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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

Morgado Gamero, Wendy Beatriz12; Cristescu, Melania E.1; Tournayre, Orianne13

Research facility: the Genome Canada BIOSCAN Canada initiative
Published Aug 15, 2025 on Dryad. https://doi.org/10.5061/dryad.kprr4xhh4

Data files

Aug 15, 2025 version files 70.76 KB

Abstract

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.