Genome-resolved ecology of an acid-tolerant nitrifying biofilm reveals cooperative nitrogen cycling at low pH

Authors: Manning, Viola; Moore Jr, Philip; Trippe, Kristin

Submitted to: Science of the Total Environment
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/8/2026
Publication Date: 6/27/2026
Citation: Manning, V., Moore Jr, P.A., Trippe, K.M. 2026. Genome-resolved ecology of an acid-tolerant nitrifying biofilm reveals cooperative nitrogen cycling at low pH. Science of the Total Environment. https://doi.org/10.1016/j.scitotenv.2026.181954.
DOI: https://doi.org/10.1016/j.scitotenv.2026.181954

Interpretive Summary: Ammonia released from animal feeding operations represents a substantial loss of nitrogen that could otherwise be recovered and reused as fertilizer. One promising approach to improve nitrogen capture is the use of microorganisms within ammonia scrubbers to convert ammonia into more stable nitrogen forms. However, because air scrubbers operate under acidic conditions, and most ammonia-converting microorganisms are inhibited at low pH, it is generally not practical to design biologically-driven air scrubbers. In this study, we examined a microbial community that was able to convert ammonia to nitrate under acidic conditions. The community was enriched in a laboratory bioreactor operating at pH values between 4 and 4.6 and had previously been shown to support nitrification. Using long-read DNA sequencing, we reconstructed the genomes of the dominant microorganisms within the bioreactor. These included several types of Nitrospira bacteria that are capable of converting ammonia to nitrate, along with a diverse group of other bacteria that rely on organic carbon for growth. Our analysis showed that different microbes perform specialized roles within the community. Some microorganisms drive ammonia and nitrite conversion, while others contribute to nitrogen transformations or recycle organic materials within the biofilm. Filamentous bacteria help form a physical framework that stabilizes the biofilm, while other microbes use enzymes to break down and reuse cellular materials. Together, these interactions allow the microbial community to remain active and stable under acidic conditions. This work improves understanding of the biological processes that support nitrification in acidic ammonia scrubbers and identifies microbial traits that may help optimize nitrogen recovery in engineered systems.

Technical Abstract: 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 4–4.6 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 revealed niche partitioning in nitrogen cycling, with comammox Nitrospira driving complete nitrification and Rhodanobacteraceae harboring denitrification potential. Acid tolerance and biofilm persistence were supported by diverse ion-transport systems, alternative respiratory complexes, extracellular polymeric substance biosynthesis, and extensive repertoires of secreted proteases and carbohydrate-active enzymes that facilitate matrix turnover and carbon scavenging. Within the biofilm, Chloroflexi likely provide structural scaffolding, while heterotrophs act as necromass foragers and metabolic partners. Together, these findings demonstrate how metabolic cooperation, functional redundancy, and biofilm-mediated resource sharing enable nitrification under acidic conditions. This work provides mechanistic insight into the microbial processes underpinning nitrification-enhanced ammonia capture and identifies genomic targets for optimizing nitrogen recovery while minimizing denitrification-driven losses in engineered systems.