Characterization of the First Candidatus Nitrotoga Isolate Reveals Metabolic Versatility and Separate Evolution of Widespread Nitrite-Oxidizing Bacteria

Nitrification is a key process of the biogeochemical nitrogen cycle and of biological wastewater treatment. The second step, nitrite oxidation to nitrate, is catalyzed by phylogenetically diverse, chemolithoautotrophic nitrite-oxidizing bacteria (NOB). Uncultured NOB from the genus Candidatus Nitrotoga are widespread in natural and engineered ecosystems. Knowledge about their biology is sparse, because no genomic information and no pure Ca. Nitrotoga culture was available. Here we obtained the first Ca. Nitrotoga isolate from activated sludge. This organism, Candidatus Nitrotoga fabula, prefers higher temperatures (>20 degrees C; optimum, 24 to 28 degrees C) than previous Ca. Nitrotoga enrichments, which were described as cold-adapted NOB. Ca. Nitrotoga fabula also showed an unusually high tolerance to nitrite (activity at 30 mM NO,-) and nitrate (up to 25 mM NO3-). Nitrite oxidation followed Michaelis-Menten kinetics, with an apparent K-m (K-m(app)) of similar to 89 mu M nitrite and a V-max of similar to 28 mu mol of nitrite per mg of protein per h. Key metabolic pathways of Ca. Nitrotoga fabula were reconstructed from the closed genome. Ca. Nitrotoga fabula possesses a new type of periplasmic nitrite oxidoreductase belonging to a lineage of mostly uncharacterized proteins. This novel enzyme indicates (i) separate evolution of nitrite oxidation in Ca. Nitrotoga and other NOB, (ii) the possible existence of phylogenetically diverse, unrecognized NOB, and (iii) together with new metagenomic data, the potential existence of nitrite-oxidizing archaea. For carbon fixation, Ca. Nitrotoga fabula uses the Calvin-Benson-Bassham cycle. It also carries genes encoding complete pathways for hydrogen and sulfite oxidation, suggesting that alternative energy metabolisms enable Ca. Nitrotoga fabula to survive nitrite depletion and colonize new niches. IMPORTANCE Nitrite-oxidizing bacteria (NOB) are major players in the biogeochemical nitrogen cycle and critical for wastewater treatment. However, most NOB remain uncultured, and their biology is poorly understood. Here, we obtained the first isolate from the environmentally widespread NOB genus Candidatus Nitrotoga and performed a detailed physiological and genomic characterization of this organism (Candidatus Nitrotoga fabula). Differences between key phenotypic properties of Ca. Nitrotoga fabula and those of previously enriched Ca. Nitrotoga members reveal an unexpectedly broad range of physiological adaptations in this genus. Moreover, genes encoding components of energy metabolisms outside nitrification suggest that Ca. Nitrotoga are ecologically more flexible than previously anticipated. The identification of a novel nitrite-oxidizing enzyme in Ca. Nitrotoga fabula expands our picture of the evolutionary history of nitrification and might lead to discoveries of novel nitrite oxidizers. Altogether, this study provides urgently needed insights into the biology of understudied but environmentally and biotechnologically important microorganisms.