Climate change is leading to habitat shifts that threaten species persistence throughout California's unique ecosystems. Baseline biodiversity data would provide opportunities for habitats to be managed under short-term and long-term environmental change. Aiming to provide biodiversity data, the UC Conservation Genomics Consortium launched the California Environmental DNA (CALeDNA) program to be a citizen and community science biomonitoring initiative that uses environmental DNA (eDNA, DNA shed from organisms such as from fur, feces, spores, pollen or leaves). Now with results from 1,000 samples shared online, California biodiversity patterns are discoverable. Soil, sediment and water collected by researchers, undergraduates and the public reveal a new catalog of thousands of organisms that only slightly overlap with traditional survey bioinventories. The CALeDNA website lets users explore the taxonomic diversity in different ways, and researchers have created tools to help people new to eDNA to analyze community ecology patterns. Although eDNA results are not always precise, the program team is making progress to fit it into California's biodiversity management toolbox, such as for monitoring ecosystem recovery after invasive species removal or wildfire.
Biodiversity monitoring in conservation projects is essential to understand environmental health, complexity, and recovery. However, traditional field surveys can be expensive, time‐consuming, biased toward visual detection, and/or only measure 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 a similar effort, but many of these approaches are still in the early stages of development and testing. Here, we used multi‐locus eDNA metabarcoding to understand how the removal of invasive red swamp crayfish using cypermethrin pesticide impacts local biodiversity of a desert oasis ecosystem, as well as to detect crayfish both directly and indirectly. We tracked crayfish DNA signatures, microbial DNA associated with crayfish, and biodiversity of plant, fungal, animal, and bacterial communities through time. We were unsuccessful in detecting crayfish directly in either control tanks or oases using targeted metabarcoding primers for invertebrates and eukaryotes, similar to previous studies which have shown variable levels of success in detecting crayfish from environmental samples. However, we were successful in discerning a suite of 90 crayfish‐associated taxa to serve as candidate bioindicators of invasive presence using 16S and fungal ITS2 metabarcoding. Ranking these 90 taxa by their geographic distribution in eDNA surveys and by evidence of crayfish associations in the literature, we support nine 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.
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.
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