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.
Highlights
Microorganisms and plants have developed symbiotic relationships to adapt to various environmental changes
To investigate the features of the microbial communities associated with different rhizocompartments of tomatoes, tomato plants were collected from 23 greenhouses located in 7 different geographic locations across South Korea (Supplementary Fig. S1 and Supplementary Table S1)
The operational taxonomic units (OTUs) datasets of endosphere samples were rarefied to 4,000 reads while those of bulk soil and rhizosphere were rarefied to 20,000 reads, both of which are close to the depth of saturation with more than 98% coverage (Supplementary Table S2)
Summary
Microorganisms and plants have developed symbiotic relationships to adapt to various environmental changes. Previous greenhouse and field studies have shown that soil type, plant genotype, plant developmental stage, and cultivation practice affect the composition and structure of microbial communities[8,9,11,15,16,17]. Among these factors, soil type is the strongest determinant of microbial community variation[8,9,11], by virtue of its close association with the physicochemical properties that exert considerable influence on soil microbial diversity and biogeography[18]. The highly connected taxa within the microbial network are considered to be keystone taxa that play an important role in the structure and function of microbial communities[30]
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