Soil metagenome
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ABSTRACT:
PROVIDER: PRJNA382207 | ENA |
REPOSITORIES: ENA
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Project description:aerobic and anaerobic condition soil metagenome in Baihua Park Metagenome
| PRJNA382209 | ENA
Project description:In this study, the recombinant Trichoderma reesei strain HJ48 was employed to investigate the differences between anaerobic and aerobic fermentation of glucose, through genome-wide transcription analysis.Analysis of the genes induced under fermentation condition has revealed novel features in T. reesei. Our results how that many genes related to ribosome were expressed more highly under aerobic condition in HJ48.
2019-07-20 | GSE84613 | GEO
Project description:This research focuses on changes in the microbial communities of tropical soils during aerobic to anaerobic transitions following wetting. Of particular interest is the natural cycling of the soil microbiome through aerobic and anaerobic metabolism over relative short time periods.
The work (proposal:https://doi.org/10.46936/10.25585/60000880) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.
2023-11-02 | MSV000093271 | MassIVE
Project description:rs11-07_opine2 - septante soil - Transcriptomic changes induced by opine production in Arabidopsis thaliana grown in natural soil - Arabidopsis thalian Col- line was transformed in order to obtain transgenic lines that produce opine compound (octopine and mannopine). Transgenic lines producing respectively octopine and mannopine and the WT line were grown in greenhouse under long-day condition in pots containing half commercial compost and half soil of la Mérantaise and watered with water. Whole plant aged of one month were harvested and frozen in liquid nitrogen. The plants were ground with a mortar an pestls and RNA extraction was performed with the RNeasy extraction kit (QIAGEN) with cristal of PVP. The RNA concentration was measured on a NANODrop spectrophotometer.
2017-01-05 | GSE93121 | GEO
Project description:Background: The soil environment is responsible for sustaining most terrestrial plant life on earth, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere and how it responds to agricultural management such as crop rotations and soil tillage will be vital for improving global food production. Methods: The rhizosphere soils of wheat and chickpea growing under + and - decaying root were collected for metagenomics sequencing. A gene catalogue was established by de novo assembling metagenomic sequencing. Genes abundance was compared between bulk soil and rhizosphere soils under different treatments. Conclusions: The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the microbiome from decaying root in determining the metagenome of developing root systems, which is fundamental to plant growth, since roots preferentially inhabit previous root channels. Modifications in root microbial function through soil management, can ultimately govern plant health, productivity and food security.
2020-03-06 | GSE146427 | GEO
Project description:Purpose: Deconstructing the soil microbiome into reduced-complexity functional modules represents a novel method of microbiome analysis. The goals of this study are to confirm differences in transcriptomic patterns among five functional module consortia. Methods: mRNA profiles of 3 replicates each of functional module enrichments of soil inoculum in M9 media with either 1) xylose, 2) n-acetylglucosamine, 3) glucose and gentamycin, 4) xylan, or 5) pectin were generated by sequencing using an Illumina platform (GENEWIZ performed sequencing). Sequence reads that passed quality filters were aligned to a soil metagenome using Burrows Wheeler Aligner. Resulting SAM files were converted to raw reads using HTSeq, and annotated using Uniref90 or EGGNOG databases. Results: To reduce the size of the RNA-Seq counts table and increase its computational tractability, transcripts containing a minimum of 75 total counts, but no more than 3 zero counts, across the 15 samples were removed. The subsequent dataset was normalized using DESeq2, resulting in a dataset consisting of 6947 unique transcripts across the 15 samples, and 185,920,068 reads. We identified gene categories that were enriched in a sample type relative to the overall dataset using Fisher’s exact test. Conclusions: our dataset confirms that the functional module consortia generated from targeted enrichments of a starting soil inoculum had distinct functional trends by enrichment type.
2020-01-14 | GSE143587 | GEO
Project description:Actinobacillus pleuropneumoniae is an important porcine respiratory pathogen causing great economic losses in the pig industry worldwide. Oxygen deprivation is a stress that A. pleuropneumoniae will encounter during both early infection and the later, persistent stage. To understand modulation of A. pleuropneumoniae gene expression in response to the stress caused by anaerobic conditions, gene expression profiles under anaerobic and aerobic conditions were compared in this study. The microarray results showed that 631 genes (27.7% of the total ORFs) were differentially expressed in anaerobic conditions. Many genes encoding proteins involved in glycolysis, carbon source uptake systems, pyruvate metabolism, fermentation and the electron respiration transport chain were up-regulated. These changes led to an increased amount of pyruvate, lactate, ethanol and acetate in the bacterial cells as confirmed by metabolite detection. Genes encoding proteins involved in cell surface structures, especially biofilm formation, peptidoglycan biosynthesis and lipopolysaccharide biosynthesis were up-regulated as well. Biofilm formation was significantly enhanced under anaerobic conditions. These results indicate that induction of central metabolism is important for basic survival of A. pleuropneumoniae after a shift to an anaerobic environment. Enhanced biofilm formation may contribute to the persistence of this pathogen in the damaged anaerobic host tissue and also in the early colonization stage. These discoveries give new insights into adaptation mechanisms of A. pleuropneumoniae in response to environmental stress. Transcriptional profiles were analyzed using microarray to compare the gene expressions of A. pleuropneumoniae cultured under aerobic and anaerobic condition. The bacteria was cultured under aerobic condition to mid-log phase (3 hours) and then divided into two separate groups, one group was continually cultured under aerobic condition for 1 hour (OD600nm = 0.417 M-BM-1 0.008) and the other group was cultured under anaerobic condition for 1 hour (OD600nm = 0.333 M-BM-1 0.015). Three independent biological replicates were performed. The total RNA were extracted and hybridized with the whole genome microarray of A. pleuropneumoniae. The signal intensities were normalized and transformed into log2 values. The genes with P-value < 0.05 were selected as differentially expressed genes.
2014-06-30 | E-GEOD-39801 | biostudies-arrayexpress
Project description:Transcriptional expression of MG1655 and UTI89 harvested from various time points during aerobic or anaerobic growth in Luria-Bertani medium Keywords: time course analyses (aerobic and anaerobic)
2007-02-02 | GSE6425 | GEO
Project description:We found many binding sites for FNR under glucose fermentative anaerobic growth conditions. Also, many binding sites were identified for M-OM-^C70 under both aerobic and anaerobic growthin conditions. Descirbed in the manuscript "Genome-scale Analysis of E. coli FNR Reveals the Complexity of Bacterial Regulon Structure" Examination of occupancy of FNR adn M-OM-^C70 under aerobic and anaerobic growth in conditions.
2013-06-20 | E-GEOD-41187 | biostudies-arrayexpress