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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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The anaerobic cobalamin synthesis pathway with gene distributions within the three metagenomes by taxonomic classification. The heat map depicts presence/absence of cobalamin synthesis pathways where red = genes absent; yellow = partial pathway, less than 50% of genes detected; light green = partial pathway, greater than 50% of genes detected; and dark green = complete pathway detected. Black circles indicate the specific genes detected for each microbial group. Abbreviations: DMB = 5,6-dimethylbenzimidazole, NMN = nicotinamide mononucleotide, Dhc = Dehalococcoides, Firm = Firmicutes, EurA = Euryarchaeota, δ/γ-Prot = Proteobacteria, BC = Bacteroidetes/Chlorobi group, Cflx = Chloroflexi.
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Figure 6: The anaerobic cobalamin synthesis pathway with gene distributions within the three metagenomes by taxonomic classification. The heat map depicts presence/absence of cobalamin synthesis pathways where red = genes absent; yellow = partial pathway, less than 50% of genes detected; light green = partial pathway, greater than 50% of genes detected; and dark green = complete pathway detected. Black circles indicate the specific genes detected for each microbial group. Abbreviations: DMB = 5,6-dimethylbenzimidazole, NMN = nicotinamide mononucleotide, Dhc = Dehalococcoides, Firm = Firmicutes, EurA = Euryarchaeota, δ/γ-Prot = Proteobacteria, BC = Bacteroidetes/Chlorobi group, Cflx = Chloroflexi.

Mentions: An examination of the prokaryotic corrinoid synthesis pathway [59] within the three metagenomes demonstrated the absence of a complete de novo synthesis pathway in the strains of Dhc contained in these cultures. The beginning of the anaerobic corrinoid synthesis pathway, from uroporphyrinogen-III or siroheme through to cobyrinate (10 genes of a total of 17) is categorically absent from all sequenced Dhc genomes, including strain 195 from the DonnaII consortium [8,12]. An in-house draft genome of the Dehalococcoides in KB-1 also lacks homologs to this portion of the corrinoid synthesis pathway. In addition, all isolated Dehalococcoides strains require the addition of cobalamin for growth, including strain 195, two strains from ANAS, and an in-house isolate from KB-1 [14][13]. In contrast, the genes required for synthesis of adenosylcobalamin from partially synthesized corrin-containing products including cobyrinate, cobinamide, 5,6-dimethylbenzimidazole, and cobalamin are all present within Dhc in these metagenomes and sequenced genomes, as are the genes for import of these corrin-containing precursors into the cell (Figure 6, Dhc column). An exception to this is aquacobalamin, which does not appear to be utilized as a precursor by Dhc. This indicates that while Dhc are typically incapable of de novo synthesis of a corrinoid [12], they encode multiple options for import and subsequent adaptation of varied cobalamin molecules, suggesting Dhc are highly versatile in their ability to scavenge corrinoids from an environment and repurpose them for insertion in a reductive dehalogenase enzyme.


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)

The anaerobic cobalamin synthesis pathway with gene distributions within the three metagenomes by taxonomic classification. The heat map depicts presence/absence of cobalamin synthesis pathways where red = genes absent; yellow = partial pathway, less than 50% of genes detected; light green = partial pathway, greater than 50% of genes detected; and dark green = complete pathway detected. Black circles indicate the specific genes detected for each microbial group. Abbreviations: DMB = 5,6-dimethylbenzimidazole, NMN = nicotinamide mononucleotide, Dhc = Dehalococcoides, Firm = Firmicutes, EurA = Euryarchaeota, δ/γ-Prot = Proteobacteria, BC = Bacteroidetes/Chlorobi group, Cflx = Chloroflexi.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: The anaerobic cobalamin synthesis pathway with gene distributions within the three metagenomes by taxonomic classification. The heat map depicts presence/absence of cobalamin synthesis pathways where red = genes absent; yellow = partial pathway, less than 50% of genes detected; light green = partial pathway, greater than 50% of genes detected; and dark green = complete pathway detected. Black circles indicate the specific genes detected for each microbial group. Abbreviations: DMB = 5,6-dimethylbenzimidazole, NMN = nicotinamide mononucleotide, Dhc = Dehalococcoides, Firm = Firmicutes, EurA = Euryarchaeota, δ/γ-Prot = Proteobacteria, BC = Bacteroidetes/Chlorobi group, Cflx = Chloroflexi.
Mentions: An examination of the prokaryotic corrinoid synthesis pathway [59] within the three metagenomes demonstrated the absence of a complete de novo synthesis pathway in the strains of Dhc contained in these cultures. The beginning of the anaerobic corrinoid synthesis pathway, from uroporphyrinogen-III or siroheme through to cobyrinate (10 genes of a total of 17) is categorically absent from all sequenced Dhc genomes, including strain 195 from the DonnaII consortium [8,12]. An in-house draft genome of the Dehalococcoides in KB-1 also lacks homologs to this portion of the corrinoid synthesis pathway. In addition, all isolated Dehalococcoides strains require the addition of cobalamin for growth, including strain 195, two strains from ANAS, and an in-house isolate from KB-1 [14][13]. In contrast, the genes required for synthesis of adenosylcobalamin from partially synthesized corrin-containing products including cobyrinate, cobinamide, 5,6-dimethylbenzimidazole, and cobalamin are all present within Dhc in these metagenomes and sequenced genomes, as are the genes for import of these corrin-containing precursors into the cell (Figure 6, Dhc column). An exception to this is aquacobalamin, which does not appear to be utilized as a precursor by Dhc. This indicates that while Dhc are typically incapable of de novo synthesis of a corrinoid [12], they encode multiple options for import and subsequent adaptation of varied cobalamin molecules, suggesting Dhc are highly versatile in their ability to scavenge corrinoids from an environment and repurpose them for insertion in a reductive dehalogenase enzyme.

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
Related in: MedlinePlus