Host and symbiont genetic determinants of nutritional phenotype in a natural population of the pea aphid

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.

Molecular Mechanisms Underlying Host Plant Specificity in Aphids

Aphids are serious pests of agricultural and ornamental plants and important model systems for hemipteran-plant interactions. The long evolutionary history of aphids with their host plants has resulted in a variety of systems that provide insight into the different adaptation strategies of aphids to plants and vice versa. In the past, various plant-aphid interactions have been documented, but lack of functional tools has limited molecular studies on the mechanisms of plant-aphid interactions. Recent technological advances have begun to reveal plant-aphid interactions at the molecular level and to increase our knowledge of the mechanisms of aphid adaptation or specialization to different host plants. In this article, we compile and analyze available information on plant-aphid interactions, discuss the limitations of current knowledge, and argue for new research directions. We advocate for more work that takes advantage of natural systems and recently established molecular techniques to obtain a comprehensive view of plant-aphid interaction mechanisms.

Microbe Profile: Buchnera aphidicola: ancient aphid accomplice and endosymbiont exemplar

Buchnera aphidicola is an obligate endosymbiont of aphids that cannot be cultured outside of hosts. It exists as diverse strains in different aphid species, and phylogenetic reconstructions show that it has been maternally transmitted in aphids for >100 million years. B. aphidicola genomes are highly reduced and show conserved gene order and no gene acquisition, but encoded proteins undergo rapid evolution. Aphids depend on B. aphidicola for biosynthesis of essential amino acids and as an integral part of embryonic development. How B. aphidicola populations are regulated within hosts remains little known.

Concepts and Consequences of a Core Gut Microbiota for Animal Growth and Development

Animal microbiomes are occasionally considered as an extension of host anatomy, physiology, and even their genomic architecture. Their compositions encompass variable and constant portions when examined across multiple hosts. The latter, termed the core microbiome, is viewed as more accommodated to its host environment and suggested to benefit host fitness. Nevertheless, discrepancies in its definitions, characteristics, and importance to its hosts exist across studies. We survey studies that characterize the core microbiome, detail its current definitions and available methods to identify it, and emphasize the crucial need to upgrade and standardize the methodologies among studies. We highlight ruminants as a case study and discuss the link between the core microbiome and host physiology and genetics, as well as potential factors that shape it. We conclude with main directives of action to better understand the host-core microbiome axis and acquire the necessary insights into its controlled modulation. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Intraspecific variation in immune gene expression and heritable symbiont density

Host genetic variation plays an important role in the structure and function of heritable microbial communities. Recent studies have shown that insects use immune mechanisms to regulate heritable symbionts. Here we test the hypothesis that variation in symbiont density among hosts is linked to intraspecific differences in the immune response to harboring symbionts. We show that pea aphids (Acyrthosiphon pisum) harboring the bacterial endosymbiont Regiella insecticola (but not all other species of symbionts) downregulate expression of key immune genes. We then functionally link immune expression with symbiont density using RNAi. The pea aphid species complex is comprised of multiple reproductively-isolated host plant-adapted populations. These ‘biotypes’ have distinct patterns of symbiont infections: for example, aphids from the Trifolium biotype are strongly associated with Regiella. Using RNAseq, we compare patterns of gene expression in response to Regiella in aphid genotypes from multiple biotypes, and we show that Trifolium aphids experience no downregulation of immune gene expression while hosting Regiella and harbor symbionts at lower densities. Using F1 hybrids between two biotypes, we find that symbiont density and immune gene expression are both intermediate in hybrids. We propose that in this system, Regiella symbionts are suppressing aphid immune mechanisms to increase their density, but that some hosts have adapted to prevent immune suppression in order to control symbiont numbers. This work therefore suggests that antagonistic coevolution can play a role in host-microbe interactions even when symbionts are transmitted vertically and provide a clear benefit to their hosts. The specific immune mechanisms that we find are downregulated in the presence of Regiella have been previously shown to combat pathogens in aphids, and thus this work also highlights the immune system’s complex dual role in interacting with both beneficial and harmful microbes.

Insects frequently form beneficial partnerships with heritable microbes that are passed from mothers to offspring. Natural populations exhibit a great deal of variation in the frequency of heritable microbes and in the within-host density of these infections. Uncovering the mechanisms underlying variation in host-microbe interactions is key to understanding how they evolve. We study a model host-microbe interaction: the pea aphid and a heritable bacterium that makes aphids resistant to fungal pathogens. We show that aphids harboring bacteria show sharply reduced expression of innate immune system genes, and that this leads to increased densities of symbionts. We further show that populations of aphids that live on different species of plants vary in differential immune gene expression and in the density of their symbiont infections. This study contributes to our mechanistic understanding of an important model of host-microbe symbiosis and suggests that hosts and heritable microbes are evolving antagonistically. This work also sheds light on how invertebrate immune systems evolve to manage the complex task of combatting harmful pathogens while accommodating potentially beneficial microbes.

Wing plasticity and associated gene expression varies across the pea aphid biotype complex

Developmental phenotypic plasticity is a widespread phenomenon that allows organisms to produce different adult phenotypes in response to different environments. Investigating the molecular mechanisms underlying plasticity has the potential to reveal the precise changes that lead to the evolution of plasticity as a phenotype. Here, we study wing plasticity in multiple host-plant adapted populations of pea aphids as a model for understanding adaptation to different environments within a single species. We describe the wing plasticity response of different "biotypes" to a crowded environment and find differences within as well as among biotypes. We then use transcriptome profiling to compare a highly plastic pea aphid genotype to one that shows no plasticity and find that the latter exhibits no gene expression differences between environments. We conclude that the loss of plasticity has been accompanied by a loss of differential gene expression and therefore that genetic assimilation has occurred. Our gene expression results generalize previous studies that have shown a correlation between plasticity in morphology and gene expression.

Essential Amino Acid Enrichment and Positive Selection Highlight Endosymbiont's Role in a Global Virus-Vectoring Pest

Host-associated microbes display remarkable convergence in genome repertoire resulting from selection to supplement missing host functions. Nutritional supplementation has been proposed in the verrucomicrobial endosymbiont Xiphinematobacter sp., which lives within a globally widespread group of plant-parasitic nematodes that vector damaging nepoviruses to plants. Only one genome sequence has been published from this symbiont, leaving unanswered questions about its diversity, host range, role, and selective pressures within its hosts. Because its hosts are exceptionally resistant to culturing, this symbiont is best studied through advanced genomic approaches. To analyze the role of Xiphinematobacter sp. in its host, sequencing was performed on nematode communities, and then genomes were extracted for comparative genomics, gene ontology enrichment tests, polymorphism analysis, de Bruijn-based genome-wide association studies, and tests of pathway- and site-specific selection on genes predicted play a role in the symbiosis. Results showed a closely clustered set of Xiphinematobacter isolates with reduced genomes of ∼917 kbp, for which a new species was proposed. Symbionts shared only 2.3% of genes with outgroup Verrucomicrobia, but comparative analyses showed high conservation of all 10 essential amino acid (EAA) biosynthesis pathways plus several vitamin pathways. These findings were supported by gene ontology enrichment tests and high polymorphisms in these pathways compared with background. Genome-wide association analysis confirmed high between-species fixation of alleles with significant functional enrichment for EAA and thiamine synthesis. Strong positive selection was detected on sites within these pathways, despite several being under increased purifying selection. Together, these results suggest that supplementation of EAAs missing in the host diet may drive this widespread symbiosis.IMPORTANCE Xiphinematobacter spp. are distinctly evolved intracellular symbionts in the phylum Verrucomicrobia, which includes the important human gut-associated microbe Akkermansia muciniphila and many highly abundant free-living soil microbes. Like Akkermansia sp., Xiphinematobacter sp. is obligately associated with the gut of its hosts, which in this case consists of a group of plant-parasitic nematodes that are among the top 10 most destructive species to global agriculture, by vectoring plant viruses. This study examined the hypothesis that the key to this symbiont's stable evolutionary association with its host is through provisioning nutrients that its host cannot make that may be lacking in the nematode's plant phloem diet, such as essential amino acids and several vitamins. The significance of our research is in demonstrating, using population genomics, the signatures of selective pressure on these hypothesized roles to ultimately learn how this independently evolved symbiont functionally mirrors symbionts of phloem-feeding insects.

Similar Gut Bacterial Microbiota in Two Fruit-Feeding Moth Pests Collected from Different Host Species and Locations

Simple Summary

The peach fruit moth, Carposina sasakii, and the oriental fruit moth, Grapholita molesta are two co-occurring pests in orchards. Larvae of both species bore into fruits and cause damage to fruit production. Understanding the gut microbes, as well as the influencing factors between these co-occurring pests, may provide insight into their occurrence and control. In this study, we found that the two pests shared many bacteria in their gut from the genera Pseudomonas, Gluconobacter, Acetobacter, and Pantoea. The composition of the gut microbiota is similar between the two species collected from the same host plant and orchard; however, the gut microbiota of individuals collected from different orchards of the same host plant can be different within pest species. These results show that the two fruit moth pests have similar gut bacteria and varied environment in orchards can influence their gut microbiota.

Abstract

Numerous gut microbes are associated with insects, but their composition remains largely unknown for many insect groups, along with factors influencing their composition. Here, we compared gut bacterial microbiota of two co-occurring agricultural pests, the peach fruit moth (PFM), Carposina sasakii, and the oriental fruit moth (OFM), Grapholita molesta, collected from different orchards and host plant species. Gut microbiota of both species was mainly composed of bacteria from Proteobacteria, followed by Firmicutes. The two species shared bacteria from the genera Pseudomonas, Gluconobacter, Acetobacter, and Pantoea. When we compared two pairs of PFM and OFM populations collected from the same host species and the same orchard, there is no difference in alpha and beta diversity in gut microbiota. When we compared gut microbiota of the same species and host plant from different orchards, alpha and beta diversity was different in populations of PFM collected from two pear orchards but not in other comparisons. Our study suggests that the two pests share many features of gut microbiota and environment in orchards is a main factor influencing their gut microbiota.

Extreme developmental instability associated with wing plasticity in pea aphids

A key focus of evolutionary developmental biology is on how phenotypic diversity is generated. In particular, both plasticity and developmental instability contribute to phenotypic variation among genetically identical individuals, but the interactions between the two phenomena and their general fitness impacts are unclear. We discovered a striking example of asymmetry in pea aphids: the presence of wings on one side and the complete or partial absence of wings on the opposite side. We used this asymmetric phenotype to study the connection between plasticity, developmental instability and fitness. We found that this asymmetric wing development (i) occurred equally on both sides and thus is a developmental instability; (ii) is present in some genetically unique lines but not others, and thus has a genetic basis; and (iii) has intermediate levels of fecundity, and thus does not necessarily have negative fitness consequences. We conclude that this dramatic asymmetry may arise from incomplete switching between developmental targets, linking plasticity and developmental instability. We suspect that what we have observed may be a more widespread phenomenon, occurring across species that routinely produce distinct, alternative phenotypes.

Evaluation of RNA Interference for Control of the Grape Mealybug Pseudococcus maritimus (Hemiptera: Pseudococcidae)

Simple Summary

RNA interference (RNAi) is a defense mechanism that protects insects from viruses by targeting and degrading RNA. This feature has been exploited to reduce the expression of endogenous RNA for determining functions of various genes and for killing insect pests by targeting genes that are vital for insect survival. When dsRNA matching perfectly to the target RNA is administered, the RNAi machinery dices the dsRNA into ~21 bp fragments (known as siRNAs) and one strand of siRNA is employed by the RNAi machinery to target and degrade the target RNA. In this study we used a cocktail of dsRNAs targeting grape mealybug’s aquaporin and sucrase genes to kill the insect. Aquaporins and sucrases are important genes enabling these insects to maintain water relations indispensable for survival and digest complex sugars in the diet of plant sap-feeding insects, including mealybugs. In our experiments, administration of dsRNA caused a reduction in expression of the target genes and an increase in insect mortality. These results provide support for the application of RNAi to control the grape mealybug.

Abstract

The grape mealybug Pseudococcus maritimus (Ehrhorn, 1900) (Hemiptera: Pseudococcidae) is a significant pest of grapevines (Vitis spp.) and a vector of disease-causing grape viruses, linked to its feeding on phloem sap. The management of this pest is constrained by the lack of naturally occurring resistance traits in Vitis. Here, we obtained proof of concept that RNA interference (RNAi) using double-stranded RNA (dsRNA) molecules against essential genes for phloem sap feeding can depress insect survival. The genes of interest code for an aquaporin (AQP) and a sucrase (SUC) that are required for osmoregulation in related phloem sap-feeding hemipteran insects (aphids and whiteflies). In parallel, we investigated the grape mealybug genes coding non-specific nucleases (NUC), which reduce RNAi efficacy by degrading administered dsRNA. Homologs of AQP and SUC with experimentally validated function in aphids, together with NUC, were identified in the published transcriptome of the citrus mealybug Planococcus citri by phylogenetic analysis, and sequences of the candidate genes were obtained for Ps. maritimus by PCR with degenerate primers. Using this first sequence information for Ps. maritimus, dsRNA was prepared and administered to the insects via an artificial diet. The treatment comprising dsRNA against AQP, SUC and NUC significantly increased insect mortality over three days, relative to dsRNA-free controls. The dsRNA constructs for AQP and NUC were predicted, from sequence analysis to have some activity against other mealybugs, but none of the three dsRNA constructs have predicted activity against aphids. This study provides the basis to develop in planta RNAi strategies against Ps. maritimus and other mealybug pests of grapevines.

B-vitamin nutrition in the pea aphid-Buchnera symbiosis

Various insects that utilize vitamin-deficient diets derive a supplementary supply of these micronutrients from their symbiotic microorganisms. Here, we tested the inference from genome annotation that the symbiotic bacterium Buchnera aphidicola in the pea aphid Acyrthosiphon pisum provides the insect with vitamins B₂ and B₅ but no other B-vitamins. Contrary to expectation, aphid survival over five days of larval development on artificial diets individually lacking each B-vitamin not synthesized by Buchnera was not significantly reduced, despite significantly lower carcass B₁, B₃, B₆ and B₇ concentrations in the aphids on diets lacking each of these B-vitamins than on the vitamin-complete diet. Aphid survival was, however, significantly reduced on diet containing low concentrations (≤0.2 mM) or no pantothenate (B₅). Complementary transcriptome analysis revealed low abundance of the sense-transcript, but high abundance of the antisense transcript, of the Buchnera gene panC encoding the enzyme mediating the terminal reaction in pantothenate synthesis. We hypothesize that metabolic constraints or antisense transcripts may reduce Buchnera-mediated production of pantothenate, resulting in poor aphid performance on pantothenate-free diets. The discrepancy between predictions from genome data and empirical data illustrates the need for physiological study to test functional inferences made from genome annotations.

Candidate genetic determinants of intraspecific variation in pea aphid susceptibility to RNA interference

RNA interference (RNAi) plays a key role in insect defense against viruses and transposable elements, and it is being applied as an experimental tool and for insect pest control. However, RNAi efficiency is highly variable for some insects, notably the pea aphid Acyrthosiphon pisum. In this study, we used natural variation in RNAi susceptibility of pea aphids to identify genes that influence RNAi efficiency. Susceptibility to orally-delivered dsRNA against the gut aquaporin gene AQP1 (ds-AQP1) varied widely across a panel of 83 pea aphid genotypes, from zero to total mortality. Genome-wide association between aphid performance on ds-AQP1 supplemented diet and aphid genetic variants yielded 103 significantly associated single nucleotide polymorphisms (SNPs), including variants in 55 genes, at the 10^-4 probability cut-off. When ds-AQP1 was co-administered with dsRNA against six candidate genes, aphid mortality was reduced for three (50%) genes: the orthologs of the Drosophila genes trachealess (CG42865), headcase (CG15532) and a gene coding a peritrophin-A domain (CG8192), indicating that these genes function to promote RNAi efficiency against AQP1 in the pea aphid. Aphid susceptibility (quantified as mortality) to ds-AQP1 was correlated with RNAi against a further gene, snakeskin with essential gut function unrelated to AQP1, for some but not all aphid genotypes tested, suggesting that the determinants of RNAi efficiency may be partly gene-specific. This study demonstrates high levels of natural variation in susceptibility to RNAi and demonstrates the value of harnessing this variation to identify genes influencing RNAi efficiency.

Impact of Facultative Bacteria on the Metabolic Function of an Obligate Insect-Bacterial Symbiosis

Beneficial microorganisms associated with animals derive their nutritional requirements entirely from the animal host, but the impact of these microorganisms on host metabolism is largely unknown. The focus of this study was the experimentally tractable tripartite symbiosis between the pea aphid Acyrthosiphon pisum, its obligate intracellular bacterial symbiont Buchnera, and the facultative bacterium Hamiltonella which is localized primarily to the aphid hemolymph (blood). Metabolome experiments on, first, multiple aphid genotypes that naturally bear or lack Hamiltonella and, second, one aphid genotype from which Hamiltonella was experimentally eliminated revealed no significant effects of Hamiltonella on aphid metabolite profiles, indicating that Hamiltonella does not cause major reconfiguration of host metabolism. However, the titer of just one metabolite, 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR), displayed near-significant enrichment in Hamiltonella-positive aphids in both metabolome experiments. AICAR is a by-product of biosynthesis of the essential amino acid histidine in Buchnera and, hence, an index of histidine biosynthetic rates, suggesting that Buchnera-mediated histidine production is elevated in Hamiltonella-bearing aphids. Consistent with this prediction, aphids fed on [¹³C]histidine yielded a significantly elevated ¹²C/¹³C ratio of histidine in Hamiltonella-bearing aphids, indicative of increased (∼25%) histidine synthesized de novo by Buchnera However, in silico analysis predicted an increase of only 0.8% in Buchnera histidine synthesis in Hamiltonella-bearing aphids. We hypothesize that Hamiltonella imposes increased host demand for histidine, possibly for heightened immune-related functions. These results demonstrate that facultative bacteria can alter the dynamics of host metabolic interactions with co-occurring microorganisms, even when the overall metabolic homeostasis of the host is not substantially perturbed.IMPORTANCE Although microbial colonization of the internal tissues of animals generally causes septicemia and death, various animals are persistently associated with benign or beneficial microorganisms in their blood or internal organs. The metabolic consequences of these persistent associations for the animal host are largely unknown. Our research on the facultative bacterium Hamiltonella, localized primarily to the hemolymph of pea aphids, demonstrated that although Hamiltonella imposed no major reconfiguration of the aphid metabolome, it did alter the metabolic relations between the aphid and its obligate intracellular symbiont, Buchnera Specifically, Buchnera produced more histidine in Hamiltonella-positive aphids to support both Hamiltonella demand for histidine and Hamiltonella-induced increase in host demand. This study demonstrates how microorganisms associated with internal tissues of animals can influence specific aspects of metabolic interactions between the animal host and co-occurring microorganisms.