What is Environmental DNA?

Every organism continuously sheds DNA into its environment through skin cells, mucus, gametes, waste, and decomposition. This shed material, collectively termed environmental DNA or eDNA, can be captured from water samples and analyzed to determine which species are present in an ecosystem without ever observing or capturing the organisms themselves.

For natural resource managers, regulators, and researchers, eDNA offers a non-invasive, highly sensitive, and increasingly cost-effective alternative to traditional survey methods, particularly for rare, cryptic, or hard-to-sample species.

Why Digital PCR for eDNA?

Digital PCR has emerged as the analytical platform of choice for eDNA quantification, and for good reason:

• Sensitivity at low DNA concentrations: eDNA is often present at vanishingly low levels. dPCR routinely detects single-digit copy numbers per reaction.
• Absolute quantification without standard curves means copy-number results are directly comparable across labs, projects, and years, essential for trend monitoring and regulatory reporting.
• Inhibitor resistance: environmental samples are rich in PCR inhibitors (humic acids, tannins, sediment particulates). dPCR handles these substantially better than qPCR.
• Reproducibility: dPCR results are reproducible across operators and instruments, which matters for multi-year monitoring programs.
• Multiplexing: multiple species can be quantified from a single reaction, increasing throughput and reducing per-sample cost.

[Read more about species-level eDNA quantification using digital PCR] (link to your July 2025 blog post)

Applications

Endangered & Threatened Species Monitoring

Non-invasive detection of species, recovery monitoring, and habitat assessment. Examples of species we have assays for or can design assays for include:

• Anadromous fish: Chinook salmon, coho salmon, steelhead
• Native freshwater fish: Delta smelt, Tidewater goby
• Amphibians: California red-legged frog, foothill yellow-legged frog, California tiger salamander
• Invertebrates: vernal pool tadpole shrimp, vernal pool fairy shrimp, western ridged mussel, western pearlshell

Invasive Species Detection

Early-warning detection of invasive species before they become established, when management is still feasible:

• Invasive mussels: zebra mussel, quagga mussel, golden mussel (recently introduced to California)
• Invasive fish: common carp, black crappie, smallmouth bass, eastern brook trout, bluegill, yellow bullhead, yellow perch, American shad, goldfish, brown bullhead, grass carp
• Invasive invertebrates: New Zealand mudsnail, rusty crayfish, red swamp crayfish
• Invasive amphibians: American bullfrog (in non-native ranges)

Aquaculture & Fisheries

Pathogen surveillance, parasite detection, and stock assessment support for aquaculture operations and fisheries managers.

Environmental Gene Expression

Quantification of functional gene transcripts (eRNA) for monitoring ecological processes and stress responses in environmental microbiomes.

[See Resources for our full list of eDNA assays]

Custom Assay Design

If your target species or gene is not on our existing panel, our team designs and validates custom dPCR assays end-to-end:

• Target sequence identification and primer/probe design
• In silico and empirical specificity testing against non-target species
• Sensitivity validation and limit of detection determination
• Field validation against samples from known-positive and known-negative sites
• Documentation and transferable assay protocols

[Talk to a Scientist]

Sample Collection & Handling

eDNA results are only as good as the samples that arrive at the lab. We provide:

• Sample collection guidance tailored to your target species, water type, and sampling design
• Filter and preservative recommendations
• Field QA/QC protocols including blanks and replicates
• Chain-of-custody documentation
• Shipping logistics for time-sensitive samples

Reporting & Data Interpretation

Our reports include raw copy number data, technical replicates, QA/QC results (extraction blanks, no-template controls, inhibition checks), and interpretive context appropriate to your application. For programs with regulatory or litigation implications, we provide expanded documentation and expert support.

Sample Types We Analyze

Surface freshwater · Marine and coastal water · Groundwater and hyporheic samples · Sediment · Snow melt · Stream substrate biofilm · Aquaculture pond water · Treated effluent · Air filter samples (where applicable)

Who We Work With

State and federal natural resource agencies · Tribal natural resource departments · Environmental consultants and engineering firms · Water and wastewater utilities (for invasive species monitoring) · Researchers and academic institutions · Conservation NGOs · Aquaculture operations