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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

Journal Article · · Applied and Environmental Microbiology
DOI:https://doi.org/10.1128/AEM.03508-16· OSTI ID:1379788
 [1];  [1];  [2];  [3];  [4];  [2];  [1];  [5];  [6];  [7];  [8]
  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)
+ Show Author Affiliations

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 interactions and roles played by members of dechlorinating communities under cobalamin-limited conditions.

Research Organization:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
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)
Grant/Contract Number:
AC02-05CH11231; CBET-1336709; S10RR029668; S10RR027303; R42 ES004705-19; R01 ES024255-01; 09-069890
OSTI ID:
1379788
Journal Information:
Applied and Environmental Microbiology, Vol. 83, Issue 8; ISSN 0099-2240
Publisher:
American Society for MicrobiologyCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 17 works
Citation information provided by
Web of Science

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Cited By (5)

Synthetic microbial consortia for biosynthesis and biodegradation: promises and challenges journal July 2019
Growth of Dehalococcoides mccartyi species in an autotrophic consortium producing limited acetate journal August 2018
Sustained Dechlorination of Vinyl Chloride to Ethene in Dehalococcoides -Enriched Cultures Grown without Addition of Exogenous Vitamins and at Low pH journal August 2019
An integrative overview of genomic, transcriptomic and proteomic analyses in organohalide respiration research journal January 2018
An integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community journal February 2019

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Dehalococcoides
reductive dechlorination
corrinoid
Veillonellaceae
metagenome
metatranscriptome