Soil metagenome
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REPOSITORIES: ENA
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Project description:The purpose of this study is to analyze maize shoots growth under negative pressure to stabilize soil water content，Maize plants were subjected to two irrigation treatments. The first treatment was soil moisture dry-wet cycles, which was obtained using drip irrigation (control, DW). The second treatment was negative pressure to stabilize soil water content treatment (SW), which was obtained using the negative pressure irrigation (NPI) system.
2021-10-03 | ST001955 | MetabolomicsWorkbench
Project description:GCMS datasets for the soil depth manuscript
Abstract
Two factors that are well-known to influence soil microbiomes include the depth of the soil as well as the level of moisture. Previous works have demonstrated that climate change will increase the incidence of drought in soils, but it is unknown how fluctuations in moisture availability affect soil microbiome composition and functioning down the depth profile. Here, we investigated soil and wheatgrass rhizosphere microbiomes in a common field setting under four different irrigation regimes and three depths. We demonstrated that there is a significant interactive effect, where fluctuations in soil moisture more strongly influence soil microbiomes at the surface layer than in deeper layers, including for soil community composition, diversity, and for functional profiles. Meanwhile, in rhizosphere communities the influence of irrigation was similar across the different depths, although there were slight discrepancies between the two cultivars of wheatgrass used. The lessened response of deeper soil microbiomes to changes in irrigation may be due to higher incidence of slow-growing, stress-resistant microbes.
2022-11-07 | MSV000090655 | MassIVE
Project description:Increasing concern about pollution of our environment calls for advanced and rapid methods to estimate ecological toxicity. The use of gene expression microarrays in environmental studies can potentially meet this challenge. We present a novel method to examine soil toxicity. We exposed the collembolan Folsomia candida to soil containing an ecologically relevant cadmium concentration, and found a cumulative total of 1586 differentially expressed transcripts across three exposure durations, including transcripts involved in stress response, detoxification, and hypoxia. Additional enrichment analysis of gene ontology (GO) terms revealed that antibiotic biosynthesis is important at all time points examined. Interestingly, genes involved in the "penicillin and cephalosporin biosynthesis pathway" have never been identified in animals before, but are expressed in F. candida’s tissue. The synthesis of antibiotics can possibly be a response to increased cadmium-induced susceptibility to invading pathogens, which might be caused by repression of genes involved in the immune-system (C-type lectins and Toll receptor). This study presents a first global view on the environmental stress response of an arthropod species exposed to contaminated soil,and provides a mechanistic basis for the development of a gene expression soil quality test. Keywords: cadmium, soil, Collembola, environmental genomics
2008-08-08 | GSE11122 | GEO
Project description:Soil fungal diversity under nitrogen and irrigation
| PRJNA328182 | ENA
Project description:Soil microbiome of tomato fields under irrigation
| PRJNA578949 | ENA
Project description:Genome-wide microarray analysis was performed using RNA extracted from soil cultures of Streptomyces coelicolor A3(2) in the presence or absence of chitin. The vast majority of genes in chitin and amino sugar metabolism, as well as many other genes for carbon and energy, nitrogen and sulfur metabolism, were differentially expressed in response to addition of chitin. Moreover, the gene expressions of eight gene clusters for secondary metabolites were also significantly up-regulated in the chitin amended soil. To reveal the role of a pleiotropic transcriptional regulator, DasR, which has been reported to be involved in regulation of chitin metabolism, antibiotic production and morphological differentiation, the gene expression patterns of wild type and dasR mutant in soil amended with chitin were compared by microarray analysis. The dasR mutation resulted in up-regulation of four antibiotic gene clusters and down-regulation of chitin metabolism.
2012-11-07 | GSE39164 | GEO
Project description:A cultivation facility that can assist users in controlling the soil water condition is needed for accurately phenotyping plants under drought stress in an artificial environment. Here we report the Internet of Things (IoT)-based pot system controlling optional treatment of soil water condition (iPOTs), an automatic irrigation system that mimics the drought condition in a growth chamber. The Wi-Fi-enabled iPOTs system allows water supply from the bottom of the pot, based on the soil water level set by the user, and automatically controls the soil water level at a desired depth. The iPOTs also allows users to monitor environmental parameters, such as soil temperature, air temperature, humidity, and light intensity, in each pot. To verify whether the iPOTs mimics the drought condition, we conducted a drought stress test on rice varieties and near-isogenic lines, with diverse root system architecture, using the iPOTs system installed in a growth chamber. Similar to the results of a previous drought stress field trial, the growth of shallow-rooted rice accessions was severely affected by drought stress compared with that of deep-rooted accessions. The microclimate data obtained using the iPOTs system increased the accuracy of plant growth evaluation. Transcriptome analysis revealed that pot positions in the growth chamber had little impact on plant growth. Together, these results suggest that the iPOTs system represents a reliable platform for phenotyping plants under drought stress.
2021-08-24 | GSE171578 | GEO
Project description:The experiment at three long-term agricultural experimental stations (namely the N, M and S sites) across northeast to southeast China was setup and operated by the Institute of Soil Science, Chinese Academy of Sciences. This experiment belongs to an integrated project (The Soil Reciprocal Transplant Experiment, SRTE) which serves as a platform for a number of studies evaluating climate and cropping effects on soil microbial diversity and its agro-ecosystem functioning. Soil transplant serves as a proxy to simulate climate change in realistic climate regimes. Here, we assessed the effects of soil type, soil transplant and landuse changes on soil microbial communities, which are key drivers in Earth’s biogeochemical cycles.
2016-02-04 | GSE77546 | GEO
Project description:Genome-wide microarray analysis was performed using RNA extracted from soil cultures of Streptomyces coelicolor A3(2) in the presence or absence of chitin. The vast majority of genes in chitin and amino sugar metabolism, as well as many other genes for carbon and energy, nitrogen and sulfur metabolism, were differentially expressed in response to addition of chitin. Moreover, the gene expressions of eight gene clusters for secondary metabolites were also significantly up-regulated in the chitin amended soil. To reveal the role of a pleiotropic transcriptional regulator, DasR, which has been reported to be involved in regulation of chitin metabolism, antibiotic production and morphological differentiation, the gene expression patterns of wild type and dasR mutant in soil amended with chitin were compared by microarray analysis. The dasR mutation resulted in up-regulation of four antibiotic gene clusters and down-regulation of chitin metabolism. A study using total RNA extracted from soil cultures of Streptomyces ceolicolor A3(2). A whole genome microarray of S. coelicolor (NimbleGen Custom Prokaryotic Gene Expression 72K 4-plex Arrays) was designed and manufactured by Roche (Roche NimbleGen, Madison, WI). Each array contained four sets of 8 sequence-specific 60-mer probes per gene corresponding to 7825 genes from the S. coelicolor A3(2) genome.
2012-11-07 | E-GEOD-39164 | biostudies-arrayexpress