Environmental DNA (eDNA) removal rates in streams differ by particle size under varying substrate and light conditions

Elise D Snyder; Jennifer L Tank; Pedro F P Brandão-Dias; Kyle Bibby; Arial J Shogren; Aaron W Bivins; Brett Peters; Erik M Curtis; Diogo Bolster; Scott P Egan; Gary A Lamberti

doi:10.1016/j.scitotenv.2023.166469

Environmental DNA (eDNA) removal rates in streams differ by particle size under varying substrate and light conditions

Sci Total Environ. 2023 Dec 10:903:166469. doi: 10.1016/j.scitotenv.2023.166469. Epub 2023 Aug 24.

Authors

Affiliations

¹ Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA. Electronic address: esnyder4@nd.edu.
² Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA. Electronic address: tank.1@nd.edu.
³ Department of BioSciences, Rice University, 6100 Main St, Houston, TX 77005-1827, USA. Electronic address: pb21@rice.edu.
⁴ Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall of Engineering, Notre Dame, IN 46556, USA. Electronic address: kbibby@nd.edu.
⁵ Department of Biological Sciences, The University of Alabama, Science and Engineering Complex,1325 Hackberry Ln, Tuscaloosa, AL 35401, USA. Electronic address: ashogren@ua.edu.
⁶ Department of Civil and Environmental Engineering, Louisiana State University, 3255 Patrick F. Taylor Hall, Baton Rouge, LA 70803, USA. Electronic address: abivins@lsu.edu.
⁷ Environmental Change Initiative, University of Notre Dame, 721 Flanner Hall, Notre Dame, IN 46556, USA. Electronic address: bpeters2@nd.edu.
⁸ Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA. Electronic address: ecurtis@nd.edu.
⁹ Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA; Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall of Engineering, Notre Dame, IN 46556, USA. Electronic address: dbolster@nd.edu.
¹⁰ Department of BioSciences, Rice University, 6100 Main St, Houston, TX 77005-1827, USA. Electronic address: spe1@rice.edu.
¹¹ Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA. Electronic address: glambert@nd.edu.

PMID: 37633388
DOI: 10.1016/j.scitotenv.2023.166469

Abstract

The use of environmental DNA (eDNA) as a sampling tool offers insights into the detection of invasive and/or rare aquatic species and enables biodiversity assessment without traditional sampling approaches, which are often labor-intensive. However, our understanding of the environmental factors that impact eDNA removal (i.e., how rapidly eDNA is removed from the water column by the combination of decay and physical removal) in flowing waters is limited. This limitation constrains predictions about the location and density of target organisms after positive detection. To address this question, we spiked Common Carp (Cyprinus carpio) eDNA into recirculating mesocosms (n = 24) under varying light (shaded versus open) and benthic substrate conditions (no substrate, bare substrate, and biofilm-colonized substrate). We then collected water samples from each mesocosm at four time points (40 min, 6 h, 18 h, and 48 h), and sequentially filtered the samples through 10, 1.0, and 0.2 μm filters to quantify removal rates for different eDNA particle sizes under varying light and substrate conditions. Combining all size classes, total eDNA removal rates were higher for mesocosms with biofilm-colonized substrate compared to those with no substrate or bare (i.e., no biofilm) substrate, which is consistent with previous findings linking biofilm colonization with increased eDNA removal and degradation. Additionally, when biofilm was present, light availability increased eDNA removal; eDNA levels fell below detection after 6-18 h for open mesocosms versus 18-48 h for shaded mesocosms. Among size classes, larger particles (>10 μm) were removed faster than small particles (1.0-0.2 μm). These results suggest that changes in the distribution of eDNA size classes over time (e.g., with downstream transport) and with differing environmental conditions could be used to predict the location of target organisms in flowing waters, which will advance the use of eDNA as a tool for species monitoring and management.

Keywords: Aquatic biomonitoring; Particle size distribution; ddPCR; eDNA ecology; eDNA transport.