Enrichment and identification of a moderately acidophilic nitrite-oxidizing bacterium

• Identification of a novel nitrite-oxidizing bacterium (NOB) Nitrobacter. • This NOB optimally grows at a slightly acidic condition of pH 5. • Discovery of a mutualistic relationship between acidophilic NOB and AOA. • Enhanced nitrification rate under acidic conditions via co-culture. This study enriched a novel nitrite-oxidizing bacterium (NOB, ‘ Candidatus Nitrobacter acidophilus’) in a laboratory reactor operating at pH 4.5 for treating low-strength ammonia wastewater. Batch experiments showed that ‘ Ca . N. acidophilus’ oxidized nitrite to nitrate at a rate of 20.7 ± 2.3 μM/h with optimal growth at pH 5, distinguishing it from most previously known NOB strains. Phylogenetic analysis showed that this Nitrobacter strain clustered with other Nitrobacter strains obtained from acidic environments but was divergent from each other with an average nucleotide identity (ANI) below 85 %. Genomic characteristics revealed that ‘ Ca. N. acidophilus’ possesses versatile transporter systems. They are different from previously reported Nitrobacter strains and indicate acid adaptation mechanisms. Interestingly, the mutualistic interaction with acidophilic ammonia-oxidizing archaea (AOA) Nitrosotalea markedly increased the archaeal amo A gene expression by 149 times and enhanced ammonia oxidation rates by 5 times, highlighting the NOB's role in alleviating nitrite inhibition on the acidophilic AOA. These findings expand our understanding of bacterial nitrite oxidation and provide valuable insights into an important partnership between acidophilic AOA and NOB in acidic environments.