Metagenomic analysis of a stable trichloroethene-degrading microbial community

Abstract

Dehalococcoides bacteria are the only organisms known to completely reduce chlorinated ethenes to the harmless product ethene. However, Dehalococcoides dechlorinate these chemicals more effectively and grow more robustly in mixed microbial communities than in isolation. In this study, the phylogenetic composition and gene content of a functionally stable trichloroethene-degrading microbial community was examined using metagenomic sequencing and analysis. For phylogenetic classification, contiguous sequences (contigs) longer than 2500 bp were grouped into classes according to tetranucleotide frequencies and assigned to taxa based on rRNA genes and other phylogenetic marker genes. Classes were identified for Clostridiaceae, Dehalococcoides, Desulfovibrio, Methanobacterium, Methanospirillum, as well as a Spirochete, a Synergistete, and an unknown Deltaproteobacterium. Dehalococcoides contigs were also identified based on sequence similarity to previously sequenced genomes, allowing the identification of 170 kb on contigs shorter than 2500 bp. Examination of metagenome sequences affiliated with Dehalococcoides revealed 406 genes not found in previously sequenced Dehalococcoides genomes, including 9 cobalamin biosynthesis genes related to corrin ring synthesis. This is the first time that a Dehalococcoides strain has been found to possess genes for synthesizing this cofactor critical to reductive dechlorination. Besides Dehalococcoides, several other members of this community appear to have genes for complete or near-complete cobalamin biosynthesis pathways. In all, 17 genes for putative reductive dehalogenases were identified, including 11 novel ones, all associated with Dehalococcoides. Genes for hydrogenase components (271 in total) were widespread, highlighting the importance of hydrogen metabolism in this community. PhyloChip analysis confirmed the stability of this microbial community.

Effects of Sulfate Reduction on Trichloroethene Dechlorination by Dehalococcoides-Containing Microbial Communities

“…This agrees with the observations made using constructed consortia that reductive dechlorination rates are not affected by sulfate amendment (2 and 5 mM) under electron donor limitation. Also, the higher abundance of D. mccartyi (Ͼ30%) in the enrichment culture compared to the co-and tricultures may be another reason that dechlorination outcompetes sulfate reduction (53).…”

“…The methanogenic dechlorinating community ANAS was previously enriched from contaminated soil obtained from the Alameda Naval Air Station (CA). The culture has been maintained in the laboratory for more than 15 years in a continuously stirred semibatch fed reactor, and its community structure and dechlorination performance have been previously described (53,56,57).…”

Characterization of a Highly Enriched Microbial Consortium Reductively Dechlorinating 2,3-Dichlorophenol and 2,4,6-Trichlorophenol and the Corresponding cprA Genes from River Sediment

“…The metagenomes of microbial communities are currently under investigation to reveal the metabolic interactions within organohalide-respiring consortia. Some consortia have been developed and characterized for organohalide-respiring populations and associated bacteria (Duhamel and Edwards, 2007;Rowe et al, 2008;Brisson et al, 2012;Hug, 2012;Maphosa et al, 2012). PCR-DGGE analysis using 16S rRNA genes usually yields patterns that reflect the composition of dominant microorganisms, including the nonculturable members (Gelsomino et al, 1999).…”

Genomic insights into organohalide respiration

“…Metaanalyses highlighted two high plasticity regions (HPR) around the origin of replication but otherwise the strains show high synteny and identity (1029 genes conserved in all strains) [16,17,18 ,19]. Metagenomes for Dehalococcoides-containing enrichment cultures have also been recently described for the cultures called KB1, DonnaII, and ANAS [20,21].…”

“…Metagenome analyses of chloroethene-respiring, Dehalococcoides-enriched cultures showed that multiple non-Dehalococcoides populations (e.g. Firmicutes; methanogens; delta-proteobacteria) harbor pathways for cobalamin synthesis [20,21] and Men [63] observed that Dehalococcoides in coculture with Desulfovibrio benefitted from corrinoid salvage and amino acid pathways in the latter organism. Yan [75] showed specific cobamide transfer to Dehalococcoides from G. lovleyi strains but not G. sulfurreducens.…”