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Development and Testing of Species-specific Quantitative PCR Assays for Environmental DNA Applications
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Comparative Decay Dynamics and Detectability of eDNA and eRNA in Connected and Isolated Freshwater Mesocosms Using

Wendy B Morgado-Gamero1, Orianne Tournayre1,2, Melania E Cristescu1

  • 1Department of Biology, McGill University, Montreal, Quebec, Canada.

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|August 13, 2025
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Summary

Environmental RNA (eRNA) degrades faster than environmental DNA (eDNA), but digital PCR (dPCR) detects both across diluted freshwater networks, showing eRNA

Keywords:
aquatic ecosystemsbiomonitoringdecay ratesdigital PCRenvironmental DNAenvironmental RNAmesocosmsmolecular markers

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Area of Science:

  • Environmental molecular biology
  • Freshwater ecosystem monitoring
  • Biodiversity assessment

Background:

  • Environmental nucleic acids (eNAs) are crucial for freshwater biodiversity monitoring.
  • Understanding eNA degradation and detectability in interconnected systems is vital.
  • Field-scale assays are needed to assess eNA dynamics in ecologically relevant settings.

Purpose of the Study:

  • To compare environmental DNA (eDNA) and environmental RNA (eRNA) decay rates and detectability.
  • To assess the influence of ecosystem connectivity on eNA detectability over time.
  • To evaluate eNA transport and detection in a connected mesocosm network.

Main Methods:

  • Novel field-scale assay using 1000-L connected and isolated mesocosms.
  • Comparison of four genetic markers (16S, 18S, COI, LDHA) and transcript types (mRNA, rRNA).
  • Quantification of eNA decay and detectability using digital PCR (dPCR).

Main Results:

  • eRNA degraded significantly faster than eDNA across all markers and mesocosm types.
  • mRNA degraded faster than rRNA; eDNA showed biphasic decay for nuclear markers and monophasic for mitochondrial.
  • eNA transport was effective across the network, with detection after 10,000-fold dilution.

Conclusions:

  • eRNA's rapid degradation is offset by high detectability using dPCR, indicating its potential for monitoring active communities.
  • Ecosystem connectivity facilitates eNA transport, but detectability decreases with dilution.
  • Field-scale mesocosm networks provide ecologically relevant insights into eNA dynamics.