An aquatic environmental DNA filtration system to maximize recovery potential and promote filtration approach standardization

PeerJ. 2023 Jul 12:11:e15360. doi: 10.7717/peerj.15360. eCollection 2023.


Background: Aquatic environmental DNA (eDNA) has emerged as a promising approach to identify organisms in freshwater and marine environments. While the recovery of eDNA from water most commonly involves capture of biological debris on a filter matrix, practitioners are yet to converge on standardized approaches for filtration, particularly in the field. This lack of standardization has resulted in inconsistent handling of samples following collection, limiting interpretation of results across studies and burdening groups with inconvenient storage and transport logistics that may compromise eDNA integrity.

Methods: A simple to assemble and low-cost ($350 USD) water filtration system is demonstrated that can be used in field and laboratory settings to reduce time between sample acquisition and eDNA filtration, maximizing eDNA sample recovery. Quantitative PCR is used to show the utility of the platform for laboratory and marine eDNA analysis.

Results: The resulting eDNA collection system is easily transported in a rugged water-resistant case, operates for more than eight hours on a 12-volt lead-acid battery, and has an unobstructed filtration rate of 150.05 ± 7.01 mL/min and 151.70 ± 6.72 mL/min with 0.22 µm and 0.45 µm Sterivex filters, respectively. We show that immediate sample filtration increases eDNA recovery in the laboratory, and demonstrate collections in aquaria and marine environments. We anticipate that providing easy to obtain, open hardware designs for eDNA sample collection will increase standardization of aquatic eDNA collection methods and improve cross-study comparisons.

Keywords: Biodiversity; Environmental DNA; Field analysis; Invasive species; eDNA.

Publication types

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

MeSH terms

  • DNA, Environmental* / genetics
  • Fresh Water
  • Nucleic Acid Amplification Techniques
  • Polymerase Chain Reaction
  • Water


  • DNA, Environmental
  • Water

Grants and funding

This study was funded by JHU/APL Internal Research and Development and the Department of Navy award N00014-21-1-2610 issued by the Office of Naval Research. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.