Competition Between Ammonia-Oxidizing Archaea and Comammox

Ammonia oxidizers perform the first and rate-limiting step of nitrification, which is a crucial process in the global nitrogen cycle. This process is carried out by ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and complete ammonia oxidizers (comammox). In the ammonia oxidizer’s native environment, the different groups of ammonia oxidizers are often competing for limiting amounts of ammonium. The comammox strain Nitrospira sp. BO4 was able to outcompete the AOA Nitrosarchaeum sp. BO1 under limiting and excess ammonium (Ghimire-Kafle et al., 2024). 

However, this experiment was only conducted with one pair of strains under optimal growth conditions. Therefore, we conducted two additional experiments to investigate (1) the impact of starvation as environmental stressor on the outcome of the competition between Nitrospira sp. BO4 and Nitrosarchaeum sp. BO1 and (2) the competition between additional AOA and comammox strains.

Pre-cultures for all experiments were grown in medium with 500 µM ammonium. For the competition experiment, the cultures were mixed in a 1:1 ratio of AOA and comammox and grown again in batch culture with 500 µM ammonium. In parallel the non-mixed cultures were grown under the same conditions.

The cultures BO1 and BO4 were starved as mixed culture and individual cultures for 3 weeks. The individual starved cultures were mixed at the end of the starvation period. To investigate the recovery from starvation, all mixed and individual cultures were grown in medium with 500 µM ammonium.

The ammonium consumption was monitored in all cultures. When ammonium was completely consumed, the cultures were filtered and DNA was isolated. qPCR was used to determine the abundance of the ammonia oxidizers and 16S rRNA gene amplicon sequencing to describe the community composition of the heterotrophic community in the enrichment cultures. The sequencing data were analyzed with QIIME2  (Boylen et al., 2019).