Ontology highlight
ABSTRACT:
PROVIDER: PRJNA859261 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR20462137_1.fastq.gz | Fastqsanger.gz | |||
| SRR20462137_2.fastq.gz | Fastqsanger.gz | |||
| SRR20462138_1.fastq.gz | Fastqsanger.gz | |||
| SRR20462138_2.fastq.gz | Fastqsanger.gz | |||
| SRR20462139_1.fastq.gz | Fastqsanger.gz |
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Project description:<p>Carbonate-type saline-alkaline stress severely constrains maize production; however, the synergistic response mechanisms between rhizosphere microorganisms and metabolites remain unclear. This study focused on maize fields in the carbonate chernozem region of the Songnen Plain in Northeast China. Through field experiments and the integration of soil chemical factor analysis, microbial high-throughput sequencing (16S rRNA and ITS), and non-targeted metabolomics (LC-MS), we systematically investigated the response mechanisms of the rhizosphere micro-ecosystem under saline-alkaline stress. The results indicated that saline-alkaline stress significantly increased soil pH and electrical conductivity (EC), and led to decreases in soil organic matter (SOM), total nitrogen (TN), and total phosphorus (TP) contents. However, the rhizosphere zone exhibited a certain buffering capacity, maintaining a higher cation exchange capacity (CEC). Microbial community analysis revealed that bacterial alpha diversity increased under stress. In contrast, fungal diversity significantly decreased, and the community structure shifted towards a pathogen-dominated community, primarily within Ascomycota, especially the genus Fusarium. Co-occurrence network analysis further revealed that saline-alkaline conditions enhanced the complexity and connectivity of bacterial networks but led to the contraction and structural simplification of fungal networks. Metabolite analysis showed that saline-alkaline stress induced significant reprogramming of the rhizosphere metabolic profile. Organophosphorus compounds, nucleotides, and their analogs were significantly enriched, while defensive secondary metabolites such as Cajanol specifically accumulated in the saline-alkaline rhizosphere. Pathway analysis indicated the activation of stress resistance and oxidative stress mitigation-related pathways, including Betalain biosynthesis, flavonoid biosynthesis, tryptophan metabolism, and arginine metabolism. Multi-omics integration analysis identified soil EC and total potassium (TK) as key environmental factors driving the differentiation of microbial and metabolite communities. Key differential metabolites showed significant positive correlations with saline-alkaline-enriched microbial taxa (e.g., Sphingomonas), revealing a metabolite-mediated microbial recruitment mechanism. This study, through multi-omics analysis, discovered that the maize rhizosphere, under saline-alkaline stress, undergoes metabolic reprogramming (e.g., enriching defensive metabolites like Cajanol) to directionally recruit beneficial bacteria such as Sphingomonas and maintains higher bacterial network complexity, while also leading to the pathologization of the fungal community. Our study reveals that maize recruits beneficial microbes via rhizosphere metabolic reprogramming, providing a mechanistic basis for microbiome-assisted saline-alkaline soil remediation.</p>
2026-06-08 | MTBLS13956 | MetaboLights
Project description:Bacterial community structure in saline-alkaline fumigated soil
| PRJNA242210 | ENA
Project description:To study long-term elevated CO2 and enriched N deposition interactive effects on microbial community and soil ecoprocess, here we investigated soil microbial community in a grassland ecosystem subjected to ambient CO2 (aCO2, 368 ppm), elevated CO2 (eCO2, 560 ppm), ambient nitrogen deposition (aN) or elevated nitrogen deposition (eN) treatments for a decade. There exist antagonistic CO2×N interactions on microbial functional genes associated with C, N, P S cycling processes. More strong antagonistic CO2×N interactions are observed on C degradation genes than other genes. Remarkably antagonistic CO2×N interactions on soil microbial communities could enhance soil C accumulation.
2018-05-01 | GSE98512 | GEO
Project description:Saline-alkaline soil microbial community diversity
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Project description:Anthropogenic nutrient inputs alter soil biodiversity; however, it remains largely unknown whether changes in soil microeukaryotes (fungi and protists) are primarily driven by direct effects, such as modifications in soil properties, or by indirect effects, such as plant diversity loss. To disentangle these mechanisms, we investigated the long-term effects (11 years) of fertilization and manipulated plant diversity (1, 2, or 4 plant species) on soil microeukaryote communities in a temperate grassland experiment using long-amplicon rRNA sequencing. Our results indicate that fertilization generally had a stronger influence on microeukaryote communities than plant species richness. Fertilization altered the community composition of fungi and protists, increased OTU richness by 20.8% and 52.7%, respectively, and shifted community dominance from fungi to protists. Regarding plant diversity, we observed an effect exclusively on the protist community. Changes were primarily explained by increased plant biomass (driven by both fertilization and plant diversity) and by higher soil phosphorus and lower soil pH levels (driven exclusively by fertilization). Regarding life strategies, we observed synergistic treatment effects: fertilization primarily enhanced fungal saprophytes (only richness), fungal animal pathogens, and protist consumers, whereas plant diversity affected phototrophic protists (reduction) and protist animal pathogens (enhancement). Notably, fertilization and plant diversity decline together led to a cumulative increase in fungal plant pathogens. In conclusion, we highlight that fertilisation alone has a significant effect on soil microeukaryotes, while the additional decline in plant diversity affects different soil groups that are not directly affected by fertilisation. This synergistic pattern indicates that fertilization can influence the entire microeukaryote community through direct and indirect mechanisms, with a cumulative enhancement on certain groups, such as plant pathogens.
2026-07-06 | E-MTAB-15101 | biostudies-arrayexpress
Project description:Anthropogenic activities have dramatically increased the inputs of reactive nitrogen (N) into terrestrial ecosystems, with potentially important effects on the soil microbial community and consequently soil C and N dynamics. Our analysis of microbial communities in soils subjected to 14 years of 7 g N m-2 year-1 Ca(NO3)2 amendment in a Californian grassland showed that the taxonomic composition of bacterial communities, examined by 16S rRNA gene amplicon sequencing, was significantly altered by nitrate amendment, supporting the hypothesis that N amendment- induced increased nutrient availability, yielded more fast-growing bacterial taxa while reduced slow-growing bacterial taxa. Nitrate amendment significantly increased genes associated with labile C degradation (e.g. amyA and xylA) but had no effect or decreased the relative abundances of genes associated with degradation of more recalcitrant C (e.g. mannanase and chitinase), as shown by data from GeoChip targeting a wide variety of functional genes. The abundances of most N cycling genes remained unchanged or decreased except for increases in both the nifH gene (associated with N fixation), and the amoA gene (associated with nitrification) concurrent with increases of ammonia-oxidizing bacteria. Based on those observations, we propose a conceptual model to illustrate how changes of functional microbial communities may correspond to soil C and N accumulation.
2017-11-21 | GSE107168 | GEO
Project description:<p>Background</p><p>Soil salinization and alkalization severely threaten soybean growth and yield. Arbuscular mycorrhizal fungi (AMF), specifically Rhizophagus intraradices (Ri), enhance stress tolerance and soil quality, yet their mechanisms in regulating microbial-metabolite interactions during critical soybean growth stages remain unclear.</p><p>Results</p><p>This research employed partitioned (rhizosphere and hyphosphere) pot experiments in natural saline-alkaline soil, integrating high-throughput sequencing and untargeted metabolomics to analyze Ri effects on microbial communities and metabolic functions at branching (V5), pod development (R4), and mature pod (R8) stages. Results revealed V5 stage for Ri to activate host resistance, R4 for hyphal expansion (density 21.13 m/g), enhancing nutrient uptake, and R8 stage for increased spore and glomalin-related soil protein (GRSP) secretion to alleviate stress. Ri differentially regulates bacterial-fungal networks, enriching biomarker and driving stochastic microbial assembly. Ri shifted bacterial assembly toward stochasticity and enriched biomarkers. Bacterial richness peaked under RiRR4 (+Ri, R4 rhizosphere; +27.06% vs CRR4). Fungal assembly showed a different trend, peaking under RiRV5 (+Ri, V5 rhizosphere; +39.75% vs CRV5). Ri enhanced plant resistance and soybean growth via bacterial diversity in rhizosphere soil. Metabolomics identified phenylalanine metabolism as a core Ri-regulated pathway under saline-alkaline stress, facilitating carbon-nitrogen cycling and secondary metabolite accumulation.</p><p>Conclusions</p><p>This research reveals how Ri coordinates microbial and metabolic processes to enhance saline-alkaline resistance in soybean.</p>
2026-01-12 | MTBLS13661 | MetaboLights
Project description:Tibet is one of the most threatened regions by climate warming, thus understanding how its microbial communities function may be of high importance for predicting microbial responses to climate changes. Here, we report a study to profile soil microbial structural genes, which infers functional roles of microbial communities, along four sites/elevations of a Tibetan mountainous grassland, aiming to explore potential microbial responses to climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 4.0, we showed that microbial communities were distinct for most but not all of the sites. Substantial variations were apparent in stress, N and C cycling genes, but they were in line with the functional roles of these genes. Cold shock genes were more abundant at higher elevations. Also, gdh converting ammonium into urea was more abundant at higher elevations while ureC converting urea into ammonium was less abundant, which was consistent with soil ammonium contents. Significant correlations were observed between N-cycling genes (ureC, gdh and amoA) and nitrous oxide flux, suggesting that they contributed to community metabolism. Lastly, we found by CCA, Mantel tests and the similarity tests that soil pH, temperature, NH4+M-bM-^@M-^SN and vegetation diversity accounted for the majority (81.4%) of microbial community variations, suggesting that these four attributes were major factors affecting soil microbial communities. Based on these observations, we predict that climate changes in the Tibetan grasslands are very likely to change soil microbial community functional structure, with particular impacts on microbial N cycling genes and consequently microbe-mediated soil N dynamics. Twelve samples were collected from four elevations (3200, 3400, 3600 and 3800 m) along a Tibetan grassland; Three replicates in every elevation
2013-07-13 | E-GEOD-48820 | biostudies-arrayexpress
Project description:Tibet is one of the most threatened regions by climate warming, thus understanding how its microbial communities function may be of high importance for predicting microbial responses to climate changes. Here, we report a study to profile soil microbial structural genes, which infers functional roles of microbial communities, along four sites/elevations of a Tibetan mountainous grassland, aiming to explore potential microbial responses to climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 4.0, we showed that microbial communities were distinct for most but not all of the sites. Substantial variations were apparent in stress, N and C cycling genes, but they were in line with the functional roles of these genes. Cold shock genes were more abundant at higher elevations. Also, gdh converting ammonium into urea was more abundant at higher elevations while ureC converting urea into ammonium was less abundant, which was consistent with soil ammonium contents. Significant correlations were observed between N-cycling genes (ureC, gdh and amoA) and nitrous oxide flux, suggesting that they contributed to community metabolism. Lastly, we found by CCA, Mantel tests and the similarity tests that soil pH, temperature, NH4+–N and vegetation diversity accounted for the majority (81.4%) of microbial community variations, suggesting that these four attributes were major factors affecting soil microbial communities. Based on these observations, we predict that climate changes in the Tibetan grasslands are very likely to change soil microbial community functional structure, with particular impacts on microbial N cycling genes and consequently microbe-mediated soil N dynamics.
2013-07-13 | GSE48820 | GEO
Project description:integrated soil metagenomics and metaproteomics to study grassland soil microbial communities
2019-03-27 | PXD013110 | Pride