Environmental RNA: Monitoring Ecosystems with eRNA


Traditional methods for monitoring ecological health, like catching or observing organisms, can be time-consuming, disruptive, and miss rare or elusive species. Environmental DNA (eDNA) analysis offered a non-invasive alternative, detecting DNA shed by organisms in their environment. However, eDNA can persist for a long time, potentially indicating organisms no longer present. Environmental RNA (eRNA) addresses this limitation by offering a new approach to ecological monitoring.

What is eRNA?

eRNA consists of messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA) molecules found in the environment. Unlike eDNA, which can last weeks or months, eRNA degrades quickly, typically within hours or days. This makes eRNA ideal for detecting organisms currently living within an ecosystem. By analyzing the eRNA profile of a sample, researchers can gain insights into the species present and their activity.

Schematic of experimental design, in which the degradation rates of environmental (e)DNA and (e)RNA were compared across multiple genes collected in environmental genomic material released from dreissenid mussels. The concentration of eRNA depletes faster than eDNA, providing a predictor for estimating time since genomic material release

Applications of eRNA in Ecosystem Monitoring

  • Species Detection and Biodiversity Assessment: eRNA sequencing allows for the identification of organisms present in a sample through their unique RNA signatures. This provides a more accurate picture of biodiversity compared to eDNA, as eRNA reflects the living portion of the community.
  • Functional Monitoring: eRNA analysis goes beyond just identifying species. By studying the expressed genes (transcripts) in the eRNA pool, researchers can assess the physiological state and activity of organisms within the ecosystem. This can provide valuable insights into ecosystem health and how organisms respond to environmental changes.
  • Pathogen Detection: eRNA analysis has the potential for rapid and sensitive detection of pathogens in environmental samples. By identifying specific RNA sequences associated with known pathogens, researchers can implement early intervention strategies to mitigate disease outbreaks.

Advantages of eRNA Monitoring

  • High Spatiotemporal Resolution: The rapid degradation of eRNA allows for a more precise understanding of the current ecological state compared to eDNA. This enables researchers to detect changes in communities over shorter timescales.
  • Minimally Invasive: eRNA analysis can be conducted using water, soil, or sediment samples, eliminating the need to directly capture organisms, which can be disruptive and potentially harm sensitive species.
  • Cost-Effective: With advancements in sequencing technologies, eRNA analysis is becoming increasingly affordable, making it a viable tool for large-scale ecological monitoring programs.

Environmental RNA (eRNA) has the potential to significantly improve population and community biological monitoring applications by moving beyond environmental DNA (eDNA) detection of species presence, abundance, and diversity towards enhanced detection and diagnostics of population and community characteristics.

Challenges and Future Directions

Despite its promise, eRNA analysis faces challenges. Standardizing sampling and data analysis methods is crucial for reliable comparisons across studies. Additionally, reference databases for eRNA sequences are still being developed, particularly for complex microbial communities.

Future research should focus on expanding reference databases, refining extraction and analysis techniques, and understanding how environmental factors influence eRNA degradation rates. Overcoming these challenges will unlock the full potential of eRNA as a transformative tool for ecosystem monitoring and conservation efforts.

Analysis of differentially expressed eRNAs and identification of subtype-related eRNA-target gene pairs in GC (A) The volcano plot showed 1,724 differentially expressed eRNAs between Immune_M and no_Immune_M subtypes. Each red dot showed an upregulated eRNA, and each blue dot showed a downregulated eRNA (p<0.05). (B) The volcano plot showed 1,114 differentially expressed eRNAs between Immune_H and no_Immune_H subtypes. Each red dot showed an upregulated eRNA, and each blue dot showed a downregulated eRNA (p<0.05). (C) The volcano plot showed 71 differentially expressed eRNAs between Immune_L and no_Immune_L subtypes. Each red dot showed an upregulated eRNA, and each blue dot showed a downregulated eRNA (p<0.05). (D) The Venn plot showed 1,766 unique differentially expressed eRNAs between the three eRNA subtypes. (E) Sankey plot showed subtype-related eRNA-target gene pairs in three eRNA subtypes. The GO terms were regulated by the target gene, also shown in this plot.


eRNA analysis is a significant advancement in ecological monitoring. By providing a direct measure of the living components of an ecosystem and their activity, eRNA offers valuable insights into biodiversity, ecosystem health, and potential threats. As research progresses and methodologies are refined, eRNA analysis has the potential to revolutionize how we monitor and manage our ecosystems.

Environmental RNA: Monitoring Ecosystems with eRNA
Gen store May 27, 2024
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