DOI: 10.5061/dryad.qfttdz0vk
title: Raw data and code for: Arbuscular mycorrhizal fungus alters the phyllosphere microbial community of alfalfa and modifies plant defenses against dual pea aphid and pathogen attack

description: The dataset contains multiple classes of measurements: (i) plant biomass
 traits, including shoot dry weight (g/pot), root dry weight (g/pot), root
 length, and mycorrhizal colonization (%); (ii) disease-related indices,
 including disease incidence (%) and disease index; (iii) plant defense
 parameters, such as activities of POD (peroxidase), SOD (superoxide
 dismutase), PPO (polyphenol oxidase), as well as concentrations of JA
 (jasmonic acid), SA (salicylic acid), and TI (trypsin inhibitor); and (iv)
 microbial community diversity indices, including Chao1 richness, Shannon
 diversity, Simpson index, and Pielou evenness for both fungi and bacteria.
description: # Raw data and code for: Arbuscular mycorrhizal fungus alters the
 phyllosphere microbial community of alfalfa and modifies plant defenses
 against dual pea aphid and pathogen attack Dataset DOI:
 [10.5061/dryad.qfttdz0vk](10.5061/dryad.qfttdz0vk) ## Description of the
 data and file structure This dataset originates from a greenhouse
 experiment investigating how **arbuscular mycorrhizal fungi (AMF)**
 influence the **phyllosphere microbial community of alfalfa** and modulate
 **plant defenses** against **pea aphid and pathogen attack**. The data
 include plant growth measurements, disease assessments, AMF colonization,
 enzyme activities, plant hormone levels, protease inhibitor levels, and
 microbial alpha diversity indices. Additional files contain pyllosphere
 microbiome rawdata for statistical analysis. * **Treatment groups**: *
 **NM**: No AMF, no aphid, no pathogen * **NMA**: No AMF + aphid * **NMP**:
 No AMF + pathogen * **NMAP**: No AMF + aphid + pathogen * **AM**: AMF only
 * **AMA**: AMF + aphid * **AMP**: AMF + pathogen * **AMAP**: AMF + aphid +
 pathogen * **Plant growth and disease**: * *Shoot dry weight (g/pot)*:
 Aboveground biomass * *Root dry weight (g/pot)*: Belowground biomass *
 *Disease incidence (%)*: Percentage of diseased plants * *Disease index*:
 Composite index of disease severity * *Mycorrhizal colonization (%)*:
 Proportion of roots colonized by AMF * *Root length*: Total root length
 (cm) * **Defense enzymes and hormones**: * *POD, SOD, PPO*: Antioxidant
 and defense-related enzyme activities * *JA*: Jasmonic acid content *
 *SA*: Salicylic acid content * *TI*: Trypsin inhibitor activity *
 **Microbial community indices**: * *Fungi/Bacteria Chao1*: Richness
 estimator * *Fungi/Bacteria Shannon*: Diversity index * *Fungi/Bacteria
 Simpson*: Dominance index * *Fungi/Bacteria Pielou*: Evenness index 
 
 ## Analysis workflow 1. **Alpha diversity** * Calculation of Chao1,
 Shannon, Simpson, Pielou, and Good’s coverage using `vegan`. 2. **Beta
 diversity** * Bray–Curtis distance matrix and PCoA visualization. * Group
 comparison via PERMANOVA (`adonis2`). 3. **Differential abundance
 (DESeq2)** * Normalization and statistical testing of OTU counts. *
 Identification of significantly enriched taxa. 4. **Co-occurrence
 network** * Spearman correlation among OTUs (`psych`, `Hmisc`). * Network
 construction with `igraph` (GraphML export). 5. **Random forest analysis**
 * Classification of treatments using OTU features. * Ranking of important
 OTUs (`%IncMSE`). 6. **Structural Equation Modeling (SEM)** * Piecewise
 SEM analysis linking AMF, aphids, pathogen, plant hormones, enzymes, and
 microbial diversity (`piecewiseSEM`). The following R packages are
 required: * `vegan` (alpha and beta diversity, PERMANOVA) * `ggplot2`
 (visualization) * `DESeq2` (differential abundance analysis) * `igraph`
 (co-occurrence network) * `psych`, `Hmisc` (correlation analysis) *
 `randomForest`, `rfPermute` (random forest analysis) * `piecewiseSEM`
 (structural equation modeling) ### Files and variables #### File: code.txt
 **Description:** R script containing the code used for statistical
 analyses. #### File: Functional_ecology-data.xlsx **Description:** Excel
 spreadsheet containing the experimental dataset. Each row corresponds to
 an individual replicate, and each column represents a measured variable,
 including plant growth traits (shoot/root dry weight, root length,
 mycorrhizal colonization), disease indices (incidence, index), plant
 defense parameters (POD, SOD, PPO, JA, SA, TI), and microbial diversity
 indices (Chao1, Shannon, Simpson, Pielou for both fungi and bacteria). ##
 Code/software R (version ≥ 4.0.0) ## Access information Other publicly
 accessible locations of the data: * NCBI Sequence Read Archive under
 accession number PRJNA1055717 and PRJNA1303415.