Integrating Microbial Ecology and Sustainability: Linking Agricultural Waste Gas Streams to Microbial Community Shifts in a Photobioreactor

Photobioreactors (PBRs) functionally coupled animal housing offer great potential as sustainable technologies to mitigate gaseous emissions such as CO2 and NH3 while simultaneously producing value-added biomass. Here, we present the first systematic investigation of microbial community shifts in such a system, with a specific focus on carbon and nitrogen metabolism. Using a cone-shaped, helical PBR continuously cultivating Arthrospira platensis (Spirulina) and coupled to a chicken house, we introduced controlled perturbations (exhaust-air input and biomass harvesting) to probe community resilience. Time-resolved microbiome and functional profiling revealed marked, perturbation-dependent reorganizations of the microbial community, including signatures of enhanced carbon fixation and nitrogen cycling, while integrated biochemical and genomic analyses of Arthrospira provided mechanistic insights into these dynamics. We also show that the use of cultivation matrices stabilizes the microbiome, maintaining community composition and functional profiles under perturbation. Overall, our results demonstrate that coupling PBRs to agricultural exhaust streams not only enables valorization of CO2 and NH3 into biomass but also fosters a resilient microbial ecosystem, thereby establishing a novel framework that links sustainable emission-mitigation technologies with microbial ecology and opens new avenues for circular bioeconomy strategies.