Combined read- and assembly-based metagenomics to reconstruct aDehalococcoides mccartyigenome from PCB-contaminated sediments and evaluate functional differences among organohalide-respiring consortia in the presence of different halogenated contaminants

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.

Genome-Resolved Metagenomics and Metatranscriptomics Reveal Insights into the Ecology and Metabolism of Anaerobic Microbial Communities in PCB-Contaminated Sediments

“…Four microcosms were prepared anaerobically in 160 mL serum bottles with a modified reduced anaerobic mineral medium (RAMM; 100 mL). , The RAMM composition is described in Section S1. PCB-contaminated sediment samples (10 g each) from two different freshwater lagoon locations (F4 and E2) that previously showed dechlorination activity were added to duplicate bottles for each location (i.e., F4–1, F4–2, E2–1, and E2–2).…”

“…A mixture of organic acids (acetate, propionate, butyrate, and lactate) was added into the bottles with an initial concentration of 2.5 mM each . Site location, sediment sampling protocols, and microcosm preparation details exist elsewhere. ,, Aroclor 1248 is the likely contaminating PCB mixture . No exogenous PCB congeners or microorganisms were added to the microcosms.…”

“…A liquid–liquid PCB extraction method was applied to microcosm slurry samples (2 mL), followed by addition of surrogate and internal standards as described previously. , Each extracted batch of samples contained at least one laboratory blank comprised of hexane spiked with surrogate standards. PCBs in slurry extracts were quantified with a modified US EPA method 1668C. , Surrogate standard recoveries and method blanks allowed us to evaluate extraction procedure efficiencies and quantify background PCB concentrations .…”

“…The Dehalococcoides MAGs were placed in the Cornell subgroup (Figure S5). The ANI among the three Dehalococcoides MAGs was >99.8% and was >98% with PCB-dechlorinating strain CG4 MAG 25 but not from the individually assembled Dehalococcoides MAGs. A total of 27 RDase genes with >90% identity to each other were annotated in the Dehalococcoides MAGs (Figure S6).…”

“…Comparing PCB congener profiles at day 0 and at final sampling day 200 revealed greater differences in the HPCBM congener profile after 200 days 25 than in the LPCBM, where few congeners diverged from the initial profile (Figure 1). In a previous microcosm study with these sediments over a 430-day incubation period, the mass fractions of tetrachlorinated PCB 66 and PCB 61/70/74/66 decreased, while mass fractions of trichlorinated dechlorination products PCB25 and PCB26/29 increased.…”