Due to pervasive anthropogenic influences (e.g., habitat alteration, climate change), current rates of biodiversity loss in the Sacramento-San Joaquin Delta are unprecedented. Application of appropriate management regimes and mitigation measures thus require effective biological monitoring to adaptively manage systems. Non-invasive environmental DNA (eDNA)-based tools for endangered species monitoring have gained attention as a complementary approach to traditional sampling because of their increased sensitivity and accurate quantification. However, the unique characteristics of environmental RNA (eRNA) make it a novel tool, allowing us to gain additional information that is not possible to obtain with eDNA. Using novel eRNA tools to improve detection and quantify health status of Smelt has only been theorized and remains to be empirically tested. Both Delta and Longfin Smelt species were historically ubiquitous in the Sacramento-San Joaquin Delta, but have declined precipitously over the past several decades. One source of mortality is entrainment into the south Delta water export pumps. Although the entrainment of juvenile and adult smelt has been regularly monitored at fish salvage facilities, entrainment of larval smelt (< 20 mm) is not quantified, thus remains largely unknown. Moreover, given the current climate change effect (e.g., increased heat stress), an understanding of how these endangered species will respond to acute stress response in the wild is lacking.
