A preliminary examination of bacterial, archaeal, and fungal communities inhabiting different rhizocompartments of tomato plants under real-world environments

Abstract

Plant microbiota is a key determinant of plant health and productivity. The composition and structure of plant microbiota varies according to plant tissue and compartment, which are specific habitats for microbial colonization. To investigate the structural composition of the microbiome associated with tomato roots under natural systems, we characterized the bacterial, archaeal, and fungal communities of three belowground compartments (rhizosphere, endosphere, and bulk soil) of tomato plants collected from 23 greenhouses in 7 geographic locations of South Korea. The microbial diversity and structure varied by rhizocompartment, with the most distinctive community features found in the endosphere. The bacterial and fungal communities in the bulk soil and rhizosphere were correlated with soil physicochemical properties, such as pH, electrical conductivity, and exchangeable cation levels, while this trend was not evident in the endosphere samples. A small number of core bacterial operational taxonomic units (OTUs) present in all samples from the rhizosphere and endosphere represented more than 60% of the total relative abundance. Among these core microbes, OTUs belonging to the genera Acidovorax , Enterobacter , Pseudomonas , Rhizobium , Streptomyces , and Variovorax , members of which are known to have beneficial effects on plant growth, were more relatively abundant in the endosphere samples. A co-occurrence network analysis indicated that the microbial community in the rhizosphere had a larger and more complex network than those in the bulk soil and endosphere. The analysis also identified keystone taxa that might play important roles in microbe-microbe interactions in the community. Additionally, profiling of predicted gene functions identified many genes associated with membrane transport in the endospheric and rhizospheric communities. Overall, the data presented here provide preliminary insight into bacterial, archaeal, and fungal phylogeny, functionality, and interactions in the rhizocompartments of tomato roots under real-world environments.

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

“…It is widely accepted core microbial communities presented in the gut microbiomes of humans and other animals, as well as root microbiomes of plants [4,5,7,8,19,20]. Assembly of rhizosphere microbiome in plant is driven by many aspects, including climate environment, soil source, host developmental stage, cultivation practice, and root architecture [5][6][7][8]11,14,[21][22][23][24]. Biotic factors, such as plant genotypes, pathogens, biocontrol microorganisms, and seed bacteria also alter and influence the microbial communities in rhizosphere environment [5][6][7][8][12][13][14][26][27][28][29][30][46][47][48].…”

“…The rhizosphere microbiota of the plant is mainly dominated by the bacterial phyla Proteobacteria, Bacteroidetes, and Acidobacteria [2,5,19,20]. In tomato, some studies on the community composition of the rhizosphere microbiota have reached the same conclusion using both culture-dependent and culture-independent approaches [15,[22][23][24][25][26]. Qiao et al [26] found that the three most abundant core phyla in the tomato (Solanum lycopersicum cv.…”

“…In a comprehensive study of 4 tomato cultivars (S. lycopersicum) from 4 geographically separated greenhouses, Lee et al [25] compared rhizobacterial communities by using culture-dependent and culture-independent approaches, revealing that only 22% of the total OTUs in the MiSeq dataset were recovered in the culture collection and the most dominant phylum in the tomato rhizosphere microbiota was Proteobacteria (78.5%), followed by Actinobacteria (8.5%), Bacteroidetes (3.6%), and Acidobacteria (3.5%). Furthermore, Lee et al [24] examined the microbial communities of three compartments of tomato plants collected from a broad range of geographical distributions. The results showed that the rhizosphere microbiota of the tomato plant was constituted by the bacterial phyla of Proteobacteria, Actinobacteria, Bacteoidetes, Fimicutes, and Acidobacteria.…”

“…The assembly and composition of rhizosphere microbial communities in tomato are affected by soil, plant genotype, and root system architecture [24,25,[27][28][29]. In addition, the effects of pathogens, biocontrol microorganisms, and nutrient amendment on the tomato microbiota have been demonstrated [15,22,23].…”

Quantitative partition of the rhizosphere microbiota assembly processes

“…An experimental design where bulk soil, rhizosphere soil and plant roots are sampled and microbial communities determined for each of the three compartments can easily produce a contingency matrix [10, 11]. Based on the matrix, beta-diversity are usually calculated, showing the compositional similarity of microbial community between each other.…”