Petroleum hydrocarbon-contaminated soil
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PROVIDER: PRJNA1064703 | ENA |
REPOSITORIES: ENA
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Project description:Petroleum hydrocarbon-contaminated ecopiles Raw sequence reads
| PRJNA925022 | ENA
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:The experiment was designed to test the interactions of Spartina alterniflora, its microbiome, and the interaction of the plant-microbe relationship with oil from the Deepwater Horizon oil spill (DWH). Total RNA was extracted from leaf and root microbiome of S. alterniflora in soils that were oiled in DWH oil spill with or without added oil, as well as those grown in unoiled soil with or without added oil. The work in its entirety characterizes the transport, fate and catabolic activities of bacterial communities in petroleum-polluted soils and within plant tissues.
2020-04-10 | GSE148431 | GEO
Project description:Microbial consortium assembly and functional analysis
| PRJNA1091787 | ENA
Project description:Petroleum contaminated soils Metagenomic assembly
| PRJNA721029 | ENA
Project description:Metabolic Characterization and Geochemical Drivers of Active Hydrocarbon-Degrading Microorganisms
| PRJNA1098919 | ENA
Project description:Soil health deteriorates through the contamination and remediation processes, resulting in the limitation of the reuse and recycling of the remediated soils. Therefore, soil health should be recovered for the intended purposes of reuse and recycling. This study aimed to evaluate the applicability and effectiveness of several amendments to revitalize total petroleum hydrocarbon contaminated soils remediated by the landfarming process. Ten inorganic, organic, and biological amendments were investigated for their dosage and duration, and nine physicochemical, four fertility, and seven microbial (soil enzyme activity) factors were compared before and after the treatment of amendments. Finally, the extent of recovery was quantitatively estimated, and the significance of results was confirmed with statistical methods, such as simple regression and correlation analyses assisted by principal component analysis. The landfarming process is considered a somewhat environmentally friendly remediation technology to minimize the adverse effect on soil quality, but four soil properties-such as water holding capacity (WHC), exchangeable potassium (Ex. K), nitrate-nitrogen (NO3-N), available phosphorus (Av. P), and urease-were confirmed to deteriorate through the landfarming process. The WHC was better improved by organic agents, such as peat moss, biochar, and compost. Zeolite was evaluated as the most effective material for improving Ex. K content. The vermicompost showed the highest efficacy in recovering the NO3-N content of the remediated soil. Chlorella, vermicompost, and compost were investigated for their ability to enhance urease activity effectively. Although each additive showed different effectiveness according to different soil properties, their effect on overall soil properties should be considered for cost-effectiveness and practical implementation. Their overall effect was evaluated using statistical methods, and the results showed that compost, chlorella, and vermicompost were the most relevant amendments for rehabilitating the overall health of the remediated soil for the reuse and/or recycling of agricultural purposes. This study highlighted how to practically improve the health of remediated soils for the reuse and recycling of agricultural purposes.
| S-EPMC8951262 | biostudies-literature
Project description:Methanogenic activity was investigated in a petroleum hydrocarbon-contaminated aquifer by using a series of four push-pull tests with acetate, formate, H(2) plus CO(2), or methanol to target different groups of methanogenic Archaea. Furthermore, the community composition of methanogens in water and aquifer material was explored by molecular analyses, i.e., fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes amplified with the Archaea-specific primer set ARCH915 and UNI-b-rev, and sequencing of DNA from dominant DGGE bands. Molecular analyses were subsequently compared with push-pull test data. Methane was produced in all tests except for a separate test where 2-bromoethanesulfonate, a specific inhibitor of methanogens, was added. Substrate consumption rates were 0.11 mM day(-1) for methanol, 0.38 mM day(-1) for acetate, 0.90 mM day(-1) for H(2), and 1.85 mM day(-1) for formate. Substrate consumption and CH(4) production during all tests suggested that at least three different physiologic types of methanogens were present: H(2) plus CO(2) or formate, acetate, and methanol utilizers. The presence of 15 to 20 bands in DGGE profiles indicated a diverse archaeal population. High H(2) and formate consumption rates agreed with a high diversity of methanogenic Archaea consuming these substrates (16S rRNA gene sequences related to several members of the Methanomicrobiaceae) and the detection of Methanomicrobiaceae by using FISH (1.4% of total DAPI [4',6-diamidino-2-phenylindole]-stained microorganisms in one water sample; probe MG1200). Considerable acetate consumption agreed with the presence of sequences related to the obligate acetate degrader Methanosaeata concilii and the detection of this species by FISH (5 to 22% of total microorganisms; probe Rotcl1). The results suggest that both aceticlastic and CO(2)-type substrate-consuming methanogens are likely involved in the terminal step of hydrocarbon degradation, while methanogenesis from methanol plays a minor role. DGGE profiles further indicate similar archaeal community compositions in water and aquifer material. The combination of hydrogeological and molecular methods employed in this study provide improved information on the community and the potential activity of methanogens in a petroleum hydrocarbon-contaminated aquifer.
| S-EPMC544196 | biostudies-literature
Project description:Prokaryotic community in hydrocarbon polluted seawater
| PRJNA893820 | ENA
Project description:Bacterial endophytes (BEs) are non-pathogenic residents of healthy plant tissues that can confer benefits to plants. Many Bacterial endophytes have been shown to contribute to plant growth and health, alleviation of plant stress and to in-planta contaminant-degradation. This study examined the endophytic bacterial communities of plants growing abundantly in a heavily hydrocarbon contaminated site, and compared them to those found in the same species at a non-contaminated. We used culture- dependent and independent methods to characterize the community structure, hydrocarbon degrading capabilities, and plant growth promoting traits of cultivable endophytes isolated from Achillea millefolium, Solidago Canadensis, and Daucus carota plants from these two sites. Culture- dependent and independent analyses revealed class Gammaproteobacteria predominated in all the plants regardless of the presence of petroleum hydrocarbon, with Pantoea spp. as largely dominant. It was interesting to note a >50% taxonomic overlap (genus level) of 16s rRNA high throughput amplicon sequences with cultivable endophytes. PERMANOVA analysis of TRFLP fragments revealed significant structural differences between endophytic bacterial communities from hydrocarbon-contaminated and non-contaminated soils-however, there was no marked difference in their functional capabilities. Pantoea spp. demonstrated plant beneficial characteristics, such as P solubilization, indole-3-acetic acid production and presence of 1-aminocyclopropane-1-carboxylate deaminase. Our findings reveal that functional capabilities of bacterial isolates being examined were not influenced by the presence of contamination; and that the stem endosphere supports ubiquitous BEs that were consistent throughout plant hosts and sites.
| S-EPMC6115521 | biostudies-literature