Ontology highlight
ABSTRACT:
PROVIDER: PRJNA638431 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11972628_1.fastq.gz | Fastqsanger.gz | |||
| SRR11972628_2.fastq.gz | Fastqsanger.gz | |||
| SRR11972629_1.fastq.gz | Fastqsanger.gz | |||
| SRR11972629_2.fastq.gz | Fastqsanger.gz | |||
| SRR11972630_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:The experiment was designed to test the interactions of Spartina alterniflora, its microbiome, and the interaction of the plant-microbe relationship with oil from the Deepwater Horizon oil spill (DWH). Total RNA was extracted from leaf and root microbiome of S. alterniflora in soils that were oiled in DWH oil spill with or without added oil, as well as those grown in unoiled soil with or without added oil. The work in its entirety characterizes the transport, fate and catabolic activities of bacterial communities in petroleum-polluted soils and within plant tissues.
2020-04-10 | GSE148431 | GEO
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.
2021-07-09 | GSE179685 | GEO
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:The leaf transcriptome of the nickel hyperaccumulator specie Noccaea caerulescens subsp. fimiensis living on serpentine soils were compared to the closely related non-nickel-accumulators Noccaea caerulescens "Viviez" growing on a zinc mining site and Noccaea montana living on serpentine soil, to identity differentially expressed genes potentially involved in Ni hyperaccumulation.
2019-06-05 | GSE115411 | GEO
Project description:In this study, Solexa sequencing technology has been used to discover small RNA populations of self-grafted watermelon and grafted watermelon (bottle gourd and squash were used as rootstocks). A total of 11,458,476, 11,614,094 and 9,339,089 raw reads representing 2,957,751, 2,880,328 and 2,964,990 unique sequences were obtained from the scions of self-grafted watermelon and watermelon grafted on-to bottle gourd and squash at two true-leaf stage, respectively. 39 known miRNAs belonging to 30 miRNA families and 80 novel miRNAs were identified in our small RNA dataset. Compared with self-grafted watermelon, 20 (5 known and 15 novel miRNAs) and 51 (21 known miRNAs and 30 novel miRNAs) miRNAs were expressed significantly different with higher abundance or lower abundance in watermelon grafted on to bottle gourd and squash, respectively. The differentially expressed miRNA target various transcriptional factors and other genes which involved in a wide range of biological processes. This study was firstly conducted to identify and compare miRNAs on genome-wide scale in watermelon grafting system. The miRNAs expressed differentially when watermelon was grafted onto different rootstocks suggesting that miRNAs might play an important role in diverse biological and metabolic processes in watermelon and grafting may possibly by changing miRNAs expression to regulate plant growth and response to stresses. The small RNA transcriptomes obtained in this study provided insights into molecular basis of miRNA regulation of genes expressed in self-grafted and grafted watermelon.
2011-10-26 | GSE33209 | GEO