A Comparison of Ribosomal Gene and Transcript Abundance during High and Low Nitrite Oxidizing Activity Using a Newly Designed Real-Time PCR Detection System Targeting the Nitrobacter spp. 16S–23S Intergenic Spacer Region

Abstract

The Nitrobacter ribosomal RNA transcript (rRNAt) abundance reflected nitrite oxidizing activity in a bench-scale nitrification reactor (BSNR) biomass. A newly designed real-time PCR detection system targeting the Nitrobacter 16S–23S intergenic spacer region (ISR) was used to assess transcript levels. In a batch nitrite oxidation experiment, the Nitrobacter rRNAt abundance varied dramatically (32-fold) as the growth prospect changed from unfavorable (nitrite starvation: 4.21 ± 0.85 × 10⁸ copies/L), to favorable (excess nitrite: 1.35 ± 0.24 × 10¹⁰ copies/L), and back to unfavorable (nitrite starvation: 5.88 ± 1.01 × 10⁸ copies/L) over a 15-h time period. The Nitrobacter ribosomal gene (rDNA) abundance varied comparatively little (less than twofold) during this time. Further, when nitrifying activity was pH inhibited in the BSNR, the Nitrobacter rRNAt abundance varied significantly (35-fold) as the growth prospect changed from unfavorable (pH 6.2: 3.71 ± 1.35 × 10⁸ copies/L) to favorable (pH 7.2: 1.29 ± 0.16 × 10¹⁰ copies/L), while the Nitrobacter rDNA abundance again varied comparatively little (less than twofold). The results indicate that real-time PCR is better suited to measure activity rather than population changes in slow growing bacteria such as nitrite oxidizers. Utilization of rRNAt as an in situ measure of nitrite oxidizing activity could be used to improve the implementation of traditional nitrification, where high NOB activity is promoted, as well as alternate N-conversion pathways which suppress nitrite oxidation.