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 log2 fold 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 the Archaea domain increased 4.7 log2 fold, dominated by methanogens. Prior to remediation, classes Alphaproteobacteria and Betaproteobacteria dominated the community but exhibit significant decreases five months after biostimulation. Geobacter and Sulfurospirillum replace “Sideroxydans” and Burkholderia as the most abundant genera. As a result of biostimulation, Deltaproteobacteria and Epsilonproteobacteria capable 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.

Abundance of Chlorinated Solvent and 1,4-Dioxane Degrading Microorganisms at Five Chlorinated Solvent Contaminated Sites Determined via Shotgun Sequencing

“…Similar to many previous studies examining microbial communities at chlorinated solvent sites (undergoing some kind of bioremediation), the genera Dehalococcoides, Dehalogenimonas and Geobacter were found in groundwater from all five sites. ,− The current study identified Desulfitobacterium and Anaeromyxobacter in the majority of samples and these genera have also been frequently detected at contaminated sites. ,− , In contrast, fewer previous studies have reported the presence of Polaromonas and Nocardioides . ,, Previous researchers have also detected methanotrophs in situ. ,, It was surprising that Dehalobacter was absent in the MG-RAST data, as this genus has been commonly reported in groundwater from chlorinated solvent contaminated sites. ,,,, However, cprA and pceA from Dehalobacter were found in the functional gene analysis, suggesting this genus could be present, but at levels undetectable by the MG-RAST analysis.…”

“…However, only a limited number of researchers have adopted this approach for describing chlorinated solvent groundwater microbial communities. Notably, these studies have primarily focused on taxonomic data, without specifically addressing RDases or other functional genes related to chlorinated solvent degradation. , Others have examined dehalogenating genes in forest soils using shotgun sequencing . To our knowledge, the current work represents the first study to target contaminant degrading functional genes in groundwater from chlorinated solvent contaminated sites using shotgun sequencing.…”

In Situ Bioremediation of a Chlorinated Hydrocarbon Plume: A Superfund Site Field Pilot Test

“…Select groundwater samples from the site were subjected to shotgun metagenomic analysis. Results from baseline to five months after the start of full-scale remedial action have already been published [20]. The MMM results in the present study are supported by the metagenomic analyses.…”

Short-term high fat diet alters genes associated with metabolic and vascular dysfunction during adolescence in rats: a pilot study

“…The resulting data files were downloaded and opened with JMP version 14 (SAS Institute, Cary, NC, USA) for data filtering and further analyses. Zipf’s power law is a graphic method employed to model complex phenomena ( Adamic, 2011 ) that has been used to identify low count theshold in environmental metagenomic shotgun sequence data ( Reiss, Guerra & Makhnin, 2016 ) and in a study of cell response to nanostructured titanium ( Reiss et al, 2020 ). Transcription profiles of tissue qualifies as a complex system and a low count cutoff was determined by a Ziph graph, in which the log abundance per gene, as measured counts per million (CPM) for all samples, is graphed against the log rank of each gene ( Fig.…”