Research ArticlePLANT SCIENCES

Initial soil microbiome composition and functioning predetermine future plant health

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Science Advances  25 Sep 2019:
Vol. 5, no. 9, eaaw0759
DOI: 10.1126/sciadv.aaw0759
  • Fig. 1 Schematic figure of the rhizobox sampling system and the experimental design.

    (A) The rhizobox consisted of a three-layer cylinder with a height of 136 mm and a diameter of 110 mm. The inner layer (root compartment) is made of a 50-μm nylon mesh net, which prevents roots from entering into the middle layer, and the outer layer is made of a 4-mm metal mesh to support the rhizobox. (B) The middle sampling layer consisted of 18 individual nylon mesh bags (150 μm nylon mesh; height, 136 mm; width, 18 to 21 mm; thickness, 1 to 2 mm) containing homogenized and sterilized field soil. The soil in the nylon mesh bags of the middle layer was thus in close contact with plant roots and root exudates and was used as a proxy of rhizosphere bacterial community. (C) The central root compartment was densely colonized by plant roots after 3 weeks of transplantation of tomato seedlings to the field (photo credit: Yian Gu, Nanjing Agricultural University). (D) Initial bulk soil was collected when the experiment was conducted (0 weeks), and three middle-layer nylon bags from each rhizobox were randomly collected at every sampling time point (3, 4, 5, and 6 weeks after planting) to sample the rhizosphere soil.

  • Fig. 2 The outcome of plant-pathogen interaction is associated with the initial soil microbiome composition and functioning.

    (A) The population dynamics of R. solanacearum bacterial pathogen in the rhizosphere of healthy and diseased plants. (B) The initial soil microbiomes associated with healthy and diseased plants were clearly distinct (F1,22 = 2.3, P < 0.001, AMOVA on unweighted UniFrac); the percentage of explained variation is shown on the x and y axes. (C) Differences in the abundances of rare discriminating OTUs (linear discriminant analysis score ≥ 2, fold change ≥ 2, and significance test P < 0.05) in the initial soils (week 0) that later became associated with healthy and diseased plants. P values were calculated using Student’s t test (P < 0.05), and significantly associated phyla are highlighted in bold. (D) Co-occurrence networks of initial microbiomes that later became associated with healthy (left) and diseased plants (right). (E) Potential “driver taxa” behind pathogen suppression based on bacterial network analysis of initial microbiomes that later became associated with healthy and diseased plants. Node sizes are proportional to their scaled NESH (neighbor shift) score (a score identifying important microbial taxa of microbial association networks), and a node is colored red if its betweenness increases when comparing soil microbiomes associated with diseased to healthy plants. As a result, large red nodes denote particularly important driver taxa behind pathogen suppression, and these taxa names are shown in bold. Line colors indicate node (taxa) connections as follows: association present only in healthy plant microbiomes (red edges), association present only in diseased plant microbiomes (green edges), and association present in both healthy and diseased plant microbiomes (blue edges). (F) Distinct functional gene profiles associated with the initial microbiomes of future healthy and diseased plants. (G) The abundance of representative genes related to secondary metabolism synthesis in the initial soil microbiomes of future healthy and diseased plants. (H) The percentage of R. solanacearum pathogen-suppressing Bacillus and Pseudomonas bacteria isolated from the initial soil microbiomes of healthy and diseased plants (pairwise t test, mean ± SD, n = 3; N.S., nonsignificant; *P < 0.05; ***P < 0.001).

  • Fig. 3 Taxonomic and functional differences between healthy and diseased plant microbiomes persist throughout the tomato growth season and can be transferred to the next plant generation via soil transplantation.

    (A) Decay in the phylogenetic distance (unweighted UniFrac distance) between microbiomes associated with healthy and diseased plants. (B) Temporal dynamics of the relative abundance of rare OTUs enriched in the initial microbiomes of healthy and diseased plants. (C) Differences in the abundances of rare discriminating OTUs (linear discriminant analysis score ≥ 2, fold change ≥ 2, and significance test P < 0.05) associated with healthy and diseased plant microbiomes at the end of the experiment (week 6). P values were calculated using Student’s t test (P < 0.05), and significantly associated phyla are highlighted in bold. (D) Co-occurrence networks associated with healthy (left) and diseased plants (right) at the end of the experiment (week 6). (E) Potential driver taxa behind pathogen suppression based on bacterial network analysis of healthy and diseased plant microbiomes at the end of the experiment (week 6). Node sizes are proportional to their scaled NESH score (a score identifying important microbial taxa of microbial association networks), and a node is colored red if its betweenness increases when comparing soil microbiomes associated with diseased to healthy plants. As a result, large red nodes denote particularly important driver taxa behind pathogen suppression, and these taxa names are shown in bold. Line colors indicate node (taxa) connections as follows: association present only in healthy plant microbiomes (red edges), association present only in diseased plant microbiomes (green edges), and association present in both healthy and diseased plant microbiomes (blue edges). (F) Distinct functional gene profiles associated with healthy and diseased plant microbiomes at the end of the experiment (week 6). (G) The abundance of representative genes related to secondary metabolism synthesis of healthy and diseased plant microbiomes at the end of the experiment (week 6). (H) The disease incidence in the second plant generation after transplantation of soil from the first-generation healthy, diseased, or sterilized healthy soil (mean ± SD, n = 4). Different lowercase letters denote significance at P < 0.05 (Duncan’s multiple range test).

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/5/9/eaaw0759/DC1

    Fig. S1. The placement of rhizoboxes and observed disease dynamics during the field experiment.

    Fig. S2. Differences in the physicochemical soil properties, total bacterial abundances, and bacterial diversity between healthy and diseased plants during the field experiment.

    Fig. S3. Relationships between physical distance and bacterial phylogenetic distance (unweighted UniFrac distance) between rhizoboxes within three replicated plots.

    Fig. S4. Differences in the abundances of bacterial phyla in the initial soils (week 0) that later became associated with healthy and diseased plants (week 6).

    Fig. S5. Rare OTUs discriminate the initial soil microbiomes that later become associated with healthy and diseased plants.

    Fig. S6. Ten best discriminant OTUs linked to future plant disease outcomes based on random forest analysis.

    Fig. S7. The total abundance of Bacillus and Pseudomonas bacteria and their ability to inhibit the growth of Ralstonia solanacearum.

    Fig. S8. Differences in bacterial community composition associated with healthy and diseased plants persisted throughout the field experiment.

    Fig. S9. Temporal changes in discriminating rare OTUs observed in the initial microbiomes associated with healthy and diseased plants.

    Fig. S10. Heatmaps showing the dynamics of discriminating rare OTUs associated with healthy and diseased plants during the field experiment.

    Fig. S11. PCoA of Bray-Curtis distances of bacterial functional gene profiles in the beginning (week 0) and at the end of the field experiment (week 6).

    Fig. S12. Comparison of bacterial community between initial bulk soil and 5-day old nylon bag samples.

    Table S1. Physicochemical properties of initial soils that later became associated with healthy and diseased plants.

    Table S2. Topological properties of networks associated with healthy and diseased plant microbiomes at weeks 0 and 6.

    Data file S1. Screened OTUs enriched in initial soil microbiome associated with later healthy and diseased plants.

    Data file S2. Functional genes significantly different in initial soil microbiome associated with later healthy and diseased plants.

    Data file S3. Screened OTUs enriched in soil microbiome associated with later healthy and diseased plants at 6 week after planting.

    Data file S4. Functional genes significantly different in soil microbiome associated with later healthy and diseased plants at 6 weeks after planting.

    Movie S1. Method of sampling middle-layer nylon bags from rhizobox.

  • Supplementary Materials

    The PDF file includes:

    • Fig. S1. The placement of rhizoboxes and observed disease dynamics during the field experiment.
    • Fig. S2. Differences in the physicochemical soil properties, total bacterial abundances, and bacterial diversity between healthy and diseased plants during the field experiment.
    • Fig. S3. Relationships between physical distance and bacterial phylogenetic distance (unweighted UniFrac distance) between rhizoboxes within three replicated plots.
    • Fig. S4. Differences in the abundances of bacterial phyla in the initial soils (week 0) that later became associated with healthy and diseased plants (week 6).
    • Fig. S5. Rare OTUs discriminate the initial soil microbiomes that later become associated with healthy and diseased plants.
    • Fig. S6. Ten best discriminant OTUs linked to future plant disease outcomes based on random forest analysis.
    • Fig. S7. The total abundance of Bacillus and Pseudomonas bacteria and their ability to inhibit the growth of Ralstonia solanacearum.
    • Fig. S8. Differences in bacterial community composition associated with healthy and diseased plants persisted throughout the field experiment.
    • Fig. S9. Temporal changes in discriminating rare OTUs observed in the initial microbiomes associated with healthy and diseased plants.
    • Fig. S10. Heatmaps showing the dynamics of discriminating rare OTUs associated with healthy and diseased plants during the field experiment.
    • Fig. S11. PCoA of Bray-Curtis distances of bacterial functional gene profiles in the beginning (week 0) and at the end of the field experiment (week 6).
    • Fig. S12. Comparison of bacterial community between initial bulk soil and 5-day old nylon bag samples.
    • Table S1. Physicochemical properties of initial soils that later became associated with healthy and diseased plants.
    • Table S2. Topological properties of networks associated with healthy and diseased plant microbiomes at weeks 0 and 6.

    Download PDF

    Other Supplementary Material for this manuscript includes the following:

    • Data file S1 (Microsoft Excel format). Screened OTUs enriched in initial soil microbiome associated with later healthy and diseased plants.
    • Data file S2 (Microsoft Excel format). Functional genes significantly different in initial soil microbiome associated with later healthy and diseased plants.
    • Data file S3 (Microsoft Excel format). Screened OTUs enriched in soil microbiome associated with later healthy and diseased plants at 6 week after planting.
    • Data file S4 (Microsoft Excel format). Functional genes significantly different in soil microbiome associated with later healthy and diseased plants at 6 weeks after planting.
    • Movie S1 (.mp4 format). Method of sampling middle-layer nylon bags from rhizobox.

    Files in this Data Supplement:

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