Real-Time PCR Quantification of Nitrifying Bacteria in a Municipal Wastewater Treatment Plant

• Published in: Environmental science & technology Vol. 37; no. 2; pp. 343 - 351
• Main Authors: Harms, Gerda, Layton, Alice C, Dionisi, Hebe M, Gregory, Igrid R, Garrett, Victoria M, Hawkins, Shawn A, Robinson, Kevin G, Sayler, Gary S
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 15.01.2003
• Subjects: Activated sludge; Ammonia; Applied sciences; Assaying; Bacteria; Biological and medical sciences; Biological Assay; Biological treatment of waters; Biotechnology; DNA, Bacterial - analysis; Environment and pollution; Environmental Monitoring; Exact sciences and technology; Fundamental and applied biological sciences. Psychology; Industrial applications and implications. Economical aspects; Nitrogen - metabolism; Nitrosomonas; Nitrosomonas - genetics; Other wastewaters; Oxidation; Plants; Pollution; Polymerase Chain Reaction - methods; Population Dynamics; RNA, Ribosomal, 16S - analysis; rRNA 16S; Sludge; Waste Disposal, Fluid; Wastewater treatment; Wastewaters; Water treatment; Water treatment and pollution; Nitrobacteraceae; Ribosomal DNA; Microbial biomass; Real time system; Biological purification; Polymerase chain reaction; Ribosomal RNA; Nitrification; Nitrosomonas; 16S-RNA; Bacteria; Population dynamics; Urban waste water; Molecular probe; Waste water purification; Microbial community
• ISSN: 0013-936X; 1520-5851
• DOI: 10.1021/es0257164

Real-time PCR assays using TaqMan or Molecular Beacon probes were developed and optimized for the quantification of total bacteria, the nitrite-oxidizing bacteria Nitrospira, and Nitrosomonas oligotropha-like ammonia oxidizing bacteria (AOB) in mixed liquor suspended solids (MLSS) from a municipal wastewater treatment plant (WWTP) using a single-sludge nitrification process. The targets for the real-time PCR assays were the 16S rRNA genes (16S rDNA) for bacteria and Nitrospira spp. and the amoA gene for N. oligotropha. A previously reported assay for AOB 16S rDNA was also tested for its application to activated sludge. The Nitrospira 16S rDNA, AOB 16S rDNA, and N. oligotropha-like amoA assays were log- linear over 6 orders of magnitude and the bacterial 16S rDNA real-time PCR assay was log-linear over 4 orders of magnitude with DNA standards. When these real-time PCR assays were applied to DNA extracted from MLSS, dilution of the DNA extracts was necessary to prevent PCR inhibition. The optimal DNA dilution range was broad for the bacterial 16S rDNA (1000-fold) and Nitrospira 16S rDNA assays (2500-fold) but narrow for the AOB 16S rDNA assay (10-fold) and N. oligotropha- like amoA real-time PCR assay (5-fold). In twelve MLSS samples collected over one year, mean cell per L values were 4.3 ± 2.0 × 1011 for bacteria, 3.7 ± 3.2 × 1010 for Nitrospira, 1.2 ± 0.9 × 1010 for all AOB, and 7.5 ± 6.0 × 109 for N. oligotropha-like AOB. The percent of the nitrifying population was 1.7% N. oligotropha-like AOB based on the N. oligotropha amoA assay, 2.9% total AOB based on the AOB 16S rDNA assay, and 8.6% nitrite-oxidizing bacteria based on the Nitrospira 16S rDNA assay. Ammonia-oxidizing bacteria in the wastewater treatment plant were estimated to oxidize 7.7 ± 6.8 fmol/hr/cell based on the AOB 16S rDNA assay and 12.4 ± 7.3 fmol/hr/cell based on the N. oligotropha amoA assay.