Bacterial communities in the rhizosphere, phyllosphere and endosphere of tomato plants

Abstract

Plants harbor diverse bacterial communities, which play crucial roles in plant health and growth, in their rhizosphere, phyllosphere and endosphere. Tomato is an important model for studying plant-microbe interactions, but comparison of its associated bacterial community is still lacking. In this study, using Illumina sequencing of 16S rRNA amplicons, we characterized and compared the bacterial size and community from rootzone soil as well as the rhizosphere, phyllosphere and endosphere of roots, stems, leaves, fruits and seeds of tomato plants that were grown in greenhouse conditions. Habitat (soil, phyllospheric, and endophytic) structured the community. The bacterial communities from the soil-type samples (rootzone soil and rhizosphere) showed the highest richness and diversity. The lowest bacterial diversity occurred in the phyllospheric samples, while the lowest richness occurred in the endosphere. Among the endophytic samples, both bacterial diversity and richness varied in different tissues, with the highest values in roots. The most abundant phyla in the tomato-associated community was Proteobacteria, with the exception of the seeds and jelly, where both Proteobacteria and Firmicutes were dominant. At the genus level, the sequences of Pseudomonas and Acinetobacter were prevalent in the rhizosphere, and in the phyllosphere, more than 97% of the sequences were assigned to Acinetobacter. For the endophytes, Acinetobacter, Enterobacter, and Pseudomonas were the abundant genera in the roots, stems and leaves. In the fruits, the bacterial endophytes varied in different compartments, with Enterobacter being enriched in the pericarp and seeds, Acinetobacter in the placenta, and Weissella in the jelly. The present data provide a comprehensive description of the tomato-associated bacterial community and will be useful for better understanding plant-microbe interactions and selecting suitable bacterial taxa for tomato production.

Bacterial Communities in the Rhizosphere and Phyllosphere of Halophytes and Drought-Tolerant Plants in Mediterranean Ecosystems

“…In almost all plant species, the rhizospheric bacterial diversity, in terms of species richness, was much higher than the respective phyllopsheric communities. This is a common finding in similar studies of native and/or cultivated plants in different environments [53][54][55][56][57][58][59][60]. These differences in species richness between the two plant compartments have been attributed to their fundamental physiological and functional differences, as well as the direct impact of their surrounding environments (soil vs air environment).…”

The Endophytic Microbiome as a Hotspot of Synergistic Interactions, with Prospects of Plant Growth Promotion

“…Rice endophytic microbiome was observed to consist of diverse genes related to hydrolytic plant-polymer-degrading enzymes, detoxification of reactive oxygen species (ROS), glutathione synthases, and glutathione- S -transferases (GST), autoinducer molecules, and iron acquisition [ 229 ]. Illumina-based 16 rRNA analysis of bacterial community structure of rhizosphere, phyllosphere, and endosphere of tomato plants showed that bacterial richness decreased from root zone soil to rhizosphere to phyllosphere to endosphere, whereas diversity was decreased from root zone soil to rhizosphere to endosphere to phyllosphere [ 230 ]. Proteobacteria was found to be the most abundant phyla associated with tomato plants.…”

Microbial Diversity of Psychrotolerant Bacteria Isolated from Wild Flora of Andes Mountains and Patagonia of Chile towards the Selection of Plant Growth-Promoting Bacterial Consortia to Alleviate Cold Stress in Plants

“…plant. Several reports point to a higher richness and microbial diversity in the rhizosphere than the phyllosphere of plants [ 41 , 64 , 65 , 66 ]. This bacterial diversity is correlated with the total community size.…”