title: Metagenome phylogenetic profiling of microbial community evolution in a tetrachloroethene-contaminated aquifer responding to enhanced reductive dechlorination protocols.
abstract: Chlorinated solvent contamination of potable water supplies is a serious problem worldwide. Biostimulation protocols can successfully remediate chlorinated solvent contamination through enhanced reductive dechlorination pathways, however the process is poorly understood and sometimes stalls creating a more serious problem. Whole metagenome techniques have the potential to reveal details of microbial community changes induced by biostimulation. Here we compare the metagenome of a tetrachloroethene contaminated Environmental Protection Agency Superfund Site before and after the application of biostimulation protocols. Environmental DNA was extracted from uncultured microbes that were harvested by on-site filtration of groundwater one month prior to and five months after the injection of emulsified vegetable oil, nutrients, and hydrogen gas bioamendments. Pair-end libraries were prepared for high-throughput DNA sequencing and 90 basepairs from both ends of randomly fragmented 400 basepair DNA fragments were sequenced. Over 31 millions reads were annotated with Metagenome Rapid Annotation using Subsystem Technology representing 32 prokaryotic phyla, 869 genera, and 3,181 species. A 3.6 log2fold increase in biomass as measured by DNA yield per mL water was measured, but there was a 9% decrease in the number of genera detected post-remediation. We apply Bayesian statistical methods to assign false discovery rates to fold-change abundance data and use Zipf's power law to filter genera with low read counts. Plotting the log-rank against the log-fold-change facilitates the visualization of the changes in the community in response to the enhanced reductive dechlorination protocol. Members of theArchaeadomain increased 4.7 log2fold, dominated by methanogens. Prior to remediation, classesAlphaproteobacteriaandBetaproteobacteriadominated the community but exhibit significant decreases five months after biostimulation.GeobacterandSulfurospirillumreplace "Sideroxydans" andBurkholderiaas the most abundant genera. As a result of biostimulation,DeltaproteobacteriaandEpsilonproteobacteriacapable of dehalogenation, iron and sulfate reduction, and sulfur oxidation increase. Matches to thermophilic, haloalkane respiring archaea is evidence for additional species involved in biodegradation of chlorinated solvents. Additionally, potentially pathogenic bacteria increase, indicating that there may be unintended consequences of bioremediation.
authors.affiliation: New Mexico Institute of Mining and Technology, 801 Leroy Place, Socorro, NM 87801 USA.
authors.forename: Rebecca A
authors.initials: RA
authors.lastname: Reiss
authors.affiliation: AMEC Foster Wheeler Environment & Infrastructure, Inc, 8519 Jefferson NE, Albuquerque, NM 87113 USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Guerra
authors.affiliation: New Mexico Institute of Mining and Technology, 801 Leroy Place, Socorro, NM 87801 USA.
authors.forename: Oleg
authors.initials: O
authors.lastname: Makhnin
keywords: Enhanced reductive dechlorination; Metagenomics