Soil metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA269683 | ENA |
REPOSITORIES: ENA
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Project description:Green manure is widely advocated as a sustainable alternative to chemical fertilizers in crop systems, yet the mechanisms underlying its yield benefits remain unclear. Moreover, vigorous vegetative growth under green manure can elevate lodging risk, undermining yield and harvest efficiency. Here, we describe mechanisms by which hairy vetch–based green manure enhances yield and evaluate the practical value of deploying functionally weak alleles of gibberellin 20-oxidase (GA20ox) in this management context. We conducted field comparisons of green manure and conventional chemical fertilization to evaluate effects on rice productivity, grain appearance quality, and canopy physiology. Green manure significantly increased grain yield and grain appearance quality in the leading Japanese cultivar ‘Koshihikari’, accompanied by higher lodging. By contrast, high-yielding cultivars homozygous for a single-copy GA20ox1 allele and/or a non-functional GA20ox2 allele maintained superior lodging resistance under green manure treatment while improving yield and grain appearance quality, indicating an effective combination of its treatment and genotypes. Physiologically, green manure increased chlorophyll index during vegetative growth and at the reproductive stage, and nitrogen (N) concentration on the whole plant. Furthermore, green manure increased flag-leaf width and tiller number; these canopy changes were associated with reduced panicle temperature at the ripening stage. Green manure treatment induced upregulation of OsNADH-GOGAT2, a known gene associated with increased N loading to grains, and more grain storage proteins, providing a positive link to improved grain appearance quality. Collectively, this study demonstrates that integrating hairy vetch with functionally weak GA20ox alleles can enhance productivity and grain appearance quality while mitigating lodging risk. This sheds light on the importance of aligning green-manure treatment with targeted allelic selection to stabilize performance across intensive-farming systems and reduce chemical fertilizer dependency.
2026-01-19 | GSE313855 | GEO
Project description:A5_Microorganisms under Farm yard manure (FYM) treated soil Metagenome
| PRJNA269682 | ENA
Project description:Metagenome data from soil samples were collected at 0 to 10cm deep from 2 avocado orchards in Channybearup, Western Australia, in 2024. Amplicon sequence variant (ASV) tables were constructed based on the DADA2 pipeline with default parameters.
2025-06-15 | GSE298403 | GEO
Project description:Soil microorganisms in mountain tea garden under green manure cover
| PRJNA1156325 | 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:Effects of green manure rotation on soil metagenome (PRJCA031341)
| PRJDB33089 | ENA
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:We present the draft genome of Nitrospirae bacterium Nbg-4 as a representative of this clade and couple this to in situ protein expression under sulfate-enriched and sulfate-depleted conditions in rice paddy soil. The proteins were extracted from the soil and analysed via LC-MS/MS measurements.
2018-01-08 | PXD007817 | Pride
Project description:<p>Common vetch (Vicia sativa L.) is an important annual leguminous forage crop commonly used for green manure, fodder, and soil improvement. It is widely cultivated as a green manure and forage crop in Yunnan Province during winter and spring. However, the dry conditions and minimal rainfall during these seasons greatly limit common vetch growth. Therefore, screening for drought-tolerant, high-yielding common vetch varieties is a critical objective in breeding programs.</p>
2026-01-31 | MTBLS13368 | MetaboLights