Sorting states of environmental DNA: Effects of isolation method and water matrix on recovery of membrane-bound, dissolved, and adsorbed states of eDNA

Environmental DNA (eDNA) once shed can exist in numerous states with varying behaviors including degradation rates and transport potential. In this study we consider three states of eDNA: 1) a membrane-bound state referring to DNA enveloped in a cellular or organellar membrane, 2) a dissolved state defined as the extracellular DNA molecule in the environment without any interaction with other particles, and 3) an adsorbed state defined as extracellular DNA adsorbed to a particle surface in the environment. Capturing, isolating, and analyzing a target state of eDNA provides utility for better interpretation of eDNA degradation rates and transport potential. While methods for separating different states of DNA have been developed, they remain poorly evaluated due to the lack of state-controlled experimentation. We evaluated the methods for separating states of eDNA from a single sample by spiking DNA from three different species to represent the three states of eDNA as state-specific cont...,       Adsorbed DNA State: Sheared salmon sperm DNA (Invitrogen, Waltham, MA) was diluted to 100 ng/µL in 6 mL nuclease-free molecular grade water (Sigma-Aldrich, St. Louis, MO) in a 15 mL tube with 300 g (50 mg/mL) montmorillonite clay K10 (Fluka, Buchs, CH). One no-adsorbent control tube was created by diluting salmon DNA to 100 ng/µL in 1 mL nuclease-free molecular grade water, but with no clay. The tubes were shaken at 600 rpm for 48 hours. Previous work demonstrated that most of the DNA adsorption in similar concentrations reached equilibrium well within this timeframe (Kirtane et al., 2020). At 48 hours, the tube with the salmon DNA and clay was centrifuged at 4500 xg for five minutes and the supernatant was separated from the pelleted clay with a pipette. The pelleted clay was then washed using 6 mL nuclease-free molecular grade water by vortexing followed by centrifugation at 4500 xg for five minutes and the supernatant was separated to remove any non-adsorbed salmon DNA. This wa..., , # Data from: Sorting states of environmental DNA: Effects of isolation method and water matrix on recovery of membrane-bound, dissolved, and adsorbed states of eDNA

[https://doi.org/10.5061/dryad.wstqjq2rq](https://doi.org/10.5061/dryad.wstqjq2rq)

 This dataset contains the qPCR amplification results of mouse, salmon and chicken targets. The data is presented in two separate files, one for the standard curves and one for the quantification of the samples.

 **Description of the data and file structure**

 This data contains the following fields described below  

1\) all_samples_combined.csv

 name: code name for each sample. Please refer to the experimental setup and methodology described in the publication for better understanding of the sample ID.

cp - exported cp values. These are the fluorosence values exported at a given threshold showing the level of qPCR amplification

ID - unique identifier for the fluorophore, spike, water matrix, state extraction protocol, qPCR plate numbe...