Project description:Earthworms enhance plant growth but the precise mechanism by which this occurs is not known. An understanding of the mechanism could potentially support changes in agricultural management reducing fertiliser usage and therefore costs and the carbon footprint of agriculture. We conducted a factorial experiment in which 5 strains of wheat were grown in the presence and absence of earthworms under regular watering and droughted conditions. The different wheat strains all responded in a similar fashion. Plant biomass was greater in the presence of earthworms and under regular watering. The presence of earthworms reduced the impact of drought on plant biomass and also slowed down the rate of drying of the droughted soils. Plant nutrient content (N, P, Si) showed no consistent pattern with treatments but total N, P and Si mirrored plant biomass and decreased in the order earthworm-present watered > earthworm-present droughted > earthworm-absent watered > earthworm-absent droughted. Nutrient availability in the soil, as assessed by chemical extractions showed no consistent pattern with treatments. Differential gene expression of plants was greater between watering treatments than between earthworm treatments. Genes that were differentially expressed between the earthworm treatments predominantly related to plant defences, abiotic stress and control of plant growth though a couple were linked to both nitrogen cycling and stress responses. The soil microbiome of the earthworm-present treatments was more associated with nutrient-rich environments, the promotion of plant growth and the suppression of plant pathogens. Our data suggest that enhanced plant growth was due to changes in the microbiome due to earthworm processing of the soil rather than changes in nutrient availability due to the presence of earthworms.

2025-03-03 | GSE214932 | GEO

RNA-Seq Analysis to confirm Different Transcriptomic Profiles of Soil-Derived Functional Module Consortia.

Project description:Purpose: Deconstructing the soil microbiome into reduced-complexity functional modules represents a novel method of microbiome analysis. The goals of this study are to confirm differences in transcriptomic patterns among five functional module consortia. Methods: mRNA profiles of 3 replicates each of functional module enrichments of soil inoculum in M9 media with either 1) xylose, 2) n-acetylglucosamine, 3) glucose and gentamycin, 4) xylan, or 5) pectin were generated by sequencing using an Illumina platform (GENEWIZ performed sequencing). Sequence reads that passed quality filters were aligned to a soil metagenome using Burrows Wheeler Aligner. Resulting SAM files were converted to raw reads using HTSeq, and annotated using Uniref90 or EGGNOG databases. Results: To reduce the size of the RNA-Seq counts table and increase its computational tractability, transcripts containing a minimum of 75 total counts, but no more than 3 zero counts, across the 15 samples were removed. The subsequent dataset was normalized using DESeq2, resulting in a dataset consisting of 6947 unique transcripts across the 15 samples, and 185,920,068 reads. We identified gene categories that were enriched in a sample type relative to the overall dataset using Fisher’s exact test. Conclusions: our dataset confirms that the functional module consortia generated from targeted enrichments of a starting soil inoculum had distinct functional trends by enrichment type.

2020-01-14 | GSE143587 | GEO

earthworm and soil

Project description:earthworm and soil

| PRJNA914475 | ENA

earthworm gut

Project description:earthworm gut metagenomes Raw sequence reads

| PRJNA782213 | ENA

earthworm gut content

Project description:earthworm gut content Raw sequence reads

| PRJNA847348 | ENA