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1. The toxins of vertically transmitted Spiroplasma

   https://doi.org/10.3389/fmicb.2023.1148263  

   Moore, Logan D.; Ballinger, Matthew J. (May 2023, Frontiers in Microbiology)

   Vertically transmitted (VT) microbial symbionts play a vital role in the evolution of their insect hosts. A longstanding question in symbiont research is what genes help promote long-term stability of vertically transmitted lifestyles. Symbiont success in insect hosts is due in part to expression of beneficial or manipulative phenotypes that favor symbiont persistence in host populations. In Spiroplasma, these phenotypes have been linked to toxin and virulence domains among a few related strains. However, these domains also appear frequently in phylogenetically distant Spiroplasma, and little is known about their distribution across the Spiroplasma genus. In this study, we present the complete genome sequence of the Spiroplasma symbiont of Drosophila atripex, a non-manipulating member of the Ixodetis clade of Spiroplasma, for which genomic data are still limited. We perform a genus-wide comparative analysis of toxin domains implicated in defensive and reproductive phenotypes. From 12 VT and 31 non-VT Spiroplasma genomes, ribosome-inactivating proteins (RIPs), OTU-like cysteine proteases (OTUs), ankyrins, and ETX/MTX2 domains show high propensity for VT Spiroplasma compared to non-VT Spiroplasma. Specifically, OTU and ankyrin domains can be found only in VT Spiroplasma, and RIP domains are found in all VT Spiroplasma and three non-VT Spiroplasma. These domains are frequently associated with Spiroplasma plasmids, suggesting a possible mechanism for dispersal and maintenance among heritable strains. Searching insect genome assemblies available on public databases uncovered uncharacterized Spiroplasma genomes from which we identified several spaid-like genes encoding RIP, OTU, and ankyrin domains, suggesting functional interactions among those domain types. Our results suggest a conserved core of symbiont domains play an important role in the evolution and persistence of VT Spiroplasma in insects. 

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2. Diverse toxin repertoire but limited metabolic capacities inferred from the draft genome assemblies of three Spiroplasma (Citri clade) strains associated with Drosophila

   https://doi.org/10.1099/mgen.0.001408  

   Ramirez, Paulino; Martinez_Montoya, Humberto; Aramayo, Rodolfo; Mateos, Mariana (June 2025, Microbial Genomics)

   Spiroplasma(classMollicutes) is a diverse wall-less bacterial genus whose members are strictly dependent on eukaryotic hosts (mostly arthropods and plants), with which they engage in pathogenic to mutualistic interactions.Spiroplasmaare generally fastidious to culturein vitro, especially those that are vertically transmitted by their hosts, which include flies in the genusDrosophila.Drosophilahas been invaded by at least three independent clades ofSpiroplasma: Poulsonii (the best studied, contains reproductive manipulators and defensive mutualists associated with two major clades ofDrosophilaand has amongst the highest substitution rates within bacteria), Citri (restricted to therepletagroup ofDrosophila) and Ixodetis. We report the first genome drafts ofDrosophila-associated Citri cladeSpiroplasma: strainsMoj fromDrosophila mojavensis, strainsAld-Tx fromDrosophila aldrichifrom Texas (newly discovered; also associated withDrosophila mulleri) and strainsHy2 fromDrosophila hydei(the onlyDrosophilaspecies known to naturally also harbour a Poulsonii clade strain, thereby providing an arena for horizontal gene transfer). Compared to their Poulsonii clade counterparts, we infer that the three Citri clade strains have the following: (1) equal or worse DNA repair abilities; (b) more limited metabolic capacities, which may underlie their comparatively lower titres and transmission efficiency; and (c) similar content of toxin domains, including at least one ribosome-inactivating protein, which is implicated in the Poulsonii-conferred defence against natural enemies. As a byproduct of our phylogenomic analyses and exhaustive search for certain toxin domains in public databases, we document the toxin repertoire in close relatives ofDrosophila-associatedSpiroplasma, and in a very divergent newly discovered lineage (i.e. ‘clade X’). Phylogenies of toxin-encoding genes or domains imply substantial exchanges between closely and distantly related strains. Surprisingly, despite encoding several toxin genes and achieving relatively high prevalences in certain natural populations (sAld-Tx in this study;sMoj in prior work), fitness assays ofsMoj (this study) andsAld-Tx (prior work) in the context of wasp parasitism fail to detect a beneficial effect to their hosts. Thus, how Citri clade strains persist in theirDrosophilahost populations remains elusive. 

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3. Genomes of Single-Stranded DNA Viruses in a Fecal Sample from South Polar Skua (Stercorarius maccormicki) on Ross Island, Antarctica

   https://doi.org/10.1128/mra.00299-23  

   Shick, Sarah R.; Elrod, Megan L.; Schmidt, Annie; Kraberger, Simona; Ainley, David G.; Ballard, Grant; Varsani, Arvind (June 2023, Microbiology Resource Announcements)

   Roux, Simon (Ed.)

   ABSTRACT South polar skuas migrate from subtropical regions to breed along coastal Antarctica. In a fecal sample collected on Ross Island, Antarctica, we identified 20 diverse microviruses ( Microviridae ) that share low levels of similarity to currently known microviruses; 6 appear to use a Mycoplasma/Spiroplasma codon translation table. 

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4. Context‐dependent vertical transmission shapes strong endosymbiont community structure in the pea aphid, Acyrthosiphon pisum

   https://doi.org/10.1111/mec.14449  

   Rock, Danielle I.; Smith, Andrew H.; Joffe, Jonah; Albertus, Amie; Wong, Narayan; O'Connor, Michael; Oliver, Kerry M.; Russell, Jacob A. (December 2017, Molecular Ecology)

   Abstract Animal‐associated microbiomes are often comprised of structured, multispecies communities, with particular microbes showing trends of co‐occurrence or exclusion. Such structure suggests variable community stability, or variable costs and benefits—possibilities with implications for symbiont‐driven host adaptation. In this study, we performed systematic screening for maternally transmitted, facultative endosymbionts of the pea aphid,Acyrthosiphon pisum. Sampling across six locales, with up to 5 years of collection in each, netted significant and consistent trends of community structure. Co‐infections betweenSerratia symbioticaandRickettsiella viridiswere more common than expected, whileRickettsiaand X‐type symbionts colonized aphids withHamiltonella defensamore often than expected.Spiroplasmaco‐infected with other endosymbionts quite rarely, showing tendencies to colonize as a single species monoculture. Field estimates of maternal transmission rates help to explain our findings: whileSerratiaandRickettsiellaimproved each other's transmission,Spiroplasmareduced transmission rates of co‐infecting endosymbionts. In summary, our findings show that North American pea aphids harbour recurring combinations of facultative endosymbionts. Common symbiont partners play distinct roles in pea aphid biology, suggesting the creation of “generalist” aphids receiving symbiont‐based defence against multiple ecological stressors. Multimodal selection, at the host level, may thus partially explain our results. But more conclusively, our findings show that within‐host microbe interactions, and their resulting impacts on transmission rates, are an important determinant of community structure. Widespread distributions of heritable symbionts across plants and invertebrates hint at the far‐reaching implications for these findings, and our work further shows the benefits of symbiosis research within a natural context. 

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5. Conserved microbiota among young Heliconius butterfly species

   https://doi.org/10.7717/peerj.5502  

   van Schooten, Bas; Godoy-Vitorino, Filipa; McMillan, W. Owen; Papa, Riccardo (January 2018, PeerJ)

   Background Insects are the most diverse group of animals which have established intricate evolutionary interactions with bacteria. However, the importance of these interactions is still poorly understood. Few studies have focused on a closely related group of insect species, to test the similarities and differences between their microbiota. Heliconius butterflies are a charismatic recent insect radiation that evolved the unique ability to use pollen as a protein source, which affected life history traits and resulted in an elevated speciation rates. We hypothesize that different Heliconius butterflies sharing a similar trophic pollen niche, harbor a similar gut flora within species, population and sexes. Methods To test our hypothesis, we characterized the microbiota of 38 adult male and female butterflies representing six species of Heliconius butterflies and 2 populations of the same species. We sequenced the V4 region of the 16S rRNA gene with the Roche 454 system and analyzed the data with standard tools for microbiome analysis. Results Overall, we found a low microbial diversity with only 10 OTUs dominating across all individuals, mostly Proteobacteria and Firmicutes, which accounted for  99.5% of the bacterial reads. When rare reads were considered, we identified a total of 406 OTUs across our samples. We identified reads within Phyla Chlamydiae , found in 5 butterflies of four species. Interestingly, only three OTUs were shared among all 38 individuals ( Bacillus, Enterococcus and Enterobacteriaceae ). Altogether, the high individual variation overshadowed species and sex differences. Thus, bacterial communities were not structured randomly with 13% of beta-diversity explained by species, and 40 rare OTUs being significantly different across species. Finally, 13 OTUs, including the intercellular symbiont Spiroplasma, varied significantly in relative abundance between males and females. Discussion The Heliconius microbial communities in these 38 individuals show a low diversity with few differences in the rare microbes between females, males, species or populations. Indeed, Heliconius butterflies, similarly to other insects, are dominated by few OTUs, mainly from Proteobacteria and Firmicutes. The overall low microbial diversity observed contrasts with the high intra-species variation in microbiome composition. This could indicate that much of the microbiome maybe acquired from their surroundings. The significant differences between species and sexes were restricted to rare taxa, which could be important for microbial community stability under changing conditions as seen in other host-microbiome systems. The presence of symbionts like Spiroplasma or Chlamydiae , identified in this study for the first time in Heliconius , could play a vital role in their behavior and evolution by vertical transmission. Altogether, our study represents a step forward into the description of the microbial diversity in a charismatic group of closely related butterflies. 

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