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To explore the relationships between community composition and the environment in a reservoir ecosystem,plankton communities from the Three Gorges Reservoir Region were studied by PCR-denaturing gradient gel electrophoresis fingerprinting.Bacterial and eukaryotic operational taxonomic units(OTUs),generated by DGGE analysis of the PCR-amplified 16S and 18S rRNA genes,were used as surrogates for the dominant biodiversity units.OTU composition among the sites was heterogeneous;46.7% of the total bacterial OTUs (45)and 64.1% of the eukaryotic OTUs (39) were identified in less than half of the sampling sites.Unweighted pair group method with arithmetic averages (UPGMA) clustering of the OTUs suggested that the plankton communities in the Xiangxi Rive sites were not always significantly different from those from the Yangtze River sites,despite clear difierences in their environmental characterizations.Canonical correspondence analysis (CCA) Was applied to further investigate the relationships between OTU composition and the environmental factors.The first two CCA ordination axes suggested that the bacterial community composition was primadly correlated with the variables of NO3--N,dissolved oxygen (DO),and SiO32--Si,whereas,the eukaryotic community was mainly correlated with the concentrations of DO, PO43--P, and SiO32--Si.