Response of Nitrobacter spp. Ribosomal Gene and Transcript Abundance Following Nitrite Starvation and Exposure to Mechanistically Distinct Inhibitors

Abstract

The Nitrobacter spp. rRNA gene (rDNA) and relative rRNA transcript abundance (rRNAt/rDNA ratio) were evaluated in response to sudden changes in the nitrite oxidation rate. The rDNA abundance poorly indicated sudden transitions in the rate, whereas the relative rRNAt abundance usually varied quickly and significantly. In response to changes in nitrite concentration, 8 h were required for the rRNAt/rDNA ratio to transition from a minimum value at nitrite starvation (approximately 0.07) to a maximum value with excess nitrite present (approximately 4), and 5 h were required for this metric to return to the minimum value after nitrite starvation re-ensued. Generally, the relative rRNAt abundance dropped significantly after 4.5 h of exposure to three different inhibitors. A sharp decline in the rRNAt/rDNA ratio occurred during exposure to 3,5-DCP (from 4 down to 0.2) even as the fractional inhibition level remained low (< 0.10); the minimum ratio value was observed when nitrite oxidation was completely inhibited. The ratio decreased significantly during exposure to azide (from 4 to 0.5) and H+ (from 2 to 0.2), but only when the fractional inhibition levels were high (> 0.8). Interestingly, when the pH was suddenly changed to 4.5, inhibiting nitrite oxidation completely, the rRNAt/rDNA metric did not decline suggesting that rRNAt processing was inhibited. This effect was not observed during severe inhibition with 3,5-DCP and azide. Overall, the findings indicate the relative rRNAt abundance can be used to closely track in situ Nitrobacter spp. activity and in most instances will reveal inhibition events with the potential to impact treatment performance in reactors where Nitrobacter spp. are dominant.

Vertical distribution of metabolically active eukaryotes in the water column and sediments of the Black Sea

“…rRNA is an essential structural component of the ribosome, which is the organelle responsible for protein synthesis in all prokaryotes and eukaryotes. The number of cellular ribosomes, and thus also the rRNA content, increases with growth rate and decreases with starvation (Wagner, 1994;Muttray & Mohn, 1998;Buckley & Szmant, 2004;Chicharo & Chicharo, 2008;Hawkins et al, 2008). Therefore, rRNA extracted from environmental samples serves as a phylogenetic marker for the identification and relative abundance of metabolically active members within complex microbial communities.…”

Acclimatization of communities of ammonia oxidizing bacteria to seasonal changes in optimal conditions in a coke wastewater treatment plant

“…Contrary to expectations, our data showed no correlation between the quantity of AOB and AOR, demonstrating that the activated sludge with a high percentage of AOB did not produce higher potential/actual AORs than that which had a low percentage of AOB. This result may be associated with the known low growth rate and yield of nitrifying bacteria (Hawkins et al, 2008).…”

Ameliorating Risk: Culturable and Metagenomic Monitoring of the 14 Year Decline of a Genetically Engineered Microorganism at a Bioremediation Field Site

“…Primers and probes were designed to target the nahA, tetA, and luxA genes found on the pUTK21 plasmid of strain HK44 (GenBank accession numbers AFOY01000001-AFOY01000130) ( Table 1). Quantitative PCR (qPCR) reactions were prepared and run following previously published protocols that included duplicate six point standard curves generated from HK44 genomic DNA and spike controls for each sample [7,8]. For each assay, duplicate wells for six individual DNA extracts from each lysimeter were tested (total of 36 DNA extracts).…”