Data for: Agricultural intensification reduces selection of putative plant growth-promoting rhizobacteria in wheat

Data and Resources

This Dataset is currently private and won't be accessible to anyone outside the organization. If you want to publish this dataset, please send an email to data.stewards@rothamsted.ac.uk

Cite this as

Retrieved: 21:29 22 Nov 2024 (UTC)
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Abstract

This repository contains all the data files used and generated for the analysis in Reid et al., 2024.

## QIIME2 Output
The following files are from the QIIME2 output, separated into culture-independent (CI) and culture-dependent (CD) amplicon sequence analyses. Text files include amplicon sequence variant (ASV) abundances and corresponding taxonomic classification (SILVA138). Newick format files contain the rooted phylogenetic tree. Import these files into R to create a phyloseq object with corresponding sample data.

### Culture-Dependent (CD)
- `asv_abundances_CD.txt`
- `asv_taxonomy_CD.txt`
- `tree_CD.nwk`
- `sample_data_CD.txt`

### Culture-Independent (CI)
- `asv_abundances_CI.txt`
- `asv_taxonomy_CI.txt`
- `tree_CI.nwk`
- `sample_data_CI.txt`

## Filtered Phyloseq Objects

The following files contain final, filtered phyloseq objects that can be directly imported into R:
- `phyloseq_CI.rds`
- `phyloseq_CD.rds`

## Normalized Abundance
The following file contains a phyloseq object with ASV abundances normalized by DESeq VST:
- `phyloseq_CI_norm.rds`

## Miscellaneous
- `wheat_pheno_data.csv`: Phenotypic data for sampled wheat plants.
- `functional_bioassay_abundance.csv`: Abundance information for rhizobacterial isolates tested for plant growth-promoting traits.

## Prism Files

The following files include analysis and final figures generated in Graphpad Prism and can only be opened with the Prism application ([Download Prism](https://www.graphpad.com/features)):

- `Figure1.prism`
- `Figure2.pzfx`
- `Figure3.prism`
- `Figure4.prism`
- `Figure5.pzfx`
- `Wheat_pheno_graphs.prism`

Methods

QIIMI2 was used to analyse the amplicon sequence data. QIIMI2 is a is a microbiome multi-omics bioinformatics and data science platform.
GraphPrism was used to generate the analysis and final figure files.
Soil sample was collected from Woburn, Stackyard bare-fallow soil mine (latitude: 52°00′04.3"N, 0°36′49.0"W). This is located at the Rothamsted Research experimental farm, UK.
Several Triticum aestivum cultivars (Avalon, Cadenza, Chidham, Crusoe, Red Lammas, Gallant, Hereward, Malacca, and Victor), 2 wild grasses (Aegilops speltoides and Aegilops tauschii) and other wheat species (T.carthilicum, T.dicoccoides, T.macha, T.monococcum, T.polonicum, T.spelta, T.turanicum and T.urartu) were phenotyped. Plant height, ear length, dry weight and weeks to flowering were recorded.
R package Phyloseq was used to construct the phylogentic tree.
The functional bioassay abundance tested for the ability of the rhizobacteria to solubilize casein, phosphate, potassium, iron, and zinc as described by https://doi.org/10.3389/fmicb.2021.642587.

Technical Information

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Funder Information
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Private Information
Responsible Person Tim Mauchline
Research Infrastructure Used Harpenden & Brooms Barn Farms,Harpenden & Brooms Barn Farms
Data Locations Rothamsted Research shared drives
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