Bacterial community structures in hydrogenotrophic dechlorinating membrane-biofilm reactors revealed by massively parallel pyrosequencing and real-time PCR

Recent studies showed that chlorinated compounds including trichloroethene (TCE), 1,1,1-trichloroethane (TCA), and chloroform (CF) were reductively dehalogenated in the H2-based membrane biofilm reactor (MBfR) under denitrifying conditions with H2 as the sole electron donor, but a comprehensive understanding of the structure of the H2-fueled dechlorinating bacterial communities in an engineered system has been lacking. Using massively parallel pyrosequencing of the V6 region of the 16S rRNA gene, we detected 312, 592, and 639 operational taxonomic units (OTU) in biofilms of three MBfRs that reduced nitrate, nitrate and TCE, or nitrate, sulfate, and all three chlorinated solvents together, respectively. Comparative community analysis revealed that 13% of the total OTUs were shared by all MBfRs, regardless of the feed. Chlorinated solvents in a single or a mixture increased the bacterial diversity in the biofilm. Pyrosequencing and real-time quantitative PCR showed that Dehalococcoides were markedly enriched in the TCE-only biofilm. The input of a mixture of three chlorinated compounds, which coincided with the onset of sulfate reduction enriched a more diverse community that included sulfate-reducing bacteria (Desulfovibrio) and nitrate-reducing bacteria (Geothrix and Pseudomonas). Our results suggest that, as additional electron acceptors to nitrate and sulfate, chlorinated solvents increased microbial diversity by allowing specialists to grow in the biofilm. Although TCA, CF, or sulfate reduction may have inhibited Dehalococcoides, their presence stimulated a more diverse bacterial community.