Bioaugmentation on arrazine-contaminated soil
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB40333 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4586410_1.fastq.gz | Fastqsanger.gz | |||
| ERR4586410_2.fastq.gz | Fastqsanger.gz | |||
| ERR4586420_1.fastq.gz | Fastqsanger.gz | |||
| ERR4586420_2.fastq.gz | Fastqsanger.gz | |||
| ERR4586411_1.fastq.gz | Fastqsanger.gz |
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Project description:Soil samples were collected from Kuwait, Lebanon, Egypt, and Germany, and artificially polluted with 3% (w/w) crude oil. Cross-bioaugmentation was done among them, and the oil-consumption and the constituent communities of hydrocarbonoclastic bacteria were monitored periodically through 6 months. The results showed that cross-bioaugmentation did not bring about reproducible effects on oil-removal in the four soils. After 6 months, oil-removal values reached between 82 and 95% in most of the samples including the unbioaugmented controls. The numbers of hydrocarbonoclastic bacteria showed significant increases followed by significant decreases during the course of bioremediation also in the unbioaugmented controls. In most cases, the inoculated bacterial taxa failed to colonize the soils, and oil-removal was achieved mainly by the native (autochthonous) soil bacterial communities. those belonged to the genera Mycolicibacterium, Mycobacterium, Xanthobacter, Pseudoxanthomonas, Pseudomonas, Zavarzinia, and others. The microbial communities in the four soils also comprised nitrogen fixing bacteria belonging to the genera Gordonia, Rhizobium, Kocuria, and Azospirillum. Such diazotrophs are known to enrich the soils with fixed nitrogen and thus, contribute to enhancing the microbiological hydrocarbon-consumption. It was concluded that cross-bioaugmentation leads to unpredictable and inconsistent effects on oil removal. Therefore, it could not beregarded as the technology of choice for oil-bioremediation.
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Project description:Our objective was to study the bacterial community changes that determine enhanced removal of petroleum hydrocarbons from soils subjected to bioaugmentation with the hydrocarbon-degrading strains Rhodococcus erythropolis CD 130, CD 167, and their combination. To achieve this, a high-throughput sequencing of the 16S rRNA gene was performed. The changes in the bacterial community composition were most apparent the day after bacterial inoculation. These changes represented an increase in the percentage abundance of Rhodococcus and Pseudomonas genera. Surprisingly, members of the Rhodococcus genus were not present after day 91. At the end of the experiment, the bacterial communities from the CD 130, CD 167, and control soils had a similar structure. Nevertheless, the composition of the bacteria in the CD 130 + CD 167 soil was still distinct from the control. Metagenomic predictions from the 16S rRNA gene sequences showed that the introduction of bacteria had a significant influence on the predicted pathways (metabolism of xenobiotics, lipids, terpenoids, polyketides, and amino acids) on day one. On day 182, differences in the abundance of functional pathways were also detected in the CD 130 and CD 130 + CD 167 soils. Additionally, we observed that on day one, in all bioaugmented soils, the alkH gene was mainly contributed by the Rhodococcus and Mycobacterium genera, whereas in non-treated soil, this gene was contributed only by the Mycobacterium genus. Interestingly, from day 91, the Mycobacterium genus was the main contributor for the tested genes in all studied soils. Our results showed that hydrocarbon depletion from the analyzed soils resulted from the activity of the autochthonous bacteria. However, these changes in the composition and function of the indigenous bacterial community occurred under the influence of the introduced bacteria.
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Project description:Enhanced plasmid mediated bioaugmentation of RDX contaminated matrices in column studies using donor strain Gordonia sp. KTR9
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Project description:Rhizoremediation is a complex type of green clean-up technology that involves both plants and the rhizosphere-associated microorganisms to decompose hazardous compounds. The success of the strategy strongly depends on plant tolerance towards the pollutant, as well as plant's interactions with the rhizospheric microbes. The microorganisms may be stimulated by the secreted root exudates, which results in an increased breakdown of contaminants in the rhizosphere. The main goal of this study was to establish a potential rhizoremediation combination for a diesel-polluted site. Inoculation of plant roots or seeds with indigenous rhizospheric populations is a common approach in the rhizoremediation. However, we introduced hydrocarbon-degrading consortia (M10, R3, and K52) that were previously isolated from crude oil-contaminated soil instead of indigenous microbes. Bioaugmentation with these petroleum degraders was applied to screen four high biomass crop species (Indian mustard, alfalfa, high erucic acid rapeseed, HEAR, and low erucic acid rapeseed, LEAR) for their tolerance towards diesel oil. At no pollution, a promoting effect of M10 bacteria could be observed on germination and root elongation of all plant species. Moreover, M10 consortiums increased the germination index at 6,000 mg diesel oil per kilogram dry soil in the case of Indian mustard, alfalfa, and HEAR. The latter species was found to increment its dry weight upon bioaugmentation with M10 bacteria and all diesel oil treatments (6,000 and 24,000 mg diesel oil per kilogram dry soil). The initial results indicate HEAR and the M10 bacterial consortium as a promising plant-microbe tandem for a long-term rhizoremediation process.
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Project description:The survival, pollutant degradation activity and transcriptome response was monitored in Sphingomonas sp. LH128 inoculated into soil. Cultivable cell numbers were determined by plating, while phenanthrene degradation was monitored by HPLC. The genetic base for the adaptive strategy of LH128 in soil was investigated by using microarray consisting 7,200 gene-coding ORFs. During 4 hours of incubation, 510 genes were differentially expressed (317 increased and 193 reduced expression) while 610 genes were differentially expressed (318 increased and 292 reduced) after 10 days of incubation. Genes with increased expression comprised of gene encoding PAH catabolic enzymes, stress resistance, oxidative stress tolerance, outer membrane proteins/porins and efflux pump proteins while the downregulated genes comprised of genes encoding flagellar biosynthesis, ribosomal proteins and ATPase.
2012-10-20 | GSE41705 | GEO
Project description:Enhanced plasmid mediated bioaugmentation of RDX contaminated matrices in column studies using donor strain Gordonia sp. KTR9 [exp1]
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Project description:The survival, pollutant degradation activity and transcriptome response was monitored in Sphingomonas sp. LH128 inoculated into soil. Cultivable cell numbers were determined by plating, while phenanthrene degradation was monitored by HPLC. The genetic base for the adaptive strategy of LH128 in soil was investigated by using microarray consisting 7,200 gene-coding ORFs. During 4 hours of incubation, 510 genes were differentially expressed (317 increased and 193 reduced expression) while 610 genes were differentially expressed (318 increased and 292 reduced) after 10 days of incubation. Genes with increased expression comprised of gene encoding PAH catabolic enzymes, stress resistance, oxidative stress tolerance, outer membrane proteins/porins and efflux pump proteins while the downregulated genes comprised of genes encoding flagellar biosynthesis, ribosomal proteins and ATPase. Transcriptomic response of phenanthrene degrading Sphingomonas sp. LH128 inoculated into phenanthrene contaminated soil after 4h and after 10 days of incubation was studied using genome-wide gene expression analysis. For this purpose, the strain was pregrown in minimal medium and inoculated at appropriated celld densitites. RNA was extracted both from soil and and from initial inoculum and cDNA was synthesized and labeled with Cy3. Transcriptomic response in soil of three replicates per conditions after both incubation duration were analyzed and compared with the initial inoculum
2012-10-20 | E-GEOD-41705 | biostudies-arrayexpress