Biology subjects

Siozios, S.

Publications and source records attributed to Siozios, S..

14 recordsLinked to original sources

bioRxiv2026

Rapid spread of nutritional Wolbachia symbionts across and within solitary bee species

Maternally inherited, intracellular Bacteria of the genus Wolbachia are extremely widespread among arthropods. Their evolutionary success is owed to frequent host shifts and rapid subsequent spread within host populations, often facilitated by Wolbachia-induced reproductive manipulations. Theory suggests that carrying Wolbachia must also be beneficial for a successful spread, however the nature of such benefits remains unclear. Here, we demonstrate that Wolbachias success in many solitary bee species is strongly associated with the presence of a gene cassette enabling Wolbachia to synthesize Biotin (vitamin B7). This ability is absent from almost all other Wolbachia strains but common among bee associated strains. We show that Wolbachia occurs in up to 70% of all bee species and that strains carrying this rare genomic element have independently spread into numerous bee hosts recently. We further demonstrate that the presence of the biotin operon is associated with specialised diets in several bee species, suggesting a previously overlooked nutritional role of Wolbachia in this group of important pollinators. Overall, our results suggest that nutritional benefits provided by symbionts may represent a more widespread and important mechanism by which reproductive manipulators spread into new host species than previously appreciated.

evolutionary biology↗

bioRxiv2023

Genome dynamics across the evolutionary transition to endosymbiosis

Endosymbiosis - where a microbe lives and replicates within a host - is an important contributor to organismal function that has accelerated evolutionary innovations and catalysed the evolution of complex life. The evolutionary processes associated with transitions to endosymbiosis, however, are poorly understood. Here, we use comparative genomics of the genus Arsenophonus to reveal the complex processes that occur on evolution of an endosymbiotic lifestyle. We compared the genomes of 38 strains spanning diverse lifestyles from environmentally acquired infections to obligate inter-dependent endosymbionts. We observed recent endosymbionts had larger genome sizes than closely related environmentally acquired strains, consistent with evolutionary innovation and rapid gain of new function. Increased genome size was a consequence of prophage and plasmid acquisition including a cargo of type III effectors, and concomitant loss of CRISPR-Cas genome defence systems enabling mobile genetic element expansion. Persistent endosymbiosis was also associated with loss of type VI secretion, likely reflecting reduced microbe-microbe competition. Thereafter, the transition to stable endosymbiosis and vertical inheritance was associated with the expected relaxation of purifying selection, pseudogenisation of genes and reduction of metabolism, leading to genome reduction. However, reduced %GC that is typically considered a progressive linear process was observed only in obligate interdependent endosymbionts. We argue that a combination of the need for rapid horizontal gene transfer-mediated evolutionary innovation together with reduced phage predation in endosymbiotic niches drives loss of genome defence systems and rapid genome expansion upon adoption of endosymbiosis. These remodelling processes precede the reductive evolution traditionally associated with adaptation to endosymbiosis.

genomics↗

bioRxiv2022

Candidatus Megaira are diverse symbionts of algae and ciliates with the potential for defensive symbiosis

Symbiotic microbes from the genus Candidatus Megaira (Rickettsiales) are known to be common associates of algae and ciliates. However genomic resources for these bacteria are scarce, limiting our understanding of their diversity and biology. We therefore utilized SRA and metagenomic assemblies to explore the diversity of this genus. We successfully extracted four draft Ca. Megaira genomes including one complete scaffold for a Ca. Megaira and identified an additional 14 draft genomes from uncategorised environmental Metagenome-Assembled Genomes. We use this information to resolve the phylogeny for the hyper-diverse Ca. Megaira, with hosts broadly spanning ciliates, micro- and macro-algae, and find that the current single genus designation Ca. Megaira significantly underestimates their diversity. We also evaluate the metabolic potential and diversity of Ca. Megaira from this new genomic data and find no clear evidence of nutritional symbiosis. In contrast, we hypothesize a potential for defensive symbiosis in Ca. Megaira. Intriguingly, one symbiont genome revealed a proliferation of ORFs with ankyrin, tetratricopeptide and Leucine rich repeats like those observed in the genus Wolbachia where they are considered important for host-symbiont protein-protein interactions. Onward research should investigate the phenotypic interactions between Ca. Megaira and their various potential hosts, including the economically important Nemacystus decipiens, and target acquisition of genomic information to reflect the diversity of this massively variable group. Data SummaryGenomes assembled in this project have been deposited in bioproject PRJNA867165 Impact statementBacteria that live inside larger organisms commonly form symbiotic relationships that impact the hosts biology in fundamental ways, such as improving defences against natural enemies or altering host reproduction. Certain groups like ciliates and algae are known to host symbiotic bacteria commonly, but our knowledge of their symbionts evolution and function is limited. One such bacteria is Candidatus Megaira, a Rickettsiales that was first identified in ciliates, then later in algae. To improve the available data for this common but understudied group, we searched the genomes of potential hosts on online databases for Rickettsiales and assembled their genomes. We found 4 Ca. Megaira this way and then used these to find a further 14 genomes in environmental metagenomic data. Overall, we increased the number of known Ca. Megaira draft genomes from 2 to 20. These new genomes show us that Ca. Megaira is far more diverse than previously thought and that it is potentially involved in defensive symbioses. In addition, one genome shows striking resemblance to well characterized symbiont, Wolbachia, in encoding many proteins predicted to interact directly with host proteins. The genomes we have identified and examined here provide baseline resources for future work investigating the real-world interactions between the hyper diverse Ca. Megaira and its various potential hosts, like the economically important Nemacystus decipiens.

microbiology↗

bioRxiv2022

Isolation, culture and characterization of Arsenophonus symbionts from two insect species reveal loss of infectious transmission and extended host range in the apicola-nasoniae group.

Vertically transmitted Heritable microbial symbionts represent an important component of the biology and ecology of invertebrates. These symbioses evolved from ones where infection/acquisition processes occurred within the environment (horizontal transmission). However, the pattern of evolution that follows transition from horizontal to vertical transmission is commonly obscured by the distant relationship between microbes with differing transmission modes. In contrast, the genus Arsenophonus provides an opportunity to investigate these processes with clarity, as it includes members that are obligate vertically transmitted symbionts, facultative vertically transmitted symbionts, strains with mixed modes of transmission and ones that are purely horizontally transmitted. Significantly, some of the strains are culturable and amenable to genetic analysis. We first report the isolation of Arsenophonus nasoniae strain Pv into culture from the ectoparasitic wasp Pachycrepoideus vindemmiae and characterize the symbiosis. We demonstrate maternal vertical transmission and find no evidence for paternal inheritance, infectious transmission or reproductive parasitism phenotypes. This leads us to conclude this strain, in contrast to related strains, is a facultative heritable symbiont which is likely to be beneficial. We then report the serendipitous discovery and onward culture of a strain of Arsenophonus (strain Pb) from the blue butterfly, Polyommatus bellargus. This association extends the range of host species carrying A. nasoniae/A. apicola symbionts beyond the Hymenoptera for the first time. We perform basic metabolic analysis of the isolated strains using Biolog plates. This analysis indicates all strains utilize a restricted range of carbon sources, but these restrictions are particularly pronounced in the A. nasoniae Pv strain that is solely vertically transmitted. Finally, we demonstrate the Arsenophonus strain Pb from the blue butterfly can infect Galleria waxworms, providing a model system for investigating the functional genetics of Arsenophonus-insect interactions.

microbiology↗

bioRxiv2022

Culture and genomic analysis of Arsenophonus apicola sp. nov. isolated from the honeybee Apis mellifera

The genus Arsenophonus has been traditionally considered to be comprised of heritable bacterial symbionts of arthropods. Recent work has reported a microbe related to the type species A. nasoniae as infecting the honey bee, Apis mellifera. The association was unusual for members of the genus in that the microbe-host interaction arose through environmental and social exposure rather than vertical transmission. In this study, we describe the in vitro culture of ArsBeeUS, a strain of this microbe isolated from A. mellifera in the USA. The 16S rRNA sequence of the isolated strain clearly indicates it falls within the genus Arsenophonus. Biolog analysis indicates the bacterium has a restricted range of nutrients that support growth. In vivo experiments demonstrate the strain proliferates rapidly on injection into A. mellifera hosts. We further report the closed genome sequence for the strain. The genome is 3.3 MB and 37.6% GC, which is smaller than A. nasoniae but larger than the genomes reported for non-culturable Arsenophonus symbionts. The genome is complex, with 6 plasmids and 11 predicted intact phage elements, but notably less complex than A. nasoniae. With 92% average nucleotide identity (ANI) to the type strain A. nasoniae, the ArsBeeUS strain isolated is clearly distinct from the type species, and we propose the name Arsenophonus apicola sp. nov. (CECT 30499; LMG 32504).

microbiology↗

bioRxiv2022

Culture and genomic analysis of Symbiopectobacterium purcellii, gen.nov. sp. nov., isolated from the leafhopper Empoasca decipiens

Bacterial endosymbionts are found in multiple arthropod species, where they play crucial roles as nutritional symbionts, defensive symbionts or reproductive parasites. Recent work has highlighted a new clade of heritable microbes within the gammaproteobacteria that enter into both obligate and facultative symbioses, with an obligately required unculturable symbiont recently given the name Cand. Symbiopectobacterium. In this study, we describe a culturable rod shaped non-flagellated bacterial symbiont from this clade isolated from the leafhopper Empoasca decipiens. The symbiont is related to the transovarially-transmitted BEV bacterium that was first isolated from the leafhopper Euscelidius variegatus by Alexander Purcell, and we therefore name the symbiont Symbiopectobacterium purcellii sp. nov. gen. nov. We further report the closed genome sequence for S. purcellii. The genome is atypical for a heritable microbe, being large in size, without profound AT bias and with little evidence of pseudogenization. The genome is predicted to encode Type II, III and VI secretion systems and associated effectors and a non-ribosomal peptide synthase array likely to produce bioactive small molecules. Predicted metabolism is more complete than for other symbionts in the Symbiopectobacterium clade, and the microbe is predicted to synthesize a range of B vitamins. However, Biolog plate analysis indicate metabolism is depauperate compared to the sister clade, represented by Pectobacterium carotovorum. A quorum-sensing pathway related to that of Pectobacterium spp. (containing an overlapping expI-expR1 pair in opposite directions and a "solo" expR2) is evidenced, and LC-MS/MS analysis reveals the presence of 3-hydroxy-C10-HSL as the sole N-acylhomoserine lactone (AHL) in our strain. This AHL profile is profoundly divergent from that of other Erwinia and Pectobacterium spp., which produce mostly 3-oxo-C6- and 3-oxo-C8-HSL and could aid group identification. Thus, this microbe denotes one that has lost certain pathways associated with a saprophytic lifestyle but represents an important baseline against which to compare other members of the genus Symbiopectobacterium that show more profound integration into host biology.

microbiology↗

bioRxiv2021

Large-scale comparative genomics unravels great genomic diversity across the Rickettsia and Ca. Megaira genera and identifies Torix group as an evolutionarily distinct clade.

Rickettsia are intracellular bacteria originally described as arthropod borne pathogens that are emerging as a diverse group of often biologically important, non-pathogenic symbionts of invertebrates and microeukaryotes. However, sparse genomic resources for symbiotic strains and for the sister genus (Candidatus Megaira) inhibit our understanding of Rickettsia evolution and biology. Here, we present the first closed genomes of Ca. Megaira from an alga (Mesostigma viride), and Torix Rickettsia from midge (Culicoides impunctatus) and bed bug (Cimex lectularius) hosts. Additionally, we sequenced and constructed draft genomes for Ca. Megaira from another alga (Carteria cerasiformis), Transitional group Rickettsia from tsetse fly (Glossina morsitans submorsitans), and Torix Rickettsia from a spider mite (Bryobia graminum). We further extract 22 draft genomes from arthropod genome sequencing projects, including 1 Adalia, 4 Transitional, 1 Spotted Fever, 7 Torix, 7 Belli and the first Rhyzobius and Meloidae Rickettsia group genomes. We used new and existing Rickettsia genomes to estimate the phylogeny and metabolic potential across groups and reveal transitions in genomic properties. These data reveal Torix as unique amongst currently described Rickettsia, with highly distinct and diverse accessory genomes. We confirm the presence of a third subclade of Torix, previously only known from gene marker sequences. Further, Torix share an intact pentose phosphate pathway with Ca. Megaira, not observed in other Rickettsia. Considering the distinctness and diversity of Torix, we propose that the group be named Candidatus Tisiphia. The wide host range of Ca. Tisiphia symbionts necessitates onward research to understand the biological and physiological bases of Ca. Tisiphia-host interactions. Importance statementMembers of the genus Rickettsia were originally identified as causative agents of mammalian vector-borne disease. In the last 25 years we have recognised that many Rickettsia are arthropod symbionts, and sit alongside a sister taxon, Ca. Megaira, which are symbiotic associates of microeukaryotes. The lack of genomic information for symbiotic strains affects our ability to determine the evolutionary relationships between strains and understand the biological underpinnings of the different symbioses. We clarify these relationships by assembling 26 genomes of Rickettsia from understudied groups, and the first two Ca. Megaira, from various insects and microeukaryotes. Of note, the accessory genome diversity and broad host range of Torix Rickettsia parallels all other Rickettsia combined. This diversity, alongside the breadth of host species, make the Torix clade an important hidden player in invertebrate biology and physiology. We argue this clade should be given its own genus status, for which we propose Ca. Tisiphia.

microbiology↗

bioRxiv2021

Structure of an ant-myrmecophile-microbe community

Superorganismal ant colonies play host to a menagerie of symbiotic arthropods, termed myrmecophiles, which exhibit varying degrees of social integration into colony life. Such systems permit examination of how animal community interactions influence microbial assemblages. Here, we present an ecologically and phylogenetically comprehensive characterization of an ant-myrmecophile-microbe community in Southern California. Using 16S rRNA profiling, we find that microbiotas of the velvety tree ant (Liometopum occidentale) and its cohort of myrmecophiles are distinguished by species-specific characteristics but nevertheless bear signatures of their behavioral interactions. We found that the host ant microbiome was diverse at all taxonomic levels; that of a myrmecophilous cricket was moderately diverse, while microbiotas of three myrmecophilous rove beetles (Staphylinidae), which have convergently evolved symbiosis with Liometopum, were dominated by intracellular endosymbionts. Yet, despite these compositional differences, similarities between ant and myrmecophile microbiotas correlated with the nature and intimacy of their behavioral relationships. Physical interactions such as grooming and trophallaxis likely facilitate cross-species extracellular microbial sharing. Further, phylogenetic comparisons of microbiotas from myrmecophile rove beetles and outgroups revealed a lack of co-cladogenesis of beetles and intracellular endosymbionts, and limited evidence for convergence among the myrmecophiles intracellular microbiotas. Comparative genomic analyses of the dominant Rickettsia endosymbiont of the most highly socially integrated myrmecophile imply possible functions unrelated to nutrient-provisioning in the host beetles specialized lifestyle. Our findings indicate that myrmecophile microbiotas evolve largely independently of the constraints of deep evolutionary history, and that the transition to life inside colonies, including social interactions with hosts, plays a significant role in structuring bacterial assemblages of these symbiotic insects.

ecology↗

bioRxiv2020

Identifying candidate Culicoides spp. (Diptera: Ceratopogonidae) for the study of interactions with Candidatus Cardinium hertigii (Bacteroidetes).

Culicoides biting midges (Diptera: Ceratopogonidae) are disease vectors responsible for the transmission of several viruses of economic and animal health importance. The recent deployment of Wolbachia with pathogen-blocking capacity to control viral disease transmission by mosquitoes has led to a focus on the potential use of endosymbionts to control arboviruses transmitted by other vector species. Previous screens of Culicoides have described the presence of Candidatus Cardinium hertigii (Bacteroidetes). However, the biological impact of this symbiont is yet to be uncovered and awaits a suitable system to study Cardinium-midge interactions. To identify candidate species to investigate these interactions, accurate knowledge of the distribution of the symbiont within Culicoides populations is needed. We used a sensitive nested PCR assay to screen Cardinium infection in 337 individuals of 25 Culicoides species from both Palearctic and Afrotropical regions. Infections were observed in several vector species including C. imicola and the pulicaris complex (C. pulicaris, C. bysta, C. newsteadi and C. punctatus) with prevalence ranging from low and intermediate, to fixation. Infection in C. pulicaris was very rare in comparison to a previous study, and there is evidence the prior record of high prevalence represents a laboratory contamination error. Phylogenetic analysis based on the Gyrase B gene sequence grouped all new isolates within "group C" of the genus, a clade which has to date been exclusively described in Culicoides. Through a comparison of our results with previous screens, we evaluate the suitability of Cardinium-infected species for future work pertaining to the symbiont.

microbiology↗

bioRxiv2020

Cardinium symbiosis as a potential confounder of mtDNA based phylogeographic inference in Culicoides imicola (Diptera: Ceratopogonidae), a vector of veterinary viruses

Culicoides imicola (Diptera: Ceratopogonidae) is an important Afrotropical and Palearctic vector of disease, transmitting viruses of animal health and economic significance. The apparent incursions of C. imicola into mainland Europe via wind-movement events has made it important to trace this species to better predict new areas of arbovirus outbreaks. A widely used method for tracking dispersal patterns of C. imicola employs a phylogeographic approach anchored on the mtDNA marker COI (cytochrome c oxidase subunit I). However, a problem with this approach is that maternally-inherited symbiotic bacteria can alter the frequency of COI mitochondrial haplotypes (mitotypes), masking the true patterns of movement and gene flow. In this study, we investigate possible associations of the symbiont Cardinium with C. imicola mitotype distribution. Haplotype network analysis indicates the concordance of specific mitotypes with Cardinium infection status in C. imicola populations from the Mediterranean basin and South Africa. This observation urges caution on the single usage of the COI marker to determine population structure and movement in C. imicola, and instead suggests the complementary utilisation of additional molecular markers (e.g. microsatellites and nuclear markers).

microbiology↗

bioRxiv2020

Transitions in symbiosis: evidence for environmental acquisition and social transmission within a clade of heritable symbionts

A dynamic continuum exists from free-living environmental microbes to strict host associated symbionts that are vertically inherited. However, knowledge of the forces that drive transitions in the modes by which symbioses form is lacking. Arsenophonus is a diverse clade of bacterial symbionts, comprising reproductive parasites to coevolving obligate mutualists, in which the predominant mode of transmission is vertical. We describe a symbiosis between a member of the genus Arsenophonus and the Western honey bee. We then present multiple lines of evidence that this symbiont deviates from a heritable model of transmission. Field sampling uncovered marked spatial and seasonal dynamics in symbiont prevalence, and rapid infection loss events were observed in field colonies and individuals in the laboratory. Fluorescent in-situ hybridization showed Arsenophonus localised in the gut, and detection of the bacterium was rare in screens of early honey bee life stages. We directly show horizontal transmission of Arsenophonus between bees under varying social conditions. We conclude that honey bees acquire Arsenophonus through a combination of environmental exposure and social contacts. Together these findings uncover a key link in the Arsenophonus clades trajectory from free-living ancestral life to obligate mutualism, and provide a foundation for studying transitions in symbiotic lifestyle.

evolutionary biology↗

bioRxiv2020

The Paracaedibacter-like endosymbiont of Bodo saltans (Kinetoplastida) uses multiple putative toxin-antitoxin systems to maintain its host association

Bacterial endosymbiosis has been instrumental in eukaryotic evolution, and includes both mutualistic, dependent and parasitic associations. Here we characterize an intracellular bacterium inhabiting the flagellated protist Bodo saltans (Kinetoplastida). We present a complete bacterial genome comprising a 1.39 Mb circular chromosome with 40.6% GC content. Fluorescent in situ hybridisation confirms that the endosymbiont is located adjacent to the nuclear membrane, and a detailed model of its intracellular niche is generated using serial block-face scanning electron microscopy. Phylogenomic analysis shows that the endosymbiont belongs to the Holosporales, most closely related to other -proteobacterial endosymbionts of ciliates and amoebae. Comparative genomics indicates that it has a limited metabolism and is nutritionally host-dependent. However, the endosymbiont genome does encode diverse symbiont-specific secretory proteins, including a type VI secretion system and three separate toxin-antitoxin systems. We show that these systems are actively transcribed and hypothesize they represent a mechanism by which B. saltans becomes addicted to its endosymbiont. Consistent with this idea, attempts to cure Bodo of endosymbionts led to rapid and uniform cell death. This study adds kinetoplastid flagellates to ciliates and amoebae as hosts of Paracaedibacter-like bacteria, suggesting that these antagonistic endosymbioses became established very early in Eukaryotic evolution.

ecology↗

bioRxiv2020

Rapid molecular evolution of Spiroplasma symbionts of Drosophila

Spiroplasma are a group of Mollicutes whose members include plant pathogens, insect pathogens, and endosymbionts of animals. Spiroplasma phenotypes have been repeatedly observed to be spontaneously lost in Drosophila cultures, and several studies have documented a high genomic turnover in Spiroplasma symbionts and plant pathogens. These observations suggest that Spiroplasma evolves quickly in comparison to other insect symbionts. Here, we systematically assess evolutionary rates and patterns of Spiroplasma poulsonii, a natural symbiont of Drosophila. We analysed genomic evolution of sHy within flies, and sMel within in vitro culture over several years. We observed that S. poulsonii substitution rates are among the highest reported for any bacteria, and around two orders of magnitude higher compared with other inherited arthropod endosymbionts. The absence of mismatch repair loci mutS and mutL is conserved across Spiroplasma and likely contributes to elevated substitution rates. Further, the closely related strains sMel and sHy (>99.5% sequence identity in shared loci) show extensive structural genomic differences, which potentially indicates a higher degree of host adaptation in sHy, a protective symbiont of Drosophila hydei. Finally, comparison across diverse Spiroplasma lineages confirms previous reports of dynamic evolution of toxins, and identifies loci similar to the male-killing toxin Spaid in several Spiroplasma lineages and other endosymbionts. Overall, our results highlight the peculiar nature of Spiroplasma genome evolution, which may explain unusual features of its evolutionary ecology.

evolutionary biology↗

bioRxiv2020

The Tissue Tropisms and Transstadial Transmission of a Rickettsia Endosymbiont in the Highland Midge, Culicoides impunctatus (Diptera: Ceratopogonidae)

Rickettsia are a group of intracellular bacteria which can manipulate host reproduction and alter sensitivity to natural enemy attack in a diverse range of arthropods. The maintenance of Rickettsia endosymbionts in insect populations can be achieved through both vertical and horizontal transmission routes. For example, the presence of the symbiont in the follicle cells and salivary glands of Bemisia whiteflies allows Belli group Rickettsia transmission via the germline and plants, respectively. However, the transmission routes of other Rickettsia, such as those in the Torix group of the genus, remain underexplored. Through fluorescence in-situ hybridisation (FISH) and transmission electron microscopy (TEM) screening, this study describes the pattern of Torix Rickettsia tissue tropisms in the highland midge, Culicoides impunctatus (Diptera: Ceratopogonidae). Of note is high intensity of infection of the ovarian suspensory ligament, suggestive of a novel germline targeting strategy. Additionally, localisation of the symbiont in tissues of several developmental stages suggests transstadial transmission is a major route of ensuring maintenance of Rickettsia within C. impunctatus populations. Aside from providing insights into transmission strategies, Rickettsia presence in the fat body of larvae indicates potential host fitness and vector capacity impacts to be investigated in the future. Importance StatementMicrobial symbionts of disease vectors have garnered recent attention due to their ability to alter vectorial capacity. Their consideration as a means of arbovirus control depends on symbiont vertical transmission which leads to spread of the bacteria through a population. Previous work has identified a Rickettsia symbiont present in several vector species of biting midges (Culicoides spp.), however, symbiont transmission strategies and host effects remain underexplored. In this study, we describe the presence of Rickettsia in the ovarian suspensory ligament and the ovarian epithelial sheath of Culicoides impunctatus. Infection of these organs suggest the connective tissue surrounding developing eggs is important for ensuring vertical transmission of the symbiont in midges and possibly other insects. Additionally, our results indicate Rickettsia localisation in the fat body of Culicoides impunctatus. As viruses spread by midges often replicate in the fat body, this implies possible vector competence effects to be further investigated.

microbiology↗