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Nitrification is a two step process namely ammoniacal oxidation and nitrite oxidation. Oxidation of ammonium to nitrite is carried out by autotrophic bacterium mainly Nitrosomonas (e.g. N. europaea, N.oligocarbogenes) and Nitrosospira while conversion of nitrite to nitrate is performed by Nitrobacter (e.g. N. agilis, N. winogradski) and Nitrospira. However, ammoniacal oxidation is considered as the limiting or critical process in nitrification since the ammonia-oxidizing bacteria (AOB) has very low growth rate (Metcalf and Eddy 1991). Various approaches, both culture dependent and independent have been applied to analyze and compare the microbial structure of biomass. However, culture dependent methods are biased by the selection of species which obviously do not represent the real dominant structure (Wagner et al 1995; Lipponen et al 2002). Recently, the development of culture independent molecular techniques, like fluorescence in situ hybridization (FISH), polymerase chain reaction (PCR) or denaturing gradient gel electrophoresis (DGGE) improved the analysis of environmental samples. Whole cell fluorescene in situ hybridization (FISH) is a technique that uses fluorescently labelled phylogenetic oligonucleotide probes to detect specific whole cells/organisms in biological samples. It can be a valuable tool for the study of microbial dynamics in natural environments (Li et al 1999; Liu et al 2002, Eschenhagen et al 2003). These probes could be designed using the wealth of 16S and 23S rDNA sequence data available to target species, genera subdivisions or divisions in-situ and could be labelled with fluorescent groups, radioactive groups or antigens for immunological detection (Amann 1995). A combination of the FISH approach with the application of scanning confocal laser microscopy (SCLM) allows non-destructive studies of the three dimensional arrangements of bacterial population identified and out-of-focus fluorescence (Wagner et al 1995). Biological Aerated Filters (BAFs) also have a long history of successfully removing nitrogen in wastewater treatment plants (Chen et al 2000; Quyang et al 2000; Chui et al 2001). Biofilm in the reactors bears great potential for simultaneous and efficient removal of nitrogen (FdzPolanco et al 2000). Therefore, an assessment of nitrogen removal efficiency has been made to detect any deterioration to the performance. A possible adverse effect of reduced mass of biofilm in the partial-bed reactor was foreseen for the reason that the slow-growing nitrifiers

Detection of Ammonia-oxidizing Bacteria (AOB) in the Biofilm and Suspended Growth Biomass of Fully- and Partially-packed Biological Aerated Filters