Comparative genomics suggests an independent origin of cytoplasmic incompatibility in Cardinium hertigii

A novel Erwiniaceae gut symbiont modulates gene expression of the intracellular bacterium Cardinium in the stored product mite Tyrophagus putrescentiae

We examined host and bacterial gene expression profiles in the stored product mite Tyrophagus putrescentiae co-infected with Wolbachia (wTPut) and Cardinium (cTPut) while varying the presence of the Erwiniaceae symbiont (SLS). SLS, a novel symbiont in the family Erwiniaceae, with a genome size of 1.7 Mb, is found in 16% of mite species in infected cultures. In addition, SLS was detected in mite feces but not in their eggs. Although Wolbachia expression remained unchanged, the presence or absence of SLS significantly affected Cardinium expression. It indicated that the effect of Wolbachia on SLS was neutral. In SLS-positive samples, Cardinium exhibited 29 upregulated and 48 downregulated genes compared to SLS-negative samples. Furthermore, Cardinium gene expression strongly correlated with mite KEGG gene expression in SLS-positive samples. Positive Spearman's correlations between Cardinium gene expression and mite KEGG immune and regulatory pathways were doubled in SLS-positive compared to SLS-negative samples. The diversity of expressed genes in the mite host decreased in the presence of SLS. Cardinium had more interacting genes to mite host in SLS-positive samples than without SLS. Transposases are the most affected Cardinium genes, showing upregulation in the presence of SLS. Correlation analyses revealed interactions between Cardinium and SLS via mite immune and regulatory pathways, including lysosome, ubiquitin-mediated proteolysis, PIK3_Akt, and cGMP-PKG. The results showed that Cardinium indirectly affects the gut symbionts of mites.IMPORTANCEThis study introduces a new model to analyze interactions between intracellular bacterial symbionts, gut bacterial symbionts, and their mite hosts. Using gene expression correlations, we investigated how the intracellular Cardinium responds to the novel Erwiniaceae gut symbiont in the mold mite Tyrophagus putrescentiae. The data showed that both mite and Cardinium gene expression are different in the samples with and without Erwiniaceae symbionts. In the presence of Erwiniaceae symbionts, Cardinium increased the interaction with the mite host in terms of changes in gene expression. The mite immune and regulatory pathway gene expression is differently correlated to Cardinium genes in relation to Erwiniaceae symbionts. As a well-known producer of allergens, T. putrescentiae physiology and thus its allergen production are influenced by both symbionts, potentially affecting the release of allergens into human environments.

Cardinium disrupts Wolbachia-host dynamics in the domestic mite Tyrophagus putrescentiae: evidence from manipulative experiments

We investigated the tripartite interactions between two intracellular bacterial symbionts, Cardinium and Wolbachia in Tyrophagus putrescentiae. Cultures of Tyrophagus putrescentiae are typically single-infected by one intracellular symbiont. However, co-infection can be experimentally induced by mixing single-infected cultures, resulting in 10% of mite individuals being double-infected (Cardinium + Wolbachia) and a corresponding reduction in host fitness. Here, we assembled the genomes of Cardinium and Wolbachia and analyzed their gene expression in parental single-infected and mixed mite cultures using population-level samples (ranging from 7,500 to 10,000 mites). Wolbachia interacts more extensively with its mite host than Cardinium in single-infected cultures. However, in mixed cultures, (i) Wolbachia exhibited reduced regulation of the host compared with Cardinium; (ii) the gene expression profile of Cardinium shifted, increasing its interactions with the host, whereas the gene expression profile of Wolbachia remained unchanged; and (iii) Wolbachia genes exhibited a loss of interactions with mite gene expression, as indicated by reduced correlations (for example with host MAPK, endocytosis, and calcium signaling pathways). The experiments show that at the mite population level, symbiont infection disrupts gene expression interaction between the two symbionts and their host in different ways. Wolbachia was more influenced by Cardinium gene expression than vice versa. Cardinium can inhibit the growth of Wolbachia by disrupting its interaction with the host, leading to a loss of Wolbachia's influence on mite immune and regulatory pathways. The reasons for responses are due to co-infection or the reduced frequency of Wolbachia single-infected individuals due to the analyses of population-level samples.

IMPORTANCE

We found that Cardinium disrupts the interaction between Wolbachia and mite host. In Wolbachia single-infected cultures, strong correlations exist between symbiont and host gene expressions. Interestingly, although Cardinium can also interact with the host, this interaction appears weaker compared with Wolbachia in single-infected cultures. These results suggest that both symbionts affect mite host gene expression, particularly in immune and regulatory pathways. In mixed samples, Cardinium appears to outcompete Wolbachia by disrupting its host interaction. It indicates competition between these two intracellular symbionts in mite populations. Wolbachia belongs to a mite-specific supergroup Q, distinct from the more commonly studied Wolbachia supergroups. As these mite-specific bacteria exhibit pathogen-blocking effects, our findings may have relevance for other systems, such as ticks and tick-borne diseases. The study sheds light on intracellular symbiont interaction within a novel mite-symbiont model.

Limited Variation in Bacterial Communities of Scaphoideus titanus (Hemiptera: Cicadellidae) Across European Populations and Different Life Stages

The Nearctic leafhopper Scaphoideus titanus (Hemiptera: Cicadellidae) is the primary vector of 'Candidatus Phytoplasma vitis', the causative agent of Flavescence doreé in Europe. Although microorganisms play an important role in the ecology and behavior of insects, knowledge about the interaction between S. titanus and microbes is limited. In this study, we employed an amplicon metabarcoding approach for profiling the V4 region of the 16S rRNA gene to characterize the bacterial communities of S. titanus across several populations from four European localities. Additionally, we investigated changes in bacterial communities between nymphal and adult stages. In total, we identified 7,472 amplicon sequence variants (ASVs) in adults from the European populations. At the genus level, 'Candidatus Karelsulcia' and 'Candidatus Cardinium' were the most abundant genera, with both being present in every individual. While we found significant changes in the microbial composition of S. titanus across different European populations, no significant differences were observed between nymphal and adult stages. Our study reveals new insights into the microbial composition of S. titanus and highlights the role of geography in influencing its bacterial community.

Warm temperature inhibits cytoplasmic incompatibility induced by endosymbiotic Rickettsiella in spider hosts

Bacterial endosymbionts manipulate reproduction in arthropods to increase their prevalence in the host population. One such manipulation is cytoplasmic incompatibility (CI), wherein the bacteria sabotage sperm in infected males to reduce the hatch rate when mated with uninfected females, but zygotes are 'rescued' when that male mates with an infected female. In the spider Mermessus fradeorum (Linyphiidae), Rickettsiella symbionts cause variable levels of CI. We hypothesised that temperature affects the strength of CI and its rescue in M. fradeorum, potentially mediated by bacterial titre. We reared Rickettsiella-infected spiders in two temperature conditions (26°C vs. 20°C) and tested CI induction in males and rescue in females. In incompatible crosses between infected males and uninfected females, the hatch rate from warm males was doubled (mean ± standard error = 0.687 ± 0.052) relative to cool males (0.348 ± 0.046), indicating that CI induction is weaker in warm males. In rescue crosses between infected females and infected males, female rearing temperature had a marginal effect on CI rescue, but the hatch rate remained high for both warm (0.960 ± 0.023) and cool females (0.994 ± 0.004). Bacterial titre, as measured by quantitative polymerase chain reaction, was lower in warm than cool spiders, particularly in females, suggesting that bacterial titre may play a role in causing the temperature-mediated changes in CI.

Rickettsia induces strong cytoplasmic incompatibility in a predatory insect

Rickettsia, a group of intracellular bacteria found in eukaryotes, exhibits diverse lifestyles, with some acting as vertebrate pathogens transmitted by arthropod vectors and others serving as maternally transmitted arthropod endosymbionts, some of which manipulate host reproduction for their own benefit. Two phenotypes, namely male-killing and parthenogenesis induction are known as Rickettsia-induced host reproductive manipulations, but it remains unknown whether Rickettsia can induce other types of host manipulation. In this study, we discovered that Rickettsia induced strong cytoplasmic incompatibility (CI), in which uninfected females produce no offspring when mated with infected males, in the predatory insect Nesidiocoris tenuis (Hemiptera: Miridae). Molecular phylogenetic analysis revealed that the Rickettsia strain was related to Rickettsia bellii, a common insect endosymbiont. Notably, this strain carried plasmid-encoded homologues of the CI-inducing factors (namely cifA-like and cifB-like genes), typically found in Wolbachia, which are well-known CI-inducing endosymbionts. Protein domain prediction revealed that the cifB-like gene encodes PD-(D/E)XK nuclease and deubiquitinase domains, which are responsible for Wolbachia-induced CI, as well as ovarian tumour-like (OTU-like) cysteine protease and ankyrin repeat domains. These findings suggest that Rickettsia and Wolbachia endosymbionts share underlying mechanisms of CI and that CI-inducing ability was acquired by microbes through horizontal plasmid transfer.

Molecular Biology of Cytoplasmic Incompatibility Caused by Wolbachia Endosymbionts

Among endosymbiotic bacteria living within eukaryotic cells, Wolbachia is exceptionally widespread, particularly in arthropods. Inherited through the female germline, it has evolved ways to increase the fraction of bacterially infected offspring by inducing parthenogenesis, feminization, male killing, or, most commonly, cytoplasmic incompatibility (CI). In CI, Wolbachia infection of males causes embryonic lethality unless they mate with similarly infected females, creating a relative reproductive advantage for infected females. A set of related Wolbachia bicistronic operons encodes the CI-inducing factors. The downstream gene encodes a deubiquitylase or nuclease and is responsible for CI induction by males, while the upstream product when expressed in females binds its sperm-introduced cognate partner and rescues viability. Both toxin-antidote and host-modification mechanisms have been proposed to explain CI. Interestingly, male killing by either Spiroplasma or Wolbachia endosymbionts involves deubiquitylases as well. Interference with the host ubiquitin system may therefore be a common theme among endosymbiont-mediated reproductive alterations.

Egg provisioning explains the penetrance of symbiont-mediated sex allocation distortion in haplodiploids

Maternally transmitted symbionts such as Wolbachia can alter sex allocation in haplodiploid arthropods. By biasing population sex ratios towards females, these changes in sex allocation may facilitate the spread of symbionts. In contrast to symbiont-induced cytoplasmic incompatibility (CI), the mechanisms that underpin sex allocation distortion remain poorly understood. Using a nuclear genotype reference panel of the haplodiploid mite Tetranychus urticae and a single Wolbachia variant that is able to simultaneously induce sex allocation distortion and CI, we unraveled the mechanistic basis of Wolbachia-mediated sex allocation distortion. Host genotype was an important determinant for the strength of sex allocation distortion. We further show that sex allocation distortion by Wolbachia in haplodiploid mites is driven by increasing egg size, hereby promoting egg fertilization. This change in reproductive physiology was also coupled to increased male and female adult size. Our results echo previous work on Cardinium symbionts, suggesting that sex allocation distortion by regulating host investment in egg size is a common strategy among symbionts that infect haplodiploids. To better understand the relevance that sex allocation distortion may have for the spread of Wolbachia in natural haplodiploid populations, we parametrized a model based on generated phenotypic data. Our simulations show that empirically derived levels of sex allocation distortion can be sufficient to remove invasion thresholds, allowing CI to drive the spread of Wolbachia independently of the initial infection frequency. Our findings help elucidate the mechanisms that underlie the widespread occurrence of symbionts in haplodiploid arthropods and the evolution of sex allocation.

Complete De Novo Assembly of Wolbachia Endosymbiont of Frankliniella intonsa

As an endosymbiont, Wolbachia exerts significant effects on the host, including on reproduction, immunity, and metabolism. However, the study of Wolbachia in Thysanopteran insects, such as flower thrips Frankliniella intonsa, remains limited. Here, we assembled a gap-free looped genome assembly of Wolbachia strain wFI in a length of 1,463,884 bp (GC content 33.80%), using Nanopore long reads and Illumina short reads. The annotation of wFI identified a total of 1838 protein-coding genes (including 85 pseudogenes), 3 ribosomal RNAs (rRNAs), 35 transfer RNAs (tRNAs), and 1 transfer-messenger RNA (tmRNA). Beyond this basic description, we identified mobile genetic elements, such as prophage and insertion sequences (ISs), which make up 17% of the entire wFI genome, as well as genes involved in riboflavin and biotin synthesis and metabolism. This research lays the foundation for understanding the nutritional mutualism between Wolbachia and flower thrips. It also serves as a valuable resource for future studies delving into the intricate interactions between Wolbachia and its host.

Endogenous Plasmids and Chromosomal Genome Reduction in the Cardinium Endosymbiont of Dermatophagoides farinae

Cardinium bacteria are well known as endosymbionts that infect a wide range of arthropods and can manipulate host reproduction to promote their vertical transmission. As intracellular bacteria, Cardinium species undergo dramatic genome evolution, especially their chromosomal genome reduction. Although Cardinium plasmids have been reported to harbor important genes, the role of these plasmids in the genome evolution is yet to be fully understood. In this study, 2 genomes of Cardinium endosymbiont bacteria in astigmatic mites were de novo assembled, including the complete circular chromosomal genome of Cardinium sp. DF that was constructed in high quality using high-coverage long-read sequencing data. Intriguingly, 2 circular plasmids were assembled in Cardinium sp. DF and were identified to be endogenous for over 10 homologous genes shared with the chromosomal genome. Comparative genomics analysis illustrated an outline of the genome evolution of Cardinium bacteria, and the in-depth analysis of Cardinium sp. DF shed light on the multiple roles of endogenous plasmids in the molecular process of the chromosomal genome reduction. The endogenous plasmids of Cardinium sp. DF not only harbor massive homologous sequences that enable homologous recombination with the chromosome, but also can provide necessary functional proteins when the coding genes decayed in the chromosomal genome. IMPORTANCE As bacterial endosymbionts, Cardinium typically undergoes genome reduction, but the molecular process is still unclear, such as how plasmids get involved in chromosome reduction. Here, we de novo assembled 2 genomes of Cardinium in astigmatic mites, especially the chromosome of Cardinium sp. DF was assembled in a complete circular DNA using high-coverage long-read sequencing data. In the genome assembly of Cardinium sp. DF, 2 circular endogenous plasmids were identified to share at least 10 homologous genes with the chromosomal genome. In the comparative analysis, we identified a range of genes decayed in the chromosomal genome of Cardinium sp. DF but preserved in the 2 plasmids. Taken together with in-depth analyses, our results unveil that the endogenous plasmids harbor homologous sequences of chromosomal genome and can provide a structural basis of homologous recombination. Overall, this study reveals that endogenous plasmids participate in the ongoing chromosomal genome reduction of Cardinium sp. DF.

Distribution of Bacterial Endosymbionts of the Cardinium Clade in Plant-Parasitic Nematodes

Bacteria of the genus "Candidatus Cardinium" and related organisms composing the Cardinium clade are intracellular endosymbionts frequently occurring in several arthropod groups, freshwater mussels and plant-parasitic nematodes. Phylogenetic analyses based on two gene sequences (16S rRNA and gyrB) showed that the Cardinium clade comprised at least five groups: A, B, C, D and E. In this study, a screening of 142 samples of plant-parasitic nematodes belonging to 93 species from 12 families and two orders using PCR with specific primers and sequencing, revealed bacteria of Cardinium clade in 14 nematode samples belonging to 12 species of cyst nematodes of the family Heteroderidae. Furthermore, in this study, the genome of the Cardinium cHhum from the hop cyst nematode, Heterodera humuli, was also amplified, sequenced and analyzed. The comparisons of the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values for the strain Cardinium cHhum with regard to related organisms with available genomes, combined with the data on 16S rRNA and gyrB gene sequence identities, showed that this strain represents a new candidate species within the genus "Candidatus Paenicardinium". The phylogenetic position of endosymbionts of the Cardinium clade detected in nematode hosts was also compared to known representatives of this clade from other metazoans. Phylogenetic reconstructions based on analysis of 16S rRNA, gyrB, sufB, gloEL, fusA, infB genes and genomes and estimates of genetic distances both indicate that the endosymbiont of the root-lesion nematode Pratylenchus penetrans represented a separate lineage and is designated herein as a new group F. The phylogenetic analysis also confirmed that endosymbionts of ostracods represent the novel group G. Evolutionary relationships of bacterial endosymbionts of the Cardinium clade within invertebrates are presented and discussed.

A Novel Widespread MITE Element in the Repeat-Rich Genome of the Cardinium Endosymbiont of the Spider Oedothorax gibbosus

Free-living bacteria have evolved multiple times to become host-restricted endosymbionts. The transition from a free-living to a host-restricted lifestyle comes with a number of different genomic changes, including a massive loss of genes. In host-restricted endosymbionts, gene inactivation and genome reduction are facilitated by mobile genetic elements, mainly insertion sequences (ISs). ISs are small autonomous mobile elements, and one of, if not the most, abundant transposable elements in bacteria. Proliferation of ISs is common in some facultative endosymbionts, and is likely driven by the transmission bottlenecks, which increase the level of genetic drift. In this study, we present a manually curated genome annotation for a Cardinium endosymbiont of the dwarf spider Oedothorax gibbosus. Cardinium species are host-restricted endosymbionts that, similarly to ColbachiaWolbachia spp., include strains capable of manipulating host reproduction. Through the focus on mobile elements, the annotation revealed a rampant spread of ISs, extending earlier observations in other Cardinium genomes. We found that a large proportion of IS elements are pseudogenized, with many displaying evidence of recent inactivation. Most notably, we describe the lineage-specific emergence and spread of a novel IS-derived Miniature Inverted repeat Transposable Element (MITE), likely being actively maintained by intact copies of its parental IS982-family element. This study highlights the relevance of manual curation of these repeat-rich endosymbiont genomes for the discovery of novel MITEs, as well as the possible role these understudied elements might play in genome streamlining. IMPORTANCE Cardinium bacteria, a widespread symbiont lineage found across insects and nematodes, have been linked to reproductive manipulation of their hosts. However, the study of Cardinium has been hampered by the lack of comprehensive genomic resources. The high content of mobile genetic elements, namely, insertion sequences (ISs), has long complicated the analyses and proper annotations of these genomes. In this study, we present a manually curated annotation of the Cardinium symbiont of the spider Oedothorax gibbosus. Most notably, we describe a novel IS-like element found exclusively in this strain. We show that this mobile element likely evolved from a defective copy of its parental IS and then spread throughout the genome, contributing to the pseudogenization of several other mobile elements. We propose this element is likely being maintained by the intact copies of its parental IS element and that other similar elements in the genome could potentially follow this route.

Sex-based de novo transcriptome assemblies of the parasitoid wasp Encarsia suzannae, a host of the manipulative heritable symbiont Cardinium hertigii

Parasitoid wasps in the genus Encarsia are commonly used as biological pest control agents of whiteflies and armored scale insects in greenhouses or the field. They are also hosts of the bacterial endosymbiont Cardinium hertigii, which can cause reproductive manipulation phenotypes, including parthenogenesis, feminization, and cytoplasmic incompatibility (the last is mainly studied in Encarsia suzannae). Despite their biological and economic importance, there are no published Encarsia genomes and only one public transcriptome. Here, we applied a mapping-and-removal approach to eliminate known contaminants from previously-obtained Illumina sequencing data. We generated de novo transcriptome assemblies for both female and male E. suzannae which contain 45,986 and 54,762 final coding sequences, respectively. Benchmarking Single-Copy Orthologs results indicate both assemblies are highly complete. Preliminary analyses revealed the presence of homologs of sex-determination genes characterized in other insects and putative venom proteins. Our male and female transcriptomes will be valuable tools to better understand the biology of Encarsia and their evolutionary relatives, particularly in studies involving insects of only one sex.

Genome sequencing and comparative analysis of Wolbachia strain wAlbA reveals Wolbachia-associated plasmids are common

Wolbachia are widespread maternally-transmitted bacteria of arthropods that often spread by manipulating their host's reproduction through cytoplasmic incompatibility (CI). Their invasive potential is currently being harnessed in field trials aiming to control mosquito-borne diseases. Wolbachia genomes commonly harbour prophage regions encoding the cif genes which confer their ability to induce CI. Recently, a plasmid-like element was discovered in wPip, a Wolbachia strain infecting Culex mosquitoes; however, it is unclear how common such extra-chromosomal elements are in Wolbachia. Here we sequenced the complete genome of wAlbA, a strain of the symbiont found in Aedes albopictus, after eliminating the co-infecting and higher density wAlbB strain that previously made sequencing of wAlbA challenging. We show that wAlbA is associated with two new plasmids and identified additional Wolbachia plasmids and related chromosomal islands in over 20% of publicly available Wolbachia genome datasets. These plasmids encode a variety of accessory genes, including several phage-like DNA packaging genes as well as genes potentially contributing to host-symbiont interactions. In particular, we recovered divergent homologues of the cif genes in both Wolbachia- and Rickettsia-associated plasmids. Our results indicate that plasmids are common in Wolbachia and raise fundamental questions around their role in symbiosis. In addition, our comparative analysis provides useful information for the future development of genetic tools to manipulate and study Wolbachia symbionts.

Highly transmissible cytoplasmic incompatibility by the extracellular insect symbiont Spiroplasma

Cytoplasmic incompatibility (CI) is a form of reproductive manipulation caused by maternally inherited endosymbionts infecting arthropods, like Wolbachia, whereby matings between infected males and uninfected females produce few or no offspring. We report the discovery of a new CI symbiont, a strain of Spiroplasma causing CI in the parasitoid wasp Lariophagus distinguendus. Its extracellular occurrence enabled us to establish CI in uninfected adult insects by transferring Spiroplasma-infected hemolymph. We sequenced the CI-Spiroplasma genome and did not find any homologues of any of the cif genes discovered to cause CI in Wolbachia, suggesting independent evolution of CI. Instead, the genome contains other potential CI-causing candidate genes, such as homologues of high-mobility group (HMG) box proteins that are crucial in eukaryotic development but rare in bacterial genomes. Spiroplasma's extracellular nature and broad host range encompassing medically and agriculturally important arthropods make it a promising tool to study CI and its applications.

Cryptic Genes for Interbacterial Antagonism Distinguish Rickettsia Species Infecting Blacklegged Ticks From Other Rickettsia Pathogens

Background

The genus Rickettsia (Alphaproteobacteria: Rickettsiales) encompasses numerous obligate intracellular species with predominantly ciliate and arthropod hosts. Notable species are pathogens transmitted to mammals by blood-feeding arthropods. Mammalian pathogenicity evolved from basal, non-pathogenic host-associations; however, some non-pathogens are closely related to pathogens. One such species, Rickettsia buchneri, is prevalent in the blacklegged tick, Ixodes scapularis. While I. scapularis transmits several pathogens to humans, it does not transmit Rickettsia pathogens. We hypothesize that R. buchneri established a mutualism with I. scapularis, blocking tick superinfection with Rickettsia pathogens.

Methods

To improve estimates for assessing R. buchneri infection frequency in blacklegged tick populations, we used comparative genomics to identify an R. buchneri gene (REIS_1424) not present in other Rickettsia species present throughout the I. scapularis geographic range. Bioinformatic and phylogenomics approaches were employed to propose a function for the hypothetical protein (263 aa) encoded by REIS_1424.

Results

REIS_1424 has few analogs in other Rickettsiales genomes and greatest similarity to non-Proteobacteria proteins. This cohort of proteins varies greatly in size and domain composition, possessing characteristics of Recombination hotspot (Rhs) and contact dependent growth inhibition (CDI) toxins, with similarity limited to proximal C-termini (~145 aa). This domain was named CDI-like/Rhs-like C-terminal toxin (CRCT). As such proteins are often found as toxin-antidote (TA) modules, we interrogated REIS_1423 (151 aa) as a putative antidote. Indeed, REIS_1423 is similar to proteins encoded upstream of CRCT domain-containing proteins. Accordingly, we named these proteins CDI-like/Rhs-like C-terminal toxin antidotes (CRCA). R. buchneri expressed both REIS_1423 and REIS_1424 in tick cell culture, and PCR assays showed specificity for R. buchneri over other rickettsiae and utility for positive detection in three tick populations. Finally, phylogenomics analyses uncovered divergent CRCT/CRCA modules in varying states of conservation; however, only R. buchneri and related Tamurae/Ixodes Group rickettsiae carry complete TA modules.

Conclusion

We hypothesize that Rickettsia CRCT/CRCA modules circulate in the Rickettsia mobile gene pool, arming rickettsiae for battle over arthropod colonization. While its functional significance remains to be tested, R. buchneri CRCT/CRCA serves as a marker to positively identify infection and begin deciphering the role this endosymbiont plays in the biology of the blacklegged tick.

Quality over quantity: unraveling the contributions to cytoplasmic incompatibility caused by two coinfecting Cardinium symbionts

Cytoplasmic incompatibility (CI) is a common form of reproductive sabotage caused by maternally inherited bacterial symbionts of arthropods. CI is a two-step manipulation: first, the symbiont modifies sperm in male hosts which results in the death of fertilized, uninfected embryos. Second, when females are infected with a compatible strain, the symbiont reverses sperm modification in the fertilized egg, allowing offspring of infected females to survive and spread the symbiont to high frequencies in a population. Although CI plays a role in arthropod evolution, the mechanism of CI is unknown for many symbionts. Cardinium hertigii is a common CI-inducing symbiont of arthropods, including parasitoid wasps like Encarsia partenopea. This wasp harbors two Cardinium strains, cEina2 and cEina3, and exhibits strong CI. The strains infect wasps at different densities, with the cEina3 present at a lower density than cEina2, and it was previously not known which strain caused CI. By differentially curing wasps of cEina3, we found that this low-density symbiont is responsible for CI and modifies males during their pupal stage. cEina2 does not modify host reproduction and may spread by 'hitchhiking' with cEina3 CI or by conferring an unknown benefit. The cEina3 strain also shows a unique localization pattern in male reproductive tissues. Instead of infecting sperm like other CI-inducing symbionts, cEina3 cells are found in somatic cells at the testis base and around the seminal vesicle. This may allow the low-density cEina3 to efficiently modify host males and suggests that cEina3 uses a different modification strategy than sperm-infecting CI symbionts.

Endosymbionts moderate constrained sex allocation in a haplodiploid thrips species in a temperature-sensitive way

Maternally inherited bacterial endosymbionts that affect host fitness are common in nature. Some endosymbionts colonise host populations by reproductive manipulations (such as cytoplasmic incompatibility; CI) that increase the reproductive fitness of infected over uninfected females. Theory predicts that CI-inducing endosymbionts in haplodiploid hosts may also influence sex allocation, including in compatible crosses, however, empirical evidence for this is scarce. We examined the role of two common CI-inducing endosymbionts, Cardinium and Wolbachia, in the sex allocation of Pezothrips kellyanus, a haplodiploid thrips species with a split sex ratio. In this species, irrespective of infection status, some mated females are constrained to produce extremely male-biased broods, whereas other females produce extremely female-biased broods. We analysed brood sex ratio of females mated with males of the same infection status at two temperatures. We found that at 20 °C the frequency of constrained sex allocation in coinfected pairs was reduced by 27% when compared to uninfected pairs. However, at 25 °C the constrained sex allocation frequency increased and became similar between coinfected and uninfected pairs, resulting in more male-biased population sex ratios at the higher temperature. This temperature-dependent pattern occurred without changes in endosymbiont densities and compatibility. Our findings indicate that endosymbionts affect sex ratios of haplodiploid hosts beyond the commonly recognised reproductive manipulations by causing female-biased sex allocation in a temperature-dependent fashion. This may contribute to a higher transmission efficiency of CI-inducing endosymbionts and is consistent with previous models that predict that CI by itself is less efficient in driving endosymbiont invasions in haplodiploid hosts.

A dual endosymbiosis supports nutritional adaptation to hematophagy in the invasive tick Hyalomma marginatum

Many animals are dependent on microbial partners that provide essential nutrients lacking from their diet. Ticks, whose diet consists exclusively on vertebrate blood, rely on maternally inherited bacterial symbionts to supply B vitamins. While previously studied tick species consistently harbor a single lineage of those nutritional symbionts, we evidence here that the invasive tick Hyalomma marginatum harbors a unique dual-partner nutritional system between an ancestral symbiont, Francisella, and a more recently acquired symbiont, Midichloria. Using metagenomics, we show that Francisella exhibits extensive genome erosion that endangers the nutritional symbiotic interactions. Its genome includes folate and riboflavin biosynthesis pathways but deprived functional biotin biosynthesis on account of massive pseudogenization. Co-symbiosis compensates this deficiency since the Midichloria genome encompasses an intact biotin operon, which was primarily acquired via lateral gene transfer from unrelated intracellular bacteria commonly infecting arthropods. Thus, in H. marginatum, a mosaic of co-evolved symbionts incorporating gene combinations of distant phylogenetic origins emerged to prevent the collapse of an ancestral nutritional symbiosis. Such dual endosymbiosis was never reported in other blood feeders but was recently documented in agricultural pests feeding on plant sap, suggesting that it may be a key mechanism for advanced adaptation of arthropods to specialized diets.

Interactions of the Intracellular Bacterium Cardinium with Its Host, the House Dust Mite Dermatophagoides farinae, Based on Gene Expression Data

Dermatophagoides farinae is inhabited by an intracellular bacterium, Cardinium. Using correlations between host and symbiont gene expression profiles, we identified several important molecular pathways that potentially regulate/facilitate their interactions. The expression of Cardinium genes collectively explained 95% of the variation in the expression of mite genes assigned to pathways for phagocytosis, apoptosis, the MAPK signaling cascade, endocytosis, the tumor necrosis factor (TNF) pathway, the transforming growth factor beta (TGF-β) pathway, lysozyme, and the Toll/Imd pathway. In addition, expression of mite genes explained 76% of the variability in Cardinium gene expression. In particular, the expression of the Cardinium genes encoding the signaling molecules BamD, LepA, SymE, and VirD4 was either positively or negatively correlated with the expression levels of mite genes involved in endocytosis, phagocytosis, and apoptosis. We also found that Cardinium possesses a complete biosynthetic pathway for lipoic acid and may provide lipoate, but not biotin, to mites. Cardinium gene expression collectively explained 84% of the variation in expression related to several core mite metabolic pathways, and, most notably, a negative correlation was observed between bacterial gene expression and expression of mite genes assigned to the glycolysis and citric acid cycle pathways. Furthermore, we showed that Cardinium gene expression is correlated with expression levels of genes associated with terpenoid backbone biosynthesis. This pathway is important for the synthesis of pheromones, thus providing an opportunity for Cardinium to influence mite reproductive behavior to facilitate transmission of the bacterium. Overall, our study provided correlational gene expression data that can be useful for future research on mite-Cardinium interactions. IMPORTANCE The molecular mechanisms of mite-symbiont interactions and their impacts on human health are largely unknown. Astigmatid mites, such as house dust and stored-product mites, are among the most significant allergen sources worldwide. Although mites themselves are the main allergen sources, recent studies have indicated that mite-associated microbiomes may have implications for allergen production and human health. The major medically important house dust mite, D. farinae, is known to harbor a highly abundant intracellular bacterium belonging to the genus Cardinium. Expression analysis of the mite and symbiont genes can identify key mite molecular pathways that facilitate interactions with this endosymbiont and possibly shed light on how this bacterium affects mite allergen production and physiology in general.

Evaluation of RNAlater as a Field-Compatible Preservation Method for Metaproteomic Analyses of Bacterium-Animal Symbioses

Field studies are central to environmental microbiology and microbial ecology, because they enable studies of natural microbial communities. Metaproteomics, the study of protein abundances in microbial communities, allows investigators to study these communities "in situ," which requires protein preservation directly in the field because protein abundance patterns can change rapidly after sampling. Ideally, a protein preservative for field deployment works rapidly and preserves the whole proteome, is stable in long-term storage, is nonhazardous and easy to transport, and is available at low cost. Although these requirements might be met by several protein preservatives, an assessment of their suitability under field conditions when targeted for metaproteomic analyses is currently lacking. Here, we compared the protein preservation performance of flash freezing and the preservation solution RNAlater using the marine gutless oligochaete Olavius algarvensis and its symbiotic microbes as a test case. In addition, we evaluated long-term RNAlater storage after 1 day, 1 week, and 4 weeks at room temperature (22°C to 23°C). We evaluated protein preservation using one-dimensional liquid chromatography-tandem mass spectrometry. We found that RNAlater and flash freezing preserved proteins equally well in terms of total numbers of identified proteins and relative abundances of individual proteins, and none of the test time points was altered, compared to time zero. Moreover, we did not find biases against specific taxonomic groups or proteins with particular biochemical properties. Based on our metaproteomic data and the logistical requirements for field deployment, we recommend RNAlater for protein preservation of field-collected samples targeted for metaproteomic analyses. IMPORTANCE Metaproteomics, the large-scale identification and quantification of proteins from microbial communities, provide direct insights into the phenotypes of microorganisms on the molecular level. To ensure the integrity of the metaproteomic data, samples need to be preserved immediately after sampling to avoid changes in protein abundance patterns. In laboratory setups, samples for proteomic analyses are most commonly preserved by flash freezing; however, liquid nitrogen or dry ice is often unavailable at remote field locations, due to their hazardous nature and transport restrictions. Our study shows that RNAlater can serve as a low-hazard, easy-to-transport alternative to flash freezing for field preservation of samples for metaproteomic analyses. We show that RNAlater preserves the metaproteome equally well, compared to flash freezing, and protein abundance patterns remain stable during long-term storage for at least 4 weeks at room temperature.

Genome Features of Asaia sp. W12 Isolated from the Mosquito Anopheles stephensi Reveal Symbiotic Traits

Asaia bacteria commonly comprise part of the microbiome of many mosquito species in the genera Anopheles and Aedes, including important vectors of infectious agents. Their close association with multiple organs and tissues of their mosquito hosts enhances the potential for paratransgenesis for the delivery of antimalaria or antivirus effectors. The molecular mechanisms involved in the interactions between Asaia and mosquito hosts, as well as Asaia and other bacterial members of the mosquito microbiome, remain underexplored. Here, we determined the genome sequence of Asaia strain W12 isolated from Anopheles stephensi mosquitoes, compared it to other Asaia species associated with plants or insects, and investigated the properties of the bacteria relevant to their symbiosis with mosquitoes. The assembled genome of strain W12 had a size of 3.94 MB, the largest among Asaia spp. studied so far. At least 3585 coding sequences were predicted. Insect-associated Asaia carried more glycoside hydrolase (GH)-encoding genes than those isolated from plants, showing their high plant biomass-degrading capacity in the insect gut. W12 had the most predicted regulatory protein components comparatively among the selected Asaia, indicating its capacity to adapt to frequent environmental changes in the mosquito gut. Two complete operons encoding cytochrome bo₃-type ubiquinol terminal oxidases (cyoABCD-1 and cyoABCD-2) were found in most Asaia genomes, possibly offering alternative terminal oxidases and allowing the flexible transition of respiratory pathways. Genes involved in the production of 2,3-butandiol and inositol have been found in Asaia sp. W12, possibly contributing to biofilm formation and stress tolerance.

Evolution of Wolbachia mutualism and reproductive parasitism: insight from two novel strains that co-infect cat fleas

Wolbachiae are obligate intracellular bacteria that infect arthropods and certain nematodes. Usually maternally inherited, they may provision nutrients to (mutualism) or alter sexual biology of (reproductive parasitism) their invertebrate hosts. We report the assembly of closed genomes for two novel wolbachiae, wCfeT and wCfeJ, found co-infecting cat fleas (Ctenocephalides felis) of the Elward Laboratory colony (Soquel, CA, USA). wCfeT is basal to nearly all described Wolbachia supergroups, while wCfeJ is related to supergroups C, D and F. Both genomes contain laterally transferred genes that inform on the evolution of Wolbachia host associations. wCfeT carries the Biotin synthesis Operon of Obligate intracellular Microbes (BOOM); our analyses reveal five independent acquisitions of BOOM across the Wolbachia tree, indicating parallel evolution towards mutualism. Alternately, wCfeJ harbors a toxin-antidote operon analogous to the wPip cinAB operon recently characterized as an inducer of cytoplasmic incompatibility (CI) in flies. wCfeJ cinB and three adjacent genes are collectively similar to large modular toxins encoded in CI-like operons of certain Wolbachia strains and Rickettsia species, signifying that CI toxins streamline by fission of large modular toxins. Remarkably, the C. felis genome itself contains two CI-like antidote genes, divergent from wCfeJ cinA, revealing episodic reproductive parasitism in cat fleas and evidencing mobility of CI loci independent of WO-phage. Additional screening revealed predominant co-infection (wCfeT/wCfeJ) amongst C. felis colonies, though fleas in wild populations mostly harbor wCfeT alone. Collectively, genomes of wCfeT, wCfeJ, and their cat flea host supply instances of lateral gene transfers that could drive transitions between parasitism and mutualism.

Cardinium Localization During Its Parasitoid Wasp Host's Development Provides Insights Into Cytoplasmic Incompatibility

Arthropods harbor heritable intracellular symbionts that may manipulate host reproduction to favor symbiont transmission. In cytoplasmic incompatibility (CI), the symbiont sabotages the reproduction of infected males such that high levels of offspring mortality result when they mate with uninfected females. In crosses with infected males and infected females, however (the “rescue” cross), normal numbers of offspring are produced. A common CI-inducing symbiont, Cardinium hertigii, causes variable levels of CI mortality in the parasitoid wasp, Encarsia suzannae. Previous work correlated CI-induced mortality with male development time in this system, although the timing of Cardinium CI-induction and the relationship between development time and CI mortality was not well understood. Here, using a combination of crosses, manipulation of development time, and fluorescence microscopy, we identify the localization and the timing of the CI-induction step in the Cardinium-E. suzannae system. Antibiotic treatment of adult Cardinium-infected males did not reduce the mortality associated with the CI phenotype, suggesting that CI-alteration occurs prior to adulthood. Our results suggest that the alteration step occurs during the pupal period, and is limited by the duration of pupal development: 1) Encarsia produces most sperm prior to adulthood, 2) FISH localization of Cardinium in testes showed an association with sperm nuclei throughout spermatogenesis but not with mature sperm, and 3) two methods of prolonging the pupal period (cool temperatures and the juvenile hormone analog methoprene) both caused greater CI mortality, suggesting the degree of alteration is limited by the duration of the pupal stage. Based on these results, we compare two models for potential mechanisms of Cardinium sperm modification in the context of what is known about analogous mechanisms of Wolbachia, a more extensively studied CI-inducing symbiont.

A Role for Maternal Factors in Suppressing Cytoplasmic Incompatibility

Wolbachia are maternally transmitted bacterial endosymbionts, carried by approximately half of all insect species. Wolbachia prevalence in nature stems from manipulation of host reproduction to favor the success of infected females. The best known reproductive modification induced by Wolbachia is referred to as sperm-egg Cytoplasmic Incompatibility (CI). In CI, the sperm of Wolbachia-infected males cause embryonic lethality, attributed to paternal chromatin segregation defects during early mitotic divisions. Remarkably, the embryos of Wolbachia-infected females “rescue” CI lethality, yielding egg hatch rates equivalent to uninfected female crosses. Several models have been discussed as the basis for Rescue, and functional evidence indicates a major contribution by Wolbachia CI factors. A role for host contributions to Rescue remains largely untested. In this study, we used a chemical feeding approach to test for CI suppression capabilities by Drosophila simulans. We found that uninfected females exhibited significantly higher CI egg hatch rates in response to seven chemical treatments that affect DNA integrity, cell cycle control, and protein turnover. Three of these treatments suppressed CI induced by endogenous wRi Wolbachia, as well as an ectopic wMel Wolbachia infection. The results implicate DNA integrity as a focal aspect of CI suppression for different Wolbachia strains. The framework presented here, applied to diverse CI models, will further enrich our understanding of host reproductive manipulation by insect endosymbionts.

Biotin provisioning by horizontally transferred genes from bacteria confers animal fitness benefits

Insect symbionts are widespread in nature and lateral gene transfer is prevalent in insect symbiosis. However, the function of horizontally transferred genes (HTGs) in insect symbiosis remains speculative, including the mechanism that enables insects to feed on plant phloem deficient in B vitamins. Previously, we found there is redundancy in biotin synthesis pathways from both whitefly Bemisia tabaci and symbiotic Hamiltonella due to the presence of whitefly HTGs. Here, we demonstrate that elimination of Hamiltonella decreased biotin levels but elevated the expression of horizontally transferred biotin genes in whiteflies. HTGs proteins exhibit specific expression patterns in specialized insect cells called bacteriocytes housing symbionts. Complementation with whitefly HTGs rescued E. coli biotin gene knockout mutants. Furthermore, silencing whitefly HTGs in Hamiltonella-infected whiteflies reduced biotin levels and hindered adult survival and fecundity, which was partially rescued by biotin supplementation. Each of horizontally transferred biotin genes are conserved in various laboratory cultures and species of whiteflies with geographically diverse distributions, which shares an evolutionary origin. We provide the first experimental evidence that biotin synthesized through acquired HTGs is important in whiteflies and may be as well in other animals. Our findings suggest that B vitamin provisioning in animal-microbe symbiosis frequently evolved from bacterial symbionts to animal hosts through horizontal gene transfer events. This study will also shed light on how the animal genomes evolve through functional transfer of genes with bacterial origin in the wider contexts of microbial ecology.

A Bacterial Phage Tail-like Structure Kills Eukaryotic Cells by Injecting a Nuclease Effector

Many bacteria interact with target organisms using syringe-like structures called contractile injection systems (CISs). CISs structurally resemble headless bacteriophages and share evolutionarily related proteins such as the tail tube, sheath, and baseplate complex. In many cases, CISs mediate trans-kingdom interactions between bacteria and eukaryotes by delivering effectors to target cells. However, the specific effectors and their modes of action are often unknown. Here, we establish an ex vivo model to study an extracellular CIS (eCIS) called metamorphosis-associated contractile structures (MACs) that target eukaryotic cells. MACs kill two eukaryotic cell lines, fall armyworm Sf9 cells and J774A.1 murine macrophage cells, by translocating an effector termed Pne1. Before the identification of Pne1, no CIS effector exhibiting nuclease activity against eukaryotic cells had been described. Our results define a new mechanism of CIS-mediated bacteria-eukaryote interaction and are a step toward developing CISs as novel delivery systems for eukaryotic hosts.

Convergence of Nutritional Symbioses in Obligate Blood Feeders

Symbiosis with intracellular or gut bacteria is essential for the nutrition of animals with an obligate blood-feeding habit. Divergent bacterial lineages have independently evolved functional interactions with obligate blood feeders, but all converge to an analogous biochemical feature: the provisioning of B vitamins. Although symbionts and blood feeders coevolved interdependently for millions of years we stress that their associations are not necessarily stable. Ancestral symbionts can be replaced by recently acquired bacteria with similar biochemical features, a dynamic that emerges through a combination of phylogenetic and ecological constraints. Specifically, we highlight the lateral transfer of a streamlined biotin (B₇ vitamin) operon, and conjecture that its extensive spread across bacterial lineages may drive the emergence of novel nutritional symbioses with blood feeders.

A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes

Many commensal bacteria antagonize each other or their host by producing syringe-like secretion systems called contractile injection systems (CIS). Members of the Bacteroidales family have been shown to produce only one type of CIS-a contact-dependent type 6 secretion system that mediates bacterium-bacterium interactions. Here, we show that a second distinct cluster of genes from Bacteroidales bacteria from the human microbiome may encode yet-uncharacterized injection systems that we term Bacteroidales injection systems (BIS). We found that BIS genes are present in the gut microbiomes of 99% of individuals from the United States and Europe and that BIS genes are more prevalent in the gut microbiomes of healthy individuals than in those individuals suffering from inflammatory bowel disease. Gene clusters similar to that of the BIS mediate interactions between bacteria and diverse eukaryotes, like amoeba, insects, and tubeworms. Our findings highlight the ubiquity of the BIS gene cluster in the human gut and emphasize the relevance of the gut microbiome to the human host. These results warrant investigations into the structure and function of the BIS and how they might mediate interactions between Bacteroidales bacteria and the human host or microbiome.IMPORTANCE To engage with host cells, diverse pathogenic bacteria produce syringe-like structures called contractile injection systems (CIS). CIS are evolutionarily related to the contractile tails of bacteriophages and are specialized to puncture membranes, often delivering effectors to target cells. Although CIS are key for pathogens to cause disease, paradoxically, similar injection systems have been identified within healthy human microbiome bacteria. Here, we show that gene clusters encoding a predicted CIS, which we term Bacteroidales injection systems (BIS), are present in the microbiomes of nearly all adult humans tested from Western countries. BIS genes are enriched within human gut microbiomes and are expressed both in vitro and in vivo Further, a greater abundance of BIS genes is present within healthy gut microbiomes than in those humans with with inflammatory bowel disease (IBD). Our discovery provides a potentially distinct means by which our microbiome interacts with the human host or its microbiome.

Endosymbiotic Rickettsiella causes cytoplasmic incompatibility in a spider host

Many arthropod hosts are infected with bacterial endosymbionts that manipulate host reproduction, but few bacterial taxa have been shown to cause such manipulations. Here, we show that a bacterial strain in the genus Rickettsiella causes cytoplasmic incompatibility (CI) between infected and uninfected hosts. We first surveyed the bacterial community of the agricultural spider Mermessus fradeorum (Linyphiidae) using high throughput sequencing and found that individual spiders can be infected with up to five different strains of maternally inherited symbiont from the genera Wolbachia, Rickettsia, and Rickettsiella. The Rickettsiella strain was pervasive, found in all 23 tested spider matrilines. We used antibiotic curing to generate uninfected matrilines that we reciprocally crossed with individuals infected only with Rickettsiella. We found that only 13% of eggs hatched when uninfected females were mated with Rickettsiella-infected males; in contrast, at least 83% of eggs hatched in the other cross types. This is the first documentation of Rickettsiella, or any Gammaproteobacteria, causing CI. We speculate that induction of CI may be much more widespread among maternally inherited bacteria than previously appreciated. Further, our results reinforce the importance of thoroughly characterizing and assessing the inherited microbiome before attributing observed host phenotypes to well-characterized symbionts such as Wolbachia.

A chromosome-level assembly of the cat flea genome uncovers rampant gene duplication and genome size plasticity

BACKGROUND

Fleas (Insecta: Siphonaptera) are small flightless parasites of birds and mammals; their blood-feeding can transmit many serious pathogens (i.e., the etiological agents of bubonic plague, endemic and murine typhus). The lack of flea genome assemblies has hindered research, especially comparisons to other disease vectors. Accordingly, we sequenced the genome of the cat flea, Ctenocephalides felis, an insect with substantial human health and veterinary importance across the globe.

RESULTS

By combining Illumina and PacBio sequencing of DNA derived from multiple inbred female fleas with Hi-C scaffolding techniques, we generated a chromosome-level genome assembly for C. felis. Unexpectedly, our assembly revealed extensive gene duplication across the entire genome, exemplified by ~ 38% of protein-coding genes with two or more copies and over 4000 tRNA genes. A broad range of genome size determinations (433-551 Mb) for individual fleas sampled across different populations supports the widespread presence of fluctuating copy number variation (CNV) in C. felis. Similarly, broad genome sizes were also calculated for individuals of Xenopsylla cheopis (Oriental rat flea), indicating that this remarkable "genome-in-flux" phenomenon could be a siphonapteran-wide trait. Finally, from the C. felis sequence reads, we also generated closed genomes for two novel strains of Wolbachia, one parasitic and one symbiotic, found to co-infect individual fleas.

CONCLUSION

Rampant CNV in C. felis has dire implications for gene-targeting pest control measures and stands to complicate standard normalization procedures utilized in comparative transcriptomics analysis. Coupled with co-infection by novel Wolbachia endosymbionts-potential tools for blocking pathogen transmission-these oddities highlight a unique and underappreciated disease vector.

Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil

Soil ecosystems harbor diverse microorganisms and yet remain only partially characterized as neither single-cell sequencing nor whole-community sequencing offers a complete picture of these complex communities. Thus, the genetic and metabolic potential of this "uncultivated majority" remains underexplored. To address these challenges, we applied a pooled-cell-sorting-based mini-metagenomics approach and compared the results to bulk metagenomics. Informatic binning of these data produced 200 mini-metagenome assembled genomes (sorted-MAGs) and 29 bulk metagenome assembled genomes (MAGs). The sorted and bulk MAGs increased the known phylogenetic diversity of soil taxa by 7.2% with respect to the Joint Genome Institute IMG/M database and showed clade-specific sequence recruitment patterns across diverse terrestrial soil metagenomes. Additionally, sorted-MAGs expanded the rare biosphere not captured through MAGs from bulk sequences, exemplified through phylogenetic and functional analyses of members of the phylum Bacteroidetes Analysis of 67 Bacteroidetes sorted-MAGs showed conserved patterns of carbon metabolism across four clades. These results indicate that mini-metagenomics enables genome-resolved investigation of predicted metabolism and demonstrates the utility of combining metagenomics methods to tap into the diversity of heterogeneous microbial assemblages.IMPORTANCE Microbial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of untapped genetic diversity. To address some of the challenges associated with bulk metagenomics as well as low throughput of single-cell genomics, we applied flow cytometry-enabled mini-metagenomics to capture expanded microbial diversity from forest soil and compare it to soil bulk metagenomics. Our resulting data from this pooled-cell sorting approach combined with bulk metagenomics revealed increased phylogenetic diversity through novel soil taxa and rare biosphere members. In-depth analysis of genomes within the highly represented Bacteroidetes phylum provided insights into conserved and clade-specific patterns of carbon metabolism.

Wolbachia supplement biotin and riboflavin to enhance reproduction in planthoppers

Symbiont-mediated nutritional mutualisms can contribute to the host fitness of insects, especially for those that feed exclusively on nutritionally unbalanced diets. Here, we elucidate the importance of B group vitamins in the association of endosymbiotic bacteria Wolbachia with two plant-sap feeding insects, the small brown planthopper, Laodelphax striatellus (Fallén), and the brown planthopper, Nilaparvata lugens (Stål). Infected planthoppers of both species laid more eggs than uninfected planthoppers, while the experimental transfer of Wolbachia into uninfected lines of one planthopper species rescued this fecundity deficit. The genomic analysis showed that Wolbachia strains from the two planthopper species encoded complete biosynthesis operons for biotin and riboflavin, while a metabolic analysis revealed that Wolbachia-infected planthoppers of both species had higher titers of biotin and riboflavin. Furthermore, experimental supplementation of food with a mixture of biotin and riboflavin recovered the fecundity deficit of Wolbachia-uninfected planthoppers. In addition, comparative genomic analysis suggested that the riboflavin synthesis genes are conserved among Wolbachia supergroups. Biotin operons are rare in Wolbachia, and those described share a recent ancestor that may have been horizontally transferred from Cardinium bacteria. Our research demonstrates a type of mutualism that involves a facultative interaction between Wolbachia and plant-sap feeding insects involving vitamin Bs.

Whole genomic sequencing and sex-dependent abundance estimation of Cardinium sp., a common and hyperabundant bacterial endosymbiont of the American house dust mite, Dermatophagoides farinae

The two common species of house dust mites (HDMs), Dermatophagoides farinae and D. pteronyssinus, are major sources of allergens in human dwellings worldwide. Many allergens from HDMs have been described, but their extracts vary in immunogens. Mite strains may differ in their microbiomes, which affect mite allergen expression and contents of bacterial endotoxins. Some bacteria, such as the intracellular symbiont Cardinium, can affect both the sex ratio and biochemical pathways of mites, resulting in abundance variations of mite allergens/immunogens. Here, we investigated the bacterial microbiomes of D. farinae and D. pteronyssinus males and females using barcode 16S rDNA sequencing, qPCR, and genomic data analysis. We found a single species of Cardinium associated with D. farinae strains from the USA, China and Europe. Cardinium had high abundance relative to other bacterial taxa and represented 99% of all bacterial DNA reads from female mites from the USA. Cardinium was also abundant with respect to the number of host cells-we estimated 10.4-11.8 cells of Cardinium per single female mite cell. In a European D. farinae strain, Cardinium was more prevalent in females than in males (representing 92 and 67% of all bacterial taxa in females and males, respectively). In contrast, D. pteronyssinus lacked any Cardinium species, and the microbiomes of male and female mites were similar. We produced a Cardinium genome assembly (1.48 Mb; GenBank: PRJNA555788, GCA_007559345.1) associated with D. farinae. The ascertained ubiquity and abundance of Cardinium strongly suggest that this intracellular bacterium plays an important biological role in D. farinae.

Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids' di-symbiotic systems

Many insects depend on obligate mutualistic bacteria to provide essential nutrients lacking from their diet. Most aphids, whose diet consists of phloem, rely on the bacterial endosymbiont Buchnera aphidicola to supply essential amino acids and B vitamins. However, in some aphid species, provision of these nutrients is partitioned between Buchnera and a younger bacterial partner, whose identity varies across aphid lineages. Little is known about the origin and the evolutionary stability of these di-symbiotic systems. It is also unclear whether the novel symbionts merely compensate for losses in Buchnera or carry new nutritional functions. Using whole-genome endosymbiont sequences of nine Cinara aphids that harbour an Erwinia-related symbiont to complement Buchnera, we show that the Erwinia association arose from a single event of symbiont lifestyle shift, from a free-living to an obligate intracellular one. This event resulted in drastic genome reduction, long-term genome stasis, and co-divergence with aphids. Fluorescence in situ hybridisation reveals that Erwinia inhabits its own bacteriocytes near Buchnera's. Altogether these results depict a scenario for the establishment of Erwinia as an obligate symbiont that mirrors Buchnera's. Additionally, we found that the Erwinia vitamin-biosynthetic genes not only compensate for Buchnera's deficiencies, but also provide a new nutritional function; whose genes have been horizontally acquired from a Sodalis-related bacterium. A subset of these genes have been subsequently transferred to a new Hamiltonella co-obligate symbiont in one specific Cinara lineage. These results show that the establishment and dynamics of multi-partner endosymbioses can be mediated by lateral gene transfers between co-ocurring symbionts.

Development of a multi-locus sequence typing system helps reveal the evolution of Cardinium hertigii, a reproductive manipulator symbiont of insects

Background

Cardinium is an intracellular bacterial symbiont in the phylum Bacteroidetes that is found in many different species of arthropods and some nematodes. This symbiont is known to be able to induce three reproductive manipulation phenotypes, including cytoplasmic incompatibility. Placing individual strains of Cardinium within a larger evolutionary context has been challenging because only two, relatively slowly evolving genes, 16S rRNA gene and Gyrase B, have been used to generate phylogenetic trees, and consequently, the relationship of different strains has been elucidated in only its roughest form.

Results

We developed a Multi Locus Sequence Typing (MLST) system that provides researchers with three new genes in addition to Gyrase B for inferring phylogenies and delineating Cardinium strains. From our Cardinium phylogeny, we confirmed the presence of a new group D, a Cardinium clade that resides in the arachnid order harvestmen (Opiliones). Many Cardinium clades appear to display a high degree of host affinity, while some show evidence of host shifts to phylogenetically distant hosts, likely associated with ecological opportunity. Like the unrelated reproductive manipulator Wolbachia, the Cardinium phylogeny also shows no clear phylogenetic signal associated with particular reproductive manipulations.

Conclusions

The Cardinium phylogeny shows evidence of diversification within particular host lineages, and also of host shifts among trophic levels within parasitoid-host communities. Like Wolbachia, the relatedness of Cardinium strains does not necessarily predict their reproductive phenotypes. Lastly, the genetic tools proposed in this study may help future authors to characterize new strains and add to our understanding of Cardinium evolution.

Molecular host mimicry and manipulation in bacterial symbionts

It is common among intracellular bacterial pathogens to use eukaryotic-like proteins that mimic and manipulate host cellular processes to promote colonization and intracellular survival. Eukaryotic-like proteins are bacterial proteins with domains that are rare in bacteria, and known to function in the context of a eukaryotic cell. Such proteins can originate through horizontal gene transfer from eukaryotes or, in the case of simple repeat proteins, through convergent evolution. Recent studies of microbiomes associated with several eukaryotic hosts suggest that similar molecular strategies are deployed by cooperative bacteria that interact closely with eukaryotic cells. Some mimics, like ankyrin repeats, leucine rich repeats and tetratricopeptide repeats are shared across diverse symbiotic systems ranging from amoebae to plants, and may have originated early, or evolved independently in multiple systems. Others, like plant-mimicking domains in members of the plant microbiome are likely to be more recent innovations resulting from horizontal gene transfer from the host, or from microbial eukaryotes occupying the same host. Host protein mimics have only been described in a limited set of symbiotic systems, but are likely to be more widespread. Systematic searches for eukaryote-like proteins in symbiont genomes could lead to the discovery of novel mechanisms underlying host-symbiont interactions.

Dynamics of the microbial community during growth of the house dust mite Dermatophagoides farinae in culture

The variation in house dust mite microbial communities is important because various microorganisms modulate the production of allergens by their mite hosts and/or contaminate immunotherapeutic extracts. Temporal changes in mite microbiomes and the mite culture environment occurring at different stages of mite culture development are particularly understudied in this system. Here, we analyzed the dynamics of microbial communities during the culture growth of Dermatophagoides farinae. Changes in microbiomes were related to three key variables: the mite population density, microbial microcosm respiration and concentration of guanine (the mite nitrogenous waste metabolite). Mite populations exhibited the following phases: exponential growth, plateau and exponential decline. The intracellular bacterium Cardinium and the yeast Saccharomyces cerevisiae prevailed in the internal mite microbiomes, and the bacterium Lactobacillus fermentum was prevalent in the mite diet. The reduction in the mite population size during the late phases of culture development was related to the changes in their microbial profiles: the intracellular bacterium Cardinium was replaced by Staphylococcus, Oceanobacillus and Virgibacillus, and S. cerevisiae was replaced by the antagonistic fungi Aspergillus penicillioides and Candida. Increases in the guanine content were positively correlated with increases in the Staphylococcus and A. penicillioides profiles in the culture environment. Our results show that the mite microbiome exhibits strong, dynamic alterations in its profiles across different mite culture growth stages.

Exposure to opposing temperature extremes causes comparable effects on Cardinium density but contrasting effects on Cardinium-induced cytoplasmic incompatibility

Terrestrial arthropods, including insects, commonly harbor maternally inherited intracellular symbionts that confer benefits to the host or manipulate host reproduction to favor infected female progeny. These symbionts may be especially vulnerable to thermal stress, potentially leading to destabilization of the symbiosis and imposing costs to the host. For example, increased temperatures can reduce the density of a common reproductive manipulator, Wolbachia, and the strength of its crossing incompatibility (cytoplasmic incompatibility, or CI) phenotype. Another manipulative symbiont, Cardinium hertigii, infects ~ 6–10% of Arthropods, and also can induce CI, but there is little homology between the molecular mechanisms of CI induced by Cardinium and Wolbachia. Here we investigated whether temperature disrupts the CI phenotype of Cardinium in a parasitic wasp host, Encarsia suzannae. We examined the effects of both warm (32°C day/ 29°C night) and cool (20°C day/ 17°C night) temperatures on Cardinium CI and found that both types of temperature stress modified aspects of this symbiosis. Warm temperatures reduced symbiont density, pupal developmental time, vertical transmission rate, and the strength of both CI modification and rescue. Cool temperatures also reduced symbiont density, however this resulted in stronger CI, likely due to cool temperatures prolonging the host pupal stage. The opposing effects of cool and warm-mediated reductions in symbiont density on the resulting CI phenotype indicates that CI strength may be independent of density in this system. Temperature stress also modified the CI phenotype only if it occurred during the pupal stage, highlighting the likely importance of this stage for CI induction in this symbiosis.

Insects often harbor heritable symbiotic bacteria that infect their cells and/or bodily fluids. These heritable bacteria are passed from mother to offspring and can have substantial effects on host insect biology, and include bacteria like Cardinium that cause mating incompatibilities between symbiont-infected and uninfected individuals. Often, the extent of these symbiont-conferred modifications correlates with the bacterial density in the host. The appearance of these phenotypes is also affected by temperature stress, which often reduces bacterial density. However, here we find that temperature-altered strength of Cardinium-induced mating incompatibility in a whitefly parasitoid wasp can be independent of Cardinium density. While heat treatment reduced the symbiont density and the phenotype, as expected, cold treatment also reduced symbiont density but increased the degree of mating incompatibility. Here, the prolonged duration of the host pupal development in the cold treatments appeared to be more important for phenotype strength. These results suggest that the connection between bacterial density and phenotype strength may not be as general as previously thought. Furthermore, the modification of this manipulative phenotype has implications for the effectiveness of the host, Encarsia suzannae, as a biological control agent.

First Evidence of Intracellular Bacteria Cardinium in Thermophilic Mite Microzetorchestes emeryi (Acari: Oribatida): Molecular Screening of Bacterial Endosymbiont Species

We undertook the issue of the distribution of intracellular bacteria among Oribatida (Acari). Six genera of bacteria were detected by PCR and Sanger DNA sequencing: Wolbachia, Cardinium, Rickettsia, Spiroplasma, Arsenophonus, and Hamiltonella. Our research, for the first time, revealed the presence of Cardinium in Microzetorchestes emeryi in two subpopulations separated from each other by 300 m. The percentages of infected animals were the same in both subpopulations-ca. 20%. The identity of 16S rDNA sequences of Cardinium between these two subpopulations of M. emeryi was 97%. Phylogenetic analysis showed that the Cardinium in M. emeryi was clustered into the group A. The occurrence of M. emeryi in Poland has not been reported before and our report is the first one. Cardinium maybe help the thermophilic M. emeryi to adapt to low temperatures in the Central Europe.

Population and Culture Age Influence the Microbiome Profiles of House Dust Mites

Interactions with microorganisms might enable house dust mites (HDMs) to derive nutrients from difficult-to-digest structural proteins and to flourish in human houses. We tested this hypothesis by investigating the effects of changes in the mite culture growth and population of two HDM species on HDM microbiome composition and fitness. Growing cultures of laboratory and industrial allergen-producing populations of Dermatophagoides farinae (DFL and DFT, respectively) and Dermatophagoides pteronyssinus (DPL and DPT, respectively) were sampled at four time points. The symbiotic microorganisms of the mites were characterized by DNA barcode sequencing and quantified by qPCR using universal/specific primers. The population growth of mites and nutrient contents of mite bodies were measured and correlated with the changes in bacteria in the HDM microbiome. The results showed that both the population and culture age significantly influenced the microbiome profiles. Cardinium formed 93% and 32% of the total sequences of the DFL and DFT bacterial microbiomes, respectively, but this bacterial species was less abundant in the DPL and DPT microbiomes. Staphylococcus abundance was positively correlated with increased glycogen contents in the bodies of mites, and increased abundances of Aspergillus, Candida, and Kocuria were correlated with increased lipid contents in the bodies of mites. The xerophilic fungus Wallemia accounted for 39% of the fungal sequences in the DPL microbiome, but its abundance was low in the DPT, DFL, and DFT microbiomes. With respect to the mite culture age, we made three important observations: the mite population growth from young cultures was 5-8-fold higher than that from old cultures; specimens from old cultures had greater abundances of fungi and bacteria in their bodies; and yeasts predominated in the gut contents of specimens from young cultures, whereas filamentous mycelium prevailed in specimens from old cultures. Our results are consistent with the hypothesis that mites derive nutrients through associations with microorganisms.

The draft genome of strain cCpun from biting midges confirms insect Cardinium are not a monophyletic group and reveals a novel gene family expansion in a symbiont

BACKGROUND

It is estimated that 13% of arthropod species carry the heritable symbiont Cardinium hertigii. 16S rRNA and gyrB sequence divides this species into at least four groups (A-D), with the A group infecting a range of arthropods, the B group infecting nematode worms, the C group infecting Culicoides biting midges, and the D group associated with the marine copepod Nitocra spinipes. To date, genome sequence has only been available for strains from groups A and B, impeding general understanding of the evolutionary history of the radiation. We present a draft genome sequence for a C group Cardinium, motivated both by the paucity of genomic information outside of the A and B group, and the importance of Culicoides biting midge hosts as arbovirus vectors.

METHODS

We reconstructed the genome of cCpun, a Cardinium strain from group C that naturally infects Culicoides punctatus, through Illumina sequencing of infected host specimens.

RESULTS

The draft genome presented has high completeness, with BUSCO scores comparable to closed group A Cardinium genomes. Phylogenomic analysis based on concatenated single copy core proteins do not support Cardinium from arthropod hosts as a monophyletic group, with nematode Cardinium strains nested within the two groups infecting arthropod hosts. Analysis of the genome of cCpun revealed expansion of a variety of gene families classically considered important in symbiosis (e.g., ankyrin domain containing genes), and one set-characterized by DUF1703 domains-not previously associated with symbiotic lifestyle. This protein group encodes putative secreted nucleases, and the cCpun genome carried at least 25 widely divergent paralogs, 24 of which shared a common ancestor in the C group. The genome revealed no evidence in support of B vitamin provisioning to its haematophagous host, and indeed suggests Cardinium may be a net importer of biotin.

DISCUSSION

These data indicate strains of Cardinium within nematodes cluster within Cardinium strains found in insects. The draft genome of cCpun further produces new hypotheses as to the interaction of the symbiont with the midge host, in particular the biological role of DUF1703 nuclease proteins that are predicted as being secreted by cCpun. In contrast, the coding content of this genome provides no support for a role for the symbiont in provisioning the host with B vitamins.

The Mite Tyrophagus putrescentiae Hosts Population-Specific Microbiomes That Respond Weakly to Starvation

The effect of short-term nutrient deprivation was studied in five populations of the mite Tyrophagus putrescentiae with different microbiomes. The fresh weight, nutrient status, respiration, and population growth of the mites were observed for the five mite population-scale samples. The starvation caused the larvae and nymphs to be eliminated, resulting in a significant increase in the fresh weight of starved adult specimens. Three populations were negatively influenced by starvation, and the starved specimens were characterized by a decrease in nutrient status, respiration, and population growth. One population was not influenced or was slightly influenced by starvation, which had no effect on population growth or nutrient contents but caused a significant decrease in respiration. One population was positively influenced by starvation; the population growth increased in starved specimens, and starvation had no effect on respiration. Although starvation altered the bacterial profiles of the microbiomes, these differences were much smaller than those between the populations. The bacterial profiles of Staphylococcus, Bacillus, Kocuria, Brevibacterium, and unidentified Micrococcaceae and Enterobacteriaceae increased in starved specimens, whereas those of Bartonella and Solitalea-like genera were reduced in the starved mite populations. The profiles of the intracellular symbiont Cardinium decreased in the starved specimens, and the Wolbachia profile changes were dependent on the mite population. In mite populations, when the symbionts were rare, their profiles varied stochastically. Correlations between changes in the profiles of the bacterial taxa and mite fitness parameters, including nutrient status (lipids, proteins, saccharides, and glycogen contents), mite population growth, and respiration, were observed. Although the microbiomes were resistant to the perturbations caused by nutrition deficiency, the responses of the mites differed in terms of their population growth, respiration, and nutrient status.

The Toxin-Antidote Model of Cytoplasmic Incompatibility: Genetics and Evolutionary Implications

Wolbachia bacteria inhabit the cells of about half of all arthropod species, an unparalleled success stemming in large part from selfish invasive strategies. Cytoplasmic incompatibility (CI), whereby the symbiont makes itself essential to embryo viability, is the most common of these and constitutes a promising weapon against vector-borne diseases. After decades of theoretical and experimental struggle, major recent advances have been made toward a molecular understanding of this phenomenon. As pieces of the puzzle come together, from yeast and Drosophila fly transgenesis to CI diversity patterns in natural mosquito populations, it becomes clearer than ever that the CI induction and rescue stem from a toxin-antidote (TA) system. Further, the tight association of the CI genes with prophages provides clues to the possible evolutionary origin of this phenomenon and the levels of selection at play.

Legionella Becoming a Mutualist: Adaptive Processes Shaping the Genome of Symbiont in the Louse Polyplax serrata

Legionellaceae are intracellular bacteria known as important human pathogens. In the environment, they are mainly found in biofilms associated with amoebas. In contrast to the gammaproteobacterial family Enterobacteriaceae, which established a broad spectrum of symbioses with many insect taxa, the only instance of legionella-like symbiont has been reported from lice of the genus Polyplax. Here, we sequenced the complete genome of this symbiont and compared its main characteristics to other Legionella species and insect symbionts. Based on rigorous multigene phylogenetic analyses, we confirm this bacterium as a member of the genus Legionella and propose the name Candidatus Legionella polyplacis, sp.n. We show that the genome of Ca. Legionella polyplacis underwent massive degeneration, including considerable size reduction (529.746 bp, 484 protein coding genes) and a severe decrease in GC content (23%). We identify several possible constraints underlying the evolution of this bacterium. On one hand, Ca. Legionella polyplacis and the louse symbionts Riesia and Puchtella experienced convergent evolution, perhaps due to adaptation to similar hosts. On the other hand, some metabolic differences are likely to reflect different phylogenetic positions of the symbionts and hence availability of particular metabolic function in the ancestor. This is exemplified by different arrangements of thiamine metabolism in Ca. Legionella polyplacis and Riesia. Finally, horizontal gene transfer is shown to play a significant role in the adaptive and diversification process. Particularly, we show that Ca. L. polyplacis horizontally acquired a complete biotin operon (bioADCHFB) that likely assisted this bacterium when becoming an obligate mutualist.

Genome-Wide Profiling of Cardinium-Responsive MicroRNAs in the Exotic Whitefly, Bemisia tabaci (Gennadius) Biotype Q

Although the bacterial symbiont Cardinium has profound effects on the ecological adaptation of its host, the whitefly Bemisia tabaci (Gennadius) biotype Q (hereafter referred to as B. tabaci Q), the molecular mechanism underlying interactions between these two organisms is not yet fully understood. In this study, sRNA libraries were constructed, amplified, and sequenced for Cardinium-infected (C⁺) and uninfected (C^∗−) B. tabaci Q with identical genetic backgrounds. Subsequently, the genes targeted by the differentially expressed miRNAs were predicted by integrating the B. tabaci Q genome data. A total of 125 known and 100 novel miRNAs were identified, among which 23 significant differentially expressed miRNAs were identified in both libraries. It is noteworthy that an analysis of target genes showed that Cardinium-responsive miRNA-regulated genes were functional in apoptosis, reproduction, development, immune response, thermotolerance and insecticide resistance. GO and KEGG pathway analysis revealed that some miRNA-target genes are closely associated with energy metabolism. A major finding of this study was the identification of several miRNAs that may be involved in physiological processes in response to environmental stress, i.e., insecticides and high temperatures. This information will provide a foundation to help further elucidate the functions of Cardinium in B. tabaci Q.

A new Cardinium group of bacteria found in Achipteria coleoptrata (Acari: Oribatida)

The understanding of the biology of arthropods requires an understanding of their bacterial associates. We determined the distribution of bacteria Wolbachia sp., Rickettsia sp., Cardinium sp., Spiroplasma sp., Arsenophonus sp., Hamiltonella sp., and Flavobacterium in oribatid mites (Acari: Oribatida). We identified Cardinium sp. in Achipteria coleoptrata. This is the first report of this bacterium in A. coleoptrata. Approximately 30% of the mite population was infected by Cardinium sp. The Cardinium 16S rDNA was examined for the presence of two sequences unique for this microorganism. One of them was noted in Cardinium sp. of A. coleoptrata. In the second sequence, we found nucleotide substitution in the 7th position: A instead of T. In our opinion, this demonstrated the unique nature of Cardinium sp. of A. coleoptrata. We also determined phylogenetic relationship between Cardinium sp., including the strain found in A. coleoptrata by studying the 16S rRNA and gyrB gene sequences. It revealed that Cardinium from A. coleoptrata did not cluster together with strains from groups A, B, C or D, and constituted a separate clade E. These observations make A. coleoptrata a unique Cardinium host in terms of the distinction of the strain.

Comparative Genomics of Wolbachia-Cardinium Dual Endosymbiosis in a Plant-Parasitic Nematode

Wolbachia and Cardinium are among the most important and widespread of all endosymbionts, occurring in nematodes and more than half of insect and arachnid species, sometimes as coinfections. These symbionts are of significant interest as potential biocontrol agents due to their abilities to cause major effects on host biology and reproduction through cytoplasmic incompatibility, sex ratio distortion, or obligate mutualism. The ecological and metabolic effects of coinfections are not well understood. This study examined a Wolbachia-Cardinium coinfection in the plant-parasitic nematode (PPN), Pratylenchus penetrans, producing the first detailed study of such a coinfection using fluorescence in situ hybridization (FISH), polymerase chain reaction (PCR), and comparative genomic analysis. Results from FISH and single-nematode PCR showed 123/127 individuals in a focal population carried Cardinium (denoted strain cPpe), and 48% were coinfected with Wolbachia strain wPpe. Both endosymbionts showed dispersed tissue distribution with highest densities in the anterior intestinal walls and gonads. Phylogenomic analyses confirmed an early place of cPpe and long distance from a sister strain in another PPN, Heterodera glycines, supporting a long history of both Cardinium and Wolbachia in PPNs. The genome of cPpe was 1.36 Mbp with 35.8% GC content, 1,131 predicted genes, 41% having no known function, and missing biotin and lipoate synthetic capacity and a plasmid present in other strains, despite having a slightly larger genome compared to other sequenced Cardinium. The larger genome revealed expansions of gene families likely involved in host-cellular interactions. More than 2% of the genes of cPpe and wPpe were identified as candidate horizontally transferred genes, with some of these from eukaryotes, including nematodes. A model of the possible Wolbachia-Cardinium interaction is proposed with possible complementation in function for pathways such as methionine and fatty acid biosynthesis and biotin transport.