Ontology highlight
ABSTRACT:
PROVIDER: PRJNA908107 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22577100_1.fastq.gz | Fastqsanger.gz | |||
| SRR22577100_2.fastq.gz | Fastqsanger.gz | |||
| SRR22577200_1.fastq.gz | Fastqsanger.gz | |||
| SRR22577200_2.fastq.gz | Fastqsanger.gz | |||
| SRR22577101_1.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: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:Cover Crop Fungal Assemblages Metagenome
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Project description:The rate, timing, and mode of species dispersal is recognized as a key driver of the structure and function of communities of macroorganisms, and may be one ecological process that determines the diversity of microbiomes. Many previous studies have quantified the modes and mechanisms of bacterial motility using monocultures of a few model bacterial species. But most microbes live in multispecies microbial communities, where direct interactions between microbes may inhibit or facilitate dispersal through a number of physical (e.g., hydrodynamic) and biological (e.g., chemotaxis) mechanisms, which remain largely unexplored. Using cheese rinds as a model microbiome, we demonstrate that physical networks created by filamentous fungi can impact the extent of small-scale bacterial dispersal and can shape the composition of microbiomes. From the cheese rind of Saint Nectaire, we serendipitously observed the bacterium Serratia proteamaculans actively spreads on networks formed by the fungus Mucor. By experimentally recreating these pairwise interactions in the lab, we show that Serratia spreads on actively growing and previously established fungal networks. The extent of symbiotic dispersal is dependent on the fungal network: diffuse and fast-growing Mucor networks provide the greatest dispersal facilitation of the Serratia species, while dense and slow-growing Penicillium networks provide limited dispersal facilitation. Fungal-mediated dispersal occurs in closely related Serratia species isolated from other environments, suggesting that this bacterial-fungal interaction is widespread in nature. Both RNA-seq and transposon mutagenesis point to specific molecular mechanisms that play key roles in this bacterial-fungal interaction, including chitin utilization and flagellin biosynthesis. By manipulating the presence and type of fungal networks in multispecies communities, we provide the first evidence that fungal networks shape the composition of bacterial communities, with Mucor networks shifting experimental bacterial communities to complete dominance by motile Proteobacteria. Collectively, our work demonstrates that these strong biophysical interactions between bacterial and fungi can have community-level consequences and may be operating in many other microbiomes.
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Project description:Impacts of cover crop residue management on the arbuscular mycorrhizal fungal communities of maize
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