Modelling the transport of environmental DNA through a porous substrate using continuous flow-through column experiments

Arial J Shogren; Jennifer L Tank; Elizabeth A Andruszkiewicz; Brett Olds; Christopher Jerde; Diogo Bolster

doi:10.1098/rsif.2016.0290

Modelling the transport of environmental DNA through a porous substrate using continuous flow-through column experiments

J R Soc Interface. 2016 Jun;13(119):20160290. doi: 10.1098/rsif.2016.0290.

Authors

Arial J Shogren¹, Jennifer L Tank², Elizabeth A Andruszkiewicz³, Brett Olds⁴, Christopher Jerde⁵, Diogo Bolster⁶

Affiliations

¹ Department of Biological Sciences, Environmental Change Initiative, University of Notre Dame, Notre Dame, IN, USA ashogren@nd.edu.
² Department of Biological Sciences, Environmental Change Initiative, University of Notre Dame, Notre Dame, IN, USA.
³ Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA.
⁴ Department of Biological Sciences, Environmental Change Initiative, University of Notre Dame, Notre Dame, IN, USA Oceanic Institute of Hawai'i Pacific University, Waimanalo, HI, USA.
⁵ Department of Biological Sciences, Environmental Change Initiative, University of Notre Dame, Notre Dame, IN, USA Biology Department, Aquatic Ecosystems Analysis Laboratory, University of Nevada, Reno, NV, USA.
⁶ Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA.

Abstract

Detecting environmental DNA (eDNA) in water samples is a powerful tool in determining the presence of rare aquatic species. However, many open questions remain as to how biological and physical conditions in flowing waters influence eDNA. Motivated by what one might find in a stream/river benthos we conducted experiments in continuous flow columns packed with porous substrates to explore eDNA transport and ask whether substrate type and the presence of colonized biofilms plays an important role for eDNA retention. To interpret our data, and for modelling purposes, we began with the assumption that eDNA could be treated as a classical tracer. Comparing our experimental data with traditional transport models, we found that eDNA behaves anomalously, displaying characteristics of a heterogeneous, polydisperse substance with particle-like behaviour that can be filtered by the substrate. Columns were quickly flushed of suspended eDNA particles while a significant amount of particles never made it through and were retained in the column, as calculated from a mass balance. Suspended eDNA was exported through the column, regardless of biofilm colonization. Our results indicate that the variable particle size of eDNA results in stochastic retention, release and transport, which may influence the interpretation eDNA detection in biological systems.

Keywords: anomalous transport; eDNA; porous media.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
DNA / analysis*
DNA / chemistry*
Models, Chemical*
Perciformes*
Rivers*

Substances

DNA