Bacterial growth kinetics estimation by fluorescence in situ hybridization and spectrofluorometric quantification

Ammonia-oxidizing bacteria in wastewater

Ammonia-oxidizing bacteria (AOB) have a key role in the conversion of ammonia to nitrite in wastewater treatment plants (WWTPs). The characterization of AOB communities in such systems requires the use of genomic methods as AOB are difficult to isolate from environmental samples. Fluorescence in situ hybridization (FISH) using fluorescently labeled probes targeting 16S rRNA molecules provides a robust tool for the detection and quantification of AOB populations in biofilms and activated sludge flocs. The abundance of AOB may be also determined by real-time quantitative polymerase chain reaction (qPCR) using primers that amplify either the 16S rRNA or amoA genes. The evaluation of changes in the AOB community in time and space can be undertaken by PCR amplification of these gene fragments followed by denaturing gradient gel electrophoresis (PCR-DGGE). In this chapter, we summarize the most commonly applied procedures for the analysis of the AOB in wastewater, emphasizing their advantages and limitations.