ENVIRONMENTAL BIOTECHNOLOGY Structure and dynamics of nitrifier populations in a full-scale submerged membrane bioreactor during start-up Tao Yu & Dong Li & Rong Qi & Sheng-tao Li & Shi-wei Xu & Min Yang Received: 27 August 2010 / Revised: 21 November 2010 / Accepted: 22 November 2010 / Published online: 23 December 2010 # Springer-Verlag 2010 Abstract Changes of microbial characteristics in a full- scale submerged membrane bioreactor system (capacity, 60,000 m 3 day -1 ) treating sewage were monitored over the start-up period (96 days). Fluorescence in situ hybridiza- tion analysis showed that the percentages of ammonia- oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (nitrobacter-related population) in total bacteria counted with DAPI staining increased significantly from 1.9% and 0.9% to 4.5% and 2.8%, corresponding to an increase of the specific ammonium oxidizing rate (from 0.06 to 0.12 kg N kg -1 mixed liquor suspended solids (MLSS) per day) and the specific nitrate forming rate (from 0.05 to 0.10 kg N kg -1 MLSS day -1 ). Both the denaturing gradient gel electrophoresis of polymerase chain reaction and clone library results showed that the AOB was dominated by the genus Nitrosomonas, the diversity of which increased markedly with operational time. Most of the day 2 clones were closely related with the uncultured Nitrosomonas sp. clone Ninesprings-49S amoA gene (AY356450.1) originated from activated sludge, while the day 96 clone library showed a more diverse distribu- tion characterized by the appearance of the oligotrophic nitrifiers like the Nitrosomonas oligotropha- and Nitro- somonas ureae-like bacteria, perhaps due to the intercep- tion by membrane and the low food-to-microorganisms ratio environment. The above results show that the membrane bioreactor system was characterized by the increased diversity and percentage of nitrifiers, which made it possible to achieve a stable and high efficient nitrification. Ammonia-oxidizing archaea with the chang- ing population structures were also detected, but their roles for ammonia oxidation in the system need further studies. Keywords Membrane bioreactor . Nitrification . Ammonia- oxidizing bacteria . Ammonia-oxidizing archaea . Sludge characteristics Introduction The membrane bioreactor (MBR) process has recently been focused because of its merits of smaller footprint, complete removal of solids, reduced sludge production, rapid start-up of biological processes, and better effluent quality in comparison with the conventional activated sludge (CAS) process (Pollice et al. 2008). This process has shown a wide application in both industrial and municipal wastewater treatment (Lyko et al. 2008). In comparison with the CAS process, the MBRs are characterized by a complete retention of biomass inside the bioreactor through mem- brane interception, which controls and increases the solids retention time (SRT) independently from the hydraulic retention time. This feature allows the systems to keep sufficient amounts of slow-growing microbes, such as ammonia-oxidizing bacteria (AOB; Chen and Lapara 2008). At the same time, high SRTs make it possible to acquire a high concentration of biomass, which permits stable operations and strong tolerance to shock loads (Xue et al. 2009; Rosenberger et al. 2002). However, there are T. Yu : D. Li : R. Qi : M. Yang (*) State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Science, Chinese Academy of Science, 18 Shuangqing Road, Haidian District, Beijing 100085, China e-mail: yangmin@rcees.ac.cn S.-t. Li : S.-w. Xu Beijing Drainage Group Co. Ltd., Beijing, China Appl Microbiol Biotechnol (2011) 90:369–376 DOI 10.1007/s00253-010-3030-4