Ontology highlight
ABSTRACT:
PROVIDER: PRJNA561072 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9998350_1.fastq.gz | Fastqsanger.gz | |||
| SRR9998350_2.fastq.gz | Fastqsanger.gz | |||
| SRR9998360_1.fastq.gz | Fastqsanger.gz | |||
| SRR9998360_2.fastq.gz | Fastqsanger.gz | |||
| SRR9998370_1.fastq.gz | Fastqsanger.gz |
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Project description:The spread of antibiotic resistance genes (ARG) into agricultural soils, products, and foods severely limits the use of organic fertilizers in agriculture. In this study, experimental land plots were fertilized, sown, and harvested for two consecutive agricultural cycles using either mineral or three types of organic fertilizers: sewage sludge, pig slurry, or composted organic fraction of municipal solid waste. The analysis of the relative abundances of more than 200,000 ASV (Amplicon Sequence Variants) allowed the identification of a small, but significant (<10%) overlap between soil and fertilizer microbiomes, particularly in soils sampled the same day of the harvest (post-harvest soils). Loads of clinically relevant ARG were significantly higher (up to 100 fold) in fertilized soils relative to the initial soil. The highest increases corresponded to post-harvest soils treated with organic fertilizers, and they correlated with the extend of the contribution of fertilizers to the soil microbiome. Edible products (lettuce and radish) showed low, but measurable loads of ARG (sul1 for lettuces and radish, tetM for lettuces). These loads were minimal in mineral fertilized soils, and strongly dependent on the type of fertilizer. We concluded that at least part of the observed increase on ARG loads in soils and foodstuffs were actual contributions from the fertilizer microbiomes. Thus, we propose that adequate waste management and good pharmacological and veterinarian practices may significantly reduce the potential health risk posed by the presence of ARG in agricultural soils and plant products.
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Project description:The soil samples of different fertilizer treatments Genome sequencing
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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:Drought is an increasing threat to soybean (Glycine max) production worldwide. In addition to methods such as breeding and genetic modification, inoculation of plants or soils with single microbes and microbial consortia are being explored to mitigate the impacts of drought stress on crop plants. One criterion for selecting microbes within a consortium is to select hub taxa, which are those whose abundances appear to be highly correlated with abundances of other taxa in the microbiome. To assess the impact of microbial inoculations with hub taxa on soybean, I identified five hub taxa from soybean roots which were then used to inoculate soybeans grown in 75% sand and 25% no-till soil from the KBS LTER. No-till soil was used to match the environment from which hub taxa were identified and isolated, and because no-till soils are known to confer resilience to low-moisture stress. Inoculated and control plants were then exposed to low-moisture stress as seedlings. Selected hub taxa included two fungi (Humicola sp., and Gibellulopsis sp.) and three bacteria (Streptomyces sp., Massilia sp., and Caulobacter segnis). The impact of inoculation on plant hosts was assessed with phenotype measures (aboveground and belowground) and plant functional measures (transcriptomics and non-target metabolomics of roots). The impact on the microbiome was assessed using amplicon sequencing of DNA as well as cDNA created from RNA extracted from roots. Inoculation had a minor impact on the microbiome that was most apparent when a more active fraction of the microbiome was analyzed using cDNA. cDNA amplicon sequencing demonstrated that Bradyrhizobium was enriched earlier in inoculated samples compared to control samples and that Glomus was enriched earlier in control samples. Transcriptomics of soybean roots demonstrated that genes related to nodulation were upregulated in inoculated samples, and non-targeted metabolomics appeared to show a possible signal of increased nodulation related metabolites in inoculated samples. Molecular and metabolomics data agreed with phenotypic data which showed increases in nodulation as well as increased aboveground growth, likely related to increased nitrogen fixation activity. Experiments using field soils and enriching individual hub taxa revealed that this effect of increased resilience to drought and nodulation was reproducible with both Caulobacter segnis and Streptomyces treatments. Overall, these results support the hypothesis that hub taxa can be used as inocula to improve the performance and resilience of the host plants.
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