title: 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 betweenDehalococcoidesand 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 theVeillonellaceaebin-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 corrinoidde novobiosynthesis pathway was also assigned to theVeillonellaceaebin-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 ofDehalococcoideswas 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.IMPORTANCEThe key chloroethene-dechlorinating bacteriumDehalococcoides mccartyiis a cobalamin auxotroph, thus acquiring corrinoids from other community members. Therefore, it is important to investigate the microbe-microbe interactions betweenDehalococcoidesand 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 ofVeillonellaceaespecies in the communities compared to other coexisting community members in producing and providing corrinoids forDehalococcoidesspecies under cobalamin-limited conditions.
authors.affiliation: Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, California, USA ymen2@illinois.edu.
authors.forename: Yujie
authors.initials: Y
authors.lastname: Men
authors.affiliation: Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, California, USA.
authors.forename: Ke
authors.initials: K
authors.lastname: Yu
authors.affiliation: Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
authors.forename: Jacob
authors.initials: J
authors.lastname: Bælum
authors.affiliation: Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, California, USA.|School of Environment, Tsinghua University, Beijing, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Gao
authors.affiliation: National Research Council Canada, Montreal, Quebec, Canada.
authors.forename: Julien
authors.initials: J
authors.lastname: Tremblay
authors.affiliation: Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Prestat
authors.affiliation: Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, California, USA.
authors.forename: Ben
authors.initials: B
authors.lastname: Stenuit
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Susannah G
authors.initials: SG
authors.lastname: Tringe
authors.affiliation: Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.
authors.forename: Janet
authors.initials: J
authors.lastname: Jansson
authors.affiliation: The University of Hong Kong, Hong Kong.
authors.forename: Tong
authors.initials: T
authors.lastname: Zhang
authors.affiliation: Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, California, USA.|Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
authors.forename: Lisa
authors.initials: L
authors.lastname: Alvarez-Cohen
mesh_terms: D001419:Bacteria / Q000378:metabolism; D001673:Biodegradation, Environmental; D053898:Biosynthetic Pathways / Q000235:genetics; D041862:Chloroflexi / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism*; D045728:Corrinoids / Q000378:metabolism; D020869:Gene Expression Profiling; D016680:Genome, Bacterial; D054879:Halogenation; D056186:Metagenomics; D059013:Microbial Consortia / Q000187:drug effects / Q000235:genetics; D014241:Trichloroethylene / Q000378:metabolism; D045854:Veillonellaceae / Q000235:genetics / Q000378:metabolism; D014805:Vitamin B 12 / Q000378:metabolism* / Q000494:pharmacology
chemical_list: D045728:Corrinoids; D014241:Trichloroethylene; D014805:Vitamin B 12
keywords: Dehalococcoides; Veillonellaceae; corrinoid; metagenome; metatranscriptome; reductive dechlorination