Domestication and evolutionary histories of specialized gut symbionts across cephalotine ants.

The evolution of animals and their gut symbionts is a complex phenomenon, obscured by lability and diversity. In social organisms, transmission of symbionts among relatives may yield systems with more stable associations. Here, we study the history of a social insect symbiosis involving cephalotine ants and their extracellular gut bacteria, which come predominantly from host-specialized lineages. We perform multi-locus phylogenetics for symbionts from nine bacterial orders, and map prior amplicon sequence data to lineage-assigned symbiont genomes, studying distributions of rigorously defined symbionts across 20 host species. Based on monophyly and additional hypothesis testing, we estimate that these specialized gut bacteria belong to 18 distinct lineages, of which 15 have been successfully isolated and cultured. Several symbiont lineages showed evidence for domestication events that occurred later in cephalotine evolutionary history, and only one lineage was ubiquitously detected in all 20 host species and 48 colonies sampled with amplicon 16S rRNA sequencing. We found evidence for phylogenetically constrained distributions in four symbionts, suggesting historical or genetic impacts on community composition. Two lineages showed evidence for frequent intra-lineage co-infections, highlighting the potential for niche divergence after initial domestication. Nearly all symbionts showed evidence for occasional host switching, but four may, more often, co-diversify with their hosts. Through our further assessment of symbiont localization and genomic functional profiles, we demonstrate distinct niches for symbionts with shared evolutionary histories, prompting further questions on the forces underlying the evolution of hosts and their gut microbiomes.

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, role assignment within multi-species microbiomes remains challenging due to genomic redundancy and the uncertainties of in vivo impacts. 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: Burkholderiales: Alcaligenaceae)-and its in vivo physiological context. A re-analysis of amplicon sequencing data, with precisely assigned Ischyrobacter reads, revealed a seemingly ubiquitous distribution across the turtle ant genus Cephalotes, suggesting ≥50 million years since domestication. Through new genome sequencing, we also show that divergent I. davidsoniae lineages are conserved in their uricolytic and urea-generating capacities. With phylogenetically refined definitions of Ischyrobacter and separately domesticated Burkholderiales symbionts, our FISH microscopy revealed a distinct niche for I. davidsoniae, with dense populations at the anterior ileum. Being positioned at the site of host N-waste delivery, in vivo metatranscriptomics and metabolomics further implicate I. davidsoniae within a symbiont-autonomous N-recycling pathway. While encoding much of this pathway, I. davidsoniae expressed only a subset of the requisite steps in mature adult workers, including the penultimate step deriving urea from allantoate. The remaining steps were expressed by other specialized gut symbionts. Collectively, this assemblage converts inosine, made from midgut symbionts, into urea and ammonia in the hindgut. With urea supporting host amino acid budgets and cuticle synthesis, and with the ancient nature of other active N-recyclers discovered here, I. davidsoniae emerges as a central player in a conserved and impactful, multipartite symbiosis.

Turtle ants harbor metabolically versatile microbiomes with conserved functions across development and phylogeny.

Gut bacterial symbionts can support animal nutrition by facilitating digestion and providing valuable metabolites. However, changes in symbiotic roles between immature and adult stages are not well documented, especially in ants. Here, we explored the metabolic capabilities of microbiomes sampled from herbivorous turtle ant (Cephalotes sp.) larvae and adult workers through (meta)genomic screening and in vitro metabolic assays. We reveal that larval guts harbor bacterial symbionts with impressive metabolic capabilities, including catabolism of plant and fungal recalcitrant dietary fibers and energy-generating fermentation. Additionally, several members of the specialized adult gut microbiome, sampled downstream of an anatomical barrier that dams large food particles, show a conserved potential to depolymerize many dietary fibers. Symbionts from both life stages have the genomic capacity to recycle nitrogen and synthesize amino acids and B-vitamins. With help of their gut symbionts, including several bacteria likely acquired from the environment, turtle ant larvae may aid colony digestion and contribute to colony-wide nitrogen, B-vitamin and energy budgets. In addition, the conserved nature of the digestive capacities among adult-associated symbionts suggests that nutritional ecology of turtle ant colonies has long been shaped by specialized, behaviorally-transferred gut bacteria with over 45 million years of residency.

Seeds and seedlings of oaks suffer from mammals and molluscs close to phylogenetically isolated, old adults.

BACKGROUND AND AIMS: Mammals and molluscs (MaM) are abundant herbivores of tree seeds and seedlings, but how the trees and their environment affect MaM herbivory has been little studied. MaM tend to move much larger distances during the feeding stage than the more frequently studied insect herbivores. We hypothesize that MaM (1) select and stay within the patches that promise to be relatively the richest in seeds and seedlings, i.e. patches around adult trees that are old and within a distantly related, less productive neighborhood; and (2) try to remain sheltered from predators while foraging, i.e. mammals remain close to adult trees or to cover by herbs while foraging, and might force their mollusc prey to show the opposite distribution. METHODS: We exposed oak acorns and seedlings in a temperate forest along transects from adult conspecifics in different neighbourhoods. We followed acorn removal and leaf herbivory. We used exclusion experiments to separate acorn removal by ungulates vs. rodents and leaf herbivory by insects vs. molluscs. We measured the size of the closest conspecific adult tree, its phylogenetic isolation from the neighbourhood and the herbaceous ground cover. KEY RESULTS: Consistent with our hypothesis, rodents removed seeds around adult trees surrounded by phylogenetically distant trees and by a dense herb cover. Molluscs grazed seedlings surrounding large conspecific adults and where herb cover is scarce. Contrary to our hypothesis, the impact of MaM did not change from 1 to 5 m distance from adult trees. CONCLUSIONS: We suggest that foraging decisions of MaM repulse seedlings from old adults, and mediate the negative effects of herbaceous vegetation on tree recruitment. Also, an increase in mammalian seed predation might prevent trees from establishing in the niches of phylogenetically distantly related species, contrary to what is known from insect enemies.

Habitats shape taxonomic and functional composition of Neotropical ant assemblages.

Determining assembly rules of co-occurring species persists as a fundamental goal in community ecology. At local scales, the relative importance of environmental filtering vs. competitive exclusion remains a subject of debate. In this study, we assessed the relative importance of habitat filtering and competition in structuring understory ant communities in tropical forests of French Guiana. Leaf-litter ants were collected using pitfall and Winkler traps across swamp, slope and plateau forests near Saül, French Guiana. We used a combination of univariate and multivariate analyses to evaluate trait response of ants to habitat characteristics. Null model analyses were used to investigate the effects of habitat filtering and competitive interactions on community assembly at the scale of assemblages and sampling points, respectively. Swamp forests presented a much lower taxonomic and functional richness compared to slope and plateau forests. Furthermore, marked differences in taxonomic and functional composition were observed between swamp forests and slope or plateau forests. We found weak evidence for competitive exclusion based on null models. Nevertheless, the contrasting trait composition observed between habitats revealed differences in the ecological attributes of the species in the different forest habitats. Our analyses suggest that competitive interactions may not play an important role in structuring leaf-litter ant assemblages locally. Rather, habitats are responsible for driving both taxonomic and functional composition of ant communities.