91Lu/Soil-suppressive-of-banana-root-knot-nematode: Siderophore-producing Bacillus and free-living nematodes mediate soil suppressiveness to banana root-knot nematodes

Description : 📄 Overview This release contains the R scripts and source data necessary to reproduce the statistical analyses and figures presented in the manuscript: Title: Soil suppressiveness to root-knot nematode in banana is associated with enrichment of free-living nematodes and siderophore-producing Bacillus under continuous cropping Authors: Qiaofang Lu, Kunguang Wang, Shaohua Gu, et al. Journal: Nature Communications 📊 Contents The code in this repository covers the following analyses described in the study: Field Data Analysis: Processing of disease incidence, gall index, and soil nematode abundance across 11 years of continuous banana cropping. Nematode Community Analysis: Calculation of Shannon diversity indices, PCoA based on Bray-Curtis distances, and trophic group abundance (Bacterivores, Fungivores, Plant-parasites, Omnivores-predators). Rhizosphere Microbiome Analysis: Analysis of 16S rRNA (bacteria) and 18S rRNA (nematode) amplicon sequencing data, including alpha/beta diversity and taxonomic classification. Network & Indicator Analysis: Co-occurrence network construction to identify ecological clusters (Modules 1 & 2). Indicator species analysis and Likelihood Ratio Tests (LRTs) to pinpoint key taxa (e.g., ASV1467 Bacillus velezensis). Machine Learning: Random Forest regression models to predict Meloidogyne abundance based on microbial ASVs. Full Changelog: https://github.com/91Lu/Soil-suppressive-of-banana-root-knot-nematode/commits/v1.0.0