Diversity of oil contaminated site in Sikkim
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PROVIDER: PRJEB22227 | ENA |
REPOSITORIES: ENA
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Project description:The Galicia seashore, in northwestern Spain, was one of the shorelines affected by the Prestige oil spill in November 2002. The diversity of autochthonous Pseudomonas populations present at two beaches (Carnota municipality) was analyzed using culture-independent and culture-dependent methods. The first analysis involved the screening of an rpoD gene library. The second involved the isolation of 94 Pseudomonas strains that were able to grow on selective media by direct plating or after serial enrichments on several carbon sources: biphenyl, gentisate, hexadecane, methylnaphthalene, naphthalene, phenanthrene, salicylate, xylene, and succinate. Eight denitrifying Pseudomonas strains were also isolated by their ability to grow anaerobically with nitrate. The calculated coverage index for Pseudomonas species was 89% when clones and isolates were considered together, and there were 29 phylospecies detected. The most abundant were members of the species P. stutzeri, P. putida, P. anguilliseptica, and P. oleovorans. Thirty-one isolates could not be identified at the species level and were considered representatives of 16 putative novel Pseudomonas species. One isolate was considered representative of a novel P. stutzeri genomovar. Concordant results were obtained when the diversities of the cloned DNA library and the cultured strains were compared. The clone library obtained by the rpoD PCR method was a useful tool for evaluating Pseudomonas communities and also for microdiversity studies of Pseudomonas populations.
| S-EPMC3028729 | biostudies-literature
Project description:The widespread use and consumption of crude oil draws the public's attention to the fate of petroleum hydrocarbons in the environment, as they can permeate the soil environment in an uncontrollable manner. Contamination of soils with petroleum products, including diesel oil (DO), can cause changes in the microbiological soil properties. The effect of diesel oil on the functional diversity of fungi was tested in a model experiment during 270 days. Fungi were isolated from soil and identified. The functional diversity of fungal communities was also determined. Fungi were identified with the MALDI-TOF method, while the functional diversity was determined using FF-plates made by Biolog®, with 95 carbon sources. Moreover, the diesel oil degradation dynamics was assessed. The research showed that soil contaminated with diesel oil is characterized by a higher activity of oxireductases and a higher number of fungi than soil not exposed to the pressure of this product. The DO pollution has an adverse effect on the diversity of fungal community. This is proved by significantly lower values of the Average Well-Color Development, substrates Richness (R) and Shannon-Weaver (H) indices at day 270 after contamination. The consequences of DO affecting soil not submitted to remediation are persistent. After 270 days, only 64% of four-ringed, 28% of five-ringed, 21% of 2-3-ringed and 16% of six-ringed PAHs underwent degradation. The lasting effect of DO on communities of fungi led to a decrease in their functional diversity. The assessment of the response of fungi to DO pollution made on the basis of the development of colonies on Petri dishes [Colony Development (CD) and Eco-physiological Diversity (EP) indices] is consistent with the analysis based on the FF MicroPlate system by Biolog®. Thus, a combination of the FF MicroPlate system by Biolog® with the simultaneous calculation of CD and EP indices alongside the concurrent determination of the content of PAHs and activity of oxireductases provides an opportunity to achieve relatively complete characterization of the consequences of a long-term impact of diesel oil on soil fungi.
| S-EPMC5623761 | biostudies-literature
Project description:oil-contaminated sediment Transcriptome
| PRJNA587015 | ENA
Project description:Oil contaminated sands Raw sequence reads
| PRJNA690167 | ENA
Project description:Oil-contaminated sediment Raw sequence reads
| PRJNA587011 | ENA
Project description:oil contaminated soil Genome sequencing and assembly
| PRJNA983866 | ENA
Project description:Soils and groundwater contamination modifies the physical-chemical conditions of the environment, altering natural biogeochemical processes of the ground. As a result, several mineral transformations occur, in which iron plays a decisive role. The presence of iron enables the study of magnetic properties, improving the understanding of the geophysical signatures of highly dynamic environments (e.g., biogeochemical hotspots and contamination plumes). In this work, we seek to identify creosote biodegradation related to the precipitation of magnetic minerals on sediments at a contaminated site in São Paulo, Brazil. Several rock magnetism analyses were carried out to provide the magnetic mineralogy of the samples in terms of their composition, size, and abundance. We conducted high-temperature thermomagnetic curves, frequency-dependent magnetic susceptibility, anesthetic remanent magnetization (ARM) and isothermal remanent magnetization (IRM) data, superparamagnetic concentration and dipole moment (SPCDM), and scanning electron microscopy (SEM) analyses. The magnetic signatures of the contaminated samples suggest an increase of superparamagnetic grains in the water table fluctuation zone if compared to the magnetic signatures of the uncontaminated samples. Thermomagnetic curves of contaminated samples showed a lower heterogeneity of the magnetic mineral phases than the uncontaminated ones. This work contributes to the advancement of the understanding of how natural biogeochemical processes are impacted by human actions, such as soil contamination, and even by climate change, which should affect soil redox conditions in periods of drought and flooding.
| S-EPMC9759522 | biostudies-literature