Particle size distribution and optimal capture of aqueous macrobial eDNA

By C. Turner, M. Barnes, Charles C.Y. Xu, S. Jones, C. Jerde, David M. Lodge. bioRxiv, 2014

429 citations recorded by the source corpus.

Detecting aquatic macroorganisms with environmental DNA (eDNA) 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, for the first time, 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 1-10 μm. Total eDNA was most abundant below 0.2 μm and SPM was most abundant above 100 μm. SPM was ≤0.1% total eDNA, and total eDNA was ≤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 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 plays 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.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0f441c611a3414adec437eea58eaab58d6304e2e

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Citations in the corpus

Environmental DNA particle size distribution from Brook Trout (Salvelinus fontinalis) (2015, background): “Particles 1–10 lm across, corresponding to the size of individual mitochondria or small cells, constituted the most common size class of Common Carp eDNA (Turner et al. 2014).”
Long‐range PCR allows sequencing of mitochondrial genomes from environmental DNA (2017, background): “In a recent study based on water from a fish pond, most of the eDNA detected was from particles that ranged in size from 1 to 10 μm, consistent with the presence of intact tissues or cells in aquatic environments (Turner et al., 2014).”
Experimental observations on the decay of environmental DNA from bighead and silver carps (2017, background): “The significant role of microbial communities on decay of extracellular DNA is wellrecognized (reviewed in Nielsen et al. 2007), though its role in degrading mitochondrial membranes, the structures within which much of eDNA may be initially found (Turner et al. 2014), is not as welldescribed.”
Environmental DNA monitoring and management of invasive fish: comparison of eDNA and fyke netting (2017, background): “This has been shown previously where a patchy distribution and highly variable carp DNA concentrations ranging from zero to thousands of DNA copies in samples from the same site were found (Turner et al. 2014b).”
Towards the Optimization of eDNA/eRNA Sampling Technologies for Marine Biosecurity Surveillance (2021, background): “[94] determined that the molecular signal (via qPCR) was most abundant from fractions captured between 1 and 10 microns.”
Environmental DNA metabarcoding: Transforming how we survey animal and plant communities (2017, background): “…that aqueous eDNA is either derived from cellular or organellar sources (e.g., mitochondria, Lacoursiere-Roussel, Rosabal, & Bernatchez, 2016; Turner et al., 2014; Wilcox, McKelvey, Young, Lowe, & Schwartz, 2015), and precipitation protocols suggest extracellular sources (Torti et al., 2015).”
Quantifying relative fish abundance with eDNA: a promising tool for fisheries management (2016, background): “Indeed, significant seasonal change in fish eDNA concentration has previously been reported (Turner et al. 2014).”
The ecology of environmental DNA and implications for conservation genetics (2016, methodology): “A notable exception is the work of Turner et al. (2014a) who looked at the particle size distribution of Common Carp eDNA in a small lake and zoo pond using serial filtration of water samples through filters of decreasing pore sizes (180–0.2 lm) and concluding with an ethanol precipitation .”
Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA (2020, background): “It is considered that some of aqueous eDNA-bearing particles, such as feces, are too large to remain suspended in water (Maggi, 2013) and consequently precipitate onto the sediments (Turner et al., 2014).”