Exaggeration and cooption of innate immunity for social defense

Comparative genomics of the primary endosymbiont Buchnera aphidicola in aphid hosts and their coevolutionary relationships

BACKGROUND

Coevolution between modern aphids and their primary obligate, bacterial endosymbiont, Buchnera aphidicola, has been previously reported at different classification levels based on molecular phylogenetic analyses. However, the Buchnera genome remains poorly understood within the Rhus gall aphids.

RESULTS

We assembled the complete genome of the endosymbiont Buchnera in 16 aphid samples, representing 13 species in all six genera of Rhus gall aphids by shotgun genome skimming method. We compared the newly assembled genomes with those from GenBank to comprehensively investigate patterns of coevolution between the bacteria Buchnera and their aphid hosts. Buchnera genomes were mostly collinear, and the pan-genome contained 684 genes, in which the core genome contained 256 genes with some lineages having large numbers of tandem gene duplications. There has been substantial gene-loss in each Buchnera lineage. We also reconstructed the phylogeny for Buchnera and their host aphids, respectively, using 72 complete genomes of Buchnera, along with the complete mitochondrial genomes and three nuclear genes of 31 corresponding host aphid accessions. The cophylogenetic test demonstrated significant coevolution between these two partner groups at individual, species, generic, and tribal levels.

CONCLUSIONS

Buchnera exhibits very high levels of genomic sequence divergence but relative stability in gene order. The relationship between the symbionts Buchnera and its aphid hosts shows a significant coevolutionary pattern and supports complexity of the obligate symbiotic relationship.

Single-cell RNA-seq revealed heterogeneous responses and functional differentiation of hemocytes against white spot syndrome virus infection in Litopenaeus vannamei

Shrimp hemocytes are the vital immune cells participating in innate immune response to defend against viruses. However, the lack of specific molecular markers for shrimp hemocyte hindered the insightful understanding of their functional clusters and differential roles in combating microbial infections. In this study, we used single-cell RNA sequencing to map the transcriptomic landscape of hemocytes from the white spot syndrome virus (WSSV)-infected Litopenaeus vannamei and conjointly analyzed with our previous published single-cell RNA sequencing technology data from the healthy hemocytes. A total of 16 transcriptionally distinct cell clusters were identified, which occupied different proportions in healthy and WSSV-infected hemocytes and exerted differential roles in antiviral immune response. Following mapping of the sequencing data to the WSSV genome, we found that all types of hemocytes could be invaded by WSSV virions, especially the cluster 8, which showed the highest transcriptional levels of WSSV genes and exhibited a cell type-specific antiviral response to the viral infection. Further evaluation of the cell clusters revealed the delicate dynamic balance between hemocyte immune response and viral infestation. Unsupervised pseudo-time analysis of hemocytes showed that the hemocytes in immune-resting state could be significantly activated upon WSSV infection and then functionally differentiated to different hemocyte subsets. Collectively, our results revealed the differential responses of shrimp hemocytes and the process of immune-functional differentiation post-WSSV infection, providing essential resource for the systematic insight into the synergistic immune response mechanism against viral infection among hemocyte subtypes.

IMPORTANCE

Current knowledge of shrimp hemocyte classification mainly comes from morphology, which hinder in-depth characterization of cell lineage development, functional differentiation, and different immune response of hemocyte types during pathogenic infections. Here, single-cell RNA sequencing was used for mapping hemocytes during white spot syndrome virus (WSSV) infection in Litopenaeus vannamei, identifying 16 cell clusters and evaluating their potential antiviral functional characteristics. We have described the dynamic balance between viral infestation and hemocyte immunity. And the functional differentiation of hemocytes under WSSV stimulation was further characterized. Our results provided a comprehensive transcriptional landscape and revealed the heterogeneous immune response in shrimp hemocytes during WSSV infection.

Lipids as a key element of insect defense systems

The relationship between insect pathogenic fungi and their insect hosts is a classic example of a co-evolutionary arms race between pathogen and target host: parasites evolve towards mechanisms that increase their advantage over the host, and the host increasingly strengthens its defenses. The present review summarizes the literature data describing the direct and indirect role of lipids as an important defense mechanism during fungal infection. Insect defense mechanisms comprise anatomical and physiological barriers, and cellular and humoral response mechanisms. The entomopathogenic fungi have the unique ability to digest the insect cuticle by producing hydrolytic enzymes with chitin-, lipo- and proteolytic activity; besides the oral tract, cuticle pays the way for fungal entry within the host. The key factor in insect resistance to fungal infection is the presence of certain types of lipids (free fatty acids, waxes or hydrocarbons) which can promote or inhibit fungal attachment to cuticle, and might also have antifungal activity. Lipids are considered as an important source of energy, and as triglycerides are stored in the fat body, a structure analogous to the liver and adipose tissue in vertebrates. In addition, the fat body plays a key role in innate humoral immunity by producing a range of bactericidal proteins and polypeptides, one of which is lysozyme. Energy derived from lipid metabolism is used by hemocytes to migrate to the site of fungal infection, and for phagocytosis, nodulation and encapsulation. One polyunsaturated fatty acid, arachidonic acid, is used in the synthesis of eicosanoids, which play several crucial roles in insect physiology and immunology. Apolipoprotein III is important compound with antifungal activity, which can modulate insect cellular response and is considered as important signal molecule.

Host’s demand for essential amino acids is compensated by an extracellular bacterial symbiont in a hemipteran insect model

Plant sap is a nutritionally unbalanced diet that constitutes a challenge for insects that feed exclusively on it. Sap-sucking hemipteran insects generally overcome this challenge by harboring beneficial microorganisms in their specialized symbiotic organ, either intracellularly or extracellularly. Genomic information of these bacterial symbionts suggests that their primary role is to supply essential amino acids, but empirical evidence has been virtually limited to the intracellular symbiosis between aphids and Buchnera. Here we investigated the amino acid complementation by the extracellular symbiotic bacterium Ishikawaella harbored in the midgut symbiotic organ of the stinkbug Megacopta punctatissima. We evaluated amino acid compositions of the phloem sap of plants on which the insect feeds, as well as those of its hemolymph, whole body hydrolysate, and excreta. The results highlighted that the essential amino acids in the diet are apparently insufficient for the stinkbug development. Experimental symbiont removal caused severe shortfalls of some essential amino acids, including branched-chain and aromatic amino acids. In vitro culturing of the isolated symbiotic organ demonstrated that hemolymph-circulating metabolites, glutamine and trehalose, efficiently fuel the production of essential amino acids. Branched-chain amino acids and aromatic amino acids are the ones preferentially synthesized despite the symbiont’s synthetic capability of all essential amino acids. These results indicate that the symbiont-mediated amino acid compensation is quantitatively optimized in the stinkbug-Ishikawaella gut symbiotic association as in the aphid-Buchnera intracellular symbiotic association. The convergence of symbiont functions across distinct nutritional symbiotic systems provides insight into how host-symbiont interactions have been shaped over evolutionary time.

Aphid hologenomics: current status and future challenges

Aphids are important model organisms in ecological, developmental, and evolutionary studies of, for example, symbiosis, insect-plant interactions, pest management, and developmental polyphenism. Here, we review the recent progress made in the genomics of aphids and their symbionts: hologenomics. The reference genome of Acyrthosiphon pisum has been greatly improved, and chromosome-level assembly is now available. The genomes of over 20 aphid species have been sequenced, and comparative genomic analyses have revealed pervasive gene duplication and dynamic chromosomal rearrangements. Over 120 symbiont genomes (both obligate and facultative) have been sequenced, and modern deep-sequencing technologies have identified novel symbionts. The advances in hologenomics have helped to elucidate the dynamic evolution of facultative and co-obligate symbionts with the ancient obligate symbiont Buchnera.

Defense in Social Insects: Diversity, Division of Labor, and Evolution

All social insects defend their colony from predators, parasites, and pathogens. In Oster and Wilson's classic work, they posed one of the key paradoxes about defense in social insects: Given the universal necessity of defense, why then is there so much diversity in mechanisms? Ecological factors undoubtedly are important: Predation and usurpation have imposed strong selection on eusocial insects, and active defense by colonies is a ubiquitous feature of all social insects. The description of diverse insect groups with castes of sterile workers whose main duty is defense has broadened the purview of social evolution in insects, in particular with respect to caste and behavior. Defense is one of the central axes along which we can begin to organize and understand sociality in insects. With the establishment of social insect models such as the honey bee, new discoveries are emerging regarding the endocrine, neural, and gene regulatory mechanisms underlying defense in social insects. The mechanisms underlying morphological and behavioral defense traits may be shared across diverse groups, providing opportunities for identifying both conserved and novel mechanisms at work. Emerging themes highlight the context dependency of and interaction between factors that regulate defense in social insects.

Linoleic acid as corpse recognition signal in a social aphid

Social insect colonies constantly produce dead insects, which cause sanitary problems and potentially foster deadly pathogens and parasites. Hence, many social insects have evolved a variety of hygienic behaviors to remove cadavers from the colonies. To that end, they have to discriminate dead insects from live ones, where chemical cues should play important roles. In ants, bees and termites, such corpse recognition signals, also referred to as "death pheromones" or "necromones", have been identified as fatty acids, specifically oleic acid and/or linoleic acid. Meanwhile, there has been no such report on social aphids. Here we attempted to identify the "death pheromone" of a gall-forming social aphid with second instar soldiers, Tuberaphis styraci, by making use of an artificial diet rearing system developed for this species. On the artificial diet plates, soldiers exhibited the typical cleaning behavior, pushing colony wastes with their heads continuously, against dead aphids but not against live aphids. GC-MS and GC-FID analyses revealed a remarkable increase of linoleic acid on the body surface of the dead aphids in comparison with the live aphids. When glass beads coated with either linoleic acid or body surface extract of the dead aphids were placed on the artificial diet plates, soldiers exhibited the cleaning behavior against the glass beads. A series of behavioral assays showed that (i) soldiers exhibit the cleaning behavior more frequently than non-soldiers, (ii) young soldiers perform the cleaning behavior more frequently than old soldiers, and (iii) the higher the concentration of linoleic acid is, the more active cleaning behavior is induced. Analysis of the lipids extracted from the aphids revealed that linoleic acid is mainly derived from phospholipids that constitute the cell membranes. In conclusion, we identified linoleic acid as the corpse recognition factor of the social aphid T. styraci. The commonality of the death pheromones across the divergent social insect groups (Hymenoptera, Blattodea and Hemiptera) highlights that these unsaturated fatty acids are generally produced by enzymatic autolysis of cell membranes after death and therefore amenable to utilization as a reliable signal of dead insects.

Hosting certain facultative symbionts modulates the phenoloxidase activity and immune response of the pea aphid Acyrthosiphon pisum

The pea aphid Acyrthosiphon pisum hosts different facultative symbionts (FS) which provide it with various benefits, such as tolerance to heat or protection against natural enemies (e.g., fungi, parasitoid wasps). Here, we investigated whether and how the presence of certain FS could affect phenoloxidase (PO) activity, a key component of insect innate immunity, under normal and stressed conditions. For this, we used clones of A. pisum of different genetic backgrounds (LL01, YR2 and T3-8V1) lacking FS or harboring one or two (Regiella insecticola, Hamiltonella defensa, Serratia symbiotica + Rickettsiella viridis). Gene expression and proteomics analyses of the aphid hemolymph indicated that the two A. pisum POs, PPO1 and PPO2, are expressed and translated into proteins. The level of PPO genes expression as well as the amount of PPO proteins and phenoloxidase activity in the hemolymph depended on both the aphid genotype and FS species. In particular, H. defensa and R. insecticola, but not S. symbiotica + R. viridis, caused a sharp decrease in PO activity by interfering with both transcription and translation. The microinjection of different types of stressors (yeast, Escherichia coli, latex beads) in the YR2 lines hosting different symbionts affected the survival rate of aphids and, in most cases, also decreased the expression of PPO genes after 24 h. The amount and activity of PPO proteins varied according to the type of FS and stressor, without clear corresponding changes in gene expression. These data demonstrate that the presence of certain FS influences an important component of pea aphid immunity.

Immune properties of invertebrate phenoloxidases

Melanin production from different types of phenoloxidases (POs) confers immunity from a variety of pathogens ranging from viruses and microorganisms to parasites. The arthropod proPO expresses a variety of activities including cytokine, opsonin and microbiocidal activities independent of and even without melanin production. Proteolytic processing of proPO and its activating enzyme gives rise to several peptide fragments with a variety of separate activities in a process reminiscent of vertebrate complement system activation although proPO bears no sequence similarity to vertebrate complement factors. Pathogens influence proPO activation and thereby what types of immune effects that will be produced. An increasing number of specialised pathogens - from parasites to viruses - have been identified who can synthesise compounds specifically aimed at the proPO-system. In invertebrates outside the arthropods phylogenetically unrelated POs are participating in melanization reactions obviously aimed at intruders and/or aberrant tissues.

Triple RNA-Seq characterizes aphid gene expression in response to infection with unequally virulent strains of the endosymbiont Hamiltonella defensa

Background

Secondary endosymbionts of aphids provide benefits to their hosts, but also impose costs such as reduced lifespan and reproductive output. The aphid Aphis fabae is host to different strains of the secondary endosymbiont Hamiltonella defensa, which encode different putative toxins. These strains have very different phenotypes: They reach different densities in the host, and the costs and benefits (protection against parasitoid wasps) they confer to the host vary strongly.

Results

We used RNA-Seq to generate hypotheses on why four of these strains inflict such different costs to A. fabae. We found different H. defensa strains to cause strain-specific changes in aphid gene expression, but little effect of H. defensa on gene expression of the primary endosymbiont, Buchnera aphidicola. The highly costly and over-replicating H. defensa strain H85 was associated with strongly reduced aphid expression of hemocytin, a marker of hemocytes in Drosophila. The closely related strain H15 was associated with downregulation of ubiquitin-related modifier 1, which is related to nutrient-sensing and oxidative stress in other organisms. Strain H402 was associated with strong differential regulation of a set of hypothetical proteins, the majority of which were only differentially regulated in presence of H402.

Conclusions

Overall, our results suggest that costs of different strains of H. defensa are likely caused by different mechanisms, and that these costs are imposed by interacting with the host rather than the host’s obligatory endosymbiont B. aphidicola.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07742-8.

Something old, something new, something borrowed, something red: the origin of ecologically relevant novelties in Hemiptera

Comparative transcriptomics, applied in an evolutionary context, has transformed the possibilities for studying phenotypic evolution in non-model taxa. We review recent discoveries about the development of novel, ecologically relevant phenotypes in hemipteran insects. These discoveries highlight the diverse genomic substrates of novelty: 'something old', when novelty results from changes in the regulation of existing genes or gene duplication; 'something new', wherein lineage-restricted genes contribute to the evolution of new phenotypes; and 'something borrowed', showcasing contributions of horizontal gene transfer to the evolution of novelty, including carotenoid synthesis (resulting in 'something red'). These findings show the power and flexibility of comparative transcriptomic approaches for expanding beyond the 'toolkit' model for the evolution of development. We conclude by raising questions about the relationship between new genes and new traits and outlining a research framework for answering them in Hemiptera.

Evidence for reduced immune gene diversity and activity during the evolution of termites

The evolution of biological complexity is associated with the emergence of bespoke immune systems that maintain and protect organism integrity. Unlike the well-studied immune systems of cells and individuals, little is known about the origins of immunity during the transition to eusociality, a major evolutionary transition comparable to the evolution of multicellular organisms from single-celled ancestors. We aimed to tackle this by characterizing the immune gene repertoire of 18 cockroach and termite species, spanning the spectrum of solitary, subsocial and eusocial lifestyles. We find that key transitions in termite sociality are correlated with immune gene family contractions. In cross-species comparisons of immune gene expression, we find evidence for a caste-specific social defence system in termites, which appears to operate at the expense of individual immune protection. Our study indicates that a major transition in organismal complexity may have entailed a fundamental reshaping of the immune system optimized for group over individual defence.

Temporal division of labor in an aphid social system

Temporal division of labor, or age polyethism, in which altruistic caste individuals change their tasks with aging, is widely found in bees and ants (Hymenoptera) and also in other social insects. Here we report the discovery of elaborate age polyethism in a social aphid (Hemiptera). Tuberaphis styraci is a gall-forming aphid in which monomorphic first instar nymphs differentiate into normal nymphs and soldiers upon second instar molt. Soldiers neither grow nor reproduce but perform gall cleaning and colony defense. Using an artificial diet rearing system, we collected age-defined groups of soldiers and monitored their social behaviors. We observed that young soldiers tend to clean whereas old soldiers preferentially attack, thereby verifying age-dependent task switching from housekeeping to defense. Strategic sampling, age estimation and behavioral observation of soldiers from natural galls revealed that (1) young cleaning soldiers tend to inhabit upper gall regions with adult insects, (2) old attacking soldiers tend to be distributed in lower gall regions, particularly around the gall openings, and (3) the gall structure is linked to intra-nest movement, aging and task switching of soldiers in an adaptive manner. These results highlight an evolutionary parallelism comparable to the sophisticated temporal division of labor observed in honeybee colonies.

Immune challenge reduces gut microbial diversity and triggers fertility-dependent gene expression changes in a social insect

Background

The gut microbiome can influence life history traits associated with host fitness such as fecundity and longevity. In most organisms, these two life history traits are traded-off, while they are positively linked in social insects. In ants, highly fecund queens can live for decades, while their non-reproducing workers exhibit much shorter lifespans. Yet, when fertility is induced in workers by death or removal of the queen, worker lifespan can increase. It is unclear how this positive link between fecundity and longevity is achieved and what role the gut microbiome and the immune system play in this. To gain insights into the molecular regulation of lifespan in social insects, we investigated fat body gene expression and gut microbiome composition in workers of the ant Temnothorax rugatulus in response to an experimental induction of fertility and an immune challenge.

Results

Fertile workers upregulated several molecular repair mechanisms, which could explain their extended lifespan. The immune challenge altered the expression of several thousand genes in the fat body, including many immune genes, and, interestingly, this transcriptomic response depended on worker fertility. For example, only fertile, immune-challenged workers upregulated genes involved in the synthesis of alpha-ketoglutarate, an immune system regulator, which extends the lifespan in Caenorhabditis elegans by down-regulating the TOR pathway and reducing oxidant production. Additionally, we observed a dramatic loss in bacterial diversity in the guts of the ants within a day of the immune challenge. Yet, bacterial density did not change, so that the gut microbiomes of many immune challenged workers consisted of only a single or a few bacterial strains. Moreover, the expression of immune genes was linked to the gut microbiome composition, suggesting that the ant host can regulate the microbiome in its gut.

Conclusions

Immune system flare-ups can have negative consequence on gut microbiome diversity, pointing to a previously underrated cost of immunity. Moreover, our results provide important insights into shifts in the molecular regulation of fertility and longevity associated with insect sociality.

JNK pathway plays a key role in the immune system of the pea aphid and is regulated by microRNA-184

Different from holometabolous insects, the hemipteran species such as pea aphid Acyrthosiphon pisum exhibit reduced immune responses with the absence of the genes coding for antimicrobial peptide (AMP), immune deficiency (IMD), peptidoglycan recognition proteins (PGRPs), and other immune-related molecules. Prior studies have proved that phenoloxidase (PO)-mediated melanization, hemocyte-mediated phagocytosis, and reactive oxygen species (ROS) participate in pea aphid defense against bacterial infection. Also, the conserved signaling, Jun N-terminal kinase (JNK) pathway, has been suggested to be involved in pea aphid immune defense. However, the precise role of the JNK signaling, its interplay with other immune responses and its regulation in pea aphid are largely unknown. In this study, using in vitro biochemical assays and in vivo bioassays, we demonstrated that the JNK pathway regulated hemolymph PO activity, hydrogen peroxide concentration and hemocyte phagocytosis in bacteria infected pea aphids, suggesting that the JNK pathway plays a central role in regulating immune responses in pea aphid. We further revealed the JNK pathway is regulated by microRNA-184 in response to bacterial infection. It is possible that in common the JNK pathway plays a key role in immune system of hemipteran insects and microRNA-184 regulates the JNK pathway in animals.

Plants make galls to accommodate foreigners: some are friends, most are foes

At the colonization site of a foreign entity, plant cells alter their trajectory of growth and development. The resulting structure - a plant gall - accommodates various needs of the foreigner, which are phylogenetically diverse: viruses, bacteria, protozoa, oomycetes, true fungi, parasitic plants, and many types of animals, including rotifers, nematodes, insects, and mites. The plant species that make galls also are diverse. We assume gall production costs the plant. All is well if the foreigner provides a gift that makes up for the cost. Nitrogen-fixing nodule-inducing bacteria provide nutritional services. Gall wasps pollinate fig trees. Unfortunately for plants, most galls are made for foes, some of which are deeply studied pathogens and pests: Agrobacterium tumefaciens, Rhodococcus fascians, Xanthomonas citri, Pseudomonas savastanoi, Pantoea agglomerans, 'Candidatus' phytoplasma, rust fungi, Ustilago smuts, root knot and cyst nematodes, and gall midges. Galls are an understudied phenomenon in plant developmental biology. We propose gall inception for discovering unifying features of the galls that plants make for friends and foes, talk about molecules that plants and gall-inducers use to get what they want from each other, raise the question of whether plants colonized by arbuscular mycorrhizal fungi respond in a gall-like manner, and present a research agenda.

Defensive Symbioses in Social Insects Can Inform Human Health and Agriculture

Social animals are among the most successful organisms on the planet and derive many benefits from living in groups, including facilitating the evolution of agriculture. However, living in groups increases the risk of disease transmission in social animals themselves and the cultivated crops upon which they obligately depend. Social insects offer an interesting model to compare to human societies, in terms of how insects manage disease within their societies and with their agricultural symbionts. As living in large groups can help the spread of beneficial microbes as well as pathogens, we examine the role of defensive microbial symbionts in protecting the host from pathogens. We further explore how beneficial microbes may influence other pathogen defenses including behavioral and immune responses, and how we can use insect systems as models to inform on issues relating to human health and agriculture.

Plant Manipulation by Gall-Forming Social Aphids for Waste Management

Many social aphids form spectacular galls on their host plants, in which hundreds to thousands of aphids thrive for several months or even for over a year. Here, in addition to colony defense against natural enemies, waste disposal is an important task for the gall dwellers to sustain their social life. In open galls, soldier nymphs actively clean colony wastes such as honeydew droplets, cast-off skins, and cadavers by pushing them with their head out of the gall opening. In the gall, the excreted honeydew is coated with aphid-derived powdery wax to form "honeydew balls," which prevents the aphids from wetting and drowning with their own excretion. How the aphids deal with the accumulated honeydew in closed galls has been a mystery. Here, we report a novel gall-cleaning mechanism: the gall inner surface absorbs and removes the liquid waste through the plant vascular system. Such a plant-mediated water-absorbing property is commonly found in aphids forming closed galls, which must have evolved at least three times independently. By contrast, the inner surface of open galls is wax-coated and water-repelling, and in some cases, the inner surface is covered with dense trichomes, which further enhance the water repellency. In conclusion, gall-forming aphids induce novel plant phenotypes to manage the waste problems by manipulating plant morphogenesis and physiology for their own sake. This review describes our recent studies on waste management strategies by gall-forming social aphids and discusses future directions of this research topic.