Phylogeny of Wolbachia pipientis based on gltA, groEL and ftsZ gene sequences: clustering of arthropod and nematode symbionts in the F supergroup, and evidence for further diversity in the Wolbachia tree

Genetic characterization of Anaplasma marginale strains from Tunisia using single and multiple gene typing reveals novel variants with an extensive genetic diversity

Anaplasma marginale, which is responsible for bovine anaplasmosis in tropical and subtropical regions, is a tick-borne obligatory intraerythrocytic bacterium of cattle and wild ruminants. In Tunisia, information about the genetic diversity and the phylogeny of A. marginale strains are limited to the msp4 gene analysis. The purpose of this study is to investigate A. marginale isolates infecting 16 cattle located in different bioclimatic areas of northern Tunisia with single gene analysis and multilocus sequence typing methods on the basis of seven partial genes (dnaA, ftsZ, groEL, lipA, secY, recA and sucB). The single gene analysis confirmed the presence of different and novel heterogenic A. marginale strains infecting cattle from the north of Tunisia. The concatenated sequence analysis showed a phylogeographical resolution at the global level and that most of the Tunisian sequence types (STs) formed a separate cluster from a South African isolate and from all New World isolates and strains. By combining the characteristics of each single locus with those of the multi-loci scheme, these results provide a more detailed understanding on the diversity and the evolution of Tunisian A. marginale strains.

First detection of Wolbachia in the New Zealand biota

Wolbachia is one of the most widespread intracellular bacteria on earth, estimated to infect between 40 and 66% of arthropod species in most ecosystems that have been surveyed. Their significance rests not only in their vast distribution, but also in their ability to modify the reproductive biology of their hosts, which can ultimately affect genetic diversity and speciation of infected populations. Wolbachia has yet to be formally identified in the fauna of New Zealand which has high levels of endemic biodiversity and this represents a gap in our understanding of the global biology of Wolbachia. Using High Throughput Sequencing (HTS) of host DNA in conjunction with traditional molecular techniques we identified six endemic Orthoptera species that were positive for Wolbachia infection. In addition, short-sequence amplification with Wolbachia specific primers applied to New Zealand and introduced invertebrates detected a further 153 individuals positive for Wolbachia. From these short-range DNA amplification products sequence data was obtained for the ftsZ gene region from 86 individuals representing 10 host species. Phylogenetic analysis using the sequences obtained in this study reveals that there are two distinct Wolbachia bacteria lineages in New Zealand hosts belonging to recognised Wolbachia supergroups (A and B). These represent the first described instances of Wolbachia in the New Zealand native fauna, including detection in putative parasitoids of infected Orthoptera suggesting a possible transmission path. Our detection of Wolbachia infections of New Zealand species provides the opportunity to study local transmission of Wolbachia and explore their role in the evolution of New Zealand invertebrates.

A novel bacterial symbiont association in the hispid beetle, Octodonta nipae (Coleoptera: Chrysomelidae), their dynamics and phylogeny

The hispid leaf beetle, Octodonta nipae (Maulik), (Coleoptera: Chrysomelidae), is a devastating pest of palm cultivation worldwide. Endosymbiotic bacteria in the genus Wolbachia are arguably one of the most abundant bacterial group associated with arthropods. Owing to its critical effects on host reproduction, Wolbachia has garnered much attention as a prospective future tool for insect pest management. However, their association, infection dynamics, and functionality remain unknown in this insect pest. Here, we diagnosis for the first time, the infection prevalence, and occurrence of Wolbachia in O. nipae. Experimental evidence by the exploration of wsp gene vindicate that O. nipae is naturally infected with bacterial symbiont of genus Wolbachia, showing a complete maternal inheritance with shared a common Wolbachia strain (wNip). Moreover, MLST (gatB, fbpA, coxA, ftsZ, and hcpA) analysis enabled the detections of new sequence type (ST-484), suggesting a particular genotypic association of O. nipae and Wolbachia. Subsequently, quantitative real-time PCR (qPCR) assay demonstrated variable infection density across different life stages (eggs, larvae, pupae and adult male and female), body parts (head, thorax, abdomen), and tissues (ovaries, testes, and guts). Infection density was higher in egg and female adult stage, as well as abdomen and reproductive tissues as compared to other samples. Interestingly, Wolbachia harbored dominantly in a female than the male adult, while, no significant differences were observed between male and female body parts and tissues. Phylogeny of Wolbachia infection associated with O. nipae rectified from all tested life stages were unique and fall within the same monophyletic supergroup-A of Wolbachia clades. The infection density of symbiont is among the valuable tool to understand their biological influence on hosts, and this latest discovery would facilitate the future investigations to understand the host-symbiont complications and its prospective role as a microbiological agent to reduce pest populations.

Biological characterization of Aedes albopictus (Diptera: Culicidae) in Argentina: implications for arbovirus transmission

Aedes albopictus (Diptera: Culicidae) is an invasive mosquito, native to Asia, that has expanded its range worldwide. It is considered to be a public health threat as it is a competent vector of viruses of medical importance, including dengue, chikungunya, and Zika. Despite its medical importance there is almost no information on biologically important traits of Ae. albopictus in Argentina. We studied life cycle traits, demographic parameters and analyzed the competence of this mosquito as a virus vector. In addition, we determined the prevalence of Wolbachia strains in Ae. albopictus as a first approach to investigate the potential role of this bacteria in modulating vector competence for arboviruses. We observed low hatch rates of eggs, which led to a negative growth rate. We found that Ae. albopictus individuals were infected with Wolbachia in the F1 but while standard superinfection with wAlbA and wAlbB types was found in 66.7% of the females, 16.7% of the females and 62.5% of the males were single-infected with the wAlbB strain. Finally, despite high levels of infection and dissemination, particularly for chikungunya virus, Ae. albopictus from subtropical Argentina were found to be relatively inefficient vectors for transmission of both chikungunya and dengue viruses.

Validation of onchocerciasis biomarker N-acetyltyramine-O-glucuronide (NATOG)

The Neglected Tropical Disease onchocerciasis is a parasitic disease. Despite many control programmes by the World Health Organization (WHO), large communities in West and Central Africa are still affected. Besides logistic challenges during biannual mass drug administration, the lack of a robust, point-of-care diagnostic is limiting successful eradication of onchocerciasis. Towards the implementation of a non-invasive and point-of-care diagnostic, we have recently reported the discovery of the biomarker N-acetyltyramine-O-glucuronide (NATOG) in human urine samples using a metabolomics-mining approach. NATOG's biomarker value was enhanced during an investigation in a rodent model. Herein, we further detail the specificity of NATOG in active onchocerciasis infections as well as the co-infecting parasites Loa loa and Mansonella perstans. Our results measured by liquid chromatography coupled with mass spectrometry (LC-MS) reveal elevated NATOG values in mono- and co-infection samples only in the presence of the nematode Onchocerca volvulus. Metabolic pathway investigation of l-tyrosine/tyramine in all investigated nematodes uncovered an important link between the endosymbiotic bacterium Wolbachia and O. volvulus for the biosynthesis of NATOG. Based on these extended studies, we suggest NATOG as a biomarker for tracking active onchocerciasis infections and provide a threshold concentration value of NATOG for future diagnostic tool development.

Unique clade of alphaproteobacterial endosymbionts induces complete cytoplasmic incompatibility in the coconut beetle

Maternally inherited bacterial endosymbionts in arthropods manipulate host reproduction to increase the fitness of infected females. Cytoplasmic incompatibility (CI) is one such manipulation, in which uninfected females produce few or no offspring when they mate with infected males. To date, two bacterial endosymbionts, Wolbachia and Cardinium, have been reported as CI inducers. Only Wolbachia induces complete CI, which causes 100% offspring mortality in incompatible crosses. Here we report a third CI inducer that belongs to a unique clade of Alphaproteobacteria detected within the coconut beetle, Brontispa longissima This beetle comprises two cryptic species, the Asian clade and the Pacific clade, which show incompatibility in hybrid crosses. Different bacterial endosymbionts, a unique clade of Alphaproteobacteria in the Pacific clade and Wolbachia in the Asian clade, induced bidirectional CI between hosts. The former induced complete CI (100% mortality), whereas the latter induced partial CI (70% mortality). Illumina MiSeq sequencing and denaturing gradient gel electrophoresis patterns showed that the predominant bacterium detected in the Pacific clade of B. longissima was this unique clade of Alphaproteobacteria alone, indicating that this endosymbiont was responsible for the complete CI. Sex distortion did not occur in any of the tested crosses. The 1,160 bp of 16S rRNA gene sequence obtained for this endosymbiont had only 89.3% identity with that of Wolbachia, indicating that it can be recognized as a distinct species. We discuss the potential use of this bacterium as a biological control agent.

A Small Wolbachia Protein Directly Represses Phage Lytic Cycle Genes in "Candidatus Liberibacter asiaticus" within Psyllids

Huanglongbing (HLB) is a severe disease of citrus caused by an uncultured alphaproteobacterium "Candidatus Liberibacter asiaticus" and transmitted by Asian citrus psyllids (Diaphorina citri). Two prophage genomes, SC1 and SC2, integrated in "Ca. Liberibacter asiaticus" strain UF506 were described previously, and very similar prophages are found resident in the majority of "Ca. Liberibacter asiaticus" strains described worldwide. The SC1 lytic cycle is marked by upregulation of prophage late genes, including a functional holin (SC1_gp110); these late genes are activated when "Ca. Liberibacter asiaticus" is in planta, but not when infecting the psyllid host. We previously reported that the holin promoter is strongly and constitutively active in Liberibacter crescens (a cultured proxy for uncultured "Ca. Liberibacter asiaticus") but is suppressed in a dose-dependent manner by crude aqueous extracts from D. citri applied exogenously. Here we report that the suppressor activity of the crude psyllid extract was heat labile and abolished by proteinase K treatment, indicating a proteinaceous repressor and of a size smaller than 30 kDa. The repressor was affinity captured from D. citri aqueous extracts using biotinylated holin promoter DNA immobilized on magnetic beads and subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS). Protein database interrogation was used to identify a small DNA-binding protein encoded by a gene carried by Wolbachia strain wDi, a resident endosymbiont of D. citri as the repressor. The in vitro-translated Wolbachia repressor protein was able to penetrate L. crescens cells, bind to "Ca. Liberibacter asiaticus" promoter DNA, and partially suppress holin promoter-driven β-glucuronidase (GUS) activity, indicating potential involvement of an additional interacting partner(s) or posttranslational modification(s) for complete suppression. Expression of the Wolbachia repressor protein appeared to be constitutive irrespective of "Ca. Liberibacter asiaticus" infection status of the insect host. IMPORTANCE Host acquisition of a new microbial species can readily perturb the dynamics of preexisting microbial associations. Molecular cross talk between microbial associates may be necessary for efficient resource allocation and enhanced survival. Classic examples involve quorum sensing (QS), which detects population densities and is both used and coopted to control expression of bacterial genes, including host adaptation factors. We report that a 56-amino-acid repressor protein made by the resident psyllid endosymbiont Wolbachia can enter cells of Liberibacter crescens, a cultured proxy for the uncultured psyllid endosymbiont "Ca. Liberibacter asiaticus" and repress "Ca. Liberibacter asiaticus" phage lytic cycle genes. Such repression in "Ca. Liberibacter asiaticus" may be critical to survival of both endosymbionts, since phage-mediated lysis would likely breach the immunogenic threshold of the psyllid, invoking a systemic and nonspecific innate immune reaction.

Molecular diversity of Wolbachia in Lepidoptera: Prevalent allelic content and high recombination of MLST genes

Wolbachia are common endosymbiotic bacteria of Arthropoda and Nematoda that are ordinarily transmitted vertically in host lineages through the egg cytoplasm. Despite the great interest in the Wolbachia symbiont, many issues of its biology remain unclear, including its evolutionary history, routes of transfer among species, and the molecular mechanisms underlying the symbiont's effect on its host. In this report, we present data relating to Wolbachia infection in 120 species of 13 Lepidoptera families, mostly butterflies, from West Siberian localities based on Multilocus sequence typing (MLST) and the wsp locus and perform a comprehensive survey of the distribution of Wolbachia and its genetic diversity in Lepidoptera worldwide. We observed a high infection incidence in the studied region; this finding is probably also true for other temperate latitude regions because many studied species have broad Palearctic and even Holarctic distribution. Although 40 new MLST alleles and 31 new STs were described, there was no noticeable difference in the MLST allele content in butterflies and probably also in moths worldwide. A genetic analysis of Wolbachia strains revealed the MLST allele core in lepidopteran hosts worldwide, viz. the ST-41 allele content. The key finding of our study was the detection of rampant recombination among MLST haplotypes. High rates of homologous recombination between Wolbachia strains indicate a substantial contribution of genetic exchanges to the generation of new STs. This finding should be considered when discussing issues related to the reconstruction of Wolbachia evolution, divergence time, and the routes of Wolbachia transmission across arthropod hosts.

Multigenetic characterization of 'Candidatus Xenohaliotis californiensis'

'Candidatus Xenohaliotis californiensis' (or Ca.Xc) is the aetiological agent of withering syndrome, a chronic wasting disease affecting most if not all North American species of abalone, and has been described as a Rickettsiales-like prokaryote. Genetic data regarding this species are limited to the 16S rRNA gene. The inability to grow it axenically has hindered its genetic and genomic characterization and, in consequence, a thorough analysis of its systematics. Here, we amplified and sequenced five genes (16S rRNA, 23S rRNA, ftsZ, virD4 and virB11) of Ca.Xc from infected abalone to analyse its phylogenetic position. Phylogenies from concatenated DNA and amino acid sequences with representative genera of most Rickettsiales unequivocally place Ca.Xc in the family Anaplasmataceae. Furthermore, the family has two reciprocally monophyletic lineages: one leading to (Neorickettsia, Ca.Xc) and the other to ((Ehrlichia, Anaplasma), Wolbachia)). A molecular-clock Bayesian reconstruction places Ca.Xc as the most basal lineage in Anaplasmataceae. These phylogenetic hypotheses shed light on patterns of host evolution and of ecological transitions. Specifically, Neorickettsia and Ca.Xc inhabit aquatic hosts whereas the remaining Anaplasmataceae are found in terrestrial hosts. Additionally, our evolutionary timeline places the directly transmitted marine Ca.Xc as the basal Anaplasmataceae, ancestral to both freshwater and terrestrial species with adaptations leading to more complex life cycles involving intermediate vectors or reservoir species; this supports the hypothesis of a marine origin for this bacterial family.

Comparative Genomics of a Parthenogenesis-Inducing Wolbachia Symbiont

Wolbachia is an intracellular symbiont of invertebrates responsible for inducing a wide variety of phenotypes in its host. These host-Wolbachia relationships span the continuum from reproductive parasitism to obligate mutualism, and provide a unique system to study genomic changes associated with the evolution of symbiosis. We present the genome sequence from a parthenogenesis-inducing Wolbachia strain (wTpre) infecting the minute parasitoid wasp Trichogramma pretiosum. The wTpre genome is the most complete parthenogenesis-inducing Wolbachia genome available to date. We used comparative genomics across 16 Wolbachia strains, representing five supergroups, to identify a core Wolbachia genome of 496 sets of orthologous genes. Only 14 of these sets are unique to Wolbachia when compared to other bacteria from the Rickettsiales. We show that the B supergroup of Wolbachia, of which wTpre is a member, contains a significantly higher number of ankyrin repeat-containing genes than other supergroups. In the wTpre genome, there is evidence for truncation of the protein coding sequences in 20% of ORFs, mostly as a result of frameshift mutations. The wTpre strain represents a conversion from cytoplasmic incompatibility to a parthenogenesis-inducing lifestyle, and is required for reproduction in the Trichogramma host it infects. We hypothesize that the large number of coding frame truncations has accompanied the change in reproductive mode of the wTpre strain.

Detection and Localization of Wolbachia in Thrips palmi Karny (Thysanoptera: Thripidae)

Thrips palmi Karny is a globally distributed polyphagous agricultural pest. It causes huge economic loss by its biological behaviors like feeding, reproduction and transmission of tospoviruses. Since T. palmi shows close morphological similarities with other thrips species, we employed mitochondrial cytochrome oxidase 1 (mtCO1) gene as a molecular marker. BLAST analysis of this sequence helped us to identify the collected specimen as T. palmi. We observed the female to male ratio of about 3:1 from collected samples and suspected the presence of Wolbachia. The presence of Wolbachia was detected by PCR using genus specific primers of 16S rRNA gene. Further confirmation of Wolbachia strain was achieved by conducting PCR amplification of three ubiquitous genes ftsZ, gatB and groEL. A phylogenetic tree was constructed with concatenated sequences of ftsZ and gatB gene to assign supergroup to Wolbachia. Finally, we localized Wolbachia in abdominal region of the insect using fluorescent in situ hybridization with the help of confocal microscope. Our result confirmed the presence of Wolbachia supergroup B strain for the first time in T. palmi.

Breakdown of coevolution between symbiotic bacteria Wolbachia and their filarial hosts

Wolbachia is an alpha-proteobacterial symbiont widely distributed in arthropods. Since the identification of Wolbachia in certain animal-parasitic nematodes (the Onchocercidae or filariae), the relationship between arthropod and nematode Wolbachia has attracted great interest. The obligate symbiosis in filariae, which renders infected species susceptible to antibiotic chemotherapy, was held to be distinct from the Wolbachia-arthropod relationship, typified by reproductive parasitism. While co-evolutionary signatures in Wolbachia-arthropod symbioses are generally weak, reflecting horizontal transmission events, strict co-evolution between filariae and Wolbachia has been reported previously. However, the absence of close outgroups for phylogenetic studies prevented the determination of which host group originally acquired Wolbachia. Here, we present the largest co-phylogenetic analysis of Wolbachia in filariae performed to date including: (i) a screening and an updated phylogeny of Wolbachia; (ii) a co-phylogenetic analysis; and (iii) a hypothesis on the acquisition of Wolbachia infection. First, our results show a general overestimation of Wolbachia occurrence and support the hypothesis of an ancestral absence of infection in the nematode phylum. The accuracy of supergroup J is also underlined. Second, although a global pattern of coevolution remains, the signal is derived predominantly from filarial clades associated with Wolbachia in supergroups C and J. In other filarial clades, harbouring Wolbachia supergroups D and F, horizontal acquisitions and secondary losses are common. Finally, our results suggest that supergroup C is the basal Wolbachia clade within the Ecdysozoa. This hypothesis on the origin of Wolbachia would change drastically our understanding of Wolbachia evolution.

Discovery of a new Wolbachia supergroup in cave spider species and the lateral transfer of phage WO among distant hosts

Wolbachia are widespread intracellular bacteria infecting the major classes of arthropods and some filarial nematodes. In arthropods, Wolbachia have evolved various intriguing reproductive manipulations, including cytoplasmic incompatibility, parthenogenesis, feminization, and male killing. Sixteen supergroups of Wolbachia have been identified, named A-Q (except G). Though Wolbachia present great diversity in arthropods, spiders, especially cave spiders, are still a poorly surveyed group of Wolbachia hosts. Here, we report a novel Wolbachia supergroup from nine Telema cave spiders (Araneae: Telemidae) based on five molecular markers (16S rRNA, ftsZ, gltA, groEL, and coxA). In addition, phage WO, which was previously reported only in Wolbachia supergroups A, B, and F, infects this new Wolbachia supergroup. We detected a 100% infection rate for phage WO and Wolbachia in Telema species. The phylogenetic trees of phage WO and Wolbachia are not congruent, which suggests that horizontal transfer of phage WO has occurred in these secluded species. Additionally, these data indicate Telema-Wolbachia-phage WO may be a good model for exploring the horizontal transfer history of WO among different host species.

Closely coupled evolutionary history of ecto- and endosymbionts from two distantly related animal phyla

The level of integration between associated partners can range from ectosymbioses to extracellular and intracellular endosymbioses, and this range has been assumed to reflect a continuum from less intimate to evolutionarily highly stable associations. In this study, we examined the specificity and evolutionary history of marine symbioses in a group of closely related sulphur-oxidizing bacteria, called Candidatus Thiosymbion, that have established ecto- and endosymbioses with two distantly related animal phyla, Nematoda and Annelida. Intriguingly, in the ectosymbiotic associations of stilbonematine nematodes, we observed a high degree of congruence between symbiont and host phylogenies, based on their ribosomal RNA (rRNA) genes. In contrast, for the endosymbioses of gutless phallodriline annelids (oligochaetes), we found only a weak congruence between symbiont and host phylogenies, based on analyses of symbiont 16S rRNA genes and six host genetic markers. The much higher degree of congruence between nematodes and their ectosymbionts compared to those of annelids and their endosymbionts was confirmed by cophylogenetic analyses. These revealed 15 significant codivergence events between stilbonematine nematodes and their ectosymbionts, but only one event between gutless phallodrilines and their endosymbionts. Phylogenetic analyses of 16S rRNA gene sequences from 50 Cand. Thiosymbion species revealed seven well-supported clades that contained both stilbonematine ectosymbionts and phallodriline endosymbionts. This closely coupled evolutionary history of marine ecto- and endosymbionts suggests that switches between symbiotic lifestyles and between the two host phyla occurred multiple times during the evolution of the Cand. Thiosymbion clade, and highlights the remarkable flexibility of these symbiotic bacteria.

Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius

The common bed bug (Cimex lectularius) has been a persistent pest of humans for thousands of years, yet the genetic basis of the bed bug's basic biology and adaptation to dense human environments is largely unknown. Here we report the assembly, annotation and phylogenetic mapping of the 697.9-Mb Cimex lectularius genome, with an N50 of 971 kb, using both long and short read technologies. A RNA-seq time course across all five developmental stages and male and female adults generated 36,985 coding and noncoding gene models. The most pronounced change in gene expression during the life cycle occurs after feeding on human blood and included genes from the Wolbachia endosymbiont, which shows a simultaneous and coordinated host/commensal response to haematophagous activity. These data provide a rich genetic resource for mapping activity and density of C. lectularius across human hosts and cities, which can help track, manage and control bed bug infestations.

Flea-Associated Bacterial Communities across an Environmental Transect in a Plague-Endemic Region of Uganda

The vast majority of human plague cases currently occur in sub-Saharan Africa. The primary route of transmission of Yersinia pestis, the causative agent of plague, is via flea bites. Non-pathogenic flea-associated bacteria may interact with Y. pestis within fleas and it is important to understand what factors govern flea-associated bacterial assemblages. Six species of fleas were collected from nine rodent species from ten Ugandan villages between October 2010 and March 2011. A total of 660,345 16S rRNA gene DNA sequences were used to characterize bacterial communities of 332 individual fleas. The DNA sequences were binned into 421 Operational Taxonomic Units (OTUs) based on 97% sequence similarity. We used beta diversity metrics to assess the effects of flea species, flea sex, rodent host species, site (i.e. village), collection date, elevation, mean annual precipitation, average monthly precipitation, and average monthly temperature on bacterial community structure. Flea species had the greatest effect on bacterial community structure with each flea species harboring unique bacterial lineages. The site (i.e. village), rodent host, flea sex, elevation, precipitation, and temperature also significantly affected bacterial community composition. Some bacterial lineages were widespread among flea species (e.g. Bartonella spp. and Wolbachia spp.), but each flea species also harbored unique bacterial lineages. Some of these lineages are not closely related to known bacterial diversity and likely represent newly discovered lineages of insect symbionts. Our finding that flea species has the greatest effect on bacterial community composition may help future investigations between Yersinia pestis and non-pathogenic flea-associated bacteria. Characterizing bacterial communities of fleas during a plague epizootic event in the future would be helpful.

Broader prevalence of Wolbachia in insects including potential human disease vectors

Wolbachia are intracellular, maternally transmitted bacteria considered the most abundant endosymbionts found in arthropods. They reproductively manipulate their host in order to increase their chances of being transmitted to the offspring, and currently are being used as a tool to control vector-borne diseases. Studies on distribution of Wolbachia among its arthropod hosts are important both for better understanding why this bacterium is so common, as well as for its potential use as a biological control agent. Here, we studied the incidence of Wolbachia in a broad range of insect species, collected from different regions of Brazil, using three genetic markers (16S rRNA, wsp and ftsZ), which varied in terms of their sensitivity to detect this bacterium. The overall incidence of Wolbachia among species belonging to 58 families and 14 orders was 61.9%. The most common positive insect orders were Coleoptera, Diptera, Hemiptera and Hymenoptera, with Diptera and Hemiptera having the highest numbers of Wolbachia-positive families. They included potential human disease vectors whose infection status has never been reported before. Our study further shows the importance of using quantitative polymerase chain reaction for high-throughput and sensitive Wolbachia screening.

A screen of maternally inherited microbial endosymbionts in oribatid mites (Acari: Oribatida)

We determined the distribution of microbial endosymbionts as possible agents of parthenogenesis in Oribatida. We screened mites from 20 species of 14 families suspected to be parthenogenetic from the absence or rarity of males. Our research included parthenogenesis-inducing bacteria Wolbachia spp., Cardinium spp., Rickettsia spp., and additionally Arsenophonus, Spiroplasma and microsporidia that can also manipulate host reproduction. We detected the endosymbionts by PCR-based methods and transmission electron microscopy (TEM) observation of fixed and stained preparations of host cells. We detected Wolbachia only in one Oribatida species, Oppiella nova, by identifying Wolbachia genes using PCR. TEM observations confirmed infection by the endosymbiont in O. nova and its lack in other Oribatida species. Sequence analysis of hcpA and fbpA genes showed that the Wolbachia strain from O. nova was different from strains characterized in some insects, crustaceans (Isopoda), mites (Tetranychidae), springtails (Hexapoda) and roundworms (Nematoda). The analysis strongly suggested that the Wolbachia sp. strain found in O. nova did not belong to supergroups A, B, C, D, E, F, H or M. We found that the sequences of Wolbachia from O. nova were clearly distantly related to sequences from the bacteria of the other supergroups. This observation makes O. nova a unique Wolbachia host in terms of the distinction of the strain. The role of these micro-organisms in O. nova remains unknown and is an issue to investigate.

Genetic variation amongst biotypes of Dactylopius tomentosus

The tomentose cochineal scale insect, Dactylopius tomentosus (Lamarck) (Hemiptera: Dactylopiidae), is an important biological control agent against invasive species of Cylindropuntia (Caryophyllales: Cactaceae). Recent studies have demonstrated that this scale is composed of host-affiliated biotypes with differential host specificity and fitness on particular host species. We investigated genetic variation and phylogenetic relationships among D. tomentosus biotypes and provenances to examine the possibility that genetic diversity may be related to their host-use pattern, and whether their phylogenetic relationships would give insights into taxonomic relatedness of their host plants. Nucleotide sequence comparison was accomplished using sequences of the mitochondrial cytochrome c oxidase I (COI) gene. Sequences of individuals from the same host plant within a region were identical and characterized by a unique haplotype. Individuals belonging to the same biotype but from different regions had similar haplotypes. However, haplotypes were not shared between different biotypes. Phylogenetic analysis grouped the monophyletic D. tomentosus into 3 well-resolved clades of biotypes. The phylogenetic relationships and clustering of biotypes corresponded with known taxonomic relatedness of their hosts. Two biotypes, Fulgida and Mamillata, tested positive for Wolbachia (α-Proteobacteria), a common endosymbiont of insects. The Wolbachia sequences were serendipitously detected by using insect-specific COI DNA barcoding primers and are most similar to Wolbachia Supergroup F strains. This study is the first molecular characterization of cochineal biotypes that, together with Wolbachia sequences, contribute to the better identification of the biotypes of cochineal insects and to the biological control of cacti using host-specific biotypes of the scale.

Identification and ultrastructural characterization of the Wolbachia symbiont in Litomosoides chagasfilhoi

BACKGROUND

Filarial nematodes are arthropod-transmitted parasites of vertebrates that affect more than 150 million people around the world and remain a major public health problem throughout tropical and subtropical regions. Despite the importance of these nematodes, the current treatment strategies are not efficient in eliminating the parasite. The main strategy of control is based on chemotherapy with diethylcarbamazine, albendazole and ivermectin. In the 1970s, it was found that some filarids possess endosymbiotic bacteria that are important for the development, survival and infectivity of the nematodes. These bacteria belong to the genus Wolbachia, which is a widespread and abundant intracellular symbiont in worms. Knowledge about the structure of the bacteria and their relationship with their nematode hosts may allow new perspectives for the control of filarial nematodes.

METHODS

In this study, we used transmission electron microscopy combined with three-dimensional approaches to observe the structure of the endosymbiont of the filarial nematode Litomosoides chagasfilhoi, an experimental model for the study of lymphatic filariasis. In addition, the bacterium was classified based on PCR analyses.

RESULTS

The bacterium was mainly found in the hypodermis and in the female reproductive system in close association with host cell structures, such as the nucleus and endoplasmic reticulum. Our ultrastructural data also showed that the symbiont envelope is composed of two membrane units and is enclosed in a cytoplasmic vacuole, the symbiosome. Molecular data revealed that the bacterium of L. chagasfilhoi shares 100% identity with the Wolbachia endosymbiont of Litomosoides galizai.

CONCLUSIONS

Here we described ultrastructural aspects of the relationship of the Wolbachia with the filarial nematode Litomosoides chagasfilhoi and the findings lead us to consider this relationship as a mutualistic symbiosis.

Phylogenomic analyses uncover origin and spread of the Wolbachia pandemic

Of all obligate intracellular bacteria, Wolbachia is probably the most common. In general, Wolbachia are either widespread, opportunistic reproductive parasites of arthropods or essential mutualists in a single group of filarial nematodes, including many species of medical significance. To date, a robust phylogenetic backbone of Wolbachia is lacking and consequently, many Wolbachia-related phenomena cannot be discussed in a broader evolutionary context. Here we present the first comprehensive phylogenomic analysis of Wolbachia supergroup relationships based on new whole-genome-shotgun data. Our results suggest that Wolbachia has switched between its two major host groups at least twice. The ability of some arthropod-infecting Wolbachia to universally infect and to adapt to a broad range of hosts quickly is restricted to a single monophyletic lineage (containing supergroups A and B). Thus, the currently observable pandemic has likely a single evolutionary origin and is unique within the radiation of Wolbachia strains.

Anterior foregut microbiota of the glassy-winged sharpshooter explored using deep 16S rRNA gene sequencing from individual insects

The glassy-winged sharpshooter (GWSS) is an invasive insect species that transmits Xylella fastidiosa, the bacterium causing Pierce's disease of grapevine and other leaf scorch diseases. X. fastidiosa has been shown to colonize the anterior foregut (cibarium and precibarium) of sharpshooters, where it may interact with other naturally-occurring bacterial species. To evaluate such interactions, a comprehensive list of bacterial species associated with the sharpshooter cibarium and precibarium is needed. Here, a survey of microbiota associated with the GWSS anterior foregut was conducted. Ninety-six individual GWSS, 24 from each of 4 locations (Bakersfield, CA; Ojai, CA; Quincy, FL; and a laboratory colony), were characterized for bacteria in dissected sharpshooter cibaria and precibaria by amplification and sequencing of a portion of the 16S rRNA gene using Illumina MiSeq technology. An average of approximately 150,000 sequence reads were obtained per insect. The most common genus detected was Wolbachia; sequencing of the Wolbachia ftsZ gene placed this strain in supergroup B, one of two Wolbachia supergroups most commonly associated with arthropods. X. fastidiosa was detected in all 96 individuals examined. By multilocus sequence typing, both X. fastidiosa subspecies fastidiosa and subspecies sandyi were present in GWSS from California and the colony; only subspecies fastidiosa was detected in GWSS from Florida. In addition to Wolbachia and X. fastidiosa, 23 other bacterial genera were detected at or above an average incidence of 0.1%; these included plant-associated microbes (Methylobacterium, Sphingomonas, Agrobacterium, and Ralstonia) and soil- or water-associated microbes (Anoxybacillus, Novosphingobium, Caulobacter, and Luteimonas). Sequences belonging to species of the family Enterobacteriaceae also were detected but it was not possible to assign these to individual genera. Many of these species likely interact with X. fastidiosa in the cibarium and precibarium.

Redescription of Cercopithifilaria rugosicauda (Böhm & Supperer, 1953) (Spirurida: Onchocercidae) of roe deer, with an emended diagnosis of the genus Cercopithifilaria and a genetic characterisation

Newly collected material of Cercopithifilaria rugosicauda from roe deer Capreolus capreolus was analysed and compared to descriptions of C. rugosicauda from Austria and Hungary. The present specimens were assigned to the genus Cercopithifilaria using both morphological and molecular analyses. Complementary morphological data on the males and microfilariae of C. rugosicauda were described. The main morphological characters of different species of Cercopithifilaria were outlined and an emended generic diagnosis proposed. A genetic characterisation based on the analyses of cox1 and 12S rDNA sequences was reported supporting that C. rugosicauda was included in the clade of the genus Cercopithifilaria distinctly from other congeneric species available. However, these molecular analyses did not solve the relationships between the species of Cercopithifilaria. These could be approached using morphological characters that might be representative of their evolutionary history. In addition, Wolbachia was not seen in C. rugosicauda, either by immunohistological or by molecular approaches.

Wolbachia infection status and genetic structure in natural populations of Polytremis nascens (Lepidoptera: Hesperiidae)

The maternally inherited obligate bacteria Wolbachia is known for infecting the reproductive tissues of a wide range of arthropods. In this study, we surveyed Wolbachia infections in Polytremis nascens (Lepidoptera: Hesperiidae) from 14 locations in China by amplifying the 16S rRNA gene with a nested PCR method and revealed the effect of Wolbachia on host mitochondrial DNA. The results show that 31% (21/67) are Wolbachia positive among all specimens and mainly prevails in southern populations in China. No significant difference in the prevalence is found between the sexes. Notably, the nucleotide diversity of Wolbachia infected butterflies is smaller compared to that of uninfected butterflies. The mitochondrial DNA of infected group appear to be not evolving neutrally (Tajima's D value=-2.3303 and Fu's F values=-3.7068). The analysis of molecular variance shows significant differentiation of mitochondrial haplotypes between infected and uninfected specimens (FST=0.6064). The mismatch analysis speculated the different expansion pattern in Wolbachia infected specimens and all P. nascens specimens. These results suggest that the populations of P. nascens may have recently been subjected to a Wolbachia-induced sweep. Additionally, phylogenetic analysis differentiated the mitochondrial haplotypes of P. nascens into three major clades. The clades are in perfect agreement with the pattern of Wolbachia infection. One of the clades grouped with the butterflies infected with Wolbachia. The remaining two clades grouped with uninfected butterflies from the central-west of China populations and Eastern and Southern China populations respectively, which are isolated mainly by the Yangtze River. The analysis of haplotype networks, geographic distribution and population size change shows that Haplotype 1 in central-west of China is the ancestral haplotype and the populations of P. nascens are expanded.

Diversity and evolution of the Wolbachia endosymbionts of Bemisia (Hemiptera: Aleyrodidae) whiteflies

Wolbachia is the most prevalent symbiont described in arthropods to date. Wolbachia can manipulate host reproduction, provide nutrition to insect hosts and protect insect hosts from pathogenic viruses. So far, 13 supergroups of Wolbachia have been identified. The whitefly Bemisia tabaci is a complex containing more than 28 morphologically indistinguishable cryptic species. Some cryptic species of this complex are invasive. In this study, we report a comprehensive survey of Wolbachia in B. tabaci and its relative B. afer from 1658 insects representing 54 populations across 13 provinces of China and one state of Australia. Based on the results of PCR or sequencing of the 16S rRNA gene, the overall rates of Wolbachia infection were 79.6% and 0.96% in the indigenous and invasive Bemisia whiteflies, respectively. We detected a new Wolbachia supergroup by sequencing five molecular marker genes including 16S rRNA, groEL, gltA, hcpA, and fbpA genes. Data showed that many protein-coding genes have limitations in detecting and classifying newly identified Wolbachia supergroups and thus raise a challenge to the known Wolbachia MLST standard analysis system. Besides, the other Wolbachia strains detected from whiteflies were clustered into supergroup B. Phylogenetic trees of whitefly mitochondrial cytochrome oxidase subunit I and Wolbachia multiple sequencing typing genes were not congruent. In addition, Wolbachia was also detected outside the special bacteriocytes in two cryptic species by fluorescence in situ hybridization, indicating the horizontal transmission of Wolbachia. Our results indicate that members of Wolbachia are far from well explored.

Palaeosymbiosis revealed by genomic fossils of Wolbachia in a strongyloidean nematode

Wolbachia are common endosymbionts of terrestrial arthropods, and are also found in nematodes: the animal-parasitic filaria, and the plant-parasite Radopholus similis. Lateral transfer of Wolbachia DNA to the host genome is common. We generated a draft genome sequence for the strongyloidean nematode parasite Dictyocaulus viviparus, the cattle lungworm. In the assembly, we identified nearly 1 Mb of sequence with similarity to Wolbachia. The fragments were unlikely to derive from a live Wolbachia infection: most were short, and the genes were disabled through inactivating mutations. Many fragments were co-assembled with definitively nematode-derived sequence. We found limited evidence of expression of the Wolbachia-derived genes. The D. viviparus Wolbachia genes were most similar to filarial strains and strains from the host-promiscuous clade F. We conclude that D. viviparus was infected by Wolbachia in the past, and that clade F-like symbionts may have been the source of filarial Wolbachia infections.

Bovine lungworms are economically important nematode parasites of cattle. We have sequenced the genome of the bovine lungworm to provide information for drug and vaccine discovery. Within the lungworm genome we found extensive evidence of an ancient association between the lungworm and a bacterium called Wolbachia. The lungworm Wolbachia is now a “fossil” in the genome, but tells of an ancient infection. Association between lungworms, and related nematode worms, and Wolbachia was not known previously. We have used the lungworm Wolbachia sequence to explore the history of nematode-Wolbachia interactions, particularly the jumping of these symbionts between arthropods and nematodes.

Microsatellite and Wolbachia analysis in Rhagoletis cerasi natural populations: population structuring and multiple infections

Rhagoletis cerasi (Diptera: Tephritidae) is a major pest of sweet and sour cherries in Europe and parts of Asia. Despite its economic significance, there is a lack of studies on the genetic structure of R. cerasi populations. Elucidating the genetic structure of insects of economic importance is crucial for developing phenological-predictive models and environmental friendly control methods. All natural populations of R. cerasi have been found to harbor the endosymbiont Wolbachia pipientis, which widely affects multiple biological traits contributing to the evolution of its hosts, and has been suggested as a tool for the biological control of insect pests and disease vectors. In the current study, the analysis of 18 R. cerasi populations collected in Greece, Germany, and Russia using 13 microsatellite markers revealed structuring of R. cerasi natural populations, even at close geographic range. We also analyzed the Wolbachia infection status of these populations using 16S rRNA-, MLST- and wsp-based approaches. All 244 individuals screened were positive for Wolbachia. Our results suggest the fixation of the wCer1 strain in Greece while wCer2, wCer4, wCer5, and probably other uncharacterized strains were also detected in multiply infected individuals. The role of Wolbachia and its potential extended phenotypes needs a thorough investigation in R. cerasi. Our data suggest an involvement of this symbiont in the observed restriction in the gene flow in addition to a number of different ecological factors.

Phylogenomics and analysis of shared genes suggest a single transition to mutualism in Wolbachia of nematodes

Wolbachia, endosymbiotic bacteria of the order Rickettsiales, are widespread in arthropods but also present in nematodes. In arthropods, A and B supergroup Wolbachia are generally associated with distortion of host reproduction. In filarial nematodes, including some human parasites, multiple lines of experimental evidence indicate that C and D supergroup Wolbachia are essential for the survival of the host, and here the symbiotic relationship is considered mutualistic. The origin of this mutualistic endosymbiosis is of interest for both basic and applied reasons: How does a parasite become a mutualist? Could intervention in the mutualism aid in treatment of human disease? Correct rooting and high-quality resolution of Wolbachia relationships are required to resolve this question. However, because of the large genetic distance between Wolbachia and the nearest outgroups, and the limited number of genomes so far available for large-scale analyses, current phylogenies do not provide robust answers. We therefore sequenced the genome of the D supergroup Wolbachia endosymbiont of Litomosoides sigmodontis, revisited the selection of loci for phylogenomic analyses, and performed a phylogenomic analysis including available complete genomes (from isolates in supergroups A, B, C, and D). Using 90 orthologous genes with reliable phylogenetic signals, we obtained a robust phylogenetic reconstruction, including a highly supported root to the Wolbachia phylogeny between a (A + B) clade and a (C + D) clade. Although we currently lack data from several Wolbachia supergroups, notably F, our analysis supports a model wherein the putatively mutualist endosymbiotic relationship between Wolbachia and nematodes originated from a single transition event.

Distribution and evolutionary impact of wolbachia on butterfly hosts

Wolbachia are maternally inherited endosymbiotic alpha-proteobacteria found in terrestrial arthropods and filarial nematodes. They are transmitted vertically through host cytoplasm and alter host biology by inducing various reproductive alterations, like feminization, parthenogenesis, male killing (MK) and cytoplasmic incompatibility. In butterflies, some effects especially MK and sperm-egg incompatibility are well established. All these effects skew the sex ratio towards female and subsequently favor the vertical transmission of Wolbachia. Some of the insects are also infected with multiple Wolbachia strains which may results in some complex phenomenon. In the present review the potential of Wolbachia for promoting evolutionary changes in its hosts with emphasis on recent advances in interactions of butterfly-Wolbachia is discussed. In addition to this, strain diversity of Wolbachia and its effects on various butterfly hosts are also highlighted.

Localization of a filarial phosphate permease that is up-regulated in response to depletion of essential Wolbachia endobacteria

Wolbachia of filarial nematodes are essential, obligate endobacteria. When depleted by doxycycline worm embryogenesis, larval development and worm survival are inhibited. The molecular basis governing the endosymbiosis between Wolbachia and their filarial host is still being deciphered. In rodent filarial nematode Litomosoides sigmodontis, a nematode encoded phosphate permease gene (Ls-ppe-1) was up-regulated at the mRNA level in response to Wolbachia depletion and this gene promises to have an important role in Wolbachia-nematode endosymbiosis. To further characterize this gene, the regulation of phosphate permease during Wolbachia depletion was studied at the protein level in L. sigmodontis and in the human filaria Onchocerca volvulus. And the localization of phosphate permease (PPE) and Wolbachia in L. sigmodontis and O. volvulus was investigated in untreated and antibiotic treated worms. Depletion of Wolbachia by tetracycline (Tet) resulted in up-regulation of Ls-ppe-1 in L. sigmodontis. On day 36 of Tet treatment, compared to controls (Con), >98% of Wolbachia were depleted with a 3-fold increase in mRNA levels of Ls-ppe-1. Anti-Ls-PPE serum used in Western blots showed up-regulation of Ls-PPE at the protein level in Tet worms on day 15 and 36 of treatment. Immunohistology revealed the localization of Wolbachia and Ls-PPE in the embryos, microfilariae and hypodermis of L. sigmodontis female worms and up-regulation of Ls-PPE in response to Wolbachia depletion. Expression of O. volvulus phosphate permease (Ov-PPE) studied using anti-Ov-PPE serum, showed up-regulation of Ov-PPE at the protein level in doxycycline treated Wolbachia depleted O. volvulus worms and immunohistology revealed localization of Ov-PPE and Wolbachia and up-regulation of Ov-PPE in the hypodermis and embryos of doxycycline treated worms. Ls-PPE and Ov-PPE are upregulated upon Wolbachia depletion in same tissues and regions where Wolbachia are located in untreated worms, reinforcing a link between Wolbachia and this nematode encoded protein. The function of nematode phosphate permease in the endosymbiosis is unknown but could involve transportation of phosphate to Wolbachia, which encode all the genes necessary for de novo nucleotide biosynthesis. Electron microscopic localization of PPE and Wolbachia and RNAi mediated knock-down of PPE in filarial nematodes will bring further insights to the functions of PPE in the Wolbachia-nematode symbiosis.

Presence of Wolbachia in three hymenopteran species: Diprion pini (Hymenoptera: Diprionidae), Neodiprion sertifer (Hymenoptera: Diprionidae), and Dahlbominus fuscipennis (Hymenoptera: Eulophidae)

Sawflies are important pests of various plant species. Diprion pini (L.) and Neodiprion sertifer (Geoffroy) (Hymenoptera: Diprionidae) are two of the most important sawfly pests in Italy, and both species are parasitized by the hymenopteran parasitoid Dahlbominus fuscipennis (Zetterstedt). Bacterial endosymbionts are currently studied for their high potential in strategies of biocontrol in a number of insect species. In this study, we investigated the presence of symbiotic bacteria (Wolbachia and Cardinium) in the three species of hymenoptera mentioned earlier, both in wild and laboratory populations. Although all samples were negative for the presence of Cardinium, 100% prevalence for Wolbachia was detected, as all examined individuals resulted to be PCR positive. Furthermore, 16S rDNA and ftsZ gene sequencing indicated that all individuals from the three hymenopteran species are infected by a single Wolbachia strain. Additionally, we report the presence of gynandromorphic individuals in D. pini, both in wild and laboratory-reared populations. Heat treatments on D. pini colonies removed the Wolbachia symbionts, but they also prevented the development of adults.

A phylogenomic approach to bacterial subspecies classification: proof of concept in Mycobacterium abscessus

Background

Mycobacterium abscessus is a rapidly growing mycobacterium that is often associated with human infections. The taxonomy of this species has undergone several revisions and is still being debated. In this study, we sequenced the genomes of 12 M. abscessus strains and used phylogenomic analysis to perform subspecies classification.

Results

A data mining approach was used to rank and select informative genes based on the relative entropy metric for the construction of a phylogenetic tree. The resulting tree topology was similar to that generated using the concatenation of five classical housekeeping genes: rpoB, hsp65, secA, recA and sodA. Additional support for the reliability of the subspecies classification came from the analysis of erm41 and ITS gene sequences, single nucleotide polymorphisms (SNPs)-based classification and strain clustering demonstrated by a variable number tandem repeat (VNTR) assay and a multilocus sequence analysis (MLSA). We subsequently found that the concatenation of a minimal set of three median-ranked genes: DNA polymerase III subunit alpha (polC), 4-hydroxy-2-ketovalerate aldolase (Hoa) and cell division protein FtsZ (ftsZ), is sufficient to recover the same tree topology. PCR assays designed specifically for these genes showed that all three genes could be amplified in the reference strain of M. abscessus ATCC 19977^T.

Conclusion

This study provides proof of concept that whole-genome sequence-based data mining approach can provide confirmatory evidence of the phylogenetic informativeness of existing markers, as well as lead to the discovery of a more economical and informative set of markers that produces similar subspecies classification in M. abscessus. The systematic procedure used in this study to choose the informative minimal set of gene markers can potentially be applied to species or subspecies classification of other bacteria.

The symbiotic role of Wolbachia in Onchocercidae and its impact on filariasis

Symbiotic associations between eukaryotes and microorganisms are frequently observed in nature, and range along the continuum between parasitism and mutualism. The genus Wolbachia contains well-known intracellular bacteria of arthropods that induce several reproductive phenotypes that benefit the transmission of the bacteria. Interestingly, Wolbachia bacteria have been found in the Onchocercidae, a family of filarial nematodes, including species that cause human filarial diseases, e.g. lymphatic filariasis and onchocerciasis. The endosymbiont is thought to be mutualistic in the Onchocercidae, and to provide essential metabolites to the filariae. Currently, Wolbachia bacteria are targets of antibiotic therapy with tetracyclines, which have profound effects on the development, viability and fertility of filarial parasites. This overview article presents the Onchocercidae and Wolbachia, and then discusses the origin and the nature of the symbiosis. It highlights the contribution of Wolbachia to the survival of the filariae and to the development of pathology. Finally, the infection control implications for filariases are debated. Potential directions for future research are also discussed.

Wolbachia, filariae and Leishmania coinfection in dogs from a Mediterranean area

OBJECTIVES

In an endemic area for leishmaniosis and filariasis, coinfection can occur and the immunomodulation triggered by Wolbachia infection might influence the clinical signs and progression of both diseases. The aims of this study were to determine the prevalence of Wolbachia in dogs infected with Dirofilaria immitis and other filarial nematodes, to evaluate the prevalence of coinfection of Leishmania infantum, filariae and Wolbachia and their association with clinical presentation.

METHODS

Polymerase chain reaction assays were performed to detect filarial species, Wolbachia species and Leishmania in 118 samples of dogs from southeastern Spain with leishmaniosis and/or filariasis.

RESULTS

Ninety-eight dogs were infected with Leishmania and 49 had filarial infection (29 were coinfected with both). Wolbachia DNA was detected in 30·6% of filariae-positive dogs (15/49). Dogs coinfected with Leishmania and filaria had more severe clinical signs. Wolbachia infection was significantly (P=0·026) more frequent in dogs that were not infected with Leishmania. There was no correlation between outcome and coinfection with these pathogens.

CLINICAL SIGNIFICANCE

This study highlights the increased sensitivity of polymerase chain reaction in the diagnosis of filariasis, confirms the presence of Wolbachia in dogs from the Mediterranean basin, shows the increased severity of clinical signs when Leishmania-filarial coinfection is present and suggests a protective role of Wolbachia in leishmaniosis.

Wolbachia association with the tsetse fly, Glossina fuscipes fuscipes, reveals high levels of genetic diversity and complex evolutionary dynamics

Background

Wolbachia pipientis, a diverse group of α-proteobacteria, can alter arthropod host reproduction and confer a reproductive advantage to Wolbachia-infected females (cytoplasmic incompatibility (CI)). This advantage can alter host population genetics because Wolbachia-infected females produce more offspring with their own mitochondrial DNA (mtDNA) haplotypes than uninfected females. Thus, these host haplotypes become common or fixed (selective sweep). Although simulations suggest that for a CI-mediated sweep to occur, there must be a transient phase with repeated initial infections of multiple individual hosts by different Wolbachia strains, this has not been observed empirically. Wolbachia has been found in the tsetse fly, Glossina fuscipes fuscipes, but it is not limited to a single host haplotype, suggesting that CI did not impact its population structure. However, host population genetic differentiation could have been generated if multiple Wolbachia strains interacted in some populations. Here, we investigated Wolbachia genetic variation in G. f. fuscipes populations of known host genetic composition in Uganda. We tested for the presence of multiple Wolbachia strains using Multi-Locus Sequence Typing (MLST) and for an association between geographic region and host mtDNA haplotype using Wolbachia DNA sequence from a variable locus, groEL (heat shock protein 60).

Results

MLST demonstrated that some G. f. fuscipes carry Wolbachia strains from two lineages. GroEL revealed high levels of sequence diversity within and between individuals (Haplotype diversity = 0.945). We found Wolbachia associated with 26 host mtDNA haplotypes, an unprecedented result. We observed a geographical association of one Wolbachia lineage with southern host mtDNA haplotypes, but it was non-significant (p = 0.16). Though most Wolbachia-infected host haplotypes were those found in the contact region between host mtDNA groups, this association was non-significant (p = 0.17).

Conclusions

High Wolbachia sequence diversity and the association of Wolbachia with multiple host haplotypes suggest that different Wolbachia strains infected G. f. fuscipes multiple times independently. We suggest that these observations reflect a transient phase in Wolbachia evolution that is influenced by the long gestation and low reproductive output of tsetse. Although G. f. fuscipes is superinfected with Wolbachia, our data does not support that bidirectional CI has influenced host genetic diversity in Uganda.

Targeted genome enrichment for efficient purification of endosymbiont DNA from host DNA

Wolbachia endosymbionts are widespread in arthropods and are generally considered reproductive parasites, inducing various phenotypes including cytoplasmic incompatibility, parthenogenesis, feminization and male killing, which serve to promote their spread through populations. In contrast, Wolbachia infecting filarial nematodes that cause human diseases, including elephantiasis and river blindness, are obligate mutualists. DNA purification methods for efficient genomic sequencing of these unculturable bacteria have proven difficult using a variety of techniques. To efficiently capture endosymbiont DNA for studies that examine the biology of symbiosis, we devised a parallel strategy to an earlier array-based method by creating a set of SureSelect™ (Agilent) 120-mer target enrichment RNA oligonucleotides ("baits") for solution hybrid selection. These were designed from Wolbachia complete and partial genome sequences in GenBank and were tiled across each genomic sequence with 60 bp overlap. Baits were filtered for homology against host genomes containing Wolbachia using BLAT and sequences with significant host homology were removed from the bait pool. Filarial parasite Brugia malayi DNA was used as a test case, as the complete sequence of both Wolbachia and its host are known. DNA eluted from capture was size selected and sequencing samples were prepared using the NEBNext® Sample Preparation Kit. One-third of a 50 nt paired-end sequencing lane on the HiSeq™ 2000 (Illumina) yielded 53 million reads and the entirety of the Wolbachia genome was captured. We then used the baits to isolate more than 97.1 % of the genome of a distantly related Wolbachia strain from the crustacean Armadillidium vulgare, demonstrating that the method can be used to enrich target DNA from unculturable microbes over large evolutionary distances.

Identification of Wolbachia strains in mosquito disease vectors

Wolbachia bacteria are common endosymbionts of insects, and some strains are known to protect their hosts against RNA viruses and other parasites. This has led to the suggestion that releasing Wolbachia-infected mosquitoes could prevent the transmission of arboviruses and other human parasites. We have identified Wolbachia in Kenyan populations of the yellow fever vector Aedes bromeliae and its relative Aedes metallicus, and in Mansonia uniformis and Mansonia africana, which are vectors of lymphatic filariasis. These Wolbachia strains cluster together on the bacterial phylogeny, and belong to bacterial clades that have recombined with other unrelated strains. These new Wolbachia strains may be affecting disease transmission rates of infected mosquito species, and could be transferred into other mosquito vectors as part of control programs.

Survey of endosymbionts in the Diaphorina citri metagenome and assembly of a Wolbachia wDi draft genome

Diaphorina citri (Hemiptera: Psyllidae), the Asian citrus psyllid, is the insect vector of Ca. Liberibacter asiaticus, the causal agent of citrus greening disease. Sequencing of the D. citri metagenome has been initiated to gain better understanding of the biology of this organism and the potential roles of its bacterial endosymbionts. To corroborate candidate endosymbionts previously identified by rDNA amplification, raw reads from the D. citri metagenome sequence were mapped to reference genome sequences. Results of the read mapping provided the most support for Wolbachia and an enteric bacterium most similar to Salmonella. Wolbachia-derived reads were extracted using the complete genome sequences for four Wolbachia strains. Reads were assembled into a draft genome sequence, and the annotation assessed for the presence of features potentially involved in host interaction. Genome alignment with the complete sequences reveals membership of Wolbachia wDi in supergroup B, further supported by phylogenetic analysis of FtsZ. FtsZ and Wsp phylogenies additionally indicate that the Wolbachia strain in the Florida D. citri isolate falls into a sub-clade of supergroup B, distinct from Wolbachia present in Chinese D. citri isolates, supporting the hypothesis that the D. citri introduced into Florida did not originate from China.

A new type F Wolbachia from Splendidofilariinae (Onchocercidae) supports the recent emergence of this supergroup

Wolbachia are vertically transmitted endosymbiotic bacteria of arthropods and onchocercid nematodes. It is commonly accepted that they co-evolved with their filarial hosts, and have secondarily been lost in some species. However, most of the data on the Wolbachia/Onchocercidae relationship have been derived from studies on two subfamilies, the Dirofilariinae and the Onchocercinae, which harbour parasites of humans and domestic animals. Within the last few years, analyses of more diverse material have suggested that some groups of Onchocercidae do not have Wolbachia, such as recently studied Splendidofilariinae from birds. This study takes advantage of the analysis of additional Splendidofilariinae, Rumenfilaria andersoni from a Finnish reindeer and Madathamugadia hiepei from a South African gecko, using PCR, immunohistochemical staining and whole-mount fluorescent analysis to detect Wolbachia and describe its strains. A DNA barcoding approach and phylogenetic analyses were used to investigate the symbiosis between Wolbachia and the Onchocercidae. A new supergroup F Wolbachia was demonstrated in M. hiepei, representing the first filarial nematode harbouring Wolbachia described in a non-mammalian host. In the adult, Wolbachia infects the female germline but not the hypodermis, and intestinal cells are also infected. The phylogenetic analyses confirmed a recent emergence of supergroup F. They also suggested several events of horizontal transmission between nematodes and arthropods in this supergroup, and the existence of different metabolic interactions between the filarial nematodes and their symbionts.

Tsetse-Wolbachia symbiosis: comes of age and has great potential for pest and disease control

Tsetse flies (Diptera: Glossinidae) are the sole vectors of African trypanosomes, the causative agent of sleeping sickness in human and nagana in animals. Like most eukaryotic organisms, Glossina species have established symbiotic associations with bacteria. Three main symbiotic bacteria have been found in tsetse flies: Wigglesworthia glossinidia, an obligate symbiotic bacterium, the secondary endosymbiont Sodalis glossinidius and the reproductive symbiont Wolbachia pipientis. In the present review, we discuss recent studies on the detection and characterization of Wolbachia infections in Glossina species, the horizontal transfer of Wolbachia genes to tsetse chromosomes, the ability of this symbiont to induce cytoplasmic incompatibility in Glossina morsitans morsitans and also how new environment-friendly tools for disease control could be developed by harnessing Wolbachia symbiosis.

Association of a new Wolbachia strain with, and its effects on, Leptopilina victoriae, a virulent wasp parasitic to Drosophila spp

Wolbachia bacteria are ubiquitous intracellular bacteria of arthropods. Often considered reproductive parasites, they can benefit certain host species. We describe a new Wolbachia strain from Leptopilina victoriae, a Drosophila wasp. The strain is closely related to Wolbachia from Culex sp. Located to the posterior poles of oocytes, it manipulates its host's reproduction by inducing a male development type of cytoplasmic incompatibility. We also report its diverse effects on the wasp's life history traits.

Filarial and Wolbachia genomics

Filarial nematode parasites, the causative agents for a spectrum of acute and chronic diseases including lymphatic filariasis and river blindness, threaten the well-being and livelihood of hundreds of millions of people in the developing regions of the world. The 2007 publication on a draft assembly of the 95-Mb genome of the human filarial parasite Brugia malayi- representing the first helminth parasite genome to be sequenced - has been followed in rapid succession by projects that have resulted in the genome sequencing of six additional filarial species, seven nonfilarial nematode parasites of animals and nearly 30 plant parasitic and free-living species. Parallel to the genomic sequencing, transcriptomic and proteomic projects have facilitated genome annotation, expanded our understanding of stage-associated gene expression and provided a first look at the role of epigenetic regulation of filarial genomes through microRNAs. The expansion in filarial genomics will also provide a significant enrichment in our knowledge of the diversity and variability in the genomes of the endosymbiotic bacterium Wolbachia leading to a better understanding of the genetic principles that govern filarial-Wolbachia mutualism. The goal here is to provide an overview of the trends and advances in filarial and Wolbachia genomics.

Identification and biological role of the endosymbionts Wolbachia in rice water weevil (Coleoptera: Curculionidae)

Wolbachia spp. are obligate intracellular bacteria present in reproductive tissues of many arthropod species. Wolbachia infection status and roles in host reproduction were studied in the rice water weevil, Lissorhoptrus oryzophilus Kuschel (Coleoptera, Curculionidae), an introduced species in China. We examined Wolbachia infection status in five populations in China where it reproduces parthenogenetically, and one native population in Southeast Texas, where it reproduces bisexually. All populations were infected by Wolbachia, and all specimens in each population were infected by Wolbachia of a single strain. Phylogenetic analyses based on multilocus sequence typing system indicated that Wolbachia in non-native L. oryzophilus weevils diverges evidently from those in native weevils. After treatments with tetracycline, parthenogenetic weevils reduced the fecundity significantly and eggs were not viable. Our results suggest that Wolbachia are necessary for oocyte production in L oryzophilus.

Implications of microfauna-host interactions for trypanosome transmission dynamics in Glossina fuscipes fuscipes in Uganda

Tsetse flies (Diptera: Glossinidae) are vectors for African trypanosomes (Euglenozoa: kinetoplastida), protozoan parasites that cause African trypanosomiasis in humans (HAT) and nagana in livestock. In addition to trypanosomes, two symbiotic bacteria (Wigglesworthia glossinidia and Sodalis glossinidius) and two parasitic microbes, Wolbachia and a salivary gland hypertrophy virus (SGHV), have been described in tsetse. Here we determined the prevalence of and coinfection dynamics between Wolbachia, trypanosomes, and SGHV in Glossina fuscipes fuscipes in Uganda over a large geographical scale spanning the range of host genetic and spatial diversity. Using a multivariate analysis approach, we uncovered complex coinfection dynamics between the pathogens and statistically significant associations between host genetic groups and pathogen prevalence. It is important to note that these coinfection dynamics and associations with the host were not apparent by univariate analysis. These associations between host genotype and pathogen are particularly evident for Wolbachia and SGHV where host groups are inversely correlated for Wolbachia and SGHV prevalence. On the other hand, trypanosome infection prevalence is more complex and covaries with the presence of the other two pathogens, highlighting the importance of examining multiple pathogens simultaneously before making generalizations about infection and spatial patterns. It is imperative to note that these novel findings would have been missed if we had employed the standard univariate analysis used in previous studies. Our results are discussed in the context of disease epidemiology and vector control.