16S rRNA gene data for aerobic BTEX-degrading enrichments exposed to sulfonamide polyfluorinated substances in fire-fighting foams and transformation products
Data files
Apr 12, 2024 version files 383.37 MB
Abstract
Per- and polyfluoroalkyl substances (PFASs) from aqueous film forming foams (AFFFs) can hinder bioremediation of co-contaminants, such as trichloroethene (TCE) and benzene, toluene, ethylbenzene, and xylene (BTEX). Anaerobic dechlorination can require bioaugmentation of Dehalococcoides and for BTEX, oxygen is often sparged to stimulate in-situ aerobic biodegradation. We tested PFAS inhibition to TCE and BTEX bioremediation by exposing an anaerobic TCE-dechlorinating co-culture, an aerobic BTEX-degrading enrichment culture, and an anaerobic toluene-degrading enrichment culture to n-dimethyl perfluorohexane sulfonamido amine (AmPr-FHxSA), perfluorohexane sulfonamide (FHxSA), perfluorohexane sulfonic acid (PFHxS), or non-fluorinated surfactant sodium dodecyl sulfate (SDS). The anaerobic TCE-dechlorinating co-culture was resistant to individual PFASs exposures but was inhibited by >1,000x diluted AFFF. FHxSA and AmPr-FHxSA inhibited the aerobic BTEX-degrading enrichment. The anaerobic toluene-degrading enrichment was not inhibited by AFFF or individual PFASs. Increases in amino acids in the anaerobic TCE-dechlorinating co-culture compared to the control indicated stress response, while the BTEX culture exhibited lower concentrations of all amino acids upon exposure to most surfactants (both fluorinated and non-fluorinated) compared to the control. These data suggest the main mechanisms of microbial toxicity are related to interactions with cell membrane synthesis as well as protein stress signaling.
README: 16S rRNA gene data for aerobic BTEX-degrading enrichments exposed to sulfonamide polyfluorinated substances in fire-fighting foams and transformation products
https://doi.org/10.5061/dryad.0k6djhb7j
Description of the data
The data reported consist of 16S rRNA gene sequences from an aerobic enrichment culture that is able to degrade benzene, toluene, ethylbenzene, and xylenes under aerobic conditions. The enrichment was developed from a PFAS fire-fighting foam impacted site. The microcosm experiments evaluated inhibition to BTEX biodegradation upon exposure of individual sulfonamide-PFAS present int fire-fighting foam as well as their transformation products, perfluoroalkyl sulfonates.
Folder Structure:
- Raw_16S_data (.zip): This zipped folder contains the following files:
- Folders (named B1a, B1b, etc.,) corresponding to specific samples which contain FASTQ files (raw files, and primers, barcodes removed) (.fq). These FASTQ files contain raw sequencing data from the 16S rRNA gene region of the samples. Each FASTQ file represents a set of sequencing reads obtained from DNA samples. The reads typically include both forward and reverse reads.
- * B1a, B1b: Control (unexposed to PFASs or SDS) BTEX-degrading enrichment after six days.
- * B2a, B2b: SDS exposed BTEX-degrading enrichment after six days
- * B3a, B3b: PFHxS exposed BTEX-degrading enrichment after six days.
- * B4a,B4b: FHxSA exposed BTEX-degrading enrichment after six days.
- * B5a, B5b: Ampr-FHxSA exposed BTEX-degrading enrichment after six days.
- * BIa, BIb: BTEX-degrading enrichment (inoculum).
- SampleSeq_info (.xls ): Sample ID, Barcode Sequence, LinkerPrimerSequence
- Rawdata_Readme (.txt): Overview of raw data reads showing folder structure
- Folders (named B1a, B1b, etc.,) corresponding to specific samples which contain FASTQ files (raw files, and primers, barcodes removed) (.fq). These FASTQ files contain raw sequencing data from the 16S rRNA gene region of the samples. Each FASTQ file represents a set of sequencing reads obtained from DNA samples. The reads typically include both forward and reverse reads.
- Taxa_Abundances_Processed (.xlsx): This Excel file shows processed 16S data with assigned Taxa and relative abundances per sample. A tab is also included with Sample codes and Experimental/Control group information.
Code/Software
All downstream processing of the raw data in the manuscript used MOTHUR v.1.43.0 following the MiSeq SOP.4. Raw reads were merged, trimmed, and 302 filtered for quality. Unique sequences were aligned against the SILVA 16S rRNA reference database (v.132),5 clustered into operational taxonomic units based on 97% similarity and assigned taxonomic identities to the genus level using the RDP v.18 reference training set. Singletons were removed and the data was transferred to R for all downstream analysis. The phyloseq package in R was used to process output files from MOTHUR into relative abundance using the averaged triplicates and plotted using ggplot2. Diversity indices were calculated using the microbiome package. Statistical analysis was performed using base R using ANOVA and Tukey’s HSD Test for post-hoc analysis
Results
At the Phylum level, Actinobacteria and Proteobacteria were the most abundant . Exposures to FHxSA, AmPr-FHxSA increased relative abundance of Proteobacteria and Bacteriodetes, gram-negative bacterial genera. AmPr-FHxSA also had detectable percentage of Firmicutes, which was undetected in the inoculum and in FHxSA exposures. Cultures exposed to PFHxS and SDS, the DNA extraction and amplification efficiency was not acceptable and thus not reported.
Methods
At the end of the BTEX enrichment experiments with 10 μM of each PFAS, 4 mL slurry samples were centrifuged at 10,000g for 10 minutes, decanted, and extracted for DNA using a DNeasy PowerSoil Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. Extracted DNA was stored at -80°C and sent to Novogene Corporation Inc. (Sacramento, CA, USA) for bacterial 16S rRNA amplification and sequencing. At Novogene Corporation Inc. (Sacramento, CA, USA), DNA concentrations were normalized to 10 ng/μL and amplified targeting the V3-V4 region (470bp fragment length). At Novogene Corporation Inc. (Sacramento, CA, USA), DNA concentrations were normalized to 297 10 ng/μL and amplified targeting the V3-V4 region (470bp fragment length). The amplicons 298 were then assessed for quality on an Agilent 5400 Fragment Analyzer (Agilent, Palo Alto, CA, 299 USA) before library preparation and sequencing on an Illumina NovaSeq6000 PE250 platform 300 (Illumina, San Diego, CA, USA).