Title: Differential gene expression of dechlorinating communities with Dehalococcoides mccartyi species

Accession Number: GSE94143

Link to Dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE94143

Repository: Gene Expression Omnibus (GEO)

Data Type(s): Gene Expression

Experiment Type(s): Expression profiling by array

Organism(s): Dehalococcoides

Summary: The aim of this study is to obtain a systems level understanding of the interactions between Dehalococcoides 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 draft genomes were binned from the metagenomes. At an early stage (2 d), more transcripts of genes in the Veillonellaceae bin-genome were detected in the metatranscriptome of the enrichment with exogenous cobalamin compared to the one without cobalamin addition. 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 de novo biosynthesis pathway was also assigned to the Veillonellaceae bin-genome. Targeted qPCR analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin. Furthermore, Dehalococcoides' corrinoid salvaging and modification pathway was upregulated in response to the cobalamin stress. This study provides important insights into the microbial interactions and roles of members of dechlorinating communities under cobalamin-limited conditions.

Publication(s) associated with this dataset:

• Men Y, Yu K, Baelum J, Gao Y, Tremblay J, Prestat E, Stenuit B, Tringe SG, Jansson J, Zhang T, Alvarez-Cohen L. 2017. Metagenomic and metatranscriptomic analyses reveal the structure and dynamics of a dechlorinating community containing Dehalococcoides mccartyi and corrinoid-providing microorganisms under cobalamin-limited conditions. Appl Environ Microbiol 83(8):e03508-16. doi:10.1128/aem.03508-16 PMID:28188205 PMCID:PMC5377501

Project(s) associated with this dataset:

• University of California-Berkeley: Metabolic Interactions Supporting Effective TCE Bioremediation under Various Biogeochemical Conditions
• University of California-Berkeley: Microbial Communities that Bioremediate Chemical Mixtures