The CALeDNA program: Citizen scientists and researchers inventory California's biodiversity

Abstract

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.

Landscape analyses using eDNA metabarcoding and Earth observation predict community biodiversity in California

“…2016, Meyer et␣al. 2021), which can be probed for nearly any taxonomic group using multi‐locus metabarcoding methods (Bohmann et␣al. 2014, Deiner et␣al.…”

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

“…Our highest ranked candidate bioindicators, with rank values of 6 ( Cynobium sp., Aspergillus flavus , and Talaromyces helicus ) were previously identified as key associated taxa in invasive P. clarkii or C. chelax in Italy and Australia (Dörr et al, 2012; Foysal et al, 2019; Garzoli et al, 2014). In our study, out of 1003 total eDNA samples from across the state of California (Meyer et al, 2021), Cynobium sp . and Talaromyces helicus were only found in samples in the Coachella Valley, suggesting that they may thrive in desert environments where crayfish are present.…”

“…We vetted these candidate bioindicator taxa in multiple ways. 1) We scored geographic distribution by cross referencing each taxon within 1000 eDNA samples collected across California that used the same assay (CALeDNA publicly available data, ucedna.com; Meyer et al, 2021). Bioindicators that were present in most of these samples were given a low score because they are clearly not likely to be crayfish-specific based on distribution.…”

“…Environmental DNA (eDNA) is an increasingly popular tool for biodiversity monitoring across landscapes and taxa. Using eDNA, reliable biodiversity surveys can be quickly and easily obtained by land managers and community scientists without need for expertise in field methods or taxonomy (Meyer et al, 2021; Suarez-Menendez et al, 2020). These approaches are particularly promising for invasive species monitoring and conservation projects (Ficetola et al, 2008; Sepulveda et al, 2020) because they make it possible for managers to simultaneously monitor biodiversity and detect invasive species using a single technique.…”

Environmental DNA Methods for Ecological Monitoring and Biodiversity Assessment in Estuaries

“…Some methodological testing and optimization (for example, determining primer sets that could efficiently detect organisms to the required taxonomic level) would be needed to apply this robustly for SFE management purposes, but there are published methods that provide a path forward for such "Tree of Life" ecosystem biomonitoring (Stat et al 2017). For example, the California Environmental DNA (CALeDNA) project is large-scale, taxonomically broad biodiversity monitoring program that uses eDNA metabarcoding to detect microbes, fungi, plants, and animals across the state of California from soil and sediment samples (Meyer et al 2021). Programs such as this, providing eDNA results as open data, can help show which substrates and molecular markers have been successfully used to detect target taxa and could inform how to efficiently implement eDNA metabarcoding biomonitoring in the SFE.…”