Journal article
Genome-Resolved Metagenomics and Metatranscriptomics Reveal Insights into the Ecology and Metabolism of Anaerobic Microbial Communities in PCB-Contaminated Sediments
Environmental science & technology, Vol.57(43), pp.16386-16398
10/19/2023
DOI: 10.1021/acs.est.3c05439
PMCID: PMC10621002
PMID: 37856784
Appears in UI Libraries Support Open Access
Abstract
Growth of organohalide-respiring bacteria such as Dehalococcoides mccartyi on halogenated organics (e.g., polychlorinated biphenyls (PCBs)) at contaminated sites or in enrichment culture requires interaction and support from other microbial community members. To evaluate naturally occurring interactions between Dehalococcoides and key supporting microorganisms (e.g., production of H2, acetate, and corrinoids) in PCB-contaminated sediments, metagenomic and metatranscriptomic sequencing was conducted on DNA and RNA extracted from sediment microcosms, showing evidence of both Dehalococcoides growth and PCB dechlorination. Using a genome-resolved approach, 160 metagenome-assembled genomes (MAGs), including three Dehalococcoides MAGs, were recovered. A novel reductive dehalogenase gene, distantly related to the chlorophenol dehalogenase gene cprA (pairwise amino acid identity: 23.75%), was significantly expressed. Using MAG gene expression data, 112 MAGs were assigned functional roles (e.g., corrinoid producers, acetate/H2 producers, etc.). A network coexpression analysis of all 160 MAGs revealed correlations between 39 MAGs and the Dehalococcoides MAGs. The network analysis also showed that MAGs assigned with functional roles that support Dehalococcoides growth (e.g., corrinoid assembly, and production of intermediates required for corrinoid synthesis) displayed significant coexpression correlations with Dehalococcoides MAGs. This work demonstrates the power of genome-resolved metagenomic and metatranscriptomic analyses, which unify taxonomy and function, in investigating the ecology of dehalogenating microbial communities.
Details
- Title: Subtitle
- Genome-Resolved Metagenomics and Metatranscriptomics Reveal Insights into the Ecology and Metabolism of Anaerobic Microbial Communities in PCB-Contaminated Sediments
- Creators
- Hongyu Dang - University of IowaJessica M. Ewald - University of IowaTimothy E. Mattes - University of Iowa
- Resource Type
- Journal article
- Publication Details
- Environmental science & technology, Vol.57(43), pp.16386-16398
- DOI
- 10.1021/acs.est.3c05439
- PMID
- 37856784
- PMCID
- PMC10621002
- NLM abbreviation
- Environ Sci Technol
- ISSN
- 0013-936X
- eISSN
- 1520-5851
- Publisher
- American Chemical Society
- Grant note
- DOI: 10.13039/100000066, name: National Institute of Environmental Health Sciences, award: P42ES013661, R01ES032671
- Language
- English
- Date published
- 10/19/2023
- Academic Unit
- Civil and Environmental Engineering; IIHR--Hydroscience and Engineering; Iowa Superfund Research Program
- Record Identifier
- 9984500083202771
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