Environmental RNA as a Tool for Marine Community Biodiversity Assessments

Abstract

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.

Environmental RNA as a Noninvasive Tool for Assessing Toxic Effects in Fish: A Proof-of-concept Study Using Japanese Medaka Exposed to Pyrene

“…Unlike DNA, RNA is only produced for genes that are actively being transcribed, making it a useful tool for understanding the “real time” status of the organisms. Recent studies reported that the degradation of eRNA for some genes was slower than previously expected. − eRNA has been detected for a wide range of aquatic species, including fish, ,, water fleas, , polychaetas, ,, mussels, ascidians, algae, and others . Also, eRNA has been detected for both mitochondrial and nuclear genes ,, and for several microRNAs .…”

“…Recent studies reported that the degradation of eRNA for some genes was slower than previously expected. 14−17 eRNA has been detected for a wide range of aquatic species, including fish, 16,18,19 water fleas, 17,20 polychaetas, 14,21,22 mussels, 15 ascidians, 14 algae, 23 and others. 22 Also, eRNA has been detected for both mitochondrial and nuclear genes 15,16,18 and for several microRNAs.…”

“…14−17 eRNA has been detected for a wide range of aquatic species, including fish, 16,18,19 water fleas, 17,20 polychaetas, 14,21,22 mussels, 15 ascidians, 14 algae, 23 and others. 22 Also, eRNA has been detected for both mitochondrial and nuclear genes 15,16,18 and for several microRNAs. 24 In addition, eRNA may originate from various tissues including gills, skin, and mucus.…”

Harnessing decay rates for coastal marine biosecurity applications: A review of environmental DNA and RNA fate

“…Analysis of eRNA ecology and fate within an aquatic environment and particularly in marine environments, is still in its infancy, and the lack of data on its basic ecological properties, such as common forms present in the environment (e.g., particulate, cellular or extracellular), persistence and degradation mechanism, means its biomonitoring performance remains unclear (Jo, Tsuri, et al, 2022). However, recent proof‐of‐concept studies have demonstrated that eRNA, combined with eDNA, is a promising tool for biodiversity assessment and marine biosecurity programs (Giroux et al, 2022; Laroche et al, 2018; Miyata et al, 2021; Veilleux et al, 2021; Yates et al, 2021). Environmental RNA's faster decay rate allows for inferences about the presence or absence of species in “real‐time,” enabling better identification of living and viable organisms/assemblages, increased sensitivity, reducing false positives and enabling the estimate of species abundance with more precision (Bowers et al, 2021; Farrell et al, 2021; Kagzi et al, 2022; Miyata et al, 2021; Qian et al, 2022; Wood et al, 2020).…”

“…However, recent proof-of-concept studies have demonstrated that eRNA, combined with eDNA, is a promising tool for biodiversity assessment and marine biosecurity programs (Giroux et al, 2022;Laroche et al, 2018;Miyata et al, 2021;Veilleux et al, 2021;Yates et al, 2021). Environmental RNA's faster decay rate allows for inferences about the presence or absence of species in "real-time," enabling better identification of living and viable organisms/assemblages, increased sensitivity, reducing false positives and enabling the estimate of species abundance with more precision (Bowers et al, 2021;Farrell et al, 2021;Kagzi et al, 2022;Miyata et al, 2021;Qian et al, 2022;Wood et al, 2020).…”