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Microbial communities in polychlorinated biphenyl (PCB)-contaminated wastewater lagoon sediments: PCB congener, quantitative PCR, and 16S rRNA gene amplicon sequencing datasets

ABSTRACT: The potential for aerobic and anaerobic microbial natural attenuation of PCBs in freshwater sediments is described by PCB congener, quantitative PCR, and 16S rRNA gene amplicon sequencing datasets generated, in duplicate, from 27 sediment samples collected from a PCB-contaminated freshwater lagoon (54 samples total). Sediment samples were subjected to a hexane PCB extraction protocol and the concentrations of 209 PCB congeners were determined in hexane extracts by gas chromatography with a tandem mass spectrometry detection. DNA was extracted from sediments sediment samples and used for qPCR and 16S rRNA amplicon sequencing. The abundance of 16S rRNA genes (i.e., Dehalococcoides and putative dechlorinating Chloroflexi) and functional genes (i.e., reductive dehalogenase (rdhA) and biphenyl dioxygenase (bphA)) associated with aerobic and anaerobic PCB biodegradation, along with the total 16S rRNA genes abundance, was determined by SYBR green qPCR. The microbial community composition and structure in all sediment samples was obtained by 16S rRNA gene amplicon sequencing. Primers targeting the 16S rRNA gene V4 region were used to produce 16S rRNA gene amplicons that were sequencing with the high-throughput Illumina MiSeq platform and sequencing chemistry. The 16S rRNA gene sequencing dataset along with PCB congener and qPCR datasets included as metadata, could be reused in meta-analyses that aim to determine microbial community interactions in contaminated environments, and uncover relationships between microbial community structure and environmental variable (e.g., PCB congener concentrations).

SUBMITTER: Mattes T

PROVIDER: S-EPMC8601980 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:We analyzed the transcriptional response of the actinomycete Rhodococcus aetherivorans I24 to biphenyl and polychlorinated biphenyls (PCBs). This species has not been extensively exposed to PCBs, as it was first isolated from a toluene contaminated aquifer, rather than a site contaminated with polychlorinated hydrocarbons. Using a microarray targeting 3524 genes, we assessed gene expression in minimal medium supplemented with various substrates (e.g. PCBs) and in both PCB-contaminated and non-contaminated sediment slurries. Relative to the reference condition (minimal medium supplemented with glucose), 408 genes were up-regulated in the various treatments. In medium and in sediment, PCBs elicited the up-regulation of a common set of 100 genes, including chaperones (groEL), a superoxide dismutase (sodA), alkyl hydroperoxide reductase protein C (ahpC), and a catalase/peroxidase (katG). Analysis of the R. aetherivorans I24 genome sequence identified orthologs of many of the genes in the canonical biphenyl pathway, but very few of these genes were up-regulated in response to PCBs or biphenyl. This study is one of the first which utilizes microarrays to assess the transcriptional response of a soil bacterium to a pollutant under conditions which more closely resemble the natural environment. Our results indicate that the transcriptional response of R. aetherivorans I24 to PCBs, in both medium and sediment, is primarily directed towards reducing oxidative stress, rather than catabolism. In addition, the identification of numerous genes expressed in contaminated soil specifically may have implications for the development of biosensors. Finally, comparative genomic and transcriptomic analyses suggest that the mere presence of orthologs of the required enzymes may not be sufficient to confer a vigorous biphenyl/PCB metabolism. RNA was isolated from cells incubated in the following: sediment from a PCB-contaminated industrial site, uncontaminated sediment from a comparable site, and defined media supplemented with glucose (3 g/L), glucose and biphenyl (3 g/L, 4.5 Î¼M), or glucose and PCBs (3 g/L, 5 mg/L Aroclor 1254). In all cases, there were 3 biological replicates and 2 technical replicates (repeat hybridizations). A total of 3524 genes are represented on the arrays; of these, 41 and 176 are found on the plasmids pRA2 and pRA3, respectively. On average, there are 3 distinct 24nt probes per gene.

Project description:BackgroundExposure to persistent organic pollutants (POPs) is known to increase risk of diabetes.ObjectiveTo determine which POPs are most associated with prevalence of diabetes in 601 Akwesasne Native Americans.MethodsMultiple logistic regression analysis was used to assess associations between quartiles of concentrations of 101 polychlorinated biphenyl (PCBs) congeners, congener groups and three chlorinated pesticides [dichlorodiphenyldichloroethylene (DDE), hexachlorobenzene (HCB) and mirex] with diabetes. In Model 1, the relationship between quartiles of exposure and diabetes were adjusted only for sex, age, body mass index (BMI), and total serum lipids. Model 2 included additional adjustment for either total PCBs or total pesticides.ResultsTotal serum PCB and pesticide concentrations were each significantly associated with prevalence of diabetes when adjusted only for covariates (Model 1), but neither showed a significant OR for highest to lowest quartiles after additional adjustment for the other (Model 2). When applying Model 2 to PCB congener groups and individual pesticides, there were significant omnibus differences between the four quartiles (all ps < 0.042) for most groups, with the exception of penta- and hexachlorobiphenyls, DDE and mirex. However, when comparing highest to lowest quartiles only non- and mono-ortho PCBs [OR = 4.55 (95% CI: 1.48, 13.95)], tri- and tetrachloro PCBs [OR = 3.66 (95% CI: 1.37, -9.78)] and HCB [OR = 2.64 (95% CI: 1.05, 6.61)] showed significant associations with diabetes. Among the non- and mono-ortho congeners, highest to lowest quartile of dioxin TEQs was not significant [OR = 1.82 (95% CI: 0.61, 5.40)] but the OR for the non-dioxin-like congeners was [OR = 5.01 (95% CI: 1.76, 14.24)].ConclusionThe associations with diabetes after adjustment for other POPs were strongest with the more volatile, non-dioxin-like, low-chlorinated PCB congeners and HCB. Because low-chlorinated congeners are more volatile, these observations suggest that inhalation of vapor-phase PCBs is an important route of exposure.CitationAminov Z, Haase R, Rej R, Schymura MJ, Santiago-Rivera A, Morse G, DeCaprio A, Carpenter DO, and the Akwesasne Task Force on the Environment. 2016. Diabetes prevalence in relation to serum concentrations of polychlorinated biphenyl (PCB) congener groups and three chlorinated pesticides in a Native American population. Environ Health Perspect 124:1376-1383; http://dx.doi.org/10.1289/ehp.1509902.

Dataset Information

Microbial communities in polychlorinated biphenyl (PCB)-contaminated wastewater lagoon sediments: PCB congener, quantitative PCR, and 16S rRNA gene amplicon sequencing datasets

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