Surveillance of a federally protected freshwater fish using
loop-mediated isothermal amplification (LAMP) and eDNA
Abstract
Environmental DNA (eDNA) has increasingly been used in the surveillance
of imperiled aquatic species. Despite recent efforts in drawing genetic
material from the environment, there are still pitfalls surrounding this
field. We created a novel protocol which implements loop-mediated
isothermal amplification (LAMP) to detect target DNA. Our methods are
applied here in the surveillance of Etheostoma trisella, the
Trispot Darter, a freshwater fish that recently received protection
under the U.S. Endangered Species Act. Water samples (n = 256) were
collected at sites in Alabama and Georgia to determine whether E.
trisella still occupies historic sites and whether it inhabits
previously unknown areas. We found evidence of E. trisella
presence in 69 water samples while 187 were negative. Our LAMP protocol
is capable of amplifying low quantities of DNA in the water, and is a
robust technique for freshwater species surveillance. Verification of
positive results from eDNA experiments is essential to confirm reaction
reliability. Application of methods such as ours are necessary for
recognizing species under threat that require conservation.