ORIGINAL ARTICLE Bacterial and archaeal assemblages in sediments of a large shallow freshwater lake, Lake Taihu, as revealed by denaturing gradient gel electrophoresis F.H. Liu 1,2 , G.H. Lin 1 , G. Gao 3 , B.Q. Qin 3 , J.S. Zhang 1 , G.P. Zhao 1 , Z.H. Zhou 1 and J.H. Shen 1 1 Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China 2 Graduate School of the Chinese Academy of Sciences, Beijing, China 3 Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China Introduction Lake Taihu, the third largest (2338 km 2 ) freshwater lake in China, is a shallow (average depth about 1Æ9 m) and eutrophic lake (McCarthy et al. 2007). The lake conse- quently receives heavy allochthonous inputs of agricul- tural chemicals (pesticides and chemical fertilizers), in addition to rapidly increasing sewage inputs from munici- pal and industrial sources. Meiliang Bay, a deep-bedded lake bay (surface area 220 km 2 ), receives inputs from two major industrial cities, Wuxi and Changzhou, primarily via the Liangxi and Zhihugang rivers respectively. The close proximity of fisheries, aquaculture and tourism on the lake further intensify nutrient inputs. For the last two decades, cyanobacterial blooms have occurred frequently from year to year in the west lake bays, in particular Meiliang Bay (Wu et al. 2007). Microorganisms are among the most important con- tributors to the recycling of nutrients and decomposition of organic matter in freshwater sediments (Nealson 1997; Tamaki et al. 2005). Sediments represent some of the most diverse microbial habitats (Torsvik et al. 2002) and play a pivotal role in the decomposition of organic matter and in biogeochemical cycles of the main elements, including carbon, nitrogen and phosphorus. Therefore, sediments are important in energy and nutrient exchanges (Ranjard et al. 2000; Urakawa et al. 2000). In addition to the geographical location and morphology of a lake, the chemical composition of the water and the sediment environment are also important in determining the Keywords 16S rDNA, DGGE, eutrophication, microbial assemblages, shallow freshwater lake. Correspondence Jianhua Shen, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China. E-mail: jhshen@sibs.ac.cn Zhihua Zhou, Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China. E-mail: zhouzhihua@sippe.ac.cn 2008 ⁄ 0645: received 15 April 2008, revised 8 August 2008 and accepted 8 September 2008 doi:10.1111/j.1365-2672.2008.04069.x Abstract Aims: To explore the association of microbial community structure with the development of eutrophication in a large shallow freshwater lake, Lake Taihu. Methods and Results: The bacterial and archaeal assemblages in sediments of different lake areas were analysed using denaturing gradient gel electrophoresis (DGGE) of amplified 16S rDNA fragments. The bacterial DGGE profiles showed that eutrophied sites, grass-bottom areas and relatively clean sites with a eutrophic (albeit dredged) site are three respective clusters. Fifty-one domi- nant bacterial DGGE bands were detected and 92 corresponding clones were sequenced, most of which were affiliated with bacterial phylotypes commonly found in freshwater ecosystems. Actinobacteria were detected in the centre of the lake and not at eutrophied sites whereas the opposite was found with respect to Verrucomicrobiales. Twenty-five dominant archaeal DGGE bands were detected and 31 corresponding clones were sequenced, most of which were affiliated with freshwater archaeal phylotypes. Conclusions: The bacterial community structures in the sediments of different areas with similar water quality and situation tend to be similar in Taihu Lake. Significance and Impact of the Study: This study may expand our knowledge on the relationship between the overall microbial assemblages and the develop- ment of eutrophication in the shallow freshwater lake. Journal of Applied Microbiology ISSN 1364-5072 1022 Journal compilation ª 2009 The Society for Applied Microbiology, Journal of Applied Microbiology 106 (2009) 1022–1032 ª 2009 The Authors