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 paper 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 putative draft genomes were binned from the metagenomes. At an early stage (2 days), more transcripts of genes in the Veillonellaceae 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 de novo biosynthesis pathway was also assigned to the Veillonellaceae 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 Dehalococcoides was upregulated in response to the cobalamin stress. Finally, this study provides important insights into the microbial interactionsmore » and roles played by members of dechlorinating communities under cobalamin-limited conditions.« less

Authors:

Men, Yujie ^[1]; Yu, Ke ^[1]; Bælum, Jacob ^[2]; Gao, Ying ^[3]; Tremblay, Julien ^[4]; Prestat, Emmanuel ^[2]; Stenuit, Ben ^[1]; Tringe, Susannah G. ^[5]; Jansson, Janet ^[6]; Zhang, Tong ^[7]; Alvarez-Cohen, Lisa ^[8]

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+ Show Author Affiliations

1. Univ. of California, Berkeley, CA (United States)
2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
3. Univ. of California, Berkeley, CA (United States); Tsinghua Univ., Beijing (China)
4. National Research Council Canada, Montreal, QC (Canada)
5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
6. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
7. Univ. of Hong Kong (China)
8. Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Publication Date:

Fri Feb 10 00:00:00 EST 2017

Research Org.:

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Sponsoring Org.:

USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF); National Inst. of Health (NIH) (United States); Danish Research Council (Denmark)

OSTI Identifier:

1379788

Grant/Contract Number:  

AC02-05CH11231; CBET-1336709; S10RR029668; S10RR027303; R42 ES004705-19; R01 ES024255-01; 09-069890

Resource Type:

Accepted Manuscript

Journal Name:

Applied and Environmental Microbiology

Additional Journal Information:

Journal Volume: 83; Journal Issue: 8; Journal ID: ISSN 0099-2240

Publisher:

American Society for Microbiology

Country of Publication:

United States

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES; Dehalococcoides; reductive dechlorination; corrinoid; Veillonellaceae; metagenome; metatranscriptome