Journal article
Combined read- and assembly-based metagenomics to reconstruct a Dehalococcoides mccartyi genome from PCB-contaminated sediments and evaluate functional differences among organohalide-respiring consortia in the presence of different halogenated contaminants
FEMS microbiology ecology, Vol.98(7), fiac067
07/2022
DOI: 10.1093/femsec/fiac067
PMCID: PMC9279884
PMID: 35665806
Abstract
Microbial communities that support respiration of halogenated organic contaminants by Dehalococcoides sp. facilitate full-scale bioremediation of chlorinated ethenes and demonstrate the potential to aid in bioremediation of halogenated aromatics like polychlorinated biphenyls (PCBs). However, it remains unclear if Dehalococcoides-containing microbial community dynamics observed in sediment-free systems quantitatively resemble that of sediment environments. To evaluate that possibility we assembled, annotated, and analyzed a Dehalococcoides sp. metagenome-assembled genome (MAG) from PCB-contaminated sediments. Phylogenetic analysis of reductive dehalogenase gene (rdhA) sequences within the MAG revealed that pcbA1 and pcbA4/5-like rdhA were absent, while several candidate PCB dehalogenase genes and potentially novel rdhA sequences were identified. Using a compositional comparative metagenomics approach, we quantified Dehalococcoides-containing microbial community structure shifts in response to halogenated organics and the presence of sediments. Functional level analysis revealed significantly greater abundances of genes associated with cobamide remodeling and horizontal gene transfer in tetrachloroethene-fed cultures as compared to halogenated aromatic-exposed consortia with or without sediments, despite little evidence of statistically significant differences in microbial community taxonomic structure. Our findings support the use of a generalizable comparative metagenomics workflow to evaluate Dehalococcoides-containing consortia in sediments and sediment-free environments to eludicate functions and microbial interactions that facilitate bioremediation of halogenated organic contaminants.
Details
- Title: Subtitle
- Combined read- and assembly-based metagenomics to reconstruct a Dehalococcoides mccartyi genome from PCB-contaminated sediments and evaluate functional differences among organohalide-respiring consortia in the presence of different halogenated contaminants
- Creators
- Jessica M Ewald - University of IowaJerald L Schnoor - University of IowaTimothy E Mattes - University of Iowa
- Resource Type
- Journal article
- Publication Details
- FEMS microbiology ecology, Vol.98(7), fiac067
- DOI
- 10.1093/femsec/fiac067
- PMID
- 35665806
- PMCID
- PMC9279884
- NLM abbreviation
- FEMS Microbiol Ecol
- eISSN
- 1574-6941
- Grant note
- DOI: 10.13039/100000066, name: NIEHS, award: P42ES013661, R01ES032671
- Language
- English
- Electronic publication date
- 06/06/2022
- Date published
- 07/2022
- Academic Unit
- Civil and Environmental Engineering; Occupational and Environmental Health; IIHR--Hydroscience and Engineering; Iowa Superfund Research Program
- Record Identifier
- 9984267486302771
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