Urban multidimensional stress disrupts cross-domain microbial networks in river sediments

Freshwater sediments are increasingly exposed to anthropogenic stressors, yet their effects on cross-domain microbial interactions remain poorly understood. We analyzed microbial co-occurrence networks—including bacteria, protists, and fungi—in sediments from two urban river systems in Central Chile (Aconcagua and Maipo) using high-throughput metabarcoding. Sites under multidimensional stress exhibited fragmented networks with isolated modules, reduced cross-domain connectivity, and a predominance of positive correlations. Potential keystone taxa under micropollutant stress include members of Firmicutes, Ciliophora and Rozellomycota, which may drive the microbiome stability. Negative co-occurrences between protists and bacteria suggested ecological competition or niche partitioning in contaminated zones. In contrast, reference sites showed more cohesive networks with highly connected modules and strong negative co-occurrences, particularly between Proteobacteria, Ascomycota and Basidiomycota. These findings underscore the vulnerability of cross-domain microbial assemblages to urban contamination and point to specific microbial groups as candidate bioindicators for monitoring ecosystem integrity under modern anthropogenic pressures.