JonahWater: Next Generation Sequencing

JonahWater Next Generation Sequencing (NGS) delivers insight into aquatic ecosystems assemblages

Our JonahWater NGS services answer questions about aquatic assemblages

NGS is useful for quantifying the composition of aquatic assemblages

NGS taxonomic groups include bacteria, phytoplankton, zooplankton, macroinvertebrates, higher plants, fish, and vertebrates

Our Next Generation Sequencing Assays

We pride ourselves in our transparancy. Take a look at the assays we offer to detect groups of species using 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. 


Amphibians are another species often used as indicator species due to their general intolerance of disturbance and poor water quality, whether it’s caused by habitat disturbance or pollution. Traditional surveys typically involve turning over rocks and disturbing aquatic habitats. eDNA sampling is minimally invasive, allowing researchers to leave habitat exactly as they found it. eDNA detects DNA from eggs, larvae, or adults indiscriminately.

Unionidae Mussels (under development)

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. 

Vertebrates (Vert12S)

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. 


Monitoring bacteria can be useful for evaluating changes across the landscape and can tell you a lot about the communities upstream, possible inputs, and disturbances. There is still a fair amount of work to do to interpret differences in aquatic bacterial assemblages though. 

Our Next Generation Sequencing Process

Example Next Generation Sequencing Data

Next Generation Sequencing excels at quantifying the relative abundance of species in an assemblage. Shown here are data on the proportions of different phytoplankton species from the length of the Potomac River. For each sample, approximately 100 mL of water were filtered. After collecting we then sequenced the filtered DNA using primers specific to all phytoplankton. Top four taxa are shown.


The phytoplankton assemblage was dominated by diatoms (Bacillariophyta), but different taxa dominated different regions. We also quantified abundances of cyanobacteria, chlorophytes, and eustigmatophyte. The patterns observed in the Potomac showed clear patterns of the effects of river size and eutrophication.


Whether it is for quantifying changes in assemblages over time, detecting invasive species, or comparing assemblages across sites, we can reconstruct the abundances of aquatic organisms using our JonahWater services.

Our Standard Deliverables

NGS Report Explained

Next Generation Sequencing Pricing

Batches of <15 samples require a fee of $150 for bioinformatics setup per taxonomic group

$5 surcharge for processing 45mm filters

Discounts available for large orders. Please contact to discuss.

If providing extracted DNA, samples are discounted $25/sample.

*Surcharge of $10 for fish metabarcoding due to increased number of replicates

Request your free quote today!

Water bodies to sample

Desired Technique

Organisms To Measure

Jonah Ventures
5485 Conestoga Ct #210, 
Boulder, CO 80301
(720) 515-6624