The Wolbachia protein TomO interacts with a host RNA to induce polarization defects in Drosophila oocytes

Wolbachia is an endosymbiont prevalent in arthropods. To maximize its transmission thorough the female germline, Wolbachia induces in infected hosts male‐to‐female transformation, male killing, parthenogenesis, and cytoplasmic incompatibility, depending on the host species and Wolbachia strain involved. However, the molecular mechanisms underlying these host manipulations by Wolbachia remain largely unknown. The Wolbachia strain wMel, an inhabitant of Drosophila melanogaster, impairs host oogenesis only when transplanted into a heterologous host, for example, Drosophila simulans. We found that egg polarity defects induced by wMel infection in D. simulans can be recapitulated in the natural host D. melanogaster by transgenic overexpression of a variant of the Wolbachia protein Toxic manipulator of oogenesis (TomO), TomO_wMel^?HS, in the female germline. RNA immunoprecipitation assays demonstrated that TomO physically associates with orb mRNA, which, as a result, fails to interact with the translation repressor Cup. This leads to precocious translation of Orb, a posterior determinant, and thereby to the misspecification of oocytes and accompanying polarity defects. We propose that the ability of TomO to bind to orb mRNA might provide a means for Wolbachia to enter the oocyte located at the posterior end of the egg chamber, thereby accomplishing secure maternal transmission thorough the female germline.     

Effects of Wolbachia on fitness of the Mediterranean fruit fly (Diptera: Tephritidae)

Wolbachia pipientis is a widespread endosymbiont of insects and other arthropods exerting a wide range of biological effects on their hosts. A growing number of recent studies document the influence of Wolbachia on reproduction and lifespan of insect host species. However, little is known regarding effects of Wolbachia on the demographic traits of different host populations. Moreover, whether different Wolbachia strains exert different effects on fitness components of their hosts remains largely unknown. We studied the effects of (a) the Wolbachia strain wCer2 on fitness components of two laboratory lines of the Mediterranean fruit fly, Ceratitis capitata (Diptera: Tephritidae) and (b) two different Wolbachia strains (wCer2 and wCer4) on one of the Mediterranean fruit fly lines. Wolbachia infection (wCer2) shortens the egg‐to‐adult developmental duration of both C. capitata lines, although it prolongs embryonic development. In one of the two lines, egg‐to‐adult mortality increased. Wolbachia infection shortens adult lifespan (to a different extent in males and females) and reduces female fecundity. The different Wolbachia strains differentially affect both immature mortality and developmental duration, and adult longevity and female fecundity. Our findings demonstrate both differential response of two C. capitata lines to Wolbachia infection and differential effects of two Wolbachia strains on the same Mediterranean fruit fly line. Practical and theoretical implications of our findings are discussed.     

Transinfection of the olive fruit fly Bactrocera oleae with Wolbachia: towards a symbiont‐based population control strategy

The olive fruit fly Bactrocera oleae is responsible for worldwide economic damage. In this report, we describe the first B. oleae lines transinfected with the Wolbachia strain wCer2, an endosymbiont of the cherry fruit fly Rhagoletis cerasi. Immunostaining followed by confocal microscopy, detects high numbers of Wolbachia in embryos as well as in ovarioles and sperm from individuals of both transinfected lines. wCer2 was uniformly distributed in B. oleae egg chambers and the cortex of preblastoderm embryos. Wolbachia is known to manipulate host reproduction with several strategies, one of which is cytoplasmic incompatibility (CI), resulting in embryonic mortality in incompatible crosses. Wolbachia was found to induce complete CI in the novel host, suggesting that symbiont‐based approaches can be used as novel environmentally friendly tools for the control of natural olive fruit fly populations.     

Host tissues as microhabitats for Wolbachia and quantitative insights into the bacterial community in terrestrial isopods

Animal–bacterial symbioses are highly dynamic in terms of multipartite interactions, both between the host and its symbionts as well as between the different bacteria constituting the symbiotic community. These interactions will be reflected by the titres of the individual bacterial taxa, for example via host regulation of bacterial loads or competition for resources between symbionts. Moreover, different host tissues represent heterogeneous microhabitats for bacteria, meaning that host‐associated bacteria might establish tissue‐specific bacterial communities. Wolbachia are widespread endosymbiotic bacteria, infecting a large number of arthropods and filarial nematodes. However, relatively little is known regarding direct interactions between Wolbachia and other bacteria. This study represents the first quantitative investigation of tissue‐specific Wolbachia–microbiota interactions in the terrestrial isopod Armadillidium vulgare. To this end, we obtained a more complete picture of the Wolbachia distribution patterns across all major host tissues, integrating all three feminizing Wolbachia strains (wVulM, wVulC, wVulP) identified to date in this host. Interestingly, the different Wolbachia strains exhibited strain‐specific tissue distribution patterns, with wVulM reaching lower titres in most tissues. These patterns were consistent across different host genetic backgrounds and might reflect different co‐evolutionary histories between the Wolbachia strains and A. vulgare. Moreover, Wolbachia‐infected females carried higher total bacterial loads in several, but not all, tissues, irrespective of the Wolbachia strain. Taken together, this quantitative approach indicates that Wolbachia is part of a potentially more diverse bacterial community, as exemplified by the presence of highly abundant bacterial taxa in the midgut caeca of several A. vulgare populations.     

Drosophila melanogaster brain invasion: pathogenic Wolbachia in central nervous system of the fly

The pathogenic Wolbachia strain wMelPop rapidly over‐replicates in the brain, muscles, and retina of Drosophila melanogaster, causing severe tissue degeneration and premature death of the host. The unique features of this endosymbiont make it an excellent tool to be used for biological control of insects, pests, and vectors of human diseases. To follow the dynamics of bacterial morphology and titer in the nerve cells we used transmission electron microscopy of 3‐d‐old female brains. The neurons and glial cells from central brain of the fly had different Wolbachia titers ranging from single bacteria to large accumulations, tearing cell apart and invading extracellular space. The neuropile regions of the brain were free of wMelPop. Wolbachia tightly interacted with host cell organelles and underwent several morphological changes in nerve cells. Based on different morphological types of bacteria described we propose for the first time a scheme of wMelPop dynamics within the somatic tissue of the host.     

Drosophila melanogaster infected with Wolbachia strain wMelCS prefer cooler temperatures

1. Temperature plays a fundamental role in the dynamics of host–pathogen interactions. Wolbachia is an endosymbiotic bacteria that infects about 40% of arthropod species, which can affect host behaviour and reproduction. Yet, the effect of Wolbachia on host thermoregulatory behaviour is largely unknown, despite its use in disease vector control programs in thermally variable environments. 2. Here, a thermal gradient was used to test whether Drosophila melanogaster infected with Wolbachia strain wMelCS exhibited different temperature preferences (T_p) to uninfected flies. 3. It was found that Wolbachia‐infected flies preferred a cooler mean temperature (T_p = 25.06 ± 0.25 °C) than uninfected flies (T_p = 25.78 ± 0.24 °C). 4. This finding suggests that Wolbachia‐infected hosts might seek out cooler microclimates to reduce exposure to, and lessen the consequences of, high temperatures. This finding has generated hypotheses that will be fruitful in areas of research for exploring the mechanisms by which the change in T_p occurs in this complex and significant host–pathogen–environment interaction.     

Loss of cytoplasmic incompatibility and minimal fecundity effects explain relatively low Wolbachia frequencies in Drosophila mauritiana

Maternally transmitted Wolbachia bacteria infect about half of all insect species. Many Wolbachia cause cytoplasmic incompatibility (CI) and reduced egg hatch when uninfected females mate with infected males. Although CI produces a frequency‐dependent fitness advantage that leads to high equilibrium Wolbachia frequencies, it does not aid Wolbachia spread from low frequencies. Indeed, the fitness advantages that produce initial Wolbachia spread and maintain non‐CI Wolbachia remain elusive. wMau Wolbachia infecting Drosophila mauritiana do not cause CI, despite being very similar to CI‐causing wNo from Drosophila simulans (0.068% sequence divergence over 682,494 bp), suggesting recent CI loss. Using draft wMau genomes, we identify a deletion in a CI‐associated gene, consistent with theory predicting that selection within host lineages does not act to increase or maintain CI. In the laboratory, wMau shows near‐perfect maternal transmission; but we find no significant effect on host fecundity, in contrast to published data. Intermediate wMau frequencies on the island of Mauritius are consistent with a balance between unidentified small, positive fitness effects and imperfect maternal transmission. Our phylogenomic analyses suggest that group‐B Wolbachia, including wMau and wPip, diverged from group‐A Wolbachia, such as wMel and wRi, 6–46 million years ago, more recently than previously estimated.     

SYTO11 staining vs FISH staining: a comparison of two methods to stain Wolbachia pipientis in cell cultures

Aims: The Aedes albopictus C7‐10 cell line was infected with Wolbachia strains wRi and wAlbB to create C7‐10R and C7‐10B cell lines, respectively. We compared two different methods, fluorescence in situ hybridization staining and SYTO11 staining, to describe these new Wolbachia infections in C7‐10. Methods and Results: Both staining methods were as efficient to stain Wolbachia. A formula was developed to quantify Wolbachia infection. The infection levels in C7‐10B and C7‐10R differed. The live stain SYTO11 was found to be useful to visualize Wolbachia in replicating host cells. Its potential cytotoxic effect at high concentration was investigated. Conclusions: C7‐10 supported two Wolbachia infections, constituting new tools to study Wolbachia–host interactions. The different infection levels suggest that wRi and wAlbB have different requirements for their survival in C7‐10 host cell line. Observation of SYTO11‐stained live cells gave new insights on Wolbachia segregation pattern during host cell mitosis. Significance and Impact of the Study: Wolbachia‐induced phenotypes in their arthropod and worm hosts could potentially be used to control pest populations. However, the mechanisms underlying these phenotypes are difficult to study because of Wolbachia’s intracellular lifestyle. The Wolbachia infections in C7‐10 described here could be used as in vitro models to investigate Wolbachia biology.     

Wolbachia affect behavior and possibly reproductive compatibility but not thermoresistance,fecundity, and morphology in a novel transinfected host,Drosophila nigrosparsa

Wolbachia, intracellular endosymbionts, are estimated to infect about half of all arthropod species. These bacteria manipulate their hosts in various ways for their maximum benefits. The rising global temperature may accelerate species migration, and thus, horizontal transfer of Wolbachia may occur across species previously not in contact. We transinfected and then cured the alpine fly Drosophila nigrosparsa with Wolbachia strain wMel to study its effects on this species. We found low Wolbachia titer, possibly cytoplasmic incompatibility, and an increase in locomotion of both infected larvae and adults compared with cured ones. However, no change in fecundity, no impact on heat and cold tolerance, and no change in wing morphology were observed. Although Wolbachia increased locomotor activities in this species, we conclude that D. nigrosparsa may not benefit from the infection. Still, D. nigrosparsa can serve as a host for Wolbachia because vertical transmission is possible but may not be as high as in the native host of wMel, Drosophila melanogaster.     

Tracing the history and ecological context of Wolbachia double infection in a specialist host (Urophora cardui)—parasitoid (Eurytoma serratulae) system

The endosymbiotic bacterium Wolbachia is the most widespread bacteria in insects, yet the ecology of novel acquisitions in natural host populations is poorly understood. Using temporal data separated by 12 years, I tested the hypothesis that immigration of a parasitoid wasp led to transmission of its Wolbachia strain to its dipteran host, resulting in double‐strain infection, and I used geographic and community surveys to explore the history of transmission in fly and parasitoid. Double infection in the fly host was present before immigration of the parasitoid. Equal prevalence of double infection in males and females, constant prevalence before and after immigration in two regions, and increase in one region of immigration indicate little if no competition between strains. Double infection was present throughout the fly's distribution range, but proportions varied highly (0–0.71, mean = 0.26). Two fly‐specific MLST strains, observed in Eastern and Western Europe, respectively, differed at hcpA only. Flies with either fly‐strain could be double infected with the parasitoid's strain. The geographic distribution of double infection implies that it is older than the fly host's extent distribution range and that different proportions of double infection are caused by demographic fluctuations in the fly. The geographic data in combination with community surveys of infections and strains further suggest that the parasitoid strain was the fly's ancestral strain that was transmitted to the parasitoid, that is, the reverse transmission route as first hypothesized. Based on these findings together with a comparison of oviposition strategies of other hosts harboring related Wolbachia strains, I hypothesize that trans‐infection during an insect host's puparial metamorphosis might be important in promoting horizontal transmission among diverse holometabolic taxa.     

Stable coexistence of incompatible Wolbachia along a narrow contact zone in mosquito field populations

In arthropods, the intracellular bacteria Wolbachia often induce cytoplasmic incompatibility (CI) between sperm and egg, which causes conditional embryonic death and promotes the spatial spread of Wolbachia infections into host populations. The ability of Wolbachia to spread in natural populations through CI has attracted attention for using these bacteria in vector‐borne disease control. The dynamics of incompatible Wolbachia infections have been deeply investigated theoretically, whereas in natural populations, there are only few examples described, especially among incompatible infected hosts. Here, we have surveyed the distribution of two molecular Wolbachia strains (wPip11 and wPip31) infecting the mosquito Culex pipiens in Tunisia. We delineated a clear spatial structure of both infections, with a sharp contact zone separating their distribution areas. Crossing experiments with isofemale lines from different localities showed three crossing types: wPip11‐infected males always sterilize wPip31‐infected females; however, while most wPip31‐infected males were compatible with wPip11‐infected females, a few completely sterilize them. The wPip11 strain was thus expected to spread, but temporal dynamics over 7 years of monitoring shows the stability of the contact zone. We examined which factors may contribute to the observed stability, both theoretically and empirically. Population cage experiments, field samples and modelling did not support significant impacts of local adaptation or assortative mating on the stability of wPip infection structure. By contrast, low dispersal probability and metapopulation dynamics in the host Cx. pipiens probably play major roles. This study highlights the need of understanding CI dynamics in natural populations to design effective and sustainable Wolbachia‐based control strategies.     

Wolbachia effects on thermal preference of natural Drosophila melanogaster are influenced by host genetic background,Wolbachia type,and bacterial titer

Temperature plays a fundamental role in the fitness of all organisms. In particular, it strongly affects metabolism and reproduction in ectotherms that have limited physiological capabilities to regulate their body temperature. The influence of temperature variation on the physiology and behaviour of ectotherms is well studied but we still know little about the influence of symbiotic interactions on thermal preference (T_p) of the host. A growing number of studies focusing on the Wolbachia-Drosophila host-symbiont system found that Wolbachia can influence T_p in Drosophila laboratory strains. Here, we investigated the effect of Wolbachia on T_p in wild-type D. melanogaster flies recently collected from nature. Consistent with previous data, we found reduced T_p compared to an uninfected control in one of two fly strains infected with the wMelCS Wolbachia type. Additionally, we, for the first time, found that Wolbachia titer variation influences the thermal preference of the host fly. These data indicate that the interaction of Wolbachia and Drosophila resulting in behavioural variation is strongly influenced by the genetic background of the host and symbiont. More studies are needed to better understand the evolutionary significance of T_p variation influenced by Wolbachia in natural Drosophila populations.     

Wolbachia in wasps parasitic on filth flies with emphasis on Spalangia cameroni

The house fly, Musca domestica L., and the stable fly, Stomoxys calcitrans (L.) (Diptera: Muscidae), are cosmopolitan pests parasitized by a guild of more than two dozen species of wasps. Several species of these wasps have been commercialized as biocontrol agents or are being studied for this purpose. Wolbachia bacteria are known to infect at least some of these wasps and are of interest because infections can dramatically affect insect reproduction. A survey in this parasitoid–fly system detected Wolbachia in 15 of 21 species of wasps and in three of nine species of flies parasitized by these wasps. Phylogenetic analyses using wsp gene sequences identified single isolate infections in most cases. Infections of two and four isolates were detected in Nasonia vitripennis (Walker) and Spalangia cameroni Perkins (Hymenoptera: Pteromalidae), respectively. Laboratory experiments showed infections in S. cameroni to cause an incomplete form of female‐mortality (FM) type cytoplasmic incompatibility (CI). Crosses between uninfected female and infected male partners (♀×♂^w) produced fewer progeny, which had a strong male‐biased sex ratio. Crosses between ♀×♂, ♀^w×♂^w, and ♀^w×♂ produced more progeny, which had a female‐biased sex ratio. Developmental times of progeny were increased when the paternal parent was infected with Wolbachia, regardless of whether the maternal parent was infected or whether offspring developed from fertilized eggs. This result may reflect the action of Wolbachia on components of the seminal fluid that then affect the development of offspring from inseminated females. It is hoped that future studies of Wolbachia in this guild will facilitate the rearing and application of these wasps as biocontrol agents of house fly and stable fly.     

Evidence for a recent horizontal transmission and spatial spread of Wolbachia from endemic Rhagoletis cerasi (Diptera: Tephritidae) to invasive Rhagoletis cingulata in Europe

The widespread occurrence of Wolbachia in arthropods and nematodes suggests that this intracellular, maternally inherited endosymbiont has the ability to cross species boundaries. However, direct evidence for such a horizontal transmission of Wolbachia in nature is scarce. Here, we compare the well‐characterized Wolbachia infection of the European cherry fruit fly, Rhagoletis cerasi, with that of the North American eastern cherry fruit fly, Rhagoletis cingulata, recently introduced to Europe. Molecular genetic analysis of Wolbachia based on multilocus sequence typing and the Wolbachia surface protein wsp showed that all R. cingulata individuals are infected with wCin2 identical to wCer2 in R. cerasi. In contrast, wCin1, a strain identical to wCer1 in R. cerasi, was present in several European populations of R. cingulata, but not in any individual from the United States. Surveys of R. cingulata from Germany and Hungary indicated that in some populations, the frequency of wCin1 increased significantly in just a few years with at least two independent horizontal transmission events. This is corroborated by the analysis of the mitochondrial cytochrome oxidase II gene that showed association of wCin1 with two distinct haplotypes in Germany, one of which is also infected with wCin1 in Hungary. In summary, our study provides strong evidence for a very recent inter‐specific Wolbachia transmission with a subsequent spatial spread in field populations.     

Various infection status and molecular evidence for horizontal transmission and recombination of Wolbachia and Cardinium among rice planthoppers and related species

Wolbachia and Cardinium are widely distributed and are considered important for their ability to disturb reproduction and affect other fitness‐related traits of their hosts. By using multilocus sequence typing (MLST), RFLP (restriction fragment length polymorphism) and 16S ribosomal DNA gene sequencing methods, we extensively surveyed Wolbachia and Cardinium infection status of four predominant rice planthoppers and one kind of leafhopper in different rice fields. The results demonstrated that Sogatella furcifera (Horváth) and Laodelphax striatellus (Fallén) were infected with the same Wolbachia strain (wStri), while Nilaparvata lugens (Stål) and its closely related species Nilaparvata muiri China were infected with two phylogeneticlly distant strains, wLug and wMui, respectively. Three new Wolbachia strains (provisionally named wMfas1, wMfas2 and wMfas3) were detected in the leafhopper Macrosteles fascifrons (Stål). Only S. furcifera was co‐infected with Cardinium, which indicated that the distribution of Cardinium in these rice planthoppers was narrower than that of Wolbachia. Unambiguous intragenic recombination events among these Wolbachia strains and incongruent phylogenetic relationships show that the connections between different Wolbachia strains and hosts were more complex than we expected. These results suggest that horizontal transmission and host associated specialization are two factors affecting Wolbachia and Cardinium infections among planthoppers and their related species.     

Mapping Wolbachia distributions in the adult Drosophila brain

The maternally inherited bacterium Wolbachia infects the germline of most arthropod species. Using Drosophila simulans and D. melanogaster, we demonstrate that localization of Wolbachia to the fat bodies and adult brain is likely also a conserved feature of Wolbachia infection. Examination of three Wolbachia strains (W_Mel, W_Riv, W_Pop) revealed that the bacteria preferentially concentrate in the central brain with low titres in the optic lobes. Distribution within regions of the central brain is largely determined by the Wolbachia strain, while the titre is influenced by both, the host species and the bacteria strain. In neurons of the central brain and ventral nerve cord, Wolbachia preferentially localizes to the neuronal cell bodies but not to axons. All examined Wolbachia strains are present intracellularly or in extracellular clusters, with the pathogenic W_Pop strain exhibiting the largest and most abundant clusters. We also discovered that 16 of 40 lines from the Drosophila Genetic Reference Panel are Wolbachia infected. Direct comparison of Wolbachia infected and cured lines from this panel reveals that differences in physiological traits (chill coma recovery, starvation, longevity) are partially due to host line influences. In addition, a tetracycline‐induced increase in Drosophila longevity was detected many generations after treatment.     

Wolbachia modifies thermal preference in Drosophila melanogaster

Environmental variation can have profound and direct effects on fitness, fecundity, and host–symbiont interactions. Replication rates of microbes within arthropod hosts, for example, are correlated with incubation temperature but less is known about the influence of host–symbiont dynamics on environmental preference. Hence, we conducted thermal preference (T_p) assays and tested if infection status and genetic variation in endosymbiont bacterium Wolbachia affected temperature choice of Drosophila melanogaster. We demonstrate that isogenic flies infected with Wolbachia preferred lower temperatures compared with uninfected Drosophila. Moreover, T_p varied with respect to three investigated Wolbachia variants (wMel, wMelCS, and wMelPop). While uninfected individuals preferred 24.4°C, we found significant shifts of −1.2°C in wMel- and −4°C in flies infected either with wMelCS or wMelPop. We, therefore, postulate that Wolbachia-associated T_p variation within a host species might represent a behavioural accommodation to host–symbiont interactions and trigger behavioural self-medication and bacterial titre regulation by the host.     

Presence of the endosymbiont Wolbachia among some fruit flies (Diptera: Tephritidae) from Iran: A multilocus sequence typing approach

Wolbachia is a widespread endosymbiont of insects with a diverse range of biological effects on its hosts. We studied the prevalence of Wolbachia in some important species of tephritids in Iran. Among different populations of five fruit fly species, Dacus ciliatus (cucurbit fly), Rhagoletis cerasi (cherry fruit fly), Ceratitis capitata (Mediterranean fruit fly), Myiopardalis pardalina (melon fly) and Carypomya vesuviana (jujube fly), two species, R. cerasi and C. vesuviana, showed infection with separate Wolbachia strains, namely wCer6 and wVes1, respectively. C. vesuviana is introduced here as a novel host for Wolbachia. Genotyping of Wolbachia strains in 12 populations of five fruit fly species, using multilocus sequence typing (MLST) and the wsp gene sequence showed the occurrence of two new strains as well as a new strain type (ST) belonging to the A supergroup. On the basis of the results of this study, 12 barcodes under five species of Iranian tephritids have been added to the database of DNA barcodes. Inter- and intra-specific differences among COI sequences showed a clear gap in barcoding among most fruit flies.     

Transinfection and growth discrepancy of Drosophila Wolbachia strain wMel in cell lines of the mosquito Aedes albopictus

Aim: The Wolbachia strain wMel can protect Drosophila melanogaster against pathogenic RNA viruses. To analyse the potential of this inhibitory effect against arboviruses vectorized by these mosquitoes, we here first transinfected the Aedes albopictus Aa23 and C6/36 cell lines with the Wolbachia strain wMel and then monitored their infection dynamics. Methods and Results: Wolbachia strain wMel was transferred into A. albopictus Aa23 and C6/36 cell lines using the shell vial technique. The presence of the bacterium in the transinfected cells was monitored by quantitative PCR and fluorescence in situ hybridization. Bacteria could be detected in the cytoplasm of both the Aa23 and C6/36 cell lines. However, the dynamics and stability of the bacterial infection differed depending on the initial cell background. The Aa23 cell line, which had been treated with a tetracycline antibiotic 2 years previously to eliminate its natural Wolbachia wAlbB‐infecting strain, lost the introduced Wolbachia wMel strain after 12 passages postinfection. In contrast, the C6/36 cell line, which had originally been aposymbiotic, displayed a stable infection with Wolbachia wMel. The bacterial density in C6/36 was greater than that of the A. albopictus RML12 cell line from which the wMel strain had originated. Conclusions: Transient or persistent transinfection of A. albopictus Aa23 and C6/36 cell lines with Wolbachia wMel strain was achieved. The results indicate the influence of the genetic background of mosquito cells in maintaining Wolbachia originating from a distant dipteral host. Significance and Impact of the Study: The cell model built here can now be used to investigate the viral inhibitory effect of the Wolbachia wMel strain against arboviruses such as dengue and chikungunya, which are transmitted by the mosquito A. albopictus.     

The mushroom habitat as an ecological arena for global exchange of Wolbachia

Wolbachia infect a variety of arthropod and nematode hosts, but in arthropods, host phylogenetic relationships are usually poor predictors of strain similarity. This suggests that new infections are often established by horizontal transmission. To gain insight into the factors affecting the probability of horizontal transmission among host species, we ask how host phylogeny, geographical distribution and ecology affect patterns of Wolbachia strain similarity. We used multilocus sequence typing (MLST) to characterize Wolbachia strain similarity among dipteran hosts associated with fleshy mushrooms. Wolbachia Supergroup A was more common than Supergroup B in Diptera, and also more common in mycophagous than non‐mycophagous Diptera. Within Supergroup A, host family within Diptera had no effect on strain similarity, and there was no tendency for Wolbachia strains from sympatric host species to be more similar to one another than to strains from hosts in different biogeographical realms. Supergroup A strains differed between mycophagous and non‐mycophagous Diptera more than expected by chance, suggesting that ecological associations can facilitate horizontal transmission of Wolbachia within mycophagous fly communities. For Supergroup B, there were no significant associations between strain similarity and host phylogeny, biogeography, or ecology. We identified only two cases in which closely related hosts carried closely related Wolbachia strains, evidence that Wolbachia‐host co‐speciation or early introgression can occur but may not be a major contributor to overall strain diversity. Our results suggest that horizontal transmission of Wolbachia can be influenced by host ecology, thus leading to partial restriction of Wolbachia strains or strain groups to particular guilds of insects.