Spatiotemporal intermittence effect on periphyton microbial communities in a tropical drying river network

Drying river networks (DRNs) are globally expanding ecosystems where hydrological intermittence, including surface-flow cessation and habitat fragmentation, profoundly shapes biodiversity, ecological functions, and biogeochemical processes. Despite growing knowledge, the role of microbial communities inhabiting periphyton in tropical DRNs remains poorly understood. Here, we conducted the first spatiotemporal metabarcoding assessment (16S & 18S V4 amplicon sequencing) of bacteria, phototrophs, and fungi in stream periphyton across the Cube Drying River Network, located in Ecuador’s Chocó–Darién biodiversity hotspot. We sampled 20 reaches spanning perennial and intermittent sites during six campaigns across an intermittence gradient. Microbial α-diversity increased with drying, peaking at the highest intermittence (45%), with phototrophs and fungi exhibiting significant gains compared to wetter phases. Community β-diversity declined as intermittence intensified, indicating homogenization of assemblages under sustained hydric stress and restricted dispersal due to disconnection of surface flow. Variation partitioning showed that major dissolved constituents (e.g., Ca²⁺, Mg²⁺, NO₃⁻, TOC) explained ~6% of compositional shifts, while environmental variables and trace elements accounted for smaller fractions. Co-occurrence network analyses revealed that interactions among microbial groups intensified with drying, culminating in highly connected yet low-modularity networks, which suggests reduced resilience under prolonged intermittence. Our results contrast with patterns reported in temperate and arid systems, where drying typically reduces microbial diversity, underscoring the particular dynamics of tropical DRNs, which are dominated by isolated pools and incomplete drying. These findings underscore the role of periphyton as critical microbial hubs that regulate ecosystem functioning under fluctuating flow regimes and emphasize the urgent need to integrate microbial dynamics into global assessments of river network resilience in the face of climate change.