Amoeba/amoebal symbiont genetic transfers: lessons from giant virus neighbours.

Free-living amoebae serve as hosts for a variety of amoebae-resisting microorganisms, including giant viruses and certain bacteria. The latter include symbiotic bacteria as well as bacteria exhibiting a pathogenic phenotype towards amoebae. Amoebae-resisting bacteria have been shown to be widespread in water and to use the amoebae as a reservoir, a replication niche, a protective armour as well as a training ground to select virulence traits allowing survival in the face of microbicidal effects of macrophages, the first line of defense against invading pathogens. More importantly, amoebae play a significant role as a melting pot for genetic exchanges. These ecological and evolutionary roles of amoebae might also be at play for giant viruses and knowledge derived from the study of amoebae-resisting bacteria is useful for the study and understanding of interactions between amoebae and giant viruses. This is especially important since some genes have spread in all domains of life and the exponential availability of eukaryotic genomes and metagenomic sequences will allow researchers to explore these genetic exchanges in a more comprehensive way, thus completely changing our perception of the evolutionary history of organisms. Thus, a large part of this review is dedicated to report current known gene exchanges between the different amoebae-resisting organisms and between amoebae and the internalized bacteria.

Endosymbiotic bacteria associated with nematodes, ticks and amoebae.

Endosymbiosis is a mutualistic, parasitic or commensal symbiosis in which one symbiont is living within the body of another organism. Such symbiotic relationship with free-living amoebae and arthropods has been reported with a large biodiversity of microorganisms, encompassing various bacterial clades and to a lesser extent some fungi and viruses. By contrast, current knowledge on symbionts of nematodes is still mainly restricted to Wolbachia and its interaction with filarial worms that lead to increased pathogenicity of the infected nematode. In this review article, we aim to highlight the main characteristics of symbionts in term of their ecology, host cell interactions, parasitism and co-evolution, in order to stimulate future research in a field that remains largely unexplored despite the availability of modern tools.

Gut symbionts from distinct hosts exhibit genotoxic activity via divergent colibactin biosynthetic pathways.

Secondary metabolites produced by nonribosomal peptide synthetase (NRPS) or polyketide synthase (PKS) pathways are chemical mediators of microbial interactions in diverse environments. However, little is known about their distribution, evolution, and functional roles in bacterial symbionts associated with animals. A prominent example is "colibactin", a largely unknown family of secondary metabolites produced by Escherichia coli via a hybrid NRPS-PKS biosynthetic pathway, inflicting DNA damage upon eukaryotic cells and contributing to colorectal cancer and tumor formation in the mammalian gut. Thus far, homologs of this pathway have only been found in closely related Enterobacteriaceae, while a divergent variant of this gene cluster was recently discovered in a marine alphaproteobacterial Pseudovibrio strain. Herein, we sequenced the genome of Frischella perrara PEB0191, a bacterial gut symbiont of honey bees, and identified a homologous colibactin biosynthetic pathway related to those found in Enterobacteriaceae. We show that the colibactin genomic island (GI) has conserved gene synteny and biosynthetic module architecture across F. perrara, Enterobacteriaceae and the Pseudovibrio strain. Comparative metabolomics analyses of F. perrara and E. coli further reveal that these two bacteria produce related colibactin pathway-dependent metabolites. Finally, we demonstrate that F. perrara, like E. coli, causes DNA damage in eukaryotic cells in vitro in a colibactin pathway-dependent manner. Together, these results support that divergent variants of the colibactin biosynthetic pathway are widely distributed among bacterial symbionts, producing related secondary metabolites and likely endowing its producer with functional capabilities important for diverse symbiotic associations.

Absence of intestinal PPARγ aggravates acute infectious colitis in mice through a lipocalin-2-dependent pathway.

To be able to colonize its host, invading Salmonella enterica serovar Typhimurium must disrupt and severely affect host-microbiome homeostasis. Here we report that S. Typhimurium induces acute infectious colitis by inhibiting peroxisome proliferator-activated receptor gamma (PPARγ) expression in intestinal epithelial cells. Interestingly, this PPARγ down-regulation by S. Typhimurium is independent of TLR-4 signaling but triggers a marked elevation of host innate immune response genes, including that encoding the antimicrobial peptide lipocalin-2 (Lcn2). Accumulation of Lcn2 stabilizes the metalloproteinase MMP-9 via extracellular binding, which further aggravates the colitis. Remarkably, when exposed to S. Typhimurium, Lcn2-null mice exhibited a drastic reduction of the colitis and remained protected even at later stages of infection. Our data suggest a mechanism in which S. Typhimurium hijacks the control of host immune response genes such as those encoding PPARγ and Lcn2 to acquire residence in a host, which by evolution has established a symbiotic relation with its microbiome community to prevent pathogen invasion.

Arbuscular mycorrhiza-specific signaling in rice transcends the common symbiosis signaling pathway.

Knowledge about signaling in arbuscular mycorrhizal (AM) symbioses is currently restricted to the common symbiosis (SYM) signaling pathway discovered in legumes. This pathway includes calcium as a second messenger and regulates both AM and rhizobial symbioses. Both monocotyledons and dicotyledons form symbiotic associations with AM fungi, and although they differ markedly in the organization of their root systems, the morphology of colonization is similar. To identify and dissect AM-specific signaling in rice (Oryza sativa), we developed molecular phenotyping tools based on gene expression patterns that monitor various steps of AM colonization. These tools were used to distinguish common SYM-dependent and -independent signaling by examining rice mutants of selected putative legume signaling orthologs predicted to be perturbed both upstream (CASTOR and POLLUX) and downstream (CCAMK and CYCLOPS) of the central, calcium-spiking signal. All four mutants displayed impaired AM interactions and altered AM-specific gene expression patterns, therefore demonstrating functional conservation of SYM signaling between distant plant species. In addition, differential gene expression patterns in the mutants provided evidence for AM-specific but SYM-independent signaling in rice and furthermore for unexpected deviations from the SYM pathway downstream of calcium spiking.

Mycorrhizal ecology and evolution: the past, the present, and the future.

1406 I. 1407 II. 1408 III. 1410 IV. 1411 V. 1413 VI. 1416 VII. 1418 1418 References 1419 SUMMARY: Almost all land plants form symbiotic associations with mycorrhizal fungi. These below-ground fungi play a key role in terrestrial ecosystems as they regulate nutrient and carbon cycles, and influence soil structure and ecosystem multifunctionality. Up to 80% of plant N and P is provided by mycorrhizal fungi and many plant species depend on these symbionts for growth and survival. Estimates suggest that there are c. 50 000 fungal species that form mycorrhizal associations with c. 250 000 plant species. The development of high-throughput molecular tools has helped us to better understand the biology, evolution, and biodiversity of mycorrhizal associations. Nuclear genome assemblies and gene annotations of 33 mycorrhizal fungal species are now available providing fascinating opportunities to deepen our understanding of the mycorrhizal lifestyle, the metabolic capabilities of these plant symbionts, the molecular dialogue between symbionts, and evolutionary adaptations across a range of mycorrhizal associations. Large-scale molecular surveys have provided novel insights into the diversity, spatial and temporal dynamics of mycorrhizal fungal communities. At the ecological level, network theory makes it possible to analyze interactions between plant-fungal partners as complex underground multi-species networks. Our analysis suggests that nestedness, modularity and specificity of mycorrhizal networks vary and depend on mycorrhizal type. Mechanistic models explaining partner choice, resource exchange, and coevolution in mycorrhizal associations have been developed and are being tested. This review ends with major frontiers for further research.

Evolutionary forces affect multigenomic arbuscular mycorhizal fungi : an experimental approach using Glomus intraradices

Abstract Arbuscular Mycorhizal Fungi (AMF) are important plant symbionts that can improve floristic diversity and ecosystem productivity. These important fungi are obligate biotrophs and form symbioses with roots of the majority of plant species, improving plant nutrient acquisition in exchange of photosynthates. AM fungi are successful both ecologically as they occupy a very large spectrum of environments as well as host range and evolutionarily, as this symbiosis is over 400 million years old. These fungi grow and reproduce clonally by hyphae and multinucleate spores. AMF are coenocytic and recent work has shown that they harbor genetically different nuclei and that AMF populations are genetically diverse. How AMF species diversity is maintained has been addressed theoretically and experimentally at the community level. Much less attention has been drawn to understand how genetic diversity is maintained within populations although closely related individuals are more likely to compete for the same resources and occupy similar niches. How infra-individual genetic diversity is shaped and maintained has received even less attention. In Chapter 2, we show that individuals from a field population may differ in their symbiotic efficiency under reduced phosphate availability: We show there is genetic variation in an AMF field population for fitness-related growth traits in response to different phosphate availability acid host species. Furthermore, AFLP fingerprints of the same individuals growing in contrasting environments diverged suggesting that the composition in nuclei of AMF is dynamical and affected by environmental factors. Thus environmental heterogeneity is likely to play an important role for the maintenance of genetic diversity at the population level. In Chapter 3 we show that single spores do not inherit necessarily the same genetic material. We have found genetic divergences using two different types of molecular marker, as well as phenotypic divergences among single spore lines. Our results stress the importance of considering these organisms as a multilevel hierarchical system and of better knowing their life cycle. They have important consequences for the understanding of AMF genetics, ecology and the development of commercial AMF inocculum. Résumé Les champignons endomycorhiziens arbusculaires (CEA) sont d'importants symbiontes pour les plantes, car ils augmentent la diversité et la productivité des écosystèmes. Ces importants symbiontes sont des biotrophes obligatoires et forment une symbiose avec la plupart des plantes terrestres. Ils améliorent l'acquisition de substances nutritives de leurs hôtes en échange de sucres obtenus par photosynthèse. Ces champignons ont un grand succès écologique, ils colonisent une grande rangée d'environnements ainsi que d'hôtes. Ils ont aussi un succès évolutif certain de part le fait que cette symbiose existe depuis plus de 400 millions d'années. Les CEA sont asexués et croissent clonalement en formant des hyphes et des spores multinuclées. Les CEA sont des coenocytes et des travaux de recherche récents ont montré qu'ils possèdent des noyaux génétiquement différents. D'autres travaux ont aussi révélé que les populations de CEA sont génétiquement diversifiées. Comment la diversité des CEA est maintenue a seulement été adressée par des études théoriques et expérimentalement au niveau des communautés. Très peu d'attention a été portée sur le maintien de la diversité génétique infra et inter populationnelle, or ce sont les individus les plus proches génétiquement qui vont entrer en compétition pour des ressources et niches similaires. La formation et le maintien de la diversité intra-individu des CEA a reçu très peu d'attention. Dans le chapitre 2, nous montrons que des individus CEA d'un même champ différent dans leur efficacité symbiotique lorsque la concentration en phosphoré est réduite. Nous montrons qu'il existe de la variance génétique dans une population de CEA provenant d'un même champ en réponse à différentes concentrations de phosphore, ainsi qu'en réponse à différentes espèces d'hôtes, et ceci pour des traits de croissance vraisemblablement liés au succès reproducteur. De plus grâce à des AFLP nous avons pu montrer que le génome de ces individus subissent des changements lorsqu'ils croissent dans des environnements contrastés. Ceci suggère que les noyaux génétiquement différents des CEA sont des entités dynamiques. Il est fort probable que l'hétérogénéité environnementale joue un rôle dans le maintien de la diversité génétique des populations de CEA. Dans le chapitre 3, nous montrons que toutes les spores d'un même mycélium parental de CEA ne reçoivent pas exactement le même contenu génétique. Nous avons mis en évidence des divergences entre des Lignées monosporales en utilisant deux types de marqueur moléculaires, ainsi que des différences phénotypiques. Nos résutats soulignent l'importance de considézer ces organismes comme dés systëmes hiérarchiques mufti-niveaux, ainsi que de mieux connaître leur cycle de vie. Nos résultats ont d'importantes conséquences pour la compréhension du système génétique des CEA, ainsi que de leur évolution, leur écológie, mais également des conséquences pour la production d' inoccultim commercial.

Additive genetic effects on embryo viability in a whitefish (Salmonidae) influenced by the water mould Saprolegnia ferax

Animals and plants are associated with symbiotic microbes whose roles range from mutualism to commensalism to parasitism. These roles may not only be taxon-specific but also dependent on environmental conditions and host factors. To experimentally test these possibilities, we drew a random sample of adult whitefish from a natural population, bred them in vitro in a full-factorial design in order to separate additive genetic from maternal environmental effects on offspring, and tested the performance of the resulting embryos under different environmental conditions. Enhancing the growth of symbiotic microbes with supplemental nutrients released cryptic additive genetic variance for viability in the fish host. These effects vanished with the concurrent addition of the water mould Saprolegnia ferax. Our findings demonstrate that the heritability of host fitness is environment-specific and critically depends on the interaction between symbiotic microbes.

Contribution to the geology of Southern Turkey: new insights from the Mersin mélanges and from the Lycian and Antalya nappes

Abstract The study of fossil Tethyan continental margins implies the consideration of the oceanic domains to which they were connected. The advent of plate tectonics confirmed the importance of the detection of accretion-related mélanges. Ophiolitic mélanges are derived from both an upper ophiolitic obducting plate and a lower oceanic plate. Besides ophiolitic elements, the mélanges may incorporate parts of a magmatic arc and dismembered fragments of a passive continental margin. As the lower plate usually totally disappears during the obduction process, it can only be reconstructed from its elements found in the mélanges. Because of their key location at active margin boundaries, preserved accretion-related mélanges provide strong constraints on the geological evolution of former oceanic domains and their adjacent margins. The identification of Palaeotethyan remnants as accretionary series or reworked during the Late Triassic Eo-Cimmerian event, as well as the recognition of HugluPindos marginal sequences in southern Turkey and in the external Hellenides represent the main achievements of this work, making possible to establish new palaeogeographical correlations. The Mersin mélanges (Turkey), together with the Antalya and Mamonia (Cyprus) domains, are characterized by a series of exotic units found now south of the main Taurus range and compose the South-Taurides Exotic Units. The Mersin mélanges are subdivided in a Triassic and a Late Cretaceous unit. These units consist of the remnants of three major Tethyan oceans, the Palaeotethys, the Neotethys and the Huglu-Pindos. The definition and inventory of the Upper Antalya Nappes (Turkey) are still a matter of controversies and often conflicting interpretations. The recognition of Campanian radiolarians on top of the Kerner Gorge unit directly overlain by the Ordovician Seydi§ehir Fm. of the Tahtah Dag Nappe outlines a tectonic contact and demonstrates that the Upper Antalya Nappes system is composed of three different nappes, the Kerner Gorge, Bakirli and the Tahtah Dag nappes. Additionally, a limestone block in a doubtful tectonic position at the base of the Upper Antalya Nappes yielded for the first time two middle Viséan associations of foraminifers and problematic algae. The Tavas Nappe in the Lycian Nappes (Turkey) is classically divided into the Karadag, Teke Dere, Köycegiz and Haticeana units. As for the Mersin mélanges, the Tavas Nappe is highly composite and includes dismembered units belonging to the Palaeotethyan, Neotethyan and HugluPindos realms. The Karadag unit consists of a Gondwana-type platform succession ranging from the Late Devonian to the Late Triassic. It belongs to the Cimmerian Taurus terrane and was part of the northern passive margin of the Neotethys. The Teke Dere unit is composed of different parts of the Palaeotethyan succession including Late Carboniferous OIB-type basalts, Carboniferous MORB-type basalts, an Early Carboniferous siliciclastic series and a Middle Permian arc sequence. The microfauna and microflora identified in different horizons within the Teke Dere unit share strong biogeographical affinities with the northern Palaeotethyan borders. Kubergandian limestones in primary contact above the Early Carboniferous siliciclastics yielded a rich and diverse microfauna and microflora also identified in reworked cobbles within the Late Triassic Gevne Fm. of the Aladag unit (Turkey). The sedimentological evolution of the Köycegiz and Haticeana series is in many points similar to classical Pindos sequences. These series originated in the Huglu-Pindos Ocean along the northern passive margin of the Anatolian (Turkish transect) and Sitia-Pindos (Greek transect) terranes. Conglomerates at the base of the Lentas Unit in southern Crete (Greece) yielded a microfauna and microflora presenting also strong affinities with the northern borders of the Palaeotethys. This type of reworked sediments at the base of Pindos-like series would suggest a derivation from the Palaeotethyan active margin. -Résumé (French abstract) L'étude des marges continentales fossiles de l'espace téthysien implique d'étudier les domaines océaniques qui y étaient rattachés. Les progrès de la tectonique des plaques ont confirmé l'importance de la reconnaissance des mélanges d'accrétion. Les mélanges ophiolitiques dérivent d'une plaque supérieure ophiolitique qui obducte, et d'une plaque inférieure océanique. En plus d'éléments ophiolitiques, les mélanges peuvent aussi incorporer des parties d'un arc magmatique, ou des fragments d'une marge continentale passive. Comme la plaque inférieure disparaît généralement complètement durant le processus d'obduction, elle ne peut être reconstruite qu'au travers de ses éléments trouvés dans les mélanges. A cause de leur situation aux limites de marges actives, les mélanges d'accrétion bien préservés permettent de contraindre l'évolution géologique d'anciens océans et de leurs marges. L'identification de vestiges de la Paléotéthys en série d'accrétion ou remaniés lors de l'orogenèse éo-cimmérienne au Trias supérieur, ainsi que l'observation de séquences marginales de Huglu-Pinde en Turquie du sud et dans les Hellénides externes représentent les principaux résultats de ce travail, permettant d'établir de nouvelles corrélations paléogéographiques. Les mélanges de Mersin (Turquie), avec les domaines d'Antalya et de Mamonia (Chypre), sont caractérisés par des unités exotiques se trouvant au sud de la chaîne taurique, et forment les Unités Exotiques Sud-Tauriques. Les mélanges de Mersin sont subdivisés en une unité triasique, et une autre du Crétacé supérieur. Ces unités comprennent les reliques de trois principaux océans téthysiens, la Paléotéthys, la Néotéthys et Huglu-Pinde. L'inventaire et la définition des nappes supérieures d'Antalya (Turquie) sont encore matière à controverse et donne lieu à des interprétations conflictuelles. La découverte de radiolaires campaniens au sommet de l'unité de la Gorge de Kemer, directement recouverts par la formation ordovicienne de Seydisehir de la nappe du Tahtali Dag met en évidence un contact tectonique et démontre que les nappes supérieures sont composées de trois différentes nappes, celle de la Gorge de Kemer, celle du Bakirli et celle Tahtali Dag. De plus, un bloc de calcaire dont la position tectonique demeure incertaine à la base des nappes supérieures a fourni pour la première fois deux associations viséennes de foraminifères et d'algues problématiques. La nappe de Tavas dans les nappes lyciennes (Turquie) est séparée en unités du Karadag, du Teke Dere, de Köycegiz et d'Haticeana. Comme pour les mélanges de Mersin, la nappe de Tavas est composite et inclut des unités appartenant à la Paléotéthys, à la Néotéthys et à Huglu-Pinde. L'unité du Karadag est une plateforme carbonatée de type Gondwana se développant du Dévonien supérieur au Trias supérieur. Elle appartient au domaine cimmérien du Taurus et formait la marge nord de la Néotéthys. L'unité du Teke Dere est composée de différentes écailles paléotéthysiennes et inclut des basaltes d'île océanique du Carbonifère supérieur, des basaltes de ride océanique du Carbonifère, une série siliciclastique du Carbonifère supérieur et un arc du Permien moyen. Les microfaunes et -flores trouvées à différents niveaux de la série du Teke Dere partagent de fortes affinités paléogéographiques avec les marges nord de la Paléotéthys. Des calcaires du Kubergandien en contact primaire au-dessus de la série siliciclastique a donné de riches microfaunes et -flores, également identifiées dans des galets remaniés dans la formation de Gevne du Trias supérieur de l'Aladag. L'évolution sédimentologique des séries de Köycegiz et d'Haticeana sont très similaires aux séries classiques du Pinde. Ces séquences prennent leur racine dans l'océan de Huglu-Pinde, le long de la marge passive nord anatolienne (profil turc) et de la marge de Sitia-Pinde (profil grec). Des conglomérats à la base de l'unité de Lentas au sud de la Crète (Grèce) ont donné des microfaunes et flores partageant également de fortes similitudes avec les bordures nord de la Paléotéthys. Le type de sédiments remaniés à la base d'unités de type Pinde suggère une dérivation depuis la marge active de la Paléotéthys. -Résumé grand public (non-specialized abstract) Au début du 20ème siècle, Alfred Wegener bouleverse les croyances géologiques de l'époque et publie plusieurs articles sur la dérive ou la translation des continents. En utilisant des arguments géographiques (similarités des lignes de côte), paléontologiques (faunes et flores similaires) et climatiques (dépôts tropicaux et glaciaires), Wegener explique qu'il y a plusieurs millions d'années, les terres émergées actuelles ne devaient former qu'un seul et grand continent. La fin du 20ème siècle verra l'avènement de la théorie de la tectonique des plaques suite à la reconnaissance du cycle de Wilson, des rides médio-océaniques, des anomalies magnétiques dans les océans et des sutures océaniques qui représentent les reliques d'océans disparus. Le Cycle de Wilson se caractérise par une suite d'évènements géologiques majeurs pouvant se résumer de la manière suivante : (1) séparation d'un craton continental en deux parties, créant une limite de plaque divergente. C'est ce que l'on appelle un rift; (2) développement et croissance d'un océan entre ces deux blocs. Des roches magmatiques remontent à la surface de la terre et forment une chaîne de montagne sous-marine que l'on appelle ride médio-océanique ou dorsale. L'océan continue de se développer, et des sédiments se déposent à sa surface formant la suite ophiolitique ou trinité de Steinmann; (3) après une phase d'expansion plus ou moins longue, les conditions imposées aux limites des plaques à la surface de la terre changent, et l'océan se met à se refermer par disparition progressive (subduction) de sa croûte océanique sous une croûte continentale par exemple. Ceci crée une nouvelle limite de plaque, convergente cette fois; (4) la subduction de la plaque océanique sous la plaque continentale provoque une remontée de magma formant des chaînes volcaniques à la surface de la Terre ; (5) une fois que la plaque océanique a complètement disparu, les deux blocs préalablement séparés par l'océan font collision, formant ainsi une chaîne de montagne. Les chaînes de montagnes sont de manière générale formées par un empilement plus ou moins complexe de nappes. C'est au coeur de certaines de ces nappes que se trouvent les vestiges de l'océan disparu. Un des objectifs de ce travail était la recherche de ces vestiges dans le domaine téthysien de la Méditerranée orientale. Pour ce faire, nous avons parcourus une grande partie du sud de la Turquie, nous sommes allés à Chypre, dans le Sultanat d'Oman, en Iran, en Crète, et nous avons visités quelques îles grecques du Dodécanèse. La région de la Méditerranée orientale est une zone qui a été tectoniquement très active, et qui continue de l'être de nos jours par des phénomènes de subduction (ex. les volcans de Santorin), et par des mouvements coulissants entre des plaques continentales (ex. la faille nord-anatolienne) qui donnent régulièrement lieu à des tremblements de terre. Pour le géologue, la complexité de ces zones d'étude réside dans le fait que les chaînes de montagne actuelles ne contiennent en général pas seulement les restes d'un océan, mais bien de plusieurs bassins océaniques qui se sont succédés dans l'espace et dans le temps. Les nappes qui se trouvent au sud de la Turquie et dans le Dodécanèse forment un important jalon dans la chaîne alpine qui s'étend depuis les Alpes jusque dans l'Himalaya. L'idée d'un continuum au coeur de ce système se basait principalement sur l'âge des océans et sur la reconnaissance de similarités dans l'évolution des séries sédimentaires. La localisation des vestiges de la Paléotéthys ainsi que l'identification des séries sédimentaires ayant appartenu à l'océan de HugluPinde repris sous forme de nappes en Turquie et en Grèce sont cruciales pour permettre de bonnes corrélations locales et régionales. La reconnaissance, la compréhension et l'interprétation de ces séries sédimentaires permettront d'élaborer un modèle d'évolution géodynamique régional, s'appuyant sur des faits de terrains indiscutables, et prenant en compte les contraintes globales que ce genre d'exercice implique.

Lausannevirus, a giant amoebal virus encoding histone doublets.

Large viruses infecting algae or amoebae belong to the NucleoCytoplasmic Large DNA Viruses (NCLDV) and present genotypic and phenotypic characteristics that have raised major interest among microbiologists. Here, we describe a new large virus discovered in Acanthamoeba castellanii co-culture of an environmental sample. The virus, referred to as Lausannevirus, has a very limited host range, infecting Acanthamoeba spp. but being unable to infect other amoebae and mammalian cell lines tested. Within A. castellanii, this icosahedral virus of about 200 nm exhibits a development cycle similar to Mimivirus, with an eclipse phase 2 h post infection and a logarithmic growth leading to amoebal lysis in less than 24 h. The 346 kb Lausannevirus genome presents similarities with the recently described Marseillevirus, sharing 89% of genes, and thus belongs to the same family as confirmed by core gene phylogeny. Interestingly, Lausannevirus and Marseillevirus genomes both encode three proteins with predicted histone folds, including two histone doublets, that present similarities to eukaryotic and archaeal histones. The discovery of Lausannevirus and the analysis of its genome provide some insight in the evolution of these large amoebae-infecting viruses.

Genetic exchange in an arbuscular mycorrhizal fungus results in increased rice growth and altered mycorrhiza-specific gene transcription.

Arbuscular mycorrhizal fungi (AMF) are obligate symbionts with most terrestrial plants. They improve plant nutrition, particularly phosphate acquisition, and thus are able to improve plant growth. In exchange, the fungi obtain photosynthetically fixed carbon. AMF are coenocytic, meaning that many nuclei coexist in a common cytoplasm. Genetic exchange recently has been demonstrated in the AMF Glomus intraradices, allowing nuclei of different Glomus intraradices strains to mix. Such genetic exchange was shown previously to have negative effects on plant growth and to alter fungal colonization. However, no attempt was made to detect whether genetic exchange in AMF can alter plant gene expression and if this effect was time dependent. Here, we show that genetic exchange in AMF also can be beneficial for rice growth, and that symbiosis-specific gene transcription is altered by genetic exchange. Moreover, our results show that genetic exchange can change the dynamics of the colonization of the fungus in the plant. Our results demonstrate that the simple manipulation of the genetics of AMF can have important consequences for their symbiotic effects on plants such as rice, which is considered the most important crop in the world. Exploiting natural AMF genetic variation by generating novel AMF genotypes through genetic exchange is a potentially useful tool in the development of AMF inocula that are more beneficial for crop growth.

Cost-effective experimental design to support modeling of concentration-response functions

Modeling concentration-response function became extremely popular in ecotoxicology during the last decade. Indeed, modeling allows determining the total response pattern of a given substance. However, reliable modeling is consuming in term of data, which is in contradiction with the current trend in ecotoxicology, which aims to reduce, for cost and ethical reasons, the number of data produced during an experiment. It is therefore crucial to determine experimental design in a cost-effective manner. In this paper, we propose to use the theory of locally D-optimal designs to determine the set of concentrations to be tested so that the parameters of the concentration-response function can be estimated with high precision. We illustrated this approach by determining the locally D-optimal designs to estimate the toxicity of the herbicide dinoseb on daphnids and algae. The results show that the number of concentrations to be tested is often equal to the number of parameters and often related to the their meaning, i.e. they are located close to the parameters. Furthermore, the results show that the locally D-optimal design often has the minimal number of support points and is not much sensitive to small changes in nominal values of the parameters. In order to reduce the experimental cost and the use of test organisms, especially in case of long-term studies, reliable nominal values may therefore be fixed based on prior knowledge and literature research instead of on preliminary experiments

Cereal mycorrhiza: an ancient symbiosis in modern agriculture.

The majority of terrestrial plants live in association with symbiotic fungi that facilitate mineral nutrient uptake. The oldest and most prevalent of these associations are the arbuscular mycorrhizal (AM) symbioses that first evolved approximately 400 million years ago, coinciding with the appearance of the first land plants. Crop domestication, in comparison, is a relatively recent event, beginning approximately 10000 years ago. How has the dramatic change from wild to cultivated ecosystems impacted AM associations, and do these ancient symbioses potentially have a role in modern agriculture? Here, we review recent advances in AM research and the use of breeding approaches to generate new crop varieties that enhance the agronomic potential of AM associations.

Molecular players shaping the arbuscular mycorrhizal symbiosis of rice

SUMMARY : The arbuscular mycorrhizal (AM) symbiosis is an evolutionarily ancient association between most land plants and Glomeromycotan fungi that is based on the mutual exchange of nutrients between the two partners. Its structural and physiological establishment is a multi-step process involving a tightly regulated signal exchange leading to intracellular colonization of roots by the fungi. Most research on the molecular biology and genetics of symbiosis development has been performed in dicotyledonous model legumes. In these, a plant signaling pathway, the common SYM pathway, has been found to be required for accommodation of both root symbionts rhizobia and AM fungi. Rice, a monocotyledon model and the world's most important staple crop also forms AM symbioses, has been largely ignored for studies of the AM symbiosis. Therefore in this PhD work functional conservation of the common SYM pathway in rice was addressed and demonstrated. Mycorrhiza-specific marker genes were established that are expressed at different stages of AM development and therefore represent readouts for various AM-specific signaling events. These tools were successfully used to obtain evidence for a yet unknown signaling network comprising common SYM-dependent and -independent events. In legumes AM colonization induces common SYM signaling dependent changes in root system architecture. It was demonstrated that also in rice, root system architecture changes in response to AM colonization but these alterations occur independently of common SYM signaling. The rice root system is complex and contains three different root types. It was shown that root type identity influences the quantity of AM colonization, indicating root type specific symbiotic properties. Interestingly, the root types differed in their transcriptional responses to AM colonization and the less colonized root type responded more dramatically than the more strongly colonized root type. Finally, in an independent project a novel mutant, inhospitable (iho), was discovered. It is perturbed at the most early step of AM colonization, namely differentiation of the AM fungal hyphae into a hyphopodium at the root surface. As plant factors required for this early step are not known, identification of the IHO gene will greatly contribute to the advance of mycorrhiza RÉSUMÉ : La symbiose mycorhizienne arbusculaire (AM) est une association évolutionnairement ancienne entre la majorité des plantes terrestres et les champignons du type Glomeromycota, basée sur l'échange mutuel d'éléments nutritifs entre les deux partenaires. Son établissement structural et physiologique est un processus en plusieurs étapes, impliquant des échanges de signaux étroitement contrôlés, aboutissant à la colonisation intracellulaire des racines par le champignon. La plupart des recherches sur la biologie moléculaire et la génétique du développement de la symbiose ont été effectuées sur des légumineuses dicotylédones modèles. Dans ces dernières, une voie de signalisation, la voie SYM, s'est avérée nécessaire pour permettre la mise en place de la symbiose mycorhizienne. Chez les plantes monocotylédones, comme le riz, une des céréales les plus importantes, nourrissant la moitié de la population mondiale, peu de recherches ont été effectuées sur les bases de la cette symbiose. Dans ce travail de thèse, la conservation fonctionnelle de la voie commune SYM chez le riz a été étudiée et démontrée. De plus, des gènes marqueurs spécifiques des différentes étapes du développement de l'AM ont été identifiés, permettant ainsi d'avoir des traceurs de la colonisation. Ces outils ont été utilisés avec succès pour démontrer l'existence d'un nouveau réseau de signalisation, comprenant des éléments SYM dépendant et indépendant. Chez les légumineuses, la colonisation par les AM induit des changements dans l'architecture du système racinaire, via la signalisation SYM dépendantes. Cependant chez le riz, il a été démontré que l'architecture de système racinaire changeait suite à la colonisation de l'AM, mais ceux, de façon SYM indépendante. Le système racinaire du riz est complexe et contient trois types différents de racines. Il a été démontré que le type de racine pouvait influencer l'efficacité de la colonisation par l'AM, indiquant que les racines ont des propriétés symbiotiques spécifiques différentes. De façon surprenante, les divers types de racines répondent de différemment suite à colonisation par l'AM avec des changements de la expression des gènes. Le type de racine le moins colonisé, répondant le plus fortement a la colonisation, et inversement. En parallèle, dans un projet indépendant, un nouveau mutant, inhospitable (iho), a été identifié. Ce mutant est perturbé lors de l'étape la plus précoce de la colonisation par l'AM, à savoir la différentiation des hyphes fongiques de l'AM en hyphopodium, à la surface des racines. Les facteurs d'origine végétale requis pour cette étape étant encore inconnus, l'identification du gène IHO contribuera considérablement a accroître nos connaissance sur les bases de la mise en place de cette symbiose.

What uses are mating types? The "developmental switch" model.

Why mating types exist at all is subject to much debate. Among hypotheses, mating types evolved to control organelle transmission during sexual reproduction, or to prevent inbreeding or same-clone mating. Here I review data from a diversity of taxa (including ciliates, algae, slime molds, ascomycetes, and basidiomycetes) to show that the structure and function of mating types run counter the above hypotheses. I argue instead for a key role in triggering developmental switches. Genomes must fulfill a diversity of alternative programs along the sexual cycle. As a haploid gametophyte, an individual may grow vegetatively (through haploid mitoses), or initiate gametogenesis and mating. As a diploid sporophyte, similarly, it may grow vegetatively (through diploid mitoses) or initiate meiosis and sporulation. Only diploid sporophytes (and not haploid gametophytes) should switch on the meiotic program. Similarly, only haploid gametophytes (not sporophytes) should switch on gametogenesis and mating. And they should only do so when other gametophytes are ready to do the same in the neighborhood. As argued here, mating types have evolved primarily to switch on the right program at the right moment.