Groundwater metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA649362 | ENA |
REPOSITORIES: ENA
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Project description:HiSpOD is a new efficient functional microarrays probe design algorithm especially dedicated for the microbial ecology and environmental studies. It was used to design 3392 probes targeting 21 genes involved in chlorinated solvent biodegradation pathways and synthesized on a nimblegen microarray. In order to test the probe specificity, the microarray was firstly hybridized to 6 M-BM-5g of labelled aRNA from sheep rumen content (background aRNA). Secondly, hybridization of 1011 copies of labelled aRNA derived from in vitro transcription of three synthetic genes (mmoC, vcrA and tceA) and mixed with 6 M-BM-5g of the same complex background material were performed to test their sensibility. Finally, the expression analysis of a contaminated groundwater sample was performed. A 3 chip study was realized. The first one is a negative control performed with a complex background material (labelled antisense mRNA from sheep rumen content). The second one is a positive control realized with labelled antisense RNA derived from in vitro transcription of three synthetic genes mixed the same complex background material. The third consists in the hybridization of antisense mRNA retrieved from a contaminated groundwater. Each probe (3392) was synthetized in triplicate, and a total of 8,863 random probes was used to determine the background noise.
2011-04-13 | E-GEOD-21492 | biostudies-arrayexpress
Project description:HiSpOD is a new efficient functional microarrays probe design algorithm especially dedicated for the microbial ecology and environmental studies. It was used to design 3392 probes targeting 21 genes involved in chlorinated solvent biodegradation pathways and synthesized on a nimblegen microarray. In order to test the probe specificity, the microarray was firstly hybridized to 6 µg of labelled aRNA from sheep rumen content (background aRNA). Secondly, hybridization of 1011 copies of labelled aRNA derived from in vitro transcription of three synthetic genes (mmoC, vcrA and tceA) and mixed with 6 µg of the same complex background material were performed to test their sensibility. Finally, the expression analysis of a contaminated groundwater sample was performed.
2011-04-13 | GSE21492 | GEO
Project description:Pristine groundwater is a highly stable environment with microbes adapted to dark, oligotrophic conditions. Input events like heavy rainfalls can introduce excess particulate organic matter including surface-derived microbes into the groundwater, hereby creating a disturbance to the groundwater microbiome. Some of the translocated bacteria are not able to thrive in groundwater and will form necromass. Here, we investigated the effects of necromass addition to the microbial community in fractured bedrock groundwater, using groundwater mesocosms as model systems. We followed the uptake of 13C-labeled necromass by the bacterial and eukaryotic groundwater community quantitatively and over time by employing a combined protein and DNA stable isotope probing approach. Necromass was rapidly depleted in the mesocosms within four days, accompanied by a strong decrease of Shannon diversity and an increase of bacterial 16S rRNA gene copy numbers by one order of magnitude. Species of Flavobacterium, Massilia, Rheinheimera, Rhodoferax and Undibacterium dominated the microbial community within two days and were identified as key players in necromass degradation, based on a 13C incorporation of > 90% in their peptides. Their proteomes showed various uptake and transport related proteins, and many proteins involved in metabolizing amino acids. After four and eight days of incubation, autotrophic and mixotrophic groundwater species of Nitrosomonas, Limnohabitans, Paucibacter and Acidovorax increased in abundance, with a 13C incorporation between 0.5 and 23%. Our data point towards a very fast and exclusive uptake of labeled necromass by a few specialists followed by a concerted action of groundwater microorganisms, including autotrophs presumably fueled by released, reduced nitrogen and sulfur compounds generated during necromass degradation.
2022-05-31 | PXD031173 | Pride
Project description:A functional microarray targeting 24 genes involved in chlorinated solvent biodegradation pathways has been developed and used to monitor the gene diversity present in four trichloroethylene (TCE) contaminated sites under ERD (enhanced reductive dechlorination) treatment. The microarray format provided by NimbleGen and used in this study is 12x135K. 2 µg of labelled gDNA from 30 groundwater samples were hybridized on the microarrays.
2012-04-03 | GSE28606 | GEO
Project description:Uranium-contaminated groundwater metagenome
| PRJNA39533 | ENA
Project description:Metagenomes from contaminated groundwater
| PRJNA329043 | ENA
Project description:Arsenic contaminated groundwater Raw sequence reads
| PRJNA291121 | ENA
Project description:Groundwater-derived microorganisms are known to play an important role in biogeochemical C, S and N cycling. Thereby, the presence and majorly the activity of microorganisms in aquifers affect enormously the nutrient cycling. However, the diversity and their functional capability in natural aquifers are still rare and therefore a better knowledge of the core microbial communities is urgently needed. Metaproteome analysis was applied to characterize the repertoire of microbes in the depth and to identify the key drivers of major biogeochemical processes. Therefore, 1000 L water from the aquifer was sampled by filtration on 0.3 µm glass filters. After protein extraction, proteolytic cleavage and mass spectrometric analysis (Ultimate 3000 nanoRSLC coupled to Q Exactive HF instrument), 3808 protein groups (2371 proteins with ≥2 peptides) were identified from 13,204 peptides. The findings of our study have broad implications for the understanding of aquifer cycling’s which finally leads to a greatly improved understanding of the ecosystem services provided by the microbial communities present in aquifers. In the future, functional results would allow to monitor and to assess pollution effects which would beneficially assist groundwater resource management.
2016-12-23 | PXD004351 | Pride
Project description:Metagenome analysis of BTEX contaminated hypoxic groundwater
| PRJNA251795 | ENA