Computational protocol: Suppression of Fusarium wilt of cucumber by ammonia gas fumigation via reduction of Fusarium population in the field

Similar protocols

Protocol publication

[…] Sequences were processed using the RDPipeline initial process to assemble paired-end reads and to remove low quality (Q score < 25) and short reads ( <220 bp). Chimera reads were removed through UCHIME running in de novo mode. Singletons were filtered and all samples were rarefied to the same number of reads as the sample with the lowest reads (32,427 reads per sample). Singletons were defined where only one sequence was present among all samples. [...] Fungal alpha-diversity (Chao1 estimator and Shannon diversity) indices were calculated based on the rarefied OTU table. Principle component analysis (PCA) was performed to examine beta-diversities (Bray-Curtis distances) between individual samples. Permutational multivariate analyses of variance (PERMANOVA) was used to determine the significance of community composition differences between treatments. Multiple regression tree (MRT) analysis was conducted to evaluate the effects of F treatment and time × crop growth stage on the whole soil fungal community. Permutational analysis of multivariate dispersions (PERMDISP) was applied to evaluate the significant differences in replicate dispersion among samples. Similarity percentage (SIMPER) analysis was performed to elucidate the indicator genera to the overall Bray-Curtis distances between treatments.Statistical analysis was performed using IBM SPSS statistics Version 20 (IBM Corporation, New York, United States), and complementary calculations were carried out in Microsoft Excel 2003. Two-tailed unpaired t-tests were used to compare the disease incidence and cucumber yield between CK and F treatments. Pearson correlations were performed to examine the relationships between fungal population, Fusarium abundance and Fusarium population and disease incidence as well as cucumber yield. For each variable measured in the soil, the data were analyzed by one-way ANOVA using Tukey’s HSD test (p < 0.05). […]

Pipeline specifications

Software tools RDPipeline, UCHIME, SPSS
Applications Miscellaneous, 16S rRNA-seq analysis
Organisms Cucumis sativus, Fusarium oxysporum, Fungi
Chemicals Ammonia