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Lei Cai
Institute of Microbiology Chinese Academy of Sciences
Corresponding Author
ORCiD: https://orcid.org/0000-0002-8131-7274
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Background: Plant microbiome is an integral part of the host influencing its growth and health. The increasing evidence indicates that plant rhizosphere may recruit beneficial microbes to suppress soil-borne pathogen, but the ecological mechanisms that govern plant microbiome assembly and functions under disease in both below and aboveground compartments are not fully understood. Here we examined both bacterial and fungal communities from soils (rhizosphere and bulk soil) and multiple plant compartments (e.g. root, stem, and fruit) of chili pepper (Capsicum annuum L.) at two pepper production sites, and explored how Fusarium wilt disease (FWD) affect the assembly, co-occurrence patterns, and ecological functions of plant-associated microbiomes.
Results: Our data demonstrated that FWD had less impact on reproductive organ (fruit) than on vegetative organs (root and stem), with the strongest impact in the stem upper epidermis. Fungal intra-kingdom networks presented lower stabilities and their communities were more sensitive to FWD than the bacterial communities. Moreover, the diseased pepper was more susceptible to colonization by other pathogenic fungi, but they may recruit potential beneficial bacteria to facilitate host or offspring survival, and FWD may enhance the ecological importance of fungal taxa in the interkingdom network. Further, metagenomic analysis revealed that several potential protective functional genes encoding detoxify and biofilm formation were significantly enriched in the diseased pepper.
Conclusion: Together, these results significantly advance our understanding of pepper microbiome assembly and functions under biotic stress. Our work highlights the diseased plant and the aboveground compartments harbor a potential of beneficial microbiomes and functions that, in concert, can provide potential critical data for harnessing the plant microbiome for sustainable agriculture.
Keywords
Fusarium wilt disease, compartments, microbiome assembly, microbial network, beneficial microbes, metagenomics, chilli pepper
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This is a list of supplementary files associated with this preprint. Click to download.
- SupplementaryInformation.docx
Additional file 1: Fig S1. Pathogen isolation and pathogenicity test. Fig S2. Samples were divided into different compartments for preparing of DNA extraction. Fig S3. NMDS of bacterial communities in soil, root, stem, and fruit. Fig S4. NMDS of fungal communities in soil, root, stem, and fruit. Fig S5. Changes of alpha diversity and taxonomic composition. Fig S6. The different species between healthy and diseased plant. Fig S7. Interkingdom co-occurrence networks in different organs. Fig S8. Changes of different functional profiles. Table S1. Primers information of 16S and ITS rRNA amplicon sequencing. Table S2. PERMANOVA by Adonis of all 16S and ITS rRNA samples. Table S3. PERMANOVA by Adonis of 16S rRNA conducted separately for each compartment. Table S4. PERMANOVA by Adonis of ITS rRNA conducted separately for each compartment. Table S5. Linear-mixed model for bacterial and fungal alpha diversity. Table S6. Distance to centroid using Bray-Curtis dissimilarity. Table S7. Linear-mixed model for bacterial phylum and fungal class composition. Table S8. The taxonomic characteristics of intra- and interkingdom networks. Table S9. The taxonomic composition of bacterial phylum and fungal class between healthy and diseased intra-kingdom networks. Table S10. The taxonomic position of top 10 hub ZOTUs in intra- and interkingdom networks. Table S11. Numbers of different functions calculated by the LEfSe difference analysis. Table S12. Description of different functions calculated by the LEfSe difference analysis.
- SupplementaryInformation.docx
Additional file 1: Fig S1. Pathogen isolation and pathogenicity test. Fig S2. Samples were divided into different compartments for preparing of DNA extraction. Fig S3. NMDS of bacterial communities in soil, root, stem, and fruit. Fig S4. NMDS of fungal communities in soil, root, stem, and fruit. Fig S5. Changes of alpha diversity and taxonomic composition. Fig S6. The different species between healthy and diseased plant. Fig S7. Interkingdom co-occurrence networks in different organs. Fig S8. Changes of different functional profiles. Table S1. Primers information of 16S and ITS rRNA amplicon sequencing. Table S2. PERMANOVA by Adonis of all 16S and ITS rRNA samples. Table S3. PERMANOVA by Adonis of 16S rRNA conducted separately for each compartment. Table S4. PERMANOVA by Adonis of ITS rRNA conducted separately for each compartment. Table S5. Linear-mixed model for bacterial and fungal alpha diversity. Table S6. Distance to centroid using Bray-Curtis dissimilarity. Table S7. Linear-mixed model for bacterial phylum and fungal class composition. Table S8. The taxonomic characteristics of intra- and interkingdom networks. Table S9. The taxonomic composition of bacterial phylum and fungal class between healthy and diseased intra-kingdom networks. Table S10. The taxonomic position of top 10 hub ZOTUs in intra- and interkingdom networks. Table S11. Numbers of different functions calculated by the LEfSe difference analysis. Table S12. Description of different functions calculated by the LEfSe difference analysis.
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This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Research
Lei Cai
Institute of Microbiology Chinese Academy of Sciences
Corresponding Author
ORCiD: https://orcid.org/0000-0002-8131-7274
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Complete author information
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CURRENT STATUS: Posted
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Posted 25 Nov, 2020
No community comments so far
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Subject Areas
General Microbiology
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: Plant microbiome is an integral part of the host influencing its growth and health. The increasing evidence indicates that plant rhizosphere may recruit beneficial microbes to suppress soil-borne pathogen, but the ecological mechanisms that govern plant microbiome assembly and functions under disease in both below and aboveground compartments are not fully understood. Here we examined both bacterial and fungal communities from soils (rhizosphere and bulk soil) and multiple plant compartments (e.g. root, stem, and fruit) of chili pepper (Capsicum annuum L.) at two pepper production sites, and explored how Fusarium wilt disease (FWD) affect the assembly, co-occurrence patterns, and ecological functions of plant-associated microbiomes.
Results: Our data demonstrated that FWD had less impact on reproductive organ (fruit) than on vegetative organs (root and stem), with the strongest impact in the stem upper epidermis. Fungal intra-kingdom networks presented lower stabilities and their communities were more sensitive to FWD than the bacterial communities. Moreover, the diseased pepper was more susceptible to colonization by other pathogenic fungi, but they may recruit potential beneficial bacteria to facilitate host or offspring survival, and FWD may enhance the ecological importance of fungal taxa in the interkingdom network. Further, metagenomic analysis revealed that several potential protective functional genes encoding detoxify and biofilm formation were significantly enriched in the diseased pepper.
Conclusion: Together, these results significantly advance our understanding of pepper microbiome assembly and functions under biotic stress. Our work highlights the diseased plant and the aboveground compartments harbor a potential of beneficial microbiomes and functions that, in concert, can provide potential critical data for harnessing the plant microbiome for sustainable agriculture.
Figure 1
Figure 1
Figure 2
Figure 2
Figure 3
Figure 3
Figure 4
Figure 4
Figure 5
Figure 5
This is a list of supplementary files associated with this preprint. Click to download.
- SupplementaryInformation.docx
Additional file 1: Fig S1. Pathogen isolation and pathogenicity test. Fig S2. Samples were divided into different compartments for preparing of DNA extraction. Fig S3. NMDS of bacterial communities in soil, root, stem, and fruit. Fig S4. NMDS of fungal communities in soil, root, stem, and fruit. Fig S5. Changes of alpha diversity and taxonomic composition. Fig S6. The different species between healthy and diseased plant. Fig S7. Interkingdom co-occurrence networks in different organs. Fig S8. Changes of different functional profiles. Table S1. Primers information of 16S and ITS rRNA amplicon sequencing. Table S2. PERMANOVA by Adonis of all 16S and ITS rRNA samples. Table S3. PERMANOVA by Adonis of 16S rRNA conducted separately for each compartment. Table S4. PERMANOVA by Adonis of ITS rRNA conducted separately for each compartment. Table S5. Linear-mixed model for bacterial and fungal alpha diversity. Table S6. Distance to centroid using Bray-Curtis dissimilarity. Table S7. Linear-mixed model for bacterial phylum and fungal class composition. Table S8. The taxonomic characteristics of intra- and interkingdom networks. Table S9. The taxonomic composition of bacterial phylum and fungal class between healthy and diseased intra-kingdom networks. Table S10. The taxonomic position of top 10 hub ZOTUs in intra- and interkingdom networks. Table S11. Numbers of different functions calculated by the LEfSe difference analysis. Table S12. Description of different functions calculated by the LEfSe difference analysis.
- SupplementaryInformation.docx
Additional file 1: Fig S1. Pathogen isolation and pathogenicity test. Fig S2. Samples were divided into different compartments for preparing of DNA extraction. Fig S3. NMDS of bacterial communities in soil, root, stem, and fruit. Fig S4. NMDS of fungal communities in soil, root, stem, and fruit. Fig S5. Changes of alpha diversity and taxonomic composition. Fig S6. The different species between healthy and diseased plant. Fig S7. Interkingdom co-occurrence networks in different organs. Fig S8. Changes of different functional profiles. Table S1. Primers information of 16S and ITS rRNA amplicon sequencing. Table S2. PERMANOVA by Adonis of all 16S and ITS rRNA samples. Table S3. PERMANOVA by Adonis of 16S rRNA conducted separately for each compartment. Table S4. PERMANOVA by Adonis of ITS rRNA conducted separately for each compartment. Table S5. Linear-mixed model for bacterial and fungal alpha diversity. Table S6. Distance to centroid using Bray-Curtis dissimilarity. Table S7. Linear-mixed model for bacterial phylum and fungal class composition. Table S8. The taxonomic characteristics of intra- and interkingdom networks. Table S9. The taxonomic composition of bacterial phylum and fungal class between healthy and diseased intra-kingdom networks. Table S10. The taxonomic position of top 10 hub ZOTUs in intra- and interkingdom networks. Table S11. Numbers of different functions calculated by the LEfSe difference analysis. Table S12. Description of different functions calculated by the LEfSe difference analysis.
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