Herbivores, the most abundant animals on Earth, use symbiotic microbes to help derive energy and nutrients from plant material. Leaf-cutter ants are a paradigmatic example of this, as they use cut leaf material to cultivate a mutualistic fungus that they use as their primary food source in subterranean fungus gardens. Some leaf-cutter ants have transitioned to cutting grasses instead of the usual dicots. These ants have adapted both morphologically and behaviorally to grass cutting, and they form a monophyletic clade, which demonstrates an evolutionary transition to a new substrate. Their fungus gardens also contain a community of bacteria, the role of which is less understood. In order to address gaps in knowledge about the roles of the bacteria, we examined the bacterial community in the fungus gardens of four species of leaf-cutter ants: Atta bisphaerica and Atta capiguara, strict grass-cutters, Atta sexdens, a strict dicot-cutter, and Atta laevigata, which is a grass and dicot-cutter. Three bacterial community metagenomes were sequenced at the Joint Genome Institute with an Illumina HiSeq 2500 sequencer. In total, we sequenced 12 metagenomes, three from each ant species. The assembled metagenomes contained a total of 5.28 Gbp of sequence, and a total of 8.19 million genes.
The metagenomes were dominated by the phylum Enterobacteriaceae. The bacterial communities in the gardens of grass-cutter ants, A. bisphaerica and A. capiguara were similar and had relatively low diversity, and were dominated by the genus Pantoea. The bacterial communities of A. sexdens, a dicot-cutter ant were more diverse, presumably because the plant substrates, and the respective plant defense compounds that the ants consume are more diverse. Interestingly, bacterial communities from A. laevigata, the grass and dicot-cutter, were the most variable, in one case being more similar to grass-cutter ant bacterial communities and in another, being more similar to dicot-cutter communities. In addition to whole community analysis, due to high sequencing depth, we have been able to generate complete composite genomes for some of the dominant bacteria, including Pantoea and Gluconobacter, and examined them for genes that are related to plant defense compound remediation. The work presented here demonstrates the connection between the functional and compositional diversity of a microbial community and how they relate to the substrate utilization of their host and can have implications for microbiome research and for functional community ecology.