Maize farming requires high amounts of N fertilizer, with adverse environmental effects and insufficient agronomic sustainability. Certain maize genotypes can be colonized endophytically by atmospheric nitrogen (N2)-fixing bacteria, but the agronomic potential of endophytic N2-fixation is not fully exploited. Our hypothesis is that a scientific understanding of the mechanisms controlling these endophytic N2-fixing associations combined with an assessment of maize genetic diversity and specificity with regards to this interaction could be useful to optimize endophytic N2-fixation and exploit it in agriculture. The aim of the project is thus to better understand the interactions between bacterial endophytes fixing N2 and maize, in order to identify and select maize genotypes that will be able to use the fixed N more efficiently and thus will be less dependent on mineral N fertilization. This will be achieved by developing a multidisciplinary approach integrating molecular physiology, the assessment of whole-plant N responses to the endophytic interaction, molecular plant-microbe ecology and agronomy. We will characterize both at the physiological and molecular levels the atmospheric N2-fixing endophytic interaction using a large-scale integrated transcriptomic, proteomic and metabolomic approach implemented with two established Herbaspirillum and Azospirillum models of N2-fixing endophytic bacteria and 19 representatives of European and American maize genetic diversity. This will allow identifying the genetic and physiological determinants required for an efficient N2-fixing endophytic association. Such study, combined to a genome-scale metabolic modelling approach, will then help obtaining an integrated view on the plant’s response to the endophytic interaction and on its adaptation to temperate climatic conditions. A molecular screening will also be conducted to obtain effective endophytic N2-fixing bacteria for agronomic improvement of maize cultivation at lower N input under temperate pedoclimatic conditions. To this end, we will implement a novel molecular screening strategy, using not only microbial traits but also the plant biological markers of the ability of the plant to utilize the fixed N more efficiently. Production of innovative fertilizers based on inoculant technology will be then undertaken to assess under agronomic conditions, if the maize genotypes exhibiting the best endophytic N2 fixation also exhibit improved performance in terms of biomass and grain production. Such an agronomic evaluation will also be conducted with commercial hybrids known for their high performance under reduced N fertilization. The project focuses on maize, a crop of major economic importance both in France and worldwide. Maize is particularly relevant for this project for four reasons. First, it has a huge genetic diversity, allowing the improvement of both its agronomic and environmental performances in terms of N fertilizer usage. Second, maize is also a model crop particularly suited to perform integrated agronomic, physiological and molecular genetic studies during the whole plant developmental cycle. Third, many maize genotypes are colonized endophytically by N2-fixing bacterial endophytes. Thus, deciphering the relationships between maize physiological status and the provision of “free” N by the bacterial endophytes will deliver science to underpin and implement novel agricultural strategies aimed at reducing the use of N mineral fertilisers in maize farming, which will be facilitated by the industrial development in this project of fertilizer micro-granules serving as carriers for N-fixing endophytic inoculant.

The microbiota can play major roles mediating host adaptation. Plants rely on the ancestral Arbuscular Mycorrhizal (AM) symbiosis to supplement their phosphorus nutrition. However, recent findings indicate that the AM symbiosis is not essential. Indeed, there are at least three ‘non-mycorrhizal’ plant families for which the loss of the AM symbiosis was not compensated by any major nutritional innovation that we know of. Certain non-mycorrhizal Brassicaceae were discovered to associate with new types of root endophytic fungi capable of transferring phosphorus to the plant, suggesting the existence of yet-unknown nutritional associations between non-mycorrhizal plants and their microbiota. This project aims to uncover and describe these associations by developing a novel approach to follow phosphorus in rhizosphere microbial communities. We hypothesize that non-mycorrhizal plants adapted to the loss of the AM symbiosis by establishing new nutritional microbial partnerships promoting their phosphorus nutrition.

Plants have developed diverse strategies to effectively uptake the scarce nitrogen (N) resource in soils with low pH and low N availability, typical for most forests. Some plant species can directly affect nitrification in soil through a process known as biological nitrification inhibition (BNI). Plants with BNI capacity release specific compounds to the soil via decomposition of plant litter or root exudation that inhibit nitrification pathways. BNI compound(s) and nitrifier group(s) targeted have been identified only for a few ecosystems and a few perennial grass or cultivated species. However, our knowledge on BNI in forest ecosystems is still very limited. Indeed, the questions about the nature of BNI compounds produced by trees and their effects on nitrifier community remains unanswered. Therefore, FORBES addresses this challenge by digging deeper than ever done before into the BNI capacity of forest tree species. More specifically, our general aim is to uncover the BNI capacity from forest tree species by identifying the compounds responsible for BNI and by testing their effect on target and off-target microbial strains and complex communities. To do so, we will use complementary approaches at the interface between microbiology, soil microbial ecology, forest science and chemical ecology, and we will address the following questions: (i) what is the relative contribution of root exudates vs litter to the production of BNI compounds by tree species?, (ii) which compounds produced by tree species explain their BNI capacity and their effect on multiple nitrifier strains? and (iii) what are the effects of BNI compounds on complex target (i.e. Nitrobacter) and off-target (i.e. other nitrifiers, denitrifiers) microbial communities in soil?

Due to sanitary risks associated with the presence of the Asian tiger mosquito Ae. albopictus in recently invaded urban areas, better knowledge is needed to evaluate the social (behavior, practices) and environmental (human impact on the environment) factors as risk factors on the emergence of vector-borne diseases. Indeed, the urban mosaic provides a wide range of water containers suitable for larval development. It was suggested for certain mosquito species that anthropogenic disturbances of the environment can have a direct effet on the physiology of mosquitoes but also an indirect effect by impacting their microbiota. However, it is now admitted that those microorganisms, which are predominantly acquired and influenced by water of breeding sites, play a key role in mosquito biology and their ability to transmit pathogens. By combining in situ observations and experiments in controlled environments, this project aims to assess the combined impact of human practices (via a survey of opinion and practices) and human activities (emission of pollutants) on the proliferation of the Asian tiger mosquito in urban areas. Improving our knowledge of the biotic and abiotic factors involved in the ecology of the tiger mosquito in urban environments could lead to a new reflection for the implementation of recommendations applicable to the inhabitants and to the actors of health and the city in order to create a durable habitat that is poorly favorable to the colonization by this mosquito.

Meiotic recombination is a key aspect of our biology. By ensuring proper chromosome segregation during meiosis and maintaining genome integrity, it plays a crucial role in our fecundity. Recombination also has an essential long-term evolutionary function, facilitating adaptation through linkage dissipation. However, recent progress in our understanding of the underlying molecular mechanisms suggests that recombination also has a dark side. Intra-genomic conflicts, mediated by two particular forms of meiotic drive called biased gene conversion, causing transmission biases at the level of the population, are now suspected to stand at the core of the dynamics of recombination. Such intra-genomic conflicts have a strong impact on the proper functioning of recombination and meiosis, as well as on genome-wide fitness landscapes, potentially contributing a substantial genetic load. More fundamentally, these conflicts are intrinsically the result of an interplay between the molecular mechanisms involved in the regulation of recombination and the long-term effects of biased gene conversion at the level of the population. As a consequence, recombination stands at the crossroad between molecular, cellular and evolutionary biology, and a full understanding of its regulation requires an integrated perspective, articulating together multiple domains of modern biology. This multi-disciplinary collaborative research project aims to arrive at an integrated understanding of recombination and biased-gene conversion, including their regulation, their impact on genome structure and their consequences on fitness, health and fecundity. The project will combine experimental, population genetic and comparative genomic approaches. It will be focused primarily on mammals and humans, while benefiting from a macro-evolutionary perspective. Its main contributions will be as follows. First, the current working model of the dynamics of recombination in mammals (the Red Queen model), which fully accounts for intra-genomic conflicts and biased gene conversion, will be extensively tested using a combination of experimental approaches (ChipSeq, sperm typing and high throughput sequencing) and comparative analyses. In parallel, statistical population genetic and phylogenetic approaches will be developed, leading to new bioinformatic tools allowing unbiased characterization of genomic fitness landscapes and selective regimes acting on protein-coding genes, correcting for the confounding effects of biased gene conversion. Finally, the taxonomic distribution and the ultimate causes of biased gene conversion will be investigated, using a combination of experimental, comparative and theoretical approaches. Altogether, this project will therefore arrive at an integrated understanding of recombination and gene conversion, organizing the proximal causes and the ultimate drivers into a coherent global view. Relying on ambitious sequencing projects, it will produce important new data pertaining to key aspects of these biological questions. It will also lead to the development of improved statistical and bioinformatic tools for decoding functional and selective features of genomes, and will therefore have a substantial impact on current bioinformatics and applied genomics. The project will be conducted by a multi-disciplinary consortium gathering four French research teams, based in Lyon (LBBE, Lartillot and Duret; LEM, Nesme) and Montpellier (IGH, de Massy; ISEM, Galtier), with complementary expertise in molecular, cellular, computational and evolutionary biology. A total budget of ~ 580 000 euros is requested.