Nitrogen removal from wastewater involves design and operational strategies that are based on the kinetic characteristics of strict ammonia oxidizer bacteria (AOB) and nitrite oxidizing bacteria (NOB). Several studies in wastewater have found complete nitrifiers related to Ca. Nitrospira nitrosa as the principal or unique comammox bacteria present in their nitrogen removal systems. The lack of diversity and, consequently, the lack of functional redundancy calls into question the feasibility of designing operational strategies that may seek to leverage the activity of comammox bacteria.
The principal objective was to assess the population and strain level diversity of comammox bacteria as compared with canonical nitrifiers.
Samples from three nitrogen removal systems were subject to DNA extraction and long and short read metagenomic sequencing. Metagenomes were assembled, binned, and dereplicated on a system-by-system basis. The average nucleotide identity (ANI) was calculated between all MAGs from the same functional group. Further, the ANI from reads (ANIr) and the nucleotide diversity calculated by inStrain were used to evaluate the micro-diversity of each group.
All AOB MAGs (n=10) were annotated as Nitrosomonas-like while the Nitrospira-like MAGs were associated with either Nitrospira lineage I (7 canonical Nitrospira) or lineage II (2 canonical and 4 comammox Nitrospira). All comammox MAGs were closely related to Ca. Nitrospira nitrosa. The average ANI value from pairwise comparisons between the comammox MAGs (90%±5) was significantly higher than between the AOB MAGs (83%±7) and between the canonical Nitrospira MAGs (82%±4). Further, all comammox MAGs and some Nitrosomonas MAGs had significantly lower intra-population diversity as compared with most canonical Nitrospira MAGs. These results suggest that comammox bacteria not only exhibit low diversity at the species/population level across wastewater systems but also at the strain/intra-population level. Therefore, Ca. Nitrospira nitrosa cluster may harbor specific adaptations to the wastewater environment.
