Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions

Abstract

The genus Nitrospira is the most widespread group of nitrite-oxidizing bacteria and thrives in diverse natural and engineered ecosystems. Nitrospira marina Nb-295T was isolated from the ocean over 30 years ago; however, its genome has not yet been analyzed. Here, we investigated the metabolic potential of N. marina based on its complete genome sequence and performed physiological experiments to test genome-derived hypotheses. Our data confirm that N. marina benefits from additions of undefined organic carbon substrates, has adaptations to resist oxidative, osmotic, and UV light-induced stress and low dissolved pCO2, and requires exogenous vitamin B12. In addition, N. marina is able to grow chemoorganotrophically on formate, and is thus not an obligate chemolithoautotroph. We further investigated the proteomic response of N. marina to low (∼5.6 µM) O2 concentrations. The abundance of a potentially more efficient CO2-fixing pyruvate:ferredoxin oxidoreductase (POR) complex and a high-affinity cbb3-type terminal oxidase increased under O2 limitation, suggesting a role in sustaining nitrite oxidation-driven autotrophy. This putatively more O2-sensitive POR complex might be protected from oxidative damage by Cu/Zn-binding superoxide dismutase, which also increased in abundance under low O2 conditions. Furthermore, the upregulation of proteins involved in alternative energy metabolisms, including Group 3b [NiFe] hydrogenase and formate dehydrogenase, indicate a high metabolic versatility to survive conditions unfavorable for aerobic nitrite oxidation. In summary, the genome and proteome of the first marine Nitrospira isolate identifies adaptations to life in the oxic ocean and provides insights into the metabolic diversity and niche differentiation of NOB in marine environments.

Investigating the Chemolithoautotrophic and Formate Metabolism of Nitrospira moscoviensis by Constraint-Based Metabolic Modeling and 13 C-Tracer Analysis

“…It has been demonstrated that several Nitrospira species can use formate as an energy source and that their genomes contain a formate transporter (FocA) and a soluble NAD + -reducing formate dehydrogenase (FDH), which catalyzes the oxidation of formate to CO 2 with concomitant reduction of NAD + to NADH ( 5 , 9 ). Notably, N. moscoviensis and the marine Nitrospira marina were reported to grow less efficiently on formate than on nitrite ( 5 , 9 ), a trend we confirmed for N. moscoviensis in batch experiments (see Fig. S4A ).…”

“…Interestingly, N. marina also showed poor growth with formate compared to that with nitrite ( 9 ), even though it possesses a cytoplasmic formate dehydrogenase that is only distantly related to the one of N. moscoviensis . Therefore, it is tempting to speculate that poor growth on formate might be a general feature of Nitrospira caused by its overall metabolism.…”

“…can use alternative substrates to fuel their carbon and energy metabolism ( 1 , 4 , 5 ). In addition to nitrite, some Nitrospira species have been experimentally shown to use formate, hydrogen, and ammonia as electron donors with oxygen or nitrate as terminal electron acceptors ( 4 – 9 ). For example, Nitrospira moscoviensis contains a soluble formate dehydrogenase and NiFe hydrogenase that allow growth with formate and H 2 , respectively ( 4 , 5 ), whereas the recently discovered complete ammonia-oxidizing (comammox) Nitrospira contains pathways for both ammonia and nitrite oxidation that enable growth via complete nitrification ( 7 , 8 ).…”

Activity-Based Cell Sorting Reveals Resistance of Functionally Degenerate Nitrospira during a Press Disturbance in Nitrifying Activated Sludge

“…Nitrospira species are well known to be metabolically versatile, with a wide range of functional potentials, including nitrite oxidation, hydrogen oxidation, urea conversion, formate oxidation, nitrate reduction, and complete ammonium oxidation ( 24 , 37 , 38 , 52 , 58 ). This metabolic diversity likely creates opportunities for functionally degenerate Nitrospira populations to coexist within a bioreactor by differentiating in niche space through auxiliary metabolic specializations while also sharing a niche space of nitrite oxidation ( 34 , 59 ).…”

Activity-based cell sorting reveals resistance of functionally degenerateNitrospiraduring a press disturbance in nitrifying activated sludge

“…These findings therefore reveal that physiological diversity at the lineage level, and possibly at the sub-lineage or strain level, within Nitrospira-dominated communities can facilitate niche-partitioning and acclimation to FA-exposure as a press-disturbance when applied as an engineering control strategy to promote low-energy nitrogen removal. Nitrospira species are well-known to be metabolically versatile, with a wide range of functional potentials including nitrite oxidation, hydrogen oxidation, urea conversion, formate oxidation, nitrate reduction, and complete ammonium oxidation (24,37,38,52,60). This metabolic diversity likely creates opportunities for functionally degenerate Nitrospira populations to co-exist within a bioreactor by differentiating in niche space through auxiliary metabolic specializations, while also sharing a common niche space of nitrite oxidation (34,61).…”