Genome Analysis of Two Phylotypes Associated with Leafcutter Ants Reveals Their Biosynthetic Potential.

The attine ants of South and Central America are ancient farmers, having evolved a symbiosis with a fungal food crop >50 million years ago. The most evolutionarily derived attines are the and leafcutter ants, which harvest fresh leaves to feed their fungus. and many other attines vertically transmit a mutualistic strain of and use antifungal compounds made by these bacteria to protect their fungal partner against co-evolved fungal pathogens of the genus . mutualists associated with the attines and make novel cyclic depsipeptide compounds called gerumycins, while a mutualist strain isolated from derived makes an unusual polyene antifungal called nystatin P1. The novelty of these antimicrobials suggests there is merit in exploring secondary metabolites of on a genome-wide scale. Here, we report a genomic analysis of the phylotypes Ps1 and Ps2 that are consistently associated with ants collected in Gamboa, Panama. These were previously distinguished solely on the basis of 16S rRNA gene sequencing but genome sequencing of five Ps1 and five Ps2 strains revealed that the phylotypes are distinct species and each encodes between 11 and 15 secondary metabolite biosynthetic gene clusters (BGCs). There are signature BGCs for Ps1 and Ps2 strains and some that are conserved in both. Ps1 strains all contain BGCs encoding nystatin P1-like antifungals, while the Ps2 strains encode novel nystatin-like molecules. Strains show variations in the arrangement of these BGCs that resemble those seen in gerumycin gene clusters. Genome analyses and invasion assays support our hypothesis that vertically transmitted Ps1 and Ps2 strains have antibacterial activity that could help shape the cuticular microbiome. Thus, our work defines the species associated with ants and supports the hypothesis that species could provide a valuable source of new antimicrobials.