Molecular phylogeny of intracellular symbiotic Gammaproteobacteria in insects

Many groups of insects harbor mutualistic intracellular bacteria. These bacteria originated mainly from two bacterial phyla: Bacteroidetes and Proteobacteria. The thesis is focused on phylogeny of Enterobacteriaceae - the most diverse group of endosymbiotic bacteria within Gammaproteobacteria. The study brings new phylogenetical data on "primary" symbionts and summarizes the current state of knowledge on their phylogeny, evolution and diversity

Multiple origins of endosymbiosis within the Enterobacteriaceae (gamma-Proteobacteria): convergence of complex phylogenetic approaches

A complex phylogenomic analysis of Enterobacteriaceae (50 taxa, 69 genes) was conducted to investigate origins of obligate intracellular symbionts within this symbiont-rich group of bacteria. Resulting topologies confirmed at least four independent origins of endosymbiosis within the Enterobacteriaceae and suggest origins of symbionts from phenotypically various bacterial ancestors including gut and pathogenic bacteria or facultative symbionts

Genomic and Cellular Integration in the Tripartite Nested Mealybug Symbiosis

The PhD thesis is composed of three publications on genomic, metabolic, and cellular integration between the host and its symbionts in the tripartite nested mealybug system. The articles revealed a path to an intimate endosymbiosis that can be compared to what we think happened before (and to some extent after) bacterial ancestors of key eukaryotic organelles, mitochondria and plastids, became highly integrated into their host cells. I argue that these much younger symbioses may tell us something about how the mitochondria and plastids came to be, at the very least by revealing what types of evolutionary events are possible as stable intracellular relationships proceed along the path of integration

Evolutionary origins of intracellular symbionts in arthropods

Intracellular symbionts are widespread among arthropods, particularly within insects. Obligate symbiotic associations are known to have originated multiple times between the arthropods feeding on nutrient-poor diets and bacteria from various groups. However, exact phylogenetic positions and relationships among these symbiotic lineages are mostly unclear or vague. This thesis consists of an exemplary case study on the most symbiont-rich bacterial group, Enterobacteriaceae, already published in BMC Biology. It uses advanced phylogenetic tools and extended taxonomic sample to establish phylogenetic relationships among individual symbiotic lineages and their phylogenetic affinity to freeliving relatives. To provide it with broader background, the publication is accompanied by a review on general evolutionary forces influencing origin and maintenance of intracellular symbiosis in arthropods. Apart from overviewing the current known diversity of the symbiotic bacteria, it also points out specific drawbacks in inferring symbionts phylogeny and consequences that can phylogeny have on our understanding of intracellular symbiosis

Multiple origins of endosymbiosis within the Enterobacteriaceae (γ-Proteobacteria): convergence of complex phylogenetic approaches

Abstract Background The bacterial family Enterobacteriaceae gave rise to a variety of symbiotic forms, from the loosely associated commensals, often designated as secondary (S) symbionts, to obligate mutualists, called primary (P) symbionts. Determination of the evolutionary processes behind this phenomenon has long been hampered by the unreliability of phylogenetic reconstructions within this group of bacteria. The main reasons have been the absence of sufficient data, the highly derived nature of the symbiont genomes and lack of appropriate phylogenetic methods. Due to the extremely aberrant nature of their DNA, the symbiotic lineages within Enterobacteriaceae form long branches and tend to cluster as a monophyletic group. This state of phylogenetic uncertainty is now improving with an increasing number of complete bacterial genomes and development of new methods. In this study, we address the monophyly versus polyphyly of enterobacterial symbionts by exploring a multigene matrix within a complex phylogenetic framework. Results We assembled the richest taxon sampling of Enterobacteriaceae to date (50 taxa, 69 orthologous genes with no missing data) and analyzed both nucleic and amino acid data sets using several probabilistic methods. We particularly focused on the long-branch attraction-reducing methods, such as a nucleotide and amino acid data recoding and exclusion (including our new approach and slow-fast analysis), taxa exclusion and usage of complex evolutionary models, such as nonhomogeneous model and models accounting for site-specific features of protein evolution (CAT and CAT+GTR). Our data strongly suggest independent origins of four symbiotic clusters; the first is formed by Hamiltonella and Regiella (S-symbionts) placed as a sister clade to Yersinia, the second comprises Arsenophonus and Riesia (S- and P-symbionts) as a sister clade to Proteus, the third Sodalis, Baumannia, Blochmannia and Wigglesworthia (S- and P-symbionts) as a sister or paraphyletic clade to the Pectobacterium and Dickeya clade and, finally, Buchnera species and Ishikawaella (P-symbionts) clustering with the Erwinia and Pantoea clade. Conclusions The results of this study confirm the efficiency of several artifact-reducing methods and strongly point towards the polyphyly of P-symbionts within Enterobacteriaceae. Interestingly, the model species of symbiotic bacteria research, Buchnera and Wigglesworthia, originated from closely related, but different, ancestors. The possible origins of intracellular symbiotic bacteria from gut-associated or pathogenic bacteria are suggested, as well as the role of facultative secondary symbionts as a source of bacteria that can gradually become obligate maternally transferred symbionts.</p

Arsenophonus and Sodalis replacements shape evolution of symbiosis in louse flies

Symbiotic interactions between insects and bacteria are ubiquitous and form a continuum from loose facultative symbiosis to greatly intimate and stable obligate symbiosis. In blood-sucking insects living exclusively on vertebrate blood, obligate endosymbionts are essential for hosts and hypothesized to supplement B-vitamins and cofactors missing from their blood diet. The role and distribution of facultative endosymbionts and their evolutionary significance as seeds of obligate symbioses are much less understood. Here, using phylogenetic approaches, we focus on the Hippoboscidae phylogeny as well as the stability and dynamics of obligate symbioses within this bloodsucking group. In particular, we demonstrate a new potentially obligate lineage of Sodalis co-evolving with the Olfersini subclade of Hippoboscidae. We also show several likely facultative Sodalis lineages closely related to Sodalis praecaptivus (HS strain) and suggest repeated acquisition of novel symbionts from the environment. Similar to Sodalis, Arsenophonus endosymbionts also form both obligate endosymbiotic lineages co-evolving with their hosts (Ornithomyini and Ornithoica groups) as well as possibly facultative infections incongruent with the Hippoboscidae phylogeny. Finally, we reveal substantial diversity of Wolbachia strains detected in Hippoboscidae samples falling into three supergroups: A, B, and the most common F. Altogether, our results prove the associations between Hippoboscoidea and their symbiotic bacteria to undergo surprisingly dynamic, yet selective, evolutionary processes strongly shaped by repeated endosymbiont replacements. Interestingly, obligate symbionts only originate from two endosymbiont genera, Arsenophonus and Sodalis, suggesting that the host is either highly selective about its future obligate symbionts or that these two lineages are the most competitive when establishing symbioses in louse flies

Phylogenetic tree derived from <i>spaPQR</i> region by BI in MrBayes.

<p>The numbers at the nodes show the posterior probabilites and bootstrap values from the identical topology obtained by ML in PhyML. New <i>Sodalis</i> lineages added in this study are printed in red.</p

<em>Candidatus</em> Sodalis melophagi sp. nov.: Phylogenetically Independent Comparative Model to the Tsetse Fly Symbiont <em>Sodalis glossinidius</em>

<div><p>Bacteria of the genus <em>Sodalis</em> live in symbiosis with various groups of insects. The best known member of this group, a secondary symbiont of tsetse flies <em>Sodalis glossinidius</em>, has become one of the most important models in investigating establishment and evolution of insect-bacteria symbiosis. It represents a bacterium in the early/intermediate state of the transition towards symbiosis, which allows for exploring such interesting topics as: usage of secretory systems for entering the host cell, tempo of the genome modification, and metabolic interaction with a coexisting primary symbiont. In this study, we describe a new <em>Sodalis</em> species which could provide a useful comparative model to the tsetse symbiont. It lives in association with <em>Melophagus ovinus</em>, an insect related to tsetse flies, and resembles <em>S. glossinidius</em> in several important traits. Similar to <em>S. glossinidius</em>, it cohabits the host with another symbiotic bacterium, the bacteriome-harbored primary symbiont of the genus <em>Arsenophonus</em>. As a typical secondary symbiont, <em>Candidatus</em> Sodalis melophagi infects various host tissues, including bacteriome. We provide basic morphological and molecular characteristics of the symbiont and show that these traits also correspond to the early/intermediate state of the evolution towards symbiosis. Particularly, we demonstrate the ability of the bacterium to live in insect cell culture as well as in cell-free medium. We also provide basic characteristics of type three secretion system and using three reference sequences (16 S rDNA, <em>groEL</em> and <em>spaPQR</em> region) we show that the bacterium branched within the genus <em>Sodalis</em>, but originated independently of the two previously described symbionts of hippoboscoids. We propose the name <em>Candidatus</em> Sodalis melophagi for this new bacterium.</p> </div

Morphology and ultrastructure of <i>Candidatus</i> Sodalis melophagi.

<p><b>A</b>: <i>In vitro</i> cell culture in Nomarski contrast. <b>B</b>, <b>C</b>: Cells of <i>Candidatus</i> Sodalis melophagi in bacteriome. Black arrows – cells of <i>Candidatus</i> Sodalis melophagi, white arrows – cells of the primary endosymbiont of the genus <i>Arsenophonus</i>.</p

16 S rDNA tree derived by BI analysis in MrBayes.

<p>Posterior probabilities are indicated by the numbers at the nodes. New <i>Sodalis</i> lineages added in this study are printed in red.</p