Abstract
The recently discovered comammox bacteria have the potential to completely oxidize ammonia to nitrate. These microorganisms are part of the Nitrospira genus and are present in a variety of environments, including biological nutrient removal (BNR) systems. However, the physiological traits within and between comammox and nitrite-oxidizing bacterium (NOB)-like Nitrospira species have not been analyzed in these ecosystems. In this study, we identified Nitrospira strains dominating the nitrifying community of a sequencing batch reactor (SBR) performing BNR under microaerobic conditions. We recovered metagenome-derived draft genomes from two Nitrospira strains: (i) Nitrospira sp. strain UW-LDO-01, a comammox-like organism classified as "Candidatus Nitrospira nitrosa," and (ii) Nitrospira sp. strain UW-LDO-02, a nitrite-oxidizing strain belonging to the Nitrospira defluvii species. A comparative genomic analysis of these strains with other Nitrospira-like genomes identified genomic differences in "Ca. Nitrospira nitrosa" mainly attributed to each strain's niche adaptation. Traits associated with energy metabolism also differentiate comammox from NOB-like genomes. We also identified several transcriptionally regulated adaptive traits, including stress tolerance, biofilm formation, and microaerobic metabolism, which might explain survival of Nitrospira under multiple environmental conditions. Overall, our analysis expanded our understanding of the genetic functional features of "Ca. Nitrospira nitrosa" and identified genomic traits that further illuminate the phylogenetic diversity and metabolic plasticity of the Nitrospira genus. IMPORTANCENitrospira-like bacteria are among the most diverse and widespread nitrifiers in natural ecosystems and the dominant nitrite oxidizers in wastewater treatment plants (WWTPs). The recent discovery of comammox-like Nitrospira strains, capable of complete oxidation of ammonia to nitrate, raises new questions about specific traits responsible for the functional versatility and adaptation of this genus to a variety of environments. The availability of new Nitrospira genome sequences from both nitrite-oxidizing and comammox bacteria offers a way to analyze traits in different Nitrospira functional groups. Our comparative genomics analysis provided new insights into the adaptation of Nitrospira strains to specific lifestyles and environmental niches.
Highlights
The recently discovered comammox bacteria have the potential to completely oxidize ammonia to nitrate
Denitrification was incomplete, with only ϳ60% of the nitrate removed in the anoxic phase (Fig. 1A), even though the reactor received acetate in this phase. This suggests that efficient acetate uptake was likely performed by glycogen-accumulating organisms (GAO), without affecting P concentrations [8]
As a confirmation of the results obtained from this analysis and to identify other ammonia and nitrite oxidizers in the reactor, key nitrifying genes were searched in assemblies from the four metagenomic samples, using hidden Markov model (HMM) profiling, and the normalized nucleotide coverages of gene-containing contigs were compared for each sample (Fig. S4)
Summary
The recently discovered comammox bacteria have the potential to completely oxidize ammonia to nitrate. The metagenomic analysis of the stage 1 sample, which corresponds to the operational stage under which nitrite and ammonia were both present under microaerobic conditions, did not result in the assembly of any other genome of nitrifying microorganisms.
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