eDNA-qPCR Reveals Spatial Biomass and Habitat Associations of the Endangered Brachymystax lenok tsinlingensis in Zhouzhi Heihe River

Brachymystax lenok tsinlingensis is an endangered salmonid endemic to China. Traditional trapping methods frequently fail to detect this rare fish in low-density mountain streams, hampering evidence-based conservation. Here, we employed environmental DNA quantitative PCR (eDNA-qPCR) with species-specific primers to assess the spatial biomass distribution of this species in the Zhouzhi Heihe River. Concurrently, we surveyed plankton, benthic macroinvertebrates, and physicochemical water parameters. eDNA detected the target species at 12 of 14 sites, with reliable quantification achieved at 9 sites, suggesting that the method may be more effective than conventional trapping for detecting this species under the studied low-density conditions. eDNA-derived relative biomass exhibited pronounced spatial heterogeneity, ranging from 6.0 × 10−4 to 1.5 × 10−2 g/cm3. Water depth showed a significant positive association with biomass (r = 0.5347), whereas phytoplankton Shannon diversity (a measure of species richness and evenness) was significantly negatively correlated (r = −0.5447). Flow velocity displayed a negative trend that did not reach statistical significance (r = −0.5009). Plankton and benthic communities indicated overall ecological conditions but did not directly explain the observed spatial variation in fish biomass. These findings indicate that the spatial pattern of B. lenok tsinlingensis is primarily shaped by local physical habitat structure, with deeper, hydraulically more complex channel units serving as key microhabitats. eDNA-qPCR thus represents an effective, low-disturbance monitoring tool for this endangered cold-water fish and provides a scientific basis for targeted habitat protection and restoration.