When you’re filtering water samples from a water body that has a lot of organic matter or suspended sediment, your filter might clog before you’re able to filter your target sample volume. For example, you want to filter 250 mL, but your filtration rate slows to a very slow drip when you’ve filtered only 150 mL. It’s impractical and sometimes impossible to wait until the target volume has been filtered. And it’s generally a bad idea to let your water sample sit at room temperature because we know that eDNA degrades quickly, especially at warmer temperatures. There are a number of options for dealing with clogged filters:
- Switch to a filter with larger pore size, such as a 5 micron filter.
- Consider setting a cutoff time or drip rate for ending filtering. For example, you might end filtering when the drip rate slows to 3 drips every 10 seconds. If you filter less than your target volume, be sure to record the volume filtered for each sample so you can later analyze it to see if the volume influences the amount of eDNA that’s captured.
- Filter your target volume through multiple filters. For example, if your target is 1000 mL, you could filter four 250 mL subsamples or two 500 mL subsamples. Label all samples carefully to identify the sample and subsample numbers as well as the volume that was filtered for each. Keep in mind that each filter is handled separately during DNA extraction, so this approach can substantially increase the cost of your sampling program.
Optimizing sampling methods for your system
Different sampling techniques work better in different systems, so building in a pilot round of field sampling can help increase effectiveness and efficiency. For example, you might find that you need to switch to a filter with a larger pore size because your filter clogs quickly, that your system is too shallow for your grab bottle (you can use a serological pipette or single-use cup instead), or that cleaning your boots between sites is taking more time than the actual sampling (you can bring multiple pairs of boots to the field or use boot covers). You might find that sample collection method you’d planned to use doesn’t work well because it re-suspends sediment, or you can’t reach the part of the water body you want to sample without a boat or special equipment, or you need to improve your ability to fully decontaminate your equipment. When trying out new collection methods, it can save a lot of time and money if you confirm that you can detect your target species at known sites and that your field blanks are not being contaminated before applying those methods to a whole field season.
With respect to modifying your sample collection methods, there are a couple of caveats:
- If you make any changes to how you collect, filter, or preserve eDNA water samples, continue to adhere to stringent measures for preventing cross-contamination among samples. Carefully think through every step of the sampling procedure and identify every possible action that could introduce eDNA from sample to sample. Develop (and follow) strict measures to avoid contamination throughout the sampling, filtration, and preservation process.
- If you’re collecting samples as part of a large scale eDNA program (such as the US Forest Service’s Rangewide Bull Trout eDNA Project), don’t deviate from the program’s sampling protocol without first consulting with the program’s managers.