The link between independent acquisition of intracellular gamma-endosymbionts and concerted evolution in Tremblaya princeps

Endogenous Plasmids and Chromosomal Genome Reduction in the Cardinium Endosymbiont of Dermatophagoides farinae

Cardinium bacteria are well known as endosymbionts that infect a wide range of arthropods and can manipulate host reproduction to promote their vertical transmission. As intracellular bacteria, Cardinium species undergo dramatic genome evolution, especially their chromosomal genome reduction. Although Cardinium plasmids have been reported to harbor important genes, the role of these plasmids in the genome evolution is yet to be fully understood. In this study, 2 genomes of Cardinium endosymbiont bacteria in astigmatic mites were de novo assembled, including the complete circular chromosomal genome of Cardinium sp. DF that was constructed in high quality using high-coverage long-read sequencing data. Intriguingly, 2 circular plasmids were assembled in Cardinium sp. DF and were identified to be endogenous for over 10 homologous genes shared with the chromosomal genome. Comparative genomics analysis illustrated an outline of the genome evolution of Cardinium bacteria, and the in-depth analysis of Cardinium sp. DF shed light on the multiple roles of endogenous plasmids in the molecular process of the chromosomal genome reduction. The endogenous plasmids of Cardinium sp. DF not only harbor massive homologous sequences that enable homologous recombination with the chromosome, but also can provide necessary functional proteins when the coding genes decayed in the chromosomal genome. IMPORTANCE As bacterial endosymbionts, Cardinium typically undergoes genome reduction, but the molecular process is still unclear, such as how plasmids get involved in chromosome reduction. Here, we de novo assembled 2 genomes of Cardinium in astigmatic mites, especially the chromosome of Cardinium sp. DF was assembled in a complete circular DNA using high-coverage long-read sequencing data. In the genome assembly of Cardinium sp. DF, 2 circular endogenous plasmids were identified to share at least 10 homologous genes with the chromosomal genome. In the comparative analysis, we identified a range of genes decayed in the chromosomal genome of Cardinium sp. DF but preserved in the 2 plasmids. Taken together with in-depth analyses, our results unveil that the endogenous plasmids harbor homologous sequences of chromosomal genome and can provide a structural basis of homologous recombination. Overall, this study reveals that endogenous plasmids participate in the ongoing chromosomal genome reduction of Cardinium sp. DF.

The Phylosymbiosis Pattern Between the Fig Wasps of the Same Genus and Their Associated Microbiota

Microbial communities can be critical for many metazoans, which can lead to the observation of phylosymbiosis with phylogenetically related species sharing similar microbial communities. Most of the previous studies on phylosymbiosis were conducted across the host families or genera. However, it is unclear whether the phylosymbiosis signal is still prevalent at lower taxonomic levels. In this study, 54 individuals from six species of the fig wasp genus Ceratosolen (Hymenoptera: Agaonidae) collected from nine natural populations and their associated microbiota were investigated. The fig wasp species were morphologically identified and further determined by mitochondrial CO1 gene fragments and nuclear ITS2 sequences, and the V4 region of 16S rRNA gene was sequenced to analyze the bacterial communities. The results suggest a significant positive correlation between host genetic characteristics and microbial diversity characteristics, indicating the phylosymbiosis signal between the phylogeny of insect hosts and the associated microbiota in the lower classification level within a genus. Moreover, we found that the endosymbiotic Wolbachia carried by fig wasps led to a decrease in bacterial diversity of host-associated microbial communities. This study contributes to our understanding of the role of host phylogeny, as well as the role of endosymbionts in shaping the host-associated microbial community.

Portiera Gets Wild: Genome Instability Provides Insights into the Evolution of Both Whiteflies and Their Endosymbionts

Whiteflies (Hemiptera: Sternorrhyncha: Aleyrodidae) are a superfamily of small phloem-feeding insects. They rely on their primary endosymbionts "Candidatus Portiera aleyrodidarum" to produce essential amino acids not present in their diet. Portiera has been codiverging with whiteflies since their origin and therefore reflects its host's evolutionary history. Like in most primary endosymbionts, the genome of Portiera stays stable across the Aleyrodidae superfamily after millions of years of codivergence. However, Portiera of the whitefly Bemisia tabaci has lost the ancestral genome order, reflecting a rare event in the endosymbiont evolution: the appearance of genome instability. To gain a better understanding of Portiera genome evolution, identify the time point in which genome instability appeared and contribute to the reconstruction of whitefly phylogeny, we developed a new phylogenetic framework. It targeted five Portiera genes and determined the presence of the DNA polymerase proofreading subunit (dnaQ) gene, previously associated with genome instability, and two alternative gene rearrangements. Our results indicated that Portiera gene sequences provide a robust tool for studying intergenera phylogenetic relationships in whiteflies. Using these new framework, we found that whitefly species from the Singhiella, Aleurolobus, and Bemisia genera form a monophyletic tribe, the Aleurolobini, and that their Portiera exhibit genome instability. This instability likely arose once in the common ancestor of the Aleurolobini tribe (at least 70 Ma), drawing a link between the appearance of genome instability in Portiera and the switch from multibacteriocyte to a single-bacteriocyte mode of inheritance in this tribe.

Mapping the bacterial metabolic niche space

The rise in the availability of bacterial genomes defines a need for synthesis: abstracting from individual taxa, to see larger patterns of bacterial lifestyles across systems. A key concept for such synthesis in ecology is the niche, the set of capabilities that enables a population's persistence and defines its impact on the environment. The set of possible niches forms the niche space, a conceptual space delineating ways in which persistence in a system is possible. Here we use manifold learning to map the space of metabolic networks representing thousands of bacterial genera. The results suggest a metabolic niche space comprising a collection of discrete clusters and branching manifolds, which constitute strategies spanning life in different habitats and hosts. We further demonstrate that communities from similar ecosystem types map to characteristic regions of this functional coordinate system, permitting coarse-graining of microbiomes in terms of ecological niches that may be filled.

The Diversity of Symbiotic Systems in Scale Insects

Most scale insects, like many other plant sap-sucking hemipterans, harbor obligate symbionts of bacterial or fungal origin, which synthesize and provide the host with substances missing in their restricted diet. Histological, ultrastructural, and molecular analyses have revealed that scale insects differ in the type of symbionts, the localization of symbionts in the host body, and the mode of transmission of symbionts from one generation to the next. Symbiotic microorganisms may be distributed in the cells of the fat body, midgut epithelium, inside the cells of other symbionts, or the specialized cells of a mesodermal origin, termed bacteriocytes. In most scale insects, their symbiotic associates are inherited transovarially, wherein the mode of transmission may have a different course-the symbionts may invade larval ovaries containing undifferentiated germ cells or ovaries of adult females containing vitellogenic or choriogenic oocytes.

Molecular characterization, ultrastructure, and transovarial transmission of Tremblaya phenacola in six mealybugs of the Phenacoccinae subfamily (Insecta, Hemiptera, Coccomorpha)

Mealybugs (Hemiptera, Coccomorpha: Pseudococcidae) are plant sap-sucking insects which require close association with nutritional microorganisms for their proper development and reproduction. Here, we present the results of histological, ultrastructural, and molecular analyses of symbiotic systems of six mealybugs belonging to the Phenacoccinae subfamily: Phenacoccus aceris, Rhodania porifera, Coccura comari, Mirococcus clarus, Peliococcus calluneti, and Ceroputo pilosellae. Molecular analyses based on bacterial 16S rRNA genes have revealed that all the investigated species of Phenacoccinae are host to only one type of symbiotic bacteria-a large pleomorphic betaproteobacteria-Tremblaya phenacola. In all the species examined, bacteria are localized in the specialized cells of the host-insect termed bacteriocytes and are transovarially transmitted between generations. The mode of transovarial transmission is similar in all of the species investigated. Infection takes place in the neck region of the ovariole, between the tropharium and vitellarium. The co-phylogeny between mealybugs and bacteria Tremblaya has been also analyzed.

Unity Makes Strength: A Review on Mutualistic Symbiosis in Representative Insect Clades

Settled on the foundations laid by zoologists and embryologists more than a century ago, the study of symbiosis between prokaryotes and eukaryotes is an expanding field. In this review, we present several models of insect⁻bacteria symbioses that allow for the detangling of most known features of this distinctive way of living, using a combination of very diverse screening approaches, including molecular, microscopic, and genomic techniques. With the increasing the amount of endosymbiotic bacteria genomes available, it has been possible to develop evolutionary models explaining the changes undergone by these bacteria in their adaptation to the intracellular host environment. The establishment of a given symbiotic system can be a root cause of substantial changes in the partners' way of life. Furthermore, symbiont replacement and/or the establishment of bacterial consortia are two ways in which the host can exploit its interaction with environmental bacteria for endosymbiotic reinvigoration. The detailed study of diverse and complex symbiotic systems has revealed a great variety of possible final genomic products, frequently below the limit considered compatible with cellular life, and sometimes with unanticipated genomic and population characteristics, raising new questions that need to be addressed in the near future through a wider exploration of new models and empirical observations.

Can social partnerships influence the microbiome? Insights from ant farmers and their trophobiont mutualists

Mutualistic interactions with microbes have played a crucial role in the evolution and ecology of animal hosts. However, it is unclear what factors are most important in influencing particular host–microbe associations. While closely related animal species may have more similar microbiota than distantly related species due to phylogenetic contingencies, social partnerships with other organisms, such as those in which one animal farms another, may also influence an organism's symbiotic microbiome. We studied a mutualistic network of Brachymyrmex and Lasius ants farming several honeydew‐producing Prociphilus aphids and Rhizoecus mealybugs to test whether the mutualistic microbiomes of these interacting insects are primarily correlated with their phylogeny or with their shared social partnerships. Our results confirm a phylogenetic signal in the microbiomes of aphid and mealybug trophobionts, with each species harbouring species‐specific endosymbiont strains of Buchnera (aphids), Tremblaya and Sodalis (mealybugs), and Serratia (both mealybugs and aphids) despite being farmed by the same ants. This is likely explained by strict vertical transmission of trophobiont endosymbionts between generations. In contrast, our results show the ants’ microbiome is possibly shaped by their social partnerships, with ants that farm the same trophobionts also sharing strains of sugar‐processing Acetobacteraceae bacteria, known from other honeydew‐feeding ants and which likely reside extracellularly in the ants’ guts. These ant–microbe associations are arguably more “open” and subject to horizontal transmission or social transmission within ant colonies. These findings suggest that the role of social partnerships in shaping a host's symbiotic microbiome can be variable and is likely dependent on how the microbes are transmitted across generations.

Yeast-like microorganisms in the scale insect Kermes quercus (Insecta, Hemiptera, Coccomorpha: Kermesidae). Newly acquired symbionts?

Scale insects, like other plant sap-consumers, are host to symbiotic microorganisms which provide them with the substances missing from their diet. In contrast to most scale insects, Kermes quercus (Linnaeus) was regarded as asymbiotic. Our histological and ultrastructural observations show that in the body of the feeding stages of K. quercus collected in two locations (Warsaw and Cracow), numerous yeast-like microorganisms occur. These microorganisms were localized in the cytoplasm of fat body cells. The yeast-like microorganisms were observed neither in other organs of the host insect nor in the eggs. These microorganisms did not cause any damage to the structure of the ovaries and the course of oogenesis of the host insect. The females infected by them produced about 1300 larvae. The lack of these microorganisms in the cytoplasm of eggs indicates that they are not transmitted transovarially from mother to offspring. Molecular analyses indicated that the microorganisms which reside in the body of K. quercus are closely related to the entomopathogenic fungi Cordyceps and Ophiocordyceps, which belong to the Sordariomycetes class within the Ascomycota. The role of yeast-like microorganisms to their host insects remains unknown; however, it has been suggested that they may represent newly acquired symbionts.

Tremblaya phenacola PPER: an evolutionary beta-gammaproteobacterium collage

Many insects rely on bacterial endosymbionts to obtain nutrients that are scarce in their highly specialized diets. The most surprising example corresponds to the endosymbiotic system found in mealybugs from subfamily Pseudococcinae in which two bacteria, the betaproteobacterium 'Candidatus Tremblaya princeps' and a gammaproteobacterium, maintain a nested endosymbiotic consortium. In the sister subfamily Phenacoccinae, however, a single beta-endosymbiont, 'Candidatus Tremblaya phenacola', has been described. In a previous study, we detected a trpB gene of gammaproteobacterial origin in 'Ca. Tremblaya phenacola' from two Phenacoccus species, apparently indicating an unusual case of horizontal gene transfer (HGT) in a bacterial endosymbiont. What we found by sequencing the genome of 'Ca. Tremblaya phenacola' PPER, single endosymbiont of Phenacoccus peruvianus, goes beyond a HGT phenomenon. It rather represents a genome fusion between a beta and a gammaproteobacterium, followed by massive rearrangements and loss of redundant genes, leading to an unprecedented evolutionary collage. Mediated by the presence of several repeated sequences, there are many possible genome arrangements, and different subgenomic sequences might coexist within the same population.

Et tu, Brute? Not Even Intracellular Mutualistic Symbionts Escape Horizontal Gene Transfer

Many insect species maintain mutualistic relationships with endosymbiotic bacteria. In contrast to their free-living relatives, horizontal gene transfer (HGT) has traditionally been considered rare in long-term endosymbionts. Nevertheless, meta-omics exploration of certain symbiotic models has unveiled an increasing number of bacteria-bacteria and bacteria-host genetic transfers. The abundance and function of transferred loci suggest that HGT might play a major role in the evolution of the corresponding consortia, enhancing their adaptive value or buffering detrimental effects derived from the reductive evolution of endosymbionts’ genomes. Here, we comprehensively review the HGT cases recorded to date in insect-bacteria mutualistic consortia, and discuss their impact on the evolutionary success of these associations.

Inside Out: Archaeal Ectosymbionts Suggest a Second Model of Reduced-Genome Evolution

Reduced-genome symbionts and their organelle counterparts, which have even smaller genomes, are essential to the lives of many organisms. But how and why have these genomes become so small? Endosymbiotic genome reduction is a product of isolation within the host, followed by massive pseudogenization and gene loss often including DNA repair mechanisms. This phenomenon can be observed in insect endosymbionts such as the bacteria Carsonella ruddii and Buchnera aphidicola. Yet endosymbionts are not the only organisms with reduced genomes. Thermophilic microorganisms experience selective pressures that cause their genomes to become more compact and efficient. Nanoarchaea are thermophilic archaeal ectosymbionts that live on the surface of archaeal hosts. Their genomes, a full order of magnitude smaller than the Escherichia coli genome, are very small and efficient. How have the genomes of nanoarchaea and late-stage insect endosymbionts, which live in drastically different environments, come to mirror each other in both genome size and efficiency? Because of their growth at extreme temperatures and their exterior association with their host, nanoarchaea appear to have experienced genome reduction differently than mesophilic insect endosymbionts. We suggest that habitat-specific mechanisms of genome reduction result in fundamentally different pathways for these two groups of organisms. With this assertion, we propose two pathways of symbiosis-driven genome reduction; isolation-symbiosis experienced by insect endosymbionts and thermal-symbiosis experienced by nanoarchaea.

Bacteria belonging to the genus Burkholderia are obligatory symbionts of the eriococcids Acanthococcus aceris Signoret, 1875 and Gossyparia spuria (Modeer, 1778) (Insecta, Hemiptera, Coccoidea)

In the fat body cells of the scale insects, Gossyparia spuria and Acanthococcus aceris, numerous rod-shaped symbiotic bacteria occur. Molecular analyses have revealed that these microorganisms are closely related to the widely distributed bacterium Burkholderia. Ultrastructural observations have revealed that the bacteria are transovarially (vertically) transmitted from the mother to offspring. The microorganisms leave the fat body cells and invade ovarioles containing vitellogenic oocytes. They pass through the follicular epithelium in the neck region of the ovariole and enter the perivitelline space. Next, the symbionts infest the anterior region of the oocyte.