Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches

Intracellular defensive symbiont is culturable and capable of transovarial, vertical transmission

Insects frequently form heritable associations with beneficial bacteria that are vertically transmitted from parent to offspring. Long-term vertical transmission has repeatedly resulted in genome reduction and gene loss, rendering many such bacteria incapable of establishment in axenic culture. Among aphids, heritable endosymbionts often provide context-specific benefits to their hosts. Although these associations have large impacts on host phenotypes, experimental approaches are often limited by an inability to cultivate these microbes. Here, we report the axenic culture of Candidatus Fukatsuia symbiotica strain WIR, a heritable bacterial endosymbiont of the pea aphid, Acyrthosiphon pisum. Whole-genome sequencing revealed similar genomic features and high sequence similarity to previously described strains, suggesting that the cultivation techniques used here may be applicable to Ca. F. symbiotica strains from distantly related aphids. Microinjection of cultured Ca. F. symbiotica into uninfected aphids revealed that it can reinfect developing embryos and that infections are maintained in subsequent generations via transovarial maternal transmission. Artificially infected aphids exhibit phenotypic and life history traits similar to those observed for native infections. Our results show that Ca. F. symbiotica may be a useful tool for experimentally probing the molecular mechanisms underlying host-symbiont interactions in a heritable symbiosis.

IMPORTANCE

Diverse eukaryotic organisms form stable, symbiotic relationships with bacteria that provide benefits to their hosts. While these associations are often biologically important, they can be difficult to probe experimentally because intimately host-associated bacteria are difficult to access within host tissues, and most cannot be cultured. This is especially true for the intracellular, maternally inherited bacteria associated with many insects, including aphids. Here, we demonstrate that a pea aphid-associated strain of the heritable endosymbiont, Candidatus Fukatsuia symbiotica, can be grown outside of its host using standard microbiology techniques and can readily re-establish infection that is maintained across host generations. These artificial infections recapitulate the effects of native infections, making this host-symbiont pair a useful experimental system.

Genomic insights into Spiroplasma endosymbionts that induce male-killing and protective phenotypes in the pea aphid

The endosymbiotic bacteria Spiroplasma (Mollicutes) infect diverse plants and arthropods, and some of which induce male killing, where male hosts are killed during development. Male-killing Spiroplasma strains belong to either the phylogenetically distant Citri-Poulsonii or Ixodetis groups. In Drosophila flies, Spiroplasma poulsonii induces male killing via the Spaid toxin. While Spiroplasma ixodetis infects a wide range of insects and arachnids, little is known about the genetic basis of S. ixodetis-induced male killing. Here, we analyzed the genome of S. ixodetis strains in the pea aphid Acyrthosiphon pisum (Aphididae, Hemiptera). Genome sequencing constructed a complete genome of a male-killing strain, sAp269, consisting of a 1.5 Mb circular chromosome and an 80 Kb plasmid. sAp269 encoded putative virulence factors containing either ankyrin repeat, ovarian tumor-like deubiquitinase, or ribosome inactivating protein domains, but lacked the Spaid toxin. Further comparative genomics of Spiroplasma strains in A. pisum biotypes adapted to different host plants revealed their phylogenetic associations and the diversity of putative virulence factors. Although the mechanisms of S. ixodetis-induced male killing in pea aphids remain elusive, this study underlines the dynamic genome evolution of S. ixodetis and proposes independent acquisition events of male-killing mechanisms in insects.

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.

Intracellular defensive symbiont is culturable and capable of transovarial, vertical transmission

Insects frequently form heritable associations with beneficial bacteria that are vertically transmitted from parent to offspring. Long term vertical transmission has repeatedly resulted in genome reduction and gene loss rendering many such bacteria incapable of independent culture. Among aphids, heritable endosymbionts often provide a wide range of context-specific benefits to their hosts. Although these associations have large impacts on host phenotypes, experimental approaches are often limited by an inability to independently cultivate these microbes. Here, we report the axenic culture of Candidatus Fukatsuia symbiotica strain WIR, a heritable bacterial endosymbiont of the pea aphid, Acyrthosiphon pisum . Whole genome sequencing revealed similar genomic features and high sequence similarity to previously described strains, suggesting the cultivation techniques used here may be applicable to Ca . F. symbiotica strains from distantly related aphids. Microinjection of the isolated strain into uninfected aphids revealed that it can reinfect developing embryos, and is maintained in subsequent generations via transovarial maternal transmission. Artificially infected aphids exhibit similar phenotypic and life history traits compared to native infections, including protective effects against an entomopathogenic Fusarium species. Overall, our results show that Ca . F. symbiotica may be a useful tool for experimentally probing the molecular mechanisms underlying heritable symbioses and antifungal defense in the pea aphid system.

IMPORTANCE

Diverse eukaryotic organisms form stable, symbiotic relationships with bacteria that provide benefits to their hosts. While these associations are often biologically important, they can be difficult to probe experimentally, because intimately host-associated bacteria are difficult to access within host tissues, and most cannot be cultured. This is especially true of the intracellular, maternally inherited bacteria associated with many insects, including aphids. Here, we demonstrate that a pea aphid-associated strain of the heritable endosymbiont, Candidatus Fukatsuia symbiotica, can be grown outside of its host using standard microbiology techniques, and can readily re-establish infection that is maintained across host generations. These artificial infections recapitulate the effects of native infections making this host-symbiont pair a useful experimental system. Using this system, we demonstrate that Ca . F. symbiotica infection reduces host fitness under benign conditions, but protects against a previously unreported fungal pathogen.

Cryptic community structure and metabolic interactions among the heritable facultative symbionts of the pea aphid

Most insects harbour influential, yet non-essential heritable microbes in their hemocoel. Communities of these symbionts exhibit low diversity. But their frequent multi-species nature raises intriguing questions on roles for symbiont-symbiont synergies in host adaptation, and on the stability of the symbiont communities, themselves. In this study, we build on knowledge of species-defined symbiont community structure across US populations of the pea aphid, Acyrthosiphon pisum. Through extensive symbiont genotyping, we show that pea aphids' microbiomes can be more precisely defined at the symbiont strain level, with strain variability shaping five out of nine previously reported co-infection trends. Field data provide a mixture of evidence for synergistic fitness effects and symbiont hitchhiking, revealing causes and consequences of these co-infection trends. To test whether within-host metabolic interactions predict common versus rare strain-defined communities, we leveraged the high relatedness of our dominant, community-defined symbiont strains vs. 12 pea aphid-derived Gammaproteobacteria with sequenced genomes. Genomic inference, using metabolic complementarity indices, revealed high potential for cooperation among one pair of symbionts-Serratia symbiotica and Rickettsiella viridis. Applying the expansion network algorithm, through additional use of pea aphid and obligate Buchnera symbiont genomes, Serratia and Rickettsiella emerged as the only symbiont community requiring both parties to expand holobiont metabolism. Through their joint expansion of the biotin biosynthesis pathway, these symbionts may span missing gaps, creating a multi-party mutualism within their nutrient-limited, phloem-feeding hosts. Recent, complementary gene inactivation, within the biotin pathways of Serratia and Rickettsiella, raises further questions on the origins of mutualisms and host-symbiont interdependencies.

Contrasting Evolutionary Patterns Between Sexual and Asexual Lineages in a Genomic Region Linked to Reproductive Mode Variation in the pea aphid

Although asexual lineages evolved from sexual lineages in many different taxa, the genetics of sex loss remains poorly understood. We addressed this issue in the pea aphid Acyrthosiphon pisum, whose natural populations encompass lineages performing cyclical parthenogenesis (CP) and producing one sexual generation per year, as well as obligate parthenogenetic (OP) lineages that can no longer produce sexual females but can still produce males. An SNP-based, whole-genome scan of CP and OP populations sequenced in pools (103 individuals from 6 populations) revealed that an X-linked region is associated with the variation in reproductive mode. This 840-kb region is highly divergent between CP and OP populations (FST = 34.9%), with >2,000 SNPs or short Indels showing a high degree of association with the phenotypic trait. In OP populations specifically, this region also shows reduced diversity and Tajima's D, consistent with the OP phenotype being a derived trait in aphids. Interestingly, the low genetic differentiation between CP and OP populations at the rest of the genome (FST = 2.5%) suggests gene flow between them. Males from OP lineages thus likely transmit their op allele to new genomic backgrounds. These genetic exchanges, combined with the selection of the OP and CP reproductive modes under different climates, probably contribute to the long-term persistence of the cp and op alleles.

Proteomic and Transcriptomic Analysis for Identification of Endosymbiotic Bacteria Associated with BYDV Transmission Efficiency by Sitobion miscanthi

Sitobion miscanthi, an important viral vector of barley yellow dwarf virus (BYDV), is also symbiotically associated with endosymbionts, but little is known about the interactions between endosymbionts, aphid and BYDV. Therefore, two aphids' geographic populations, differing in their BYDV transmission efficiency, after characterizing their endosymbionts, were treated with antibiotics to investigate how changes in the composition of their endosymbiont population affected BYDV transmission efficiency. After antibiotic treatment, Rickettsia was eliminated from two geographic populations. BYDV transmission efficiency by STY geographic population dropped significantly, by -44.2% with ampicillin and -25.01% with rifampicin, but HDZ geographic population decreased by only 14.19% with ampicillin and 23.88% with rifampicin. Transcriptomic analysis showed that the number of DEGs related to the immune system, carbohydrate metabolism and lipid metabolism did increase in the STY rifampicin treatment, while replication and repair, glycan biosynthesis and metabolism increased in the STY ampicillin treatment. Proteomic analysis showed that the abundance of symbionin symL, nascent polypeptide-associated complex subunit alpha and proteasome differed significantly between the two geographic populations. We found that the endosymbionts can mediate vector viral transmission. They should therefore be included in investigations into aphid-virus interactions and plant disease epidemiology. Our findings should also help with the development of strategies to prevent virus transmission.

Strain Tracking of 'Candidatus Liberibacter asiaticus', the Citrus Greening Pathogen, by High-Resolution Microbiome Analysis of Asian Citrus Psyllids

The Asian citrus psyllid, Diaphorina citri, is an invasive insect and a vector of 'Candidatus Liberibacter asiaticus' (CLas), a bacterium whose growth in Citrus species results in huanglongbing (HLB), also known as citrus greening disease. Methods to enrich and sequence CLas from D. citri often rely on biased genome amplification and nevertheless contain significant quantities of host DNA. To overcome these hurdles, we developed a simple pretreatment DNase and filtration (PDF) protocol to remove host DNA and directly sequence CLas and the complete, primarily uncultivable microbiome from D. citri adults. The PDF protocol yielded CLas abundances upward of 60% and facilitated direct measurement of CLas and endosymbiont replication rates in psyllids. The PDF protocol confirmed our lab strains derived from a progenitor Florida CLas strain and accumulated 156 genetic variants, underscoring the utility of this method for bacterial strain tracking. CLas genetic polymorphisms arising in lab-reared psyllid populations included prophage-encoding regions with key functions in CLas pathogenesis, putative antibiotic resistance loci, and a single secreted effector. These variants suggest that laboratory propagation of CLas could result in different phenotypic trajectories among laboratories and could confound CLas physiology or therapeutic design and evaluation if these differences remain undocumented. Finally, we obtained genetic signatures affiliated with Citrus nuclear and organellar genomes, entomopathogenic fungal mitochondria, and commensal bacteria from laboratory-reared and field-collected D. citri adults. Hence, the PDF protocol can directly inform agricultural management strategies related to bacterial strain tracking, insect microbiome surveillance, and antibiotic resistance screening.

Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium

BACKGROUND

Many animals live in intimate associations with a species-rich microbiome. A key factor in maintaining these beneficial associations is fidelity, defined as the stability of associations between hosts and their microbiota over multiple host generations. Fidelity has been well studied in terrestrial hosts, particularly insects, over longer macroevolutionary time. In contrast, little is known about fidelity in marine animals with species-rich microbiomes at short microevolutionary time scales, that is at the level of a single host population. Given that natural selection acts most directly on local populations, studies of microevolutionary partner fidelity are important for revealing the ecological and evolutionary processes that drive intimate beneficial associations within animal species.

RESULTS

In this study on the obligate symbiosis between the gutless marine annelid Olavius algarvensis and its consortium of seven co-occurring bacterial symbionts, we show that partner fidelity varies across symbiont species from strict to absent over short microevolutionary time. Using a low-coverage sequencing approach that has not yet been applied to microbial community analyses, we analysed the metagenomes of 80 O. algarvensis individuals from the Mediterranean and compared host mitochondrial and symbiont phylogenies based on single-nucleotide polymorphisms across genomes. Fidelity was highest for the two chemoautotrophic, sulphur-oxidizing symbionts that dominated the microbial consortium of all O. algarvensis individuals. In contrast, fidelity was only intermediate to absent in the sulphate-reducing and spirochaetal symbionts with lower abundance. These differences in fidelity are likely driven by both selective and stochastic forces acting on the consistency with which symbionts are vertically transmitted.

CONCLUSIONS

We hypothesize that variable degrees of fidelity are advantageous for O. algarvensis by allowing the faithful transmission of their nutritionally most important symbionts and flexibility in the acquisition of other symbionts that promote ecological plasticity in the acquisition of environmental resources. Video Abstract.

Phylosymbiotic Structures of the Microbiota in Mollitrichosiphum tenuicorpus (Hemiptera: Aphididae: Greenideinae)

Aphids harbor an array of symbionts that provide hosts with ecological benefits. Microbial community assembly generally varies with respect to aphid species, geography, and host plants. However, the influence of host genetics and ecological factors on shaping intraspecific microbial community structures has not been fully understood. In the present study, using Illumina sequencing of the V3 - V4 hypervariable region of the 16S rRNA gene, we characterized the microbial compositions associated with Mollitrichosiphum tenuicorpus from different regions and plants in China. The primary symbiont Buchnera aphidicola and the secondary symbiont Arsenophonus dominated the microbial flora in M. tenuicorpus. Ordination analyses and statistical tests suggested that geography and aphid genetics primarily contributed to the variation in the microbiota of M. tenuicorpus. We further confirmed the combined effect of aphid genetics and geography on shaping the structures of symbiont and secondary symbiont communities. Moreover, the significant correlation between aphid genetic divergence and symbiont community dissimilarity provides evidence for intraspecific phylosymbiosis in natural systems. Our study helped to elucidate the eco-evolutionary relationship between symbiont communities and aphids within one given species.

Pangenome evolution in environmentally transmitted symbionts of deep-sea mussels is governed by vertical inheritance

Microbial pangenomes vary across species; their size and structure are determined by genetic diversity within the population and by gene loss and horizontal gene transfer (HGT). Many bacteria are associated with eukaryotic hosts where the host colonization dynamics may impact bacterial genome evolution. Host-associated lifestyle has been recognized as a barrier to HGT in parentally transmitted bacteria. However, pangenome evolution of environmentally acquired symbionts remains understudied, often due to limitations in symbiont cultivation. Using high-resolution metagenomics, here we study pangenome evolution of two co-occurring endosymbionts inhabiting Bathymodiolus brooksi mussels from a single cold seep. The symbionts, sulfur-oxidizing (SOX) and methane-oxidizing (MOX) gamma-proteobacteria, are environmentally acquired at an early developmental stage and individual mussels may harbor multiple strains of each symbiont species. We found differences in the accessory gene content of both symbionts across individual mussels, which are reflected by differences in symbiont strain composition. Compared to core genes, accessory genes are enriched in genome plasticity functions. We found no evidence for recent horizontal gene transfer between both symbionts. A comparison between the symbiont pangenomes revealed that the MOX population is less diverged and contains fewer accessory genes, supporting that the MOX association with B. brooksi is more recent in comparison to that of SOX. Our results show that the pangenomes of both symbionts evolved mainly by vertical inheritance. We conclude that genome evolution of environmentally transmitted symbionts that associate with individual hosts over their lifetime is affected by a narrow symbiosis where the frequency of HGT is constrained.​.

Unraveling coevolutionary dynamics using ecological genomics

Coevolutionary interactions, from the delicate co-dependency in mutualistic interactions to the antagonistic relationship of hosts and parasites, are a ubiquitous driver of adaptation. Surprisingly, little is known about the genomic processes underlying coevolution in an ecological context. However, species comprise genetically differentiated populations that interact with temporally variable abiotic and biotic environments. We discuss the recent advances in coevolutionary theory and genomics as well as shortcomings, to identify coevolving genes that take into account this spatial and temporal variability of coevolution, and propose a practical guide to understand the dynamic of coevolution using an ecological genomics lens.

Shifts in Pseudomonas species diversity influence adaptation of brown planthopper to changing climates and geographical locations

The brown planthopper (BPH) is a monophagous sap-sucking pest of rice that causes immense yield loss. The rapid build-up of pesticide resistance combined with the ability of BPH populations to quickly overcome host plant resistance has rendered conventional control strategies ineffective. One of the likely ways in which BPH adapts to novel environments is by undergoing rapid shifts in its microbiome composition. To elucidate the rapid adaptation to novel environments and the contributions of Pseudomonas toward insect survival, we performed Pseudomonas-specific 16S rRNA gut-microbiome profiling of BPH populations. Results revealed the differential occurrence of Pseudomonas species in BPH populations with changing climates and geographical locations. Further, the observed variation in Pseudomonas species composition and abundance correlated with BPH survivability. Collectively, this study, while adding to our current understanding of symbiont-mediated insect adaptation, also demonstrated a complex interplay between insect physiology and microbiome dynamics, which likely confers BPH its rapid adaptive capacity.

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BPH, a major pest of rice, undergoes seasonal shifts in its microbiome composition

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Pseudomonas sp. in BPH microbiome varied with seasons and geographical locations

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Pseudomonas sp. composition and abundance correlated with BPH survivability

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Environment-guided microbial shifts drive rapid stress adaptations in BPH

Insights Into the Species-Specific Microbiota of Greenideinae (Hemiptera: Aphididae) With Evidence of Phylosymbiosis

Aphids and their symbionts represent an outstanding model for studies of insect–symbiont interactions. The aphid microbiota can be shaped by aphid species, geography and host plants. However, the relative importance of phylogenetic and ecological factors in shaping microbial community structures is not well understood. Using Illumina sequencing of the V3–V4 hypervariable region of the 16S rRNA gene, we characterized the microbial compositions of 215 aphid colonies representing 53 species of the aphid subfamily Greenideinae from different regions and plants in China, Nepal, and Vietnam. The primary endosymbiont Buchnera aphidicola and secondary symbiont Serratia symbiotica dominated the microbiota of Greenideinae. We simultaneously explored the relative contribution of host identity (i.e., aphid genus and aphid species), geography and host plant to the structures of bacterial, symbiont and secondary symbiont communities. Ordination analyses and statistical tests highlighted the strongest impact of aphid species on the microbial flora in Greenideinae. Furthermore, we found a phylosymbiosis pattern in natural Greenideinae populations, in which the aphid phylogeny was positively correlated with microbial community dissimilarities. These findings will advance our knowledge of host-associated microbiota assembly across both host phylogenetic and ecological contexts.

Pervasiveness of the symbiont Serratia symbiotica in the aphid natural environment: distribution, diversity and evolution at a multitrophic level

Symbioses are significant drivers of insect evolutionary ecology. Despite recent findings that these associations can emerge from environmentally derived bacterial precursors, there is still little information on how these potential progenitors of insect symbionts circulate in trophic systems. Serratia symbiotica represents a valuable model for deciphering evolutionary scenarios of bacterial acquisition by insects, as its diversity includes gut-associated strains that retained the ability to live independently of their hosts, representing a potential reservoir for symbioses emergence. Here, we conducted a field study to examine the distribution and diversity of S. symbiotica found in aphid populations, and in different compartments of their surrounding environment. Twenty % of aphids colonies were infected with S. symbiotica, including a wide diversity of strains with varied tissue tropism corresponding to different lifestyle. We also showed that the prevalence of S. symbiotica is influenced by seasonal temperatures. We found that S. symbiotica was present in non-aphid species and in host plants, and that its prevalence in these samples was higher when associated aphid colonies were infected. Furthermore, phylogenetic analyses suggest the existence of horizontal transfers between the different trophic levels. These results provide a new picture of the pervasiveness of an insect symbiont in nature.

Defensive Symbionts and the Evolution of Parasitoid Host Specialization

Insect host-parasitoid interactions abound in nature and are characterized by a high degree of host specialization. In addition to their behavioral and immune defenses, many host species rely on heritable bacterial endosymbionts for defense against parasitoids. Studies on aphids and flies show that resistance conferred by symbionts can be very strong and highly specific, possibly as a result of variation in symbiont-produced toxins. I argue that defensive symbionts are therefore an important source of diversifying selection, promoting the evolution of host specialization by parasitoids. This is likely to affect the structure of host-parasitoid food webs. I consider potential changes in terms of food web complexity, although the nature of these effects will also be influenced by whether maternally transmitted symbionts have some capacity for lateral transfer. This is discussed in the light of available evidence for horizontal transmission routes. Finally, I propose that defensive mutualisms other than microbial endosymbionts may also exert diversifying selection on insect parasitoids.

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.

The effects of captivity on the microbiome of the endangered Comal Springs riffle beetle (Heterelmis comalensis)

The gut microbiome is affected by host intrinsic factors, diet and environment, and strongly linked to host's health. Although fluctuations of microbiome composition are normal, some are due to changes in host environmental conditions. When species are moved into captive environments for conservation, education or rehabilitation, these new conditions can influence a change in gut microbiome composition. Here, we compared the microbiomes of wild and captive Comal Springs riffle beetles (Heterelmis comalensis) by using amplicon sequencing of the 16S rRNA gene. We found that the microbiome of captive beetles was more diverse than wild beetle microbiomes. We identified 24 amplicon sequence variants (ASVs) with relative abundances significantly different between the wild and captive beetles. Many of the ASVs overrepresented in captive beetle microbiomes belong to taxa linked to nitrogen-rich environments. This is one of the first studies comparing the effects of captivity on the microbiome of an endangered insect species. Our findings provide valuable information for future applications in the management of captive populations of H. comalensis.

Mechanisms and Evolution of Heritable Microbial Density in Insect Hosts

Within-host density is a critically important aspect of vertically transmitted symbioses that influences the fitness of both hosts and microbes. I review recent studies of symbiont density in insects, including my laboratory's work on pea aphids and maternally transmitted bacteria. These studies used systems approaches to uncover the molecular mechanisms of how both hosts and microbes influence symbiont density, and they shed light on whether optimal density is different from the perspective of host and microbial fitness. Mounting empirical evidence suggests that antagonistic coevolution shapes vertically transmitted symbioses even when microbes provide clear benefits to hosts. This is potentially because of differing selective pressures at the host and within-host levels. Considering these contrasting evolutionary pressures will be critically important in efforts to use vertically transmitted symbionts for biocontrol and as lessons from model systems are applied to the study of more complex microbiomes.

Metagenomic Survey of the Highly Polyphagous Anastrepha ludens Developing in Ancestral and Exotic Hosts Reveals the Lack of a Stable Microbiota in Larvae and the Strong Influence of Metamorphosis on Adult Gut Microbiota

We studied the microbiota of a highly polyphagous insect, Anastrepha ludens (Diptera: Tephritidae), developing in six of its hosts, including two ancestral (Casimiroa edulis and C. greggii), three exotic (Mangifera indica cv. Ataulfo, Prunus persica cv. Criollo, and Citrus x aurantium) and one occasional host (Capsicum pubescens cv. Manzano), that is only used when extreme drought conditions limit fruiting by the common hosts. One of the exotic hosts (“criollo” peach) is rife with polyphenols and the occasional host with capsaicinoids exerting high fitness costs on the larvae. We pursued the following questions: (1) How is the microbial composition of the larval food related to the composition of the larval and adult microbiota, and what does this tell us about transience and stability of this species’ gut microbiota? (2) How does metamorphosis affect the adult microbiota? We surveyed the microbiota of the pulp of each host fruit, as well as the gut microbiota of larvae and adult flies and found that the gut of A. ludens larvae lacks a stable microbiota, since it was invariably associated with the composition of the pulp microbiota of the host plant species studied and was also different from the microbiota of adult flies indicating that metamorphosis filters out much of the microbiota present in larvae. The microbiota of adult males and females was similar between them, independent of host plant and was dominated by bacteria within the Enterobacteriaceae. We found that in the case of the “toxic” occasional host C. pubescens the microbiota is enriched in potentially deleterious genera that were much less abundant in the other hosts. In contrast, the pulp of the ancestral host C. edulis is enriched in several bacterial groups that can be beneficial for larval development. We also report for the first time the presence of bacteria within the Arcobacteraceae family in the gut microbiota of A. ludens stemming from C. edulis. Based on our findings, we conclude that changes in the food-associated microbiota dictate major changes in the larval microbiota, suggesting that most larval gut microbiota is originated from the food.

Acautalides A-C, Neuroprotective Diels-Alder Adducts from Solid-State Cultivated Acaulium sp. H-JQSF

The solid-state cultivation of Acaulium sp. H-JQSF isolated from Armadillidium vulgare produces acautalides A-C (1-3) as skeletally unprecedented Diels-Alder adducts of a 14-membered macrodiolide to an octadeca-9,11,13-trienoic acid. The acautalide structures, along with the intramolecular transesterifications of 1-acylglycerols, were elucidated by mass spectrometry, nuclear magnetic resonance, chemical transformation, and single-crystal X-ray diffraction. Compounds 1-3 were found to be neuroprotective with antiparkinsonic potential in the 1-methyl-4-phenylpyridinium-challenged nematode model, with the magnitude impacted by the glycerol esterification.

Global patterns in genomic diversity underpinning the evolution of insecticide resistance in the aphid crop pest Myzus persicae

The aphid Myzus persicae is a destructive agricultural pest that displays an exceptional ability to develop resistance to both natural and synthetic insecticides. To investigate the evolution of resistance in this species we generated a chromosome-scale genome assembly and living panel of >110 fully sequenced globally sampled clonal lines. Our analyses reveal a remarkable diversity of resistance mutations segregating in global populations of M. persicae. We show that the emergence and spread of these mechanisms is influenced by host-plant associations, uncovering the widespread co-option of a host-plant adaptation that also offers resistance against synthetic insecticides. We identify both the repeated evolution of independent resistance mutations at the same locus, and multiple instances of the evolution of novel resistance mechanisms against key insecticides. Our findings provide fundamental insights into the genomic responses of global insect populations to strong selective forces, and hold practical relevance for the control of pests and parasites.

Genome Analysis of a Verrucomicrobial Endosymbiont With a Tiny Genome Discovered in an Antarctic Lake

Organic Lake in Antarctica is a marine-derived, cold (−13∘C), stratified (oxic-anoxic), hypersaline (>200 gl^–1) system with unusual chemistry (very high levels of dimethylsulfide) that supports the growth of phylogenetically and metabolically diverse microorganisms. Symbionts are not well characterized in Antarctica. However, unicellular eukaryotes are often present in Antarctic lakes and theoretically could harbor endosymbionts. Here, we describe Candidatus Organicella extenuata, a member of the Verrucomicrobia with a highly reduced genome, recovered as a metagenome-assembled genome with genetic code 4 (UGA-to-Trp recoding) from Organic Lake. It is closely related to Candidatus Pinguicocccus supinus (163,218 bp, 205 genes), a newly described cytoplasmic endosymbiont of the freshwater ciliate Euplotes vanleeuwenhoeki (Serra et al., 2020). At 158,228 bp (encoding 194 genes), the genome of Ca. Organicella extenuata is among the smallest known bacterial genomes and similar to the genome of Ca. Pinguicoccus supinus (163,218 bp, 205 genes). Ca. Organicella extenuata retains a capacity for replication, transcription, translation, and protein-folding while lacking any capacity for the biosynthesis of amino acids or vitamins. Notably, the endosymbiont retains a capacity for fatty acid synthesis (type II) and iron–sulfur (Fe-S) cluster assembly. Metagenomic analysis of 150 new metagenomes from Organic Lake and more than 70 other Antarctic aquatic locations revealed a strong correlation in abundance between Ca. Organicella extenuata and a novel ciliate of the genus Euplotes. Like Ca. Pinguicoccus supinus, we infer that Ca. Organicella extenuata is an endosymbiont of Euplotes and hypothesize that both Ca. Organicella extenuata and Ca. Pinguicocccus supinus provide fatty acids and Fe-S clusters to their Euplotes host as the foundation of a mutualistic symbiosis. The discovery of Ca. Organicella extenuata as possessing genetic code 4 illustrates that in addition to identifying endosymbionts by sequencing known symbiotic communities and searching metagenome data using reference endosymbiont genomes, the potential exists to identify novel endosymbionts by searching for unusual coding parameters.

A Link Between Communities of Protective Endosymbionts and Parasitoids of the Pea Aphid Revealed in Unmanipulated Agricultural Systems

In the last decade, the influence of microbial symbionts on ecological and physiological traits of their hosts has been increasingly recognized. However, most of these effects have been revealed under laboratory conditions, which oversimplifies the complexity of the factors involved in the dynamics of symbiotic associations in nature. The pea aphid, Acyrthosiphon pisum, forms a complex of plant-adapted biotypes, which strongly differ in the prevalence of their facultative endosymbionts. Some of the facultative endosymbionts of A. pisum have been shown to confer protection against natural enemies, among which Hamiltonella defensa is known to protect its host from parasitoid wasps. Here, we tested under natural conditions whether the endosymbiont communities of different A. pisum biotypes had a protective effect on their hosts and whether endosymbiotic associations and parasitoid communities associated with the pea aphid complex were linked. A space-time monitoring of symbiotic associations, parasitoid pressure and parasitoid communities was carried out in three A. pisum biotypes respectively specialized on Medicago sativa (alfalfa), Pisum sativum (pea), and Trifolium sp. (clover) throughout the whole cropping season. While symbiotic associations, and to a lesser extent, parasitoid communities were stable over time and structured mainly by the A. pisum biotypes, the parasitoid pressure strongly varied during the season and differed among the three biotypes. This suggests a limited influence of parasitoid pressure on the dynamics of facultative endosymbionts at a seasonal scale. However, we found a positive correlation between the α and β diversities of the endosymbiont and parasitoid communities, indicating interactions between these two guilds. Also, we revealed a negative correlation between the prevalence of H. defensa and Fukatsuia symbiotica in co-infection and the intensity of parasitoid pressure in the alfalfa biotype, confirming in field conditions the protective effect of this symbiotic combination.

Microbiota associated with Mollitrichosiphum aphids (Hemiptera: Aphididae: Greenideinae): diversity, host species specificity and phylosymbiosis

Symbiotic association is universal in nature, and an array of symbionts play a crucial part in host life history. Aphids and their diverse symbionts have become a good model system to study insect‐symbiont interactions. Previous symbiotic diversity surveys have mainly focused on a few aphid clades, and the relative importance of different factors regulating microbial community structure is not well understood. In this study, we collected 65 colonies representing eight species of the aphid genus Mollitrichosiphum from different regions and plants in southern China and Nepal and characterized their microbial compositions using Illumina sequencing of the V3 − V4 hypervariable region of the 16S rRNA gene. We evaluated how microbiota varied across aphid species, geography and host plants and the correlation between microbial community structure and host aphid phylogeny. Heritable symbionts dominated the microbiota associated with Mollitrichosiphum, and multiple infections of secondary symbionts were prevalent. Ordination analyses and statistical tests highlighted the contribution of aphid species in shaping the structures of bacterial, symbiont and secondary symbiont communities. Moreover, we observed a significant correlation between Mollitrichosiphum aphid phylogeny and microbial community composition, providing evidence for a pattern of phylosymbiosis between natural aphid populations and their microbial associates.

Aphid infestation differently affects the defences of nitrate-fed and nitrogen-fixing Medicago truncatula and alters symbiotic nitrogen fixation

Legumes can meet their nitrogen requirements through root nodule symbiosis, which could also trigger plant systemic resistance against pests. The pea aphid Acyrthosiphon pisum, a legume pest, can harbour different facultative symbionts (FS) influencing various traits of their hosts. It is therefore worth determining if and how the symbionts of the plant and the aphid modulate their interaction. We used different pea aphid lines without FS or with a single one (Hamiltonella defensa, Regiella insecticola, Serratia symbiotica) to infest Medicago truncatula plants inoculated with Sinorhizobium meliloti (symbiotic nitrogen fixation, SNF) or supplemented with nitrate (non-inoculated, NI). The growth of SNF and NI plants was reduced by aphid infestation, while aphid weight (but not survival) was lowered on SNF compared to NI plants. Aphids strongly affected the plant nitrogen fixation depending on their symbiotic status, suggesting indirect relationships between aphid- and plant-associated microbes. Finally, all aphid lines triggered expression of Pathogenesis-Related Protein 1 (PR1) and Proteinase Inhibitor (PI), respective markers for salicylic and jasmonic pathways, in SNF plants, compared to only PR1 in NI plants. We demonstrate that the plant symbiotic status influences plant-aphid interactions while that of the aphid can modulate the amplitude of the plant's defence response.

MinYS: mine your symbiont by targeted genome assembly in symbiotic communities

Most metazoans are associated with symbionts. Characterizing the effect of a particular symbiont often requires getting access to its genome, which is usually done by sequencing the whole community. We present MinYS, a targeted assembly approach to assemble a particular genome of interest from such metagenomic data. First, taking advantage of a reference genome, a subset of the reads is assembled into a set of backbone contigs. Then, this draft assembly is completed using the whole metagenomic readset in a de novo manner. The resulting assembly is output as a genome graph, enabling different strains with potential structural variants coexisting in the sample to be distinguished. MinYS was applied to 50 pea aphid resequencing samples, with variable diversity in symbiont communities, in order to recover the genome sequence of its obligatory bacterial symbiont, Buchnera aphidicola. It was able to return high-quality assemblies (one contig assembly in 90% of the samples), even when using increasingly distant reference genomes, and to retrieve large structural variations in the samples. Because of its targeted essence, it outperformed standard metagenomic assemblers in terms of both time and assembly quality.

Induced Systemic Resistance by a Plant Growth-Promoting Rhizobacterium Impacts Development and Feeding Behavior of Aphids

The effects of microorganisms on plant-insect interactions have usually been underestimated. While plant growth-promoting rhizobacteria (PGPR) are known to induce plant defenses, endosymbiotic bacteria hosted by herbivorous insects are often beneficial to the host. Here, we aimed to assess whether PGPR-induced defenses in broad bean plants impact the pea aphid, depending on its genotype and the presence of endosymbionts. We estimated aphid reproduction, quantified defense- and growth-related phytohormones by GC-MS, and measured different plant growth and physiology parameters, after PGPR treatment. In addition, we recorded the feeding behavior of aphids by electropenetrography. We found that the PGPR treatment of broad bean plants reduced the reproduction of one of the pea aphid clones. We highlighted a phenomenon of PGPR-induced plant defense priming, but no noticeable plant growth promotion. The main changes in aphid probing behavior were related to salivation events into phloem sieve elements. We suggest that the endosymbiont Hamiltonella defensa played a key role in plant-insect interactions, possibly helping aphids to counteract plant-induced resistance and allowing them to develop normally on PGPR-treated plants. Our results imply that plant- and aphid-associated microorganisms add greater complexity to the outcomes of aphid-plant interactions.

A large genomic insertion containing a duplicated follistatin gene is linked to the pea aphid male wing dimorphism

Wing dimorphisms have long served as models for examining the ecological and evolutionary tradeoffs associated with alternative phenotypes. Here, we investigated the genetic cause of the pea aphid (Acyrthosiphon pisum) male wing dimorphism, wherein males exhibit one of two morphologies that differ in correlated traits that include the presence or absence of wings. We mapped this trait difference to a single genomic region and, using third generation, long-read sequencing, we identified a 120 kb insertion in the wingless allele. This insertion includes a duplicated follistatin gene, which is a strong candidate gene in the minimal mapped interval to cause the dimorphism. We found that both alleles were present prior to pea aphid biotype lineage diversification, we estimated that the insertion occurred millions of years ago, and we propose that both alleles have been maintained in the species, likely due to balancing selection.

Horizontally transmitted symbiont populations in deep-sea mussels are genetically isolated

Eukaryotes are habitats for bacterial organisms where the host colonization and dispersal among individual hosts have consequences for the bacterial ecology and evolution. Vertical symbiont transmission leads to geographic isolation of the microbial population and consequently to genetic isolation of microbiotas from individual hosts. In contrast, the extent of geographic and genetic isolation of horizontally transmitted microbiota is poorly characterized. Here we show that chemosynthetic symbionts of individual Bathymodiolus brooksi mussels constitute genetically isolated subpopulations. The reconstruction of core genome-wide strains from high-resolution metagenomes revealed distinct phylogenetic clades. Nucleotide diversity and strain composition vary along the mussel life span and individual hosts show a high degree of genetic isolation. Our results suggest that the uptake of environmental bacteria is a restricted process in B. brooksi, where self-infection of the gill tissue results in serial founder effects during symbiont evolution. We conclude that bacterial colonization dynamics over the host life cycle is thus an important determinant of population structure and genome evolution of horizontally transmitted symbionts.

Thermal plasticity of a freshwater cnidarian holobiont: detection of trans-generational effects in asexually reproducing hosts and symbionts

Understanding factors affecting the susceptibility of organisms to thermal stress is of enormous interest in light of our rapidly changing climate. When adaptation is limited, thermal acclimation and deacclimation abilities of organisms are critical for population persistence through a period of thermal stress. Holobionts (hosts plus associated symbionts) are key components of various ecosystems, such as coral reefs, yet the contributions of their two partners to holobiont thermal plasticity are poorly understood. Here, we tested thermal plasticity of the freshwater cnidarian Hydra viridissima (green hydra) using individual behavior and population responses. We found that algal presence initially reduced hydra thermal tolerance. Hydra with algae (symbiotic hydra) had comparable acclimation rates, deacclimation rates, and thermal tolerance after acclimation to those without algae (aposymbiotic hydra) but they had higher acclimation capacity. Acclimation of the host (hydra) and/or symbiont (algae) to elevated temperatures increased holobiont thermal tolerance and these effects persisted for multiple asexual generations. In addition, acclimated algae presence enhanced hydra fitness under prolonged sublethal thermal stress, especially when food was limited. Our study indicates while less intense but sublethal stress may favor symbiotic organisms by allowing them to acclimate, sudden large, potentially lethal fluctuations in climate stress likely favor aposymbiotic organisms. It also suggests that thermally stressed colonies of holobionts could disperse acclimated hosts and/or symbionts to other colonies, thereby reducing their vulnerability to climate change.

Host-microbiota interactions: from holobiont theory to analysis

In the recent years, the holobiont concept has emerged as a theoretical and experimental framework to study the interactions between hosts and their associated microbial communities in all types of ecosystems. The spread of this concept in many branches of biology results from the fairly recent realization of the ubiquitous nature of host-associated microbes and their central role in host biology, ecology, and evolution. Through this special series "Host-microbiota interactions: from holobiont theory to analysis," we wanted to promote this field of research which has considerable implications for human health, food production, and ecosystem protection. In this preface, we highlight a collection of articles selected for this special issue that show, use, or debate the concept of holobiont to approach taxonomically and ecologically diverse organisms, from humans and plants to sponges and insects. We also identify some theoretical and methodological challenges and propose directions for future research on holobionts.