22Various plant species establish intimate symbioses with bacteria within their aerial organs. The 23 bacteria are contained within nodules or glands often present in distinctive patterns on the leaves in 24 what is commonly referred to as leaf nodule symbiosis. We describe here a highly specific symbiosis 25 between a wild yam species from Madagascar, Dioscorea sansibarensis and bacteria of the species 26Orrella dioscoreae. Using whole genome sequencing of plastids and bacteria from wild-collected 27 samples, we show phylogenetic patterns consistent with a dominant vertical mode of transmission of 28 the symbionts. Unique so far among leaf nodule symbioses, the bacteria can be cultured and are 29 amenable to comparative transcriptomics, revealing a potential role in complementing the host's 30 arsenal of secondary metabolites. We propose a recent establishment of a vertical mode of 31 transmission in this symbiosis which, together with a large effective population size explains the 32 cultivability and apparent lack of genome reductive evolution in O. dioscoreae. We leverage these 33 unique features to reveal pathways and functions under positive selection in these specialized 34 endophytes, highlighting the candidate mechanisms enabling a permanent association in the 35 phyllosphere. 36 37 Primulaceae (Ardisia) families, and their symbionts are members of the Burkholderiaceae family of β-47 proteobacteria. The symbionts reside in dedicated structures called leaf glands or nodules, and are 48 transmitted between generations via seeds [6]. The association is essential for both hosts and 49 symbionts: Candidatus Burkholderia (Ca. Burkholderia) species cannot be cultured outside of their host 50 and bacteria-free Psychotria kirkii and Ardisia crenata display severe growth defects [7, 8]. This co-51 dependence between host and symbiont is likely the result of co-evolution over several million years, 52 compounded by small effective population sizes and genetic drift [6]. Typical of vertically-transmitted 53 symbiotic bacteria, Ca. Burkholderia leaf nodule symbionts show extensive signs of reductive genome 54 evolution, with coding capacities ranging from 41.7% to 67.3% and an accumulation of pseudogenes 55 and insertion sequences [9][10][11]. Despite extensive genome erosion, some symbionts have been shown 56 to produce secondary metabolites, likely involved in the protection of the host from herbivory, such 57 as the insecticidal kirkamide and the depsipeptide FR900359, as well as the herbicidal streptol-58 glucoside possibly involved in allelopathic interactions [11][12][13]. Because of genomic instability and 59 evolved co-dependence, it is unclear whether secondary metabolism was present in the ancestor of 60 leaf nodule Burkholderia or acquired as a secondary trait [6]. 61We recently described a leaf nodule symbiosis in the monocot species Dioscorea sansibarensis [14]. D. 62 sansibarensis, or the Zanzibar yam, is a true yam native to Madagascar and tropical Africa [15]. This 63 fast growing vine, like many yam ...

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.