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Many parasitic insects, including lice, form close relationships with endosymbiotic bacteria that are crucial for their survival. In this study, we used genomic sequencing to investigate the distribution and evolutionary history of the bacterial genusSodalisacross a broad range of feather louse species spanning 140 genera. Phylogenomic analysis revealed significant diversity amongSodalislineages in feather lice and robust evidence for their independent and repeated acquisition by different louse clades throughout their radiation. Among the 1020 louse genomes analysed, at least 22% containedSodalis, distributed across 57 louse genera. Cophylogenetic analyses between theSodalisand feather louse phylogenies indicated considerable mismatch. This phylogenetic incongruence between lice andSodalis, along with the presence of distantly relatedSodalislineages in otherwise closely related louse species, strongly indicates repeated independent acquisition of this endosymbiont. Additionally, evidence of cospeciation among a few closely related louse species, coupled with frequent acquisition of these endosymbionts from free-living bacteria, further highlights the diverse evolutionary processes shapingSodalisendosymbiosis in feather lice. 

An endosymbiotic bacterium of the genusSodalis, designated as strain HZ^T, was cultured from the parasitoid waspSpalangia cameroni, which develops on the pupae of various host flies. The bacterium was detected inS. cameronideveloped on houseflies,Musca domestica, in a poultry facility in Hazon, northern Israel. After culturing, this bacterium displayed no surface motility on Luria–Bertani agar and was rod-shaped and irregular in size, ~10–30 nm in diameter and 5–20 µm in length. Phylogenetic analyses revealed that strain HZ^Tis closely related toSodalis praecaptivusstrain HS^T, a free-living species of the genusSodalisthat includes many insect endosymbionts. Although these bacteria maintain >98% sequence identity in shared genes, genomic characterization revealed that strain HZ^Thas undergone substantial reductive evolution, such that it lacks many gene functions that are maintained inS. praecaptivusstrain HS^T. Based on the results of phylogenetic, genomic and chemotaxonomic analyses, we propose that this endosymbiont should be classified in a new subspecies asS. praecaptivussubsp. spalangiaesubsp. nov. The type strain for this new subspecies is HZ^T(=ATCC TSD-398^T=NCIMB 15482^T). The subspeciesSodalis praecaptivussubsp.praecaptivusstrain HS^Tis created automatically with the type strain ATCC BAA-2554^T(=DSMZ 27494^T). 

Abstract Evolution results from the interaction of stochastic and deterministic processes that create a web of historical contingency, shaping gene content and organismal function. To understand the scope of this interaction, we examine the relative contributions of stochasticity, determinism, and contingency in shaping gene inactivation in 34 lineages of endosymbiotic bacteria,Sodalis, found in parasitic lice,Columbicola, that are independently undergoing genome degeneration. Here we show that the process of genome degeneration in this system is largely deterministic: genes involved in amino acid biosynthesis are lost while those involved in providing B-vitamins to the host are retained. In contrast, many genes encoding redundant functions, including components of the respiratory chain and DNA repair pathways, are subject to stochastic loss, yielding historical contingencies that constrain subsequent losses. Thus, while selection results in functional convergence between symbiont lineages, stochastic mutations initiate distinct evolutionary trajectories, generating diverse gene inventories that lack the functional redundancy typically found in free-living relatives. 

We present a protocol to establish a synthetic symbiosis between the mCherry-expressing Sodalis praecaptivus and the grain weevil host, Sitophilus zeamais. We describe steps to isolate grain weevil eggs, followed by microinjecting the bacterial symbiont into insect eggs using a modified Drosophila injection protocol, which leads to localization of bacteria in female insect ovaries. We then detail larval transplantation and visualization of bacteria in live insects using a fluorescence dissection microscope to assess the transgenerational transmission to offspring in weevils. For complete details on the use and execution of this protocol, please refer to Su et al. (2022).1 

The microbiome is critical for host survival and fitness, but gaps remain in our understanding of how this symbiotic community is structured. Despite evidence that related hosts often harbor similar bacterial communities, it is unclear whether this pattern is due to genetic similarities between hosts or to common ecological selection pressures. Here, using herbivorous rodents in the genusNeotoma, we quantify how geography, diet, and host genetics, alongside neutral processes, influence microbiome structure and stability under natural and captive conditions. Using bacterial and plant metabarcoding, we first characterized dietary and microbiome compositions for animals from 25 populations, representing seven species from 19 sites across the southwestern United States. We then brought wild animals into captivity, reducing the influence of environmental variation. In nature, geography, diet, and phylogeny collectively explained ∼50% of observed microbiome variation. Diet and microbiome diversity were correlated, with different toxin-enriched diets selecting for distinct microbial symbionts. Although diet and geography influenced natural microbiome structure, the effects of host phylogeny were stronger for both wild and captive animals. In captivity, gut microbiomes were altered; however, responses were species specific, indicating again that host genetic background is the most significant predictor of microbiome composition and stability. In captivity, diet effects declined and the effects of host genetic similarity increased. By bridging a critical divide between studies in wild and captive animals, this work underscores the extent to which genetics shape microbiome structure and stability in closely related hosts.