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Open Access Highly Accessed Research article

Metagenome analyses of corroded concrete wastewater pipe biofilms reveal a complex microbial system

Vicente Gomez-Alvarez, Randy P Revetta and Jorge W Santo Domingo*

Author Affiliations

U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268, USA

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BMC Microbiology 2012, 12:122  doi:10.1186/1471-2180-12-122

Published: 22 June 2012

Additional files

Additional file 1:

Figure S1. Distribution (%) of sequences identified to particular subsystems (SEED) in metagenomes of wastewater biofilms.Figure S2. Distribution of bacterial classes on concrete wastewater pipes as determined by taxonomic identification of 16S rRNA genes recovered from metagenome libraries. Numbers in brackets represent percentage of each group from the total number of sequences. Legend: 1. unclassified Bacteria domain, 2. Actinobacteria, 3a. Bacteroidia, 3b. Flavobacteria, 3c. Sphingobacteria, 4. Chloroflexi, 5a. Bacilli, 5b. Clostridia, 6. Fusobacteria, 7a. Alphaproteobacteria, 7b. Betaproteobacteria, 7c. Deltaproteobacteria, 7d. Epsilonproteobacteria, 7e. Gammaproteobacteria, 8. Synergistia and 9. other classes each representing <1%. Groups (phylum): 3. Bacteroidetes, 5. Firmicutes, 7. Proteobacteria . Figure S3. UPGMA cluster analysis of Bray-Curtis similarity coefficients for biofilms in wastewater systems. Sample types were classified by their taxonomic dominant group within the sulfur biogeochemical cycle: sulfur-reducing bacteria (SRB) and sulfur/sulfide-oxidizing bacteria (SOB). Location of biofilm: bottom (a), middle (b), top (c) and outdoor (d). Figure S4. Phylogenetic affiliation of phylotypes identified as Bacteroidetes from each biofilm: top pipe (TP, gray) and bottom pipe (BP, black). Clones were identified by genus or order (*) and percentage of each representative sequence in their respective libraries is provided in the brackets. The tree was inferred using maximum likelihood analysis of aligned 16S rRNA gene sequences with bootstrap values from 100 replicates. Box indicates the two most dominant phylotypes. Figure S5. Phylogenetic affiliation of Deltaproteobacteria phylotypes identified as sulfate-reducing bacteria (SRB) from each biofilm: top pipe (TP, gray) and bottom pipe (BP, black). Clones were identified by genus or family (*) and percentage of each representative sequence in their respective libraries is provided in the brackets. The tree was inferred using maximum likelihood analysis of aligned 16S rRNA gene sequences with bootstrap values from 100 replicates. Box indicates dominant phylotype. Figure S6. Phylogenetic affiliation of the top 20 most abundant Proteobacteria phylotypes identified as sulfur/sulfide-oxidizing bacteria (SOB) from each biofilm: top pipe (TP, gray) and bottom pipe (BP, black). Clones were identified by genus (*family) and percentage of each representative sequence in their respective libraries is provided in the brackets. The tree was inferred using maximum likelihood analysis of aligned 16S rRNA gene sequences with bootstrap values from 100 replicates. Box indicates dominant phylotype Figure S7. Relative abundance of taxonomic groups based on MEGAN analysis of protein families associated with the sulfur pathway. Each circle is scaled logarithmically to represent the number of reads that were assigned to each taxonomic group. Wastewater biofilms: top pipe (TP, white) and bottom pipe (BP, black). EC = Enzyme Commission number. Figure S8. Relative abundance of taxonomic groups based on MEGAN analysis of protein families associated with the nitrogen pathway. Each circle is scaled logarithmically to represent the number of reads that were assigned to each taxonomic group. Wastewater biofilms: top pipe (TP, white) and bottom pipe (BP, black). EC = Enzyme Commission number.

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