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ABSTRACT:
PROVIDER: PRJNA1139963 | ENA |
REPOSITORIES: ENA
Similar Datasets
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: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.
2009-08-07 | GSE17532 | GEO
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.
2009-08-07 | GSE17517 | GEO
Project description:Iron-rich pelagic aggregates (iron snow) were collected directly onto silicate glass filters using an electronic water pump installed below the redoxcline. RNA was extracted and library preparation was done using the NEBNext Ultra II directional RNA library prep kit for Illumina. Data was demultiplied by GATC sequencing company and adaptor was trimmed by Trimgalore. After trimming, data was processed quality control by sickle and mRNA/rRNA sequences were sorted by SortmeRNA. mRNA sequences were blast against NCBI-non redundant protein database and the outputs were meganized in MEGAN to do functional analysis. rRNA sequences were further sorted against bacterial/archeal 16S rRNA, eukaryotic 18S rRNA and 10,000 rRNA sequences of bacterial 16S rRNA, eukaryotic 18S rRNA were subset to do taxonomy analysis.
2021-10-15 | E-MTAB-9686 | biostudies-arrayexpress
Project description:Comparison of probe-target dissociations of probe Eub338 and Gam42a with native RNA of P. putida, in vitro transcribed 16s rRNA of P. putida, in vitro transcribed 16S rRNA of a 2,4,6-trinitrotoluene contaminated soil and an uncontaminated soil sample. Functional ANOVA revealed no significant differences in the dissociation curves of probe Eub338 when hybridised to the different samples. On the opposite, the dissociation curve of probe Gam42a with native RNA of P. putida was significantly different than the dissociation curves obtained with in vitro transcribed 16S rRNA samples. Keywords: Microbial diversity, thermal dissociation analysis, CodeLink microarray
2005-11-05 | GSE3525 | GEO
Project description:Soils collected from a petroleum hydrocarbon contaminated site in Greenland.
| PRJEB18076 | ENA
Project description:The goal of this growth chamber experiment was to investigate the effects of diverse soil microbial communities on the transcriptional responses of plants to drought. Specifically, we sought to understand how soil microbiomes' past exposure to water-limited conditions (either long-term exposure to dry conditions in low-precipitation sites, or recent acute drought) impacted their interactions with plants. Six soils collected from remnant prairies crossing a steep precipitation gradient in Kansas, USA were used as the starting microbial communities. Thirty-two pots (or mesocosms) of each soil were divided among four treatments: droughted or well-watered, and with or without a host plant (Tripsacum dactyloides) in a factorial design. The soil mesocosms were "conditioned" in these treatments for five months. (Metagenome and metatranscriptome data from the baseline soils and the post-conditioning soils are available in a separate BioProject on NCBI SRA and GEO). Then, a microbial slurry extracted from each of the 192 conditioned soils was used to inoculate 4 plants in a subsequent experiment (the “Test Phase”): one pot per combination of watering treatment (droughted or control) and host species (Zea mays or Tripsacum dactyloides). After 4 weeks (for maize) or 5 weeks (for eastern gamagrass) we harvested one crown root per plant for 16S rRNA sequencing and another crown root for RNA-seq. The 16S and RNA-seq data for these plants (both species) are contained in this BioProject. Note that 16S rRNA sequencing data are available for all plants in this experiment, but we conducted RNA-seq only for a subset (all plants grown in microbiomes originating from the 2 driest and 2 wettest collection sites).
2025-05-28 | GSE282586 | GEO
Project description:The goal of this growth chamber experiment was to investigate the effects of diverse soil microbial communities on the transcriptional responses of plants to drought. Specifically, we sought to understand how soil microbiomes' past exposure to water-limited conditions (either long-term exposure to dry conditions in low-precipitation sites, or recent acute drought) impacted their interactions with plants. Six soils collected from remnant prairies crossing a steep precipitation gradient in Kansas, USA were used as the starting microbial communities. Thirty-two pots (or mesocosms) of each soil were divided among four treatments: droughted or well-watered, and with or without a host plant (Tripsacum dactyloides) in a factorial design. The soil mesocosms were "conditioned" in these treatments for five months. (Metagenome and metatranscriptome data from the baseline soils and the post-conditioning soils are available in a separate BioProject on NCBI SRA and GEO). Then, a microbial slurry extracted from each of the 192 conditioned soils was used to inoculate 4 plants in a subsequent experiment (the “Test Phase”): one pot per combination of watering treatment (droughted or control) and host species (Zea mays or Tripsacum dactyloides). After 4 weeks (for maize) or 5 weeks (for eastern gamagrass) we harvested one crown root per plant for 16S rRNA sequencing and another crown root for RNA-seq. The 16S and RNA-seq data for these plants (both species) are contained in this BioProject. Note that 16S rRNA sequencing data are available for all plants in this experiment, but we conducted RNA-seq only for a subset (all plants grown in microbiomes originating from the 2 driest and 2 wettest collection sites).
2025-05-28 | GSE282587 | GEO
Project description:Total bacterial DNA was isolated from water and sediment samples from a local watershed and 16S rRNA sequences were analyzed using the Illumina MiSeq v3 platform in order to generate snapshots of bacterial community profiles. A total of 56 samples were collected that represent water and sediment samples from 14 sample sites over two different time points (November 18 and 25, 2011).
2016-07-03 | E-GEOD-73842 | biostudies-arrayexpress