Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions

Abstract

The aim of this study is to obtain a systems-level understanding of the interactions between and corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities, and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 days), more transcripts of genes in the bin-genome were detected in the metatranscriptome of the enrichment without exogenous cobalamin than in the one with the addition of cobalamin. Among these genes, sporulation-related genes exhibited the highest differential expression when cobalamin was not added, suggesting a possible release route of corrinoids from corrinoid producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoid biosynthesis pathway was also assigned to the bin-genome. Targeted quantitative PCR (qPCR) analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin than in the enrichment with cobalamin. Furthermore, the corrinoid salvaging and modification pathway of was upregulated in response to the cobalamin stress. This study provides important insights into the microbial interactions and roles played by members of dechlorinating communities under cobalamin-limited conditions. The key chloroethene-dechlorinating bacterium is a cobalamin auxotroph, thus acquiring corrinoids from other community members. Therefore, it is important to investigate the microbe-microbe interactions between and the corrinoid-providing microorganisms in a community. This study provides systems-level information, i.e., taxonomic and functional compositions and dynamics of the supportive microorganisms in dechlorinating communities under different cobalamin conditions. The findings shed light on the important roles of species in the communities compared to other coexisting community members in producing and providing corrinoids for species under cobalamin-limited conditions.

Sustained Dechlorination of Vinyl Chloride to Ethene in Dehalococcoides-Enriched Cultures Grown without Addition of Exogenous Vitamins and at Low pH

“…Dechlorinating cultures that grow in the absence of cobalamin have been reported before, yet incomplete dechlorination and VC accumulation occurred. 46,47 To our knowledge, this is the first report of complete and sustained dechlorination to ethene in dechlorinating mixed cultures grown without any exogenous vitamins.…”

An integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community

“…To exclude the bias of comparison of gene expression level caused by cellular growth, we normalized the number of mapped reads of a certain ORF against mapped reads of total ORFs from a certain genome for RPKM value calculation [48]. For instance, if gene a is present in genome A, the RPKM value will be calculated by the following equation:…”

Growth of Dehalococcoides mccartyi species in an autotrophic consortium producing limited acetate

“…A clone library analysis indicated that D. mccartyi species (57%) and Desulfovibrio species (22%) are the two dominant populations in culture EC195 (Table 1). Spirochaeta also occurred in culture EC195, which has commonly been found in other dechlorinating enrichment cultures (Men et al 2017;Kaufhold et al 2013).…”