Citation:

Giroux, M., J. Reichman, T. Langknecht, R. Burgess, AND K. Ho. Environmental RNA as a Tool for Marine Community Biodiversity Assessments. Scientific Reports. Nature Publishing Group, London, Uk, 12(1):17782, (2022). https://doi.org/10.1038/s41598-022-22198-w

Impact/Purpose:

Identifying microscopic organisms using traditional microscopy-based methods is a time consuming and difficult process. Molecular identification using DNA collected from environmental samples (environemental DNA/ eDNA) is an emerging method for the rapid identification of organisms. However, eDNA can be detected from organisms no longer in the environment (i.e. deceased or migrated) at the time of sampling, so it may not give an accurate snapshot of the organisms present in the study site of interest. Environmental RNA (eRNA) can also be collected and sequenced for identification, and may be favorable to eDNA because RNA is only produced by living organisms. This study compares the organsisms detected using eDNA and eRNA in order to better develop accurate methods for rapid detection of biodiversity. 

Description:

Microscopic organisms are often overlooked in traditional diversity assessments due to the difficulty of identifying them based on morphology. Metabarcoding is a method for rapidly identifying organisms where Environmental DNA (eDNA) is used as a template. However, legacy DNA is problematically detected from organisms no longer in the environment during sampling. Environmental RNA (eRNA), which is only produced by living organisms, can also be collected from environmental samples and used for metabarcoding. The aim of this study was to determine differences in community composition and diversity between eRNA and eDNA templates for metabarcoding. Using mesocosms containing field-collected communities from an estuary, RNA and DNA were co-extracted from sediment, libraries were prepared for two loci (18S and COI), and sequenced using an Illumina MiSeq. Results show a higher number of unique sequences detected from eRNA in both markers and higher α-diversity compared to eDNA. Significant differences between eRNA and eDNA for all β-diversity metrics were also detected. This study is the first to demonstrate community differences detected with eRNA compared to eDNA from an estuarine system and illustrates the broad applications of eRNA as a tool for assessing benthic community diversity, particularly for environmental conservation and management applications.

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