Downstream uptake rate of environmental DNA
estimated by simple stream channel metrics
Alexander K Fremier1
Katherine M Strickler1
Joseph Parzych1
Caren S Goldberg1
1
School of the Environment, Washington State University, Pullman WA
Department of Defense
Traditional versus eDNA methods
VS
Processes affecting eDNA detection
Production
cells
Degradation
Transport
Uptake
cells
cells
Detection
eDNA Transport and Uptake in Streams
What stream characteristics control uptake?
• H1: Uptake is controlled by channel complexity through changes in water residence time.
Uptake – absorption of eDNA to the stream bed
Channel complexity – geomorphic and vegetative
patterns that both influence flow and flow
interactions with the channel
Residence time – mean time an average water
molecule resides in the stream study reach
Uptake ‘eDNA tracer’ experiment
Pulled 200 liters of water with sturgeon DNA
▫ UI Aquaculture Center
▫ High eDNA loads
▫ Novel eDNA to stream ecosystems
Added a conservative tracer (rhodamine - RWT)
▫ RWT is inert so does not interact with the stream bed
▫ Visual tracer to estimate expected eDNA concentrations
▫ Easy to measure concentration
Uptake ‘eDNA tracer’ experiment
Selected FIVE 200m stream reaches with variable complexity
▫ GEOMORPH: Sinuosity, longitudinal roughness, AWSC, all three
▫ FLOW: Mean travel time, Transient storage (Fmed200)
Poured 200L slug into each reach & measured concentrations
▫ 200m downstream, 2L samples every 3-5 min
Uptake ‘eDNA tracer’ experiment
Measured DNA concentration using qPCR
▫ Filtered water samples
▫ Performed qPCR in lab dedicated to low quantity DNA (WSU)
▫ Triplicate samples were taken and values averaged
Measured RWT concentrations for 20+ water samples
▫ Calculate expected eDNA concentration from RWT concentration
▫ Calculate Spiral Length (m) and Uptake Velocity (m/s) in OTIS
Uptake ‘eDNA tracer’ experiment
[EDNA] : REPLICATES OF EDNA PER LITER
0.0025
0.002
0.0015
Expected [eDNA]
Observed [eDNA]
0.001
0.0005
0
22
32
42
52
EXPERIMENT TIME (MINUTES)
62
72
Calculations for FLOW and eDNA uptake
eDNA Uptake - Spiral Length (m)
• Calculated average distance [eDNA] travels before uptake
Hydrology - Fmed 200 (m/s)
• Fraction of median travel time due to transient storage standardized by
reach length
Geomorphology – topographic roughness (m) and sinuosity (m/m)
• Average of the absolute value of the differences mean slope and
observed topography
• Curvilinear distance / straight line distance
Transient storage predicts eDNA uptake
350
y = -323.87x + 336.59
R² = 0.2204
p < 0.001
Spiraling Length (m)
300
250
200
150
100
50
0
0.30
0.35
0.40
0.45
0.50
Fmed200 (fraction)
0.55
0.60
0.65
Longitudinal roughness correlates with eDNA uptake
Spiraling Length (m)
350
y = -61.602x + 245.6
R² = 0.2519
p < 0.001
300
250
200
150
100
50
0
0
0.5
1
1.5
Longitudinal Roughness (m)
2
Channel sinuosity is a good predictor of eDNA uptake
350
y = -516.94x + 760.92
R² = 0.1584
p < 0.01
Spiraling Length (m)
300
250
200
150
100
50
0
1
1.05
1.1
1.15
Sinuosity (m/m)
1.2
1.25
Findings… sinuosity influences ‘loss’ of eDNA
• Novel method for determining eDNA transport/uptake
• Stream geomorphology a good predictor of uptake
• Stream properties influence ‘loss’ and thereby detection
• Results could be use to inform sampling
Downstream uptake rate of environmental DNA
estimated by simple stream channel metrics
Alexander K Fremier1
Katherine M Strickler1
Joseph Parzych1
Caren S Goldberg1
1
School of the Environment, Washington State University, Pullman WA
Department of Defense