Improve Your Understanding of Water
JonahWater delivers insight into aquatic ecosystems
Our JonahWater services answer questions about species in aquatic ecosystems
We quantify aquatic assemblages by sequencing aquatic environmental DNA .
Using both Quantitative PCR and Next Generation Sequencing, we quantify phytoplankton, macroinvertebrates, fish, and other vertebrates in water.
JonahWater gives you the capacity to quantify
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Phytoplankton such as cyanobacteria, diatoms, and green algae
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Macroinvertebrates such as mayflies, chironomids, and mussels
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Vertebrates such as fish, mammals, reptiles, and amphibians
River miles sampled so far
Sequencing of environmental DNA has the potential to transform our understanding of aquatic ecosystems. Using NGS and qPCR gives managers better data cheaper and faster than traditional techniques. All from 250 milliliters of water…
Joe Craine, PhDOur NGS Process
1. Collect
Collect water and filter through syringe.
Send to Jonah Ventures Lab.
2. Extract
We extract DNA from sample.
3. Amplify
Specific regions of DNA are amplified into ampliconsusing pairs of primers.
Each primer pair is specific to a broad taxonomic group.
4. Index
Short, unique segments of DNA are attached to each amplicon to index from which sample it originated.
5. Pool
Indexed amplicons from multiple samples are pooled together
6. Sequence
Amplicons are sequenced
7. Bioinformatics
Data from sequencer is bioinformatically processed to identify groups of similar sequences called OTUs.
8. Identify
OTUs are matched against a reference database to identify the species each OTU represents.
Example NGS Data
NGS 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.
NGS Deliverables
OTU Table
Describes number of times the sequences for each OTU was read for each sample
OTU Taxonomy
Details the species that have the sequences that comprise each OTU
OTU Sequences
Observed genetic sequences that map to each OTU
NGS Pricing
One group
- 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
- 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 group
- 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
Orders of <25 samples require an additional fee of $150 for bioinformatics setup per taxonomic group
Discounts available for large orders. Please contact to discuss.
If providing extracted DNA, samples are discounted $25/sample.
Our qPCR Process
1. Collect
Collect water and filter through syringe.
Send to Jonah Ventures Lab.
2. Extract
We extract DNA from sample.
3. qPCR
Specific regions of DNA are amplified into amplicons using pairs of primers.
Each primer pair is specific to a taxonomic group. Probes then fluoresce if there are matches to individual species.
4. Cq Value
The amount of fluorescence for each cycle is quantified and the cycles repeated to generate a fluorescence curve.
The Cq value is the number of cycles it takes to detect fluorescence.
5. Calibrate
A calibration curve is used to relate the number of cycles it takes before fluorescence is detected (Cq) and the abundance of specific DNA sequences.
6. Calculate
Together, the Cq values and the calibration curves determine for each sample if the DNA of a species is present in the sample and the number of copies of DNA per mL water.
qPCR Deliverables
qPCR Report
Quantifies the number of reads found for a given sequence for each sample
qPCR Pricing
One species
- Includes qPCR assay for one species from the same sample
- eDNA sampling kit provide. Includes barcoded sample cups, desiccant, syringes, and filters
- 5-point Pisces™ standard curve
- Easy-to-read qPCR report
Two species
- Includes qPCR assay for two species from the same sample
- eDNA sampling kit provide. Includes barcoded sample cups, desiccant, syringes, and filters
- 5-point Pisces™ standard curve
- Easy-to-read qPCR report
Three species
- Includes qPCR assay for three species from the same sample
- eDNA sampling kit provide. Includes barcoded sample cups, desiccant, syringes, and filters
- 5-point Pisces™ standard curve
- Easy-to-read qPCR report
Minimum number of samples is 10.
Discounts available for large orders. Please contact to discuss.
Same-sample replicates discounted $10
Handling fees for non-standard samples are variable. Please contact.
Our JonahWater services now include qPanels
qPanels simultaneously quantify the DNA of multiple species via qPCR
We currently offer a SourceTracking qPanel for quantifying sources of fecal coliform bacteria, but are working to add capacity for additional panels
qPanel Deliverables
qPanel Report
Quantifies the number of reads found for a given sequence for each sample
qPanel Pricing
Single qPanel
- Includes qPCR assay for up to 6 species from the same sample
- eDNA sampling kit provide. Includes barcoded sample cups, desiccant, syringes, and filters
- 5-point standard curve
- Easy-to-read qPanel report
Minimum number of samples is 10.
Discounts available for large orders. Please contact to discuss.
Same-sample replicates discounted $10
Handling fees for non-standard samples are variable. Please contact.
Request your free quote today!
Boulder, CO 80301