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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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Three-way statistical comparisons of phylogenetic differences within the enrichment culture metagenomes at different taxonomic levels. Points are displayed as the relative proportional enrichment among the metagenomes, where the closer to a corner of the plot a point falls, the more highly proportionally enriched that category is within the metagenome affiliated with that corner (arrows). Points located in the center of the plot are not enriched in one metagenome compared to the others. Only categories in which at least one metagenome’s proportion was above a threshold of 0.1% were plotted. Taxonomic levels were taken from MG-RAST phylogenetic profiles from the SEED database. Black circles indicate categories for which no pair-wise statistical significance between proportions was determined. Coloring of points indicates statistical significance for that category given a biological effect size filter in pair-wise comparisons conducted using the STAMP interface. Colors and shapes are as follows: Yellow = KB-1, Blue = ANAS, Red = DonnaII; up-pointing triangle = enriched in that metagenome above the other two, down-pointing triangle = depleted in the metagenome colored compared to the other two.
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Figure 3: Three-way statistical comparisons of phylogenetic differences within the enrichment culture metagenomes at different taxonomic levels. Points are displayed as the relative proportional enrichment among the metagenomes, where the closer to a corner of the plot a point falls, the more highly proportionally enriched that category is within the metagenome affiliated with that corner (arrows). Points located in the center of the plot are not enriched in one metagenome compared to the others. Only categories in which at least one metagenome’s proportion was above a threshold of 0.1% were plotted. Taxonomic levels were taken from MG-RAST phylogenetic profiles from the SEED database. Black circles indicate categories for which no pair-wise statistical significance between proportions was determined. Coloring of points indicates statistical significance for that category given a biological effect size filter in pair-wise comparisons conducted using the STAMP interface. Colors and shapes are as follows: Yellow = KB-1, Blue = ANAS, Red = DonnaII; up-pointing triangle = enriched in that metagenome above the other two, down-pointing triangle = depleted in the metagenome colored compared to the other two.

Mentions: Phylogenetic and metabolic profiles of the three metagenomes, both including and excluding reads of Dhc origin, were imported into STAMP [31] for pair-wise statistical comparisons (see Additional file 1: supplemental information for STAMP parameters used). The annotated metagenomes varied in size as well as proportion of unknown proteins in each dataset (35%, 24.6%, and 18.5% for DonnaII, KB-1, and ANAS respectively). For all STAMP-based comparisons, the raw read datasets were utilized, to allow quantification of gene abundances. The strengths of the combined MG-RAST/STAMP analysis are its ability to identify the potentially interesting categories deserving of closer analysis and to bypass the differences in metagenomes’ sizes and sequence type by taking dataset size into account. As an example, KB-1 exhibits a comparatively high level of enrichment in the “Virus” category (Figure 3, #1). Although the effect size is large, the total number of reads assigned to the Virus category is small (1037 hits of a total of 1769825 assigned reads for the three metagenomes combined), and the difference among the three metagenomes cannot be confidently separated from a possible sampling effect. Hence, the apparent enrichment in KB-1 is not statistically significant. On a biological note for this example, the MG-RAST database contains limited sequence information for virus genomes, which may explain the low number of hits assigned to this category.


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)

Three-way statistical comparisons of phylogenetic differences within the enrichment culture metagenomes at different taxonomic levels. Points are displayed as the relative proportional enrichment among the metagenomes, where the closer to a corner of the plot a point falls, the more highly proportionally enriched that category is within the metagenome affiliated with that corner (arrows). Points located in the center of the plot are not enriched in one metagenome compared to the others. Only categories in which at least one metagenome’s proportion was above a threshold of 0.1% were plotted. Taxonomic levels were taken from MG-RAST phylogenetic profiles from the SEED database. Black circles indicate categories for which no pair-wise statistical significance between proportions was determined. Coloring of points indicates statistical significance for that category given a biological effect size filter in pair-wise comparisons conducted using the STAMP interface. Colors and shapes are as follows: Yellow = KB-1, Blue = ANAS, Red = DonnaII; up-pointing triangle = enriched in that metagenome above the other two, down-pointing triangle = depleted in the metagenome colored compared to the other two.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Three-way statistical comparisons of phylogenetic differences within the enrichment culture metagenomes at different taxonomic levels. Points are displayed as the relative proportional enrichment among the metagenomes, where the closer to a corner of the plot a point falls, the more highly proportionally enriched that category is within the metagenome affiliated with that corner (arrows). Points located in the center of the plot are not enriched in one metagenome compared to the others. Only categories in which at least one metagenome’s proportion was above a threshold of 0.1% were plotted. Taxonomic levels were taken from MG-RAST phylogenetic profiles from the SEED database. Black circles indicate categories for which no pair-wise statistical significance between proportions was determined. Coloring of points indicates statistical significance for that category given a biological effect size filter in pair-wise comparisons conducted using the STAMP interface. Colors and shapes are as follows: Yellow = KB-1, Blue = ANAS, Red = DonnaII; up-pointing triangle = enriched in that metagenome above the other two, down-pointing triangle = depleted in the metagenome colored compared to the other two.
Mentions: Phylogenetic and metabolic profiles of the three metagenomes, both including and excluding reads of Dhc origin, were imported into STAMP [31] for pair-wise statistical comparisons (see Additional file 1: supplemental information for STAMP parameters used). The annotated metagenomes varied in size as well as proportion of unknown proteins in each dataset (35%, 24.6%, and 18.5% for DonnaII, KB-1, and ANAS respectively). For all STAMP-based comparisons, the raw read datasets were utilized, to allow quantification of gene abundances. The strengths of the combined MG-RAST/STAMP analysis are its ability to identify the potentially interesting categories deserving of closer analysis and to bypass the differences in metagenomes’ sizes and sequence type by taking dataset size into account. As an example, KB-1 exhibits a comparatively high level of enrichment in the “Virus” category (Figure 3, #1). Although the effect size is large, the total number of reads assigned to the Virus category is small (1037 hits of a total of 1769825 assigned reads for the three metagenomes combined), and the difference among the three metagenomes cannot be confidently separated from a possible sampling effect. Hence, the apparent enrichment in KB-1 is not statistically significant. On a biological note for this example, the MG-RAST database contains limited sequence information for virus genomes, which may explain the low number of hits assigned to this category.

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