The bacterial communities of membrane-separation bioreactors (MBR) fed with raw sewage were analyzed by a pilot scale study. The community was analyzed by both Fluorescent in Situ Hybridization (FISH) and PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) techniques. Five rRNA targeted group specific oligonucleotide probes showed that the alpha- and beta- subclasses of proteobacteria were the most dominant groups among them. The identification of ammonia-oxidizing bacteria in MBR was confirmed by three probes: NEU, Nsv 443 and Nso 190. Mostly the ammonia-oxidizers were found in groups and present in the form of clusters or aggregates. The ratio of NEU/EUB was estimated by double hybridization and image analysis techniques as 6%. The Nitrobacter sp. was also identified inside the MBR with the help of a NIT3 probe and they were also found to be present in the form of a cluster. Usually the clusters formed by the Nitrobacter sp. were smaller than those of ammonia-oxidizing groups. After numerical analysis on the band pattern of DGGE, it was found that the MBR bacterial communities were different from that of conventional activated sludge (CAS) communities with dissimilarity indexes more than 0.6. The diversity of the microbial community was estimated by the Shannon-Weaver index of general diversity. It was found that the value of the diversity index for the CAS process was 1.61 while those for two MBR processes were 1.68 and 1.59.

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