Biocontrol Vs Copper Fungicide treatments comparison through amplicons
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB30496 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3015470_1.fastq.gz | Fastqsanger.gz | |||
| ERR3015470_2.fastq.gz | Fastqsanger.gz | |||
| ERR3015480_1.fastq.gz | Fastqsanger.gz | |||
| ERR3015480_2.fastq.gz | Fastqsanger.gz | |||
| ERR3015490_1.fastq.gz | Fastqsanger.gz |
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Project description:Pf-5 is an important biocontrol strain of Pseudomonas fluorsecens, that improves plant growth, mainly via the production of secondary metabolites and growth/colonisation competition. Copper is a broad-spectrum antimicrobial that is effective against bacteria, fungi and even viruses in soluble forms such as copper sulfate and to a lesser extent in solid form, such as copper surfaces. Copper sulfate is commonly sprayed on food crops to increase yield and is becoming more routinely used due to the increasing problem of resistance to standard pesticides. Thus, an obvious question that remains is: what effect is this introduced copper having on these important biocontrol strains? First, the phenotypic effects of copper on carbon utilisation and pH tolerance was tested using Biolog. Interestingly, the ability of Pf-5 to utilise amino acids as a sole carbon source was largely unaltered, but the presence of copper completely eliminated the utilisation of carbohydrates or fatty acids, and diminished the use of carboxylic acids and amines. This could be explained by copper-mediated disruptions of enzymes in metabolic pathways, such as the TCA cycle. The effect on gene expression was examined using reverse transcriptomics, which established molecular bases for the phenotypic results, and confirmed some known mechanisms for copper resistance, efflux and transporter proteins, and highlighted the delicate interplay with cellular control of iron, as well as uncovered the interesting relationship between integrated bacteriophage and copper as a molecular switch. The integrated phage, Prophage 01, was downregulated in the presence of copper and when this phage was activated with Mitomycin C, the copper appeared to stop the phage from going into lytic cycle and protected lysis of the cells. Prophage 01 is integrated between the housekeeping genes mutS and cinA and is conserved throughout many Pseudomonas. However, only Pf-5, out of the 10 strains tested seemed to be protected from cell lysis by copper, indicating that Prophage 01 in Pf-5 has unique features that interact with Cu.
2012-04-05 | GSE37024 | GEO
Project description:Pf-5 is an important biocontrol strain of Pseudomonas fluorsecens, that improves plant growth, mainly via the production of secondary metabolites and growth/colonisation competition. Copper is a broad-spectrum antimicrobial that is effective against bacteria, fungi and even viruses in soluble forms such as copper sulfate and to a lesser extent in solid form, such as copper surfaces. Copper sulfate is commonly sprayed on food crops to increase yield and is becoming more routinely used due to the increasing problem of resistance to standard pesticides. Thus, an obvious question that remains is: what effect is this introduced copper having on these important biocontrol strains? First, the phenotypic effects of copper on carbon utilisation and pH tolerance was tested using Biolog. Interestingly, the ability of Pf-5 to utilise amino acids as a sole carbon source was largely unaltered, but the presence of copper completely eliminated the utilisation of carbohydrates or fatty acids, and diminished the use of carboxylic acids and amines. This could be explained by copper-mediated disruptions of enzymes in metabolic pathways, such as the TCA cycle. The effect on gene expression was examined using reverse transcriptomics, which established molecular bases for the phenotypic results, and confirmed some known mechanisms for copper resistance, efflux and transporter proteins, and highlighted the delicate interplay with cellular control of iron, as well as uncovered the interesting relationship between integrated bacteriophage and copper as a molecular switch. The integrated phage, Prophage 01, was downregulated in the presence of copper and when this phage was activated with Mitomycin C, the copper appeared to stop the phage from going into lytic cycle and protected lysis of the cells. Prophage 01 is integrated between the housekeeping genes mutS and cinA and is conserved throughout many Pseudomonas. However, only Pf-5, out of the 10 strains tested seemed to be protected from cell lysis by copper, indicating that Prophage 01 in Pf-5 has unique features that interact with Cu. Two-condition experiment, where normal culture in rich medium versus cell treated with CuSO4. 3 biological replicates including 3 technical replicates for one of the biological replicates and 2 technical replicates for another of biological replicates. Swap-dye experiments were performed.
2012-04-04 | E-GEOD-37024 | biostudies-arrayexpress
Project description:Winemakers have long used copper as a conventional fungicide treatment on grapevine and only recently, the use of biocontrol agents depicted a promising alternative. Most of the studies that investigate the impact of fungicide treatments, focus on specific pathogenic microbes. In the present work instead, a field experiment conducted in South Africa shows the seasonal microbial change occurring on grapevine leaves, periodically treated with two different fungicide treatments: copper sulphate and Lactobacillus plantarum MW-1. In this work, NGS data were combined with strain-specific and community qPCRs to reveal the shift of the microbial communities throughout the growing season and highlight the impact of fungicides on the microbiota. Only the family of Lactobacillaceae systematically changed between treatments, while the bacterial community remained relatively stable over time. MW-1 was exclusively detected on biocontrol-sprayed leaves. Conversely, the fungal community was largely shaped by sampling time, underlining the succession of different dominant taxa over the months. Between treatments, only a few fungal taxa appeared to change significantly and the fungal load was also comparable. Monitoring the dynamics of the microbial community under different fungicide treatments may advise the best timing to apply treatments to the plants, toward the realization of more sustainable agricultural practices.
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Project description:Transcriptional changes occurring at the infection site of 2 weeks old Cabernet sauvignon grapevine cuttings infected with a wood pathogen (Phaeomoniella chlamydospora) in the presence of a root-inoculated biocontrol agent (Pythium oligandrum). Gene expression profiling was done using the Nimblegen whole genome array with 3 biological replicates of 3 pooled wood chunks harvested 0 and 14 d after treatment (pathogen infection, biocontrol agent inoculation, mock treatment).
2016-03-15 | E-MTAB-3899 | biostudies-arrayexpress
Project description:Exposure of a resistance and sensitive isolate of Penicillium to difenoconazole fungicide and acetone as a control for 24 hours.
2020-04-20 | GSE145355 | GEO
Project description:In this study, a newly developed 8x15K Fusarium graminearum Agilent microarray was applied to analyze transcriptional responses to azole fungicide treatment. Comparative statistical analysis of expression profiles from treated versus untreated fungal liquid cultures uncovered 1058 genes that were significantly differentially expressed. Among the 596 genes with significantly increased transcript levels, analyses using GeneOntology and FunCat annotations detected the ergosterol-biosynthesis pathway genes as the most significantly responding category, providing statistical confirmation of the mode-of-action of azole fungicides. Transcriptional profiling of 54 genes, which encode ABC transporters in F. graminearum, suggested that several of these might be involved in reducing intracellular fungicide concentration. In addition, several genes encoding transcription factors with similarity to yeast genes known to co-ordinate fungicide responses exhibited significant differential expression.
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Project description:Lowbush Blueberry Fungicide Trial Raw sequence reads
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Project description:To identify genes which are differentially expressed in Corynebacterium glutamicum in the absence of copper, we performed DNA microarray analyses of cells cultivated under copper starvation conditions compared to copper sufficiency.
2018-08-28 | GSE117530 | GEO
Project description:Two biocontrol agents Genome sequencing
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Project description:Background: MicroRNAs (miRNAs) are a class of single-stranded non-coding small RNAs (sRNAs) that are 20-24 nucleotides (nt) in length. Extensive studies have indicated that miRNAs play important roles in plant growth, development, and stress responses. With more copper (Cu) and copper-containing compounds used as bactericides and fungicides in viticulture, Cu stress has become one of the serious environmental problems that affect plant growth and development. In order to uncover the hidden response mechanisms of Cu stress, many Cu-responsive miRNAs have been detected in several plant species. However, there have been few reports about the grapevine miRNAs in response to Cu. Results: Here, two small RNA libraries were constructed from Cu-treated and water-treated (control) leaves of 'Summer Black' grapevine. Following high-throughput sequencing and filtering, 158 known vvi-miRNAs and 98 novel vvi-miRNAs were identified in the two libraries. Among these, 24 could only be detected in the treatment, and 63 were only detected in the control. Additionally, 100 known vvi-miRNAs were found to be clearly responsive to Cu, among which 96 were down-regulated and four were up-regulated; 47 novel vvi-miRNAs were found to be clearly responsive to Cu, among which 35 were down-regulated and 12 were up-regulated. Subsequently, expression patterns of a set of Cu-responsive vvi-miRNAs were validated by quantitative real-time PCR (qRT-PCR). There existed some consistency in expression levels of Cu-responsive vvi-miRNAs between high-throughput sequencing and qRT-PCR assays. In addition, 92 putative targets for 79 known vvi-miRNAs and 51 putative targets for 22 novel vvi-miRNAs were predicted, and most of the targets are involved in multiple biological processes including transcriptional regulation and response to biotic and abiotic stresses. Conclusions: In this study, 147 Cu-responsive vvi-miRNAs were identified using high-throughput sequencing, and their target genes were predicted, which will be helpful to understanding the molecular mechanisms of miRNAs in response to Cu stress. Furthermore, this work can also provide a foundation for further study of the networks of miRNAs involved in grapevine plant growth and breeding some Cu-tolerant grapevine cultivars. Mixed 'Summer Black' grapevine young leaves (2 weeks old), large leaves (5 weeks old), and old leaves (9 week old) in randomly-selected plants from both the Cu-treated and control groups were collected for high-throughput sequencing. Subsequently, we carried out the analysis of Solexa sequencing data, and performed the research of regulatory modes of grapevine miRNAs on their target genes during Cu stress.
2016-02-20 | E-GEOD-78133 | biostudies-arrayexpress