Real-time PCR quantification of nitrifying bacteria in wastewater treatment

GERDA HARMS; ALICE C. LAYTON; HEBE M. DIONISI; IGRID GREGORY; VICTORIA GARRET; SHAWN HAWKINS; KEVIN ROBINSON; GARY S. SAYLER

ENVIRONMENTAL SCIENCE & TECHNOLOGY

ACS Publications

Año: 2003 vol. 37 p. 343 - 351

0013-936X

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 amoAgene 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 amoAassays were loglinear 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. oligotrophalike amoAreal-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% nitriteoxidizing bacteria based on the Nitrospira16S rDNA assay. Ammonia-oxidizing bacteria in the wastewater treatmentplant 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.