TITLE: S-1 SOIL FIELD SAMPLING
AUTHORS: REDI-NET Consortium

[DESCRIPTION]
This protocol describes soil field sampling.

[GUIDELINES]
OBJECTIVE

To outline steps for properly collecting sediment samples from waterholes to evaluate the risk of zoonotic disease transmission by the detection of pathogens from environmental DNA (eDNA).

SUMMARY/SCOPE

The overarching aim of the REDI-NET is to develop a collaborative laboratory network between domestic and international partnering institutions to address disease surveillance needs in order to effectively detect, predict and contain potentially emergent zoonosis. This SOP provides guidance on the protocol for the correct sediment sampling at CONUS/OCONUS sites to evaluate and predict the risk of zoonotic disease transmission.

RESPONSIBLE PERSON

Principal Investigator, Study Coordinator, Entomology Component Lead, Managers
 

MAINTENANCE OF EQUIPMENT

BEFORE EACH COLLECTION

Clean corer and scoops
Freeze and clean ice packs
Clean cool-boxes
Fully charge all equipment (e.g., GPS unit, tablets/phone). Make sure the tablet has enough free-space for field sampling pictures.

AFTER EACH COLLECTION

Clean all equipment thoroughly between sampling sites, including boots, cooler box (inside and outside), etc.
Store sterile equipment separate from used equipment and samples.

QUALITY CONTROL

This SOP is reviewed by the applicable supervisor annually or as required in order to maintain its relevance.

 


 



[STEPS]
SECTION: SAMPLING TEAMS
1. 
 
Field sampling of eDNA sediment samples involves two people. One person serves as the ‘sampler’ and the other person serves as a ‘helper’. The helper can look up details in these instructions when needed, keep track of samples, handle objects that are contamination risks, serve as a second set of eyes for potential contamination, and ensure safety of the sampler in potentially hazardous field conditions.
SECTION: SAMPLING SITE SELECTION
2. Find two suitable sampling locations within the water body representing different ecological systems, if possible.
SECTION: SAMPLING SITE SELECTION
3. At each sampling location, soil samples should be taken from two points, one at the edge of the waterhole and the second one meter in from the edge. Sediment collection at each sampling location should be done in triplicate.
SECTION: SAMPLING SITE SELECTION
4. Because ‘the edge’ of the water body may change due to precipitation changes, the edge should be defined at each month's sampling.
SECTION: SAMPLING SITE SELECTION
5. If the water body has a "drop off" (embankment of more than 20 cm), the soil and water samples should be taken where the water "meets" the soil. Aim to collect at locations where finer sediment is present, if possible.
SECTION: SAMPLE COLLECTION
6. 
 
At each sampling location, the helper opens the bag containing the vials to have one open and ready for the sampler. The helper will open and close the bags containing the collection materials. This is to prevent potential contamination of samples.
SECTION: SAMPLE COLLECTION
7. Collect sediment using a suitable and appropriately labeled sampling device (such as a clean dipper head or corer). The Sampler takes the appropriately labeled sampling device (for example, SL1-edge would be the device for sampling location 1 at the edge).
SECTION: SAMPLE COLLECTION
7.1. If using a dipper head, scrape the surface of the bottom of the water body. Gently pour off any water within the dipper head over bare ground (not over the water body) taking care to minimize loss of fine surface sediments.
SECTION: SAMPLE COLLECTION
7.2. If using a corer, sample from the first 1-3 cm depth of the bottom of the water body. Cut the exposed sediment with a stainless steel or plastic (HDPE or PTFE) cutter.
SECTION: SAMPLE COLLECTION
8. The Sampler takes the appropriately labeled spoon or scoop (for example, SL1-edge would be the spoon or scoop for sampling location 1 at the edge) from the Helper and fills an appropriately labeled 50 mL falcon® tube with 10 mL of sediment. Do NOT place rocks in the tube. Cover sediment with water from the collection site leaving no airspace. 
 

SECTION: SAMPLE COLLECTION
9. Close the Falcon® tube and dry it using paper towels.
SECTION: SAMPLE COLLECTION
10. Label the Falcon® tube.
SECTION: SAMPLE COLLECTION
11. Place the Falcon® tube into the cooler box filled with ice for storage.
SECTION: SAMPLE COLLECTION
12. Repeat the sediment sampling 3 times per sampling location point (for example, three times at the edge and three times at the 1 m point).
SECTION: SAMPLE COLLECTION
13. Record sediment quality characteristics and information relating to samples collected. 
SECTION: SAMPLE COLLECTION
14. Repeat steps 7 to 13, 1 m away from the edge of the waterhole.
SECTION: SAMPLE COLLECTION
15. Clean boots thoroughly between sampling location sites.
SECTION: SAMPLE COLLECTION
16. Repeat steps 7 to 15 at the second sampling location until all the samples are collected.
SECTION: SOIL STORAGE
17. Keep freshly collected sediment in labeled, sealed vials at 4 °C cold chain (cooler box) until return to laboratory. Soil samples are not recommended to be stored for long periods of time at 4 °C.
SECTION: SOIL STORAGE
18. Once at the laboratory, samples can be stored at -20 °C for up to 2 weeks or -80 °C for longer periods of time.