While interactions between canonical nitrifiers have been investigated extensively, the extent to which comammox bacteria interact with canonical nitrifiers is as yet not well understood. The objectives of this study were to determine if comammox bacteria and canonical nitrifiers exhibit concentration and nitrogen source dependent interactions when subject to repeat nitrogen amendments and to determine if these interactions are consistent or variable at the clade or population level within each functional guild. Microcosms with granular activated carbon from a drinking water treatment plant were amended with two sources of electron donor across three nitrogen concentrations over a period of eight weeks. SSU rRNA and metagenomic analysis identified Nitrosomonas and Nitrospira-like bacteria as the sole nitrifiers. Phylogenomic analysis of assembled MAGs identified clade A1 (n=1) and clade A2 (n=3) comammox bacteria in co-existence with cluster 6a Nitrosomonas (n=3) and canonical NOB (n=2) belonging to sub-lineage II Nitrospira. Quantitative PCR (qPCR) analyses revealed that comammox bacteria were more abundant than strict AOB in the inocula and in microcosms across all nitrogen amendments, irrespective of electron donor loading or source. However, increase in comammox bacteria abundance did not result in an accompanying decrease in the abundance of strict AOB. Rather, increase in the abundance of comammox bacteria was associated with decrease in the abundance of canonical NOB in a nitrogen source dependent manner. Specifically, comammox bacteria exhibited negative correlations with Nitrospira-NOB in ammonia amended microcosms but not in urea amended microcosms. Overall, our study suggests that comammox bacteria will dominate nitrifier communities sourced from low nitrogen environments (e.g., drinking water) irrespective of intermittent fluctuations in nitrogen availability or source without directly competing with canonical AOB. However, canonical NOB are likely to get outcompeted by comammox bacteria in situations where AOB-NOB cross feeding is limited to nitrite.
