DOI: 10.5061/dryad.kprr4xhh4
title: Data from: Comparative patterns of temporal decay and detectability of eDNA and eRNA across molecular markers in connected and isolated freshwater mesocosms using digital PCR

description: Efficient use of environmental nucleic acids (eNAs) in freshwater
 biodiversity monitoring requires understanding their degradation and
 detectability in interconnected ecosystems. Environmental RNA (eRNA),
 which degrades faster than environmental DNA (eDNA), can enhance the
 temporal resolution of biological signals. This study employs a novel
 field-scale assay to investigate decay rates and detectability of eDNA and
 eRNA across four genetic markers (16S, 18S, COI, and LDHA) in 1000-liter
 connected and isolated mesocosms containing natural planktonic
 assemblages, assessing how connectivity influences detectability over
 time. This design bridges small-scale laboratory assays with more complex,
 ecologically relevant settings. Using digital PCR (dPCR), we captured
 fine-scale temporal patterns across mitochondrial and nuclear markers and
 transcript types (mRNA and rRNA), an approach rarely combined in previous
 research. Isolated and head mesocosms were spiked with eNAs from cultured
 Daphnia pulex, absent from the water source. Downstream mesocosms received
 eNAs via unidirectional water transfers. The experiment spanned 24 days,
 with water samples collected at nine time points post-spike (0, 1, 6, 8,
 24, 48, 72, 168, and 576 hours). From each mesocosm, four replicate water
 samples were collected at each time point—two for eDNA and two for eRNA
 analyses. eRNA degraded significantly faster than eDNA across all markers
 and mesocosm types. Among RNA types, mRNA (COI, LDHA) degraded faster than
 rRNA (16S, 18S). While decay rates remained consistent across the network,
 detectability declined with dilution. We found that eRNA followed a
 uniform monophasic decay pattern, whereas eDNA displayed biphasic decay
 for nuclear and monophasic decay for mitochondrial markers. eNA decay
 rates in this field-relevant mesocosm network exceeded those from
 laboratory scale. Both eNAs were detected in terminal mesocosms despite a
 10,000-fold dilution, demonstrating transport. Despite rapid RNA
 degradation, high detectability was achieved using dPCR across dilutions,
 highlighting eRNA's utility for detecting active biological
 communities in freshwater systems.
description: # Data from: Comparative patterns of temporal decay and detectability of
 eDNA and eRNA across molecular markers in connected and isolated
 freshwater mesocosms using digital PCR Dataset DOI:
 [10.5061/dryad.kprr4xhh4](10.5061/dryad.kprr4xhh4) ## Description of the
 data and file structure This README_file.txt file was generated on
 2025-07-22 by Wendy Morgado GENERAL INFORMATION 1\. Title: Data supporting
 "Comparative patterns of temporal decay and detectability of eDNA and
 eRNA across molecular markers in connected and isolated freshwater
 mesocosms using digital PCR" 2\. Author Information ``` Name: Wendy
 B. Morgado-Gamero Institution: Stewart Biology Building, McGill University
 Address: 1205 Dr Penfield Ave, Montreal, Quebec H3A 1B1 Email:
 wendy.morgadogamero@mail.mcgill.ca, wbmorgadogamero@gmail.com Name:
 Orianne Tournayre Institution: Stewart Biology Building, McGill University
 Address: 1205 Dr Penfield Ave, Montreal, Quebec H3A 1B1 Email:
 orianne.tournayre@gmail.com Name: Melania E. Cristescu Institution:
 Stewart Biology Building, McGill University Address: 1205 Dr Penfield Ave,
 Montreal, Quebec H3A 1B1 Email: melania.cristescu@mcgill.ca ``` 3\. Date
 of data collection (range, approximate date): 2021 - 2023 4\. Geographic
 location of data collection: Mont-Saint Hilaire, Quebec, Canada 5\.
 Keywords: environmental DNA, environmental RNA, biomonitoring, decay
 rates, aquatic ecosystems, mesocosms, molecular markers, digital PCR. 6\.
 Information about funding sources that supported the collection of the
 data: NSERC Discovery Grant, the Genome Canada BIOSCAN Canada initiative,
 as well as the Government of Canada’s New Frontiers in Research Fund
 (NFRF) T2020, BIOSCAN: Tracing the Patterns of Life on a Changing Planet.
 SHARING/ACCESS INFORMATION This is an original dataset generated using the
 methods as described in the resulting publication. DATA & FILE
 OVERVIEW 1\. File List: This file contains the following data tables
 generated for this study: \- Data summary table. Average concentration
 (copies/mL) and standard deviation (SD) between sample replicates for each
 mesocosm replicate (a, b, c), eNA molecule (eRNA, eDNA), marker (COI, 18S,
 16S, LDHA), mesocosm condition (isolated, connected), and sampling point
 (Hours). \- Filtration blank table. dPCR concentration (copies/µL)
 quantified in the filtration blanks. \- No template controls table. dPCR
 concentration (copies/µL) quantified in the no template controls. \-
 Negative control table. dPCR concentration (copies/µL) quantified in the
 negative controls. \- Duplex validation table. dPCR concentration
 (copies/µL) for each singleplex and duplex combination, and their average
 concentration and standard deviation (SD). \- LOQ table. dPCR
 concentration (copies/µL) of each duplex combination, their average
 concentration over dPCR technical replicates (“Average read”), standard
 deviation, and coefficient of variation. “Expected reads” indicated the
 concentration calculated from the initial standard concentration and the
 dilution factor. “dPCR reads” indicated concentration quantified by the
 instrument (copies/µL). 2\. Date that file was created: 2025-01
 METHODOLOGICAL INFORMATION All methods used to generate data are outlined
 in the resulting publication. ### Files and variables #### File:
 datasets.xlsx **Data summary table.** Average concentration (copies/mL)
 and standard deviation (SD) calculated across sample replicates for each
 mesocosm replicate (a, b, c), eNA molecule (eRNA, eDNA), marker (COI, 18S,
 16S, LDHA), mesocosm condition (isolated, connected), and sampling time
 point (Hours). **Negative control table**. dPCR  concentration
 (copies/µL) quantified in the negative controls. **No template controls
 table**. dPCR  concentration (copies/µL) quantified in the no
 template controls. **Filtration blank table**. dPCR 
 concentration (copies/µL) quantified in the filtration blanks. **Duplex
 validation table**. dPCR concentration (copies/µL) for each singleplex and
 duplex combination, and their average concentration and standard deviation
 (SD) calculated across singleplex and duplex. **Limit of Quantification
 Table.** dPCR concentration (copies/µL) of each duplex combination, their
 average concentration over dPCR technical replicates (“Average read”),
 standard deviation, and coefficient of variation. “Expected reads”
 indicates the concentration calculated from the initial standard
 concentration and the dilution factor. “dPCR reads” indicates the
 concentration quantified by the instrument (copies/µL).