This paper presents an analysis of the structure and microbial composition of nitrifying aggregates, formed as either flocs or granules, in sequencing batch reactors (SBR) operated with a high ammonium load. The structure and microbial community of the aggregates was determined by fluorescence in situ hybridisation (FISH). The aggregate structure and size was related to mass transfer limitations observed by measurements of OURs measured by either a titrimetric and off-gas analysis sensor (TOGA) or by microsensors. The FISH analysis showed that the spatial arrangement of the microbial consortia correlated well with the oxygen gradients inside the aggregates. In the larger aggregates, the ammoniumand nitrite-oxidising bacteria were mainly concentrated to the outer 100–200 μm, whereas in the floc system, the bacteria were distributed throughout the entire aggregate. This indicates that the internal mass transfer resistance is considerably larger when the aggregate size increases which is directly supported by TOGA measurements.

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