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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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Schematic overview of the examined metabolic processes taking place within the dechlorinating enrichment consortia, with the organisms implicated in each process highlighted. End products are boxed in light grey. Organisms are coloured by taxonomic affiliation and process: Methanogenesis and synthesis pathways encoded by methanogenic Archaea are in blue, acetogenesis and other processes largely attributed to Firmicutes are in green, and pathways encoded by ∂-Proteobacteria are in orange. NB: A hydrogen molecule is required for each dechlorination step from PCE to ethene: only the first dechlorination reaction is depicted here.
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Figure 2: Schematic overview of the examined metabolic processes taking place within the dechlorinating enrichment consortia, with the organisms implicated in each process highlighted. End products are boxed in light grey. Organisms are coloured by taxonomic affiliation and process: Methanogenesis and synthesis pathways encoded by methanogenic Archaea are in blue, acetogenesis and other processes largely attributed to Firmicutes are in green, and pathways encoded by ∂-Proteobacteria are in orange. NB: A hydrogen molecule is required for each dechlorination step from PCE to ethene: only the first dechlorination reaction is depicted here.

Mentions: A metagenome sequencing project for the KB-1 consortium was completed by the Joint Genome Institute (JGI), generating 103 Mb of sequence. Recently, the JGI has also sequenced metagenomes from two other Dehalococcoides-containing enrichment cultures: DonnaII and ANAS. The three microbial consortia, KB-1, DonnaII, and ANAS, are maintained in Toronto, Ontario, Canada, Ithaca, NY, and Berkeley, CA, respectively. They contain different strains of Dhc, with unique complements of rdh genes [7,27,28]. Prior to metagenome sequencing, a genome sequence for the Dhc strain in the DonnaII consortium was generated [7], and a draft genome sequence for the Dhc strain in the KB-1 culture has subsequently been generated from the metagenome sequence (in-house data). The consortia have each been maintained for over a decade, in different volumes, with differing growth conditions, and with different electron donors (Table 1). The KB-1 consortium is amended methanol as an electron donor, while DonnaII is amended butyrate and ANAS utilizes lactate as an electron donor. The consortia each contain methanogenic Archaea as well as acetogenic and/or fermentative organisms, but the dominant Archaea and acetogens differ taxonomically in each culture (see Figures 1, 2). In general, reference genomes for these organisms are not available from public databases. Two exceptions are the genome sequence of the δ-Proteobacterium Geobacter lovleyi strain SZ, which is a close relative to the Geobacter strain in the KB-1 consortium, and the euryarchaeote Methanospirillum hungatei in the DonnaII culture. Despite the physical differences in maintenance conditions and the taxonomic variation between the consortia, all three consortia are capable of the complete dechlorination of tetra- or trichloroethene to non-toxic ethene, indicating that the environmental differences present do not preclude sustained Dhc growth.


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)

Schematic overview of the examined metabolic processes taking place within the dechlorinating enrichment consortia, with the organisms implicated in each process highlighted. End products are boxed in light grey. Organisms are coloured by taxonomic affiliation and process: Methanogenesis and synthesis pathways encoded by methanogenic Archaea are in blue, acetogenesis and other processes largely attributed to Firmicutes are in green, and pathways encoded by ∂-Proteobacteria are in orange. NB: A hydrogen molecule is required for each dechlorination step from PCE to ethene: only the first dechlorination reaction is depicted here.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Schematic overview of the examined metabolic processes taking place within the dechlorinating enrichment consortia, with the organisms implicated in each process highlighted. End products are boxed in light grey. Organisms are coloured by taxonomic affiliation and process: Methanogenesis and synthesis pathways encoded by methanogenic Archaea are in blue, acetogenesis and other processes largely attributed to Firmicutes are in green, and pathways encoded by ∂-Proteobacteria are in orange. NB: A hydrogen molecule is required for each dechlorination step from PCE to ethene: only the first dechlorination reaction is depicted here.
Mentions: A metagenome sequencing project for the KB-1 consortium was completed by the Joint Genome Institute (JGI), generating 103 Mb of sequence. Recently, the JGI has also sequenced metagenomes from two other Dehalococcoides-containing enrichment cultures: DonnaII and ANAS. The three microbial consortia, KB-1, DonnaII, and ANAS, are maintained in Toronto, Ontario, Canada, Ithaca, NY, and Berkeley, CA, respectively. They contain different strains of Dhc, with unique complements of rdh genes [7,27,28]. Prior to metagenome sequencing, a genome sequence for the Dhc strain in the DonnaII consortium was generated [7], and a draft genome sequence for the Dhc strain in the KB-1 culture has subsequently been generated from the metagenome sequence (in-house data). The consortia have each been maintained for over a decade, in different volumes, with differing growth conditions, and with different electron donors (Table 1). The KB-1 consortium is amended methanol as an electron donor, while DonnaII is amended butyrate and ANAS utilizes lactate as an electron donor. The consortia each contain methanogenic Archaea as well as acetogenic and/or fermentative organisms, but the dominant Archaea and acetogens differ taxonomically in each culture (see Figures 1, 2). In general, reference genomes for these organisms are not available from public databases. Two exceptions are the genome sequence of the δ-Proteobacterium Geobacter lovleyi strain SZ, which is a close relative to the Geobacter strain in the KB-1 consortium, and the euryarchaeote Methanospirillum hungatei in the DonnaII culture. Despite the physical differences in maintenance conditions and the taxonomic variation between the consortia, all three consortia are capable of the complete dechlorination of tetra- or trichloroethene to non-toxic ethene, indicating that the environmental differences present do not preclude sustained Dhc growth.

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