Soil metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA394187 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Soil metagenome under phosphorus fertilization Metagenome
| PRJNA394180 | ENA
Project description:This study evaluates the transcriptome of 3 Arabidopsis thaliana genotypes (Col-0, phf1 and phr1/phl1) growing in soil treated under a gradient of fertilization regimes.
2019-04-06 | GSE129394 | GEO
Project description:Soil microbial communities under long-term fertilization
| PRJNA392976 | ENA
Project description:Soil prokaryotic communities under long-term fertilization
| PRJNA392865 | ENA
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:Soil ammonia oxidizing archaea under long-term fertilization
| PRJNA392983 | ENA
Project description:The aim of this study was to identify eQTL in Brassica rapa grown under altered soil phosphorus (P) supply, to understand better the genetic architecture of P-use efficiency (PUE) in plants. Recombinant inbred lines (RILs) of the BraIRRI mapping population were grown at adequate and growth-limiting soil P. Variation in leaf gene expression was quantified using an Agilent Brassica 95k oligonucleotide array. Informative gene expression markers (GEMs) were used to map eQTL and PUE-related QTL. Gene expression was highly dependent on soil P supply. However, the altered expression of many genes, including known P-responsive genes, was highly heritable. Interval mapping using P supply as a covariate revealed 18,876 eQTL, representing 15,912 unique probes. Notable trans-eQTL hotspots occurred on chromosomes A06 and A01; these were enriched with protein modification and phosphorus metabolism-related (A06), as well as chloroplast and photosynthesis-related (A01) transcripts. Regulatory loci and genes associated with P-use efficiency identified through eQTL analysis are potential targets for further characterisation and may have potential for crop improvement. Availability of the annotated B. rapa genome sequence will facilitate their study, including the separation of cis- and trans- effects.
2011-06-29 | GSE27052 | GEO
Project description:Microbes play key roles in diverse biogeochemical processes including nutrient cycling. However, responses of soil microbial community at the functional gene level to long-term fertilization, especially integrated fertilization (chemical combined with organic fertilization) remain unclear. Here we used microarray-based GeoChip techniques to explore the shifts of soil microbial functional community in a nutrient-poor paddy soil with long-term (21 years).The long-term fertilization experiment site (set up in 1990) was located in Taoyuan agro-ecosystem research station (28°55’N, 111°27’E), Chinese Academy of Sciences, Hunan Province, China, with a double-cropped rice system. fertilization at various regimes.
2020-09-19 | GSE104014 | GEO
Project description:Aeolian soil erosion, exacerbated by anthropogenic perturbations, has become one of the most alarming processes of land degradation and desertification. By contrast, dust deposition might confer a potential fertilization effect. To examine how they affect topsoil microbial community, we conducted a study GeoChip techniques in a semiarid grassland of Inner Mongolia, China. We found that microbial communities were significantly (P<0.039) altered and most of microbial functional genes associated with carbon, nitrogen, phosphorus and potassium cycling were decreased or remained unaltered in relative abundance by both erosion and deposition, which might be attributed to acceleration of organic matter mineralization by the breakdown of aggregates during dust transport and deposition. As a result, there were strong correlations between microbial carbon and nitrogen cycling genes. amyA genes encoding alpha-amylases were significantly (P=0.01) increased by soil deposition, reflecting changes of carbon profiles. Consistently, plant abundance, total nitrogen and total organic carbon were correlated with functional gene composition, revealing the importance of environmental nutrients to soil microbial function potentials. Collectively, our results identified microbial indicator species and functional genes of aeolian soil transfer, and demonstrated that functional genes had higher susceptibility to environmental nutrients than taxonomy. Given the ecological importance of aeolian soil transfer, knowledge gained here are crucial for assessing microbe-mediated nutrient cyclings and human health hazard.
2015-03-28 | GSE67347 | GEO
Project description:Nipponbare performs poorly in phosphorus (P) deficient soil whereas a Nipponbare-derived NIL containing the Pup1 allele of donor parent Kasalath is tolerant to P deficiency. In this experiment we compared gene expression patterns in roots of this NIL to Nipponbare, grown either in a P deficient or P fertilized soil. The aim is to separate constitutive differences in expression from those induced by P deficiency. Experiment Overall Design: Total RNA was extrancted from root that were grown under two conditions and prepared three biological replicant in each line (total 6 samples in each line). Experiment Overall Design: We used 6 slides for this experiment, in each slide, Nipponbare and 6-4 samples grown under same condition were hybridized.
2009-11-10 | E-GEOD-6187 | biostudies-arrayexpress