External link: https://youtu.be/BupozR1fnlg
Protocol Citation: susannat 2024. eDNA Sampling Protocol: Smith-Root citizen scientist sampler. protocols.io https://dx.doi.org/10.17504/protocols.io.q26g71dw9gwz/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: July 24, 2024
Last Modified: July 24, 2024
Protocol Integer ID: 104007
Keywords: root citizen scientist sampler for environmental dna, root citizen scientist sampler this protocol, environmental dna, root citizen scientist sampler, reliable edna data collection, edna sample, detailed guide on water collection, biodiversity research effort, sampler, dna, water collection, filtration step, sampling protocol, sampling, sample, preparing filter blank, edna, citizen scientist, various water source
Abstract
This protocol outlines the procedures for using the Smith-Root citizen scientist sampler for environmental DNA (eDNA) sampling. It includes a detailed guide on water collection and filtration steps, emphasizing the importance of maintaining sterility to avoid cross-contamination. The protocol specifies the use of Smith-Root 0.45 µm self-preserving filters and provides instructions for their proper handling and storage. Additionally, it includes steps for preparing filter blanks and cleaning the sampler to ensure accurate and reliable eDNA data collection. This method is designed to be accessible for citizen scientists, with clear, step-by-step instructions supported by visual aids and online resources. The protocol ensures that eDNA samples can be collected effectively from various water sources, contributing to ecological and biodiversity research efforts.
Image Attribution
Guidelines
Materials
- Smith-Root citizen scientist sampler*
- Smith-Root 0.45 um self-preserving filters
- Nitrile gloves
- MilliQ water for filter blank (~100 ml)
If not sampling directly from a stream or other water source:
- 1 L bottle or large Whirl-Pak bags for water sample collection**
- DNAway or 10% bleach for cleaning bottles
Before start
*Before heading to the field, ensure the sampler is fully charged. There is a charging cord included for the lead acid battery.
** Bottles should be sterilized before use and between sampling sites to prevent cross- contamination. To sterilize, soak in acid wash (1% solution of hydrochloric or nitric acid), rinse three times in DI H2O, and autoclave. Alternatively, soak in bleach solution (final concentration 1-5%) and rinse three times with DI H2O.
Water collection
Skip this step if sampling directly from a stream or other water source (as in Figure 1D). Wearing gloves, rinse sample bottle three times with ~10 ml of sample water; discard rinse water offshore or away from sampling site. Fill bottle with 1 L of sample water. If bottles are limited, large Whirl-Pak bags can be used instead.
Filtering
Wearing gloves, open an individually wrapped Smith-Root filter pouch.
Without touching the snorkel, attach it to the smooth end of the filter housing (Figure 1A).
Attach the sampler hose to the ridged end of the filter (Figure 1B).
Turn on the vacuum pump (Figure 1C).
Insert the snorkel into the sample water (Figure 1D).
When 2 L has been filtered (or when filter clogs), invert the filter housing so the snorkel is facing the sky. Continue to run the vacuum pump for 20 seconds to air dry the filter (Figure 1E). Record final volume in field data sheet.
After filtering
Remove the snorkel from the filter housing and discard the snorkel.
Place the filter housing back in the pouch (Figure 1F)
Label pouch with Station, Date, Depth, Replicate, and Volume filtered.
Discard the filtrate in the collection vessel.
Repeat all steps for as many replicates as requested (default = 3 replicates).
Blanks
Filter ~100 ml of MilliQ water through a clean filter as above. Process one blank for each sampling day.
Filter storage
Smith-Root self-preserving filters are stable at room temperature for six months.
Cleaning the sampler
Thoroughly wipe down the Smith-Root sampler after each field day with a wet paper towel. Note that seawater can corrode the metal parts of the sampler.