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. 2022 Oct 26:13:981615.
doi: 10.3389/fmicb.2022.981615. eCollection 2022.

Rhizospheric microbial consortium of Lilium lancifolium Thunb. causes lily root rot under continuous cropping system

Liangliang Dai  1 , Sunil K Singh  2 , Hao Gong  1 , Yuanyuan Tang  1 , Zhigang Peng  1 , Jun Zhang  1 , Dousheng Wu  3 , Huiming Zhang  2 , Danxia He  2   4
Affiliations

Rhizospheric microbial consortium of Lilium lancifolium Thunb. causes lily root rot under continuous cropping system

Liangliang Dai et al. Front Microbiol. .

Abstract

Tiger lily (Lilium lancifolium Thunb.) is a cash crop with a long history of cultivation in China. Its roots have long been used as a valuable component of Chinese medicine. Continuous cropping, the conventional planting approach for tiger lily, often leads to severe root rot disease, but it is not yet clear how this planting method leads to root rot. In this study, we analyzed the rhizosphere microbiome and predicted microbial protein function in tiger lily planted with the continuous cropping method in three different geological types of soil. In order to explore the specific rhizosphere microbiota triggering root rot disease, tiger lily was compared to maize grown in a similar system, which showed no disease development. An analysis of the chemical elements in the soil revealed that the Pseudomonas and Streptomyces genera, with pathogenic functions, were dominant in the tiger lily rhizosphere. The lower soil pH of tiger lily compared to maize supports the accumulation of pathogenic bacteria in the tiger lily rhizosphere. Meanwhile, we discovered that bacteria of the Flavobacterium genus, with their predicted phosphate transport function, specifically accumulated in the maize rhizosphere. Our findings suggest that Pseudomonas and Streptomyces bacteria may result in continuous cropping-induced root rot disease in tiger lily and that Flavobacterium could serve to protect maize from pathogenic bacteria.

Keywords: continuous cropping; geological soil; lily root rot disease; microbiota; rhizosphere.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Geological soil type and plant species are the main factors underlying distinctive variations within rhizosphere bacterial communities. (A) Principal coordinate analysis (PCoA) of the bacterial communities of rhizosphere soil in maize and tiger lily, based on weighted unifrac metrics. n = 4 biological replicates. Clily = tiger lily rhizosphere samples from Cambrian soil; Cmaize = maize rhizosphere samples from Cambrian soil; Olily = tiger lily rhizosphere samples from Ordovician soil; Omaize = maize rhizosphere samples from Ordovician soil; Slily = tiger lily rhizosphere samples from Silurian soil; Smaize = maize rhizosphere samples from Silurian soil. (B) Heatmap of weighted Unifrac distance metrics, used to measure the dissimilarity coefficient between samples. The color scale indicates the difference in species diversity between paired samples; the smaller the value, the smaller the difference. (C) Shannon index of the rhizospheric bacterial communities represents the communities’ diversity in each sample. Means ± SE, n = 4. One-way ANOVA with multiple comparison tests was used for statistical analysis; different letter indicates statistical difference, p ≤ 0.05.
FIGURE 2
FIGURE 2
Cambrian soil shows more flexible bacteria community remodeling compared to Ordovician and Silurian soils. (A) Ternary plot of the top 10 abundant genera of the tiger lily rhizosphere across different soil types. n = 4 biological replicates. (B) Ternary plot of the top 10 abundant genera in the maize rhizosphere across different soil types. n = 4 biological replicates. Different dominant species of three samples at genus level. Vertex means samples. Circles represent species, and the relative abundance of each species is indicated by the size of the circle. The distance of the circles to vertexes presents the relative content of species in the sample.
FIGURE 3
FIGURE 3
The rhizosphere bacterial community structure presents intrinsic bias according to crop species and soil type. (A) Taxonomic diversity of the top 10 phyla in different samples. n = 4 biological replicates. (B) Histogram of LDA scores of 16S rRNA sequences of tiger lily rhizosphere microbiome. (C) Histogram of LDA scores of 16S rRNA sequences of maize rhizosphere microbiome. The LDA value distribution histogram shows species whose LDA score is greater than 4, indicating a biomarker with statistical difference between the groups. The length of the histogram represents the impact size of the different species.
FIGURE 4
FIGURE 4
Microbial predicted function of the tiger lily rhizosphere microbiome using the KEGG Orthology (KO) database. (A) Heatmap of conserved virulent activities (23 Kos) of bacterial communities in tiger lily rhizosphere within the three different soil types. Color scale indicates bacterial abundance. (B) Distribution of the bacteria of 23 KOs at genus level within the Gammaproteobacteria class. (C) Distribution of the bacteria of 23 KOs at genus level within the Actinobacteria phylum.
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References

    1. Abadi V. A. J. M., Sepehri M., Rahmani H. A., Zarei M., Ronaghi A., Taghavi S. M., et al. (2020). Role of Dominant phyllosphere bacteria with plant growth–promoting characteristics on growth and nutrition of Maize (Zea mays L.). J. Soil Sci. Plant Nutr. 20 2348–2363.
    1. Alori E. T., Glick B. R., Babalola O. O. (2017). Microbial phosphorus solubilization and its potential for use in sustainable agriculture. Front. Microbiol. 8:971. 10.3389/fmicb.2017.00971 - DOI - PMC - PubMed
    1. Beirinckx S., Viaene T., Haegeman A., Debode J., Amery F., Vandenabeele S., et al. (2020). Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions. Microbiome 8:54. 10.1186/s40168-020-00833-w - DOI - PMC - PubMed
    1. Bolyen E., Rideout J. R., Dillon M. R., Bokulich N. A., Abnet C. C., Al-Ghalith G. A., et al. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37 852–857. - PMC - PubMed
    1. Cadot S., Guan H., Bigalke M., Walser J. C., Jander G., Erb M., et al. (2021). Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field. Microbiome 9:103. 10.1186/s40168-021-01049-2 - DOI - PMC - PubMed

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