Nitrification in drinking water distribution systems is a common operational problem for many utilities that use chloramines for secondary disinfection. The diversity of ammonia-oxidizing bacteria (AOB) and nitriteoxidizing bacteria (NOB) in the distribution systems of a pilot-scale chloraminated drinking water treatment system was characterized using terminal restriction fragment length polymorphism (T-RFLP) analysis and 16S rRNA gene (ribosomal DNA [rDNA]) cloning and sequencing. For ammonia oxidizers, 16S rDNA-targeted T-RFLP indicated the presence of Nitrosomonas in each of the distribution systems, with a considerably smaller peak attributable to Nitrosospira-like AOB. Sequences of AOB amplification products aligned within the Nitrosomonas oligotropha cluster and were closely related to N. oligotropha and Nitrosomonas ureae. The nitriteoxidizing communities were comprised primarily of Nitrospira, although Nitrobacter was detected in some samples. These results suggest a possible selection of AOB related to N. oligotropha and N. ureae in chloraminated systems and demonstrate the presence of NOB, indicating a biological mechanism for nitrite loss that contributes to a reduction in nitrite-associated chloramine decay.Many drinking water utilities in the United States have implemented chloramination for secondary disinfection because chloramines are less reactive than free chlorine and have been demonstrated to produce lower concentrations of disinfection by-products, such as trihalomethanes and haloacetic acids (2,23,25). However, the addition of chloramines can lead to biological instability in a drinking water distribution system by promoting the growth of nitrifying bacteria, microorganisms that oxidize ammonia to nitrite and nitrate. Chloramination introduces ammonia to the distribution system both as excess ammonia from chloramine formation and released ammonia from chloramine decay. Ammonia-oxidizing bacteria (AOB) are able to grow on the residual and released ammonia in the presence of chloramines and produce nitrite and soluble organic compounds (29, 32). The AOB cell mass and the products of AOB activity deplete the residual disinfectant concentration by exerting a chloramine demand and may sustain the growth of nitrite-oxidizing bacteria (NOB) and heterotrophs. The resulting reduction in chloramine residual and development of a microbial community in the distribution system lead to water quality deterioration and violation of drinking water regulations (49, 50).Several studies have reported on the disinfection kinetics of AOB with chloramines (4, 18, 50; P. S. Oldenburg, J. M. Regan, G. W. Harrington, and D. R. Noguera, unpublished data). In general, the results of these investigations suggest that AOB should be inactivated effectively at typical chloramine exposure times and doses. Nonetheless, nitrification episodes are common in these systems, even in the presence of high chloramine residuals (4, 36). A survey of chloraminating utilities in the United States revealed that 63% of the utilities have...
Jar testing of 31 natural waters suggests many utilities may need the proposed alternative performance criterion to comply with enhanced coagulation specified in the proposed D/DBP Rule. Jar tests were performed on 31 natural waters from a variety of sources across the United States. These tests indicate that the majority of utilities supplying samples will have difficulty meeting the Step 1 total organic carbon (TOC) removal requirements in the Disinfectants/Disinfection By‐products Rule. Utilities may need the proposed point of diminishing returns alternative performance criterion to achieve compliance with the enhanced coagulation requirement. Water sources with high TOC and low alkalinity were most likely to meet the proposed Step 1 TOC requirements. Those with low TOC were most likely to need the alternative performance criterion.
We describe a semi-empirical framework that combines thermodynamic models of primer hybridization with experimentally determined elongation biases introduced by 3'-end mismatches for improving polymerase chain reaction (PCR)-based sequence discrimination. The framework enables rational and automatic design of primers for optimal targeting of one or more sequences in ensembles of nearly identical DNA templates. In situations where optimal targeting is not feasible, the framework accurately predicts non-target sequences that are difficult to distinguish with PCR alone. Based on the synergistic effects of disparate sources of PCR bias, we used our framework to robustly distinguish between two alleles that differ by a single base pair. To demonstrate the applicability to environmental microbiology, we designed primers specific to all recognized archaeal and bacterial genera in the Ribosomal Database Project, and have made these primers available online. We applied these primers experimentally to obtain genus-specific amplification of 16S rRNA genes representing minor constituents of an environmental DNA sample. Our results demonstrate that inherent PCR biases can be reliably employed in an automatic fashion to maximize sequence discrimination and accurately identify potential cross-amplifications. We have made our framework accessible online as a programme for designing primers targeting one group of sequences in a set with many other sequences (http://DECIPHER.cee.wisc.edu).
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