Deterministic colonization arises early during the transition of soil bacteria to the phyllosphere and is shaped by plant-microbe interactions.

Background: Upon seed germination, soil bacteria are activated to transition to the plant and eventually colonize mature tissues like leaves. These bacteria are poised to significantly influence plant health, but we know little about their colonization routes. We studied the mechanisms of the transition of soil bacteria to germinating plants and leaves using an in-planta isolation approach and by experimentally manipulating inoculation times. We then tested how plant-microbe-microbe interactions shape assembly mechanisms in natural soil communities by amending soil with a trackable, labeled strain of the opportunistic pathogen Pseudomonas viridiflava (Pv3D9).

Results: We identified 27 diverse genera of leaf-associated bacteria that could transition alone from a few cells near a germinating plant to mature leaves, suggesting that the soil-to-leaf transition is probably important for them in nature. Indeed, when plants were only inoculated by soil after the emergence of true leaves, less diverse bacteria transitioned to mature leaves via different colonization mechanisms than when plants germinated in the presence of soil microorganisms. In particular, deterministic processes drove the colonization of phylogenetic bins dominated by Pedobacter, Enterobacter, Stenotrophomonas, Janthinobacterium, Pseudomonas, and Chryseobacterium only in the natural soil-to-leaf transition. Host genotype and soil amendments with Pv3D9, both of which affect host physiology, had strong effects on mainly deterministic colonization.

Conclusions: Diverse bacteria transition from soil to leaves during natural colonization, resulting in characteristic diversity in healthy leaf microbiomes. The mechanisms of colonization are a mix of stochastic processes, which will be largely shaped by competition, and deterministic processes which are more responsive to factors that shape host physiology. In the chase toward targeted manipulation of microbiomes, identifying these mechanisms for a given host and environment provides important information. Developing targeted treatments, however, will require further dissection of the pathways by which host factors drive stochastic and deterministic transitions from soil to leaves. Video Abstract.