Genomic erosion and extensive horizontal gene transfer in gut-associated Acetobacteraceae

BACKGROUND

Symbiotic relationships between animals and bacteria have profound impacts on the evolutionary trajectories of each partner. Animals and gut bacteria engage in a variety of relationships, occasionally persisting over evolutionary timescales. Ants are a diverse group of animals that engage in many types of associations with taxonomically distinct groups of bacterial associates. Here, we bring into culture and characterize two closely-related strains of gut associated Acetobacteraceae (AAB) of the red carpenter ant, Camponotus chromaiodes.

RESULTS

Genome sequencing, assembly, and annotation of both strains delineate stark patterns of genomic erosion and sequence divergence in gut associated AAB. We found widespread horizontal gene transfer (HGT) in these bacterial associates and report elevated gene acquisition associated with energy production and conversion, amino acid and coenzyme transport and metabolism, defense mechanisms, and lysine export. Both strains have acquired the complete NADH-quinone oxidoreductase complex, plausibly from an Enterobacteriaceae origin, likely facilitating energy production under diverse conditions. Conservation of several lysine biosynthetic and salvage pathways and accumulation of lysine export genes via HGT implicate L-lysine supplementation by both strains as a potential functional benefit for the host. These trends are contrasted by genome-wide erosion of several amino acid biosynthetic pathways and pathways in central metabolism. We perform phylogenomic analyses on both strains as well as several free living and host associated AAB. Based on their monophyly and deep divergence from other AAB, these C. chromaiodes gut associates may represent a novel genus. Together, our results demonstrate how extensive horizontal transfer between gut associates along with genome-wide deletions leads to mosaic metabolic pathways. More broadly, these patterns demonstrate that HGT and genomic erosion shape metabolic capabilities of persistent gut associates and influence their genomic evolution.

CONCLUSIONS

Using comparative genomics, our study reveals substantial changes in genomic content in persistent associates of the insect gastrointestinal tract and provides evidence for the evolutionary pressures inherent to this environment. We describe patterns of genomic erosion and horizontal acquisition that result in mosaic metabolic pathways. Accordingly, the phylogenetic position of both strains of these associates form a divergent, monophyletic clade sister to gut associates of honey bees and more distantly to Gluconobacter.

In it for the long haul: evolutionary consequences of persistent endosymbiosis

Phylogenetically independent bacterial lineages have undergone a profound lifestyle shift: from a free-living to obligately host-associated existence. Among these lineages, intracellular bacterial mutualists of insects are among the most intimate, constrained symbioses known. These obligate endosymbionts exhibit severe gene loss and apparent genome deterioration. Evolutionary theory provides a basis to link their unusual genomic features with shifts in fundamental mechanisms - selection, genetic drift, mutation, and recombination. This mini-review highlights recent comparative and experimental research of processes shaping ongoing diversification within these ancient associations. Recent work supports clear contributions of stochastic processes, including genetic drift and exceptionally strong mutational pressure, toward degenerative evolution. Despite possible compensatory mechanisms, genome degradation may constrain how persistent endosymbionts (and their hosts) respond to environmental fluctuations.

Deep divergence and rapid evolutionary rates in gut-associated Acetobacteraceae of ants

BACKGROUND

Symbiotic associations between gut microbiota and their animal hosts shape the evolutionary trajectories of both partners. The genomic consequences of these relationships are significantly influenced by a variety of factors, including niche localization, interaction potential, and symbiont transmission mode. In eusocial insect hosts, socially transmitted gut microbiota may represent an intermediate point between free living or environmentally acquired bacteria and those with strict host association and maternal transmission.

RESULTS

We characterized the bacterial communities associated with an abundant ant species, Camponotus chromaiodes. While many bacteria had sporadic distributions, some taxa were abundant and persistent within and across ant colonies. Specially, two Acetobacteraceae operational taxonomic units (OTUs; referred to as AAB1 and AAB2) were abundant and widespread across host samples. Dissection experiments confirmed that AAB1 and AAB2 occur in C. chromaiodes gut tracts. We explored the distribution and evolution of these Acetobacteraceae OTUs in more depth. We found that Camponotus hosts representing different species and geographical regions possess close relatives of the Acetobacteraceae OTUs detected in C. chromaiodes. Phylogenetic analysis revealed that AAB1 and AAB2 join other ant associates in a monophyletic clade. This clade consists of Acetobacteraceae from three ant tribes, including a third, basal lineage associated with Attine ants. This ant-specific AAB clade exhibits a significant acceleration of substitution rates at the 16S rDNA gene and elevated AT content. Substitutions along 16S rRNA in AAB1 and AAB2 result in ~10 % reduction in the predicted rRNA stability.

CONCLUSIONS

Combined, these patterns in Camponotus-associated Acetobacteraceae resemble those found in cospeciating gut associates that are both socially and maternally transmitted. These associates may represent an intermediate point along an evolutionary trajectory manifest most extremely in symbionts with strict maternal transmission. Collectively, these results suggest that Acetobacteraceae may be a frequent and persistent gut associate in Camponotus species and perhaps other ant groups, and that its evolution is strongly impacted by this host association.

Endosymbiont evolution: predictions from theory and surprises from genomes

Genome data have created new opportunities to untangle evolutionary processes shaping microbial variation. Among bacteria, long-term mutualists of insects represent the smallest and (typically) most AT-rich genomes. Evolutionary theory provides a context to predict how an endosymbiotic lifestyle may alter fundamental evolutionary processes--mutation, selection, genetic drift, and recombination--and thus contribute to extreme genomic outcomes. These predictions can then be explored by comparing evolutionary rates, genome size and stability, and base compositional biases across endosymbiotic and free-living bacteria. Recent surprises from such comparisons include genome reduction among uncultured, free-living species. Some studies suggest that selection generally drives this streamlining, while drift drives genome reduction in endosymbionts; however, this remains an hypothesis requiring additional data. Unexpected evidence of selection acting on endosymbiont GC content hints that even weak selection may be effective in some long-term mutualists. Moving forward, intraspecific analysis offers a promising approach to distinguish underlying mechanisms, by testing the null hypothesis of neutrality and by quantifying mutational spectra. Such analyses may clarify whether endosymbionts and free-living bacteria occupy distinct evolutionary trajectories or, alternatively, represent varied outcomes of similar underlying forces.

Genome evolution in an ancient bacteria-ant symbiosis: parallel gene loss among Blochmannia spanning the origin of the ant tribe Camponotini

Stable associations between bacterial endosymbionts and insect hosts provide opportunities to explore genome evolution in the context of established mutualisms and assess the roles of selection and genetic drift across host lineages and habitats. Blochmannia, obligate endosymbionts of ants of the tribe Camponotini, have coevolved with their ant hosts for ∼40 MY. To investigate early events in Blochmannia genome evolution across this ant host tribe, we sequenced Blochmannia from two divergent host lineages, Colobopsis obliquus and Polyrhachis turneri, and compared them with four published genomes from Blochmannia of Camponotus sensu stricto. Reconstructed gene content of the last common ancestor (LCA) of these six Blochmannia genomes is reduced (690 protein coding genes), consistent with rapid gene loss soon after establishment of the symbiosis. Differential gene loss among Blochmannia lineages has affected cellular functions and metabolic pathways, including DNA replication and repair, vitamin biosynthesis and membrane proteins. Blochmannia of P. turneri (i.e., B. turneri) encodes an intact DnaA chromosomal replication initiation protein, demonstrating that loss of dnaA was not essential for establishment of the symbiosis. Based on gene content, B. obliquus and B. turneri are unable to provision hosts with riboflavin. Of the six sequenced Blochmannia, B. obliquus is the earliest diverging lineage (i.e., the sister group of other Blochmannia sampled) and encodes the fewest protein-coding genes and the most pseudogenes. We identified 55 genes involved in parallel gene loss, including glutamine synthetase, which may participate in nitrogen recycling. Pathways for biosynthesis of coenzyme A, terpenoids and riboflavin were lost in multiple lineages, suggesting relaxed selection on the pathway after inactivation of one component. Analysis of Illumina read datasets did not detect evidence of plasmids encoding missing functions, nor the presence of coresident symbionts other than Wolbachia. Although gene order is strictly conserved in four Blochmannia of Camponotus sensu stricto, comparisons with deeply divergent lineages revealed inversions in eight genomic regions, indicating ongoing recombination despite ancestral loss of recA. In sum, the addition of two Blochmannia genomes of divergent host lineages enables reconstruction of early events in evolution of this symbiosis and suggests that Blochmannia lineages may experience distinct, host-associated selective pressures. Understanding how evolutionary forces shape genome reduction in this system may help to clarify forces driving gene loss in other bacteria, including intracellular pathogens.

Can't take the heat: high temperature depletes bacterial endosymbionts of ants

Members of the ant tribe Camponotini have coevolved with Blochmannia, an obligate intracellular bacterial mutualist. This endosymbiont lives within host bacteriocyte cells that line the ant midgut, undergoes maternal transmission from host queens to offspring, and contributes to host nutrition via nitrogen recycling and nutrient biosynthesis. While elevated temperature has been shown to disrupt obligate bacterial mutualists of some insects, its impact on the ant-Blochmannia partnership is less clear. Here, we test the effect of heat on the density of Blochmannia in two related Camponotus species in the lab. Transcriptionally active Blochmannia were quantified using RT-qPCR as the ratio of Blochmannia 16S rRNA to ant host elongation factor 1-α transcripts. Our results showed that 4 weeks of heat treatment depleted active Blochmannia by >99 % in minor workers and unmated queens. However, complete elimination of Blochmannia transcripts rarely occurred, even after 16 weeks of heat treatment. Possible mechanisms of observed thermal sensitivity may include extreme AT-richness and related features of Blochmannia genomes, as well as host stress responses. Broadly, the observed depletion of an essential microbial mutualist in heat-treated ants is analogous to the loss of zooanthellae during coral bleaching. While the ecological relevance of Blochmannia's thermal sensitivity is uncertain, our results argue that symbiont dynamics should be part of models predicting how ants and other animals will respond and adapt to a warming climate.

Sequence context of indel mutations and their effect on protein evolution in a bacterial endosymbiont

Indel mutations play key roles in genome and protein evolution, yet we lack a comprehensive understanding of how indels impact evolutionary processes. Genome-wide analyses enabled by next-generation sequencing can clarify the context and effect of indels, thereby integrating a more detailed consideration of indels with our knowledge of nucleotide substitutions. To this end, we sequenced Blochmannia chromaiodes, an obligate bacterial endosymbiont of carpenter ants, and compared it with the close relative, B. pennsylvanicus. The genetic distance between these species is small enough for accurate whole genome alignment but large enough to provide a meaningful spectrum of indel mutations. We found that indels are subjected to purifying selection in coding regions and even intergenic regions, which show a reduced rate of indel base pairs per kilobase compared with nonfunctional pseudogenes. Indels occur almost exclusively in repeat regions composed of homopolymers and multimeric simple sequence repeats, demonstrating the importance of sequence context for indel mutations. Despite purifying selection, some indels occur in protein-coding genes. Most are multiples of three, indicating selective pressure to maintain the reading frame. The deleterious effect of frameshift-inducing indels is minimized by either compensation from a nearby indel to restore reading frame or the indel's location near the 3'-end of the gene. We observed amino acid divergence exceeding nucleotide divergence in regions affected by frameshift-inducing indels, suggesting that these indels may either drive adaptive protein evolution or initiate gene degradation. Our results shed light on how indel mutations impact processes of molecular evolution underlying endosymbiont genome evolution.

First impressions in a glowing host-microbe partnership

Despite the clear significance of beneficial animal-microbe associations, mechanisms underlying their initiation and establishment are rarely understood. In this issue of Cell Host & Microbe, Kremer et al. (2013) reveal that first contact within the squid-vibrio symbiosis triggers profound molecular and chemical changes that are crucial for bacterial colonization.

Animals in a bacterial world, a new imperative for the life sciences

In the last two decades, the widespread application of genetic and genomic approaches has revealed a bacterial world astonishing in its ubiquity and diversity. This review examines how a growing knowledge of the vast range of animal-bacterial interactions, whether in shared ecosystems or intimate symbioses, is fundamentally altering our understanding of animal biology. Specifically, we highlight recent technological and intellectual advances that have changed our thinking about five questions: how have bacteria facilitated the origin and evolution of animals; how do animals and bacteria affect each other's genomes; how does normal animal development depend on bacterial partners; how is homeostasis maintained between animals and their symbionts; and how can ecological approaches deepen our understanding of the multiple levels of animal-bacterial interaction. As answers to these fundamental questions emerge, all biologists will be challenged to broaden their appreciation of these interactions and to include investigations of the relationships between and among bacteria and their animal partners as we seek a better understanding of the natural world.

Proteomic analysis of an unculturable bacterial endosymbiont (Blochmannia) reveals high abundance of chaperonins and biosynthetic enzymes

Many insect groups have coevolved with bacterial endosymbionts that live within specialized host cells. As a salient example, ants in the tribe Camponotini rely on Blochmannia, an intracellular bacterial mutualist that synthesizes amino acids and recycles nitrogen for the host. We performed a shotgun, label-free, LC/MS/MS quantitative proteomic analysis to investigate the proteome of Blochmannia associated with Camponotus chromaiodes. We identified more than 330 Blochmannia proteins, or 54% coverage of the predicted proteome, as well as 244 Camponotus proteins. Using the average intensity of the top 3 "best flier" peptides along with spiking of a surrogate standard at a known concentration, we estimated the concentration (fmol/μg) of those proteins with confident identification. The estimated dynamic range of Blochmannia protein abundance spanned 3 orders of magnitude and covered diverse functional categories, with particularly high representation of metabolism, information transfer, and chaperones. GroEL, the most abundant protein, totaled 6% of Blochmannia protein abundance. Biosynthesis of essential amino acids, fatty acids, and nucleotides, and sulfate assimilation had disproportionately high coverage in the proteome, further supporting a nutritional role of the symbiosis. This first quantitative proteomic analysis of an ant endosymbiont illustrates a promising approach to study the functional basis of intimate symbioses.

Endosymbiosis

The phenomenon of endosymbiosis, or one organism living within another, has deeply impacted the evolution of life and continues to shape the ecology of countless species. Traditionally, biologists have viewed evolution as a largely bifurcating pattern, reflecting mutations and other changes in existing genetic information and the occasional speciation and divergence of lineages. While lineage bifurcation has clearly been important in evolution, the merging of two lineages through endosymbiosis has also made profound contributions to evolutionary novelty. Mitochondria and chloroplasts are relicts of ancient bacterial endosymbionts that ultimately extended the range of acceptable habitats for life by allowing hosts to thrive in the presence of oxygen and to convert light into energy. Today, the sheer abundance of endosymbiotic relationships across diverse host lineages and habitats testifies to their continued significance.

Strategies of genomic integration within insect-bacterial mutualisms

Insects, the most diverse group of macroorganisms with 900,000 known species, have been a rich playground for the evolution of symbiotic associations. Symbionts of this enormous animal group include a range of microbial partners. Insects are prone to establishing relationships with intracellular bacteria, which include the most intimate, highly integrated mutualisms known in the biological world. In recent years, an explosion of genomic studies has offered new insights into the molecular, functional, and evolutionary consequences of these insect-bacterial partnerships. In this review, I highlight some insights from genome sequences of bacterial endosymbionts and select insect hosts. Notably, comparisons between facultative and obligate bacterial mutualists have revealed distinct genome features representing different stages along a shared trajectory of genome reduction. Bacteria associated with the cedar aphid offer a snapshot of a transition from facultative to obligate mutualism, illustrating the genomic basis of this key step along the symbiotic spectrum. In addition, genomes of stable, dual bacterial symbionts reflect independent instances of astonishing metabolic integration. In these systems, synthesis of key nutrients, and perhaps basic cellular processes, require collaboration among co-residing bacteria and their insect host. These findings provide a launching point for a new era of genomic explorations of bacterial-animal symbioses. Future studies promise to reveal symbiotic strategies across a broad ecological and phylogenetic range, to clarify key transitions along a spectrum of interaction types, and to fuel new experimental approaches to dissect the mechanistic basis of intimate host-symbiont associations.

Mutualism meltdown in insects: bacteria constrain thermal adaptation

Predicting whether and how organisms will successfully cope with climate change presents critical questions for biologists and environmental scientists. Models require knowing how organisms interact with their abiotic environment, as well understanding biotic interactions that include a network of symbioses in which all species are embedded. Bacterial symbionts of insects offer valuable models to examine how microbes can facilitate and constrain adaptation to a changing environment. While some symbionts confer plasticity that accelerates adaptation, long-term bacterial mutualists of insects are characterized by tight lifestyle constraints, genome deterioration, and vulnerability to thermal stress. These essential bacterial partners are eliminated at high temperatures, analogous to the loss of zooanthellae during coral bleaching. Recent field-based studies suggest that thermal sensitivity of bacterial mutualists constrains insect responses. In this sense, highly dependent mutualisms may be the Achilles' heel of thermal responses in insects.

Reduced selective constraint in endosymbionts: elevation in radical amino acid replacements occurs genome-wide

As predicted by the nearly neutral model of evolution, numerous studies have shown that reduced N(e) accelerates the accumulation of slightly deleterious changes under genetic drift. While such studies have mostly focused on eukaryotes, bacteria also offer excellent models to explore the effects of N(e). Most notably, the genomes of host-dependent bacteria with small N(e) show signatures of genetic drift, including elevated K(a)/K(s). Here, I explore the utility of an alternative measure of selective constraint: the per-site rate of radical and conservative amino acid substitutions (D(r)/D(c)). I test the hypothesis that purifying selection against radical amino acid changes is less effective in two insect endosymbiont groups (Blochmannia of ants and Buchnera of aphids), compared to related gamma-Proteobacteria. Genome comparisons demonstrate a significant elevation in D(r)/D(c) in endosymbionts that affects the majority (66-79%) of shared orthologs examined. The elevation of D(r)/D(c) in endosymbionts affects all functional categories examined. Simulations indicate that D(r)/D(c) estimates are sensitive to codon frequencies and mutational parameters; however, estimation biases occur in the opposite direction as the patterns observed in genome comparisons, thereby making the inference of elevated D(r)/D(c) more conservative. Increased D(r)/D(c) and other signatures of genome degradation in endosymbionts are consistent with strong effects of genetic drift in their small populations, as well as linkage to selected sites in these asexual bacteria. While relaxed selection against radical substitutions may contribute, genome-wide processes such as genetic drift and linkage best explain the pervasive elevation in D(r)/D(c) across diverse functional categories that include basic cellular processes. Although the current study focuses on a few bacterial lineages, it suggests D(r)/D(c) is a useful gauge of selective constraint and may provide a valuable alternative to K(a)/K(s) when high sequence divergences preclude estimates of K(s). Broader application of D(r)/D(c) will benefit from approaches less prone to estimation biases.

Purifying selection, sequence composition, and context-specific indel mutations shape intraspecific variation in a bacterial endosymbiont

Comparative genomics of closely related bacterial strains can clarify mutational processes and selective forces that impact genetic variation. Among primary bacterial endosymbionts of insects, such analyses have revealed ongoing genome reduction, raising questions about the ultimate evolutionary fate of these partnerships. Here, we explored genomic variation within Blochmannia vafer, an obligate mutualist of the ant Camponotus vafer. Polymorphism analysis of the Illumina data set used previously for de novo assembly revealed a second Bl. vafer genotype. To determine why a single ant colony contained two symbiont genotypes, we examined polymorphisms in 12 C. vafer mitochondrial sequences assembled from the Illumina data; the spectrum of variants suggests that the colony contained two maternal lineages, each harboring a distinct Bl. vafer genotype. Comparing the two Bl. vafer genotypes revealed that purifying selection purged most indels and nonsynonymous differences from protein-coding genes. We also discovered that indels occur frequently in multimeric simple sequence repeats, which are relatively abundant in Bl. vafer and may play a more substantial role in generating variation in this ant mutualist than in the aphid endosymbiont Buchnera. Finally, we explored how an apparent relocation of the origin of replication in Bl. vafer and the resulting shift in strand-associated mutational pressures may have caused accelerated gene loss and an elevated rate of indel polymorphisms in the region spanning the origin relocation. Combined, these results point to significant impacts of purifying selection on genomic polymorphisms as well as distinct patterns of indels associated with unusual genomic features of Blochmannia.

Unprecedented loss of ammonia assimilation capability in a urease-encoding bacterial mutualist

Background

Blochmannia are obligately intracellular bacterial mutualists of ants of the tribe Camponotini. Blochmannia perform key nutritional functions for the host, including synthesis of several essential amino acids. We used Illumina technology to sequence the genome of Blochmannia associated with Camponotus vafer.

Results

Although Blochmannia vafer retains many nutritional functions, it is missing glutamine synthetase (glnA), a component of the nitrogen recycling pathway encoded by the previously sequenced B. floridanus and B. pennsylvanicus. With the exception of Ureaplasma, B. vafer is the only sequenced bacterium to date that encodes urease but lacks the ability to assimilate ammonia into glutamine or glutamate. Loss of glnA occurred in a deletion hotspot near the putative replication origin. Overall, compared to the likely gene set of their common ancestor, 31 genes are missing or eroded in B. vafer, compared to 28 in B. floridanus and four in B. pennsylvanicus. Three genes (queA, visC and yggS) show convergent loss or erosion, suggesting relaxed selection for their functions. Eight B. vafer genes contain frameshifts in homopolymeric tracts that may be corrected by transcriptional slippage. Two of these encode DNA replication proteins: dnaX, which we infer is also frameshifted in B. floridanus, and dnaG.

Conclusions

Comparing the B. vafer genome with B. pennsylvanicus and B. floridanus refines the core genes shared within the mutualist group, thereby clarifying functions required across ant host species. This third genome also allows us to track gene loss and erosion in a phylogenetic context to more fully understand processes of genome reduction.

One nutritional symbiosis begat another: phylogenetic evidence that the ant tribe Camponotini acquired Blochmannia by tending sap-feeding insects

Background

Bacterial endosymbiosis has a recurring significance in the evolution of insects. An estimated 10-20% of insect species depend on bacterial associates for their nutrition and reproductive viability. Members of the ant tribe Camponotini, the focus of this study, possess a stable, intracellular bacterial mutualist. The bacterium, Blochmannia, was first discovered in Camponotus and has since been documented in a distinct subgenus of Camponotus, Colobopsis, and in the related genus Polyrhachis. However, the distribution of Blochmannia throughout the Camponotini remains in question. Documenting the true host range of this bacterial mutualist is an important first step toward understanding the various ecological contexts in which it has evolved, and toward identifying its closest bacterial relatives. In this study, we performed a molecular screen, based on PCR amplification of 16S rDNA, to identify bacterial associates of diverse Camponotini species.

Results

Phylogenetic analyses of 16S rDNA gave four important insights: (i) Blochmannia occurs in a broad range of Camponotini genera including Calomyrmex, Echinopla, and Opisthopsis, and did not occur in outgroups related to this tribe (e.g., Notostigma). This suggests that the mutualism originated in the ancestor of the tribe Camponotini. (ii) The known bacteriocyte-associated symbionts of ants, in Formica, Plagiolepis, and the Camponotini, arose independently. (iii) Blochmannia is nestled within a diverse clade of endosymbionts of sap-feeding hemipteran insects, such as mealybugs, aphids, and psyllids. In our analyses, a group of secondary symbionts of mealybugs are the closest relatives of Blochmannia. (iv) Blochmannia has cospeciated with its known hosts, although deep divergences at the genus level remain uncertain.

Conclusions

The Blochmannia mutualism occurs in Calomyrmex, Echinopla, and Opisthopsis, in addition to Camponotus, and probably originated in the ancestral lineage leading to the Camponotini. This significant expansion of its known host range implies that the mutualism is more ancient and ecologically diverse than previously documented. Blochmannia is most closely related to endosymbionts of sap-feeding hemipterans, which ants tend for their carbohydrate-rich honeydew. Based on phylogenetic results, we propose Camponotini might have originally acquired this bacterial mutualist through a nutritional symbiosis with other insects.

Slip into something more functional: selection maintains ancient frameshifts in homopolymeric sequences

Mutational hotspots offer significant sources of genetic variability upon which selection can act. However, with a few notable exceptions, we know little about the dynamics and fitness consequences of mutations in these regions. Here, we explore evolutionary forces shaping homopolymeric tracts that are especially vulnerable to slippage errors during replication and transcription. Such tracts are typically eliminated by selection from most bacterial sequences, yet persist in genomes of endosymbionts with small effective population sizes (N(e)) and biased base compositions. Focusing on Blochmannia, a bacterial endosymbiont of ants, we track the divergence of genes that contain frameshift mutations within long (9-11 bp) polyA or polyT tracts. Earlier experimental work documented that transcriptional slippage restores the reading frame in a fraction of messenger RNA molecules and thereby rescues the function of frameshifted genes. In this study, we demonstrate a surprising persistence of these frameshifts and associated tracts for millions of years. Across the genome of this ant mutualist, rates of indel mutation within homopolymeric tracts far exceed the synonymous mutation rate, indicating that long-term conservation of frameshifts within these tracts is inconsistent with neutrality. In addition, the homopolymeric tracts themselves are more conserved than expected by chance, given extensive neutral substitutions that occur elsewhere in the genes sampled. These data suggest an unexpected role for slippage-prone DNA tracts and highlight a new mechanism for their persistence. That is, when such tracts contain a frameshift, transcriptional slippage plays a critical role in rescuing gene function. In such cases, selection will purge nucleotide changes interrupting the slippery tract so that otherwise volatile sequences become frozen in evolutionary time. Although the advantage of the frameshift itself is less clear, it may offer a mechanism to lower effective gene expression by reducing but not eliminating transcripts that encode full-length proteins.

Remaining flexible in old alliances: functional plasticity in constrained mutualisms

Central to any beneficial interaction is the capacity of partners to detect and respond to significant changes in the other. Recent studies of microbial mutualists show their close integration with host development, immune responses, and acclimation to a dynamic external environment. While the significance of microbial players is broadly appreciated, we are just beginning to understand the genetic, ecological, and physiological mechanisms that generate variation in symbiont functions, broadly termed "symbiont plasticity" here. Some possible mechanisms include shifts in symbiont community composition, genetic changes via DNA acquisition, gene expression fluctuations, and variation in symbiont densities. In this review, we examine mechanisms for plasticity in the exceptionally stable mutualisms between insects and bacterial endosymbionts. Despite the severe ecological and genomic constraints imposed by their specialized lifestyle, these bacteria retain the capacity to modulate functions depending on the particular requirements of the host. Focusing on the mutualism between Blochmannia and ants, we discuss the roles of gene expression fluctuations and shifts in bacterial densities in generating symbiont plasticity. This symbiont variation is best understood by considering ant colony as the host superorganism. In this eusocial host, the bacteria meet the needs of the colony and not necessarily the individual ants that house them.

Toward a Wolbachia Multilocus Sequence Typing System: Discrimination of Wolbachia Strains Present in Drosophila Species

Among the diverse maternally inherited symbionts in arthropods, Wolbachia are the most common and infect over 20% of all species. In a departure from traditional genotyping or phylogenetic methods relying on single Wolbachia genes, the present study represents an initial Multilocus Sequence Typing (MLST) analysis to discriminate closely related Wolbachia pipientis strains, and additional data on sequence diversity in Wolbachia. We report a new phylogenetic characterization of four genes (aspC, atpD, sucB, and pdhB), and provide an expanded analysis of markers described in previous studies (16S rDNA, ftsZ, groEL, dnaA, and gltA). MLST analysis of the bacterial strains present in 16 different Drosophila-Wolbachia associations detected four distinct clonal complexes that also corresponded to maximum-likelihood identified phylogenetic clades. Among the 16 associations analyzed, six could not be assigned to MLST clonal complexes and were also shown to be in conflict with relationships predicted by maximum-likelihood phylogenetic inferences. The results demonstrate the discriminatory power of MLST for identifying strains and clonal lineages of Wolbachia and provide a robust foundation for studying the ecology and evolution of this widespread endosymbiont.

The tripartite associations between bacteriophage, Wolbachia, and arthropods

By manipulating arthropod reproduction worldwide, the heritable endosymbiont Wolbachia has spread to pandemic levels. Little is known about the microbial basis of cytoplasmic incompatibility (CI) except that bacterial densities and percentages of infected sperm cysts associate with incompatibility strength. The recent discovery of a temperate bacteriophage (WO-B) of Wolbachia containing ankyrin-encoding genes and virulence factors has led to intensifying debate that bacteriophage WO-B induces CI. However, current hypotheses have not considered the separate roles that lytic and lysogenic phage might have on bacterial fitness and phenotype. Here we describe a set of quantitative approaches to characterize phage densities and its associations with bacterial densities and CI. We enumerated genome copy number of phage WO-B and Wolbachia and CI penetrance in supergroup A- and B-infected males of the parasitoid wasp Nasonia vitripennis. We report several findings: (1) variability in CI strength for A-infected males is positively associated with bacterial densities, as expected under the bacterial density model of CI, (2) phage and bacterial densities have a significant inverse association, as expected for an active lytic infection, and (3) CI strength and phage densities are inversely related in A-infected males; similarly, males expressing incomplete CI have significantly higher phage densities than males expressing complete CI. Ultrastructural analyses indicate that approximately 12% of the A Wolbachia have phage particles, and aggregations of these particles can putatively occur outside the Wolbachia cell. Physical interactions were observed between approximately 16% of the Wolbachia cells and spermatid tails. The results support a low to moderate frequency of lytic development in Wolbachia and an overall negative density relationship between bacteriophage and Wolbachia. The findings motivate a novel phage density model of CI in which lytic phage repress Wolbachia densities and therefore reproductive parasitism. We conclude that phage, Wolbachia, and arthropods form a tripartite symbiotic association in which all three are integral to understanding the biology of this widespread endosymbiosis. Clarifying the roles of lytic and lysogenic phage development in Wolbachia biology will effectively structure inquiries into this research topic.

Symbiotic bacteria that are maternally inherited are widespread in terrestrial invertebrates. Such bacteria infect the cells of reproductive tissues and can have important evolutionary and developmental effects on the host. Often these inherited symbionts develop beneficial relationships with their hosts, but some species can also selfishly alter invertebrate reproduction to increase the numbers of infected females (the transmitting sex of the bacteria) in the population. Bacterial-mediated distortions such as male-killing, feminization, parthenogenesis induction, and cytoplasmic incompatibility are collectively known as “reproductive parasitism.” In this article, the investigators show that the associations between the most common reproductive parasite in the biosphere (Wolbachia) and a parasitic wasp host are affected by a mobile element—a temperate bacteriophage of Wolbachia. In contrast to recent reports that suggest bacteriophage WO-B may induce reproductive parasitism, the authors' quantitative and ultrastructural analyses indicate that lytic phage WO-B are lethal and therefore associate with a reduction in both Wolbachia densities and reproductive parasitism. Based on these data, the authors propose a phage density model in which lytic phage development specifically leads to a reduction, rather than induction, of reproductive parisitism. The study is among the first investigations to show that lytic bacteriophage inversely associate with the densities and phenotype of an obligate intracellular bacterium.

Phylogeny of Wolbachia pipientis based on gltA, groEL and ftsZ gene sequences: clustering of arthropod and nematode symbionts in the F supergroup, and evidence for further diversity in the Wolbachia tree

Current phylogenies of the intracellular bacteria belonging to the genus Wolbachia identify six major clades (A–F), termed ‘supergroups’, but the branching order of these supergroups remains unresolved. Supergroups A, B and E include most of the wolbachiae found thus far in arthropods, while supergroups C and D include most of those found in filarial nematodes. Members of supergroup F have been found in arthropods (i.e. termites), and have previously been detected in the nematode Mansonella ozzardi, a causative agent of human filariasis. To resolve the phylogenetic positions of Wolbachia from Mansonella spp., and other novel strains from the flea Ctenocephalides felis and the filarial nematode Dipetalonema gracile, the authors generated new DNA sequences of the Wolbachia genes encoding citrate synthase (gltA), heat-shock protein 60 (groEL), and the cell division protein ftsZ. Phylogenetic analysis confirmed the designation of Wolbachia from Mansonella spp. as a member of the F supergroup. In addition, it was found that divergent lineages from Dip. gracile and Cte. felis lack any clear affiliation with known supergroups, indicating further genetic diversity within the Wolbachia genus. Finally, although the data generated did not permit clear resolution of the root of the global Wolbachia tree, the results suggest that the transfer of Wolbachia spp. from arthropods to nematodes (or vice versa) probably occurred more than once.

Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects

The distinct lifestyle of obligately intracellular bacteria can alter fundamental forces that drive and constrain genome change. In this study, sequencing the 792-kb genome of Blochmannia pennsylvanicus, an obligate endosymbiont of Camponotus pennsylvanicus, enabled us to trace evolutionary changes that occurred in the context of a bacterial-ant association. Comparison to the genome of Blochmannia floridanus reveals differential loss of genes involved in cofactor biosynthesis, the composition and structure of the cell wall and membrane, gene regulation, and DNA replication. However, the two Blochmannia species show complete conservation in the order and strand orientation of shared genes. This finding of extreme stasis in genome architecture, also reported previously for the aphid endosymbiont Buchnera, suggests that genome stability characterizes long-term bacterial mutualists of insects and constrains their evolutionary potential. Genome-wide analyses of protein divergences reveal 10- to 50-fold faster amino acid substitution rates in Blochmannia compared to related bacteria. Despite these varying features of genome evolution, a striking correlation in the relative divergences of proteins indicates parallel functional constraints on gene functions across ecologically distinct bacterial groups. Furthermore, the increased rates of amino acid substitution and gene loss in Blochmannia have occurred in a lineage-specific fashion, which may reflect life history differences of their ant hosts.

Widespread recombination throughout Wolbachia genomes

Evidence is growing that homologous recombination is a powerful source of genetic variability among closely related free-living bacteria. Here we investigate the extent of recombination among housekeeping genes of the endosymbiotic bacteria Wolbachia. Four housekeeping genes, gltA, dnaA, ftsZ, and groEL, were sequenced from a sample of 22 strains belonging to supergroups A and B. Sequence alignments were searched for recombination within and between genes using phylogenetic inference, analysis of genetic variation, and four recombination detection programs (MaxChi, Chimera, RDP, and Geneconv). Independent analyses indicate no or weak intragenic recombination in ftsZ, dnaA, and groEL. Intragenic recombination affects gltA, with a clear evidence of horizontal DNA transfers within and between divergent Wolbachia supergroups. Intergenic recombination was detected between all pairs of genes, suggesting either a horizontal exchange of a genome portion encompassing several genes or multiple recombination events involving smaller tracts along the genome. Overall, the observed pattern is compatible with pervasive recombination. Such results, combined with previous evidence of recombination in a surface protein, phage, and IS elements, support an unexpected chimeric origin of Wolbachia strains, with important implications for Wolbachia phylogeny and adaptation of these obligate intracellular bacteria in arthropods.

For better or worse: genomic consequences of intracellular mutualism and parasitism

Bacteria that replicate within eukaryotic host cells include a variety of pathogenic and mutualistic species. Early genome data for these intracellular associates suggested they experience continual gene loss, little if any gene acquisition, and minimal recombination in small, isolated populations. This view of reductive evolution is itself evolving as new genome sequences clarify mechanisms and outcomes of diverse intracellular associations. Recently sequenced genomes have confirmed a trajectory of gene loss and exceptional genome stability in long-term, nutritional mutualists and certain pathogens. However, new genome data for the Rickettsiales and Chlamydiales indicate more repeated DNA, a greater abundance of mobile DNA elements, and more labile genome dynamics than previously suspected for ancient intracellular lineages. Surprising discoveries of conjugation machinery in the parasite Rickettsia felis and the amoebae symbiont Parachlamydia sp. suggest that DNA transfer might play key roles in some intracellular taxa.

The roles of positive and negative selection in the molecular evolution of insect endosymbionts

The evolutionary rate acceleration observed in most endosymbiotic bacteria may be explained by higher mutation rates, changes in selective pressure, and increased fixation of deleterious mutations by genetic drift. Here, we explore the forces influencing molecular evolution in Blochmannia, an obligate endosymbiont of Camponotus and related ant genera. Our goals were to compare rates of sequence evolution in Blochmannia with related bacteria, to explore variation in the strength and efficacy of negative (purifying) selection, and to evaluate the effect of positive selection. For six Blochmannia pairs, plus Buchnera and related enterobacteria, estimates of sequence divergence at four genes confirm faster rates of synonymous evolution in the ant mutualist. This conclusion is based on higher dS between Blochmannia lineages despite their more recent divergence. Likewise, generally higher dN in Blochmannia indicates faster rates of nonsynonymous substitution in this group. One exception is the groEL gene, for which lower dN and dN/dS compared to Buchnera indicate exceptionally strong negative selection in Blochmannia. In addition, we explored evidence for positive selection in Blochmannia using both site-and lineage-based maximum likelihood models. These approaches confirmed heterogeneity of dN/dS among codon sites and revealed significant variation in dN/dS across Blochmannia lineages for three genes. Lineage variation affected genes independently, with no evidence of parallel changes in dN/dS across genes along a given branch. Our data also reveal instances of dN/dS greater than one; however, we do not interpret these large dN/dS ratios as evidence for positive selection. In sum, while drift may contribute to an overall rate acceleration at nonsynonymous sites in Blochmannia, variable selective pressures best explain the apparent gene-specific changes in dN/dS across lineages of this ant mutualist. In the course of this study, we reanalyzed variation at Buchnera groEL and found no evidence of positive selection that was previously reported.

Mutation exposed: a neutral explanation for extreme base composition of an endosymbiont genome

The influence of neutral mutation pressure versus selection on base composition evolution is a subject of considerable controversy. Yet the present study represents the first explicit population genetic analysis of this issue in prokaryotes, the group in which base composition variation is most dramatic. Here, we explore the impact of mutation and selection on the dynamics of synonymous changes in Buchnera aphidicola, the AT-rich bacterial endosymbiont of aphids. Specifically, we evaluated three forms of evidence. (i) We compared the frequencies of directional base changes (AT-->GC vs. GC-->AT) at synonymous sites within and between Buchnera species, to test for selective preference versus effective neutrality of these mutational categories. Reconstructed mutational changes across a robust intraspecific phylogeny showed a nearly 1:1 AT-->GC:GC-->AT ratio. Likewise, stationarity of base composition among Buchnera species indicated equal rates of AT-->GC and GC-->AT substitutions. The similarity of these patterns within and between species supported the neutral model. (ii) We observed an equivalence of relative per-site AT mutation rate and current AT content at synonymous sites, indicating that base composition is at mutational equilibrium. (iii) We demonstrated statistically greater equality in the frequency of mutational categories in Buchnera than in parallel mammalian studies that documented selection on synonymous sites. Our results indicate that effectively neutral mutational pressure, rather than selection, represents the major force driving base composition evolution in Buchnera. Thus they further corroborate recent evidence for the critical role of reduced N(e) in the molecular evolution of bacterial endosymbionts.

Nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the enterobacteriales (gamma-Proteobacteria)

Standard methods of phylogenetic reconstruction are based on models that assume homogeneity of nucleotide composition among taxa. However, this assumption is often violated in biological data sets. In this study, we examine possible effects of nucleotide heterogeneity among lineages on the phylogenetic reconstruction of a bacterial group that spans a wide range of genomic nucleotide contents: obligately endosymbiotic bacteria and free-living or commensal species in the gamma-Proteobacteria. We focus on AT-rich primary endosymbionts to better understand the origins of obligately intracellular lifestyles. Previous phylogenetic analyses of this bacterial group point to the importance of accounting for base compositional variation in estimating relationships, particularly between endosymbiotic and free-living taxa. Here, we develop an approach to compare susceptibility of various phylogenetic reconstruction methods to the effects of nucleotide heterogeneity. First, we identify candidate trees of gamma-Proteobacteria groEL and 16S rRNA using approaches that assume homogeneous and stationary base composition, including Bayesian, maximum likelihood, parsimony, and distance methods. We then create permutations of the resulting candidate trees by varying the placement of the AT-rich endosymbiont Buchnera. These permutations are evaluated under the nonhomogeneous and nonstationary maximum likelihood model of Galtier and Gouy, which allows equilibrium base content to vary among examined lineages. Our results show that commonly used phylogenetic methods produce incongruent trees of the Enterobacteriales, and that the placement of Buchnera is especially unstable. However, under a nonhomogeneous model, various groEL and 16S rRNA phylogenies that separate Buchnera from other AT-rich endosymbionts (Blochmannia and Wigglesworthia) have consistently and significantly higher likelihood scores. Blochmannia and Wigglesworthia appear to have evolved from secondary endosymbionts, and represent an origin of primary endosymbiosis that is independent from Buchnera. This application of a nonhomogeneous model offers a computationally feasible way to test specific phylogenetic hypotheses for taxa with heterogeneous and nonstationary base composition.

Bacteriophage flux in endosymbionts (Wolbachia): infection frequency, lateral transfer, and recombination rates

The highly specialized genomes of bacterial endosymbionts typically lack one of the major contributors of genomic flux in the free-living microbial world-bacteriophages. This study yields three results that show bacteriophages have, to the contrary, been influential in the genome evolution of the most prevalent bacterial endosymbiont of invertebrates, Wolbachia. First, we show that bacteriophage WO is more widespread in Wolbachia than previously recognized, occurring in at least 89% (35/39) of the sampled genomes. Second, we show through several phylogenetic approaches that bacteriophage WO underwent recent lateral transfers between Wolbachia bacteria that coinfect host cells in the dipteran Drosophila simulans and the hymenopteran Nasonia vitripennis. These two cases, along with a previous report in the lepidopteran Ephestia cautella, support a general mechanism for genetic exchange in endosymbionts--the "intracellular arena" hypothesis--in which genetic material moves horizontally between bacteria that coinfect the same intracellular environment. Third, we show recombination in this bacteriophage; in the region encoding a putative capsid protein, the recombination rate is faster than that of any known recombining genes in the endosymbiont genome. The combination of these three lines of genetic evidence indicates that this bacteriophage is a widespread source of genomic instability in the intracellular bacterium Wolbachia and potentially the invertebrate host. More generally, it is the first bacteriophage implicated in frequent lateral transfer between the genomes of bacterial endosymbionts. Gene transfer by bacteriophages could drive significant evolutionary change in the genomes of intracellular bacteria that are typically considered highly stable and prone to genomic degradation.

Host-symbiont stability and fast evolutionary rates in an ant-bacterium association: cospeciation of camponotus species and their endosymbionts, candidatus blochmannia

Bacterial endosymbionts are widespread across several insect orders and are involved in interactions ranging from obligate mutualism to reproductive parasitism. Candidatus Blochmannia gen. nov. (Blochmannia) is an obligate bacterial associate of Camponotus and related ant genera (Hymenoptera: Formicidae). The occurrence of Blochmannia in all Camponotus species sampled from field populations and its maternal transmission to host offspring suggest that this bacterium is engaged in a long-term, stable association with its ant hosts. However, evidence for cospeciation in this system is equivocal because previous phylogenetic studies were based on limited gene sampling, lacked statistical analysis of congruence, and have even suggested host switching. We compared phylogenies of host genes (the nuclear EF-1alphaF2 and mitochondrial COI/II) and Blochmannia genes (16S ribosomal DNA [rDNA], groEL, gidA, and rpsB), totaling more than 7 kilobases for each of 16 Camponotus species. Each data set was analyzed using maximum likelihood and Bayesian phylogenetic reconstruction methods. We found minimal conflict among host and symbiont phylogenies, and the few areas of discordance occurred at deep nodes that were poorly supported by individual data sets. Concatenated protein-coding genes produced a very well-resolved tree that, based on the Shimodaira-Hasegawa test, did not conflict with any host or symbiont data set. Correlated rates of synonymous substitution (d(S)) along corresponding branches of host and symbiont phylogenies further supported the hypothesis of cospeciation. These findings indicate that Blochmannia-Camponotus symbiosis has been evolutionarily stable throughout tens of millions of years. Based on inferred divergence times among the ant hosts, we estimated rates of sequence evolution of Blochmannia to be approximately 0.0024 substitutions per site per million years (s/s/MY) for the 16S rDNA gene and approximately 0.1094 s/s/MY at synonymous positions of the genes sampled. These rates are several-fold higher than those for related bacteria Buchnera aphidicola and Escherichia coli. Phylogenetic congruence among Blochmannia genes indicates genome stability that typifies primary endosymbionts of insects.

Endosymbiosis: lessons in conflict resolution

Endosymbiotic bacteria live within a host species. There are many and diverse examples of such relationships, the study of which provides important lessons for ecology and evolution

A Conservative Test of Genetic Drift in the Endosymbiotic Bacterium Buchnera: Slightly Deleterious Mutations in the Chaperonin groEL

The obligate endosymbiotic bacterium Buchnera aphidicola shows elevated rates of sequence evolution compared to free-living relatives, particularly at nonsynonymous sites. Because Buchnera experiences population bottlenecks during transmission to the offspring of its aphid host, it is hypothesized that genetic drift and the accumulation of slightly deleterious mutations can explain this rate increase. Recent studies of intraspecific variation in Buchnera reveal patterns consistent with this hypothesis. In this study, we examine inter- and intraspecific nucleotide variation in groEL, a highly conserved chaperonin gene that is constitutively overexpressed in Buchnera. Maximum-likelihood estimates of nonsynonymous substitution rates across Buchnera species are strikingly low at groEL compared to other loci. Despite this evidence for strong purifying selection on groEL, our intraspecific analysis of this gene documents reduced synonymous polymorphism, elevated nonsynonymous polymorphism, and an excess of rare alleles relative to the neutral expectation, as found in recent studies of other Buchnera loci. Comparisons with Escherichia coli generally show patterns predicted by their differences in Ne. The sum of these observations is not expected under relaxed or balancing selection, selective sweeps, or increased mutation rate. Rather, they further support the hypothesis that drift is an important force driving accelerated protein evolution in this obligate mutualist.

Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia

Wigglesworthia glossinidia brevipalpis, the obligate bacterial endosymbiont of the tsetse fly Glossina brevipalpis, is characterized by extreme genome reduction and AT nucleotide composition bias. Here, multivariate statistical analyses are used to test the hypothesis that mutational bias and genetic drift shape synonymous codon usage and amino acid usage of Wigglesworthia. The results show that synonymous codon usage patterns vary little across the genome and do not distinguish genes of putative high and low expression levels, thus indicating a lack of translational selection. Extreme AT composition bias across the genome also drives relative amino acid usage, but predicted high-expression genes (ribosomal proteins and chaperonins) use GC-rich amino acids more frequently than do low-expression genes. The levels and configuration of amino acid differences between Wigglesworthia and Escherichia coli were compared to test the hypothesis that the relatively GC-rich amino acid profiles of high-expression genes reflect greater amino acid conservation at these loci. This hypothesis is supported by reduced levels of protein divergence at predicted high-expression Wigglesworthia genes and similar configurations of amino acid changes across expression categories. Combined, the results suggest that codon and amino acid usage in the Wigglesworthia genome reflect a strong AT mutational bias and elevated levels of genetic drift, consistent with expected effects of an endosymbiotic lifestyle and repeated population bottlenecks. However, these impacts of mutation and drift are apparently attenuated by selection on amino acid composition at high-expression genes.

Genome evolution in an insect cell: distinct features of an ant-bacterial partnership

Bacteria that live exclusively within eukaryotic host cells include not only well-known pathogens, but also obligate mutualists, many of which occur in diverse insect groups such as aphids, psyllids, tsetse flies, and the ant genus Camponotus (Buchner, 1965; Douglas, 1998; Moran and Telang, 1998; Baumann et al., 2000; Moran and Baumann, 2000). In contrast to intracellular pathogens, these primary (P) endosymbionts of insects are required for the survival and reproduction of the host, exist within specialized host cells called bacteriocytes, and undergo stable maternal transmission through host lineages (Buchner, 1965; McLean and Houk, 1973). Due to their long-term host associations and close phylogenetic relationship with well-characterized enterobacteria (Fig. 1), P-endosymbionts of insects are ideal model systems to examine changes in genome content and architecture that occur in the context of beneficial, intracellular associations. Since these bacteria have not been cultured outside of the host cell, they are difficult to study with traditional genetic or physiological approaches. However, in recent years, molecular and computational approaches have provided important insights into their genetic diversity and ecological significance. This review describes some recent insights into the evolutionary genetics of obligate insect-bacteria symbioses, with a particular focus on an intriguing association between the bacterial endosymbiont Blochmannia and its ant hosts.

Genome evolution in bacterial endosymbionts of insects

Many insect species rely on intracellular bacterial symbionts for their viability and fecundity. Large-scale DNA-sequence analyses are revealing the forces that shape the evolution of these bacterial associates and the genetic basis of their specialization to an intracellular lifestyle. The full genome sequences of two obligate mutualists, Buchnera aphidicola of aphids and Wigglesworthia glossinidia of tsetse flies, reveal substantial gene loss and an integration of host and symbiont metabolic functions. Further genomic comparisons should reveal the generality of these features among bacterial mutualists and the extent to which they are shared with other intracellular bacteria, including obligate pathogens.

A strong effect of AT mutational bias on amino acid usage in Buchnera is mitigated at high-expression genes

The advent of full genome sequences provides exceptionally rich data sets to explore molecular and evolutionary mechanisms that shape divergence among and within genomes. In this study, we use multivariate analysis to determine the processes driving genome-wide patterns of amino usage in the obligate endosymbiont Buchnera and its close free-living relative Escherichia coli. In the AT-rich Buchnera genome, the primary source of variation in amino acid usage differentiates high- and low-expression genes. Amino acids of high-expression Buchnera genes are generally less aromatic and use relatively GC-rich codons, suggesting that selection against aromatic amino acids and against amino acids with AT-rich codons is stronger in high-expression genes. Selection to maintain hydrophobic amino acids in integral membrane proteins is a primary factor driving protein evolution in E. coli but is a secondary factor in Buchnera. In E. coli, gene expression is a secondary force driving amino acid usage, and a correlation with tRNA abundance suggests that translational selection contributes to this effect. Although this and previous studies demonstrate that AT mutational bias and genetic drift influence amino acid usage in Buchnera, this genome-wide analysis argues that selection is sufficient to affect the amino acid content of proteins with different expression and hydropathy levels.

Small genome of Candidatus Blochmannia, the bacterial endosymbiont of Camponotus, implies irreversible specialization to an intracellular lifestyle

Blochmannia (Candidatus Blochmannia gen. nov.) is the primary bacterial endosymbiont of the ant genus CAMPONOTUS: Like other obligate endosymbionts of insects, Blochmannia occurs exclusively within eukaryotic cells and has experienced long-term vertical transmission through host lineages. In this study, PFGE was used to estimate the genome size of Blochmannia as approximately 800 kb, which is significantly smaller than its free-living relatives in the enterobacteria. This small genome implies that Blochmannia has deleted most of the genetic machinery of related free-living bacteria. Due to restricted gene exchange in obligate endosymbionts, the substantial gene loss in Blochmannia and other insect mutualists may reflect irreversible specialization to a host cellular environment.

50 million years of genomic stasis in endosymbiotic bacteria

Comparison of two fully sequenced genomes of Buchnera aphidicola, the obligate endosymbionts of aphids, reveals the most extreme genome stability to date: no chromosome rearrangements or gene acquisitions have occurred in the past 50 to 70 million years, despite substantial sequence evolution and the inactivation and loss of individual genes. In contrast, the genomes of their closest free-living relatives, Escherichia coli and Salmonella spp., are more than 2000-fold more labile in content and gene order. The genomic stasis of B. aphidicola, likely attributable to the loss of phages, repeated sequences, and recA, indicates that B. aphidicola is no longer a source of ecological innovation for its hosts.

Parallel acceleration of evolutionary rates in symbiont genes underlying host nutrition

The overproduction of essential amino acids by Buchnera aphidicola, the primary bacterial mutualist of aphids, is considered an adaptation for increased production of nutrients that are lacking in aphids' diet of plant sap. Given their shared role in host nutrition, amino acid biosynthetic genes of Buchnera are expected to experience parallel changes in selection that depend on host diet quality, growth rate, and population structure. This study evaluates the hypothesis of parallel selection across biosynthetic pathways by testing for correlated changes in evolutionary rates at biosynthetic genes of Buchnera. Previous studies show fast evolutionary rates at tryptophan biosynthetic genes among Buchnera associated with the aphid genus Uroleucon and suggest reduced purifying selection on symbiont nutritional functions in this aphid group. Here, we test for parallel rate acceleration at other amino acid biosynthetic genes of Buchnera-Uroleucon, including those for leucine (leuABC) and isoleucine/valine biosynthesis (ilvC). Ratios of nonsynonymous to synonymous substitutions (d(N)/d(S)) were estimated using codon-based maximum-likelihood methods that account for the extreme AT compositional bias of Buchnera sequences. A significant elevation in d(N)/d(S) at biosynthetic loci but not at two housekeeping genes sampled (dnaN and tuf) suggests reduced host-level selection on biosynthetic capabilities of Buchnera-Uroleucon. In addition, the discovery of trpEG pseudogenes in Buchnera-U. obscurum further supports reduced selection on amino acid biosynthesis.

Intraspecific variation in symbiont genomes: bottlenecks and the aphid-buchnera association

Buchnera are maternally transmitted bacterial endosymbionts that synthesize amino acids that are limiting in the diet of their aphid hosts. Previous studies demonstrated accelerated sequence evolution in Buchnera compared to free-living bacteria, especially for nonsynonymous substitutions. Two mechanisms may explain this acceleration: relaxed purifying selection and increased fixation of slightly deleterious alleles under drift. Here, we test the divergent predictions of these hypotheses for intraspecific polymorphism using Buchnera associated with natural populations of the ragweed aphid, Uroleucon ambrosiae. Contrary to expectations under relaxed selection, U. ambrosiae from across the United States yielded strikingly low sequence diversity at three Buchnera loci (dnaN, trpBC, trpEG), revealing polymorphism three orders of magnitude lower than in enteric bacteria. An excess of nonsynonymous polymorphism and of rare alleles was also observed. Local sampling of additional dnaN sequences revealed similar patterns of polymorphism and no evidence of food plant-associated genetic structure. Aphid mitochondrial sequences further suggested that host bottlenecks and large-scale dispersal may contribute to genetic homogenization of aphids and symbionts. Together, our results support reduced N(e) as a primary cause of accelerated sequence evolution in Buchnera. However, our study cannot rule out the possibility that mechanisms other than bottlenecks also contribute to reduced N(e) at aphid and endosymbiont loci.

Vertical transmission of biosynthetic plasmids in aphid endosymbionts (Buchnera)

This study tested for horizontal transfer of plasmids among Buchnera aphidicola strains associated with ecologically and phylogenetically related aphid hosts (Uroleucon species). Phylogenetic congruence of Buchnera plasmid (trpEG and leuABC) and chromosomal (dnaN and trpB) genes supports strictly vertical long-term transmission of plasmids, which persist due to their contributions to host nutrition rather than capacity for infectious transfer. Synonymous divergences indicate elevated mutation on plasmids relative to chromosomal genes.

Intraspecific phylogenetic congruence among multiple symbiont genomes

Eukaryotes often form intimate endosymbioses with prokaryotic organisms. Cases in which these symbionts are transmitted cytoplasmically to host progeny create the potential for co-speciation or congruent evolution among the distinct genomes of these partners. If symbionts do not move horizontally between different eukaryotic hosts, strict phylogenetic congruence of their genomes is predicted and should extend to relationships within a single host species. Conversely, even rare 'host shifts' among closely related lineages should yield conflicting tree topologies at the intraspecific level. Here, we investigate the historical associations among four symbiotic genomes residing within an aphid host: the mitochondrial DNA of Uroleucon ambrosiae aphids, the bacterial chromosome of their Buchnera bacterial endosymbionts, and two plasmids associated with Buchnera. DNA sequence polymorphisms provided a significant phylogenetic signal and no homoplasy for each data set, yielding completely and significantly congruent phylogenies for these four genomes and no evidence of horizontal transmission. This study thus provides the first evidence for strictly vertical transmission and 'co-speciation' of symbiotic organisms at the intraspecific level, and represents the lowest phylogenetic level at which such coevolution has been demonstrated. These results may reflect the obligate nature of this intimate mutualism and indicate opportunities for adaptive coevolution among linked symbiont genomes.

Lifestyle evolution in symbiotic bacteria: insights from genomics

Bacteria that live only in eukaryotic cells and tissues, including chronic pathogens and mutualistic bacteriocyte associates, often possess a distinctive set of genomic traits, including reduced genome size, biased nucleotide base composition and fast polypeptide evolution. These phylogenetically diverse bacteria have lost certain functional categories of genes, including DNA repair genes, which affect mutational patterns. However, pathogens and mutualistic symbionts retain loci that underlie their unique interaction types, such as genes enabling nutrient provisioning by mutualistic bacteria-inhabiting animals. Recent genomic studies suggest that many of these bacteria are irreversibly specialized, precluding shifts between pathogenesis and mutualism.

Decay of mutualistic potential in aphid endosymbionts through silencing of biosynthetic loci: Buchnera of Diuraphis

Buchnera, the primary bacterial endosymbiont of aphids, is known to provision essential amino acids lacking in the hosts' diet of plant sap. The recent discovery of silenced copies of genes for tryptophan biosynthesis (trpEG) in certain Buchnera lineages suggests a decay in symbiotic functions in some aphid species. However, neither the distribution of pseudogenes among lineages nor the impact of this gene silencing on amino-acid availability in hosts has been assessed. In Buchnera of the aphid Diuraphis noxia, tandem repeats of these pseudogenes have persisted in diverse lineages, and thpEG pseudogenes have originated at least twice within this aphid genus. Measures of amino-acid concentrations in Diuraphis species have shown that the presence of the pseudogene is associated with a decreased availability of tryptophan, indicating that gene silencing decreases nutrient provisioning by symbionts. In Buchnera of Diuraphis, rates of nonsynonymous substitutions are elevated in functional trpE copies, supporting the hypothesis that pseudogene origin and persistence reflect a reduced selection for symbiont biosynthetic contributions. The parallel evolution of trpEG pseudogenes in Buchnera of Diuraphis and certain other aphid hosts suggests that either selection at the host level is not effective or that fitness in these aphids is not limited by tryptophan availability.

Decoupling of genome size and sequence divergence in a symbiotic bacterium

In contrast to genome size variation in most bacterial taxa, the small genome size of Buchnera sp. was shown to be highly conserved across genetically diverse isolates (630 to 643 kb). This exceptional size conservation may reflect the inability of this obligate mutualist to acquire foreign DNA and reduced selection for genetic novelty within a static intracellular environment.

Cospeciation between bacterial endosymbionts (Buchnera) and a recent radiation of aphids (Uroleucon) and pitfalls of testing for phylogenetic congruence

Previous studies of phylogenetic congruence between aphids and their symbiotic bacteria (Buchnera) supported long-term vertical transmission of symbionts. However, those studies were based on distantly related aphids and would not have revealed horizontal transfer of symbionts among closely related hosts. Aphid species of the genus Uroleucon are closely related phylogenetically and overlap in geographic ranges, habitats, and parasitoids. To examine support for congruence of phylogenies of Buchnera and Uroleucon, sequences from four mitochondrial, one nuclear, and one endosymbiont gene (trpB) were obtained. Congruence of phylogenies based on pooled aphid genes with phylogenies based on trpB was highly significant: Most nodes resolved by trpB corresponded to nodes resolved by the pooled aphid genes. Furthermore, no nodes were both inconsistent between the trees and strongly supported in both trees. Two kinds of analyses testing the null hypothesis of perfect congruence between pairwise combinations of datasets and tree topologies were performed: the Kishino-Hasegawa test and the likelihood-ratio test. Both tests indicated significant disagreement among most pairwise combinations of mitochondrial, nuclear, and symbiont datasets. Because rampant recombination among mitochondrial genomes of different aphid species is unlikely, inaccurate assumptions in the evolutionary models underlying these tests appear to be causing the hypothesis of a shared history to be incorrectly rejected. Moreover, trpB was more consistent with the aphid genes as a set than any single aphid gene was with the others, suggesting that the symbionts show the same phylogeny as the aphids. Overall, analyses support the interpretation that symbionts and aphids have undergone strict cospeciation, with no horizontal transmission of symbionts even among closely related, ecologically similar aphid hosts.

Comparison of the evolutionary dynamics of symbiotic and housekeeping loci: a case for the genetic coherence of rhizobial lineages

In prokaryotes, lateral gene transfer across chromosomal lineages may be mediated by plasmids, phages, transposable elements, and other accessory DNA elements. However, the importance of such transfer and the evolutionary forces that may restrict gene exchange remain largely unexplored in native settings. In this study, tests of phylogenetic congruence are employed to explore the range of horizontal transfer of symbiotic (sym) loci among distinct chromosomal lineages of native rhizobia, the nitrogen-fixing symbiont of legumes. Rhizobial strains isolated from nodules of several host plant genera were sequenced at three loci: symbiotic nodulation genes (nodB and nodC), the chromosomal housekeeping locus glutamine synthetase II (GSII), and a portion of the 16S rRNA gene. Molecular phylogenetic analysis shows that each locus generally subdivides strains into the same major groups, which correspond to the genera Rhizobium, Sinorhizobium, and Mesorhizobium. This broad phylogenetic congruence indicates a lack of lateral transfer across major chromosomal subdivisions, and it contrasts with previous studies of agricultural populations showing broad transfer of sym loci across divergent chromosomal lineages. A general correspondence of the three rhizobial genera with major legume groups suggests that host plant associations may be important in the differentiation of rhizobial nod and chromosomal loci and may restrict lateral transfer among strains. The second major result is a significant incongruence of nod and GSII phylogenies within rhizobial subdivisions, which strongly suggests horizontal transfer of nod genes among congenerics. This combined evidence for lateral gene transfer within, but not between, genetic subdivisions supports the view that rhizobial genera are "reproductively isolated" and diverge independently. Differences across rhizobial genera in the specificity of host associations imply that the evolutionary dynamics of the symbiosis vary considerably across lineages in native settings.