Metabarcoding
JonahWater: Aquatic Metabarcoding
JonahWater Aquatic metabarcoding delivers insight into aquatic ecosystems assemblages
- Our JonahWater aquatic metabarcoding services answer questions about community assemblages
- Metabarcoding is useful for quantifying the composition of aquatic assemblages
- Metabarcoding taxonomic groups include bacteria, phytoplankton, zooplankton, macroinvertebrates, higher plants, fish, and vertebrates
We have more than 20 years experience in DNA Sequencing Technology.
Our Aquatic Metabarcoding Assays
We pride ourselves in our transparancy. Take a look at the assays we offer to detect groups of species using Next Generation Sequencing.
Fish
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.
Phytoplankton
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.
Macroinvertebrates
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
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
We can analyzing aquatic samples for unionid mussels. Our eDNA approach can identify species that may be difficult to observe through traditional survey methods. At Jonah Ventures, unionid metabarcoding is used to support mussel monitoring, species assessments, and conservation planning while reducing the need for invasive field efforts.
Vertebrates
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.
Plants
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.
Bacteria
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 Metabarcoding Process
Quantitative Metabarcoding
Metabarcoding has revolutionized biodiversity monitoring by allowing researchers to assess the presence of multiple taxa using a single method. Until recently, qPCR was required for quantification as metabarcoding lacked the ability to quantify absolute abundance of species. We have implemented a quantitative metabarcoding approach that solves this challlenge by introducing known quantitites of synthetic DNA spike-ins before PCR. This enables us to accurately estimate DNA concdentrations in environmental samples without the cost and complexity of running qPCR assays for every taxon of interest. The figure to the left shows how the spike-in process works. To read our full white paper about quantitative metabarcoding using DNA spike-ins click here.
Example Aquatic Metabarcoding 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.
Aquatic Metabarcoding Pricing
One Group
$95 /Sample
- Includes sequencing for one taxonomic group of the following: bacteria, phytoplankton, macroinvertebrates, fish*, vertebrates
- eDNA sampling kit provide. Includes barcoded sample cups, desiccant, syringes, and filters
- 10-point quality control
- Full bioinformatics
- 1-year storage of raw data
Two Groups
$155 /Sample
- Includes sequencing for two taxonomic groups of the following: bacteria, phytoplankton, macroinvertebrates, fish*, vertebrates
- eDNA sampling kit provide. Includes barcoded sample cups, desiccant, syringes, and filters
- 10-point quality control
- Full bioinformatics
- 1-year storage of raw data
Three Groups
$210 /Sample
- Includes sequencing for three taxonomic groups of the following: bacteria, phytoplankton, macroinvertebrates, fish*, vertebrates
- eDNA sampling kit provide. Includes barcoded sample cups, desiccant, syringes, and filters
- 10-point quality control
- Full bioinformatics
- 1-year storage of raw data
Batches of <15 samples require a fee of $150 for bioinformatics setup per taxonomic group
$5 surcharge for processing non-Jonah filters
Discounts available for large orders. Please contact to discuss.
If providing extracted DNA, samples are discounted $25/sample.
*Surcharge of $20 for fish metabarcoding due to increased number of replicates