Nitrobacter winogradskyi transcriptomic response to low and high ammonium concentrations

Abstract

Nitrobacter winogradskyi Nb-255 is a nitrite-oxidizing bacterium that can grow solely on nitrite (NO2(-)) as a source of energy and nitrogen. In most natural situations, NO2(-) oxidation is coupled closely to ammonium (NH4(+)) oxidation by bacteria and archaea and, conceptually, N. winogradskyi can save energy using NH4(+) to meet its N-biosynthetic requirements. Interestingly, NH4(+) delayed the growth of N. winogradskyi when at concentrations higher than 35 mM, but grew well at concentrations below 25 mM NH4(+) while adjusting the expression of 24% of its genes. Notable genes that changed in expression included those with roles in nitrogen and carbon assimilation. Contrary to expectations, higher expression of glutamate synthase (GOGAT), instead of glutamate dehydrogenase, was detected at higher NH4(+) concentration. Genes in assimilatory NO2(-) metabolism and the degradation of glycogen and biofilm/motility were downregulated when N. winogradskyi was grown in the presence of NH4(+). Nitrobacter winogradskyi grown in medium with 25 mM NH4(+) upregulated genes in post-translational modification, protein turnover, biogenesis and chaperons. The data suggest that N. winogradskyi physiology is modified in the presence of NH4(+) and is likely to be modified during coupled nitrification with NH3 oxidizers.

Enrichment and Physiological Characterization of a Cold-Adapted Nitrite-Oxidizing Nitrotoga sp. from an Eelgrass Sediment

“…Nitrobacter winogradskyi grew well in 1 mM NH 4 Cl-amended medium, and the expression level of Nwi_0718, which is the associated hypothetical assimilatory nitrite reductase NirBC encoded by Nwi_0719 and Nwi_0720, was 5.0-log-fold lower than that in unamended culture (44). Similarly, AM1 could save energy for assimilatory nitrite reduction using ammonium in the 1 to 30 mM NH 4 Cl-augmented treatments, so that complete depletion of nitrite was faster than in other treatments.…”

Quorum Quenching of Nitrobacter winogradskyi Suggests that Quorum Sensing Regulates Fluxes of Nitrogen Oxide(s) during Nitrification

“…N. winogradskyi was routinely cultivated in 60 mM NaNO 2 -supplemented mineral salts medium as described previously (26), with minor modifications for NO x and N 2 O measurements (see Text S1 in the supplemental material and the descriptions of AiiA QS inhibition and culturing experiments below). N. winogradskyi cultures were routinely screened for heterotrophic contamination by plating 200-µl aliquots of culture on Luria-Bertani (LB) agar plates.…”

“…N. winogradskyi is a well-studied example of NOB due to its superior growth rate and growth yield compared to other NOB, and it was the first NOB shown to produce AHLs (10, 13, 14). In addition, the genome of N. winogradskyi has been sequenced and this bacterium has been the subject of recent global transcriptome studies (6, 25, 26). Expression of N. winogradskyi genes nwiI , encoding an autoinducer synthase, and nwiR , encoding a receptor-transcriptional regulator, was shown to be cell density dependent and to correlate with the AHL concentration in culture (10).…”

Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Produces N -Acyl-Homoserine Lactone Autoinducers

“…N. winogradskyi Nb-255 was routinely cultivated in 60 mM NaNO 2 Ϫ minimal salts medium as described previously (24). Agrobacterium tumefaciens KYC55(pJZ372)(pJZ384) (pJZ410) was cultivated, preinduced, and used in detection of acyl-HSLs as described previously (25,26).…”