Targeted Environmental RNA Profiling Through RNase-Guided Depletion and Enrichment

Environmental RNA (eRNA) is rapidly emerging as a non-invasive tool for assessing biodiversity and biological function in natural systems. However, its full potential remains constrained by low RNA yields, mixed biological sources, and the compositional dominance of abundant RNA classes (especially rRNA) within complex intra- and extra-organismal RNA pools. In this article, a conceptual framework is proposed for integrating ribonuclease (RNase)-guided depletion and enrichment strategies into eRNA workflows. By selectively targeting specific RNA types through stepwise RNase application, and pairing these treatments with minimal-input-compatible enrichment techniques, the specificity and interpretability of eRNA data can be significantly enhanced. Particular attention is given to underexplored RNA molecules such as circular RNAs, tRNA fragments, and regulatory small RNAs, whose environmental signatures may be masked by more abundant counterparts. The feasibility of using RNases as both molecular filters and structure-informed functional probes is examined across a variety of RNA classes and environmental conditions. Rather than offering definitive protocols, this conceptual roadmap aims to stimulate cross-disciplinary dialogue between molecular biologists, ecologists, and environmental scientists, and to inspire future investigations into targeted eRNA profiling. In doing so, the overlooked utility of RNases is reframed not as a threat to RNA integrity, but as a powerful ally in deciphering the complexity of environmental transcriptomes.