Environmental DNA reveals invasive crayfish microbial associates and ecosystem-wide biodiversity before and after eradication

Abstract

Biodiversity monitoring in conservation projects is essential to understand environmental status and recovery. However, traditional field surveys can be biased towards visual detection and/or focused on measuring the biodiversity of a limited set of taxa. Environmental DNA (eDNA) methods provide a new approach to biodiversity monitoring that has the potential to sample a taxonomically broader set of organisms with similar effort, but these approaches are still in the early stages of development and testing. Here, we explore the utility of multilocus eDNA metabarcoding to explore the impact on local biodiversity of removal of the red swamp crayfish, a globally invasive species, from a desert oasis ecosystem. We tracked crayfish DNA signatures, microbial DNA associated with crayfish, and biodiversity changes of plant, fungal, animal, and bacterial communities through time. We were unsuccessful in detecting crayfish in control tanks or oases using targeted metabarcoding primers for invertebrates and eukaryotes. Metabarcoding of the 16S (targeting prokaryotes) and the ITS1 (targeting fungi) loci in the invaded oasis and tanks pre-removal were, however, successful in discerning a suite of 90 crayfish-associated taxa to serve as candidate bioindicators of invasive presence. Ranking these 90 taxa by their geographic distribution in eDNA surveys and by evidence of crayfish-associations in the literature, we support 9 taxa to be high-ranking, and suggest they be prioritized in future biomonitoring. Biodiversity analyses from five metabarcode loci including plants, animals, and both prokaryotic and eukaryotic microbes showed that communities differed but that species richness remained relatively similar between oases through time. Our results reveal that, while there are limitations of eDNA approaches to detect crayfish and other invasive species, microbial bioindicators offer a largely untapped biomonitoring opportunity for invasive species management, adding a valuable resource to a conservation manager’s toolkit.

Proteinase K is not essential for marine eDNA metabarcoding

“…We investigated whether the proportions of ProK typically used for blood and tissue DNA extractions were necessary for eDNA water samples from oligotrophic marine environments. We found no significant effect on the diversity and composition of recovered taxa among ProK quantities including none—even with taxa such as Malacostracan Arthropods that are known to be difficult to detect in eDNA samples (Ballare et al., 2023). Unlike studies showing that the addition of ProK increased DNA yield for targeted species (human genomic DNA in blood samples—Qamar et al., 2017; common carp, Cyptinus carpio carpio , from eDNA water samples — Tsuji et al., 2017), there is no indication in our study that higher ProK amounts increased DNA yield or influenced the quantity of reads for any given ZOTU.…”