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

Abstract

BackgroundThe 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.ResultsThe 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.ConclusionsComparative 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.

Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples

“…NAPDC, SCADC and TOLDC were more functionally similar to each other than to any other environments, including the tailings pond (MLSB) from which NAPDC and SCADC were enriched ( Figure 5). The cultures also grouped closely with methanogenic dechlorinating cultures enriched from environments that were co-contaminated with chlorinated compounds and hydrocarbons (Hug et al, 2012). This grouping presumably reflects the process of enrichment compared with unenriched samples from tailings and other environmental samples.…”

“…This likely reflects the relative abundance of different community members or the presence of closely related strains (for example, microdiversity), with more abundant members being better assembled due to a higher proportion of reads. The longest contigs ranged from 25.8 to 28.3 Kb, which is relatively short versus other comparable metagenomes (Hug et al, 2012), suggesting that these metagenomes reflect particularly biodiverse communities.…”

“…Metagenome Group 2 was further compared with Group 1 using STAMP (Parks and Beiko, 2010). For subsystem categories with rare counts (for example, ⩽ 0.1% of total counts), a fixed number of pseudocounts proportional to the total gene count was added to all categories across all groups used in comparisons to prevent selection of rare categories (Hug et al, 2012). For all comparisons, unassembled metagenomic reads were used unless stated otherwise.…”

“…To examine the individual contributions of NAPDC, SCADC and TOLDC to their aggregate functional profile, we performed a three-way comparison of the relative abundance of SEED functional categories according to the method of Hug et al (2012) (Figure 4a). Key functions related to methanogenesis, anaerobic hydrocarbon metabolism, redox condition regulation and hydrogen and formate transfer (important for syntrophy) were shared among the three cultures (Figure 4a).…”

“…Data points are colored according to the source of each metagenome or group; gray dots represent functional categories present at low, statistically non-significant (Po0.01) abundance. Points located near the vertices are enriched within the metagenome or group associated with that vertex, points along each axis are shared only between the two vertices associated with that axis (labelled as Functional Groups I, II and III in b), and points located near the center of the plot have similar proportions in all three metagenomes or groups (that is, show no specific enrichment; Hug et al, 2012).…”