Diversity of the Bacterial Microbiome Associated With the Endosphere and Rhizosphere of Different Cassava (Manihot esculenta Crantz) Genotypes.

Jingwen Ha,Rui Zhang,Xiaolei Niu,Kai Luo,Xin Chen,Yinhua Chen,Ke Li,Yu Gao,Yijie Zhang

doi:10.3389/fmicb.2021.729022

Jingwen Ha, Rui Zhang + Show 7 more

Open Access

https://doi.org/10.3389/fmicb.2021.729022

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Abstract

Root-associated microbial communities play important roles in plant growth and development. However, little attention has been paid to the microbial community structures associated with cassava, which is a staple food for approximately 800 million people worldwide. Here, we studied the diversity and structure of tuber endosphere and rhizosphere bacterial communities in fourteen cassava genotypes: SC5, SC8, SC9, SC205, KU50, R72, XL1, FX01, SC16, 4612, 587, 045, S0061, and 1110. The results of bacterial 16S rDNA sequencing showed that the richness and diversity of bacteria in the rhizosphere were higher than those in the tuber endosphere across the 14 cassava genotypes. After sequencing, 21 phyla and 310 genera were identified in the tuberous roots, and 36 phyla and 906 genera were identified in the rhizosphere soils. The dominant phylum across all tuber samples was Firmicutes, and the dominant phyla across all rhizosphere samples were Actinobacteria, Proteobacteria, and Acidobacteria. The numbers of core bacterial taxa within the tuber endospheres and the rhizospheres of all cassava genotypes were 11 and 236, respectively. Principal coordinate analysis and hierarchical cluster analysis demonstrated significant differences in the compositions of rhizosphere soil microbiota associated with the different cassava genotypes. Furthermore, we investigated the metabolic changes in tuber roots of three genotypes, KU50, SC205, and SC9. The result showed that the abundances of Firmicutes, Proteobacteria, and Actinobacteria in tuber samples were positively correlated with organic acids and lipids and negatively correlated with vitamins and cofactors. These results strongly indicate that there are clear differences in the structure and diversity of the bacterial communities associated with different cassava genotypes.

Highlights

Plants host diverse and abundant microbial communities that can be considered the “second genomes” of plants
The abundances of Firmicutes and Acidobacteria were higher in SC5, SC8, SC9, SC205, KU50, XL1, and FX01 than in the rhizospheres of the other genotypes (Figure 1A)
Based on the Venn diagram analysis, 21 phyla in the rhizosphere soil were found to be common to all tuberous samples, and 15 phyla were exclusive to the rhizosphere samples (Figure 1B)

Summary

Introduction

Plants host diverse and abundant microbial communities that can be considered the “second genomes” of plants. Plants can influence net ecosystem changes through deposition of secondary metabolites into the rhizosphere that attract or inhibit the growth of specific microorganisms This rhizodeposition was made up of small-molecular weight metabolites, amino acids, secreted enzymes, mucilage, and cell lysates (Grayston et al, 1998; Paterson and Sim, 2000). Soil microbes utilize this abundant carbon source, thereby implying that selective secretion of specific compounds may encourage beneficial symbiotic and protective relationships whereas secretion of other compounds inhibit pathogenic associations (Hoffland et al, 1992; Holden et al, 1999). Harnessing the plant microbiome to maximize crop production is increasingly considered a viable and sustainable approach for the future of agriculture (Geddes et al, 2015; Qiu et al, 2019)

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