Soil metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA503856 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8355010.fastq.gz | Fastqsanger.gz | |||
| SRR8355020.fastq.gz | Fastqsanger.gz | |||
| SRR8355030.fastq.gz | Fastqsanger.gz | |||
| SRR8355040.fastq.gz | Fastqsanger.gz | |||
| SRR8355050.fastq.gz | Fastqsanger.gz |
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Project description:Cover cropping is an effective method to protect agricultural soils from erosion, promote nutrient and moisture retention, encourage beneficial microbial activity, and maintain soil structure. Reusing winter cover crop root channels with the maize roots during the summer allows the cash crop to extract resources from farther niches in the soil horizon. In this study, we investigate how reusing winter cover crop root channels to grow maize (Zea mays L.) affects the composition and function of the bacterial communities in the rhizosphere using 16S rRNA gene amplicon sequencing and metaproteomics. We discovered that the bacterial community significantly differed among cover crop variations, soil profile depths, and maize growth stages. Re-usage of the root channels increased bacterial abundance, and it further increases as we elevate the complexity from monocultures to mixtures. Upon mixing legumes with brassicas and grasses, the overall expression of several steps of the carbon cycle (C) and the nitrogen cycle (N) improved. The deeper root channels of legumes and brassicas compared to grasses correlated with higher bacterial 16S rRNA gene copy numbers and community roles in the respective variations in the subsoil regimes due to the increased availability of root exudates secreted by maize roots. In conclusion, root channel re-use (monocultures and mixtures) improved the expression of metabolic pathways of the important C and N cycles, and the bacterial communities, which is beneficial to the soil rhizosphere as well as to the growing crops.
2025-05-02 | PXD046832 | Pride
Project description:Fire disturbances are becoming more common, more intense, and further-reaching across the globe, with consequences for ecosystem functioning. Importantly, fire can have strong effects on the soil microbiome, including community and functional changes after fire, but surprisingly little is known regarding the role of soil fire legacy in shaping responses to recent fire. To address this gap, we conducted a manipulative field experiment administering fire across 32 soils with varying fire legacies, including combinations of 1-7 historic fires and 1-33 years since most recent fire. We analyzed soil metatranscriptomes, determining for the first time how fire and fire legacy interactively affect metabolically-active soil taxa, the microbial regulation of important carbon (C), nitrogen (N) and phosphorus (P) cycling, expression of carbohydrate-cycling enzyme pathways, and functional gene co-expression networks. Experimental fire strongly downregulated fungal activity while upregulating many bacterial and archaeal phyla. Further, fire decreased soil capacity for microbial C and N cycling and P transport, and drastically rewired functional gene co-expression. Perhaps most importantly, we highlight a novel role of soil fire legacy in regulation of microbial C, N, and P responses to recent fire. We observed a greater number of functional genes responsive to the interactive effects of fire and fire legacy than those affected solely by recent fire, indicating that many functional genes respond to fire only under certain fire legacy contexts. Therefore, without incorporating fire legacy of soils, studies will miss important ways that fire shapes microbial roles in ecosystem functioning. Finally, we showed that fire caused significant downregulation of carbon metabolism and nutrient cycling genes in microbiomes under abnormal soil fire histories, producing a novel warning for the future: human manipulation of fire legacies, either indirectly through global change-induced fire intensification or directly through fire suppression, can negatively impact soil microbiome functional responses to new fires.
2024-08-12 | GSE274211 | GEO
Project description:Soil transplant serves as a proxy to simulate climate change in realistic climate regimes. Here, we assessed the effects of climate warming and cooling on soil microbial communities, which are key drivers in Earth’s biogeochemical cycles, four years after soil transplant over large transects from northern (N site) to central (NC site) and southern China (NS site) and vice versa. Four years after soil transplant, soil nitrogen components, microbial biomass, community phylogenetic and functional structures were altered. Microbial functional diversity, measured by a metagenomic tool named GeoChip, and phylogenetic diversity are increased with temperature, while microbial biomass were similar or decreased. Nevertheless, the effects of climate change was overridden by maize cropping, underscoring the need to disentangle them in research. Mantel tests and canonical correspondence analysis (CCA) demonstrated that vegetation, climatic factors (e.g., temperature and precipitation), soil nitrogen components and CO2 efflux were significantly correlated to the microbial community composition. Further investigation unveiled strong correlations between carbon cycling genes and CO2 efflux in bare soil but not cropped soil, and between nitrogen cycling genes and nitrification, which provides mechanistic understanding of these microbe-mediated processes and empowers an interesting possibility of incorporating bacterial gene abundance in greenhouse gas emission modeling.
2013-10-30 | GSE51592 | GEO
Project description:<div>Species-rich plant communities can induce unique soil biotic legacy effects through changing the abundance and composition of soil biota. These soil legacy effects can cause feedbacks to influence plant performance. In addition, soil biota can induce (defensive) secondary metabolites in shoots and roots and thus affect plant-herbivore interactions. We hypothesize that plant diversity-driven soil biotic legacy effects elicit changes in the shoot and root metabolome. <br></div><div><br></div><div>We tested this hypothesis by establishing an experiment with four plant species. We grew plants in a sterile substrate inoculated with soil conditioned by different plant species communities: (1) monocultures of either of the four species, (2) the four species in a mixture, (3) an eight species mixture including all four species, or (4) a sterile inoculum. After at least eight weeks in the field, we estimated shoot herbivory. At the same time, we took root and shoot samples for metabolomics analyses by liquid chromatography quadrupole time-of-flight mass spectrometry. <br></div><div><br></div><div>We found that shoot and root metabolomes of all plants grown in sterile soil differed significantly from those grown in living soil. The plant metabolomes in living soils differed by species and tissue. Across all species, shoots displayed a greater richness of secondary metabolites than roots. The richness of secondary metabolites differed by species and among living soils. The conditioning species richness significantly affected the Shannon diversity of secondary metabolites in Centaurea jacea. Shoot herbivory positively correlated with the richness and Shannon diversity of secondary metabolites in Leucanthemum vulgare. We detected multiple metabolites that together explained up to 88% of the variation in herbivory in the shoots of Centaurea jacea and Plantago lanceolata. <br></div><div><br></div><div>Synthesis: Our findings suggest that plant diversity-driven shifts in soil biota elicit changes in the composition and diversity of shoot and root secondary metabolites. However, these plant responses and their effect on shoot herbivores are species-specific. Tracking changes in plant secondary chemistry in response to soil biotic legacy effects will help to understand the mechanisms that govern species-specific plant-plant and plant-herbivore interactions.</div>
2019-05-30 | MTBLS544 | MetaboLights
Project description:Soil transplant serves as a proxy to simulate climate change in realistic climate regimes. Here, we assessed the effects of climate warming and cooling on soil microbial communities, which are key drivers in EarthM-bM-^@M-^Ys biogeochemical cycles, four years after soil transplant over large transects from northern (N site) to central (NC site) and southern China (NS site) and vice versa. Four years after soil transplant, soil nitrogen components, microbial biomass, community phylogenetic and functional structures were altered. Microbial functional diversity, measured by a metagenomic tool named GeoChip, and phylogenetic diversity are increased with temperature, while microbial biomass were similar or decreased. Nevertheless, the effects of climate change was overridden by maize cropping, underscoring the need to disentangle them in research. Mantel tests and canonical correspondence analysis (CCA) demonstrated that vegetation, climatic factors (e.g., temperature and precipitation), soil nitrogen components and CO2 efflux were significantly correlated to the microbial community composition. Further investigation unveiled strong correlations between carbon cycling genes and CO2 efflux in bare soil but not cropped soil, and between nitrogen cycling genes and nitrification, which provides mechanistic understanding of these microbe-mediated processes and empowers an interesting possibility of incorporating bacterial gene abundance in greenhouse gas emission modeling. Fifty four samples were collected from three soil types (Phaeozem,Cambisol,Acrisol) in three sites (Hailun, Fengqiu and Yingtan) along a latitude with reciprocal transplant; Both with and without maize cropping in each site; Three replicates in every treatments.
2013-10-30 | E-GEOD-51592 | biostudies-arrayexpress
Project description:Anthropogenic nitrogen (N) deposition may affect soil organic carbon (SOC) decomposition, thus affecting the global terrestrial carbon (C) cycle. However, it remains unclear how the level of N deposition affects SOC decomposition by regulating microbial community composition and function, especially C-cycling functional genes structure. We investigated the effects of short-term N addition on soil microbial C-cycling functional gene composition, SOC-degrading enzyme activities, and CO2 emission in a 5-year field experiment established in an artificial Pinus tabulaeformis forest on the Loess Plateau, China.
2022-03-01 | GSE147041 | GEO
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.
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Project description:Cropping soils vary in extent of natural suppression of soil-borne plant diseases. However, it is unknown whether similar variation occurs across pastoral agricultural systems. We examined soil microbial community properties known to be associated with disease suppression across 50 pastoral fields varying in management intensity. The composition and abundance of the disease-suppressive community were assessed from both taxonomic and functional perspectives.
2018-03-30 | GSE112489 | GEO
Project description:Plant growth and development depends on the availability of nutrients and water resources in the soil. The increased frequencies of drought events over recent years have affected nutrient availability soil systems. Crops reutilising winter cover crop root channels allows access to resources from distal regions in the soil horizon. However, the availability of information regarding root channel reutilisation under drought, specifically bacterial community structures and functions is unknown. In this study, we observed the changes inflicted by drought on bacterial communities in maize (Zea mays L.) rhizospheres after reusing the winter cover crop root channels. The techniques of 16S rRNA (ribosomal ribonucleic acid) gene-based microbial profiling and metaproteomics were used to study the alterations in biochemical pathways of those communities under drought at three different locations (Hohenschulen, Karkendamm and Reinshof) comprising three different soli types (Luvisol, Podzol and Phaeozem) respectively. Besides the influence of soil properties, we noticed that under drought the relative abundances of Acidobacteriota, Actinomycetota, Planctomycetota, and Pseudomonadota increased, while Chloroflexota, Methylomirabilota, Patescibacterota, and Verrucomicrobiota decreased. At drought-prone soil types Luvisol and Podzol, aerobic communities Pseudomonadota and Verrucomicrobiota increased abundance of the glyoxylate cycle as a means of conserving carbon and energy for plausible survival measures. Higher abundance of catalase-glutathione peroxidase (CAT-PER) through the methionine cycle-transsulfuration pathway possibly alleviate reactive oxygen species (ROS) levels. Overall, bacterial communities in the reused cover crop root channels respond to drought by taking mitigative measures for survival.
2025-09-22 | PXD062138 | Pride
Project description:Soil water repellency (SWR) (i.e. soil hydrophobicity or decreased soil wettability) is a major cause of global soil degradation and a key agricultural concern. This metabolomics data will support the larger effort measuring soil water repellency and soil aggregate formation caused by microbial community composition through a combination of the standard drop penetration test, transmission electron microscopy characterization and physico-chemical analyses of soil aggregates at 6 timepoints. Model soils created from clay/sand mixtures as described in Kallenbach et al. (2016, Nature Communications) with sterile, ground pine litter as a carbon/nitrogen source were inoculated with 15 different microbial communities known to have significantly different compositions based on 16S rRNA sequencing. This data will allow assessment of the direct influence of microbial community composition on soil water repellency and soil aggregate stability, which are main causes of soil degradation.
The work (proposal:https://doi.org/10.46936/10.25585/60001346) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.
2024-02-14 | MSV000094090 | MassIVE