Revealing the Variation and Stability of Bacterial Communities in Tomato Rhizosphere Microbiota.

Microorganisms that colonize the plant rhizosphere can contribute to plant health, growth and productivity. Although the importance of the rhizosphere microbiome is known, we know little about the underlying mechanisms that drive microbiome assembly and composition. In this study, the variation, assembly and composition of rhizobacterial communities in 11 tomato cultivars, combined with one cultivar in seven different sources of soil and growing substrate, were systematically investigated. The tomato rhizosphere microbiota was dominated by bacteria from the phyla Proteobacteria, Bacteroidetes, and Acidobacteria, mainly comprising Rhizobiales, Xanthomonadales, Burkholderiales, Nitrosomonadales, Myxococcales, Sphingobacteriales, Cytophagales and Acidobacteria subgroups. The bacterial community in the rhizosphere microbiota of the samples in the cultivar experiment mostly overlapped with that of tomato cultivar MG, which was grown in five natural field soils, DM, JX, HQ, QS and XC. The results supported the hypothesis that tomato harbors largely conserved communities and compositions of rhizosphere microbiota that remains consistent in different cultivars of tomato and even in tomato cultivar grown in five natural field soils. However, significant differences in OTU richness (p < 0.0001) and bacterial diversity (p = 0.0014 < 0.01) were observed among the 7 different sources of soil and growing substrate. Two artificial commercial nutrient soils, HF and CF, resulted in a distinct tomato rhizosphere microbiota in terms of assembly and core community compared with that observed in natural field soils. PERMANOVA of beta diversity based on the combined data from the cultivar and soil experiments demonstrated that soil (growing substrate) and plant genotype (cultivar) had significant impacts on the rhizosphere microbial communities of tomato plants (soil, F = 22.29, R2 = 0.7399, p < 0.001; cultivar, F = 2.04, R2 = 0.3223, p = 0.008). Of these two factors, soil explained a larger proportion of the compositional variance in the tomato rhizosphere microbiota. The results demonstrated that the assembly process of rhizosphere bacterial communities was collectively influenced by soil, including the available bacterial sources and biochemical properties of the rhizosphere soils, and plant genotype.

Analysis of the community composition and bacterial diversity of the rhizosphere microbiome across different plant taxa.

Rhizobacteria play an important role in bridging the soil and plant microbiomes and improving the health and growth of plants. In this study, the bacterial community structures and compositions of rhizosphere microbiomes associated with six plant species, representing two orders and three families of wild plants grown in the same field, were evaluated. The six plant species examined harbored a core and similar bacterial communities of the rhizosphere microbiome, which was dominated by members of Rhizobiales, Sphingomonadales, Burkholderiales, and Xanthomonadales of Proteobacteria, Subgroup 4 of Acidobacteria, and Sphingobacteriales of Bacteroidetes. Plant species had a significant effect on the microbial composition and Operational Taxonomic Unit (OTU) abundance of the rhizosphere microbiome. Statistical analysis indicated a significant differential OTU richness (Chao1, p < 0.05) and bacterial diversity (Shannon index, p < 0.0001) of the rhizosphere microbiome at the plant species, genus, or families levels. The paralleled samples from the same plant species in the PCoA and hierarchical cluster analysis demonstrated a clear tendency to group together, although the samples were not strictly separated according to their taxonomic divergence at the family or order level. The CAP analysis revealed a great proportion (44.85%) of the variations on bacterial communities could be attributed to the plant species. The results demonstrated that largely conserved and taxonomically narrow bacterial communities of the rhizosphere microbiome existed around the plant root. The bacterial communities and diversity of the rhizosphere microbiome were significantly related to the plant taxa, at least at the species levels.

Identification and genomic analysis of antifungal property of a tomato root endophyte Pseudomonas sp. p21.

Pseudomonas sp., which occupy a variety of ecological niches, have been widely studied for their versatile metabolic capacity to promote plant growth, suppress microbial pathogens, and induce systemic resistance in plants. In this study, a Pseudomonas sp. strain p21, which was isolated from tomato root endophytes, was identified as having antagonism against Aspergillus niger. Further analysis showed that this strain had the ability to biosynthesise siderophores and was less effective in inhibiting the growth of A. niger with the supplementation of Fe3+ in the agar medium. Genomic sequencing and the secondary metabolite cluster analysis demonstrated that Pseudomonas sp. p21 harboured 2 pyoverdine biosynthetic gene clusters, which encode compounds with predicted core structures and two variable tetra-peptide or eleven-peptide chains. The results indicated that siderophore-mediated competition for iron might be an important mechanism in Pseudomonas suppression of the fungal pathogen A. niger and in microbe-pathogen-plant interactions.