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Stained DNA Research Blog


The meeting I had this afternoon was funded by NSF, it is a working group with members of the IUSE and TCUs. The goal of our monthly meetings are to build relationships between TCUs.

We aim to gather information to distill and co-create recommendations for improving student success in environmental data science. Krystal Tsosie asked us to break down "Environmental Data Science", while also thinking about "Indigenous Science."

This conversation brought up many thoughts about how we can foster student success. We are each thinking about the ways that Environmental Science Data Science in tribal communities can improve the lives of tribal members.

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Spirinchus thaleicthys (also known as Longfin Smelt, “Hoolies”, and “Tiokowe”) are an anadromous forage fish. They enter the lower mainstream river of the Nooksack annually.

To determine spawning locations of smelt in the Nooksack River, this project has developed a species-specific eDNA assay to detect the extent of the upstream migration of the Hoolies.

At each sampling locality, the Smith-Root eDNA Sampler Backpack (Thomas et al., 2018) was used with the extension pole and trident (see image below). In the field, 250mL of water from the Nooksack was filtered using 5µm polyethersulfone (PES) filters.

Image 1. Rachael Mallon collecting eDNA using the Smith-Root backpack sampler in the Nooksack at Hovander Park (image from October 26, 2021)

The annual spawning event happens in November.

This year, the furthest downstream site is located at Fish Point (48.77, -122.6), followed upstream by Marine Drive Bridge (48.79, -122.59), Rayhorst Drive (48.81, -122.58), Slater Bridge (48.82, -122.58), Hovander (48.83, -122.60), and Ferndale (48.84, -122.59). The distance from Fish Point to Ferndale is 6.1 miles.

Map that shows sampling locations of in the bay and along the Nooksack.

In addition to the freshwater samples collected along the Nooksack River, 8 marine sites were sampled for Hoolie eDNA. These sites include Sandy Point (48.78, -122.70), Gooseberry point (48.73, -122.68), Lummi Shore Drive (48.73, -122.63), Smokehouse Road (48.75, -122.60), Locust Beach (48.75, -122.54), Whatcom Creek (48.75, -122.49), Bellingham Buoy (48.72, -122.58), and Fairhaven Dock (48.73, -122.51).

Fish Point and Marine Drive Bridge are the most popular locations for catching Hoolies. The distance from Fish Point to Marine Drive Bridge is 1.59 miles.

There is saline influence from tidal intrusion at the Fish Point and Marine Drive Bridge locations. Tidal range exceeds more than 3 m. During periods of large tidal changes, a wall of water up to 3 m high can occur in the study area on the incoming tide.

On 10/26/2021, the “Hoolie eDNA team” collected 250mL of water at 6 locations along the Nooksack as part of their “Pre-Hoolie Run” effort to determine the baseline signal that is captured using eDNA. This was done while the tide was going out. DNA was extracted and qPCR was conducted. No Hoolie DNA was detected.

On 11/02/2021, the “Hoolie eDNA team” filtered water samples when the tide was highest. Based on DNA extracted from samples collected at Fish Point, Hoolies were present when using the Hoolie Taqman assay. The Ct values are below the limit of quantification. LNR fisherman, Jeff Solomon, had not yet begun fishing for Hoolies.

Image 2. Jeff Solomon with his Hoolie dipnet at Fish Point.

On 11/03/2021 the first Hoolie was caught by LNR fisherman, Jeff Solomon. The tide was outgoing at the time of capture. This Hoolie was a male. No eDNA sampling was done on the Nooksack on this day, only marine sampling was done during the low tide. An egg survey was conducted and samples were collected at Hovander Park, Slater Bridge, Marine Drive Bridge. No eggs were detected.

Figure 1.Tidal heights at Bellingham Bay, WA on 10/26/2021. The yellow box indicates when samples were collected from the Nooksack at all 6 sites from 1600 to 1800.

Figure 2. Tidal heights at Bellingham Bay, WA on 11/02/2021. The yellow box indicates when samples were collected at the 6 sampling locations along the Nooksack from 1600-1800.

Figure 3. Tidal heights at Bellingham Bay, WA on 11/03/2021. The yellow box indicates when fish were caught. White box indicates when marine samples were collected at the 8 sampling locations in the Bay from 1000 to 1200.

On 11/10/2021 Jeff Solomon captured a bucketful of Hoolies within a half-hour period. This was during a peak tide. eDNA was collected at Marine Drive Bridge and Fish Point during the high tide. 20 fish were preserved from this capture event. Marine samples were also collected on this day. An egg survey was conducted and samples were collected at Hovander, Slater Bridge Marine Drive Bridge. No eggs were detected.

Figure 5. Tidal heights at Bellingham Bay, WA on 11/10/2021. The yellow box indicates when Fish Point and Marine Bridge Drive samples were collected. The blue box indicates when marine samples were collected. The white box is time period when Jeff Solomon went fishing. Image is of fish caught by Jeff Solomon.

The river has been in Flood Stage since the afternoon of 11/12/2021. Jeff hasn’t had a successful catch during this flood stage. The eDNA team has not conducted sampling since the start of the Flood Stage. The last Nooksack sampling effort was on 11/11/2021.

Figure 6. USGS gage height date from station managed by the Northwest Washington Field Office (Ferndale).
Questions left unanswered:

1. Are we sampling at the correct times during the day?

a. Should we collect in the morning and at night?

b. Should we collect when Jeff is fishing?

2. Are we sampling at the correct times during the rise and fall of the tide?

a. TEK indicates the Hoolies are present as the tide is outgoing

3. Can we detect Hoolies during the Flood Stage?

a. Field sampling is extremely dangerous in flood stage

b. No data has been collected at this time (neither TEK (fish capture) or eDNA)

4. Do Hoolies have holding patterns at certain locations on the Nooksack?

5. Are the Hoolies traveling all the way from Fish Point to Ferndale?

6. Have the Hoolies made it to Marine Drive Bridge?

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