Environmental DNA, or eDNA, refers to the trace genetic material shed by organisms into their surrounding environments. This DNA can be detected in soil, water or even air, and allows researchers to infer the recent presence of organisms without having observed them directly. This makes eDNA an especially useful tool for detecting rare or cryptic organisms within the environment, such as our native ʻoʻopu as they traverse the urban waterways of our home ahupuaʻa of Waikīkī.
Students exploring their catch with Paʻēpaʻē o Waikolu.
The primary eDNA sequencing application employed by the ʻĀina-Informatics Network is in collaboration with ʻIolani School’s Paʻēpaʻē o Waikolu Stream Biodiversity Program. Partnering schools conduct field surveys to capture fish and invertebrates in an effort to both monitor and restore 20 sites along Makiki, Pālolo and Mānoa Streams. At the same time, water is collected from each site for subsequent eDNA sequencing by the same school, with the goal of combining both physical and genetic methods to quantify the biodiversity at each sampling point.
Sample collection and preservation
For stream water samples, collections take place prior to the physical surveys in order to capture the undisturbed water column. Using sterile vessels, 400-500 mL of stream water is collected and stored on ice until the water can be passed through a 0.45 um filter, which are designed to allow smaller particles such as bacteria to pass through. The DNA can be extracted from the filter immediately, or the filter can be submerged in Longmire’s solution for longer term storage in the refrigerator.
DNA extraction from the filters can be done using typical blood and tissue kits, including those from Qiagen and NEB.
University Laboratory School student using a vacuum pump to filter stream water in the field at Ka Papa Loʻi o Kānewai.
Lab Protocols
Coming soon…
Bioinformatics
For our eDNA projects, a modified decona_plus pipeline has been tailored to cluster identical sequencing reads (i.e. the same amplicon) before classifying them using a user-submitted curated database. For the stream eDNA projects, this curated database contains both native and introduced fish and invertebrates likely to be observed in Hawaiʻi streams. The cluster depths can then serve as a rough proxy for relative abundance. Decona is currently available through our ʻIolani Bioinformatics Portal which allows our network teachers to upload their own sequencing reads and custom databases for eDNA analysis.
schools participating in stream surveys
additional applications
In addition to looking for ʻoʻopu and other native species in our streams, eDNA has been used by schools in our network to survey diverse locations across the islands. At Kauaʻi High School, students have been using eDNA to characterize fish and plankton populations in ʻAlekoko and Nōmilu fishponds. And at Kūlanihākoʻi High School, students used estuarine and nearshore seawater eDNA to survey the south shore of Maui for sharks.
Kūlanihākoʻi High School teacher Mista Fitz sampling the muliwai at Keālia during an algae bloom.
