A genomic perspective on nutrient provisioning by bacterial symbionts of insects

Widespread expression of conserved small RNAs in small symbiont genomes

Genome architecture of a microbe markedly changes when it transitions from a free-living lifestyle to an obligate symbiotic association within eukaryotic cells. These symbiont genomes experience numerous rearrangements and massive gene loss, which is expected to radically alter gene regulatory networks compared with those of free-living relatives. As such, it remains unclear whether and how these small symbiont genomes regulate gene expression. Here, using a label-free mass-spec quantification approach we found that differential protein regulation occurs in Buchnera, a model symbiont with a reduced genome, when it transitions between two distinct life stages. However, differential mRNA expression could not be detected between Buchnera life stages, despite the presence of a small number of putative transcriptional regulators. Instead a comparative analysis of small RNA expression profiles among five divergent Buchnera lineages, spanning a variety of Buchnera life stages, reveals 140 novel intergenic and antisense small RNAs and 517 untranslated regions that were significantly expressed, some of which have been conserved for ∼65 million years. In addition, the majority of these small RNAs exhibit both sequence covariation and thermodynamic stability, indicators of a potential structural RNA role. Together, these data suggest that gene regulation at the post-transcriptional level may be important in Buchnera. This is the first study to empirically identify Buchnera small RNAs, and we propose that these novel small RNAs may facilitate post-transcriptional regulation through translational inhibition/activation, and/or transcript stability. Ultimately, post-transcriptional regulation may shape metabolic complementation between Buchnera and its aphid host, thus impacting the animal's ecology and evolution.

Adenine methylation may contribute to endosymbiont selection in a clonal aphid population

BACKGROUND

The pea aphid Acyrthosiphon pisum has two modes of reproduction: parthenogenetic during the spring and summer and sexual in autumn. This ability to alternate between reproductive modes and the emergence of clonal populations under favorable conditions make this organism an interesting model for genetic and epigenetic studies. The pea aphid hosts different types of endosymbiotic bacteria within bacteriocytes which help the aphids survive and adapt to new environmental conditions and habitats. The obligate endosymbiont Buchnera aphidicola has a drastically reduced and stable genome, whereas facultative endosymbionts such as Regiella insecticola have large and dynamic genomes due to phages, mobile elements and high levels of genetic recombination. In previous work, selection toward cold adaptation resulted in the appearance of parthenogenetic A. pisum individuals characterized by heavier weights and remarkable green pigmentation.

RESULTS

Six adenine-methylated DNA fragments were isolated from genomic DNA (gDNA) extracted from the cold-induced green variant of A. pisum using deoxyadenosine methylase (Dam) by digesting the gDNA with the restriction enzymes DpnI and DpnII, which recognize the methylated and unmethylated GATC sites, respectively. The six resultant fragments did not match any sequence in the A. pisum or Buchnera genomes, implying that they came from facultative endosymbionts. The A1 fragment encoding a putative transposase and the A6 fragment encoding a putative helicase were selected for further comparison between the two A. pisum variants (green and orange) based on Dam analysis followed by PCR amplification. An association between adenine methylation and the two A. pisum variants was demonstrated by higher adenine methylation levels on both genes in the green variant as compared to the orange one.

CONCLUSION

Temperature selection may affect the secondary endosymbiont and the sensitive Dam involved in the survival and adaptation of aphids to cold temperatures. There is a high degree of adenine methylation at the GATC sites of the endosymbiont genes at 8°C, an effect that disappears at 22°C. We suggest that endosymbionts can be modified or selected to increase host fitness under unfavorable climatic conditions, and that the phenotype of the newly adapted aphids can be inherited.

Sympatric speciation in a bacterial endosymbiont results in two genomes with the functionality of one

Mutualisms that become evolutionarily stable give rise to organismal interdependencies. Some insects have developed intracellular associations with communities of bacteria, where the interdependencies are manifest in patterns of complementary gene loss and retention among members of the symbiosis. Here, using comparative genomics and microscopy, we show that a three-member symbiotic community has become a four-way assemblage through a novel bacterial lineage-splitting event. In some but not all cicada species of the genus Tettigades, the endosymbiont Candidatus Hodgkinia cicadicola has split into two new cytologically distinct but metabolically interdependent species. Although these new bacterial genomes are partitioned into discrete cell types, the intergenome patterns of gene loss and retention are almost perfectly complementary. These results defy easy classification: they show genomic patterns consistent with those observed after both speciation and whole-genome duplication. We suggest that our results highlight the potential power of nonadaptive forces in shaping organismal complexity.

Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum 'Diapherotrites'

The archaeal phylum 'Diapherotrites' was recently proposed based on phylogenomic analysis of genomes recovered from an underground water seep in an abandoned gold mine (Homestake mine in Lead, SD, USA). Here we present a detailed analysis of the metabolic capabilities and genomic features of three single amplified genomes (SAGs) belonging to the 'Diapherotrites'. The most complete of the SAGs, Candidatus 'Iainarchaeum andersonii' (Cand. IA), had a small genome (∼1.24 Mb), short average gene length (822 bp), one ribosomal RNA operon, high coding density (∼90.4%), high percentage of overlapping genes (27.6%) and low incidence of gene duplication (2.16%). Cand. IA genome possesses limited catabolic capacities that, nevertheless, could theoretically support a free-living lifestyle by channeling a narrow range of substrates such as ribose, polyhydroxybutyrate and several amino acids to acetyl-coenzyme A. On the other hand, Cand. IA possesses relatively well-developed anabolic capabilities, although it remains auxotrophic for several amino acids and cofactors. Phylogenetic analysis suggests that the majority of Cand. IA anabolic genes were acquired from bacterial donors via horizontal gene transfer. We thus propose that members of the 'Diapherotrites' have evolved from an obligate symbiotic ancestor by acquiring anabolic genes from bacteria that enabled independent biosynthesis of biological molecules previously acquired from symbiotic hosts. 'Diapherotrites' 16S rRNA genes exhibit multiple mismatches with the majority of archaeal 16S rRNA primers, a fact that could be responsible for their observed rarity in amplicon-generated data sets. The limited substrate range, complex growth requirements and slow growth rate predicted could be responsible for its refraction to isolation.

A new strain of Wolbachia in an alpine population of the viviparous Oreina cacaliae (Coleoptera: Chrysomelidae)

Microbial symbionts played a central role in insect evolution. Oreina cacaliae (Schrank, 1785) (Coleoptera: Chrysomelidae) is a rare example of a viviparous insect, able to feed on toxic plants and sequester toxic compounds. In the current study, the microbiota associated with O. cacaliae was characterized using a culture-independent approach, targeting the 16S rRNA bacterial gene. The obtained 16S rRNA gene sequences were analyzed and identified at different taxonomic levels. Wolbachia was the dominant bacterium, both in male and female (100 and 91.9%, respectively) individuals; the detected Wolbachia was described as a new sequence type based on multilocus sequence typing (Wolbachia ST375 Ocac_A_wVdO). After phylogenetic analyses, Wolbachia ST375 Ocac_A_wVdO was attributed to the supergroup A. Immunofluorescence assays and electron microscopy confirmed the presence of Wolbachia within O. cacaliae oocytes, confirming its transovarial transmission in this species. Representatives of six species of Oreina were tested for the presence of Wolbachia through specific polymerase chain reaction, and a dendrogram was generated for these species based on coxI gene sequences. The Wolbachia harbored by different species of Oreina were characterized by multilocus sequence typing. Five out of the six examined Oreina species were positive for Wolbachia, with four of these harboring the same sequence type.

Symbiont polyphyly, co-evolution, and necessity in pentatomid stinkbugs from Costa Rica

Interdomain symbioses with bacteria allow insects to take advantage of underutilized niches and provide the foundation for their evolutionary success in neotropical ecosystems. The gut microbiota of 13 micro-allopatric tropical pentatomid species, from a Costa Rican lowland rainforest, was characterized and compared with insect and host plant phylogenies. Like other families within the Pentatomomorpha, these insects (within seven genera—Antiteuchus, Arvelius, Edessa, Euschistus, Loxa, Mormidea, and Sibaria) house near-monocultures of gamma-proteobacteria in midgut crypts, comprising three distinct lineages within the family Enterobacteriaceae. Identity of the dominant bacteria (78–100% of the recovered 16S rRNA genes) was partially congruent with insect phylogeny, at the level of subfamily and tribe, with bacteria closely related to Erwinia observed in six species of the subfamily Pentatominae, and bacteria in a novel clade of Enterobacteriaceae for seven species within the subfamilies Edessinae and Discocephalinae. Symbiont replacement (i.e., bacterial “contamination” from the environment) may occur during maternal transmission by smearing of bacteria onto the egg surfaces during oviposition. This transmission strategy was experimentally confirmed for Sibaria englemani, and suspected for four species from two subfamilies, based on observation of egg probing by nymphs. Symbiont-deprived S. englemani, acquired via egg surface sterilization, exhibited significantly extended second instars (9.1 days compared with 7.9 days for symbiotic nymphs; p = 0.0001, Wilcoxon's rank with Bonferroni correction), slower linearized growth rates (p = 0.005, Welch 2-sample t-test), and qualitative differences in ceca morphology, including increased translucency of crypts, elongation of extracellular cavities, and distribution of symbionts, compared to symbiotic nymphs. Combined, these results suggest a role of the symbiont in host development, the reliable transference of symbionts via egg surfaces, and a suggestion of co-evolution between symbiont and tropical pentatomid host insects.

Evolutionary relationships of Pemphigus and allied genera (Hemiptera: Aphididae: Eriosomatinae) and their primary endosymbiont, Buchnera aphidicola

Aphids harbor primary endosymbionts, Buchnera aphidicola, in specialized cells within their body cavities. Aphids and Buchnera have strict mutualistic relationships in nutrition exchange. This ancient association has received much attention from researchers who are interested in endosymbiotic evolution. Previous studies have found parallel phylogenetic relationships between non-galling aphids and Buchnera at lower taxonomic levels (genus, species). To understand whether relatively isolated habitats such as galls have effect on the parallel relationships between aphids and Buchnera, the present paper investigated the phylogenetic relationships of gall aphids from Pemphigus and allied genera, which induce pseudo-galls or galls on Populus spp. (poplar) and Buchnera. The molecular phylogenies inferred from three aphid genes (COI, COII and EF-1α) and two Buchnera genes (gnd, 16S rRNA gene) indicated significant congruence between aphids and Buchnera at generic as well as interspecific levels. Interestingly, both aphid and Buchnera phylogenies supported three main clades corresponding to the galling locations of aphids, namely leaf, the joint of leaf blade and petiole, and branch of the host plant. The results suggest phylogenetic conservatism of gall characters, which indicates gall characters are more strongly affected by aphid phylogeny, rather than host plants.

Analysis of the gut microbiota of walking sticks (Phasmatodea)

BACKGROUND

Little is known about the Phasmatodea gut microbial community, including whether phasmids have symbiotic bacteria aiding in their digestion. While symbionts are near ubiquitous in herbivorous insects, the Phasmatodea's distinctively thin body shape precludes the gut enlargements needed for microbial fermentation. High-throughput sequencing was used to characterize the entire microbiota of the fat bodies, salivary glands, and anterior and posterior midguts of two species of walking stick.

RESULTS

Most bacterial sequences belonged to a strain of Spiroplasma (Tenericutes) found primarily in the posterior midgut of the parthenogenetic species Ramulus artemis (Phasmatidae). Beyond this, no significant differences were found between the R. artemis midgut sections or between that species and Peruphasma schultei (Pseudophasmatidae). Histological analysis further indicated a lack of bacteriocytes.

CONCLUSIONS

Phasmids are unlikely to depend on bacteria for digestion, suggesting they produce enzymes endogenously that most other herbivorous insects obtain from symbionts. This conclusion matches predictions based on phasmid anatomy. The role of Spiroplasma in insects warrants further study.

Coxiella-like endosymbionts

In the past two decades, many Coxiella-like bacteria have been found in hard ticks and soft ticks as well as in vertebrate hosts. It is interesting to note that many ticks harbor Coxiella-like bacteria with high prevalence. Coxiella-like bacteria and virulent Coxiella burnetii have high homology to each other; they form a monophyletic clade based on 16S rRNA sequence data and subsequent phylogenetic tree analyses. In this chapter, methods of detection, phylogeny, prevalence and density, distribution in tick organs, transmission routes, bacteria-host interactions, and putative functions of the Coxiella-like bacteria are reviewed.

Experimental infection of plants with an herbivore-associated bacterial endosymbiont influences herbivore host selection behavior

Although bacterial endosymbioses are common among phloeophagous herbivores, little is known regarding the effects of symbionts on herbivore host selection and population dynamics. We tested the hypothesis that plant selection and reproductive performance by a phloem-feeding herbivore (potato psyllid, Bactericera cockerelli) is mediated by infection of plants with a bacterial endosymbiont. We controlled for the effects of herbivory and endosymbiont infection by exposing potato plants (Solanum tuberosum) to psyllids infected with "Candidatus Liberibacter solanacearum" or to uninfected psyllids. We used these treatments as a basis to experimentally test plant volatile emissions, herbivore settling and oviposition preferences, and herbivore population growth. Three important findings emerged: (1) plant volatile profiles differed with respect to both herbivory and herbivory plus endosymbiont infection when compared to undamaged control plants; (2) herbivores initially settled on plants exposed to endosymbiont-infected psyllids but later defected and oviposited primarily on plants exposed only to uninfected psyllids; and (3) plant infection status had little effect on herbivore reproduction, though plant flowering was associated with a 39% reduction in herbivore density on average. Our experiments support the hypothesis that plant infection with endosymbionts alters plant volatile profiles, and infected plants initially recruited herbivores but later repelled them. Also, our findings suggest that the endosymbiont may not place negative selection pressure on its host herbivore in this system, but plant flowering phenology appears correlated with psyllid population performance.

Shared Ancestry of Symbionts? Sagrinae and Donaciinae (Coleoptera, Chrysomelidae) Harbor Similar Bacteria

When symbioses between insects and bacteria are discussed, the origin of a given association is regularly of interest. We examined the evolution of the symbiosis between reed beetles (Coleoptera, Chrysomelidae, Donaciinae) and intracellular symbionts belonging to the Enterobacteriaceae. We analyzed the partial sequence of the 16S rRNA to assess the phylogenetic relationships with bacteria we found in other beetle groups (Cerambycidae, Anobiidae, other Chrysomelidae). We discuss the ecology of each association in the context of the phylogenetic analysis. The bacteria in Sagra femorata (Chrysomelidae, Sagrinae) are very closely related to those in the Donaciinae and are located in similar mycetomes. The Sagrinae build a cocoon for pupation like the Donaciinae, in which the bacteria produce the material required for the cocoon. These aspects support the close relationship between Sagrinae and Donaciinae derived in earlier studies and make a common ancestry of the symbioses likely. Using PCR primers specific for fungi, we found Candida sp. in the mycetomes of a cerambycid beetle along with the bacteria.

Molecular and histological characterization of primary (betaproteobacteria) and secondary (gammaproteobacteria) endosymbionts of three mealybug species

Microscopic localization of endosymbiotic bacteria in three species of mealybug (Pseudococcus longispinus, the long-tailed mealybug; Pseudococcus calceolariae, the citrophilus mealybug; and Pseudococcus viburni, the obscure mealybug) showed these organisms were confined to bacteriocyte cells within a bacteriome centrally located within the hemocoel. Two species of bacteria were present, with the secondary endosymbiont, in all cases, living within the primary endosymbiont. DNA from the dissected bacteriomes of all three species of mealybug was extracted for analysis. Sequence data from selected 16S rRNA genes confirmed identification of the primary endosymbiont as "Candidatus Tremblaya princeps," a betaproteobacterium, and the secondary endosymbionts as gammaproteobacteria closely related to Sodalis glossinidius. A single 16S rRNA sequence of the primary endosymbiont was found in all individuals of each mealybug species. In contrast, the presence of multiple divergent strains of secondary endosymbionts in each individual mealybug suggests different evolutionary and transmission histories of the two endosymbionts. Mealybugs are known vectors of the plant pathogen Grapevine leafroll-associated virus 3. To examine the possible role of either endosymbiont in virus transmission, an extension of the model for interaction of proteins with bacterial chaperonins, i.e., GroEL protein homologs, based on mobile-loop amino acid sequences of their GroES homologs, was developed and used for analyses of viral coat protein interactions. The data from this model are consistent with a role for the primary endosymbiont in mealybug transmission of Grapevine leafroll-associated virus 3.

Endosymbiosis: bacteria sharing the load

A nested set of bacterial endosymbionts within mealybug cells collectively provides amino acids to their host, but their genomes show that some pathways are distributed between both endosymbionts, while other essential proteins are missing altogether. The possibility that additional functions are shared between partners warrants comparisons with organelles.

Adopting Bacteria in Order to Adapt to Water-How Reed Beetles Colonized the Wetlands (Coleoptera, Chrysomelidae, Donaciinae)

The present paper reviews the biology of reed beetles (Donaciinae), presents experimental data on the role of specific symbiotic bacteria, and describes a molecular method for the detection of those bacteria. Reed beetles are herbivores living on wetland plants, each species being mono- or oligo-phagous. They lay their eggs on the host plant and the larvae live underwater in the sediment attached to its roots. The larvae pupate there in a water-tight cocoon, which they build using a secretion that is produced by symbiotic bacteria. The bacteria are located in four blind sacs at the foregut of the larvae; in (female) adults they colonize two out of the six Malpighian tubules. Tetracycline treatment of larvae reduced their pupation rate, although the bacteria could not be fully eliminated. When the small amount of bacterial mass attached to eggs was experimentally removed before hatching, symbiont free larvae resulted, showing the external transmission of the bacteria to the offspring. Specific primers were designed to detect the bacteria, and to confirm their absence in manipulated larvae. The pupation underwater enabled the reed beetles to permanently colonize the wetlands and to diversify in this habitat underexploited by herbivorous insects (adaptive radiation).

Endosymbiont transmission mode in bacterial leaf nodulation as revealed by a population genetic study of Psychotria leptophylla

Leaf-nodulated plants are colonized by vertically inherited bacterial endosymbionts, which maintain symbioses throughout host generations. The permanent character of the interaction implies phylogenetic congruence between the host and the endosymbiont. However, the present population genetic study of Psychotria leptophylla provides evidence for a mixed symbiont transmission involving both vertical inheritance and horizontal transfers from the environment.

Comparison of midgut bacterial diversity in tropical caterpillars (Lepidoptera: Saturniidae) fed on different diets

As primary consumers of foliage, caterpillars play essential roles in shaping the trophic structure of tropical forests. The caterpillar midgut is specialized in plant tissue processing; its pH is exceptionally alkaline and contains high concentrations of toxic compounds derived from the ingested plant material (secondary compounds or allelochemicals) and from the insect itself. The midgut, therefore, represents an extreme environment for microbial life. Isolates from different bacterial taxa have been recovered from caterpillar midguts, but little is known about the impact of these microorganisms on caterpillar biology. Our long-term goals are to identify midgut symbionts and to investigate their functions. As a first step, different diet formulations were evaluated for rearing two species of tropical saturniid caterpillars. Using the polymerase chain reaction (PCR) with primers hybridizing broadly to sequences from the bacterial domain, 16S rRNA gene libraries were constructed with midgut DNA extracted from caterpillars reared on different diets. Amplified rDNA restriction analysis indicated that bacterial sequences recovered from the midguts of caterpillars fed on foliage were more diverse than those from caterpillars fed on artificial diet. Sequences related to Methylobacterium sp., Bradyrhizobium sp., and Propionibacterium sp. were detected in all caterpillar libraries regardless of diet, but were not detected in a library constructed from the diet itself. Furthermore, libraries constructed with DNA recovered from surface-sterilized eggs indicated potential for vertical transmission of midgut symbionts. Taken together, these results suggest that microorganisms associated with the tropical caterpillar midgut may engage in symbiotic interactions with these ecologically important insects.

Bacteriocyte-associated gammaproteobacterial symbionts of the Adelges nordmannianae/piceae complex (Hemiptera: Adelgidae)

Adelgids (Insecta: Hemiptera: Adelgidae) are known as severe pests of various conifers in North America, Canada, Europe and Asia. Here, we present the first molecular identification of bacteriocyte-associated symbionts in these plant sap-sucking insects. Three geographically distant populations of members of the Adelges nordmannianae/piceae complex, identified based on coI and ef1alpha gene sequences, were investigated. Electron and light microscopy revealed two morphologically different endosymbionts, coccoid or polymorphic, which are located in distinct bacteriocytes. Phylogenetic analyses of their 16S and 23S rRNA gene sequences assigned both symbionts to novel lineages within the Gammaproteobacteria sharing <92% 16S rRNA sequence similarity with each other and showing no close relationship with known symbionts of insects. Their identity and intracellular location were confirmed by fluorescence in situ hybridization, and the names 'Candidatus Steffania adelgidicola' and 'Candidatus Ecksteinia adelgidicola' are proposed for tentative classification. Both symbionts were present in all individuals of all investigated populations and in different adelgid life stages including eggs, suggesting vertical transmission from mother to offspring. An 85 kb genome fragment of 'Candidatus S. adelgidicola' was reconstructed based on a metagenomic library created from purified symbionts. Genomic features including the frequency of pseudogenes, the average length of intergenic regions and the presence of several genes which are absent in other long-term obligate symbionts, suggested that 'Candidatus S. adelgidicola' is an evolutionarily young bacteriocyte-associated symbiont, which has been acquired after diversification of adelgids from their aphid sister group.

An interdependent metabolic patchwork in the nested symbiosis of mealybugs

Highly reduced genomes of 144-416 kilobases have been described from nutrient-provisioning bacterial symbionts of several insect lineages [1-5]. Some host insects have formed stable associations with pairs of bacterial symbionts that live in specialized cells and provide them with essential nutrients; genomic data from these systems have revealed remarkable levels of metabolic complementarity between the symbiont pairs [3, 4, 6, 7]. The mealybug Planococcus citri (Hemiptera: Pseudococcidae) contains dual bacterial symbionts existing with an unprecedented organization: an unnamed gammaproteobacteria, for which we propose the name Candidatus Moranella endobia, lives inside the betaproteobacteria Candidatus Tremblaya princeps [8]. Here we describe the complete genomes and metabolic contributions of these unusual nested symbionts. We show that whereas there is little overlap in retained genes involved in nutrient production between symbionts, several essential amino acid pathways in the mealybug assemblage require a patchwork of interspersed gene products from Tremblaya, Moranella, and possibly P. citri. Furthermore, although Tremblaya has the smallest cellular genome yet described, it contains a genomic inversion present in both orientations in individual insects, starkly contrasting with the extreme structural stability typical of highly reduced bacterial genomes [4, 9, 10].

Multimodal dynamic response of the Buchnera aphidicola pLeu plasmid to variations in leucine demand of its host, the pea aphid Acyrthosiphon pisum

Aphids, important agricultural pests, can grow and reproduce thanks to their intimate symbiosis with the γ-proteobacterium Buchnera aphidicola that furnishes them with essential amino acids lacking in their phloem sap diet. To study how B. aphidicola, with its reduced genome containing very few transcriptional regulators, responds to variations in the metabolic requirements of its host, we concentrated on the leucine metabolic pathway. We show that leucine is a limiting factor for aphid growth and it displays a stimulatory feeding effect. Our metabolic analyses demonstrate that symbiotic aphids are able to respond to leucine starvation or excess by modulating the neosynthesis of this amino acid. At a molecular level, this response involves an early important transcriptional regulation (after 12 h of treatment) followed by a moderate change in the pLeu plasmid copy number. Both responses are no longer apparent after 7 days of treatment. These experimental data are discussed in the light of a re-annotation of the pLeu plasmid regulatory elements. Taken together, our data show that the response of B. aphidicola to the leucine demand of its host is multimodal and dynamically regulated, providing new insights concerning the genetic regulation capabilities of this bacterium in relation to its symbiotic functions.

Aphid resistance in Brassica crops: challenges, biotechnological progress and emerging possibilities

Aphids, (Hemiptera: Aphidoidea) a nefarious insect pest of Brassicaceae members including major vegetable and oilseed crops have coevolved with their host plant and emerged as most economically important insect pest of crop Brassicas. Their atypical feeding mechanism and unusual reproductive biology made them intractable to control below economic threshold level of damage to the crops. To a large extent aphid infestation is controlled by spraying agrochemicals of systemic mode of action and rarely by biological control. Use of systemic insecticides is highly cost intensive as well poses bigger threat of their incorporation in dietary chain. Breeding for genetic resistance against aphids has not been possible owing to the non-availability of resistance source within the crossable germplasms and lack of knowledge of the genetics of the trait. Genetic engineering with insect resistant transgenes seems to be the only potential avenue to address this difficult-to-accomplish breeding objective. Some success had been achieved in terms of developing aphid resistant cultivars through genetic engineering however, commercial utilization of such crops are still awaited. Thus protection of crops against aphids necessarily requires more research to identify either more effective insecticidal transgenes or biological phenomenon that can usher to new mechanism of resistance. The present review is an attempt to highlight the current status and possible avenues to develop aphid resistance in Brassicaceae crops.

Genome expansion and differential expression of amino acid transporters at the aphid/Buchnera symbiotic interface

In insects, some of the most ecologically important symbioses are nutritional symbioses that provide hosts with novel traits and thereby facilitate exploitation of otherwise inaccessible niches. One such symbiosis is the ancient obligate intracellular symbiosis of aphids with the γ-proteobacteria, Buchnera aphidicola. Although the nutritional basis of the aphid/Buchnera symbiosis is well understood, the processes and structures that mediate the intimate interactions of symbiotic partners remain uncharacterized. Here, using a de novo approach, we characterize the complement of 40 amino acid polyamine organocation (APC) superfamily member amino acid transporters (AATs) encoded in the genome of the pea aphid, Acyrthosiphon pisum. We find that the A. pisum APC superfamily is characterized by extensive gene duplications such that A. pisum has more APC superfamily transporters than other fully sequenced insects, including a ten paralog aphid-specific expansion of the APC transporter slimfast. Detailed expression analysis of 17 transporters selected on the basis of their phylogenetic relationship to five AATs identified in an earlier bacteriocyte expressed sequence tag study distinguished a subset of eight transporters that have been recruited for amino acid transport in bacteriocyte cells at the symbiotic interface. These eight transporters include transporters that are highly expressed and/or highly enriched in bacteriocytes and intriguingly, the four AATs that show bacteriocyte-enriched expression are all members of gene family expansions, whereas three of the four that are highly expressed but not enriched in bacteriocytes retain one-to-one orthology with transporters in other genomes. Finally, analysis of evolutionary rates within the large A. pisum slimfast expansion demonstrated increased rates of molecular evolution coinciding with two major shifts in expression: 1) a loss of gut expression and possibly a gain of bacteriocyte expression and 2) loss of expression in all surveyed tissues in asexual females. Taken together, our characterization of nutrient AATs at the aphid/Buchnera symbiotic interface provides the first examination of the processes and structures operating at the interface of an obligate intracellular insect nutritional symbiosis, offering unique insight into the types of genomic change that likely facilitated evolutionary maintenance of the symbiosis.

Genomic revelations of a mutualism: the pea aphid and its obligate bacterial symbiont

The symbiosis of the pea aphid Acyrthosphion pisum with the bacterium Buchnera aphidicola APS represents the best-studied insect obligate symbiosis. Here we present a refined picture of this symbiosis by linking pre-genomic observations to new genomic data that includes the complete genomes of the eukaryotic and prokaryotic symbiotic partners. In doing so, we address four issues central to understanding the patterns and processes operating at the A. pisum/Buchnera APS interface. These four issues include: (1) lateral gene transfer, (2) host immunity, (3) symbiotic metabolism, and (4) regulation.

Insect endosymbionts: manipulators of insect herbivore trophic interactions?

Throughout their evolutionary history, insects have formed multiple relationships with bacteria. Although many of these bacteria are pathogenic, with deleterious effects on the fitness of infected insects, there are also numerous examples of symbiotic bacteria that are harmless or even beneficial to their insect host. Symbiotic bacteria that form obligate or facultative associations with insects and that are located intracellularly in the host insect are known as endosymbionts. Endosymbiosis can be a strong driving force for evolution when the acquisition and maintenance of a microorganism by the insect host results in the formation of novel structures or changes in physiology and metabolism. The complex evolutionary dynamics of vertically transmitted symbiotic bacteria have led to distinctive symbiont genome characteristics that have profound effects on the phenotype of the host insect. Symbiotic bacteria are key players in insect-plant interactions influencing many aspects of insect ecology and playing a key role in shaping the diversification of many insect groups. In this review, we discuss the role of endosymbionts in manipulating insect herbivore trophic interactions focussing on their impact on plant utilisation patterns and parasitoid biology.

WRKY72-type transcription factors contribute to basal immunity in tomato and Arabidopsis as well as gene-for-gene resistance mediated by the tomato R gene Mi-1

WRKY transcription factors play a central role in transcriptional reprogramming associated with plant immune responses. However, due to functional redundancy, typically the contribution of individual members of this family to immunity is only subtle. Using microarray analysis, we found that the paralogous tomato WRKY genes SlWRKY72a and b are transcriptionally up-regulated during disease resistance mediated by the R gene Mi-1. Virus-induced gene silencing of these two genes in tomato resulted in a clear reduction of Mi-1-mediated resistance as well as basal defense against root-knot nematodes (RKN) and potato aphids. Using Arabidopsis T-DNA insertion mutants, we found that their Arabidopsis ortholog, AtWRKY72, is also required for full basal defense against RKN as well as to the oomycete Hyaloperonospora arabidopsidis. Despite their similar roles in basal defense against RKN in both tested plant species, WRKY72-type transcription factors in tomato, but not in Arabidopsis, clearly contributed to basal defense against the bacterial pathogen Pseudomonas syringae. Of the five R genes that we tested in tomato and Arabidopsis, only Mi-1 appeared to be dependent on WRKY72-type transcription factors. Interestingly, AtWRKY72 target genes, identified by microarray analysis of H. arabidopsidis-triggered transcriptional changes, appear to be largely non-responsive to analogs of the defense hormone salicylic acid (SA). Thus, similarly to Mi-1, which in part acts independently of SA, AtWRKY72 appears to utilize SA-independent defense mechanisms. We propose that WRKY72-type transcription factors play a partially conserved role in basal defense in tomato and Arabidopsis, a function that has been recruited to serve Mi-1-dependent immunity.

The Wolbachia endosymbiont as an anti-filarial nematode target

Human disease caused by parasitic filarial nematodes is a major cause of global morbidity. The parasites are transmitted by arthropod intermediate hosts and are responsible for lymphatic filariasis (elephantiasis) or onchocerciasis (river blindness). Within these filarial parasites are intracellular alpha-proteobacteria, Wolbachia, that were first observed almost 30 years ago. The obligate endosymbiont has been recognized as a target for anti-filarial nematode chemotherapy as evidenced by the loss of worm fertility and viability upon antibiotic treatment in an extensive series of human trials. While current treatments with doxycycline and rifampicin are not practical for widespread use due to the length of required treatments and contraindications, anti-Wolbachia targeting nevertheless appears a promising alternative for filariasis control in situations where current programmatic strategies fail or are unable to be delivered and it provides a superior efficacy for individual therapy. The mechanisms that underlie the symbiotic relationship between Wolbachia and its nematode hosts remain elusive. Comparative genomics, bioinfomatic and experimental analyses have identified a number of potential interactions, which may be drug targets. One candidate is de novo heme biosynthesis, due to its absence in the genome sequence of the host nematode, Brugia malayi, but presence in Wolbachia and its potential roles in worm biology. We describe this and several additional candidate targets, as well as our approaches for understanding the nature of the host-symbiont relationship.

Limited endosymbiont variation in Diuraphis noxia (Hemiptera: Aphididae) biotypes from the United States and South Africa

Symbiosis allows an insect access to imbalanced food sources on which other organisms cannot survive. A bacterial endosymbiont, Buchnera aphidicola, gives aphids the ability to feed on phloem depleted of certain essential amino acids by producing those required. Pseudogenes and lower plasmid copy numbers of essential amino acid genes in B. aphidicola, endosymbiont of the Russian wheat aphid, Diuraphis noxia (Kurdjumov) (Hemiptera: Aphididae), suggest that this symbiotic relationship is degenerating. The complete endosymbiont assemblages, copy numbers of plasmids (important in essential amino acid production), and sequence variation in B. aphidicola, from 10 Russian wheat aphid biotypes, were investigated. B. aphidicola was found to be monosymbiotic in the Russian wheat aphid biotypes and other Diuraphis species examined. An insert, occurring in an inverted repeat region on the leucine plasmid, was the only variation found in the approximately 10-kb B. aphidicola sequence analyzed from each Russian wheat aphid biotype. This inverted repeat was shown previously to be conserved within the family Aphididae. The insert occurred in B. aphidicola sequences isolated from four Russian wheat aphid biotypes. Copy numbers of the leucine plasmid differ between the South African and U.S. biotypes and were similar to previously reported values for biotypes from the same geographic regions. These results suggest that B. aphidicola may still contribute to Russian wheat aphid fitness when the aphid feeds on a variety of hosts.

Insect-symbiont systems: from complex relationships to biotechnological applications

Microbial symbiosis is a ubiquitous aspect of life and was a major element in the ability of insects to explore several adverse environments. To date, the study of symbiosis in insects has been impaired by the unculturability of most symbionts. However, some molecular methods represent powerful tools to help understand insect-microorganism associations and to disclose new symbiont-host systems. Beyond playing an essential role in nutrition and development of the insects, symbionts can produce bioactive compounds that protect the host against adverse environmental conditions, predators and/or direct competitors. Since the search for natural bioactive products and new enzymes is a developing area, understanding the diversity and nature of symbiont-host relationships paves the way for the exploitation of new resources in biotechnology. Furthermore, genetic transformation of the symbionts with genes that code for compounds that are toxic for pathogenic and phytopathogenic agents is also a promising area of application of the insect-symbiont relationships. The search for new bioactive compounds, the use of symbionts for pest and disease control and the molecular strategies applied for these purposes are issues of particular interest for innovative biotechnological applications and are addressed in the present review.

Prevalence of endosymbionts in Bemisia tabaci populations and their in vivo sensitivity to antibiotics

Bemisia tabaci can harbor both primary and secondary endosymbionts, and the specific endosymbionts can differ among different B. tabaci biotypes. This study determined (1) the prevalence of the primary endosymbiont Portiera aleyrodidarum and secondary endosymbionts Arsenophonus and Wolbachia in two invasive biotypes (B and Q) and one indigenous biotype (Cv) in China and (2) the in vivo effect of three antibiotics (tetracycline, ampicillin trihydrate, and rifampicin) against the endosymbionts; if an antibiotic substantially inhibits an endosymbiont, it could be used to determine the effect of that endosymbiont on B. tabaci. P. aleyrodidarum and Wolbachia were detected in all the three biotypes, while Arsenophonus was found only in the Q and Cv biotypes. P. aleyrodidarum was found in all tested individuals of the three biotypes. Infection rates of Wolbachia in the B, Cv, and Q biotypes were 58, 68, and 48%, respectively. The infection rate of Arsenophonus was 44% in the Q biotype but only 22% in the Cv biotype. The antibiotics failed to eliminate P. aleyrodidarum from any individual of the B, Cv, and Q biotypes but eliminated the secondary endosymbionts, Arsenophonus and Wolbachia, from 50 to 80% of the adult B. tabaci. The effect of the antibiotics depended on the species of endosymbiont, the antibiotic, the B. tabaci biotype, and various interactions between these factors. When used against Arsenophonus, the efficiency of rifampicin was better than ampicillin and tetracycline, regardless of B. tabaci biotype. When inactivating Wolbachia in Cv and Q biotypes, the efficiency tetracycline was better than ampicillin and rifampicin, and while the efficiency of tetracycline was better than rifampicin and ampicillin when they were used against Wolbachia in B biotype.

Cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways

Aspartokinase (Ask) exists within a variable network that supports the synthesis of 9 amino acids and a number of other important metabolites. Lysine, isoleucine, aromatic amino acids, and dipicolinate may arise from the ASK network or from alternative pathways. Ask proteins were subjected to cohesion group analysis, a methodology that sorts a given protein assemblage into groups in which evolutionary continuity is assured. Two subhomology divisions, ASK(alpha) and ASK(beta), have been recognized. The ASK(alpha) subhomology division is the most ancient, being widely distributed throughout the Archaea and Eukarya and in some Bacteria. Within an indel region of about 75 amino acids near the N terminus, ASK(beta) sequences differ from ASK(alpha) sequences by the possession of a proposed ancient deletion. ASK(beta) sequences are present in most Bacteria and usually exhibit an in-frame internal translational start site that can generate a small Ask subunit that is identical to the C-terminal portion of the larger subunit of a heterodimeric unit. Particularly novel are ask genes embedded in gene contexts that imply specialization for ectoine (osmotic agent) or aromatic amino acids. The cohesion group approach is well suited for the easy recognition of relatively recent lateral gene transfer (LGT) events, and many examples of these are described. Given the current density of genome representation for Proteobacteria, it is possible to reconstruct more ancient landmark LGT events. Thus, a plausible scenario in which the three well-studied and iconic Ask homologs of Escherichia coli are not within the vertical genealogy of Gammaproteobacteria, but rather originated via LGT from a Bacteroidetes donor, is supported.

Ultrastructural and molecular characterization of endosymbionts of the reed beetle genusMacroplea(Chrysomelidae, Donaciinae), and proposal of “CandidatusMacropleicola appendiculatae” and “CandidatusMacropleicola muticae”

Intracellular bacterial symbionts are known from various insect groups, particularly from those feeding on unbalanced diets, where the bacteria provide essential nutrients to the host. In the case of reed beetles (Coleoptera: Chrysomelidae, Donaciinae), however, the endosymbionts appear to be associated with specialized “glands” that secrete a material used for the beetles’ unusual water-tight cocoon. These glands were discovered over a century ago, but the bacteria they contain have yet to be characterized and placed in a phylogenetic context. Here, we describe the ultrastructure of two endosymbiotic species (“ Candidatus Macropleicola appendiculatae” and “ Candidatus Macropleicola muticae”) that reside in cells of the Malpighian tubules of the reed beetle species Macroplea appendiculata and Macroplea mutica , respectively. Fluorescent in situ hybridization using oligonucleotides targeting the 16S rRNA gene specific to Macroplea symbionts verified the localization of the symbionts in these organs. Phylogenetic analysis of 16S rRNA placed “Candidatus Macropleicola” in a clade of typically endosymbiotic Enterobacteriaceae (γ-proteobacteria). Finally, we discuss the evidence available for the hypothesis that the beetle larvae use a secretion produced by the bacteria for the formation of an underwater cocoon.

Microbial community profiling to investigate transmission of bacteria between life stages of the wood-boring beetle, Anoplophora glabripennis

Many insects harbor specific bacteria in their digestive tract, and these gut microbiota often play important roles in digestion and nutrient provisioning. While it is common for a given insect species to harbor a representative gut microbial community as a population, how this community is acquired and maintained from generation to generation is not known for most xylophagous insects, except termites. In this study, we examined acquisition of gut microbiota by the wood-feeding beetle, Anoplophora glabripennis, by identifying and comparing microbial community members among different life stages of the insect and with microbes it encounters in the environment. Automated ribosomal intergenic spacer analysis was employed to compare bacterial communities present in the egg and larval stages of A. glabripennis as well as with microbes found in the oviposition site and the surrounding woody tissue. Multivariate analyses were used to identify relationships between sample type and specific bacterial types (operational taxonomic units). From this analysis, bacteria that were derived from the environment, the oviposition site, and/or the egg were identified and compared with taxa found in larvae. Results showed that while some larval microbes were derived from environmental sources, other members of the larval microbial community appear to be vertically transmitted. These findings could lead to a better understanding of which microbial species are critical for the survival of this insect and to development of techniques that could be used to alter this community to disrupt the digestive physiology of the host insect as a biological control measure.

Selection for translational robustness in Buchnera aphidicola, endosymbiotic bacteria of aphids

Its strong intergenerational bottlenecks and effectively asexual reproduction have led Buchnera aphidicola, the endocellular symbiotic bacterium of aphids, to spectacular evolutionary and genomic changes in comparison with its free-living bacterial cousins. These changes summarize into high fixation rates of mildly deleterious destabilizing mutations. This predicts a sharp decline of its fitness and the consequent early demise of this endosymbiotic bacterium. Its survival for hundreds of millions of years casts doubt on genetic drift as the sole evolutionary force and seeks further explanation. We identify in Buchnera selection to increase the robustness of proteins to misfolding translation errors. Translational robustness varies between Buchnera lineages and protein functional categories. Metabolic proteins have been under selection for translational efficiency, whereas evolutionary rates of proteins involved in fundamental cellular processes have been largely determined by selection for translational robustness. We detect the strongest signal of translational robustness in B. aphidicola Cinara cedri with a very similar pattern to that inferred for the most common symbiotic ancestor of Buchnera lineages. This indicates that B. aphidicola Cinara cedri lineage may have probably reached the minimum evolutionary stable gene composition for endosymbiotic lifestyle. The evolutionary patterns from the comparative genomic analyses of these endosymbionts support a paradoxically complex dynamic for apparently simple genomes.

Bacterial communities of Bartonella-positive fleas: diversity and community assembly patterns

We investigated the bacterial communities of nine Bartonella-positive fleas (n = 6 Oropsylla hirsuta fleas and n = 3 Oropsylla montana fleas), using universal primers, clone libraries, and DNA sequencing. DNA sequences were used to classify bacteria detected in a phylogenetic context, to explore community assembly patterns within individual fleas, and to survey diversity patterns in dominant lineages.

Biochemistry and molecular biology of Arabidopsis-aphid interactions

To ensure their survival in natural habitats, plants must recognize and respond to a wide variety of insect herbivores. Aphids and other Hemiptera pose a particular challenge, because they cause relatively little direct tissue damage when inserting their slender stylets intercellularly to feed from the phloem sieve elements. Plant responses to this unusual feeding strategy almost certainly include recognition of aphid salivary components and the induction of phloem-specific defenses. Due to the excellent genetic and genomic resources that are available for Arabidopsis thaliana (Arabidopsis), this plant was chosen as a model system to study the metabolic and transcriptional responses to infestation by two aphids, Myzus persicae (green peach aphid, a broad generalist) and Brevicoryne brassicae (cabbage aphid, a crucifer-feeding specialist). Future research on Arabidopsis-aphid interactions will lead to the identification of aphid-specific elicitors, components of the defense-signaling pathway, and additional metabolic responses that are induced by aphid infestation.

Antibiotic treatment of the tick vector Amblyomma americanum reduced reproductive fitness

Background

The lone star tick Amblyomma americanum is a common pest and vector of infectious diseases for humans and other mammals in the southern and eastern United States. A Coxiella sp. bacterial endosymbiont was highly prevalent in both laboratory-reared and field-collected A. americanum. The Coxiella sp. was demonstrated in all stages of tick and in greatest densities in nymphs and adult females, while a Rickettsia sp. was less prevalent and in lower densities when present.

Methodology/Principal Findings

We manipulated the numbers of both bacterial species in laboratory-reared A. americanum by injecting engorged nymphs or engorged, mated females with single doses of an antibiotic (rifampin or tetracycline) or buffer alone. Burdens of the bacteria after molting or after oviposition were estimated by quantitative polymerase chain reaction with primers and probes specific for each bacterial species or, as an internal standard, the host tick. Post-molt adult ticks that had been treated with rifampin or tetracycline had lower numbers of the Coxiella sp. and Rickettsia sp. and generally weighed less than ticks that received buffer alone. Similarly, after oviposition, females treated previously with either antibiotic had lower burdens of both bacterial species in comparison to controls. Treatment of engorged females with either antibiotic was associated with prolonged time to oviposition, lower proportions of ticks that hatched, lower proportions of viable larvae among total larvae, and lower numbers of viable larvae per tick. These fitness estimators were associated with reduced numbers of the Coxiella sp. but not the Rickettsia sp.

Conclusion/Significance

The findings indicate that the Coxiella sp. is a primary endosymbiont, perhaps provisioning the obligately hematophagous parasites with essential nutrients. The results also suggest that antibiotics could be incorporated into an integrated pest management plan for control of these and other tick vectors of disease.

Endosymbiosis in statu nascendi: close phylogenetic relationship between obligately endosymbiotic and obligately free-living Polynucleobacter strains (Betaproteobacteria)

Bacterial strains affiliated to the phylogenetically shallow subcluster C (PnecC) of the Polynucleobacter cluster, which is characterized by a minimal 16S rRNA gene sequence similarity of approximately 98.5%, have been reported to occur as obligate endosymbionts of ciliates (Euplotes spp.), as well as to occur as free-living cells in the pelagic zone of freshwater habitats. We investigated if these two groups of closely related bacteria represent strains fundamentally differing in lifestyle, or if they simply represent different stages of a facultative endosymbiotic lifestyle. The phylogenetic analysis of 16S rRNA gene and 16S-23S ITS sequences of five endosymbiont strains from two different Euplotes species and 40 pure culture strains demonstrated host-species-specific clustering of the endosymbiont sequences within the PnecC subcluster. The sequences of the endosymbionts showed characteristics indicating an obligate endosymbiotic lifestyle. Cultivation experiments revealed fundamental differences in physiological adaptations, and determination of the genome sizes indicated a slight size reduction in endosymbiotic strains. We conclude that the two groups of PnecC bacteria represent obligately free-living and obligately endosymbiotic strains, respectively, and do not represent different stages of the same complex life cycle. These closely related strains occupy completely separated ecological niches. To our best knowledge, this is the closest phylogenetic relationship between obligate endosymbionts and obligately free-living bacteria ever revealed.

Soil potassium deficiency affects soybean phloem nitrogen and soybean aphid populations

The soybean aphid is an invasive pest in the midwest United States, with frequent population outbreaks. Previous work has shown that aphid population densities are higher on potassium-deficient soybean than on healthy soybean. The experiments reported here test the hypotheses that the potassium nutrition of the host plant affects the forms of phloem nitrogen available to soybean aphids, and subsequently, their abundance. In field surveys and an exclusion cage study when aphid populations were high, soybean plants with potassium deficiency symptoms had a higher density of soybean aphids than plants without deficiency symptoms. In clip cage experiments, this effect was caused by earlier aphid reproduction and higher numbers of aphid nymphs per mother on plants growing in lower-potassium soil. In phloem exudation samples, the percentage of asparagine, an important amino acid for aphid nutrition, increased with decreasing soil potassium, perhaps because of potassium's role in the nitrogen use of the plant. Taken together, these results show that soybean potassium deficiency can lead to higher populations of soybean aphid through a bottom-up effect. A possible mechanism for this relationship is that soybean potassium deficiency improves the nitrogen nutrition of these N-limited insects. By releasing these herbivores from N limitation, host plant potassium deficiency may allow soybean aphid populations to reach higher levels more rapidly in the field.

Co-cladogenesis spanning three phyla: leafhoppers (Insecta: Hemiptera: Cicadellidae) and their dual bacterial symbionts

Endosymbioses are a major form of biological complexity affecting the ecological and evolutionary diversification of many eukaryotic groups. These associations are exemplified by nutritional symbioses of insects for which phylogenetic studies have demonstrated numerous cases of long-term codiversification between a bacterial and a host lineage. Some insects, including most leafhoppers (Insecta: Hemiptera: Cicadellidae), have more than one bacterial symbiont within specialized host cells, raising questions regarding the patterns of codiversification of these multiple partners and the evolutionary persistence of complex symbiotic systems. Previous studies reported the presence of two dominant symbiont types in a member of the leafhopper subfamily Cicadellinae (sharpshooters). In this study, 16S rRNA sequences were obtained and used to examine the occurrence and evolutionary relationships of the two dominant symbiont types across 29 leafhopper species. Candidatus Sulcia muelleri (Bacteroidetes) was detected in all leafhopper species examined, a finding that is consistent with a previous report of its ancient association with the Auchenorrhyncha (a grouping that includes leafhoppers, treehoppers, cicadas, planthoppers, and spittlebugs). Baumannia cicadellinicola (Proteobacteria), previously known from only five sharpshooter species, was found only in the sharpshooter tribes Cicadellini and Proconiini, as well as in the subfamily Phereurhininae. Mitochondrial and nuclear gene sequences were obtained and used to reconstruct host phylogenies. Analyses of host and symbiont data sets support a congruent evolutionary history between sharpshooters, Sulcia and Baumannia and thus provide the first strong evidence for long-term co-inheritance of multiple symbionts during the diversification of a eukaryotic host. Sulcia shows a fivefold lower rate of 16S rDNA sequence divergence than does Baumannia for the same host pairs. The term 'coprimary' symbiont is proposed for such cases.

Molecular Interactions between Bacterial Symbionts and Their Hosts

Symbiotic bacteria are important in animal hosts, but have been largely overlooked as they have proved difficult to culture in the laboratory. Approaches such as comparative genomics and real-time PCR have provided insights into the molecular mechanisms that underpin symbiont-host interactions. Studies on the heritable symbionts of insects have yielded valuable information about how bacteria infect host cells, avoid immune responses, and manipulate host physiology. Furthermore, some symbionts use many of the same mechanisms as pathogens to infect hosts and evade immune responses. Here we discuss what is currently known about the interactions between bacterial symbionts and their hosts.

Antagonistic interactions between honey bee bacterial symbionts and implications for disease

Background

Honey bees, Apis mellifera, face many parasites and pathogens and consequently rely on a diverse set of individual and group-level defenses to prevent disease. One route by which honey bees and other insects might combat disease is through the shielding effects of their microbial symbionts. Bees carry a diverse assemblage of bacteria, very few of which appear to be pathogenic. Here we explore the inhibitory effects of these resident bacteria against the primary bacterial pathogen of honey bees, Paenibacillus larvae.

Results

Here we isolate, culture, and describe by 16S rRNA and protein-coding gene sequences 61 bacterial isolates from honey bee larvae, reflecting a total of 43 distinct bacterial taxa. We culture these bacteria alongside the primary larval pathogen of honey bees, Paenibacillus larvae, and show that many of these isolates severely inhibit the growth of this pathogen. Accordingly, symbiotic bacteria including those described here are plausible natural antagonists toward this widespread pathogen.

Conclusion

The results suggest a tradeoff in social insect colonies between the maintenance of potentially beneficial bacterial symbionts and deterrence at the individual and colony level of pathogenic species. They also provide a novel mechanism for recently described social components behind disease resistance in insect colonies, and point toward a potential control strategy for an important bee disease.

Plasmids in the aphid endosymbiont Buchnera aphidicola with the smallest genomes. A puzzling evolutionary story

Buchnera aphidicola, the primary endosymbiont of aphids, has undergone important genomic and biochemical changes as an adaptation to intracellular life. The most important structural changes include a drastic genome reduction and the amplification of genes encoding key enzymes for the biosynthesis of amino acids by their translocation to plasmids. Molecular characterization through different aphid subfamilies has revealed that the genes involved in leucine and tryptophan biosynthesis show a variable fate, since they can be located on plasmids or on the chromosome in different lineages. This versatility contrasts with the genomic stasis found in three distantly related B. aphidicola strains already sequenced. We present the analysis of three B. aphidicola strains (BTg, BCt and BCc) belonging to aphids from different tribes of the subfamily Lachninae, that was estimated to harbour the bacteria with the smallest genomes. The presence of both leucine and tryptophan plasmids in BTg, a chimerical leucine-tryptophan plasmid in BCt, and only a leucine plasmid in BCc, indicates the existence of many recombination events in a recA minus bacterium. In addition, these B. aphidicola plasmids are the simplest described in this species, indicating that plasmids are also involved in the genome shrinkage process.

Nutritional homeostasis and indispensable amino acid sensing: a new solution to an old puzzle

Indispensable amino acids are neither synthesized nor stored in animals and are rapidly depleted when not provided by the diet. To maintain homeostasis, organisms must sense deficiency of an indispensable amino acid and implement a repletion strategy. In rats and birds, the anterior piriform cortex houses the detector, but its mechanism has evaded description for >50 years. Recently, rapid detection of amino acid depletion was shown behaviorally when naïve animals, pre-fed a low nitrogen diet, terminated their first deficient meal within 20 min. The general amino acid control system of yeast, which is activated by amino acid deprivation via deacylated tRNA, was found to be active in rodent brain, showing conservation of amino acid sensory mechanisms across eukaryotic species.

Biology bacteriocyte-associated endosymbionts of plant sap-sucking insects

Psyllids, whiteflies, aphids, and mealybugs are members of the suborder Sternorrhyncha and share a common property, namely the utilization of plant sap as their food source. Each of these insect groups has an obligatory association with a different prokaryotic endosymbiont, and the association is the result of a single infection followed by maternal, vertical transmission of the endosymbionts. The result of this association is the domestication of the free-living bacterium to serve the purposes of the host, namely the synthesis of essential amino acids. This domestication is probably in all cases accompanied by a major reduction in genome size. The different properties of the genomes and fragments of the genomes of these endosymbionts suggest that there are different constraints on the permissible evolutionary changes that are probably a function of the gene repertoire of the endosymbiont ancestor and the gene losses that occurred during the reduction of genome size.

Chromosomal stasis versus plasmid plasticity in aphid endosymbiont Buchnera aphidicola

The study of three genomes of the aphid endosymbiont Buchnera aphidicola has revealed an extraordinary stasis: conservation of gene order and genetic composition of the chromosome, while the chromosome size and number of genes has reduced. The reduction in genome size appears to be ongoing since some lineages we now know to have even smaller chromosomes than the first B. aphidicola analysed. The current sequencing by our group of one of these smaller genomes with an estimated size of 450 kb, and its comparison with the other three available genomes provide insights into the nature of processes involved in shrinkage. We discuss whether B. aphidicola might be driven to extinction and be replaced by secondary aphid endosymbionts. In some lineages, genes encoding key enzymes in the pathways leading to tryptophan and leucine biosynthesis (trpEG and leuABCD, respectively) are located on plasmids, rather than the main chromosome. In contrast to the stasis of the main chromosome, plasmid genes have frequently been transferred to the main chromosome and undergone other gene rearrangements. We propose a two-step scenario to explain these contrasting modes of evolution. Essential genes may have escaped regulation by moving to plasmids in a moving B. aphidicola ancestor. B. aphidicola became polyploidy at a given stage of its evolution and plasmid genes have been transferred to the main chromosome through several independent events.

Mobile DNA in obligate intracellular bacteria

The small genomes of obligate intracellular bacteria are often presumed to be impervious to mobile DNA and the fluid genetic processes that drive diversification in free-living bacteria. Categorized by reductive evolution and streamlining, the genomes of some obligate intracellular bacteria manifest striking degrees of stability and gene synteny. However, recent findings from complete genome sequences of obligate intracellular species and their mobile genetic associates favour the abandonment of these wholesale terms for a more complex and tantalizing picture.

Functional genomics of Buchnera and the ecology of aphid hosts

In many animal groups, mutualistic bacterial symbionts play a central role in host ecology, by provisioning rare nutrients and thus enabling specialization on restricted diets. Among such symbionts, genomic studies are most advanced for Buchnera, the obligate symbiont of aphids, which feed on phloem sap. The contents of the highly reduced Buchnera genomes have verified its role in aphid nutrition. Comparisons of Buchnera gene sets indicate ongoing, irreversible gene losses that are expected to affect aphid nutritional needs. Furthermore, almost all regulatory genes have been eliminated, raising the question of whether and how gene expression responds to environmental change. Microarray studies on genome-wide expression indicate that Buchnera has evolved some constitutive changes in gene expression: homologues of heat stress genes have elevated transcript levels in Buchnera (relative to other bacteria) even in the absence of stress. Additionally, the microarray results indicate that responses to heat stress and to amino acid availability are both few and modest. Observed responses are consistent with control by the few ancestral regulators retained in the genome. Initial studies on the role of host genes in mediating the symbiosis reveal distinctive expression patterns in host cells harbouring Buchnera. In the near future, a complete genome of pea aphid will accelerate progress in understanding the functional integration of aphid and Buchnera genomes. Although information for other insect symbioses is relatively limited, studies on symbionts of carpenter ants and tsetse flies indicate many similarities to Buchnera.

Regulation of transcription in a reduced bacterial genome: nutrient-provisioning genes of the obligate symbiont Buchnera aphidicola

Buchnera aphidicola, the obligate symbiont of aphids, has an extremely reduced genome, of which about 10% is devoted to the biosynthesis of essential amino acids needed by its hosts. Most regulatory genes for these pathways are absent, raising the question of whether and how transcription of these genes responds to the major shifts in dietary amino acid content encountered by aphids. Using full-genome microarrays for B. aphidicola of the host Schizaphis graminum, we examined transcriptome responses to changes in dietary amino acid content and then verified behavior of individual transcripts using quantitative reverse transcriptase PCR. The only gene showing a consistent and substantial (>twofold) response was metE, which underlies methionine biosynthesis and which is the only amino acid biosynthetic gene retaining its ancestral regulator (metR). In another aphid host, Acyrthosiphon pisum, B. aphidicola has no functional metR and shows no response in metE transcript levels to changes in amino acid concentrations. Thus, the only substantial transcriptional response involves the one gene for which an ancestral regulator is retained. This result parallels that from a previous study on heat stress, in which only the few genes retaining the global heat shock promoter showed responses in transcript abundance. The irreversible losses of transcriptional regulators constrain ability to alter gene expression in the context of environmental fluctuations affecting the symbiotic partners.