Biomonitoring 3.0: From Taxa Lists to Interaction-Ready, Time-Resolved Ecosystem Monitoring

Biomonitoring has been transformed by high-throughput sequencing from morphology-based indices to scalable molecular inventories, yet monitoring has remained dominated by taxa lists. In this Perspective, Biomonitoring 3.0 is proposed as interaction-ready, time-resolved ecosystem monitoring, with environmental RNA positioned as a complementary layer through which more recent biological activity and context-dependent responses can often be reported. An inference ladder is introduced to grade interaction evidence from co-occurrence patterns to coupled signal–response dynamics and, where feasible, ecosystem-level consequences. Field designs are outlined in which time-lagged series, paired sampling of signal sources and putative recipients, and carrier-aware handling of extracellular RNA are emphasized to reduce legacy detection and strengthen attribution. Minimum reporting elements are recommended to support cross-study synthesis and benchmarking. The “3.0” designation is justified as a third step beyond Biomonitoring 2.0 inventories: monitoring is redirected from static membership toward dynamics and feedbacks that govern ecosystem function and decision-relevant change. A pragmatic agenda is provided for converting environmental nucleic acids into interaction indicators rather than presence records.