Nitrous oxide (N2O) production in autotrophic nitrogen conversion processes can be significant and requires further understanding. We operated an intermittently aerated partial nitritation/anammox (PN/A) sequencing batch reactor. Net N2O production rates increased in the aerated phase and decreased in the non-aerated phase. To put this finding in a transcriptional context, we probed the microbial community structure and function using metagenomics and metatranscriptomics analyses and targeted quantification of nitrogen cycle gene transcripts. We recovered 68 metagenome-assembled genomes (MAGs), including 4 MAGs of aerobic (AOB) and 2 MAGs of anaerobic (AnAOB) ammonium oxidation bacteria. The AOB MAGs were dominated by one MAG classified as Nitrosomonas oligotropha. During aeration, nirK expression at the AOB guild level increased ca. 20 fold and was almost exclusively associated with the dominant MAG. Furthermore, the dominant AOB MAG, unlike the other AOB MAGs, had a strong transcriptional response to the alternating redox conditions, including down-regulation of genes involved in respiration, inorganic carbon metabolism, protein synthesis, and folding, after aeration was turned off. No changes in the transcript levels of narG, nirS, norB, and nosZ were detected at the community level upon the transition to the aerated phase. A MAG classified as Brocadia caroliniensis dominated the AnAOB MAGs. Differences in the transcriptional response to the switches between the oxic and anoxic conditions imposed by the intermittent aeration strategy were also found among the AnAOB. The dominant AnOAB MAG did not show any significant change in gene regulation, while the minor AnAOB MAG down-regulated respiration and folding pathways in the aerated phase. These results suggest that nitrifier denitrification drives N2O production in intermittently-aerated PN/A reactors and highlight that variability in the transcriptional response of members within the same guild may shape reactor microbial community dynamics and performance.
