Soil metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA181328 | ENA |
REPOSITORIES: ENA
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Project description:The potential of the earthworm Eisenia andrei to reduce soil methanogens, and thus methane emissions to the atmosphere, were assayed in a microcosm experiment. Soils were incubated for 2, 4 and 6 months. We measured microarray parameters (methanogenic diversity) at the start of incubation, as well as after 2, 4 and 6 months of incubation in microcosms with or without earthworms. Methanosarcina barkeri was the most abundant genus that was revealed by AnaeroChip in our experiment.
2011-11-11 | E-MEXP-2843 | biostudies-arrayexpress
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:Purpose: Deconstructing the soil microbiome into reduced-complexity functional modules represents a novel method of microbiome analysis. The goals of this study are to confirm differences in transcriptomic patterns among five functional module consortia. Methods: mRNA profiles of 3 replicates each of functional module enrichments of soil inoculum in M9 media with either 1) xylose, 2) n-acetylglucosamine, 3) glucose and gentamycin, 4) xylan, or 5) pectin were generated by sequencing using an Illumina platform (GENEWIZ performed sequencing). Sequence reads that passed quality filters were aligned to a soil metagenome using Burrows Wheeler Aligner. Resulting SAM files were converted to raw reads using HTSeq, and annotated using Uniref90 or EGGNOG databases. Results: To reduce the size of the RNA-Seq counts table and increase its computational tractability, transcripts containing a minimum of 75 total counts, but no more than 3 zero counts, across the 15 samples were removed. The subsequent dataset was normalized using DESeq2, resulting in a dataset consisting of 6947 unique transcripts across the 15 samples, and 185,920,068 reads. We identified gene categories that were enriched in a sample type relative to the overall dataset using Fisher’s exact test. Conclusions: our dataset confirms that the functional module consortia generated from targeted enrichments of a starting soil inoculum had distinct functional trends by enrichment type.
2020-01-14 | GSE143587 | GEO
Project description:Metagenomic analysis in a soil microcosm study
| PRJNA489261 | ENA
Project description:The experiment at three long-term agricultural experimental stations (namely the N, M and S sites) across northeast to southeast China was setup and operated by the Institute of Soil Science, Chinese Academy of Sciences. This experiment belongs to an integrated project (The Soil Reciprocal Transplant Experiment, SRTE) which serves as a platform for a number of studies evaluating climate and cropping effects on soil microbial diversity and its agro-ecosystem functioning. Soil transplant serves as a proxy to simulate climate change in realistic climate regimes. Here, we assessed the effects of soil type, soil transplant and landuse changes on soil microbial communities, which are key drivers in Earth’s biogeochemical cycles.
2016-02-04 | GSE77546 | GEO
Project description:Soil microbial communities from experimental microcosm in Duke University, North Carolina, United States - NN3 metagenome
| PRJNA539697 | ENA
Project description:Soil microbial communities from experimental microcosm in Duke University, North Carolina, United States - YN3 metagenome
| PRJNA518672 | ENA
Project description:Soil microbial communities from experimental microcosm in Duke University, North Carolina, United States - NC metagenome
| PRJNA539695 | ENA
Project description:Soil microbial communities from experimental microcosm in Duke University, North Carolina, United States - YC metagenome
| PRJNA539696 | ENA