Microbial diversity in compact bentonite clay (7 years)
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PROVIDER: PRJEB76313 | ENA |
REPOSITORIES: ENA
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Project description:Polychlorinated dibenzo-p-dioxins and dibenzofurans are a group of chemcially-related pollutants categorically known as dioxins. We used Sphingomonas wittichii strain RW1 (RW1), one of the few strains able to grow on dioxin, to characterize its ability to respond to and degrade clay-bound dioxin. Strain RW1 grew on and completely degraded dioxin intercalated in smectite clay. To characterize the effects of sorption and bioavailability of dioxin on RW1, transcriptomes of RW1 either grown with dioxin intercalated to clay (DDSAP) or with free crystalline dioxin (DD) were sequenced using RNA-Seq. While either condition caused RW1 large-scale shifts in gene expression compared to succinate control (SUC), differences in gene expression between these two conditions were marked by a small number (86) of differentially expressed genes. The differences in gene expression may reflect the underlying adaptive mechanisms by which RW1 cells sense and deploy pathways to access dioxin intercalated in the clay.
2019-06-30 | GSE115658 | GEO
Project description:Bavarian Bentonite B25 Raw sequence reads
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Project description:Canada’s plan for a deep geological repository (DGR) will provide a safe, long-term storage solution for used nuclear fuel. Investigating microbial viability in Wyoming MX-80 bentonite under DGR-like conditions suggests microbial suppression in low water activities for the prevention of microbiologically influenced corrosion.
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Project description:Bentonite clay is an integral component of the engineered barrier system of deep geological repositories (DGRs) that are planned for the long-term storage of high-level radioactive waste. Although nucleic acid extraction and analysis can provide powerful qualitative and quantitative data reflecting the presence, abundance, and functional potential of microorganisms within DGR materials, extraction of microbial DNA from bentonite clay is challenging due to the low biomass and adsorption of nucleic acids to the charged clay matrix. In this study, we used quantitative PCR, gel fingerprinting, and high-throughput sequencing of 16S rRNA gene amplicons to assess DNA extraction efficiency from natural MX-80 bentonite and the same material "spiked" with Escherichia coli genomic DNA. Extraction protocols were tested without additives and with casein and phosphate as blocking agents. Although we demonstrate improved DNA recovery by blocking agents at relatively high DNA spiking concentrations, at relatively low spiking concentrations, we detected a high proportion of contaminant nucleic acids from blocking agents that masked sample-specific microbial profile data. Because bacterial genomic DNA associated with casein preparations was insufficiently removed by UV treatment, casein is not recommended as an additive for DNA extractions from low-biomass samples. Instead, we recommend a kit-based extraction protocol for bentonite clay without additional blocking agents, as tested here and validated with multiple MX-80 bentonite samples, ensuring relatively high DNA recoveries with minimal contamination.IMPORTANCE Extraction of microbial DNA from MX-80 bentonite is challenging due to low biomass and adsorption of nucleic acid molecules to the charged clay matrix. Blocking agents improve DNA recovery, but their impact on microbial community profiles from low-biomass samples has not been characterized well. In this study, we evaluated the effect of casein and phosphate as blocking agents for quantitative recovery of nucleic acids from MX-80 bentonite. Our data justify a simplified framework for analyzing microbial community DNA associated with swelling MX-80 bentonite samples within the context of a deep geological repository for used nuclear fuel. This study is among the first to demonstrate successful extraction of DNA from Wyoming MX-80 bentonite.
| S-EPMC6821930 | biostudies-literature
Project description:Impact of aggregate size and clay content on the bacterial community structure in soil microaggregates and macroaggregates of a clay catena
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Project description:Opalinus Clay-associated microbial communities
| PRJEB53941 | ENA
Project description:Sphingomonas wittichii strain RW1 (RW1) is one of few strains that can grow on dibenzo-p-dioxin (DD). We conducted a transcriptomic study of RW1 using RNA-Seq to outline transcriptional responses to DD, dibenzofuran (DF), and the smectite clay mineral saponite (SAP), an important geosorbent of toxicants in soil, with succinate as carbon source. The ability to grow on DD is rare compared to growth on the chemically similar DF even though the same initial dioxygenase may be involved in oxidation of both substrates. Therefore we hypothesized the reason for this lies beyond catabolic pathways and may concern genes involved in processes for cell-substrate interactions such as substrate recognition and transport, and detoxification. Compared to succinate (SUC) as control carbon source, DF caused over 240 protein-coding genes to be differentially expressed, whereas more than 300 were differentially expressed with DD. Stress response genes were up-regulated by both DD and DF. This effect was stronger with DD than DF, suggesting a higher toxicity of DD compared to DF. Both DD and DF caused changes in expression of genes involved in active cross-membrane transport such as TonB dependent receptor proteins, but the patterns of changes differed between the two substrates. Multiple transcription factor genes also displayed expression patterns distinct to DD and DF growth. DD and DF induced the catechol ortho- and the salicylate/gentisate pathways, respectively. Both DD and DF induced the shared down-stream aliphatic intermediate compound pathway. Clay (SAP) caused category-wide down-regulation of genes for cell motility and chemotaxis, particularly those involved in the synthesis, assembly and functioning of flagella. This is environmentally important finding because clay is a major component of soil microbes’ microenvironment influencing local chemistry and may serve as geosorbent for toxic pollutants. Similar to clay, DD and DF also affect motility and chemotaxis.
2015-11-13 | GSE74831 | GEO