Seasonal and Environmental Influences on Microbial Community Dynamics in the Dunk River Watershed, Prince Edward Island, Canada

ABSTRACT Riverine ecosystems are crucial biogeochemical hubs, with their microbial communities playing a key role in nutrient cycling and overall ecosystem health. This study used shotgun metagenomic sequencing to characterize the seasonal and environmental drivers of taxonomic and functional microbial community structure (read depth between 1.91 and 30.44 bp) in four tributaries of the Dunk River watershed in Prince Edward Island (PEI), a landscape shaped by intensive agriculture and groundwater‐dominated streamflow, where the seasonal and land‐use impacts on the river's microbiome remain understudied. Although taxonomic composition showed no significant spatial variation among sampling sites, functional profiling identified subtle but distinct spatial signatures, primarily driven at the site with the least human impacts. Mass effects driven by above‐ or below‐ground water dispersal pathways may override local selective pressures, resulting in a more uniform community structure across different locations. The study also identified significant correlations between certain rare microbial taxa and nutrient concentrations. This work provides critical baseline data on microbial ecology in PEI river systems, indicating that while temporal factors are the primary identifiable drivers among the measured variables, a substantial majority of the community variance remains unexplained, likely reflecting the inherent stochasticity of open riverine ecosystems.