Environmental DNA sample collection

While the basic requirements of environmental DNA (eDNA) sample collection are simple – pass water (or air) through a micron pore-size filter – a wide variety of apparatuses have been developed. Many of these are complicated (peristaltic pumps, filter funnels and flasks), heavy (rechargeable batteries), expensive (Smith-Root eDNA Sampler Backpack) and/or generate significant non-recyclable waste (plastic filter funnels, tubing, filter holders). Given the small and thrifty company Pisces is, we developed our own filtration apparatus, which was simple, lightweight, human-powered, inexpensive and completely reusable. As shown in the photo, it consists of a “plumbed” 1 L Nalgene bottle (Luer lock fitting on the bottom, air valve in the cap), a nylon Swinnex filter holder, and a bicycle pump. A 25 mm diameter filter of any desired pore size is loaded into the Swinnex filter holder which is then connected to the Nalgene bottle via the Luer lock fitting. After filling the bottle with water to be sampled, the bottle cap is screwed on tightly, the bicycle pump is connected to the air valve on the cap and air pressure is used to force water through the filter. After sample collection, the Swinnex filter holder is removed and sent to the lab for testing. While not fancy, the setup is highly functional: the bottles and plumbing fittings are inexpensive (<$100.00 USD). Air pressure from the pump (~35-40 psi) is sufficient to push water through the filter until it clogs. There is no handling of filters in the field, reducing contamination risk (after sample collection the unopened Swinnex is placed in a Ziploc bag and sent to the lab). Lab handling of samples is simplified (while most eDNA sample collections use 47mm diameter filters, these will not fit in a microcentrifuge tube, so all are cut in half and DNA extracted from only ½ of the filter. 25mm filters will fit whole in a microcentrifuge tube.). There is no plastic or rubber waste (both the bottles and Swinnex filter holders are reusable after cleaning with a dilute bleach solution).