Induction of antibiotic specialized metabolism by co-culturing in a collection of phyllosphere bacteria

A diverse set of bacteria live on the above-ground parts of plants, composing the phyllosphere, and play important roles for plant health. Phyllosphere microbial communities assemble in a predictable manner and diverge from communities colonizing other plant organs or the soil. However, how these communities differ functionally remains obscure. We assembled a collection of 258 bacterial isolates representative of the most abundant taxa of the phyllosphere of Arabidopsis and a shared soil inoculum. We screened the collection for the production of metabolites that inhibit the growth of Gram-positive and Gram-negative bacteria either in isolation or in co-culture. We found that isolates capable of constitutive antibiotic production in monoculture were significantly enriched in the soil fraction. In contrast, the proportion of binary cultures resulting in the production of growth inhibitory compounds differed only marginally between the phyllosphere and soil fractions. This shows that the phyllosphere may be a rich resource for potentially novel molecules with antibiotic activity, but that production or activity is dependent upon induction by external signals or cues. Finally, we describe the isolation of antimicrobial acyloin metabolites from a binary culture of Arabidopsis phyllosphere isolates, which inhibit the growth of clinically relevant Acinetobacter baumannii.

Automated summary

A diverse set of bacteria live on the above-ground parts of plants, composing the phyllosphere and play important roles for plant health. Phyllosphere microbial communities assemble predictably and differ functionally from other plant organs or soil communities. The phyllosphere may be a rich resource for potentially novel molecules with antibiotic activity, but production or activity is dependent upon external signals or cues. Through studying bacteria in the phyllosphere, isolates capable of inhibiting the growth of common bacteria were identified.