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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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Related in: MedlinePlus

Three-way comparisons of metabolic differences within the enrichment culture metagenomes with all Dhc reads removed. Points are displayed as in Figure 3, with points here corresponding to MG-RAST assignments to categories of metabolic classification within The SEED database. 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. Coloration and shapes are as in Figure 3. Labeled points correspond to all categories for which one metagenome was significantly enriched above the other two. For the metabolic level 1 class, the threshold for plotting was increased to 1% to reflect the lower number of possible categories.
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Figure 4: Three-way comparisons of metabolic differences within the enrichment culture metagenomes with all Dhc reads removed. Points are displayed as in Figure 3, with points here corresponding to MG-RAST assignments to categories of metabolic classification within The SEED database. 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. Coloration and shapes are as in Figure 3. Labeled points correspond to all categories for which one metagenome was significantly enriched above the other two. For the metabolic level 1 class, the threshold for plotting was increased to 1% to reflect the lower number of possible categories.

Mentions: The MG-RAST metabolic assignments for the three metagenomes with all Dhc-assigned reads removed were used to examine the non-Dhc community metabolic differences. The SEED subsystems are available at three levels of increasing specificity, where level 1 provides broad categories similar to COG designations (e.g., Membrane Transport), and levels 2 and 3 provide more specific categories (e.g., Level 2 = ABC transporters, Level 3 = ABC transporter iron(III) dicitrate (TC_3.A.1.14.1)). Several categories from the SEED level 1 exhibit differences in enrichment among the three metagenomes. However, it is clear from the triangle plot that, while these are statistically significant differences, the enrichment seen is not strong (Figure 4, level 1). A more in-depth examination was required to distinguish the nature of this significance. When examining specific subsystems (SEED level 3) there are only three categories for which one metagenome shows significant enrichment above the other two (Figure 4, level 3). DonnaII exhibits significant enrichment in the transposon 552-associated subsystem (Figure 4, #12). This SEED subsystem contains the common elements of tn552 transposons, including mobility elements (transposase tnpA and recombinase binL) as well as β-lactamase (blaZ) and two regulatory genes (blaI and blaR) (SEED subsystem notes). Gene-specific examination reveals this enrichment is specifically due to the Firmicute-associated β-lactamase gene (E.C. 3.5.2.6) in DonnaII. β-lactamase confers antibiotic resistance against β-lactam antibiotics, including penicillin [50]. The DonnaII bioreactor has never been exposed to antibiotics, so this resistance likely stems from the DonnaII bioreactor’s origin, the Ithaca wastewater treatment plant. Examination of the DonnaII sequences assigned to this subsystem reveals that the reads assigned to transposon-associated genes are 700x less abundant than reads assigned to the β-lactamase gene. From the assembled metagenome data, the identified β-lactamase genes are not associated with annotated transposases, either on the same contig or within the same scaffold, indicating the β-lactamase may not be associated with a transposon, and hence may not be mobile.


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 comparisons of metabolic differences within the enrichment culture metagenomes with all Dhc reads removed. Points are displayed as in Figure 3, with points here corresponding to MG-RAST assignments to categories of metabolic classification within The SEED database. 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. Coloration and shapes are as in Figure 3. Labeled points correspond to all categories for which one metagenome was significantly enriched above the other two. For the metabolic level 1 class, the threshold for plotting was increased to 1% to reflect the lower number of possible categories.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Three-way comparisons of metabolic differences within the enrichment culture metagenomes with all Dhc reads removed. Points are displayed as in Figure 3, with points here corresponding to MG-RAST assignments to categories of metabolic classification within The SEED database. 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. Coloration and shapes are as in Figure 3. Labeled points correspond to all categories for which one metagenome was significantly enriched above the other two. For the metabolic level 1 class, the threshold for plotting was increased to 1% to reflect the lower number of possible categories.
Mentions: The MG-RAST metabolic assignments for the three metagenomes with all Dhc-assigned reads removed were used to examine the non-Dhc community metabolic differences. The SEED subsystems are available at three levels of increasing specificity, where level 1 provides broad categories similar to COG designations (e.g., Membrane Transport), and levels 2 and 3 provide more specific categories (e.g., Level 2 = ABC transporters, Level 3 = ABC transporter iron(III) dicitrate (TC_3.A.1.14.1)). Several categories from the SEED level 1 exhibit differences in enrichment among the three metagenomes. However, it is clear from the triangle plot that, while these are statistically significant differences, the enrichment seen is not strong (Figure 4, level 1). A more in-depth examination was required to distinguish the nature of this significance. When examining specific subsystems (SEED level 3) there are only three categories for which one metagenome shows significant enrichment above the other two (Figure 4, level 3). DonnaII exhibits significant enrichment in the transposon 552-associated subsystem (Figure 4, #12). This SEED subsystem contains the common elements of tn552 transposons, including mobility elements (transposase tnpA and recombinase binL) as well as β-lactamase (blaZ) and two regulatory genes (blaI and blaR) (SEED subsystem notes). Gene-specific examination reveals this enrichment is specifically due to the Firmicute-associated β-lactamase gene (E.C. 3.5.2.6) in DonnaII. β-lactamase confers antibiotic resistance against β-lactam antibiotics, including penicillin [50]. The DonnaII bioreactor has never been exposed to antibiotics, so this resistance likely stems from the DonnaII bioreactor’s origin, the Ithaca wastewater treatment plant. Examination of the DonnaII sequences assigned to this subsystem reveals that the reads assigned to transposon-associated genes are 700x less abundant than reads assigned to the β-lactamase gene. From the assembled metagenome data, the identified β-lactamase genes are not associated with annotated transposases, either on the same contig or within the same scaffold, indicating the β-lactamase may not be associated with a transposon, and hence may not be mobile.

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