Complete genome sequence of "Candidatus Portiera aleyrodidarum" BT-QVLC, an obligate symbiont that supplies amino acids and carotenoids to Bemisia tabaci

Whitefly-Plant Interactions: An Integrated Molecular Perspective

The rapid advances in available transcriptomic and genomic data and our understanding of the physiology and biochemistry of whitefly-plant interactions have allowed us to gain new and significant insights into the biology of whiteflies and their successful adaptation to host plants. In this review, we provide a comprehensive overview of the mechanisms that whiteflies have evolved to overcome the challenges of feeding on phloem sap. We also highlight the evolution and functions of gene families involved in host perception, evaluation, and manipulation; primary metabolism; and metabolite detoxification. We discuss the emerging themes in plant immunity to whiteflies, focusing on whitefly effectors and their sites of action in plant defense-signaling pathways. We conclude with a discussion of advances in the genetic manipulation of whiteflies and the potential that they hold for exploring the interactions between whiteflies and their host plants, as well as the development of novel strategies for the genetic control of whiteflies.

The nutritional dimension of facultative bacterial symbiosis in aphids: Current status and methodological considerations for future research

Aphids are valuable models for studying the functional diversity of bacterial symbiosis in insects. In addition to their ancestral obligate nutritional symbiont Buchnera aphidicola, these insects can host a myriad of so-called facultative symbionts. The diversity of these heritable bacterial associates is now well known, and some of the ecologically important traits associated with them have been well documented. Some twenty years ago, it was suggested that facultative symbionts could play an important role in aphid nutrition, notably by improving feeding performance on specific host plants, thus influencing the adaptation of these insects to host plants. However, the underlying mechanisms have never been elucidated, and the nutritional role that facultative symbionts might perform in aphids remains enigmatic. In this opinion piece, I put forward a series of arguments in support of the hypothesis that facultative symbionts play a central role in aphid nutrition and emphasize methodological considerations for testing this hypothesis in future work. In particular, I hypothesize that the metabolic capacities of B. aphidicola alone may not always be able to counterbalance the nutritional deficiencies of phloem sap. The association with one or several facultative symbionts with extensive metabolic capabilities would then be necessary to buffer the insect from host plant-derived nutrient deficiencies, thus enabling it to gain access to certain host plants.

Comparative Genomics Reveals Three Genetic Groups of the Whitefly Obligate Endosymbiont Candidatus Portiera aleyrodidarum

Maternally inherited obligate endosymbionts codiverge with their invertebrate hosts and reflect their host's evolutionary history. Whiteflies (Hemiptera: Aleyrodidae) harbor one obligate endosymbiont, Candidatus Portiera aleyrodidarum (hereafter Portiera). Portiera was anciently acquired by whitefly and has been coevolving with its host ever since. Uncovering the divergence of endosymbionts provides a fundamental basis for inspecting the coevolutionary processes between the bacteria and their hosts. To illustrate the divergence of Portiera lineages across different whitefly species, we sequenced the Portiera genome from Aleyrodes shizuokensis and conducted a comparative analysis on the basic features and gene evolution with bacterial genomes from five whitefly genera, namely Aleurodicus, Aleyrodes, Bemisia, Pealius, and Trialeurodes. The results indicated that Portiera from Bemisia possessed significantly larger genomes, fewer coding sequences (CDSs), and a lower coding density. Their gene arrangement differed notably from those of other genera. The phylogeny of the nine Portiera lineages resembled that of their hosts. Moreover, the lineages were classified into three distinct genetic groups based on the genetic distance, one from Aleurodicus (Aleurodicinae), one from Bemisia (Aleyrodinae), and another from Aleyrodes, Pealius, and Trialeurrodes (Aleyrodinae). Synonymous and nonsynonymous rate analyses, parity rule 2 plot analyses, neutrality plot analyses, and effective number of codons analyses supported the distinction of the three genetic groups. Our results indicated that Portiera from distant hosts exhibit distinct genomic contents, implying codivergence between hosts and their endosymbionts. This work will enhance our understanding of coevolution between hosts and their endosymbionts.

Cadmium stimulated cooperation between bacterial endophytes and plant intrinsic detoxification mechanism in Lonicera japonica thunb

Due to the intimate association between plant physiology and metabolism, the internal colonizing microbe (endophytes) community must be adjusted to support plant productivity in response to cell damage in plants under stress. However, how endophytes coordinate their activities with plant intrinsic mechanisms such as antioxidative systems and detoxification pathways during Cd accumulation remains unknown. In this hydroponic pot study, we investigated how exposure of Lonicera japonica. thunb. to different levels of Cd (0.5, 2.5, 5, 10, and 20 mg kg^-1) affected plant growth, metabolic pathways, and endophyte community structure and function. Although Cd accumulation increased at 5 mg kg^-1 Cd, the biomass and height of L. japonica increased in association with elevated endophyte-involved plant detoxification activities. Endophytes, such as Sphingomonas, Klenkia, and Modestobacter, expressed major antioxidative regulators (superoxide dismutase and ascorbate acid) to detoxify Cd in L. japonica. Furthermore, L. japonica and its endophytes synergistically regulated the toxic effects of Cd accumulation via multiple plant metabolic defensive pathways to increase resistance to metal-induced stress.

Plant-mediated rifampicin treatment of Bemisia tabaci disrupts but does not eliminate endosymbionts

Whiteflies are among the most important global insect pests in agriculture; their sustainable control has proven challenging and new methods are needed. Bacterial symbionts of whiteflies are poorly understood potential target of novel whitefly control methods. Whiteflies harbour an obligatory bacterium, Candidatus Portiera aleyrodidarum, and a diverse set of facultative bacterial endosymbionts. Function of facultative microbial community is poorly understood largely due to the difficulty in their selective elimination without removal of the primary endosymbiont. Since the discovery of secondary endosymbionts, antibiotic rifampicin has emerged as the most used tool for their manipulation. Its effectiveness is however much less clear, with contrasting reports on its effects on the endosymbiont community. The present study builds upon most recent method of rifampicin application in whiteflies and evaluates its ability to eliminate obligatory Portiera and two facultative endosymbionts (Rickettsia and Arsenophnus). Our results show that rifampicin reduces but does not eliminate any of the three endosymbionts. Additionally, rifampicin causes direct negative effect on whiteflies, likely by disrupting mitochondria. Taken together, results signify the end of a rifampicin era in whitefly endosymbiont studies. Finally, we propose refinement of current quantification and data analysis methods which yields additional insights in cellular metabolic scaling.

Spatio-temporal changes in endosymbiont diversity and composition in the African cassava whitefly, Bemisia tabaci SSA1

Sap-sucking insects, including whiteflies, are amongst the most devastating and widely distributed organisms on the planet. They are often highly invasive and endosymbiont communities within these insects help them adapt to new or changing environments. Bemisia tabaci (Gennadius; Hemiptera: Aleyrodidae) whitefly species are vectors of more than 500 known plant-viruses and harbour highly diverse endosymbionts communities. To date, however, whitefly–endosymbiont interactions, community structure and their spatio-temporal changes are still poorly understood. In this study, we investigated the spatio-temporal changes in the composition and diversity of bacterial endosymbionts in the agricultural crop pest whitefly species, Bemisia tabaci sub-Saharan Africa 1-subgroup 1 and 2 (SSA1-SG1 and SSA1-SG2). 16S rRNA amplicon sequencing analysis was carried out to characterise endosymbiont compositionsin field-collected SSA1 (SSA1-SG1 and SSA1-SG2) populations infesting cassava in Uganda in 1997 and 2017. We detected Portiera, Arsenophonus, Wolbachia, Hamiltonella and Hemipteriphilus, with Arsenophonus and Wolbachia infections being predominant. Hemipteriphilus and Hamiltonella frequencies were very low and were detected in seven and two samples, respectively. Bacterial diversity based on three independent parameters including Simpson index, number of haplotypes and Bray–Curtis dissimilarity matrix was significantly higher in 1997 than in 2017. This period also coincided with the advent of super-abundant cassava-whitefly populations on cassava crops in Uganda. We discuss how endosymbionts may influence the biology and behaviour of whiteflies leading to population explosions.

Coevolution of Metabolic Pathways in Blattodea and Their Blattabacterium Endosymbionts, and Comparisons with Other Insect-Bacteria Symbioses

Many insects harbor bacterial endosymbionts that supply essential nutrients and enable their hosts to thrive on a nutritionally unbalanced diet. Comparisons of the genomes of endosymbionts and their insect hosts have revealed multiple cases of mutually-dependent metabolic pathways that require enzymes encoded in 2 genomes. Complementation of metabolic reactions at the pathway level has been described for hosts feeding on unbalanced diets, such as plant sap. However, the level of collaboration between symbionts and hosts that feed on more variable diets is largely unknown. In this study, we investigated amino acid and vitamin/cofactor biosynthetic pathways in Blattodea, which comprises cockroaches and termites, and their obligate endosymbiont Blattabacterium cuenoti (hereafter Blattabacterium). In contrast to other obligate symbiotic systems, we found no clear evidence of "collaborative pathways" for amino acid biosynthesis in the genomes of these taxa, with the exception of collaborative arginine biosynthesis in 2 taxa, Cryptocercus punctulatus and Mastotermes darwiniensis. Nevertheless, we found that several gaps specific to Blattabacterium in the folate biosynthetic pathway are likely to be complemented by their host. Comparisons with other insects revealed that, with the exception of the arginine biosynthetic pathway, collaborative pathways for essential amino acids are only observed in phloem-sap feeders. These results suggest that the host diet is an important driving factor of metabolic pathway evolution in obligate symbiotic systems. IMPORTANCE The long-term coevolution between insects and their obligate endosymbionts is accompanied by increasing levels of genome integration, sometimes to the point that metabolic pathways require enzymes encoded in two genomes, which we refer to as "collaborative pathways". To date, collaborative pathways have only been reported from sap-feeding insects. Here, we examined metabolic interactions between cockroaches, a group of detritivorous insects, and their obligate endosymbiont, Blattabacterium, and only found evidence of collaborative pathways for arginine biosynthesis. The rarity of collaborative pathways in cockroaches and Blattabacterium contrasts with their prevalence in insect hosts feeding on phloem-sap. Our results suggest that host diet is a factor affecting metabolic integration in obligate symbiotic systems.

Cytotype Affects the Capability of the Whitefly Bemisia tabaci MED Species To Feed and Oviposit on an Unfavorable Host Plant

The acquisition of nutritional obligate primary endosymbionts (P-symbionts) allowed phloemo-phageous insects to feed on plant sap and thus colonize novel ecological niches. P-symbionts often coexist with facultative secondary endosymbionts (S-symbionts), which may also influence their hosts' niche utilization ability. The whitefly Bemisia tabaci is a highly diversified species complex harboring, in addition to the P-symbiont "Candidatus Portiera aleyrodidarum," seven S-symbionts whose roles remain poorly understood. Here, we compare the phenotypic and metabolic responses of three B. tabaci lines differing in their S-symbiont community, reared on three different host plants, hibiscus, tobacco, or lantana, and address whether and how S-symbionts influence insect capacity to feed and produce offspring on those plants. We first show that hibiscus, tobacco, and lantana differ in their free amino acid composition. Insects' performance, as well as free amino acid profile and symbiotic load, were shown to be plant dependent, suggesting a critical role for the plant nutritional properties. Insect fecundity was significantly lower on lantana, indicating that it is the least favorable plant. Remarkably, insects reared on this plant show a specific amino acid profile and a higher symbiont density compared to the two other plants. In addition, this plant was the only one for which fecundity differences were observed between lines. Using genetically homogeneous hybrids, we demonstrate that cytotype (mitochondria and symbionts), and not genotype, is a major determinant of females' fecundity and amino acid profile on lantana. As cytotypes differ in their S-symbiont community, we propose that these symbionts may mediate their hosts' suitable plant range. IMPORTANCE Microbial symbionts are universal in eukaryotes, and it is now recognized that symbiotic associations represent major evolutionary driving forces. However, the extent to which symbionts contribute to their hosts' ecological adaptation and subsequent diversification is far from being fully elucidated. The whitefly Bemisia tabaci is a sap feeder associated with multiple coinfecting intracellular facultative symbionts. Here, we show that plant species simultaneously affect whiteflies' performance, amino acid profile, and symbiotic density, which could be partially explained by differences in plant nutritional properties. We also demonstrate that, on lantana, the least favorable plant used in our study, whiteflies' performance is determined by their cytotype. We propose that the host plant utilization in B. tabaci is influenced by its facultative symbiont community composition, possibly through its impact on the host dietary requirements. Altogether, our data provide new insights into the impact of intracellular microorganisms on their animal hosts' ecological niche range and diversification.

Whitefly endosymbionts: IPM opportunity or tilting at windmills?

Whiteflies are sap-sucking insects responsible for high economic losses. They colonize hundreds of plant species and cause direct feeding damage and indirect damage through transmission of devastating viruses. Modern agriculture has seen a history of invasive whitefly species and populations that expand to novel regions, bringing along fierce viruses. Control efforts are hindered by fast virus transmission, insecticide-resistant populations, and a wide host range which permits large natural reservoirs for whiteflies. Augmentative biocontrol by parasitoids while effective in suppressing high population densities in greenhouses falls short when it comes to preventing virus transmission and is ineffective in the open field. A potential source of much needed novel control strategies lays within a diverse community of whitefly endosymbionts. The idea to exploit endosymbionts for whitefly control is as old as identification of these bacteria, yet it still has not come to fruition. We review where our knowledge stands on the aspects of whitefly endosymbiont evolution, biology, metabolism, multitrophic interactions, and population dynamics. We show how these insights are bringing us closer to the goal of better integrated pest management strategies. Combining most up to date understanding of whitefly-endosymbiont interactions and recent technological advances, we discuss possibilities of disrupting and manipulating whitefly endosymbionts, as well as using them for pest control.

Comparative Genomics Underlines Multiple Roles of Profftella, an Obligate Symbiont of Psyllids: Providing Toxins, Vitamins, and Carotenoids

The Asian citrus psyllid Diaphorina citri (Insecta: Hemiptera: Psylloidea), a serious pest of citrus species worldwide, harbors vertically transmitted intracellular mutualists, Candidatus Profftella armatura (Profftella_DC, Gammaproteobacteria: Burkholderiales) and Candidatus Carsonella ruddii (Carsonella_DC, Gammaproteobacteria: Oceanospirillales). Whereas Carsonella_DC is a typical nutritional symbiont, Profftella_DC is a unique defensive symbiont with organelle-like features, including intracellular localization within the host, perfect infection in host populations, vertical transmission over evolutionary time, and drastic genome reduction down to much less than 1 Mb. Large parts of the 460-kb genome of Profftella_DC are devoted to genes for synthesizing a polyketide toxin; diaphorin. To better understand the evolution of this unusual symbiont, the present study analyzed the genome of Profftella_Dco, a sister lineage to Profftella_DC, using Diaphorina cf. continua, a host psyllid congeneric with D. citri. The genome of coresiding Carsonella (Carsonella_Dco) was also analyzed. The analysis revealed nearly perfect synteny conservation in these genomes with their counterparts from D. citri. The substitution rate analysis further demonstrated genomic stability of Profftella which is comparable to that of Carsonella. Profftella_Dco and Profftella_DC shared all genes for the biosynthesis of diaphorin, hemolysin, riboflavin, biotin, and carotenoids, underlining multiple roles of Profftella, which may contribute to stabilizing symbiotic relationships with the host. However, acyl carrier proteins were extensively amplified in polyketide synthases DipP and DipT for diaphorin synthesis in Profftella_Dco. This level of acyl carrier protein augmentation, unprecedented in modular polyketide synthases of any known organism, is not thought to influence the polyketide structure but may improve the synthesis efficiency.

An eco-systems biology approach for modeling tritrophic networks reveals the influence of dietary amino acids on symbiont dynamics of Bemisia tabaci

Metabolic conversions allow organisms to produce essential metabolites from the available nutrients in an environment, frequently requiring metabolic exchanges among co-inhabiting organisms. Here, we applied genomic-based simulations for exploring tri-trophic interactions among the sap-feeding insect whitefly (Bemisia tabaci), its host-plants, and symbiotic bacteria. The simplicity of this ecosystem allows capturing the interacting organisms (based on genomic data) and the environmental content (based on metabolomics data). Simulations explored the metabolic capacities of insect-symbiont combinations under environments representing natural phloem. Predictions were correlated with experimental data on the dynamics of symbionts under different diets. Simulation outcomes depict a puzzle of three-layer origins (plant-insect-symbionts) for the source of essential metabolites across habitats and stratify interactions enabling the whitefly to feed on diverse hosts. In parallel to simulations, natural and artificial feeding experiments provide supporting evidence for an environment-based effect on symbiont dynamics. Based on simulations, a decrease in the relative abundance of a symbiont can be associated with a loss of fitness advantage due to an environmental excess in amino-acids whose production in a deprived environment used to depend on the symbiont. The study demonstrates that genomic-based predictions can bridge environment and community dynamics and guide the design of symbiont manipulation strategies.

Two Deoxythymidine Triphosphate Synthesis-Related Genes Regulate Obligate Symbiont Density and Reproduction in the Whitefly Bemisia tabaci MED

Deoxythymidine triphosphate (dTTP) is essential for DNA synthesis and cellular growth in all organisms. Here, genetic capacity analysis of the pyrimidine pathway in insects and their symbionts revealed that dTTP is a kind of metabolic input in several host insect/obligate symbiont symbiosis systems, including Bemisia tabaci MED/Candidatus Portiera aleyrodidarum (hereafter Portiera). As such, the roles of dTTP on both sides of the symbiosis system were investigated in B. tabaci MED/Portiera. Dietary RNA interference (RNAi) showed that suppressing dTTP production significantly reduced the density of Portiera, significantly repressed the expression levels of horizontally transferred essential amino acid (EAA) synthesis-related genes, and significantly decreased the reproduction of B. tabaci MED adults as well as the hatchability of their offspring. Our results revealed the regulatory role of dTTP in B. tabaci MED/Portiera and showed that dTTP synthesis-related genes could be potential targets for controlling B. tabaci as well as other sucking pests.

Selective and stable elimination of endosymbionts from multiple-infected whitefly Bemisia tabaci by feeding on a cotton plant cultured in antibiotic solutions

The maternally heritable endosymbiont provides many ecosystem functions. Antibiotic elimination of a specific symbiont and establishment of experimental host lines lacking certain symbionts enable the roles of a given symbiont to be explored. The whitefly Bemisia tabaci (Gennadius) in China harbors obligate symbiont Portiera infecting each individual, as well as facultative symbionts, such as Hamiltonella, Rickettsia and Cardinium, with co-infections occurring relatively frequently. So far no studies have evaluated the selectivity and efficacy of a specific symbiont elimination using antibiotics in whiteflies co-infected with different symbionts. Furthermore, no success has been achieved in establishing certain symbiont-free B. tabaci lines. In this study, we treated Hamiltonella-infected B. tabaci line, Hamiltonella-Rickettsia-co-infected line and Hamiltonella-Cardinium co-infected line by feeding B. tabaci adults with cotton plants cultured in water containing rifampicin, ampicillin or a mixture of them, aiming to selectively curing symbiont infections and establishing stable symbiont-free lines. We found ampicillin selectively eliminated Cardinium without affecting Portiera, Hamiltonella and Rickettsia, although they coexisted in the same host body. Meanwhile, all of the symbionts considered in our study can be removed by rifampicin. The reduction of facultative symbionts occurred at a much quicker pace than obligate symbiont Portiera during rifampicin treatment. Also, we measured the stability of symbiont elimination in whitefly successive generations and established Rickettsia-infected and Cardinium-infected lines which are absent in natural populations. Our results provide new protocols for selective elimination of symbionts co-existing in a host and establishment of different symbiont-infected host lines.

Nutritional Relationship between Bemisia tabaci and Its Primary Endosymbiont, Portiera aleyrodidarum, during Host Plant Acclimation

Simple Summary

Plant sap-sucking insects commonly have established mutualistic relationships with bacteria that live within their bodies and often provide nutrients that are lacking in the insect’s diet. The sweet potato whitefly (Bemisia tabaci) harbors one primary and up to seven secondary endosymbiotic bacteria. The primary endosymbiont of B. tabaci is already known to play a critical role in providing necessary nutrients for B. tabaci. Our objective was to study the relationship among B. tabaci, its primary endosymbiont, and the host plant through the effects of host plant shifting and acclimation, that is, physiological adjustments as an insect becomes accustomed to a new host plant over several generations. The results showed that host shifting from Chinese kale to cotton plants led to a decrease in the fecundity of B. tabaci in the first generation, which was restored after 10 generations of acclimation, and that its developmental time was also decreased by the tenth generation. Furthermore, essential amino acid biosynthesis genes of its primary endosymbiont were differentially regulated after B. tabaci had become acclimated to cotton plants. We speculate that the primary endosymbiont has a close nutritional relationship with B. tabaci during host plant acclimation.

Abstract

Plant sap-sucking insects commonly have established mutualistic relationships with endosymbiotic bacteria that can provide nutrients lacking in their diet. Bemisia tabaci harbors one primary endosymbiont, Portiera aleyrodidarum, and up to seven secondary endosymbionts, including Hamiltonella defensa and Rickettsia sp. Portiera aleyrodidarum is already known to play a critical role in providing necessary nutrients for B. tabaci. In the present study, the relationship among B. tabaci, its primary endosymbiont, and the host plant were examined through the effects of host plant shifting and acclimation. Bemisia tabaci was transferred from Chinese kale to four different host plants, and the effects on both its performance and the expression levels of nutrient-related genes of P. aleyrodidarum were analyzed. The results showed that host shifting from Chinese kale to cotton plants led to a decrease in the performance of B. tabaci in the first generation, which was restored after 10 generations of acclimation. Furthermore, the expression levels of essential amino acid biosynthesis genes of P. aleyrodidarum were found to be differentially regulated after B. tabaci had acclimated to the cotton plants. Host plant shifting and acclimation to cucumber, poinsettia, and tomato plants did not affect the fecundity of B. tabaci and the expression levels of most examined genes. We speculate that P. aleyrodidarum may help B. tabaci improve its performance and acclimate to new hosts and that P. aleyrodidarum has a close nutritional relationship with its host during host plant acclimation.

Metagenomic analysis of relative abundance and diversity of bacterial microbiota in Bemisia tabaci infesting cotton crop in Pakistan

B. tabaci species complex are among the world's most devastating agricultural pests causing economic losses by direct feeding and more importantly by transmitting plant viruses like cotton leaf curl disease (CLCuD) associated viruses to cultivated cotton in Pakistan. Taxonomic diversity of B. tabaci associated bacterial communities using NGS techniques so far is reported from insects grown on artificial diet under lab conditions. In this study 16S rDNA metagenome sequencing analysis was used to characterize bacterial compositions in wild adult B. tabaci infesting cultivated cotton in eight major cotton growing districts of southern Punjab, Pakistan. We have identified 50 known and 7 unknown genera of bacteria belonging to 10 phyla, 20 classes, 30 orders and 40 families. Beta diversity analysis of our data sets reveal that whiteflies infesting cotton in geographically distinct locations had similar bacterial diversity. These results for the first time provide insights into the microbiome diversity of wild type whiteflies infesting a cultivated crop.

Reduced Genome of the Gut Symbiotic Bacterium "Candidatus Benitsuchiphilus tojoi" Provides Insight Into Its Possible Roles in Ecology and Adaptation of the Host Insect

Diverse animals, including insects, harbor microbial symbionts within their gut, body cavity, or cells. The subsocial parastrachiid stinkbug Parastrachia japonensis is well-known for its peculiar ecological and behavioral traits, including its prolonged non-feeding diapause period and maternal care of eggs/nymphs in an underground nest. P. japonensis harbors a specific bacterial symbiont within the gut cavity extracellularly, which is vertically inherited through maternal excretion of symbiont-containing white mucus. Thus far, biological roles of the symbiont in the host lifecycle has been little understood. Here we sequenced the genome of the uncultivable gut symbiont “Candidatus Benitsuchiphilus tojoi.” The symbiont has an 804 kb circular chromosome encoding 606 proteins and a 14.5 kb plasmid encoding 13 proteins. Phylogenetic analysis indicated that the bacterium is closely related to other obligate insect symbionts belonging to the Gammaproteobacteria, including Buchnera of aphids and Blochmannia of ants, and the most closely related to Ishikawaella, an extracellular gut symbiont of plataspid stinkbugs. These data suggested that the symbiont genome has evolved like highly reduced gamma-proteobacterial symbiont genomes reported from a variety of insects. The presence of genes involved in biosynthesis pathways for amino acids, vitamins, and cofactors in the genome implicated the symbiont as a nutritional mutualist, supplementing essential nutrients to the host. Interestingly, the symbiont’s plasmid encoded genes for thiamine and carotenoid synthesis pathways, suggesting the possibility of additional functions of the symbiont for protecting the host against oxidative stress and DNA damage. Finally, possible involvement of the symbiont in uric acid metabolism during diapause is discussed.

Genetic variability, community structure, and horizontal transfer of endosymbionts among three Asia II-Bemisia tabaci mitotypes in Pakistan

Endosymbionts associated with the whitefly Bemisia tabaci cryptic species are known to contribute to host fitness and environmental adaptation. The genetic diversity and population complexity were investigated for endosymbiont communities of B. tabaci occupying different micro-environments in Pakistan. Mitotypes of B. tabaci were identified by comparative sequence analysis of the mitochondria cytochrome oxidase I (mtCOI) gene sequence. Whitefly mitotypes belonged to the Asia II-1, -5, and -7 mitotypes of the Asia II major clade. The whitefly-endosymbiont communities were characterized based on 16S ribosomal RNA operational taxonomic unit (OTU) assignments, resulting in 43 OTUs. Most of the OTUs occurred in the Asia II-1 and II-7 mitotypes (r 2 = .9, p < .005), while the Asia II-5 microbiome was less complex. The microbiome OTU groups were mitotype-specific, clustering with a basis in phylogeographical distribution and the corresponding ecological niche of their whitefly host, suggesting mitotype-microbiome co-adaptation. The primary endosymbiont Portiera was represented by a single, highly homologous OTU (0%-0.67% divergence). Two of six Arsenophonus OTUs were uniquely associated with Asia II-5 and -7, and one occurred exclusively in Asia II-1, two only in Asia II-5, and one in both Asia II-1 and -7. Four other secondary endosymbionts, Cardinium, Hemipteriphilus, Rickettsia, and Wolbachia OTUs, were found at ≤29% frequencies. The most prevalent Arsenophonus OTU was found in all three Asia II mitotypes (55% frequency), whereas the same strain of Cardinium and Wolbachia was found in both Asia II-1 and -5, and a single Hemipteriphilus OTU occurred in Asia II-1 and -7. This pattern is indicative of horizontal transfer, suggestive of a proximity between mitotypes sufficient for gene flow at overlapping mitotype ecological niches.

Conservation of transcriptional elements in the obligate symbiont of the whitefly Bemisia tabaci

Background

Bacterial symbiosis is widespread in arthropods, especially in insects. Some of the symbionts undergo a long-term co-evolution with the host, resulting in massive genome decay. One particular consequence of genome decay is thought to be the elimination of transcriptional elements within both the coding region and intergenic sequences. In the whitefly Bemisia tabaci species complex, the obligate symbiont Candidatus Portiera aleyrodidarum is of vital importance in nutrient provision, and yet little is known about the regulatory capacities of it.

Methods

Portiera genomes of two whitefly species in China were sequenced and assembled. Gene content of these two Portiera genomes was predicted, and then subjected to Kyoto Encyclopedia of Genes and Genomes pathway analysis. Together with two other Portiera genomes from whitefly species available previously, four Portiera genomes were utilized to investigate regulatory capacities of Portiera, focusing on transcriptional elements, including genes related with transcription and functional elements within the intergenic spacers.

Results

Comparative analyses of the four Portiera genomes of whitefly B. tabaci indicate that the obligate symbionts Portiera is similar in different species of whiteflies, in terms of general genome features and possible functions in the biosynthesis of essential amino acids. The screening of transcriptional factors suggests compromised ability of Portiera to regulate the essential amino acid biosynthesis pathways. Meanwhile, thermal tolerance ability of Portiera is indicated with the detection of a σ³² factor, as well as two predicted σ³² binding sites. Within intergenic spacers, functional elements are predicted, including 37 Shine-Dalgarno sequences and 34 putative small RNAs.

Prevalence and Diversity of Endosymbionts in Cassava Whiteflies (Hemiptera: Aleyrodidae) From Colombia

Whiteflies cause huge economic losses for cassava (Manihot esculenta Crantz) cultivation. Damage can be caused directly when the insects feed on the phloem and/or indirectly by the transmission of viruses. It has been found that whiteflies maintain a close relationship with some endosymbiotic bacteria and that this interaction produces different effects on host biology and can also facilitate viral transmission. This study aimed to characterize the diversity of secondary endosymbionts (SE) present in whiteflies associated with cassava. Whitefly adults and nymphs were collected from cassava crops at nine locations in Southwestern Colombia. Molecular identification of insects and endosymbionts was carried out using specific mtCOI, wsp, 23s rRNA, and 16s rRNA primers. Phylogenetic trees were constructed from these sequences, both for whitefly species and the endosymbionts found. In addition, morphological identification of whitefly species was made using last instar nymphs. Molecular and morphological evaluation revealed that the most abundant whitefly species was Trialeurodes variabilis (Quaintance) followed by Aleurotrachelus socialis Bondar and Bemisia tuberculata Bondar. One hundred percent of the individuals contained the primary endosymbiont Portiera. The SE Rickettsia, Hamiltonella, Wolbachia, and Fritschea were not detected in the samples tested. Prevalence of Cardinium and Arsenophonus were variable at each locality, Cardinium being most prevalent in A. socialis adults. This study is the first report on the presence of Cardinium and Arsenophonus in A. socialis and T. variabilis. It is also the first report of endosymbiotic diversity in whiteflies associated with cassava in Colombia.

Witches' broom resistant genotype CCN51 shows greater diversity of symbiont bacteria in its phylloplane than susceptible genotype catongo

Background

Theobroma cacao L. (cacao) is a perennial tropical tree, endemic to rainforests of the Amazon Basin. Large populations of bacteria live on leaf surfaces and these phylloplane microorganisms can have important effects on plant health. In recent years, the advent of high-throughput sequencing techniques has greatly facilitated studies of the phylloplane microbiome. In this study, we characterized the bacterial microbiome of the phylloplane of the catongo genotype (susceptible to witch’s broom) and CCN51 (resistant). Bacterial microbiome was determined by sequencing the V3-V4 region of the bacterial 16S rRNA gene.

Results

After the pre-processing, a total of 1.7 million reads were considered. In total, 106 genera of bacteria were characterized. Proteobacteria was the predominant phylum in both genotypes. The exclusive genera of Catongo showed activity in the protection against UV radiation and in the transport of substrates. CCN51 presented genus that act in the biological control and inhibition in several taxonomic groups. Genotype CCN51 presented greater diversity of microorganisms in comparison to the Catongo genotype and the total community was different between both. Scanning electron microscopy analysis of leaves revealed that on the phylloplane, many bacterial occur in large aggregates in several regions of the surface and isolated nearby to the stomata.

Conclusions

We describe for the first time the phylloplane bacterial communities of T. cacao. The Genotype CCN51, resistant to the witch’s broom, has a greater diversity of bacterial microbioma in comparison to Catongo and a greater amount of exclusive microorganisms in the phylloplane with antagonistic action against phytopathogens.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1339-9) contains supplementary material, which is available to authorized users.

Effects of Endosymbiont Disruption on the Nutritional Dynamics of the Pea Aphid Acyrthosiphon pisum

Pea aphid (Acyrthosiphon pisum) is a worldwide pest that feeds exclusively on the phloem sap of numerous host plants. It harbours a well-known primary endosymbiont Buchneraaphidicola that helps to overcome the nutritional deficiency of a plant-based diet. However, how the Buchnera contributes to the nutritional and energy metabolism of its aphid host is unclear to date. In the current study, the function of Buchnera in relation to nutritional synthesis of pea aphid was investigated by disrupting the primary endosymbiont with an antibiotic rifampicin. Our findings revealed that the disruption of Buchnera led to infertility and higher loss in body mass of aphid hosts. Body length and width were also decreased significantly compared to healthy aphids. The detection of nutrition indicated that the quantity of proteins, soluble sugars, and glycogen in aposymbiotic pea aphids increased slowly with the growth of the aphid host. In comparison, the quantities of all the nutritional factors were significantly lower than those of symbiotic pea aphids, while the quantity of total lipid and neutral fat in aposymbiotic pea aphids were distinctly higher than those of symbiotic ones. Thus, we concluded that the significant reduction of the total amount of proteins, soluble sugars, and glycogen and the significant increase of neutral fats in aposymbiotic pea aphids were due to the disruption of Buchnera, which confirmed that the function of Buchnera is irreplaceable in the pea aphid.

Distribution and phylogenetics of whiteflies and their endosymbiont relationships after the Mediterranean species invasion in Brazil

The Bemisia tabaci is a polyphagous insect and a successful vector of plant viruses. B. tabaci is a species complex and in Brazil native species from the New World (NW) group, as well as the invasive species, Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED) were reported. For better understanding the distribution of the different species four years after the Mediterranean species invasion in Brazil, whiteflies were collected from 237 locations throughout the country between the years of 2013 and 2017, species were identified and the facultative endosymbionts detected. The survey revealed that MEAM1 was the prevalent species found on major crops across Brazil. It is the only species present in North, Northwestern and Central Brazil and was associated with virus-infected plants. MED was found in five States from Southeast to South regions, infesting mainly ornamental plants and was not associated with virus-infected plants. The prevalent endosymbionts identified in MEAM1 were Hamiltonella and Rickettsia; and the mtCOI analysis revealed low genetic diversity for MEAM1. In contrast, several different endosymbionts were identified in MED including Hamiltonella, Rickettsia, Wolbachia and Arsenophonus; and two distinct genetic groups were found based on the mtCOI analysis. Monitoring the distribution of the whiteflies species in Brazil is essential for proper management of this pest.

Endosymbionts of Plant-Parasitic Nematodes

Some of the most agriculturally important plant-parasitic nematodes (PPNs) harbor endosymbionts. Extensive work in other systems has shown that endosymbionts can have major effects on host virulence and biology. This review highlights the discovery, development, and diversity of PPN endosymbionts, incorporating inferences from genomic data. Cardinium, reported from five PPN hosts to date, is characterized by its presence in the esophageal glands and other tissues, with a discontinuous distribution across populations, and genomic data suggestive of horizontal gene exchange. Xiphinematobacter occurs in at least 27 species of dagger nematode in the ovaries and gut epithelial cells, where genomic data suggest it may serve in nutritional supplementation. Wolbachia, reported in just three PPNs, appears to have an ancient history in the Pratylenchidae and displays broad tissue distribution and genomic features intermediate between parasitic and reproductive groups. Finally, a model is described that integrates these insights to explain patterns of endosymbiont replacement.

Partnering With a Pest: Genomes of Hemlock Woolly Adelgid Symbionts Reveal Atypical Nutritional Provisioning Patterns in Dual-Obligate Bacteria

Nutritional bacterial symbionts enhance the diets of sap-feeding insects with amino acids and vitamins missing from their diets. In many lineages, an ancestral senior symbiont is joined by a younger junior symbiont. To date, an emergent pattern is that senior symbionts supply a majority of amino acids, and junior symbionts supply a minority. Similar to other hemipterans, adelgids harbor obligate symbionts, but have higher diversity of bacterial associates, suggesting a history of symbiont turnover. The metabolic roles of dual symbionts in adelgids and their contributions to the consortium are largely unexplored. Here, we investigate the symbionts of Adelges tsugae, the hemlock woolly adelgid (HWA), an invasive species introduced from Japan to the eastern United States, where it kills hemlock trees. The response of hemlocks to HWA feeding has aspects of a defensive reaction against pathogens, and some have speculated that symbionts may be involved. We sequenced the genomes of "Ca. Annandia adelgestsuga" and "Ca. Pseudomonas adelgestsugas" symbionts to detail their metabolic capabilities, infer ages of relationship, and search for effectors of plant defenses. We also tested the relationship of "Ca. Annandia" to symbionts of other insects. We find that both symbionts provide nutrients, but in more balanced proportions than dual symbionts of other hemipterans. The lesser contributions of the senior "Ca. Annandia" support our hypothesis for symbiont replacements in adelgids. Phylogenomic results were ambiguous regarding the position of "Ca. Annandia". We found no obvious effectors of plant defenses related to insect virulence, but hypothetical proteins in symbionts are unknown players.

Modeling trophic dependencies and exchanges among insects' bacterial symbionts in a host-simulated environment

BACKGROUND

Individual organisms are linked to their communities and ecosystems via metabolic activities. Metabolic exchanges and co-dependencies have long been suggested to have a pivotal role in determining community structure. In phloem-feeding insects such metabolic interactions with bacteria enable complementation of their deprived nutrition. The phloem-feeding whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) harbors an obligatory symbiotic bacterium, as well as varying combinations of facultative symbionts. This well-defined bacterial community in B. tabaci serves here as a case study for a comprehensive and systematic survey of metabolic interactions within the bacterial community and their associations with documented occurrences of bacterial combinations. We first reconstructed the metabolic networks of five common B. tabaci symbionts genera (Portiera, Rickettsia, Hamiltonella, Cardinium and Wolbachia), and then used network analysis approaches to predict: (1) species-specific metabolic capacities in a simulated bacteriocyte-like environment; (2) metabolic capacities of the corresponding species' combinations, and (3) dependencies of each species on different media components.

RESULTS

The predictions for metabolic capacities of the symbionts in the host environment were in general agreement with previously reported genome analyses, each focused on the single-species level. The analysis suggests several previously un-reported routes for complementary interactions and estimated the dependency of each symbiont in specific host metabolites. No clear association was detected between metabolic co-dependencies and co-occurrence patterns.

CONCLUSIONS

The analysis generated predictions for testable hypotheses of metabolic exchanges and co-dependencies in bacterial communities and by crossing them with co-occurrence profiles, contextualized interaction patterns into a wider ecological perspective.

The invasive MED/Q Bemisia tabaci genome: a tale of gene loss and gene gain

BACKGROUND

Sweetpotato whitefly, Bemisia tabaci MED/Q and MEAM1/B, are two economically important invasive species that cause considerable damages to agriculture crops through direct feeding and indirect vectoring of plant pathogens. Recently, a draft genome of B. tabaci MED/Q has been assembled. In this study, we focus on the genomic comparison between MED/Q and MEAM1/B, with a special interest in MED/Q's genomic signatures that may contribute to the highly invasive nature of this emerging insect pest.

RESULTS

The genomes of both species share similarity in syntenic blocks, but have significant divergence in the gene coding sequence. Expansion of cytochrome P450 monooxygenases and UDP glycosyltransferases in MED/Q and MEAM1/B genome is functionally validated for mediating insecticide resistance in MED/Q using in vivo RNAi. The amino acid biosynthesis pathways in MED/Q genome are partitioned among the host and endosymbiont genomes in a manner distinct from other hemipterans. Evidence of horizontal gene transfer to the host genome may explain their obligate relationship. Putative loss-of-function in the immune deficiency-signaling pathway due to the gene loss is a shared ancestral trait among hemipteran insects.

CONCLUSIONS

The expansion of detoxification genes families, such as P450s, may contribute to the development of insecticide resistance traits and a broad host range in MED/Q and MEAM1/B, and facilitate species' invasions into intensively managed cropping systems. Numerical and compositional changes in multiple gene families (gene loss and gene gain) in the MED/Q genome sets a foundation for future hypothesis testing that will advance our understanding of adaptation, viral transmission, symbiosis, and plant-insect-pathogen tritrophic interactions.

To B or Not to B: Comparative Genomics Suggests Arsenophonus as a Source of B Vitamins in Whiteflies

Insect lineages feeding on nutritionally restricted diets such as phloem sap, xylem sap, or blood, were able to diversify by acquiring bacterial species that complement lacking nutrients. These bacteria, considered obligate/primary endosymbionts, share a long evolutionary history with their hosts. In some cases, however, these endosymbionts are not able to fulfill all of their host's nutritional requirements, driving the acquisition of additional symbiotic species. Phloem-feeding members of the insect family Aleyrodidae (whiteflies) established an obligate relationship with Candidatus Portiera aleyrodidarum, which provides its hots with essential amino acids and carotenoids. In addition, many whitefly species harbor additional endosymbionts which may potentially further supplement their host's diet. To test this hypothesis, genomes of several endosymbionts of the whiteflies Aleurodicus dispersus, Aleurodicus floccissimus and Trialeurodes vaporariorum were analyzed. In addition to Portiera, all three species were found to harbor one Arsenophonus and one Wolbachia endosymbiont. A comparative analysis of Arsenophonus genomes revealed that although all three are capable of synthesizing B vitamins and cofactors, such as pyridoxal, riboflavin, or folate, their genomes and phylogenetic relationship vary greatly. Arsenophonus of A. floccissimus and T. vaporariorum belong to the same clade, and display characteristics of facultative endosymbionts, such as large genomes (3 Mb) with thousands of genes and pseudogenes, intermediate GC content, and mobile genetic elements. In contrast, Arsenophonus of A. dispersus belongs to a different lineage and displays the characteristics of a primary endosymbiont-a reduced genome (670 kb) with ~400 genes, 32% GC content, and no mobile genetic elements. However, the presence of 274 pseudogenes suggests that this symbiotic association is more recent than other reported primary endosymbionts of hemipterans. The gene repertoire of Arsenophonus of A. dispersus is completely integrated in the symbiotic consortia, and the biosynthesis of most vitamins occurs in shared pathways with its host. In addition, Wolbachia endosymbionts have also retained the ability to produce riboflavin, flavin adenine dinucleotide, and folate, and may make a nutritional contribution. Taken together, our results show that Arsenophonus hold a pivotal place in whitefly nutrition by their ability to produce B vitamins.

Et tu, Brute? Not Even Intracellular Mutualistic Symbionts Escape Horizontal Gene Transfer

Many insect species maintain mutualistic relationships with endosymbiotic bacteria. In contrast to their free-living relatives, horizontal gene transfer (HGT) has traditionally been considered rare in long-term endosymbionts. Nevertheless, meta-omics exploration of certain symbiotic models has unveiled an increasing number of bacteria-bacteria and bacteria-host genetic transfers. The abundance and function of transferred loci suggest that HGT might play a major role in the evolution of the corresponding consortia, enhancing their adaptive value or buffering detrimental effects derived from the reductive evolution of endosymbionts’ genomes. Here, we comprehensively review the HGT cases recorded to date in insect-bacteria mutualistic consortia, and discuss their impact on the evolutionary success of these associations.

Cooperative Metabolism in a Three-Partner Insect-Bacterial Symbiosis Revealed by Metabolic Modeling

An important factor determining the impact of microbial symbionts on their animal hosts is the balance between the cost of nutrients consumed by the symbionts and the benefit of nutrients released back to the host, but the quantitative significance of nutrient exchange in symbioses involving multiple microbial partners has rarely been addressed. In this study on the association between two intracellular bacterial symbionts, “Candidatus Portiera aleyrodidarum” and “Candidatus Hamiltonella defensa,” and their animal host, the whitefly Bemisia tabaci, we apply metabolic modeling to investigate host-symbiont nutrient exchange. Our in silico analysis revealed that >60% of the essential amino acids and related metabolites synthesized by “Candidatus Portiera aleyrodidarum” are utilized by the host, including a substantial contribution of nitrogen recycled from host nitrogenous waste, and that these interactions are required for host growth. In contrast, “Candidatus Hamiltonella defensa” retains most or all of the essential amino acids and B vitamins that it is capable of synthesizing. Furthermore, “Candidatus Hamiltonella defensa” suppresses host growth in silico by competition with “Candidatus Portiera aleyrodidarum” for multiple host nutrients, by suppressing “Candidatus Portiera aleyrodidarum” growth and metabolic function, and also by consumption of host nutrients that would otherwise be allocated to host growth. The interpretation from these modeling outputs that “Candidatus Hamiltonella defensa” is a nutritional parasite could not be inferred reliably from gene content alone but requires consideration of constraints imposed by the structure of the metabolic network. Furthermore, these quantitative models offer precise predictions for future experimental study and the opportunity to compare the functional organization of metabolic networks in different symbioses.

IMPORTANCE The metabolic functions of unculturable intracellular bacteria with much reduced genomes are traditionally inferred from gene content without consideration of how the structure of the metabolic network may influence flux through metabolic reactions. The three-compartment model of metabolic flux between two bacterial symbionts and their insect host constructed in this study revealed that one symbiont is structured to overproduce essential amino acids for the benefit of the host, but the essential amino acid production in the second symbiont is quantitatively constrained by the structure of its network, rendering it “selfish” with respect to these nutrients. This study demonstrates the importance of quantitative flux data for elucidation of the metabolic function of symbionts. The in silico methodology can be applied to other symbioses with intracellular bacteria.

Predictive Genomic Analyses Inform the Basis for Vitamin Metabolism and Provisioning in Bacteria-Arthropod Endosymbioses

The requirement of vitamins for core metabolic processes creates a unique set of pressures for arthropods subsisting on nutrient-limited diets. While endosymbiotic bacteria carried by arthropods have been widely implicated in vitamin provisioning, the underlying molecular mechanisms are not well understood. To address this issue, standardized predictive assessment of vitamin metabolism was performed in 50 endosymbionts of insects and arachnids. The results predicted that arthropod endosymbionts overall have little capacity for complete de novo biosynthesis of conventional or active vitamin forms. Partial biosynthesis pathways were commonly predicted, suggesting a substantial role in vitamin provisioning. Neither taxonomic relationships between host and symbiont, nor the mode of host-symbiont interaction were clear predictors of endosymbiont vitamin pathway capacity. Endosymbiont genome size and the synthetic capacity of nonsymbiont taxonomic relatives were more reliable predictors. We developed a new software application that also predicted that last-step conversion of intermediates into active vitamin forms may contribute further to vitamin biosynthesis by endosymbionts. Most instances of predicted vitamin conversion were paralleled by predictions of vitamin use. This is consistent with achievement of provisioning in some cases through upregulation of pathways that were retained for endosymbiont benefit. The predicted absence of other enzyme classes further suggests a baseline of vitamin requirement by the majority of endosymbionts, as well as some instances of putative mutualism. Adaptation of this workflow to analysis of other organisms and metabolic pathways will provide new routes for considering the molecular basis for symbiosis on a comprehensive scale.

Nature lessons: The whitefly bacterial endosymbiont is a minimal amino acid factory with unusual energetics

Reductive genome evolution is a universal phenomenon observed in endosymbiotic bacteria in insects. As the genome reduces its size and irreversibly losses coding genes, the functionalities of the cell system, including the energetics processes, are more restricted. Several energetic pathways can also be lost. How do these reduced metabolic networks sustain the energy needs of the system? Among the bacteria with reduced genomes Candidatus Portiera aleyrodidarum, obligate endosymbiont of whiteflies, represents an extreme case since lacks several key mechanisms for ATP generation. Thus, to analyze the cell energetics in this system, a genome-scale metabolic model of this endosymbiont was constructed, and its energy production capabilities dissected using stoichiometric analysis. Our results suggest that energy generation is coupled to the synthesis of essential amino acids and carotenoids, crucial metabolites in the symbiotic association. A deeper insight showed that ATP production via carotenoid synthesis is also connected with amino acid production. This unusual association of energy production with anabolism suggests that, although minimized, endosymbiont metabolic networks maintain a remarkable biosynthetic potential.

Sequencing and comparison of the Rickettsia genomes from the whitefly Bemisia tabaci Middle East Asia Minor I

The whitefly, Bemisia tabaci, harbors the primary symbiont 'Candidatus Portiera aleyrodidarum' and a variety of secondary symbionts. Among these secondary symbionts, Rickettsia is the only one that can be detected both inside and outside the bacteriomes. Infection with Rickettsia has been reported to influence several aspects of the whitefly biology, such as fitness, sex ratio, virus transmission and resistance to pesticides. However, mechanisms underlying these differences remain unclear, largely due to the lack of genomic information of Rickettsia. In this study, we sequenced the genome of two Rickettsia strains isolated from the Middle East Asia Minor 1 (MEAM1) species of the B. tabaci complex in China and Israel. Both Rickettsia genomes were of high coding density and AT-rich, containing more than 1000 coding sequences, much larger than that of the coexisted primary symbiont, Portiera. Moreover, the two Rickettsia strains isolated from China and Israel shared most of the genes with 100% identity and only nine genes showed sequence differences. The phylogenetic analysis using orthologs shared in the genus, inferred the proximity of Rickettsia in MEAM1 and Rickettsia bellii. Functional analysis revealed that Rickettsia was unable to synthesize amino acids required for complementing the whitefly nutrition. Besides, a type IV secretion system and a number of virulence-related genes were detected in the Rickettsia genome. The presence of virulence-related genes might benefit the symbiotic life of the bacteria, and hint on potential effects of Rickettsia on whiteflies. The genome sequences of Rickettsia provided a basis for further understanding the function of Rickettsia in whiteflies.

Temporal changes of symbiont density and host fitness after rifampicin treatment in a whitefly of the Bemisia tabaci species complex

Microbial symbionts are essential or important partners to phloem-feeding insects. Antibiotics have been used to selectively eliminate symbionts from their host insects and establish host lines with or without certain symbionts for investigating functions of the symbionts. In this study, using the antibiotic rifampicin we attempted to selectively eliminate certain symbionts from a population of the Middle East-Asia Minor 1 whitefly of the Bemisia tabaci species complex, which harbors the primary symbiont "Candidatus Portiera aleyrodidarum" and two secondary symbionts "Candidatus Hamiltonella defensa" and Rickettsia. Neither the primary nor the secondary symbionts were completely depleted in the adults (F0) that fed for 48 h on a diet treated with rifampicin at concentrations of 1-100 μg/mL. However, both the primary and secondary symbionts were nearly completely depleted in the offspring (F1) of the rifampicin-treated adults. Although the F1 adults produced some eggs (F2), most of the eggs failed to hatch and none of them reached the second instar, and consequently the rifampicin-treated whitefly colony vanished at the F2 generation. Interestingly, quantitative polymerase chain reaction assays showed that in the rifampicin-treated whiteflies, the density of the primary symbiont was reduced at an obviously slower pace than the secondary symbionts. Mating experiments between rifampicin-treated and untreated adults demonstrated that the negative effects of rifampicin on host fitness were expressed when the females were treated by the antibiotic, and whether males were treated or not by the antibiotic had little contribution to the negative effects. These observations indicate that with this whitefly population it is not feasible to selectively eliminate the secondary symbionts using rifampicin without affecting the primary symbiont and establish host lines for experimental studies. However, the extinction of the whitefly colony at the second generation after rifampicin treatment indicates the potential of the antibiotic as a control agent of the whitefly pest.

The gill microbiota of invasive and indigenous Spondylus oysters from the Mediterranean Sea and northern Red Sea

The gill tissue of bivalve mollusks hosts rich symbiotic microbial communities that may contribute to the animal's metabolism. Spondylus spinosus is an invasive oyster that has become highly abundant along the eastern Mediterranean Sea (EMS) coastline, but is scarce in the northern Red Sea (NRS), its indigenous region. The composition and seasonal dynamics of the gill microbial communities of S. spinosus were examined in both regions, using 16S rRNA gene amplicon sequencing. Additionally, two Red Sea Spondylus species, S. avramsingeri and S. pickeringae, were investigated using the same approach. Significant differences were found between microbial communities of the EMS S. spinosus and the three NRS species. Bacteria from the family Hahellaceae dominated the communities of the EMS S. spinosus and the NRS S. avramsingeri, oysters that are dominant in their habitat, yet were rare in the NRS S. spinosus and S. pickeringae, which are only seldom encountered. Bacterial communities of EMS S. spinosus were more similar to those of NRS S. spinosus than to those of other NRS Spondylus species, indicating that either part of the microbiota had co-invaded with their host into the Mediterranean Sea, or that there are species-specific selective constraints on microbial composition.

Slow and Fast Evolving Endosymbiont Lineages: Positive Correlation between the Rates of Synonymous and Non-Synonymous Substitution

The availability of complete genome sequences of bacterial endosymbionts with strict vertical transmission to the host progeny opens the possibility to estimate molecular evolutionary rates in different lineages and understand the main biological mechanisms influencing these rates. We have compared the rates of evolution for non-synonymous and synonymous substitutions in nine bacterial endosymbiont lineages, belonging to four clades (Baumannia, Blochmannia, Portiera, and Sulcia). The main results are the observation of a positive correlation between both rates with differences among lineages of up to three orders of magnitude and that the substitution rates decrease over long endosymbioses. To explain these results we propose three mechanisms. The first, variations in the efficiencies of DNA replication and DNA repair systems, is unable to explain most of the observed differences. The second, variations in the generation time among bacterial lineages, would be based on the accumulation of fewer DNA replication errors per unit time in organisms with longer generation times. The third, a potential control of the endosymbiont DNA replication and repair systems through the transfer of nuclear-encoded proteins, could explain the lower rates in long-term obligate endosymbionts. Because the preservation of the genomic integrity of the harbored obligate endosymbiont would be advantageous for the insect host, biological mechanisms producing a general reduction in the rates of nucleotide substitution per unit of time would be a target for natural selection.

Differential temporal changes of primary and secondary bacterial symbionts and whitefly host fitness following antibiotic treatments

Where multiple symbionts coexist in the same host, the selective elimination of a specific symbiont may enable the roles of a given symbiont to be investigated. We treated the Mediterranean species of the whitefly Bemisia tabaci complex by oral delivery of the antibiotic rifampicin, and then examined the temporal changes of its primary symbiont "Candidatus Portiera aleyrodidarum" and secondary symbiont "Ca. Hamiltonella defensa" as well as host fitness for three generations. In adults treated with rifampicin (F0), the secondary symbiont was rapidly reduced, approaching complete disappearance as adults aged. In contrast, the primary symbiont was little affected until later in the adult life. In the offspring of these adults (F1), both symbionts were significantly reduced and barely detectable when the hosts reached the adult stage. The F1 adults laid few eggs (F2), all of which failed to hatch. Mating experiments illustrated that the negative effects of rifampicin on host fitness were exerted via female hosts but not males. This study provides the first evidence of differential temporal reductions of primary and secondary symbionts in whiteflies following an antibiotic treatment. Studies that disrupt functions of bacterial symbionts must consider their temporal changes.

Metabolic Coevolution in the Bacterial Symbiosis of Whiteflies and Related Plant Sap-Feeding Insects

Genomic decay is a common feature of intracellular bacteria that have entered into symbiosis with plant sap-feeding insects. This study of the whitefly Bemisia tabaci and two bacteria (Portiera aleyrodidarum and Hamiltonella defensa) cohoused in each host cell investigated whether the decay of Portiera metabolism genes is complemented by host and Hamiltonella genes, and compared the metabolic traits of the whitefly symbiosis with other sap-feeding insects (aphids, psyllids, and mealybugs). Parallel genomic and transcriptomic analysis revealed that the host genome contributes multiple metabolic reactions that complement or duplicate Portiera function, and that Hamiltonella may contribute multiple cofactors and one essential amino acid, lysine. Homologs of the Bemisia metabolism genes of insect origin have also been implicated in essential amino acid synthesis in other sap-feeding insect hosts, indicative of parallel coevolution of shared metabolic pathways across multiple symbioses. Further metabolism genes coded in the Bemisia genome are of bacterial origin, but phylogenetically distinct from Portiera, Hamiltonella and horizontally transferred genes identified in other sap-feeding insects. Overall, 75% of the metabolism genes of bacterial origin are functionally unique to one symbiosis, indicating that the evolutionary history of metabolic integration in these symbioses is strongly contingent on the pattern of horizontally acquired genes. Our analysis, further, shows that bacteria with genomic decay enable host acquisition of complex metabolic pathways by multiple independent horizontal gene transfers from exogenous bacteria. Specifically, each horizontally acquired gene can function with other genes in the pathway coded by the symbiont, while facilitating the decay of the symbiont gene coding the same reaction.

Comparative Genomics of a Plant-Parasitic Nematode Endosymbiont Suggest a Role in Nutritional Symbiosis

Bacterial mutualists can modulate the biochemical capacity of animals. Highly coevolved nutritional mutualists do this by synthesizing nutrients missing from the host’s diet. Genomics tools have advanced the study of these partnerships. Here we examined the endosymbiont Xiphinematobacter (phylum Verrucomicrobia) from the dagger nematode Xiphinema americanum, a migratory ectoparasite of numerous crops that also vectors nepovirus. Previously, this endosymbiont was identified in the gut, ovaries, and eggs, but its role was unknown. We explored the potential role of this symbiont using fluorescence in situ hybridization, genome sequencing, and comparative functional genomics. We report the first genome of an intracellular Verrucomicrobium and the first exclusively intracellular non-Wolbachia nematode symbiont. Results revealed that Xiphinematobacter had a small 0.916-Mb genome with only 817 predicted proteins, resembling genomes of other mutualist endosymbionts. Compared with free-living relatives, conserved proteins were shorter on average, and there was large-scale loss of regulatory pathways. Despite massive gene loss, more genes were retained for biosynthesis of amino acids predicted to be essential to the host. Gene ontology enrichment tests showed enrichment for biosynthesis of arginine, histidine, and aromatic amino acids, as well as thiamine and coenzyme A, diverging from the profiles of relatives Akkermansia muciniphilia (in the human colon), Methylacidiphilum infernorum, and the mutualist Wolbachia from filarial nematodes. Together, these features and the location in the gut suggest that Xiphinematobacter functions as a nutritional mutualist, supplementing essential nutrients that are depleted in the nematode diet. This pattern points to evolutionary convergence with endosymbionts found in sap-feeding insects.

Whitefly genome expression reveals host-symbiont interaction in amino acid biosynthesis

Background

Whitefly (Bemisia tabaci) complex is a serious insect pest of several crop plants worldwide. It comprises several morphologically indistinguishable species, however very little is known about their genetic divergence and biosynthetic pathways. In the present study, we performed transcriptome sequencing of Asia 1 species of B. tabaci complex and analyzed the interaction of host-symbiont genes in amino acid biosynthetic pathways.

Methodology/Principal Findings

We obtained about 83 million reads using Illumina sequencing that assembled into 72716 unitigs. A total of 21129 unitigs were annotated at stringent parameters. Annotated unitigs were mapped to 52847 gene ontology (GO) terms and 131 Kyoto encyclopedia of genes and genomes (KEGG) pathways. Expression analysis of the genes involved in amino acid biosynthesis pathways revealed the complementation between whitefly and its symbiont partner Candidatus Portiera aleyrodidarum. Most of the non-essential amino acids and intermediates of essential amino acid pathways were supplied by the host insect to its symbiont. The symbiont expressed the pathways for the essential amino acids arginine, threonine and tryptophan and the immediate precursors of valine, leucine, isoleucine and phenyl-alanine. High level expression of the amino acid transporters in the whitefly suggested the molecular mechanisms for the exchange of amino acids between the host and the symbiont.

Conclusions/Significance

Our study provides a comprehensive transcriptome data for Asia 1 species of B. tabaci complex that focusses light on integration of host and symbiont genes in amino acid biosynthesis pathways.

Genome reduction and potential metabolic complementation of the dual endosymbionts in the whitefly Bemisia tabaci

BACKGROUND

The whitefly Bemisia tabaci is an important agricultural pest with global distribution. This phloem-sap feeder harbors a primary symbiont, "Candidatus Portiera aleyrodidarum", which compensates for the deficient nutritional composition of its food sources, and a variety of secondary symbionts. Interestingly, all of these secondary symbionts are found in co-localization with the primary symbiont within the same bacteriocytes, which should favor the evolution of strong interactions between symbionts.

RESULTS

In this paper, we analyzed the genome sequences of the primary symbiont Portiera and of the secondary symbiont Hamiltonella in the B. tabaci Mediterranean (MED) species in order to gain insight into the metabolic role of each symbiont in the biology of their host. The genome sequences of the uncultured symbionts Portiera and Hamiltonella were obtained from one single bacteriocyte of MED B. tabaci. As already reported, the genome of Portiera is highly reduced (357 kb), but has kept a number of genes encoding most essential amino-acids and carotenoids. On the other hand, Portiera lacks almost all the genes involved in the synthesis of vitamins and cofactors. Moreover, some pathways are incomplete, notably those involved in the synthesis of some essential amino-acids. Interestingly, the genome of Hamiltonella revealed that this secondary symbiont can not only provide vitamins and cofactors, but also complete the missing steps of some of the pathways of Portiera. In addition, some critical amino-acid biosynthetic genes are missing in the two symbiotic genomes, but analysis of whitefly transcriptome suggests that the missing steps may be performed by the whitefly itself or its microbiota.

CONCLUSIONS

These data suggest that Portiera and Hamiltonella are not only complementary but could also be mutually dependent to provide a full complement of nutrients to their host. Altogether, these results illustrate how functional redundancies can lead to gene losses in the genomes of the different symbiotic partners, reinforcing their inter-dependency.

Genome evolution in the primary endosymbiont of whiteflies sheds light on their divergence

Whiteflies are important agricultural insect pests, whose evolutionary success is related to a long-term association with a bacterial endosymbiont, Candidatus Portiera aleyrodidarum. To completely characterize this endosymbiont clade, we sequenced the genomes of three new Portiera strains covering the two extant whitefly subfamilies. Using endosymbiont and mitochondrial sequences we estimated the divergence dates in the clade and used these values to understand the molecular evolution of the endosymbiont coding sequences. Portiera genomes were maintained almost completely stable in gene order and gene content during more than 125 Myr of evolution, except in the Bemisia tabaci lineage. The ancestor had already lost the genetic information transfer autonomy but was able to participate in the synthesis of all essential amino acids and carotenoids. The time of divergence of the B. tabaci complex was much more recent than previous estimations. The recent divergence of biotypes B (MEAM1 species) and Q (MED species) suggests that they still could be considered strains of the same species. We have estimated the rates of evolution of Portiera genes, synonymous and nonsynonymous, and have detected significant differences among-lineages, with most Portiera lineages evolving very slowly. Although the nonsynonymous rates were much smaller than the synonymous, the genomic dN/dS ratios were similar, discarding selection as the driver of among-lineage variation. We suggest variation in mutation rate and generation time as the responsible factors. In conclusion, the slow evolutionary rates of Portiera may have contributed to its long-term association with whiteflies, avoiding its replacement by a novel and more efficient endosymbiont.

Two host clades, two bacterial arsenals: evolution through gene losses in facultative endosymbionts

Bacterial endosymbiosis is an important evolutionary process in insects, which can harbor both obligate and facultative symbionts. The evolution of these symbionts is driven by evolutionary convergence, and they exhibit among the tiniest genomes in prokaryotes. The large host spectrum of facultative symbionts and the high diversity of strategies they use to infect new hosts probably impact the evolution of their genome and explain why they undergo less severe genomic erosion than obligate symbionts. Candidatus Hamiltonella defensa is suitable for the investigation of the genomic evolution of facultative symbionts because the bacteria are engaged in specific relationships in two clades of insects. In aphids, H. defensa is found in several species with an intermediate prevalence and confers protection against parasitoids. In whiteflies, H. defensa is almost fixed in some species of Bemisia tabaci, which suggests an important role of and a transition toward obligate symbiosis. In this study, comparisons of the genome of H. defensa present in two B. tabaci species (Middle East Asia Minor 1 and Mediterranean) and in the aphid Acyrthosiphon pisum revealed that they belong to two distinct clades and underwent specific gene losses. In aphids, it contains highly virulent factors that could allow protection and horizontal transfers. In whiteflies, the genome lost these factors and seems to have a limited ability to acquire genes. However it contains genes that could be involved in the production of essential nutrients, which is consistent with a primordial role for this symbiont. In conclusion, although both lineages of H. defensa have mutualistic interactions with their hosts, their genomes follow distinct evolutionary trajectories that reflect their phenotype and could have important consequences on their evolvability.

Intracellular Oceanospirillales inhabit the gills of the hydrothermal vent snail Alviniconcha with chemosynthetic, γ-Proteobacterial symbionts

Associations between bacteria from the γ-Proteobacterial order Oceanospirillales and marine invertebrates are quite common. Members of the Oceanospirillales exhibit a diversity of interactions with their various hosts, ranging from the catabolism of complex compounds that benefit host growth to attacking and bursting host nuclei. Here, we describe the association between a novel Oceanospirillales phylotype and the hydrothermal vent snail Alviniconcha. Alviniconcha typically harbour chemoautotrophic γ- or ε-Proteobacterial symbionts inside their gill cells. Via fluorescence in situ hybridization and transmission electron microscopy, we observed an Oceanospirillales phylotype (named AOP for ‘Alviniconcha Oceanospirillales phylotype’) in membrane-bound vacuoles that were separate from the known γ- or ε-Proteobacterial symbionts. Using quantitative polymerase chain reaction, we surveyed 181 Alviniconcha hosting γ-Proteobacterial symbionts and 102 hosting ε-Proteobacterial symbionts, and found that the population size of AOP was always minor relative to the canonical symbionts (median 0.53% of the total quantified 16S rRNA genes). Additionally, we detected AOP more frequently in Alviniconcha hosting γ-Proteobacterial symbionts than in those hosting ε-Proteobacterial symbionts (96% and 5% of individuals respectively). The high incidence of AOP in γ-Proteobacteria hosting Alviniconcha implies that it could play a significant ecological role either as a host parasite or as an additional symbiont with unknown physiological capacities.

Circulative, "nonpropagative" virus transmission: an orchestra of virus-, insect-, and plant-derived instruments

Species of plant viruses within the Luteoviridae, Geminiviridae, and Nanoviridae are transmitted by phloem-feeding insects in a circulative, nonpropagative manner. The precise route of virus movement through the vector can differ across and within virus families, but these viruses all share many biological, biochemical, and ecological features. All share temporal and spatial constraints with respect to transmission efficiency. The viruses also induce physiological changes in their plant hosts resulting in behavioral changes in the insects that optimize the transmission of virus to new hosts. Virus proteins interact with insect, endosymbiont, and plant proteins to orchestrate, directly and indirectly, virus movement in insects and plants to facilitate transmission. Knowledge of these complex interactions allows for the development of new tools to reduce or prevent transmission, to quickly identify important vector populations, and to improve the management of these economically important viruses affecting agricultural and natural plant populations.

No exception to the rule: Candidatus Portiera aleyrodidarum cell wall revisited

Many insect endosymbionts described so far are gram-negative bacteria. Primary endosymbionts are obligatory bacteria usually harboured by insects inside vacuoles in specialized cells called bacteriocytes. This combination produces a typical three-membrane system with one membrane derived from the insect vacuole and the other two from the bacterial gram-negative cell envelope, composed by the cell wall (the outer membrane plus the periplasmic space) and the plasma membrane (the inner membrane). For the last 21 years, the primary endosymbiont of whiteflies 'Candidatus Portiera aleyrodidarum' was considered an exception to this rule. Previous works stated that only two membranes were present, the vacuolar membrane and one of the two bacterial membranes. The absence of the cell wall was related to the special vertical transmission of the endosymbionts in whiteflies. In this work, we present electron microscopic studies showing a complete cell envelope in 'Ca. Portiera aleyrodidarum' from the whitefly Bemisia tabaci. Additionally, comparison of the inferred metabolism from the gene content did not show any difference in cell envelope biogenesis compared with the closely related three-membrane endosymbionts 'Candidatus Carsonella ruddii' and 'Candidatus Evansia muelleri' Xc1. Our results rule out the proposal that 'Ca. Portiera aleyrodidarum' is an exception to the three-membrane system.

Nuclear and cytoplasmic differentiation among Mediterranean populations of Bemisia tabaci: testing the biological relevance of cytotypes

BACKGROUND

The taxonomy of the species complex Bemisia tabaci is still an unresolved issue. Recently, phylogenetic analysis based on mtCOI identified 31 cryptic species. However, mitochondrial diversity is observed within these species, associated with distinct symbiotic bacterial communities forming associations, which here are called cytotypes. The authors investigated the biological significance of two cytotypes (Q1 and Q2) belonging to the Mediterranean species, which have only been found in allopatry in the Western Mediterranean to date. Sampling was done over a few years in Western Europe, and sympatric situations were found that allowed their reproductive compatibility to be tested in the field with the use of microsatellites.

RESULTS

The field survey indicated that, in spite of its recent introduction, Q2 is well established in France and Spain, where it coexists with Q1. Microsatellite data showed that, in allopatry, Q1 and Q2 are highly differentiated, while there is little or no genetic differentiation when they coexist in sympatry, suggesting a high rate of hybridisation. Crossing experiments in the lab confirmed their interfertility.

CONCLUSION

Q1 and Q2 hybridise, which confirms that they belong to the same species, in spite of the high degree of genetic differentiation at both the cytoplasmic and nuclear levels, and also suggests that their symbiotic bacteria do not prevent hybridisation.

Differential genome evolution between companion symbionts in an insect-bacterial symbiosis

Obligate symbioses with bacteria allow insects to feed on otherwise unsuitable diets. Some symbionts have extremely reduced genomes and have lost many genes considered to be essential in other bacteria. To understand how symbiont genome degeneration proceeds, we compared the genomes of symbionts in two leafhopper species, Homalodisca vitripennis (glassy-winged sharpshooter [GWSS]) and Graphocephala atropunctata (blue-green sharpshooter [BGSS]) (Hemiptera: Cicadellidae). Each host species is associated with the anciently acquired "Candidatus Sulcia muelleri" (Bacteroidetes) and the more recently acquired "Candidatus Baumannia cicadellinicola" (Gammaproteobacteria). BGSS "Ca. Baumannia" retains 89 genes that are absent from GWSS "Ca. Baumannia"; these underlie central cellular functions, including cell envelope biogenesis, cellular replication, and stress response. In contrast, "Ca. Sulcia" strains differ by only a few genes. Although GWSS "Ca. Baumannia" cells are spherical or pleomorphic (a convergent trait of obligate symbionts), electron microscopy reveals that BGSS "Ca. Baumannia" maintains a rod shape, possibly due to its retention of genes involved in cell envelope biogenesis and integrity. Phylogenomic results suggest that "Ca. Baumannia" is derived from the clade consisting of Sodalis and relatives, a group that has evolved symbiotic associations with numerous insect hosts. Finally, the rates of synonymous and nonsynonymous substitutions are higher in "Ca. Baumannia" than in "Ca. Sulcia," which may be due to a lower mutation rate in the latter. Taken together, our results suggest that the two "Ca. Baumannia" genomes represent different stages of genome reduction in which many essential functions are being lost and likely compensated by hosts. "Ca. Sulcia" exhibits much greater genome stability and slower sequence evolution, although the mechanisms underlying these differences are poorly understood.

IMPORTANCE

In obligate animal-bacterial symbioses, bacteria experience extreme patterns of genome evolution, including massive gene loss and rapid evolution. However, little is known about this process, particularly in systems with complementary bacterial partners. To understand whether genome evolution impacts symbiont types equally and whether lineages follow the same evolutionary path, we sequenced the genomes of two coresident symbiotic bacteria from a plant sap-feeding insect and compared them to the symbionts from a related host species. We found that the older symbiont has a highly reduced genome with low rates of mutation and gene loss. In contrast, the younger symbiont has a larger genome that exhibits higher mutation rates and varies dramatically in the retention of genes related to cell wall biogenesis, cellular replication, and stress response. We conclude that while symbiotic bacteria evolve toward tiny genomes, this process is shaped by different selection intensities that may reflect the different ages and metabolic roles of symbiont types.