Community Structure,Diversity,Succession And Function Of The Tomato Rhizobacteria And Endophytes

The microorganisms,which inhabited in plant rhizosphere soil and root tissue,can play an important role in plant growth,development,health,and yield.Understanding the composition,structure,diversity,and function of the plant's rhizosphere and endogenous microbial communities will provide a basis for exploring the shaping mechanism and ecological function of plant-associated microbiome,the microbe-plant-disease interaction,and new microbial resources and biological control strategies for plant pathogens.In this study,the 16S-based rDNA amplicon sequencing analysis and metagenomics were first used to analysis the community composition and diversity of tomato root-associate microbiomes at different plant growth stages,and the effects of tomato cultivars and soil types on tomato rhizobacteria and root endophytes.The results showed that the tomato rhizosphere bacteria were mainly composed of Acidobacteria SubgroupsBurkholderiales?Cytophagales?Gemmatimonadales?Rhizobiales?Sphingobacteriales?Sphingomonadales and Xanthomonadales from the bacterial phyla of Acidobacteria?Bacteroidetes?Gemmatimonadetes and Proteobacteria etc.Among the root endophytic bacteria,the dominant populations include Bacillus?Burkholderiales?Enterobacteriales?Pseudomonadales?Pseudonocardiales?Rhizobiales and Streptomycetale,which belong to the three phyla of Actinobacteria,Firmicutes and Proteobacteria.Proteobacteria was the dominant population of the tomato rhizobacterial and root endophytic microbiome,accounting for 39.18%and 34.15%,respectively.Tomato cultivars had an influence on the community structure and diversity of tomato rhizosphere bacteria,but the difference was not statistically significant.However,cultivars had a significant effect on the community structure,species richness and bacterial diversity of tomato root endophytic microbiome.Soil types had a dominant effect on the community structure and bacterial diversity of tomato rhizosphere bacteria and endophytic bacteria.Same with the result demonstrated above,tomato rhizosphere microbiome,either the rhizosphere bacteria or endophytic bacteria,showed a similar microbial community structure,but with a notable differential proportions not only at phylum level,but also at lower taxonomic level.The principal coordinate analysis(PCoA)and hierarchical cluster analysis based on the combined data revealed that soil types have greater effects on tomato rhizosphere bacteria and root endophytic bacteria than tomato varieties.Majority of the variation across the samples could be attributed to the soil type.The samples were clustered into different groups based the soil types,including all the cultivars samples grown in the sample soil type,more than plant cultivars.The commercial soil sample CF and HF separated as an independent branch,and then QS further departed as a single group.The results from canonical association analysis(CCA)revealed that the variation in structure and composition of the plant rhizobacteria and root endophytes had a good correlation with soil organic matter(OM),P,and K contents of soils.The composition and diversity of tomato rhizosphere bacterial communities at different tomato growth stages did not change significantly,and they had relatively stable structural composition and diversity.In contrast,there were significant differences in the community composition and bacterial diversity of tomato root endophytic bacteria at different growth stages.The diversity and abundance showed a gradually decreasing trend,and finally they tend to stabilize about 60-70 days.The dominant microflora of tomato root endophytic bacterial communities at different growth stages also showed significant differences.The previously identified dominant endophytic bacteria groups,including Xanthomonadales,Enterobacteriales,Pseudomonadales,Rhizobiales,Pseudonocardiales,Burkholderiales and Streptomycetales,were consecutively enriched at a certain period of tomato growth and occupied a dominant position.The results suggested that colonization and formation of endophytic bacteria in tomato roots was a gradually establishing and stable process.Functional analysis of tomato rhizosphere bacteria and root endophytic bacteria was performed through Metagenome sequencing.The results showed that the plant microbiome harbored a highest ratio of functional proteins related to metabolism(accounting for 48.35%and 48.71%for tomato root tissue and rhizosphere soil samples,respectively),and then following by proteins associated with cellular processes and signaling,as well as information storage and processes.Further analysis showed that the genes related to cellulase and oligosaccharides degrading enzymes were annotated in tomato rhizosphere soil and root tissue metagenome.However,the enzymes associated with degradation of xylan backbone and lignin was not identified.One complete and 2-3 imcomplete tryptophan-based indole-acetic acid(IAA)biosynthetic pathways were also found in the studies on tryptophan metabolic pathways.