Metagenomics reveals diet-specific specialization in fungus gardens of grass- and dicot-cutter ants

Abstract Leaf-cutter ants in the genus Atta are dominant herbivores in the Neotropics. While most species of Atta cut dicots to incorporate into their fungus gardens, some species specialize on grasses. Here we examine the bacterial community associated with the fungus gardens of grass- and dicot-cutter ants to elucidate the potential role of bacteria in leaf-cutter ant substrate specialization. We sequenced the metagenomes of 12 Atta fungus gardens, across four species of ants, with a total of 5.316 Gbp of sequence data. We show significant differences in the fungus garden bacterial community composition between dicot- and grass-cutter ants, with grass-cutter ants having significantly lower diversity and a significantly higher abundance of Pantoea. Reflecting this difference in community composition, the bacterial functional profiles between the fungus gardens are significantly different. Specifically, grass-cutter ant fungus garden metagenomes are particularly enriched for genes responsible for amino acid, siderophore, and terpenoid biosynthesis while dicot-cutter ant fungus gardens metagenomes are enriched in genes involved in membrane transport. Our results suggest that bacteria in leaf-cutter ant fungus gardens aid in nutrient supplementation, a function especially relevant for the fungus gardens of ants that forage grass, a plant source relatively lower in nutrient value.