TY - JOUR
T1 - Particle size distribution and optimal capture of aqueous macrobial eDNA
AU - Turner, Cameron R.
AU - Barnes, Matthew A.
AU - Xu, Charles C.Y.
AU - Jones, Stuart E.
AU - Jerde, Christopher L.
AU - Lodge, David M.
PY - 2014/7
Y1 - 2014/7
N2 - Using environmental DNA (eDNA) to detect aquatic macroorganisms is a new survey method with broad applicability. However, the origin, state and fate of aqueous macrobial eDNA - which collectively determine how well eDNA can serve as a proxy for directly observing organisms and how eDNA should be captured, purified and assayed - are poorly understood. The size of aquatic particles provides clues about their origin, state and fate. We used sequential filtration size fractionation to measure the particle size distribution (PSD) of macrobial eDNA, specifically Common Carp (hereafter referred to as Carp) eDNA. We compared it to the PSDs of total eDNA (from all organisms) and suspended particle matter (SPM). We quantified Carp mitochondrial eDNA using a custom qPCR assay, total eDNA with fluorometry and SPM with gravimetric analysis. In a lake and a pond, we found Carp eDNA in particles from >180 to <0·2 μm, but it was most abundant from 1 to 10 μm. Total eDNA was most abundant below 0·2 μm, and SPM was most abundant above 100 μm. SPM consisted of ≤0·1% total eDNA, and total eDNA consisted of ≤0·0004% Carp eDNA. 0·2 μm filtration maximized Carp eDNA capture (85% ± 6%) while minimizing total (i.e. non-target) eDNA capture (48% ± 3%), but filter clogging limited this pore size to a sample volume <250 mL. To mitigate this limitation, we estimated a continuous PSD model for Carp eDNA and derived an equation for calculating isoclines of pore size and water volume that yield equivalent amounts of Carp eDNA. Our results suggest that aqueous macrobial eDNA predominantly exists inside mitochondria or cells, and that settling may therefore play an important role in its fate. For optimal eDNA capture, we recommend 0·2 μm filtration or a combination of larger pore size and water volume that exceeds the 0·2 μm isocline. In situ filtration of large volumes could maximize detection probability when surveying large habitats for rare organisms. Our method for eDNA particle size analysis enables future research to compare the PSDs of eDNA from other organisms and environments, and to easily apply them for ecological monitoring.
AB - Using environmental DNA (eDNA) to detect aquatic macroorganisms is a new survey method with broad applicability. However, the origin, state and fate of aqueous macrobial eDNA - which collectively determine how well eDNA can serve as a proxy for directly observing organisms and how eDNA should be captured, purified and assayed - are poorly understood. The size of aquatic particles provides clues about their origin, state and fate. We used sequential filtration size fractionation to measure the particle size distribution (PSD) of macrobial eDNA, specifically Common Carp (hereafter referred to as Carp) eDNA. We compared it to the PSDs of total eDNA (from all organisms) and suspended particle matter (SPM). We quantified Carp mitochondrial eDNA using a custom qPCR assay, total eDNA with fluorometry and SPM with gravimetric analysis. In a lake and a pond, we found Carp eDNA in particles from >180 to <0·2 μm, but it was most abundant from 1 to 10 μm. Total eDNA was most abundant below 0·2 μm, and SPM was most abundant above 100 μm. SPM consisted of ≤0·1% total eDNA, and total eDNA consisted of ≤0·0004% Carp eDNA. 0·2 μm filtration maximized Carp eDNA capture (85% ± 6%) while minimizing total (i.e. non-target) eDNA capture (48% ± 3%), but filter clogging limited this pore size to a sample volume <250 mL. To mitigate this limitation, we estimated a continuous PSD model for Carp eDNA and derived an equation for calculating isoclines of pore size and water volume that yield equivalent amounts of Carp eDNA. Our results suggest that aqueous macrobial eDNA predominantly exists inside mitochondria or cells, and that settling may therefore play an important role in its fate. For optimal eDNA capture, we recommend 0·2 μm filtration or a combination of larger pore size and water volume that exceeds the 0·2 μm isocline. In situ filtration of large volumes could maximize detection probability when surveying large habitats for rare organisms. Our method for eDNA particle size analysis enables future research to compare the PSDs of eDNA from other organisms and environments, and to easily apply them for ecological monitoring.
KW - Aquatic ecosystems
KW - Ecological monitoring
KW - Environmental DNA
KW - Genetic monitoring
KW - Particle size analysis
KW - Rare species
KW - Sampling methods
UR - http://www.scopus.com/inward/record.url?scp=84904345282&partnerID=8YFLogxK
U2 - 10.1111/2041-210X.12206
DO - 10.1111/2041-210X.12206
M3 - Article
AN - SCOPUS:84904345282
VL - 5
SP - 676
EP - 684
JO - Methods in Ecology and Evolution
JF - Methods in Ecology and Evolution
SN - 2041-210X
IS - 7
ER -