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Soil metagenome

ABSTRACT: Agricultural quality matrix-based multiomics structural analysis of carrots in soils fertilized with thermophile-fermented compost

PROVIDER: PRJDB13243 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR355178_1.fastq.gz	Fastqsanger.gz
	DRR355178_2.fastq.gz	Fastqsanger.gz
	DRR355179_1.fastq.gz	Fastqsanger.gz
	DRR355179_2.fastq.gz	Fastqsanger.gz

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Impact of oral compost-extract administration on gene expression in the rat gastrointestinal tract

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Impact of oral compost-extract administration on gene expression in the rat gastrointestinal tract

Project description:Oral administration of an extract of compost fermented with thermophiles to pigs reduces the incidence of stillbirth and promotes piglet growth. However, the mechanism by which compost extract modulates the physiological conditions of the animals remains largely unknown. Here, we investigate the effects of compost extract on the gene expression in the intestine of the rat as a mammalian model. Gene expression analyses of the intestine indicated that several immune-related genes were upregulated following compost exposure. Thus, thermophile-fermented compost can contain microbes and/or substances that activate the gut mucosal immune response in the rat. In Male Wistar rats aged 3 weeks, tap water was supplemented with 1.0% (v/v) compost extract for the experimental rats, whereas water only was given to the control rats. The rats received water ad libitum for 12 weeks. Fresh gut samples were collected from individual rats at the end of the feeding test and stored at -80Â°C. The intestine were separated from the gut and used as samples for the isolation of total RNA. otal RNA was then subjected to microarray experiments using the Whole Rat Genome (4x44k) Oligo Microarray (Agilent Technologies, Inc.)

2012-11-02 | E-GEOD-37732 | biostudies-arrayexpress

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Project description:The thermophilic filamentous fungi Myceliophthora thermophila (Sporotrichum thermophile) has an ability to decompose cellulolytic biomass. To identify the genes and proteins involved in this process, we explored the transcriptomes of M. thermophila grown at 45 °C on different agricultural straws (oat, triticale, canola, flax straws).

2016-11-28 | GSE57235 | GEO

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Project description:Feeding thermophile-fermented compost improves the water and muscle quality of cherry salmon by altering the microbiota in the gut

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Implications of the use of organic fertilizers for Antibiotic Resistant Gene dissemination in agricultural soils and fresh food products. A plot-scale study

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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Arbuscular mycorrhizal fungi and carrot demonstrate contrasting responses to drought stress as revealed through a dual transcriptomic approach

Project description:To test the impacts of drought on the host and fungus, we inoculated carrots (Daucus carota cv. ‘Napoli’) with spores of Rhizophagus irregularis DAOM 197198. Carrots grew in a greenhouse, and at the beginning of taproot development, were exposed to a 10-day water restriction. We evaluated plant growth and physiological responses, colonization level, and plant and fungal gene expression.

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