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

Hug, Laura A, Beiko, Robert G, Rowe, Annette R, Richardson, Ruth E, Edwards, Elizabeth A·2012·BMC Genomics
DOI 10.1186/1471-2164-13-327PMC PMC3475024
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Abstract

Background: The Dehalococcoides are strictly anaerobic bacteria that gain metabolic energy via the oxidation of H 2 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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Metadata

Authors
Hug, L. A., Beiko, R. G., Rowe, A. R., Richardson, R. E., & Edwards, E. A.
Venue
BMC Genomics
Publisher
Springer Science and Business Media LLC
Published
2012-07-23
Volume
13
Issue
1
ISSN
1471-2164
DOI
10.1186/1471-2164-13-327
PMC
PMC3475024
Cited by
107
References
0
Language
en

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