We report the results of pyrosequencing of DNA collected from the activated sludge basin of a wastewater treatment plant in Charlotte, NC. Using the 454-FLX technology, we generated 378,601 sequences with an average read length of 250.4 bp. Running the 454 assembly algorithm over our sequences yielded very poor assembly, with only 0.3% of our sequences participating in assembly of significant contigs. Of the 117 contigs greater than 500 bp long that were assembled, the most common annotations were to transposases and hypothetical proteins. Comparing our sequences to known microbial genomes showed nonspecific recruitment, indicating that previously described taxa are only distantly related to the most abundant microbes in this treatment plant. A comparison of proteins generated by translating our sequence set to translations of other sequenced microbiomes shows a distinct metabolic profile for activated sludge with high counts for genes involved in metabolism of aromatic compounds and low counts for genes involved in photosynthesis. Taken together, these data document the substantial levels of microbial diversity within activated sludge and further establish the great utility of pyrosequencing for investigating diversity in complex ecosystems.Although largely invisible in the urban landscape when they are functioning well, wastewater treatment plants are integral to the municipal obligation to protect public health, aquatic ecosystems, and the quality of life. At the heart of wastewater treatment plants is a process whereby a dense microbial consortium is employed to remove organic and nutrient contaminants. The microbes used to treat wastewater are a crucial tool in environmental protection. The current use of molecular techniques that do not require the isolation and cultivation of microorganisms (1, 33), including 16S rRNA analysis (6,13,20) and fluorescent in situ hybridization (8), have greatly expanded our understanding of wastewater microbial communities. Researchers have identified many bacteria of importance to wastewater treatment, including the bacteria involved in biological phosphorus removal (5, 16, 29), nitrifiers (8, 19, 25), denitrifiers (3, 12, 17), and methanogens (18, 36). Molecular techniques have also improved our understanding of fundamental processes such as nitrification and denitrification, as well as plant upsets, such as foaming (9, 24), which can decrease treatment efficiency.In this paper, we apply recently developed pyrosequencing technology to probe the molecular diversity of the aerobic basin of a wastewater treatment plant in Charlotte, NC. In line with other studies of complex microbial communities (28, 32), we observed astounding levels of diversity. We found that substantial regions of the genomes of the most prevalent microbes in the wastewater treatment plant are poorly described by existing sequence databases. Our results demonstrate that despite recent technological advances that allow identification of microorganisms, the microbial population of wastewater treatment plan...