MarVer1; µM; MiFish; MarVer3; PCR
• ISSN: 0378-1119; 1879-0038; 1879-0038
• DOI: 10.1016/j.gene.2024.148720

[Display omitted] •Implemented eDNA in areas where monitoring methods are challenging to conduct.•Detected commercial, recreational, invasive, cryptic, and endangered vertebrates.•Results support eDNA analyses as a valuable tool for ecosystem management.•Emphasizing the importance of using a multi-marker approach. Many critical aquatic habitats are in close proximity to human activity (i.e., adjacent to residences, docks, marinas, etc.), and it is vital to monitor biodiversity in these and similar areas that are subject to ongoing urbanization, pollution, and other environmental disruptions. Environmental DNA (eDNA) metabarcoding is an accessible, non-invasive genetic technique used to detect and monitor species diversity and is a particularly useful approach in areas where traditional biodiversity monitoring methods (e.g., visual surveys or video surveillance) are challenging to conduct. In this study, we implemented an eDNA approach that used a combination of three distinct PCR primer sets to detect marine vertebrates within a canal system of Biscayne Bay, Florida, an ecosystem representative of challenging sampling conditions and a myriad of impacts from urbanization. We detected fish species from aquarium, commercial, and recreational fisheries, as well as invasive, cryptobenthic, and endangered vertebrate species, including charismatic marine mammals such as the protected West Indian manatee, Trichechus manatus. Our results support the potential for eDNA analyses to supplement traditional biodiversity monitoring methods and ultimately serve as an important tool for ecosystem management. This approach minimizes stress or disturbance to organisms and removes the intrinsic risk and logical limitations of SCUBA diving, snorkeling, or deploying sensitive equipment in areas that are subject to high vessel traffic and/or low visibility. Overall, this work sets the framework to understand how biodiversity may change over different spatial and temporal scales in an aquatic ecosystem heavily influenced by urbanization and validates the use of eDNA as a complementary approach to traditional ecological monitoring methods.