Infection of <i>Plasmodiophora brassicae</i> changes the fungal endophyte community of tumourous stem mustard roots as revealed by high-throughput sequencing and culture-dependent methods - Fig 5

LefSe analysis (A) The cladogram diagram shows the taxas with marked differences in the two endophyte communities. Red and green indicate different groups, with the classification of taxas at the level of phylum, class, order, family, and genus shown from inside to the outside. The red and green nodes in the phylogenetic tree represent taxas that play an important role in the two endophyte communities, respectively. Yellow nodes represent taxas with no significant difference. (B) Species with the significant difference that have an LDA score higher than the estimated value; the default score is 3.0. The length of the histogram represents the LDA score; i.e., the degree of influence of taxas with a significant difference between different groups. R, healthy roots. C, clubroots.</p

Infection of <i>Plasmodiophora brassicae</i> changes the fungal endophyte community of tumourous stem mustard roots as revealed by high-throughput sequencing and culture-dependent methods - Fig 2

Rarefaction curves (A), Shannon index (B), Simpson index (C) and observed OTUs richness (D) of the endophyte communities associated with the healthy roots and clubroots of tumourous stem mustard infected with P. brassicae. R, healthy roots. C, clubroots. ** differences at 0.01 level.</p

Infection of <i>Plasmodiophora brassicae</i> changes the fungal endophyte community of tumourous stem mustard roots as revealed by high-throughput sequencing and culture-dependent methods - Fig 6

Co-occurrence network analysis of the two endophyte communities within the healthy roots and clubroots of tumourous stem mustard infected with P. brassicae (A) Healthy roots (B) Clubroots. Each node represents taxa affiliated at the OTU level, and the size of the nodes represents an average abundance of OTU. The lines represent the connections between each OTU. A red line indicates a positive correlation. whereas a green line indicates a negative correlation.</p

Infection of <i>Plasmodiophora brassicae</i> changes the fungal endophyte community of tumourous stem mustard roots as revealed by high-throughput sequencing and culture-dependent methods - Fig 3

Relative sequence abundance (%) of the endophyte at phylum (a), genus (B) and Circos figure at the genus level (C) in the healthy roots and clubroots of tumourous stem mustard infected with P. brassicae. R, healthy roots. C, clubroots.</p

Infection of <i>Plasmodiophora brassicae</i> changes the fungal endophyte community of tumourous stem mustard roots as revealed by high-throughput sequencing and culture-dependent methods - Fig 1

Healthy roots and clubroots of tumourous stem mustard caused by the infection of P. brassicae. (A) roots of a healthy plant (left) and a diseased plant (right) (B) resting spores (pots) in the root cells of cluboorts coloured with fast green (C) the cell of healthy roots.</p

Infection of <i>Plasmodiophora brassicae</i> changes the fungal endophyte community of tumourous stem mustard roots as revealed by high-throughput sequencing and culture-dependent methods - Fig 4

Hierarchical clustering analysis (A), UniFrac-weighted PCA (B), PCoA (C) and ANOSIM (D) of the endophyte communities associated with the healthy roots and clubroots of tumourous stem mustard infected with P. brassicae. R, healthy roots. C, clubroots.</p

Infection of <i>Plasmodiophora brassicae</i> changes the fungal endophyte community of tumourous stem mustard roots as revealed by high-throughput sequencing and culture-dependent methods - Fig 7

The endophytic fungi isolated from the clubroots (A) and healthy roots (B) by the culture-dependent method.</p

Additional file 11: Table S8. of Genome-wide analysis of microRNA targeting impacted by SNPs in cucumber genome

The primers for amplifying precursor sequences of miRNA genes. (XLSX 18 kb

Table_1_A root-knot nematode effector manipulates the rhizosphere microbiome for establishing parasitism relationship with hosts.DOCX

IntroductionRoot-knot nematode (RKN; Meloidogyne spp.) is one of the most infamous soilborne plant diseases, causing severe crop losses every year. Effector proteins secreted by RKNs play crucial roles during plant-nematode interaction. However, less is known about whether RKN effector proteins can impact the rhizosphere microbial environment.MethodsIn this study, we investigated the rhizosphere microbiome community of MiMIF-2 (a plant immunity-modulating effector) transgenic Arabidopsis thaliana with or without nematode infection using the Illumina high-throughput sequencing analysis.Results and discussionThe results showed that the bacterial species richness index increased, while the fungi species richness index decreased in M. incognita-infected MiMIF-2 transgenic A. thaliana plants. The relative abundance of genera such as Clitopilus, Komagataeibacter, Lactobacillus, Prevotella, Moritella, Vibrio, Escherichia-Shigella, and Pseudomonas was reduced in MiMIF-2 transgenic A. thaliana plants compared to wild type, but was significantly increased after inoculation with M. incognita. The Cluster of Orthologous Genes (COG) function classification analysis revealed a decrease in the relative abundance of defense mechanisms, secondary metabolite biosynthesis, transport, and nematode infection catabolism-related functions in MiMIF-2 lines compared to the wild type. These differences may be the reason for the increased susceptibility of MiMIF-2 transgenic A. thaliana to nematode infection. Our results provide a new insight into RKN effector proteins and their association with the microbial community, host, and plant pathogens, which will lead to the exploration of new innovative ideas for future biological control of RKNs.</p

DataSheet_1_Variation and stability of rhizosphere bacterial communities of Cucumis crops in association with root-knot nematodes infestation.docx

IntroductionRoot-knot nematodes (RKN) disease is a devastating disease in Cucumis crops production. Existing studies have shown that resistant and susceptible crops are enriched with different rhizosphere microorganisms, and microorganisms enriched in resistant crops can antagonize pathogenic bacteria. However, the characteristics of rhizosphere microbial communities of Cucumis crops after RKN infestation remain largely unknown.MethodsIn this study, we compared the changes in rhizosphere bacterial communities between highly RKN-resistant Cucumis metuliferus (cm3) and highly RKN-susceptible Cucumis sativus (cuc) after RKN infection through a pot experiment. ResultsThe results showed that the strongest response of rhizosphere bacterial communities of Cucumis crops to RKN infestation occurred during early growth, as evidenced by changes in species diversity and community composition. However, the more stable structure of the rhizosphere bacterial community in cm3 was reflected in less changes in species diversity and community composition after RKN infestation, forming a more complex and positively co-occurrence network than cuc. Moreover, we observed that both cm3 and cuc recruited bacteria after RKN infestation, but the bacteria enriched in cm3 were more abundant including beneficial bacteria Acidobacteria, Nocardioidaceae and Sphingomonadales. In addition, the cuc was enriched with beneficial bacteria Actinobacteria, Bacilli and Cyanobacteria. We also found that more antagonistic bacteria than cuc were screened in cm3 after RKN infestation and most of them were Pseudomonas (Proteobacteria, Pseudomonadaceae), and Proteobacteria were also enriched in cm3 after RKN infestation. We hypothesized that the cooperation between Pseudomonas and the beneficial bacteria in cm3 could inhibit the infestation of RKN.DiscussionThus, our results provide valuable insights into the role of rhizosphere bacterial communities on RKN diseases of Cucumis crops, and further studies are needed to clarify the bacterial communities that suppress RKN in Cucumis crops rhizosphere.</p