D3373: Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants

While genome sequencing has expanded our knowledge of symbiosis, studies of realized symbiont function remain challenging. Of further challenge is role assignment among multi-species microbiomes, in which microbes may fill complementary, host-beneficial functional niches despite genomic redundancy. We address such questions, here, for a specialized nitrogen (N) recycling microbiome of turtle ants, describing a new genus and species of gut symbiont—Ischyrobacter davidsoniae (Betaproteobacteria: Alcaligenaceae)—and its in vivo physiological context. Our genomics and prior amplicon sequencing data led us to conclude that I. davidsoniae has lived with turtle ants for >50 million years, exhibiting high prevalence and conserved capacity for purine- based N-recycling. Through FISH microscopy, we show that this bacterium colonizes the ileum and rectum, with highest concentrations at the presumed site of host N-waste delivery. While positioned to process such host-derived molecules, in vivo metatranscriptomics and metabolomics suggest a role for I. davidsoniae in a symbiont-autonomous N-recycling pathway. Surprisingly, I. davidsoniae expressed only a subset of the steps for this purine-based metabolism in mature adult workers; the remainder were expressed by other specialized gut symbionts. Collectively, this symbiont assemblage can convert inosine, made from midgut symbionts, into urea and ammonia in the hindgut. When administered through diet, urea was previously shown to support host amino acid budgets and cuticle synthesis. Thus, through its assisted production of urea in vivo, I. davidsoniae emerges as a central team player in an ancient N-recycling symbiosis, illustrating how cooperative microbe functioning can benefit hosts with limiting diets.