Simple Passive Environmental DNA Samplers for Marine Biomonitoring in Resource-Limited Programs

Abstract

The analysis of environmental DNA (eDNA) is a powerful tool for rapidly assessing biodiversity across aquatic ecosystems. Its implementation remains limited, however, by the logistical complexity of standard eDNA workflows, which often require specialized equipment and expertise. This protocol presents passive environmental DNA samplers (PEDS) as a simplified, low-cost alternative to conventional active water filtration methods. PEDS are designed for ease of use, enabling ambient eDNA capture without pumps or filtration systems, and allowing for rapid deployment and retrieval with short field exposures (∼15 min). We detail procedures for construction, deployment, and retrieval, alongside recommendations for minimizing contamination and optimizing DNA recovery. DNA is extracted from cotton membranes housed within the PEDS unit using a modified Qiagen DNeasy Blood & Tissue protocol. The protocol was validated at the Papahānaumokuākea Marine National Monument, Hawaiʻi, where PEDS were used to detect Chondria tumulosa, a cryptogenic nuisance alga, as part of ongoing conservation efforts. The use of simplistic PEDS and cotton membranes provides a cost-effective and scalable method for researchers seeking to implement eDNA-based monitoring in marine and other aquatic environments. © 2025 Wiley Periodicals LLC.

Basic Protocol 1: Assembly and deployment of PEDS on stationary buoys

Alternate Protocol: Assembly and deployment of PEDS on roving surveyors

Basic Protocol 2: Processing and storage of sample membranes

Support Protocol 1: Extraction of DNA from PEDS membranes

Support Protocol 2: Amplification of extracted DNA by PCR