3/25/2017 – eDNA collection trip

Trip date:  25 March 2017
Project manager:  Bill Gee
Trip purpose:  eDNA sample collection
Areas of Cave visited:  CarrollPassage
Trip participants:  Bill Gee, Shannon Brewer, Joshua Mouser, David Ashley, Rita Worden, Bill Kacerovskis
Entry Time:  9:50am
Exit Time:  4:30pm
The trip report:  About two months ago David Ashley contacted me about one of his former students, Shannon Brewer.  Shannon and Joshua Mouser are doing research with environmental DNA (eDNA) regarding populations of cave fish and cave crayfish.  Carroll Cave has a good population of cave fish and so is a good site for this research.  We exchanged emails and wound up setting a trip for March 25.
Environmental DNA is a method where DNA samples are collected from the environment rather than directly sampled from the organisms.  It is a non-invasive method of examining biodiversity.  The basic technique in a cave is to run some water through a special filter that captures biological detritus such as skin cells and feces, then analyzing the captured material in the lab.  Wikipedia has a pretty good overview.
I drove down Saturday morning arriving at the silo about 8:20.  That gave me plenty of time to rig the rope, download the rain gauge data logger and get into my cave gear.  Shannon, Joshua and David arrived shortly before 9:00am.  It has rained some overnight and the hill was a bit sloppy, so Rita parked at the bottom and walked up, arriving a few minutes later.  Bill also parked at the bottom of the hill and walked up.
We were all geared up and dropping into the cave by 9:50.  One of the goals of this trip was to find suitable sampling sites.  The work will involve at least three cave trips spread over a few weeks, and we need to visit the same sites each time.  Shannon and Joshua wanted to get samples from both Carroll and Thunder rivers, so we decided to do the drier passage (Carroll) first.
On the way down Carroll Passage, we noted several candidate sites.  We would make the final choices and collect samples on the return trip.  As it turns out, one of the sample sites is next to the data logger in Carroll River, just before getting to the Rimstone Room.  The second site is at a place where the stream goes under a rock and into a big pool, and the third site is another big pool upstream from the Bear Claw Passage.  All three sites are marked with a yellow plastic tent stake and green flagging tape.
The sample collection process is not difficult.  A measured sample of water (2 liters) is collected.  Using sterile gloves, a filter element is attached to the top of a plastic beaker.  A reservoir on top holds water to be filtered.  A hand-operated vacuum pump draws air out of the beaker which helps force water through the filter.  After running 1 liter of water, the filter element is removed and put in a sterile vial.  It is fairly important to get clear water.  Any kind of silt in the water will clog the filter element very quickly.  With clear water a liter can be filtered in about 3 or 4 minutes.  From start to finish it takes 20 minutes or so at each site.
Joshua also took notes at each site regarding stream size, flow state, substrate and more.
I had no great hopes of seeing any fish in Carroll River, but we got lucky.  There was one fish near the second sample site.  It is rare to see fish in that part of the cave.  We had lunch at the second sample site.  From the third sample site we went straight over to Thunder Falls.
The first of three sample sites in Thunder River is the pool just 30 feet upstream from Thunder Falls.  The second site is Goska’s Fish Pool and the third site is 50 feet into UL2.  We saw a dozen or more fish in Thunder River, and at least four within 10 feet of the UL2 sample site.
Since we were going by all of the data logger sites, I took the opportunity to download all of the loggers.  At UL2 Bill K. and I went on to the data logger while the others collected samples.  David Ashley examined all of the bio sites, both bait sticks and tiles, as we went past them.
As we left UL2, everyone went up the mud slope to get a look at the formations.  We left UL2 about 3:00, collected samples at Goska’s Fish Pool and were back at the ladder by 4:00 pm.  We all geared up and climbed out, with the last person out around 4:30.
When we got out of the cave it was just beginning to sprinkle.  By the time we were all changed and ready to head down the hill, it was raining moderately hard.  I put Rita and Bill’s gear in my truck and gave them a ride back to their cars.
Everyone but Bill K. went to El Espolon in Camdenton for a good Mexican dinner.

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