Biobarrier for hydrocarbon degradation
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Project description:Members of the bacterial phylum Spirochaetes are primarily studied for their commensal and pathogenic roles in animal hosts. However, Spirochaetes are also frequently detected in anoxic hydrocarbon-contaminated environments but their ecological role in such ecosystems has so far remained unclear. Here we provide a functional trait to these frequently detected organisms with an example of a sulfate-reducing, naphthalene-degrading enrichment culture consisting of a sulfate-reducing deltaproteobacterium Desulfobacterium naphthalenivorans and a novel spirochete Rectinema cohabitans. Using a combination of genomic, proteomic, and physiological studies we show that R. cohabitans grows by fermentation of organic compounds derived from biomass from dead cells (necromass). It recycles the derived electrons in the form of H2 to the sulfate-reducing D. naphthalenivorans, thereby supporting naphthalene degradation and forming a simple microbial loop. We provide metagenomic evidence that equivalent associations between Spirochaetes and hydrocarbon-degrading microorganisms are of general importance in hydrocarbon- and organohalide-contaminated ecosystems. We propose that environmental Spirochaetes form a critical component of a microbial loop central to nutrient cycling in subsurface environments. This emphasizes the importance of necromass and H2-cycling in highly toxic contaminated subsurface habitats such as hydrocarbon-polluted aquifers.
2018-05-17 | PXD005624 | Pride
Project description:We demonstrate the feasibility of total RNA-SIP in experiments where microbes from a hydrocarbon-contaminated aquifer were studied in microcosms with 13C-labelled-toluene to understand their adaptation to the simultaneous availability of low levels of different electron acceptors. SIP successfully resolved the involvement of microaerobic vs. aerobic and anaerobic populations. Under microoxic, nitrate-amended conditions hydrocarbon degradation was actually stimulated, but transcripts of denitrification showed no signs of 13C-labelling. The expression of distinct oxygenase-based catabolic pathways for toluene degradation was clearly apparent in 13C-labelled mRNA. We discuss how these direct insights into the gene expression and adaptation mechanisms within complex degrader communities can guide more integrated approaches in monitoring and restoration of contaminated sites.
2019-11-08 | GSE140055 | GEO
Project description:Enrichments of microbial communities derived from hydrocarbon degrading groundwater sediments raw sequence reads
| PRJNA312010 | ENA
Project description:High Arctic soils have low nutrient availability, low moisture content and very low temperatures and, as such, they pose a particular problem in terms of hydrocarbon bioremediation. An in-depth knowledge of the microbiology involved in this process is likely to be crucial to understand and optimize the factors most influencing bioremediation. Here, we compared two distinct large-scale field bioremediation experiments, located at Alert (ex situ approach) and Eureka (in situ approach), in the Canadian high Arctic. Bacterial community structure and function were assessed using microarrays targeting the 16S rRNA genes of bacteria found in cold environments and hydrocarbon degradation genes as well as reverse-transcriptase real-time PCR targeting key functional genes. Results indicated a large difference between sampling sites in terms of both soil microbiology and decontamination rates. A rapid reorganization of the bacterial community structure and functional potential as well as rapid increases in the expression of alkane monooxygenases and polyaromatic hydrocarbon ring-hydroxylating-dioxygenases were observed one month after the bioremediation treatment commenced in the Alert soils. In contrast, no clear changes in community structure were observed in Eureka soils, while key gene expression increased after a relatively long lag period (1 year). Such discrepancies are likely caused by differences in bioremediation treatments (i.e. ex situ vs. in situ), weathering of the hydrocarbons, indigenous microbial communities, and environmental factors such as soil humidity and temperature. In addition, this study demonstrates the value of molecular tools for the monitoring of polar bacteria and their associated functions during bioremediation. 38 soil samples from two high arctic locations that were contaminated-treated, contaminated or not contaminated followed for up to 4 years
2010-05-15 | E-GEOD-17517 | biostudies-arrayexpress
Project description:High Arctic soils have low nutrient availability, low moisture content and very low temperatures and, as such, they pose a particular problem in terms of hydrocarbon bioremediation. An in-depth knowledge of the microbiology involved in this process is likely to be crucial to understand and optimize the factors most influencing bioremediation. Here, we compared two distinct large-scale field bioremediation experiments, located at Alert (ex situ approach) and Eureka (in situ approach), in the Canadian high Arctic. Bacterial community structure and function were assessed using microarrays targeting the 16S rRNA genes of bacteria found in cold environments and hydrocarbon degradation genes as well as reverse-transcriptase real-time PCR targeting key functional genes. Results indicated a large difference between sampling sites in terms of both soil microbiology and decontamination rates. A rapid reorganization of the bacterial community structure and functional potential as well as rapid increases in the expression of alkane monooxygenases and polyaromatic hydrocarbon ring-hydroxylating-dioxygenases were observed one month after the bioremediation treatment commenced in the Alert soils. In contrast, no clear changes in community structure were observed in Eureka soils, while key gene expression increased after a relatively long lag period (1 year). Such discrepancies are likely caused by differences in bioremediation treatments (i.e. ex situ vs. in situ), weathering of the hydrocarbons, indigenous microbial communities, and environmental factors such as soil humidity and temperature. In addition, this study demonstrates the value of molecular tools for the monitoring of polar bacteria and their associated functions during bioremediation. 38 soil samples from two high arctic locations that were contaminated-treated, contaminated or not contaminated followed for up to 4 years
2010-06-19 | E-GEOD-17532 | biostudies-arrayexpress
Project description:Microbial Communities Identified at a Hydrocarbon-Contaminated Site
| PRJNA454475 | ENA
Project description:polyaromatic hydrocarbon-degrading enrichment culture Metagenome
| PRJNA691458 | ENA
Project description:A significant part of the heavier petroleum fraction resulting from offshore oil-spills sinks to the deep-sea. Its fate and biodegradation by microbial communities is unclear. In particular, the physiological and metabolic features of hydrostatic pressure (HP) adapted oil-degraders have been neglected. In this study, hydrocarbon-free sediment from 1km below surface water (bsl) was incubated at 0.1, 10 and 20MPa (equivalent to surface waters, 1 and 2km bsl) using triacontane (C30) as sole carbon source for a 3-month enrichment period. HP strongly impacted biodegration, as it selected for microbial communities with small cells, high O2 respiration and nutrients requirements, but low biomass and C30-degradation yields. The alkane-degrading metaproteome linked to β-oxidation was detected but its expression was reduced under HP contrary to several housekeeping genes. This was reflected in the enriched communities, as atmospheric pressure was dominated by hydrocarbonoclastic bacteria while non-specialized or previously unrecognized oil-degrading genera were enriched under HP.
2018-12-19 | PXD004328 | Pride
Project description:A functional microarray targeting 24 genes involved in chlorinated solvent biodegradation pathways has been developed and used to monitor the gene expression in a contaminated site (site B) under ERD (enhanced reductive dechlorination) treatment. The microarray format provided by NimbleGen and used in this study is 12x135K. 4 M-BM-5g of labelled antisense mRNA from 3 groundwater samples were hybridized on the microarray. A 3-chip study was performed, each corresponding to hybridization with 4 M-BM-5g of labelled antisense mRNA retrieved from a monitoring well of a contaminated site (site B). Each probe (760nt) on the microarray was synthesized in eight replicates, and a total of 5,707 random probes was used to determine the background noise. Groundwater samples were collected from a contaminated site (site B) from three monitoring wells (P1, P2 and P3). P1: well located upstream to the contamination source. P2: well in the contamination source. P3 : well located downstream to the contamination source.
2012-04-02 | E-GEOD-28608 | biostudies-arrayexpress
Project description:The application of chemical dispersants during marine oil spills can affect the community composition and activity of native marine microorganisms. Several studies have indicated that certain marine hydrocarbon-degrading bacteria, such as Marinobacter spp., can be inhibited by chemical dispersants, resulting in lower abundances and/or reduced hydrocarbon-biodegradation rates. In this respect, a major knowledge gap exists in understanding the mechanisms underlying these observed physiological effects. Here, we performed comparative proteomics of the Deepwater Horizon isolate Marinobacter sp. TT1 grown under different conditions that varied regarding the supplied carbon sources (pyruvate vs. n-hexadecane) and whether or not dispersant (Corexit EC9500A) was added, or that contained crude oil in the form of a water-accommodated fraction (WAF) or chemically-enhanced WAF (CEWAF). We characterized the proteins associated with alkane metabolism and alginate biosynthesis in strain TT1, report on its potential for aromatic hydrocarbon biodegradation and present a proposed metabolism of Corexit components as carbon substrates for the strain. Our findings implicate Corexit in affecting hydrocarbon metabolism, chemotactic motility, biofilm formation, and inducing solvent tolerance mechanisms like efflux pumps in strain TT1. This study provides novel insights into dispersant impacts on microbial hydrocarbon degraders that should be taken into consideration for future oil spill response actions.
2020-12-22 | PXD021108 | Pride