Genome-resolved metagenomics of an acid-tolerant nitrifying biofilm suggests cooperative nitrogen cycling at low pH

Ammonia emissions from animal feeding operations are a major source of nitrogen loss and environmental pollution. Nitrifying bacteria used within ammonia scrubbers offers a promising strategy to recover nitrogen for fertilizer; however, the acidic environment within air scrubbers generally inhibits nitrification and sustained nitrification at low pH remains poorly understood. Here, we present a genome-resolved analysis of an acid-tolerant nitrifying community (ATNC) enriched from a laboratory bioreactor operating at pH values between 4 and 4.6 that was previously shown to support nitrification. Long-read metagenomic sequencing yielded 12 high-quality metagenome-assembled genomes accounting for 94.7% of community abundance, including four phylogenetically distinct Nitrospira representing both comammox and canonical nitrite-oxidizing lineages, alongside heterotrophic species of Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and a filamentous Ktedonobacterales strain. Genomic reconstruction suggested niche partitioning in nitrogen cycling, with comammox Nitrospira encoding the capacity for complete nitrification and Rhodanobacteraceae harboring genes associated with denitrification. Acid tolerance and biofilm persistence were associated with diverse ion-transport systems, alternative respiratory complexes, extracellular polymeric substance biosynthesis, and expanded repertoires of secreted proteases and carbohydrate-active enzymes that facilitate matrix turnover and carbon scavenging. Within the biofilm, Chloroflexi likely contribute structural scaffolding, while heterotrophs appear to be adapted for extracellular organic matter turnover and to act as metabolic partners. Together, these findings suggest that metabolic cooperation, functional redundancy, and biofilm-mediated resource sharing may support nitrification under acidic conditions. This work provides genome-resolved insight into the microbial processes potentially underpinning nitrification-enhanced ammonia capture and identifies candidate genomic features relevant to optimizing nitrogen recovery while minimizing denitrification-driven losses in engineered systems.