The Recent Evolution of a Maternally-Inherited Endosymbiont of Ticks Led to the Emergence of the Q Fever Pathogen, Coxiella burnetii

International audienceQ fever is a highly infectious disease with a worldwide distribution. Its causative agent, the intracellular bacterium Coxiella burnetii, infects a variety of vertebrate species, including humans. Its evolutionary origin remains almost entirely unknown and uncertainty persists regarding the identity and lifestyle of its ancestors. A few tick species were recently found to harbor maternally-inherited Coxiella-like organisms engaged in symbiotic interactions, but their relationships to the Q fever pathogen remain unclear. Here, we extensively sampled ticks, identifying new and atypical Coxiella strains from 40 of 58 examined species, and used this data to infer the evolutionary processes leading to the emergence of C. burnetii. Phylogenetic analyses of multi-locus typing and whole-genome sequencing data revealed that Coxiella-like organisms represent an ancient and monophyletic group allied to ticks. Remarkably, all known C. burnetii strains originate within this group and are the descendants of a Coxiella-like progenitor hosted by ticks. Using both colony-reared and field-collected gravid females, we further establish the presence of highly efficient maternal transmission of these Coxiella-like organisms in four examined tick species, a pattern coherent with an endosymbiotic lifestyle. Our laboratory culture assays also showed that these Coxiella-like organisms were not amenable to culture in the vertebrate cell environment, suggesting different metabolic requirements compared to C. burnetii. Altogether, this corpus of data demonstrates that C. burnetii recently evolved from an inherited symbiont of ticks which succeeded in infecting vertebrate cells, likely by the acquisition of novel virulence factors

Implantation territoriale des terramares (Italie, provinces de Parme et Plaisance, XVIIe-XIIe siècles avant notre ère) (analyses géomorphologiques et spatiales)

Cette étude propose une synthèse sur les stratégies d'implantation des sites de la culture des Terramares selon deux axes: géomorphologique d'une part et spatial d'autre part. la culture des Terramares s'est développée, entre autres, à la suite de déplacements de populations investissant la plaine émilienne au sud du Pô et exploitant intensément ce nouvel environnement. Vers 1150 avant notre ère, soit cinq siècles après sa genèse, cette culture connaît un collapsus généralisé. l'étude des modalités d'occupation de ce territoire a pour but de mieux appréhender ces particularismes. Ce travail a ainsi montré, par la reconstitution du réseau hydrique de l'âge du Bronze, l'existence de liens étroits entre terramares et cours d'eau notamment par des détournements de torrent dans le fossé périphérique des sites. Ces aménagements sont probablement à corréler avec la mise en place de réseaux d'irrigation et de drainage. Des hypothèses ont pu être formulées quant à l'état d'activation des bourrelets alluviaux à cette période. les analyses spatiales, elles, ont mis en évidence l'existence d'axes de circulation et d'échanges aussi bien fluviaux que terrestres. Ces derniers structurent les trois territoires individualisés. De là, des propositions d'organisation sociale ont pu être émises et des éclaircissements sur certaines pratiques rituelles et votives ont pu être apportés, dans un contexte pourtant pauvre de ce type de données. Enfin, la soudaineté des phénomènes de genèse et de déclin de cette culture a pu être relativisée.PARIS1-BU Pierre Mendès-France (751132102) / SudocSudocFranceF

Shotgun metagenomics sequencing of the rhizosphere microbiota associated to seven ecotypes of <em>Medicago truncatula</em>

International audienceHealthy plants host a remarkable diversity of microorganisms known as plant microbiota, which provide host services such as pathogen protection and nutrient acquisition. Thus, plant microbiota emerges as a trait that extends the capacity of plants to adapt to their environment. So far, microbial community profiling has mostly allowed the description of the phylogenetic structure of plant microbiota, whereas functional insights were mostly obtained from experiments using model strains. Thus, the plant impact on the microbial functional genes pool in the rhizosphere remains largely unknown. The goals of the study were to (i) compare the functional genes pool of the rhizosphere microbiota of seven ecotypes of Medicago truncatulata, and (ii) identify the functional genes allowing the differentiation of the microbiota upon the plant ecotypes. Forty-two samples were analysed for their phylogenetic (454 pyrosequencing of 16S rRNA) and functional genes (2x125 bp shotgun sequencing, Illumina HiSeq) diversity. Fifty-five millions scaffolds were de novo assembled after removing reads mapped on M. truncatula genome. We used Prodigal as gene prediction from mRNA scaffolds and Kaiju for taxonomic classification of rRNA scaffolds. The three millions predicted mRNA (≥ 800 bp length) were filtered to remove scaffolds that carried transposable elements or came from organelles or Sinorhizobium sp. symbionts. A selected dataset of 6074 scaffolds ≥ 10 kb was used for statistical analyses. Results indicated that (i) the genetic structure of bacterial communities differed according to the plant ecotype, and (ii) the curation of the shotgun metagenomic dataset is necessary to have a better discrimination of the different rhizosphere microbiota. Furthermore, the membrane receptor TonB protein appeared to explain differences in the structure of the rhizosphere microbiota associated with the different ecotypes. Indeed, these proteins bind and transport ferric chelates made with siderophores, as well as various plant carbohydrates, and thus to mediate plant-microbe interactions

Different Medicago truncatula genotypes, expressing different phenotypes, modulate microbial functional genes in the rhizosphere

National audiencePlants host in their rhizosphere a remarkable diversity of microorganisms that in return promote plant growth and health. Thus, the plant microbiota emerges as a novel component that expand the capacity of plants to adapt to the environment, and thus pave the way for future breeding approaches.It is widely known that different plant species harbor different microbiota, but very few studies showed an impact of the plant genotypes on the microbiota. These contrasting results may depend on the choice of the tested genotypes.We formulate the hypothesis that only those plant genotypes showing high genetic diversity and expressing different phenotypes harbor different rhizosphere microbiota and are able to modulate the microbial functioning. In this study, we aimed to assess a possible relation between the genetic/phenotypic diversity within Medicago truncatula and their associated microbiota.Seven M. truncatula genotypes were chosen on the basis of their geographical origin, genetic and phenotypic (notably their different nutritional strategies) diversity. Plant biomass and the carbon and nitrogen content in shoot and root were measured in order to describe their phenotypes. Microbial taxonomic diversity and functional genes were analysed through 16S rRNA amplicon and shotgun metagenomic, respectively. Results show that the seven plant genotypes clustered in three different phenotypes. The taxonomic diversity and functional genes of bacterial communities differed according to the plant cluster from which they are issued. These differences were explained by the following proteins: (i) Transposase from family Tn3 (bacterial plasmids remobilization), (ii) Membrane receptor TonB dependent (iron) and (iii) metallopeptidases from families TldD/PmbA and M14. Interestingly, TonB dependent transporter proteins seem to be involved in plant-microbe interactions (as this outer membrane protein binds and transports ferric chelates called siderophore, as well as various plant carbohydrates). These results support our initial hypothesis and show that contrasting genotypes modulate microbial gene abundance

Variable and core functional rhizosphere microbiota associated with seven Medicago truncatula genotypes

National audienceThe rhizosphere microbiota emerges as a novel component that expands plant adaptation to its environment, and thus paves the way for future breeding approaches. Knowledge regarding the "functional core microbiota", which refers to the microbial taxa bearing essential functions for holobiont fitness, are required to move forward in this area. The aim of the present study was to compare the functional microbiota recruited by different plant genotypes in order to identify its core and variable components. Seven genotypes of Medicago truncatula (DZA315-16, DZA315-26, DZA045-6, F83005-5, SA028064, Jemalong A17 and J6), representatives of a core collection of 184 genotypes, were studied. Functional genes have been described using shotgun metagenomics followed by Prodigal. Core and variable functional microbiota have been identified based on shared genes and on genes explaining differences among the genotypes, respectively. Functional assignment has been obtained based on proteins annotation and Gene Onthology using BlastX and EggNOG. 76,264 genes were shared, whilst 3547 genes explained the differences between the three DZA genotypes and SA, 4662 among the three DZA and the F, A17, J6 genotypes, and 32 among SA and the three genotypes F, A17, J6. 60.5% of these genes have been assigned to biological processes, 22.6% to cellular components and 16.9% to molecular functions. Particularly, inorganic ion, amino-acid, and carbohydrate transport were the more represented in biological processes. This global analysis shows that different genotypes modulate rhizosphere microbial functional genes and provides new insights into the variable and core microbiota among different plant genotypes

Variable and core functional microbiota associated with seven Medicago truncatula genotypes

National audienceThe rhizosphere microbiota emerges as a novel component that expands plant adaptation to its environment, and thus paves the way for future breeding approaches. Knowledge regarding the "functional core microbiota", which refers to the microbial taxa bearing essential functions for holobiont fitness, is required to move forward in this area. The aim of the present study was to compare the functional microbiota recruited by different plant genotypes in order to identify itscore and variable components. Seven genotypes of Medicago truncatula (DZA315-16, DZA315-26, DZA045-6, F83005-5, SA028064, Jemalong A17 and J6), representatives of a core collection of 184 genotypes, were studied. Functional genes have been described using shotgun metagenomics followed by Prodigal. Core and variable functional microbiota have been identified based on shared genes and on genes explaining differences among the genotypes, respectively.Functional assignments have been obtained based on proteins annotation and Gene Onthology using BlastX and EggNOG. 76,264 genes were shared, whilst 3547 genes explained the differences between the three DZA genotypes and SA, 4662 among the three DZA and the F, A17, J6 genotypes, and 32 among SA and the three genotypes F, A17, J6. 60.5% of these genes have been assigned to biological processes, 22.6% to cellular components and 16.9% to molecular functions.Particularly, inorganic ion, amino-acid, and carbohydrate transport were the most represented in biological processes. This global analysis shows that different genotypes modulate rhizosphere microbial functional genes and provides new insights into the variable and core microbiota among different plant genotype

The PIWI protein Aubergine recruits eIF3 to activate translation in the germ plasm

International audiencePiwi-interacting RNAs (piRNAs) and PIWI proteins are essential in germ cells to repress transposons and regulate mRNAs. In Drosophila, piRNAs bound to the PIWI protein Aubergine (Aub) are transferred maternally to the embryo and regulate maternal mRNA stability through two opposite roles. They target mRNAs by incomplete base pairing, leading to their destabilization in the soma and stabilization in the germ plasm. Here, we report a function of Aub in translation. Aub is required for translational activation of nanos mRNA, a key determinant of the germ plasm. Aub physically interacts with the poly(A)-binding protein (PABP) and the translation initiation factor eIF3. Polysome gradient profiling reveals the role of Aub at the initiation step of translation. In the germ plasm, PABP and eIF3d assemble in foci that surround Aub-containing germ granules, and Aub acts with eIF3d to promote nanos translation. These results identify translational activation as a new mode of mRNA regulation by Aub, highlighting the versatility of PIWI proteins in mRNA regulation

Evolutionary changes in symbiont community structure in ticks

International audienceEcological specialization to restricted diet niches is driven by obligate, and often maternally inherited, symbionts in many arthropod lineages. These heritable symbionts typically form evolutionarily stable associations with arthropods that can last for millions of years. Ticks were recently found to harbour such an obligate symbiont, Coxiella-LE, that synthesizes B vitamins and cofactors not obtained in sufficient quantities from blood diet. In this study, the examination of 81 tick species shows that some Coxiella-LE symbioses are evolutionarily stable with an ancient acquisition followed by codiversification as observed in ticks belonging to the Rhipicephalus genus. However, many other Coxiella-LE symbioses are characterized by low evolutionary stability with frequent host shifts and extinction events. Further examination revealed the presence of nine other genera of maternally inherited bacteria in ticks. Although these nine symbionts were primarily thought to be facultative, their distribution among tick species rather suggests that at least four may have independently replaced Coxiella-LE and likely represent alternative obligate symbionts. Phylogenetic evidence otherwise indicates that cocladogenesis is globally rare in these symbioses as most originate via horizontal transfer of an existing symbiont between unrelated tick species. As a result, the structure of these symbiont communities is not fixed and stable across the tick phylogeny. Most importantly, the symbiont communities commonly reach high levels of diversity with up to six unrelated maternally inherited bacteria coexisting within host species. We further conjecture that interactions among coexisting symbionts are pivotal drivers of community structure both among and within tick species

First dairying in green Saharan Africa in the fifth millennium BC

In the prehistoric green Sahara of Holocene North Africa-in contrast to the Neolithic of Europe and Eurasia-a reliance on cattle, sheep and goats emerged as a stable and widespread way of life, long before the first evidence for domesticated plants or settled village farming communities(1-3). The remarkable rock art found widely across the region depicts cattle herding among early Saharan pastoral groups, and includes rare scenes of milking; however, these images can rarely be reliably dated(4). Although the faunal evidence provides further confirmation of the importance of cattle and other domesticates(5), the scarcity of cattle bones makes it impossible to ascertain herd structures via kill-off patterns, thereby precluding interpretations of whether dairying was practiced. Because pottery production begins early in northern Africa(6) the potential exists to investigate diet and subsistence practices using molecular and isotopic analyses of absorbed food residues(7). This approach has been successful in determining the chronology of dairying beginning in the 'Fertile Crescent' of the Near East and its spread across Europe(8-11). Here we report the first unequivocal chemical evidence, based on the delta C-13 and Delta C-13 values of the major alkanoic acids of milk fat, for the adoption of dairying practices by prehistoric Saharan African people in the fifth millennium BC. Interpretations are supported by a new database of modern ruminant animal fats collected from Africa. These findings confirm the importance of 'lifetime products', such as milk, in early Saharan pastoralism, and provide an evolutionary context for the emergence of lactase persistence in Africa