Ontology highlight
ABSTRACT:
PROVIDER: PRJNA884290 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21740300_1.fastq.gz | Fastqsanger.gz | |||
| SRR21740300_2.fastq.gz | Fastqsanger.gz | |||
| SRR21741600_1.fastq.gz | Fastqsanger.gz | |||
| SRR21741600_2.fastq.gz | Fastqsanger.gz | |||
| SRR21740301_1.fastq.gz | Fastqsanger.gz |
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Project description:soil metagenomic DNA Targeted loci environmental
| PRJNA295777 | ENA
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:Metagenomic sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). Here we examine native biocrust to determine if these patterns are reproduced in the environment. Overall, most soil metabolites display the expected relationship (positive or negative correlation) with four dominant bacteria following a wetting event and across biocrust developmental stages. For metabolites that were previously found to be consumed by an isolate, 70% are negatively correlated with the abundance of the isolate’s closest matching environmental relative in situ, whereas for released metabolites, 67% were positively correlated. Our results demonstrate that metabolite profiling, shotgun sequencing and exometabolomics may be successfully integrated to functionally link microbial community structure with environmental chemistry in biocrust.
2018-07-31 | MTBLS492 | MetaboLights
Project description:One of the cornerstones of an effective biodefense strategy is the ability to detect infectious agents with a high degree of sensitivity and specificity in the context of a complex sample background. The nature of the B. anthracis genome, however, renders specific detection difficult, due to close homology with B. cereus and B. thuringiensis. We therefore elected to determine the efficacy of next-generation sequencing analysis and microarrays for detection of B. anthracis in an environmental background. We applied next-generation sequencing to titrated genome copy numbers of B. anthracis in the presence of background nucleic acid extracted from aerosol and soil samples. We found next-generation sequencing to be capable of detecting as few as 10 genomic equivalents of B. anthracis DNA per nanogram of background nucleic acid. Detection was accomplished by mapping reads to either a defined subset of reference genomes or to the full GenBank database. Moreover, sequence data obtained from B. anthracis could be reliably distinguished from sequence data mapping to either B. cereus or B. thuringiensis. We also demonstrated the efficacy of a microbial census microarray in detecting B. anthracis in the same samples, representing a cost-effective and high-throughput approach, complementary to next-generation sequencing. This Series contains the NimbleGen array data only (no next-generation sequencing data). B. anthracis DNA was spiked at 6 different concentrations (1, 10, 100, 1000, 10000 and 100000 genome copies) into 1 ng of background nucleic acids extracted either from a soil sample or from an aerosol (air filter) sample. Two replicates of each combination of B. anthracis copy number and background sample were analyzed.
2013-06-27 | E-GEOD-48316 | biostudies-arrayexpress
Project description:Microbial community analysis with DNA oligonucleotide microarrays targeting ribosomal RNA (rRNA) provides a highly parallel interrogation of nucleic acids isolated from environmental samples. High fidelity readout is essential for accurate interpretation of hybridisations. We describe the hybridisation of in vitro transcribed 16S rRNA from an uncontaminated and 2,4,6-trinitrotoluene contaminated soil to an oligonucleotide microarray containing group- and species-specific perfect match (PM) probes and their 2 corresponding mismatch (MM) probes. Thermal dissociation analysis was used to determine the specificity of each PM-MM probe set. Functional ANOVA often discriminated PM-MM probe sets when Td values (temperature at 50% probe-target dissociation) could not. Maximum discrimination for many PM and MM probes often occurred at temperatures greater than the Td. Comparison of signal intensities measured prior to dissociation analysis from hybridisations of the two soil samples revealed significant differences in domain-, group- and species-specific probes. Functional ANOVA showed significantly different dissociation curves for 11 PM probes when hybridisations from the two soil samples were compared, even though initial signal intensities for 3 of the 11 did not vary. This approach provides a highly parallel, multi-level analysis that incorporates MM probes and dissociation curves into high fidelity microarray analysis of complex environmental nucleic acid profiles. Keywords: Microbial diversity, thermal dissociation analysis
2005-10-26 | GSE3499 | GEO
Project description:Understanding biological diversity and distribution patterns at multiple spatial scales is a central issue in ecology. Here, we investigated the biogeographical patterns of functional genes in soil microbes from 24 arctic heath sites using GeoChip-based metagenomics and principal coordinates of neighbour matrices (PCNM)-based analysis. Functional gene richness varied considerably among sites, while the proportions of each major functional gene category were evenly distributed. Functional gene composition varied significantly at most medium and broad spatial scales, and the PCNM analyses indicated that 14-20% of the variation in total and major functional gene categories could be attributed primarily to relatively broad-scale spatial effects that were consistent with broad-scale variation in soil pH and total nitrogen. The combination of variance partitioning and multi-scales analysis indicated that spatial distance effects contributed 12% to variation in functional gene composition，whereas environmental factors contributed only 3%. This relatively strong influence of spatial as compared to environmental variation in determining functional gene distributions contrasts sharply with typical microbial phylotype/species-based biogeographical patterns in the Arctic and elsewhere. Our results suggest that the distributions of soil functional genes cannot be predicted from phylogenetic distributions because spatial factors associated with historical contingencies are relatively important determinants of their biogeography.
2014-12-10 | GSE63927 | GEO
Project description:California Environmental DNA (CALeDNA) soil and sediment samples
| PRJNA941067 | ENA
Project description:The goal of this project was to screen soil samples for bacteria that may harbor B. anthracis virulence-associated genes (VAGs). There is currently no information about the prevalence of these types of organisms in the environment. Due to increased environmental monitoring of select agents by programs such as BioWatch and biodetection systems in place at the United States Post Offices and Department of State locations, it has become critical that we not only better understand the natural range of B. anthracis but also how widespread B. anthracis virulence genes are in environmental communities. Naturally occurring isolates containing the B. anthracis virulence genes could generate false-positive results in tests that detect the anthrax toxins, capsule or their associated genes. Understanding the true diversity and pathogenic potential of Bacillus spp. and particularly the B. cereus group is crucial not only in terms of understanding data from environmental monitoring but also diagnosing patients with clinical presentations similar to anthrax in the future. Severe and fatal disease caused by strains similar to B. anthracis could unnecessarily initiate emergency responses if anthrax was incorrectly suspected. Conversely, these strains may be used as bioterror agents requiring science-based responses; presently our limited understanding of these organisms does not permit data-driven decision making. We have investigated 700 aerobic sporoform soil isolates obtained from two areas in the Southwest of the US. Soil samples from the first site had been taken from public access land approximately 50 meters across from the work site of a fatal pneumonia case in a welding factory. This took place in year 2003 when B. cereus was isolated from a metal worker. The second site was targeted because of a recent case involving a deceased mule suspected to have died of a B. anthracis infection. Soil samples were initially analyzed at the CDC. Isolates were obtained by heating the soil at 65 degrees Celcius for 30 minutes followed by plating on agar media. All isolates were screened by PCR for the presence of B. anthracis genomic traits such as toxin genes (cya, lef and pag) as well as chromosomal markers. All isolates were also tested for their hemolytic activity as well as phage sensitivity.
2009-11-25 | GSE19071 | GEO
Project description:Local adaptation and phenotypic plasticity are important components of plant responses to variations in environmental conditions. While local adaptation has been widely studied in trees, little is known about plasticity of gene expression in adult trees in response to ever-changing environmental conditions in natural habitats. Here we investigate plasticity of gene expression in needle tissue between two douglas-fir provenances represented by 25 adult trees using deep RNA sequencing (RNA-Seq). Using linear mixed models, we investigated the effect of temperature, soil water availability and photoperiod on the abundance of 59189 detected transcripts. Expression of more than 80% of all identified transcripts revealed a response to variations in environmental conditions in the field. GO term overrepresentation analysis revealed gene expression responses to temperature, soil water availability and photoperiod that are highly conserved among many plant taxa. However, expression differences between the two Douglas-fir provenances were rather small compared to the expression differences observed between individual trees. Although the effect of environment on global transcript expression was high, the observed genotype by environment (GxE) interaction of gene expression was surprisingly low, since only 21 of all detected transcripts showed a GxE interaction.
2016-09-20 | GSE73420 | GEO