Tomato-dominant microbiota associated with commercial systems with different levels of productivity

Abstract

Tomatoes are an important economic crop, a key component of the human diet, and an important source of vitamins, minerals, and carotenoids. Tomato productivity is dependent on many abiotic and biotic factors, and soil microbiota plays important roles in nutrition, growth, and immunity. In this study, we used high-throughput 16S and ITS sequencing to assess the bulk soil and rhizosphere microbial community composition at two geographically distinct sites, each with two separate greenhouses with low and high tomato weights. As a result, the bacterial diversity in the soil community was greater than that of the fungal community. Proteobacteria, Actinobacteria, Acidobacteria, and Ascomycota were the most abundant phyla. Although the sites presented similar rootstocks (Guardião), pedology classifications (Oxisols), and cultivation systems, the bulk soil and rhizosphere differed in terms of microbiota abundance. The rhizosphere microbiota was strongly influenced by the bulk soil. In a comparison of the tomato microbiota from the two high-tomato-weight greenhouses, the genera Bradyrhizobium and Mesorhizobium camelthorni (Proteobacteria), Bacillus (Firmicutes), and Mycochlamys (Ascomycota) were enriched, whereas the relative abundance of pathogenic fungi (Fusarium and Penicillium) decreased. Although the effective interactions between dominant bacterial and fungal groups must be investigated, we highlight the importance of metagenomic studies in discovering the crop-associated microbiota related to plant production.