Conserved Meiotic Machinery in Glomus spp., a Putatively Ancient Asexual Fungal Lineage

Arbuscular mycorrhizal fungi (AMF) represent an ecologically important and evolutionarily intriguing group of symbionts of land plants, currently thought to have propagated clonally for over 500 Myr. AMF produce multinucleate spores and may exchange nuclei through anastomosis, but meiosis has never been observed in this group. A provocative alternative for their successful and long asexual evolutionary history is that these organisms may have cryptic sex, allowing them to recombine alleles and compensate for deleterious mutations. This is partly supported by reports of recombination among some of their natural populations. We explored this hypothesis by searching for some of the primary tools for a sustainable sexual cycle—the genes whose products are required for proper completion of meiotic recombination in yeast—in the genomes of four AMF and compared them with homologs of representative ascomycete, basidiomycete, chytridiomycete, and zygomycete fungi. Our investigation used molecular and bioinformatic tools to identify homologs of 51 meiotic genes, including seven meiosis-specific genes and other “core meiotic genes” conserved in the genomes of the AMF Glomus diaphanum (MUCL 43196), Glomus irregulare (DAOM-197198), Glomus clarum (DAOM 234281), and Glomus cerebriforme (DAOM 227022). Homology of AMF meiosis-specific genes was verified by phylogenetic analyses with representative fungi, animals (Mus, Hydra), and a choanoflagellate (Monosiga). Together, these results indicate that these supposedly ancient asexual fungi may be capable of undergoing a conventional meiosis; a hypothesis that is consistent with previous reports of recombination within and across some of their populations

Some considerations for analyzing biodiversity using integrative metagenomics and gene networks

<p>Abstract</p> <p>Background</p> <p>Improving knowledge of biodiversity will benefit conservation biology, enhance bioremediation studies, and could lead to new medical treatments. However there is no standard approach to estimate and to compare the diversity of different environments, or to study its past, and possibly, future evolution.</p> <p>Presentation of the hypothesis</p> <p>We argue that there are two conditions for significant progress in the identification and quantification of biodiversity. First, integrative metagenomic studies - aiming at the simultaneous examination (or even better at the integration) of observations about the elements, functions and evolutionary processes captured by the massive sequencing of multiple markers - should be preferred over DNA barcoding projects and over metagenomic projects based on a single marker. Second, such metagenomic data should be studied with novel inclusive network-based approaches, designed to draw inferences both on the many units and on the many processes present in the environments.</p> <p>Testing the hypothesis</p> <p>We reached these conclusions through a comparison of the theoretical foundations of two molecular approaches seeking to assess biodiversity: metagenomics (mostly used on prokaryotes and protists) and DNA barcoding (mostly used on multicellular eukaryotes), and by pragmatic considerations of the issues caused by the 'species problem' in biodiversity studies.</p> <p>Implications of the hypothesis</p> <p>Evolutionary gene networks reduce the risk of producing biodiversity estimates with limited explanatory power, biased either by unequal rates of LGT, or difficult to interpret due to (practical) problems caused by type I and type II grey zones. Moreover, these networks would easily accommodate additional (meta)transcriptomic and (meta)proteomic data.</p> <p>Reviewers</p> <p>This article was reviewed by Pr. William Martin, Dr. David Williams (nominated by Pr. J Peter Gogarten) & Dr. James McInerney (nominated by Pr. John Logsdon).</p

Influence of chemosynthetic substrates availability on symbiont densities, carbon assimilation and transfer in the dual symbiotic vent mussel <I>Bathymodiolus azoricus</I>

International audienceHigh densities of mussels of the genus Bathymodiolus are present at hydrothermal vents of the Mid-Atlantic Ridge. It was already proposed that the chemistry at vent sites would affect their sulphide- and methane-oxidizing endosymbionts' abundance. In this study, we confirmed the latter assumption using fluorescence in situ hybridization on Bathymodiolus azoricus specimens maintained in a controlled laboratory environment at atmospheric pressure with one, both or none of the chemical substrates. A high level of symbiosis plasticity was observed, methane-oxidizers occupying between 4 and 39% of total bacterial area and both symbionts developing accordingly to the presence or absence of their substrates. Using H13CO3- in the presence of sulphide, 13CH4 or 13CH3OH, we monitored carbon assimilation by the endosymbionts and its translocation to symbiont-free mussel tissues. Although no significant carbon assimilation could be evidenced with methanol, carbon was incorporated from methane and sulphide-oxidized inorganic carbon at rates 3 to 10 times slower in the host muscle tissue than in the symbiont-containing gill tissue. Both symbionts thus contribute actively to B. azoricus nutrition and adapt to the availability of their substrates. Further experiments with varying substrate concentrations using the same set-up should provide useful tools to study and even model the effects of changes in hydrothermal fluids on B. azoricus' chemosynthetic nutrition

Tomography of bacteria–mineral associations within the deep-sea hydrothermal vent shrimp <i>Rimicaris exoculata</i>

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Therapeutic Potential of a New Jumbo Phage That Infects Vibrio coralliilyticus, a Widespread Coral Pathogen

Biological control using bacteriophages is a promising approach for mitigating the devastating effects of coral diseases. Several phages that infect Vibrio coralliilyticus, a widespread coral pathogen, have been isolated, suggesting that this bacterium is permissive to viral infection and is, therefore, a suitable candidate for treatment by phage therapy. In this study, we combined functional and genomic approaches to evaluate the therapeutic potential of BONAISHI, a novel V. coralliilyticus phage, which was isolated from the coral reef in Van Phong Bay (Vietnam). BONAISHI appears to be strictly lytic for several pathogenic strains of V. coralliilyticus and remains infectious over a broad range of environmental conditions. This candidate has an unusually large dsDNA genome (303 kb), with no genes that encode known toxins or implicated in lysogeny control. We identified several proteins involved in host lysis, which may offer an interesting alternative to the use of whole bacteriophages for controlling V. coralliilyticus. A preliminary therapy test showed that adding BONAISHI to an infected culture of Symbiodinium sp. cells reduced the impact of V. coralliilyticus on Symbiodinium sp. photosynthetic activity. This study showed that BONAISHI is able to mitigate V. coralliilyticus infections, making it a good candidate for phage therapy for coral disease

Etude des symbioses de mytilidés des écosystèmes marins profonds à base chimiosynthétique par des techniques de FISH, de microscopie et de traitement d'images

Les symbioses impliquant des bactéries méthanotrophes et sulfoxydantes se rencontrent chez de nombreux mytilidés des écosystèmes marins profonds à base chimiosynthétiques pour lesquels elles jouent un rôle majeur dans la nutrition et l adaptation à leur environnement. Ce travail de thèse a consisté à adapter et développer différentes approches basées sur le FISH (Fluorescent in situ hybrization), la microscopie et l analyse d images. Ces techniques ont permis l identification de 6 types de bactéries symbiotiques sur une même coupe de filaments branchiaux de l éspèce Idas sp. et l étude ultrastructurale de cette symbiose. Une technique fiable de quantification de chaque type de symbiontes présent dans les bactériocytes de certains mytilidés a confirmé l existence de variations des populations symbiotiques de l espèce Bathymodiolus azoricus en fonction de certaines conditions environnementales, établissant la capacité des symbiontes à s adapter rapidement aux variations du milieu.PARIS-BIUSJ-Physique recherche (751052113) / SudocSudocFranceF

Histoire évolutive de Idas sp. Med (Bivalvia : Mytilidae), une moide de suintements froids associée à plusieurs bactéries symbiotiques.

International audienceSmall mytilids of the genus Idas are related to the large mussels found worldwide at deep-sea hydrothermal vents and cold seeps. They are therefore keys to a better understanding of the colonization of vents and seeps by symbiont-bearing organisms, but still little is known about their biology. For this study, specimens of a mytilid referred to the genus Idas were collected from various substrates in a cold seep area near the Nile deep sea fan. Based on molecular and morphological data, all specimens are confirmed to belong to a single species of the genus Idas, which was previously shown to host six distinct bacterial symbionts. Its larval shell characteristics indicate a long planktonic phase, which could explain its close relationship to a mussel species that occurs in the Gulf of Mexico. 3-D FISH indicates the dominance of sulfur-oxidizing, methane-oxidizing and methylotrophic symbionts in all specimens analysed.Les mytilidés du genre Idas forment un groupe monophylétique avec ceux associés aux sources hydrothermales et aux suintements froids. Ils sont donc la clé d'une meilleure compréhension du scénario de colonisation de ces environnements par les organismes symbiotiques. Pour autant, leur biologie est encore aujourd'hui fort peu connue. Pour la présente étude, des moules ont été collectées à partir de différents substrats aux alentours du delta profond du Nil. Nous utilisons ici une approche moléculaire et morphologique pour démontrer que ces spécimens appartiennent à une espèce du genre Idas, dont il a été montré précédemment qu'elle était en association symbiotique avec 6 lignées bactériennes, un cas sans précédent dans ce taxon. La coquille larvaire suggère une longue phase planctonique qui pourrait expliquer la parenté avec une espèce présente dans le Golfe du Mexique. Une approche de 3D-FISH indique la dominance de symbiontes de types sulfoxydants, méthanotrophes et méthylotrophes dans tous les individus analysés

EGN: a wizard for construction of gene and genome similarity networks.

International audienceBackground: Increasingly, similarity networks are being used for evolutionary analyses of molecular datasets. These networks are very useful, in particular for the analysis of gene sharing, lateral gene transfer and for the detection of distant homologs. Currently, such analyses require some computer programming skills due to the limited availability of user-friendly freely distributed software. Consequently, although appealing, the construction and analyses of these networks remain less familiar to biologists than do phylogenetic approaches. Results: In order to ease the use of similarity networks in the community of evolutionary biologists, we introduce a software program, EGN, that runs under Linux or MacOSX. EGN automates the reconstruction of gene and genome networks from nucleic and proteic sequences. EGN also implements statistics describing genetic diversity in these samples, for various user-defined thresholds of similarities. In the interest of studying the complexity of evolutionary processes affecting microbial evolution, we applied EGN to a dataset of 571,044 proteic sequences from the three domains of life and from mobile elements. We observed that, in Borrelia, plasmids play a different role than in most other eubacteria. Rather than being genetic couriers involved in lateral gene transfer, Borrelia's plasmids and their genes act as private genetic goods, that contribute to the creation of genetic diversity within their parasitic hosts. Conclusion: EGN can be used for constructing, analyzing, and mining molecular datasets in evolutionary studies. The program can help increase our knowledge of the processes through which genes from distinct sources and/or from multiple genomes co-evolve in lineages of cellular organisms

De la pensée de l’histoire au jeu littéraire. Études médiévales en l’honneur de Dominique Boutet, dir. S. Douchet, M.-P. Halary, P. Moran, S. Lefèvre, J.-R. Valette, Paris, Honoré Champion, 2019.

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De la pensée de l’histoire au jeu littéraire. Etudes médiévales en l’honneur de Dominique Boutet

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