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Comparative metagenomics of three Dehalococcoides-containing enrichment cultures: the role of the non-dechlorinating community.

Hug LA, Beiko RG, Rowe AR, Richardson RE, Edwards EA - BMC Genomics (2012)

Bottom Line: The KB-1 metagenome contained eighteen novel homologs to reductive dehalogenase genes.The metagenomes obtained from the three consortia were automatically annotated using the MG-RAST server, from which statistically significant differences in community composition and metabolic profiles were determined.This redundancy likely contributes to the robust growth and dechlorination rates in dechlorinating enrichment cultures.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Cell and Systems Biology, University of Toronto, Toronto, Canada. elizabeth.edwards@utoronto.ca.

ABSTRACT

Background: The Dehalococcoides are strictly anaerobic bacteria that gain metabolic energy via the oxidation of H2 coupled to the reduction of halogenated organic compounds. Dehalococcoides spp. grow best in mixed microbial consortia, relying on non-dechlorinating members to provide essential nutrients and maintain anaerobic conditions.A metagenome sequence was generated for the dechlorinating mixed microbial consortium KB-1. A comparative metagenomic study utilizing two additional metagenome sequences for Dehalococcoides-containing dechlorinating microbial consortia was undertaken to identify common features that are provided by the non-dechlorinating community and are potentially essential to Dehalococcoides growth.

Results: The KB-1 metagenome contained eighteen novel homologs to reductive dehalogenase genes. The metagenomes obtained from the three consortia were automatically annotated using the MG-RAST server, from which statistically significant differences in community composition and metabolic profiles were determined. Examination of specific metabolic pathways, including corrinoid synthesis, methionine synthesis, oxygen scavenging, and electron-donor metabolism identified the Firmicutes, methanogenic Archaea, and the ∂-Proteobacteria as key organisms encoding these pathways, and thus potentially producing metabolites required for Dehalococcoides growth.

Conclusions: Comparative metagenomics of the three Dehalococcoides-containing consortia identified that similarities across the three consortia are more apparent at the functional level than at the taxonomic level, indicating the non-dechlorinating organisms' identities can vary provided they fill the same niche within a consortium. Functional redundancy was identified in each metabolic pathway of interest, with key processes encoded by multiple taxonomic groups. This redundancy likely contributes to the robust growth and dechlorination rates in dechlorinating enrichment cultures.

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Principal component analysis of 25 metagenomes based on frequencies of COG categories. COG frequencies were normalized to metagenome size. Points are colored by sample type: green = contaminant-degrading microbial consortia, black = waste water/sludge samples, light blue = pristine groundwater and sediment sites, brown = soil samples, yellow = Hawaii Ocean Time Series samples, red = ammonia-oxidizing communities, purple = non-contaminant degrading microbial consortia. See Additional file 1: Table S9 for a full list of metagenomes used. All samples are publically available from the JGI IMG-M site (merced.jgi-psf.org/cgi-bin/mer/main.cgi).
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Figure 5: Principal component analysis of 25 metagenomes based on frequencies of COG categories. COG frequencies were normalized to metagenome size. Points are colored by sample type: green = contaminant-degrading microbial consortia, black = waste water/sludge samples, light blue = pristine groundwater and sediment sites, brown = soil samples, yellow = Hawaii Ocean Time Series samples, red = ammonia-oxidizing communities, purple = non-contaminant degrading microbial consortia. See Additional file 1: Table S9 for a full list of metagenomes used. All samples are publically available from the JGI IMG-M site (merced.jgi-psf.org/cgi-bin/mer/main.cgi).

Mentions: The other two significantly enriched subsystems in metabolism were overrepresented in KB-1 (Figure 4, #10 & 11). The enrichment in the reductive dehalogenation subsystem in the KB-1 consortium stems from reads identified by MG-RAST as homologs to the Geobacter (class ∂-Proteobacteria) reductive dehalogenases. The Geobacter in KB-1 is known to be capable of reductively dechlorinating PCE to cDCE [5]. Examination of the non-Dhc rdh genes detected in the three metagenomes indicated that there are no non-Dhc rdh genes within DonnaII, while the ANAS metagenome had some reads most similar to Shewanella and Desulfitobacterium-type rdh genes, indicating there may be one or more non-Dhc dechlorinating organisms within that culture which have not previously been detected [19,21], or that the Dhc strains within the ANAS consortium encode rdh genes that were potentially acquired through lateral gene transfer. The second subsystem enriched in the KB-1 culture is the Ton and Tol transport subsystem (Figure 4, #11). The enrichment is largely within genes in the Ton pathway for iron transport (The SEED subsystem notes, [51]), specifically within the ∂-Proteobacteria, which for KB-1 corresponds to a Geobacter species. This enrichment may be linked to Geobacter’s requirement for corrinoids for active reductive dechlorination, as TonB has been shown to complex with the cobalamin transporter BtuB [52]. Examination of the cobalamin synthesis pathway (described below, Figure 5) suggests Geobacter, as the dominant ∂-Proteobacterium in KB-1, is potentially capable of de novo cobalamin synthesis, but a TonB/BtuB complex may be an additional avenue for cobalamin acquisition.


Comparative metagenomics of three Dehalococcoides-containing enrichment cultures: the role of the non-dechlorinating community.

Hug LA, Beiko RG, Rowe AR, Richardson RE, Edwards EA - BMC Genomics (2012)

Principal component analysis of 25 metagenomes based on frequencies of COG categories. COG frequencies were normalized to metagenome size. Points are colored by sample type: green = contaminant-degrading microbial consortia, black = waste water/sludge samples, light blue = pristine groundwater and sediment sites, brown = soil samples, yellow = Hawaii Ocean Time Series samples, red = ammonia-oxidizing communities, purple = non-contaminant degrading microbial consortia. See Additional file 1: Table S9 for a full list of metagenomes used. All samples are publically available from the JGI IMG-M site (merced.jgi-psf.org/cgi-bin/mer/main.cgi).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3475024&req=5

Figure 5: Principal component analysis of 25 metagenomes based on frequencies of COG categories. COG frequencies were normalized to metagenome size. Points are colored by sample type: green = contaminant-degrading microbial consortia, black = waste water/sludge samples, light blue = pristine groundwater and sediment sites, brown = soil samples, yellow = Hawaii Ocean Time Series samples, red = ammonia-oxidizing communities, purple = non-contaminant degrading microbial consortia. See Additional file 1: Table S9 for a full list of metagenomes used. All samples are publically available from the JGI IMG-M site (merced.jgi-psf.org/cgi-bin/mer/main.cgi).
Mentions: The other two significantly enriched subsystems in metabolism were overrepresented in KB-1 (Figure 4, #10 & 11). The enrichment in the reductive dehalogenation subsystem in the KB-1 consortium stems from reads identified by MG-RAST as homologs to the Geobacter (class ∂-Proteobacteria) reductive dehalogenases. The Geobacter in KB-1 is known to be capable of reductively dechlorinating PCE to cDCE [5]. Examination of the non-Dhc rdh genes detected in the three metagenomes indicated that there are no non-Dhc rdh genes within DonnaII, while the ANAS metagenome had some reads most similar to Shewanella and Desulfitobacterium-type rdh genes, indicating there may be one or more non-Dhc dechlorinating organisms within that culture which have not previously been detected [19,21], or that the Dhc strains within the ANAS consortium encode rdh genes that were potentially acquired through lateral gene transfer. The second subsystem enriched in the KB-1 culture is the Ton and Tol transport subsystem (Figure 4, #11). The enrichment is largely within genes in the Ton pathway for iron transport (The SEED subsystem notes, [51]), specifically within the ∂-Proteobacteria, which for KB-1 corresponds to a Geobacter species. This enrichment may be linked to Geobacter’s requirement for corrinoids for active reductive dechlorination, as TonB has been shown to complex with the cobalamin transporter BtuB [52]. Examination of the cobalamin synthesis pathway (described below, Figure 5) suggests Geobacter, as the dominant ∂-Proteobacterium in KB-1, is potentially capable of de novo cobalamin synthesis, but a TonB/BtuB complex may be an additional avenue for cobalamin acquisition.

Bottom Line: The KB-1 metagenome contained eighteen novel homologs to reductive dehalogenase genes.The metagenomes obtained from the three consortia were automatically annotated using the MG-RAST server, from which statistically significant differences in community composition and metabolic profiles were determined.This redundancy likely contributes to the robust growth and dechlorination rates in dechlorinating enrichment cultures.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Cell and Systems Biology, University of Toronto, Toronto, Canada. elizabeth.edwards@utoronto.ca.

ABSTRACT

Background: The Dehalococcoides are strictly anaerobic bacteria that gain metabolic energy via the oxidation of H2 coupled to the reduction of halogenated organic compounds. Dehalococcoides spp. grow best in mixed microbial consortia, relying on non-dechlorinating members to provide essential nutrients and maintain anaerobic conditions.A metagenome sequence was generated for the dechlorinating mixed microbial consortium KB-1. A comparative metagenomic study utilizing two additional metagenome sequences for Dehalococcoides-containing dechlorinating microbial consortia was undertaken to identify common features that are provided by the non-dechlorinating community and are potentially essential to Dehalococcoides growth.

Results: The KB-1 metagenome contained eighteen novel homologs to reductive dehalogenase genes. The metagenomes obtained from the three consortia were automatically annotated using the MG-RAST server, from which statistically significant differences in community composition and metabolic profiles were determined. Examination of specific metabolic pathways, including corrinoid synthesis, methionine synthesis, oxygen scavenging, and electron-donor metabolism identified the Firmicutes, methanogenic Archaea, and the ∂-Proteobacteria as key organisms encoding these pathways, and thus potentially producing metabolites required for Dehalococcoides growth.

Conclusions: Comparative metagenomics of the three Dehalococcoides-containing consortia identified that similarities across the three consortia are more apparent at the functional level than at the taxonomic level, indicating the non-dechlorinating organisms' identities can vary provided they fill the same niche within a consortium. Functional redundancy was identified in each metabolic pathway of interest, with key processes encoded by multiple taxonomic groups. This redundancy likely contributes to the robust growth and dechlorination rates in dechlorinating enrichment cultures.

Show MeSH