JonahWater: Next Generation Sequencing

This assay amplifies either freshwater, or marine fish species. As a bonus, we get bycatch of mammals, birds, and amphibians. Fish are often targeted for aquatic eDNA detection as they readily shed DNA into their environment and they are already monitored in many places with traditional techniques. We’ve found that using eDNA yields comparable results to electrofishing and often picks up many species that traditional techniques miss. 

For phytoplankton, we use primers that target the 23S region, which amplify DNA for a variety of algal taxa including cyanobacteria. Monitoring periphyton and phytoplankton is useful when evaluating ecosystem health (such as nutrient loading, temperature, and salinity) and how it changes over time. Because of the difficulties of traditional identification of algae, there aren’t many Indices of Biotic Integrity based on algae. In the future, we envision phytoplankton to be a strong complement to DNA-based bioassessment based on other taxa.

Many current Indexes of Biotic Integrity depend on macroinvertebrates as indicator species. To assess macroinvertebrates with DNA, we can extract DNA from a filtered water sample, or a sample of collected macroinvertebrates, which we’ll homogenize and then sequence (no more sorting). Macroinvertebrate libraries need some improvement, but we can usually get it to family or genus level, which should be sufficient for bioassessment purposes. 

Characterizing mussel assemblages with eDNA is still a work in progress, e.g. we’re currently working on refining which mussel assay we will use to detect mussels. We know this assay is on a lot of eDNA wishlists, so contact us to find out where we’re at in the process. 

To amplify vertebrates, we can use a single, broad assay. However if you’re looking for the highest specificity for just fish or amphibians, we recommend using those assays for better resolution. For birds and mammals, the vertebrate assay is suitable. We’ve detected beavers, mountain lions, thrushes and ducks in the past. It doesn’t matter if these species are swimming in the water or getting a drink, we’re confident in our ability to detect them, provided you’re able to capture their DNA in your sample. 

Our plant eDNA assay is the same one we use for assessing the diets of herbivores (trnL). In water, detection of plants can be lower that expected. Aquatic plants seem to give off relatively little DNA for most of the year. Often, many of the hits are from terrestrial plants. Contact us to learn more about where we’re at.