Skip to main content
Dryad logo

Data supporting: Environmental RNA degrades more rapidly than environmental DNA across a broad range of pH conditions

Citation

Kagzi, Kaushar; Hechler, Robert; Fussmann, Gregor; Cristescu, Melania (2022), Data supporting: Environmental RNA degrades more rapidly than environmental DNA across a broad range of pH conditions, Dryad, Dataset, https://doi.org/10.5061/dryad.4qrfj6qc0

Abstract

Although the use and development of molecular biomonitoring tools based on environmental nucleic acids (eDNA and eRNA; collectively known as eNAs) have gained broad interest for the quantification of biodiversity in natural ecosystems, studies investigating the impact of site-specific physicochemical parameters on eNA-based detection methods (particularly eRNA) remain scarce. Here, we used a controlled laboratory microcosm experiment to comparatively assess the environmental degradation of eDNA and eRNA across an acid-base gradient following complete removal of the progenitor organism (Daphnia pulex). Using water samples collected over a 30-day period, eDNA and eRNA copy numbers were quantified using a droplet digital PCR (ddPCR) assay targeting the mitochondrial cytochrome c oxidase subunit I (COI) gene of D. pulex. We found that eRNA decayed more rapidly than eDNA at all pH conditions tested, with detectability­—predicted by an exponential decay model—for up to 57 hours (eRNA; neutral pH) and 143 days (eDNA; acidic pH) post organismal removal. Decay rates for eDNA were significantly higher in neutral and alkaline conditions than in acidic conditions, while decay rates for eRNA did not differ significantly among pH levels. Collectively, our findings provide the basis for a predictive framework assessing the persistence and degradation dynamics of eRNA and eDNA across a range of ecologically relevant pH conditions, establish the potential for eRNA to be used in spatially and temporally sensitive biomonitoring studies (as it is detectable across a range of pH levels), and may be used to inform future sampling strategies in aquatic habitats.

Methods

This dataset was assembled as described in the resulting publication and in the README file. 

Usage Notes

See the README file for a detailed account of the content of the uploaded file. 

Funding

NSERC Discovery Grant, Award: 04331-2017

CFREF Food from Thought Agricultural Systems for a Healthy Planet, Award: CFREF-2015-0004