Abstract:
The chemolithoautotrophic nitrite oxidizing bacteria (NOB) participate in the
biogeochemical cycling of nitrogen by catalyzing and conserving energy from the
oxidation of nitrite (NO₂-) to nitrate (NO₃-) via a nitrite oxidoreductase (NXR). The
main objective of this work was to comparatively annotate and analyze the genome
sequences of Nitrobacter winogradskyi NB255 and Nitrobacter hamburgensis X14 and
use this information to extend our understanding of nitrogen and carbon metabolism in NOB. Through the analysis of the N. winogradskyi genome, genes encoding pathways for known modes of lithotrophic and heterotrophic growth were identified, including multiple enzymes involved in anapleurotic reactions centered on C2 to C4 metabolism. N. winogradskyi lacked genes encoding a complete glycolysis pathway and for the active transport of sugars. The N. hamburgensis genome harbored many genes not
found in N. winogradskyi, including a complete glycolysis pathway, unique electron
transport components, and putative pathways for the catabolism of aromatic, organic
and one-carbon compounds. FAD-dependent oxidases were identified in the genome of
N. hamburgensis which suggested that lactate could be metabolized, providing reductant and carbon to the cell. Indeed, D-lactate enhanced the growth rate and yield of N. hamburgensis in the presence of NO₂- and served as a sole energy and carbon source
in the absence of NO₂-. Although lactate consumption occurred constitutively in
lithoautotrophically grown cells, evidence was obtained for physiological adaptation to
lactate. D-lactate grown cells consumed and assimilated lactate at a faster rate than NO₂- grown cells, and D-lactate-dependent O₂ uptake was significantly greater in cells grown heterotrophically or mixotrophically compared to cells grown lithoautotrophically.
However, D-lactate could not substitute for CO₂ as the sole carbon source(lithoheterotrophy) during growth in the presence of NO₂-. Through a comparative
analysis of the Nitrobacter 'core' genome, many genes involved in NO₂- metabolism
were identified, including a dissimilatory nitrite reductase (NirK). The putative nirK in N. winogradskyi was maximally transcribed under low oxygen in the presence of NO₂- and transcription was not detected under anaerobic conditions. Although production of
NO under aerobic conditions was not detected, NO was consumed in a cyanide sensitive process and reversibly inhibited NO₂-dependent O₂ uptake.
