Cytokinin drives assembly of the phyllosphere microbiome and promotes disease resistance through structural and chemical cues

Abstract

The plant hormone cytokinin (CK) is an important developmental regulator, promoting morphogenesis and delaying differentiation and senescence. From developmental processes, to growth, to stress tolerance, CKs are central in plant life. CKs are also known to mediate plant immunity and disease resistance, and several classes of microbes can also produce CKs, affecting the interaction with their plant hosts. While host species and genotype can be a driving force in shaping the plant microbiome, how plant developmental hormones such as CK can shape the microbiome is largely uninvestigated. Here, we examined the relationship between CK and the phyllosphere microbiome, finding that CK acts as a selective force in microbiome assembly, increasing richness, and promoting the presence of Firmicutes. CK-mediated immunity was found to partially depend on the microbial community, and bacilli isolated from previously described CK-rich plant genotypes, which overexpress a CK biosynthesis gene or have increased CK sensitivity, induced plant immunity, and promoted disease resistance. Using a biomimetic system, we investigated the relationship between the leaf microstructure, which is differentially patterned upon changes in CK content or signaling, and the growth of different phyllosphere microbes. We found that leaf structures derived from CK-rich plant genotypes support bacilli in the biomimetic system. CK was able to promote the growth, swarming, and biofilm formation of immunity inducing bacillus isolates in vitro. Overall, our results indicate that host genotype and hormonal profiles can act as a strong selective force in microbiome assembly, underlying differential immunity profiles, and pathogen resistance as a result.

Cytokinin-microbiome interactions regulate developmental functions

“…We previously demonstrated that high CK content, or increased CK sensitivity, both support an increase in phyllosphere community richness, Shannon index, and in the proportion of Firmicutes [ 16 ]. Generally, CKs are thought to be synthesized mainly in the roots and transported via the xylem to the shoots, where they exert developmental functions [ 32 , 33 ].…”

“…pFIL >> IPT and clausa have increased percentages of bacilli in the microbial community in both the seedling (Fig. 3 A, B) and mature [ 16 ], (Fig. 3 A, C) stages, and, unlike in the background M82 (Figs.…”

“…In the phyllopshere, age-related microbiome differentiation may be associated with the differences in the leaf structure or geometry, cuticle structure, trichome placement, or composition of the volatile substances secreted by the leaf. We recently reported that leaf structural niches influence phyllosphere microbial content in different genotypes [ 16 ].…”

“…Recently, we investigated the relationship between CK and the phyllosphere microbiome in tomato, demonstrating that CK acts as a selective force in microbiome assembly, increasing richness, and promoting the presence of Firmicutes [ 16 ]. We found CK-mediated immunity to partially depend on the microbial community.…”

“…We found CK-mediated immunity to partially depend on the microbial community. In our previous work, we characterized several bacilli isolates from different species obtained from the phyllosphere of tomato having a high cytokinin content ( pBLS >> IPT) , and found that these bacilli promote plant immunity and disease resistance [ 16 ]. Using biomimetics, we found that tomato genotypes with high CK content or increased CK sensitivity are better able to support bacilli in their phyllosphere, due to the altered leaf structures present in theses genotypes.…”