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PROVIDER: PRJNA701249 | ENA |
REPOSITORIES: ENA
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Project description:Copper has long been applied for agricultural practices. Like other metals, copper is highly persistent in the environment and biologically active long after its use has ceased. Here we present a unique study on the long-term effects (27 years) of copper and pH on soil microbial communities and on Folsomia candida, an important representative of the soil macrofauna, in an experiment with a full factorial, random block design. Bacterial communities were mostly affected by pH. These effects were prominent in Acidobacteria, while Actinobacteria and Gammaroteobacteria communities were affected by original and bioavailable copper. Reproduction and survival of the collembolan F. candida was not affected by the studied copper concentrations. However, the transcriptomic responses to copper reflected a mechanism of copper transport and detoxification, while pH exerted effects on nucleotide and protein metabolism and (acute) inflammatory response. We conclude that microbial community structure explained the history of copper contamination, while gene expression analysis of F. candida is associated with the current level of bioavailable copper. Combined analysis at various trophic levels is highly relevant in the context of assessing long-term soil pollution.
2012-04-04 | GSE29644 | GEO
Project description:The copper redhorse (Moxostoma hubbsi) is an endangered fish endemic to Quebec, Canada that is only known to spawn in two locations within the Richelieu River, a waterway draining a significant area of agricultural land. Accordingly, concerns have been raised over the impacts that agricultural pesticide contamination of spawning grounds and nursery habitats within the Richelieu River may have on early life stage copper redhorse. We assessed the effects of contaminants on early life stages of copper redhorse and river redhorse (Moxostoma carinatum), a closely related fish that shares the copper redhorse’s habitat and spawning grounds but is distributed more widely and is not yet listed as endangered. Copper and river redhorse embryos (1000 each) were exposed to either Richelieu River water in an in-situ flow-through system or to laboratory water used as a control. We assessed embryos hatching time, incidence of deformities and survival in copper and river redhorses. We then performed RNA sequencing on copper redhorse larvae to better understand changes due to river water exposure. We identified 341 compounds in the river water that were absent from lab water. Pesticide concentrations in the river peaked following rainfall during the spawning season. Embryos exposed to river water hatched prematurely at 63.0 and 59.2 cumulative degree days (CDD) compared to 65.4 and 69.9 CDD in laboratory water for river and copper redhorse, respectively. Copper redhorse exposed to river water also had a significantly lower survival rate than laboratory water (73% vs. 93%). RNA sequencing of copper redhorse revealed 18 differentially expressed genes (DEGs) following river water exposure. Eight of the upregulated DEGs (cd44, il1b, lamb3, lamc2, tgm5, orm1, saa, acod1) are linked to immune function and injury response and 7 of the downregulated DEGs (cpa2, ctrb, cela2a, ctrl, cpa1, prss1, cel) are involved with digestion and nutrient absorption. This study provided valuable data on the effects of anthropogenic contaminants present in the Richelieu River and increased our knowledge on the individual and mixture effects they have on an endangered fish.
2022-06-01 | GSE185175 | GEO
Project description:Thermomacidophilic archaea, such as Metallosphaera sedula, are lithoautotrophs that occupy metal-rich environments. In previous studies, a M. sedula mutant lacking the primary copper efflux transporter, CopA, became copper sensitive. In contrast, the basis for supra-normal copper resistance remained unclear in the spontaneous M. sedula mutant, CuR1. Here, transcriptomic analysis of copper-shocked cultures indicated that CuR1 had a unique regulatory response to metal challenge corresponding to up-regulation of 55 genes. Genome re-sequencing identified 17 confirmed mutations unique to CuR1 that were likely to change gene function. Of these, 12 mapped to genes with annotated function associated with transcription, metabolism or transport. These mutations included 7 non-synonymous substitutions, 4 insertions and 1 deletion. One of the insertion mutations mapped to pseudogene, Msed_1517, and extended its reading frame an additional 209 amino acids. The extended mutant allele was identified as a homolog of Pho4, a family of phosphate symporters that include the bacterial PitA proteins. Orthologs of this allele were apparent in related extremely thermoacidophilic species, suggesting M. sedula was naturally lacking this gene. Phosphate transport studies combined with physiologic analysis demonstrated M. sedula PitA was a low affinity high velocity secondary transporter implicated in copper resistance and arsenate sensitivity. Genetic analysis demonstrated spontaneous arsenate resistant mutants derived from CuR1 all underwent mutation in pitA and non-selectively became copper resistant. Taken together, these results point to archaeal PitA as a key requirement for the increased metal resistance of strain CuR1 and its accelerated capacity for copper bioleaching. The study comprises 5 samples, described in detail below. WT_CuR1: Differential transcriptional response of Metallosphaera sedula DSM 5348, WT, to the supra-normal copper resistant spontaneous Metallosphaera sedula mutant, CuR1 under normal growth conditions. This experiment was done to analyze the differential transcription of WT cells compared with CuR1 cells at mid log phase. WT-15_CuR1-15: Differential transcription of Metallosphaera cells under sub-inhibitory copper challenge (2.0 mM). This experiment was done to analyze the differential transcription of Metallosphaera sedula WT and CuR1 15 minutes post copper challenge. The copper cultures were harvested 15 minutes after the shock. WT-60_CuR1-60: Differential transcription of Metallosphaera cells under sub-inhibitory copper challenge (2.0 mM). This experiment was done to analyze the differential transcription of Metallosphaera sedula WT and CuR1 60 minutes post copper challenge. The copper cultures were harvested 60 minutes after the shock. WT-15_WT-60: Differential transcription of Metallosphaera cells under sub-inhibitory copper challenge (2.0 mM). This experiment was done to analyze the differential transcription of Metallosphaera sedula WT 15 and 60 minutes post copper challenge. The copper cultures were harvested 15 and 60 minutes after the shock, respectively. CuR1-15_CuR1-60: Differential transcription of Metallosphaera cells under sub-inhibitory copper challenge (2.0 mM). This experiment was done to analyze the differential transcription of Metallosphaera sedula CuR1 15 and 60 minutes post copper challenge. The copper cultures were harvested 15 and 60 minutes after the shock, respectively.
2014-07-10 | E-GEOD-59253 | biostudies-arrayexpress
Project description:Thermomacidophilic archaea, such as Metallosphaera sedula, are lithoautotrophs that occupy metal-rich environments. In previous studies, a M. sedula mutant lacking the primary copper efflux transporter, CopA, became copper sensitive. In contrast, the basis for supra-normal copper resistance remained unclear in the spontaneous M. sedula mutant, CuR1. Here, transcriptomic analysis of copper-shocked cultures indicated that CuR1 had a unique regulatory response to metal challenge corresponding to up-regulation of 55 genes. Genome re-sequencing identified 17 confirmed mutations unique to CuR1 that were likely to change gene function. Of these, 12 mapped to genes with annotated function associated with transcription, metabolism or transport. These mutations included 7 non-synonymous substitutions, 4 insertions and 1 deletion. One of the insertion mutations mapped to pseudogene, Msed_1517, and extended its reading frame an additional 209 amino acids. The extended mutant allele was identified as a homolog of Pho4, a family of phosphate symporters that include the bacterial PitA proteins. Orthologs of this allele were apparent in related extremely thermoacidophilic species, suggesting M. sedula was naturally lacking this gene. Phosphate transport studies combined with physiologic analysis demonstrated M. sedula PitA was a low affinity high velocity secondary transporter implicated in copper resistance and arsenate sensitivity. Genetic analysis demonstrated spontaneous arsenate resistant mutants derived from CuR1 all underwent mutation in pitA and non-selectively became copper resistant. Taken together, these results point to archaeal PitA as a key requirement for the increased metal resistance of strain CuR1 and its accelerated capacity for copper bioleaching.
2014-07-10 | GSE59253 | GEO
Project description:Copper has long been applied for agricultural practices. Like other metals, copper is highly persistent in the environment and biologically active long after its use has ceased. Here we present a unique study on the long-term effects (27 years) of copper and pH on soil microbial communities and on Folsomia candida, an important representative of the soil macrofauna, in an experiment with a full factorial, random block design. Bacterial communities were mostly affected by pH. These effects were prominent in Acidobacteria, while Actinobacteria and Gammaroteobacteria communities were affected by original and bioavailable copper. Reproduction and survival of the collembolan F. candida was not affected by the studied copper concentrations. However, the transcriptomic responses to copper reflected a mechanism of copper transport and detoxification, while pH exerted effects on nucleotide and protein metabolism and (acute) inflammatory response. We conclude that microbial community structure explained the history of copper contamination, while gene expression analysis of F. candida is associated with the current level of bioavailable copper. Combined analysis at various trophic levels is highly relevant in the context of assessing long-term soil pollution. A single channel, interwoven loop design was used to test animals exposed to the copper-spiked field soil samples. The field soil was spiked with 4 copper and 4 pH treatments yielding 16 combinations. Combinations are displayed in the Sample descriptions, with 1 M-bM-^@M-^S 4 representing the copper concentrations from low to high, and A-D representing the soil pH from low to high. 4 biological replicates per copper/pH combination were used. Each replicate contained 25 grams of soil and thirty 23-day-old animals.
2012-04-03 | E-GEOD-29644 | biostudies-arrayexpress
Project description:microRNAs can play a crucial role in stress response in plants, including biotic stress. Some miRNAs are known to respond to bacterial infection. This work has addressed the role of miRNAs in Manihot esculenta (cassava)-Xanthomonas axonopodis pv. manihotis (Xam) interaction. Illumina sequencing was used for analyzing small RNA libraries from cassava tissue infected and non-infected with Xam. Cassava variety MBRA685 (resistant to Xam-CIO151) Six-week-old plants were inoculated with 36h-old cultures of the aggressive Xanthomonas axonopodis pv. manihotis strain CIO151 in both leaves and stems.
2011-12-01 | GSE29379 | GEO
Project description:Cropping soils vary in extent of natural suppression of soil-borne plant diseases. However, it is unknown whether similar variation occurs across pastoral agricultural systems. We examined soil microbial community properties known to be associated with disease suppression across 50 pastoral fields varying in management intensity. The composition and abundance of the disease-suppressive community were assessed from both taxonomic and functional perspectives.
2018-03-30 | GSE112489 | GEO
Project description:Comparison of the transcriptome profiles of a widely commercialized maize MON810 variety and its non-GM near-isogenic counterpart grown in agricultural fields. The Helen variety was commercialized by Limagrain Iberica. Variety Helen B was obtained by Advanta; authorized the 11/08/2005; now commercialized by Limagrain Iberica. The insert integrated into the maize genome contains: Cauliflower Mosaic Virus 35S promoter + maize HSP70 intron (partial) + synthetic sequence coding for the Bacillus thuringensis CRYIA(b) insecticidal protein (truncated).
2010-09-21 | E-MEXP-2366 | biostudies-arrayexpress
Project description:Purpose: Investigate genes associated to resistance of Xanthomonas perforans race T4 in tomato line with different resistance level Methods: Resistant and susceptible tomato breeding lines were subjected to the inoculation with Xanthomonas perforans race T4 followed by sample collection at 48 hpi and RNA-seq analysis for screening differential expressed genes associated with inoculation of pathogen. Results: Revealed gene expression profiles associated disease resistance and susceptiblilty.
2019-08-02 | GSE135232 | GEO