Nitrite-oxidising bacteria are considered as metabolic specialists that adopt an obligately chemolithoautotrophic lifestyle dependent on nitrite oxidation. Recently, cultivation and genomic evidence nonetheless revealed a boarder metabolic flexibility of such bacteria to use alternative energy sources including hydrogen. One of such bacteria, Nitrospira moscoviensis, harbours a group 2a nickel iron hydrogenase enzyme to oxidise elevated level of hydrogen for growth. Combining comparative shotgun proteomics and high sensitivity gas chromatography, we show that this bacterium constitutively express this hydrogenase and rapidly oxidise trace atmospheric level of hydrogen during both nitrite-replete growth phase and nitrite-deplete persistence phase. Respirometry experiment supports that hydrogen oxidation is coupled with quinone reduction in the electron transport chain while genomic survey indicates a wide presence of uptake nickel iron hydrogenases among the genus Nitrospira. Together, our results suggest that atmospheric hydrogen is an important energy source for nitrite-oxidising bacteria under varied availability of preferred nitrite, and reveals Nitrospirota as the seventh bacterial phyla with the ability to perform atmospheric hydrogen oxidation.