Environmental DNA (eDNA) for Early Detection of Invasive Aquatic Species and Endemic Fish Surveillance in Mojave Desert Spring Systems.

Authors: Duane Moser, Shohreh Mahdavinia, Alireza Saidi-Mehrabad, Yusuf Umar, Michael Schwemm

Year: 2025

Abstract

Spring-fed systems of the US Great Basin are home to an extraordinary diversity of endemic and/or threatened aquatic organisms — animals whose fortunes are tied to societal and hydrologic variables and competition/predation from invasive species. Aquatic organisms continuously shed DNA into their surroundings. This “environmental DNA (eDNA)” is detectable with exquisite sensitivity through quantitative Polymerase Chain Reaction (qPCR) and metabarcoding. Here we report on optimized sampling and DNA extraction protocols (e.g. high-volume filtration) and validation of published and custom-designed molecular probes (qPCR primer sets) utilizing mitogenome targets for a range of endemic and invasive species in spring-fed environments of the Mojave Desert. Published Metabarcoding fish primers (e.g. MiFish (12S rRNA gene)) were used to quantitatively document an ongoing mosquitofish (Gambusia affinis) invasion at the Shoshone pupfish refugium (Cyprinodon nevadensis shoshone) in Shoshone, CA. This sequence-based assay was also used to verify known and cryptic populations of Amargosa speckled dace (Rhinichthys osculus navadensis) in Amargosa River headwater springs and explore diversity of endemic and invasive fish assemblages on the Muddy and Virgin Rivers in Nevada. The river work established many species, but some highlights include the detection of strong populations of Virgin River Chub (Gila seminuda) in the Muddy and Virgin Rivers and chub, desert sucker (Catostomus clarkii) and speckled dace (Rinichthys osculus) in the Virgin. A rogue’s gallery of invasives was also present in both, especially the Virgin River below Mesquite, NV, where red shiner (Cyprinella lutrensis)), common carp (Cyprinus carpio), channel catfish (Ictalurus punctatus), largemouth bass (Micropterus salmoides) and green sunfish (Lepomis cyanellus) dominated. Conversely, blue tilapia (Oreochromis aureus), which have been eradicated from the Muddy and have been detected sporadically in the middle Virgin, were not detected, although they were easily detected in the Las Vegas Wash. Specialty assays developed by the lab included a sensitive and specific qPCR assay for endangered Moapa dace (Moapa coriacea) and new qCPR and metabarcoding primers for super-invasive red swamp crayfish (Procambarus clarkii), which have been tested at Ash Meadows, the largest oasis in the Mojave. Other work includes eDNA surveillance of an Australian redclaw crayfish invasion (Cherax quadricarinatus) at ponds associated with the Las Vegas Wash and a study of the microbiome of Devils Hole pupfish (Cyprinodon diabolis). This work illustrated that captive pupfish microbiomes were dependent upon aquaculture techniques, with only recirculating tanks (vs. flow-through) establishing populations of a commensal bacterium (Cetobacterium spp.) which is thought to assist the fish with ethanol metabolism, an adaptation of the fish for survival under low-dissolved oxygen.