Structural variability and differentiation of niches in the rhizosphere and endosphere bacterial microbiome of moso bamboo (Phyllostachys edulis)

Abstract

The plant microbiota play a key role in plant productivity, nutrient uptake, resistance to stress and flowering. The flowering of moso bamboo has been a focus of study. The mechanism of flowering is related to nutrient uptake, temperature, hormone balance and regulation of key genes. However, the connection between microbiota of moso bamboo and its flowering is unknown. In this study, samples of rhizosphere soil, rhizomes, roots and leaves of flowering and nonflowering plants were collected, and 16S rRNA amplicon Illumina sequencing was utilized to separate the bacterial communities associated with different flowering stages of moso bamboo. We identified 5442 OTUs, and the number of rhizosphere soil OTUs was much higher than those of other samples. Principal component analysis (PCA) and hierarchical clustering (Bray Curtis dis) analysis revealed that the bacterial microorganisms related to rhizosphere soil and endophytic tissues of moso bamboo differed significantly from those in bulk soil and rhizobacterial and endosphere microbiomes. In addition, the PCA analyses of root and rhizosphere soil revealed different structures of microbial communities between bamboo that is flowering and not flowering. Through the analysis of core microorganisms, it was found that Flavobacterium, Bacillus and Stenotrophomonas played an important role in the absorption of N elements, which may affect the flowering time of moso bamboo. Our results delineate the complex host-microbe interactions of this plant. We also discuss the potential influence of bacterial microbiome in flowering, which can provide a basis for the development and utilization of moso bamboo.

Figure 1

Average Good’s coverage estimates (%) of each moso bamboo plant compartment. Rarefaction curves were assembled showing the number of OTUs, defined at the 97% sequence similarity cut-off in mothur, relative to the number of total sequences.

Figure 2

Alpha diversity estimates of the bacterial communities. (a) Number of observed OTUs). (b) Chao1 indices. (c) Shannon diversity indices. Alpha diversity estimates represent 3 biological replicates for the rhizosphere soil and root, rhizome, leaf samples were calculated in mothur with 10,000 iterations.

Figure 3

Plant compartment drives the composition of the bacterial communities at the OTU level. (a) Principle component analysis (PCA) of square-root transformed samples based on rarefaction to 2000 reads per sample. (b) Hierarchical clustering (group average linkage) of the samples based on Weighted Unifrac. PCA and hierarchical clusters were based on 3 biological replicates (rhizosphere soil and root, rhizome, leaf samples) and were constructed in PRIMER 7 with 10,000 iterations.

Figure 4

Dominant bacterial phyla detected in moso bamboo rhizosphere soil, root, rhizome, leaf compartments and bulk soils.

Figure 5

Top OTU members of the bacterial microbiome associated with the plant niches. Taxonomic dendrogram showing the core bacterial microbiome of each plant compartment. Color ranges identify genera within the tree.

Figure 6

PICRUSt analysis of the bacterial microbiome in each plant compartment. The top 35 the bacterial microbiome and their abundance information in each sample were mapped and clustered from the functional difference level.