ECORP has continued to expand our Environmental DNA (eDNA) services to include monitoring of aquatic and terrestrial species richness in streams, reservoirs, floodplains, tidal habitats, and beyond. Using molecular assays allows us to determine the presence of a large number of aquatic species that can be difficult and time consuming to detect using traditional survey protocols. We use both quantitative polymerase chain reaction (qPCR) assays as well as metabarcoding assays, each of which has a unique approach for determining species’ presence. Our use of eDNA has proven to be a cost-effective approach for serving our clients’ needs and providing innovative solutions to challenging and complex problems associated with finding rare, elusive, or cryptic species.
qPCR is a molecular assay where species-specific sequences of DNA are amplified. These sequences are detected using fluorescent molecules that light up when the DNA sequence is copied, allowing the computer to precisely determine the number of copies made and therefore the starting number of DNA sequences present in the sample. This allows for a high level of sensitivity in detecting specific species of interest, as extremely small amounts of initial DNA are necessary for amplification using this method. In contrast, metabarcoding is a similar molecular assay that instead amplifies a general sequence of DNA, one that is shared among multiple taxa, that is also located near DNA regions of high variation between different species/taxa. This allows the DNA of many organisms in the sample to be amplified, as well as enabling the determination of the species composition within a sample. The limitation of this method is that it is less sensitive in the detection of specific species than qPCR, however it will detect a larger variety of organisms. Using both assays we are able to detect, with a high degree of sensitivity, species of special concern using qPCR, and we are also able to look at the aquatic community as a whole using metabarcoding.
In addition to our use of eDNA for evaluating the presence of animal species, we are currently employing qPCR to determine if Cannabis molecules from illegal cultivation sites are present in California water bodies. This novel approach will be utilized to detect and locate illegal Cannabis grow sites on public lands as part of a State-wide effort to identify, remediate, and restore illegal grow sites. Illegal Cannabis cultivation practices result in degradation of our natural resources, including reduced streamflow from illegal water diversions and degradation of water quality resulting from the use of toxic and unregulated fertilizers and pesticides.
Finally, we are currently investigating the potential use of both qPCR and metabarcoding for determining presence and species composition in bumble bee surveys, as these species can also be difficult to detect through standard survey protocols. Four bumblebee species are currently candidates for listing in the California Endangered Species Act, including Crotch’s bumble bee (Bombus crotchii), which has been found in some southern California project locations. There has been a marked decline in pollinator populations in recent years due to various factors such as habitat loss and increased pesticide use. These molecular assays would consist of the collection and testing of flowers that have potentially been visited by these insects. Bumble bees are known for a special pollination method, called buzz pollination. Many species of plants are specifically adapted to this type of pollination, in which the bumble bee grabs onto a flower and vibrates its body at a certain frequency causing the release of pollen that is often otherwise inaccessible.
In response to our expanded use and widespread acknowledgement of the benefits and cost-effectiveness of eDNA and metabarcoding, ECORP has convened an internal eDNA Working Group comprising biologists in all areas of species expertise to collaboratively discuss the benefits and limitations of using these services to better serve our clients. If you have a project that you think could benefit from these services, feel free to contact Dave Thomas at (916) 764-9288 or Jen West at (916) 316-9534.