Genomic insights into bacterial isolates dominating honeypot ant crop microbiomes reveal metabolically distinct Fructilactobacillus sp.

Honeypot ants engage in a convergently-evolved phenotype called repletism, where specialized workers expand their crops and gasters to store vast amounts of food internally. They then store that food for months to support colonies during times of food scarcity. This fascinating phenotype is not well-understood and only recently have the microbial interactions been studied within the fructose-rich replete crops of these ants. Previous research using amplicon sequencing showed that Fructilactobacillus dominates the crop microbiomes of Myrmecocystus mexicanus repletes. This striking result and successful isolation of those strains led to the present investigation into the phylogenetic diversity of these strains and any clues to the nature of the symbiotic relationship between them and the ant host. We find that the isolates from these repletes represented two evolutionary lineages, both most closely related to F. fructivorans. One of those lineages was also found to be phylogenetically and metabolically distinct from all other Fructilactobacillus reference genomes used in this study. We also find evidence for three hypothesized scenarios that could lead to the dominance of these strains in this system, 1. Persistence - the ability of these organisms to exist where others would struggle, 2. Active Competition - additionally producing antimicrobial compounds to reduce competition, and 3. Host Selection - in which the microbe and host share evolutionary history and potential mutualism. These discoveries in a genus of bacteria that are highly relevant for fermented human foods will also lay the groundwork for future understanding of the convergent evolutionary mechanisms of repletism in ants.