Host-associated microbes, collectively known as the host microbiota, have manifold effects on host biology. Like other animals, insects establish various symbiotic associations with their microbial communities that shape their individual phenotype and fitness. In particular, the native gut bacteria of insect vectors were recently shown to modulate their susceptibility to human pathogens. Compared to vertebrates, insects tend to have less diverse but potentially more labile gut microbial associations. In mosquitoes, considerable variation in bacterial taxa observed in the gut of field-collected adults compared to laboratory-reared individuals suggests a strong influence of the environment. Therefore, diversity of the gut bacteria of mosquitoes could mediate an environmental influence on vector-borne pathogen transmission. This project will investigate how habitat-related gut bacteria influence vectorial capacity of the mosquito Aedes aegypti, a major vector of dengue, Zika, yellow fever and chikungunya viruses. We hypothesize that gut bacterial diversity and community structure drive variation in Ae. aegypti vectorial capacity for arboviruses. To test this hypothesis, we will take advantage of the co-existence in Sub-Saharan Africa of a ‘sylvatic’ ecotype of Ae. aegypti found in forested habitats, ecologically similar to the ancestral form of the species, and the human-adapted ‘domestic’ ecotype that thrives in urbanized environments. Sylvatic and domestic larval breeding sites will be used as the source of contrasted bacterial communities to which mosquitoes are naturally exposed. In a pilot study, we observed that the composition of bacterial communities differed significantly between sylvatic and domestic larval breeding sites. We expect that mosquitoes respond differentially at the physiological level to the presence of distinct bacterial communities during larval development, which has consequences on adult life history traits and therefore vectorial capacity. The proposed approach combines fieldwork in Senegal (Task 1), analyses of bacterial diversity by culture-dependent (isolation) and culture-independent (metataxogenomics and metatranscriptomics) methods (Task 2), and functional assays in vivo (Task 3). We will characterize the bacterial microbiota and microbiome in mosquito midguts from larvae and adult females and in the water of larval breeding sites. We will select relevant bacterial isolates from each mosquito ecotype to generate mono- and poly-associated gnotobiotic mosquitoes in the laboratory by contaminating axenic (bacteria-free) larvae derived from field-collected mosquitoes. Isolates will be prioritized according to a set of criteria including ecological distribution, prevalence, abundance and known biological properties. We will compare life history (age at pupation, adult body size, survival, fecundity), physiological (immune responses, vector competence), and behavioral (host preference) traits in gnotobiotic mosquitoes. This interdisciplinary project will provide novel information on the link between ecology, symbiotic gut bacteria and vectorial capacity of mosquitoes. The novelty of our approach is to examine the diversity of symbiotic gut bacterial communities as a driver of natural variation in vectorial capacity, using a combination of descriptive and experimental methods. This project will address a major knowledge gap that exists between simplified model systems that study the mechanistic basis of vector-virus interactions in the laboratory and the complexity of natural ecosystems.

Global change is a new challenge for sustainable agriculture. We aim at understanding/exploiting plant growth-promoting rhizobacteria (PGPR) to maintain wheat yield despite reduction of nitrogen fertilisers and irrigation water, by enabling a PGPR-based wheat breeding strategy. The rationale is that indigenous PGPR populations occur in most temperate wheat soils, but (i) wheat accessions differ in the ability to benefit from PGPR and (ii) past breeding for high-input conditions has overlooked these beneficial interactions. The objectives are to (i) screen a large panel of wheat diversity based on induction of gene expression in emblematic PGPR strains, (ii) determine wheat chromosomal regions involved in the interactions between roots and emblematic PGPR strains, (iii) validate these genetic determinants and PGPR benefits in controlled environments and (iv) assess their significance under combined abiotic constraints (nitrogen and water limitations) in field experiments. This will facilitate the breeding of genitor varieties with a successful interaction with PGPR by providing molecular markers linked to chromosomal regions associated to this interaction. The project is organized in three experimental Tasks. The first task aims at identifying wheat genotypes triggering the expression of key phytostimulation genes in PGPR. A collection of 200 bread wheat accessions mainly sub-sampled from the INRA bread wheat core collection of 372 accessions (372CC) will be screened, using an original phenotyping assay, for induction of bacterial genes important for successful functioning of Azospirillum and Pseudomonas PGPR strains on roots. Results will be validated using complementary methodology on a subset of 20 wheat lines showing a contrasted behavior with PGPR strains. The second task aims at identifying wheat genomic regions involved in plant × PGPR interactions. Candidate genes and physiological markers relevant to characterize the plant’s responses to Azospirillum and Pseudomonas PGPR (which are widely found in French arable soils) will be identified by transcriptomics (combined with metabolomics), particularly under N and water limitations. The candidate genes will be validated using quantitative RT-PCR, and new SNP markers of the wheat genome will be developed for about 100 of the most relevant genes. An association genetics approach will be carried out using PGPR gene induction data from Task 1, and wheat accessions will also be compared based on agronomic performance data already available. The third task will assess in the field the wheat lines selected in Task 1 in terms of their ability to (i) interact with functional microbial populations containing PGPR strains that occur naturally in soils and (ii) adjust to nitrogen limitation occurring alone or in combination with drought. Multilocal field experiments will be used. The CNRS Lyon partner (coordinator) has long-term experience in the genetics of Azospirillum and Pseudomonas PGPR strains and their modes of action, and has expertise in molecular analysis of indigenous PGPR populations and rhizosphere functioning. The INRA Clermont-Ferrand partner is a major actor in wheat genomic research and association genetics, and has expertise in the characterisation of wheat genetic resources and physiological aspects of yield and seed quality. Finally, Biogemma is a leading European plant biotechnology company with long standing expertise in wheat genetics and transcriptomics. Altogether, the partners’ skills and complementary expertise combined with the genetic and genomic resources available for wheat ensure a successful project that will bring new insights into key plant-PGPR interactions and enable a novel PGPR-based wheat breeding strategy adapted to global change conditions.

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.

Thanks to their particular biotic community, soils vary in their suppressiveness towards root diseases caused by phytopathogenic fungi on crop plants. However, the link between soil biodiversity and suppressiveness and the range of deleterious organisms that are controlled by this mechanism are poorly characterized. This project aims at developing an integrated understanding of the relation between soil biodiversity and crop protection, using soils of contrasting suppressiveness status in several countries, in a context of global change materialized by changes in crops and in pathogen/pest importance. Two approaches will be followed: (i) the comparison of emblematic soils known to be suppressive or conducive (such soils are available in Switzerland and France), and (ii) the comparison of soils under different agricultural management strategies (e.g. with soil organic matter-based management practices aiming at enhancing soil biodiversity, including in long-term experiments), which have the potential to result in different levels of suppressiveness (such conditions have been investigated in Germany). First, current knowledge gaps on suppressiveness will be filled, based on (i) chromatographic profiling of soil (to assess soil organic matter quality, which might represent a potential indicator of suppressiveness), (ii) assessment of disease suppressiveness in relation to crop plant physiology and defense status, (iii) metabarcoding of microbial taxonomic biodiversity, and (iv) molecular monitoring of microbial functional groups under controlled conditions. Second, the significance of suppressiveness under global change will be characterized, by assessing (i) the extent of disease suppressiveness on emerging crops (with a focus on wheat), (ii) the possibility of suppressiveness towards insect pests, and (iii) the contribution of arbuscular mycorrhizal fungi, a symbiotic partner neglected so far in this context, to disease suppressiveness. Third, the applicability of project findings to agronomic field conditions will be determined, based on specific monitoring of (i) phytopathogens and (ii) insect pest populations, (iii) metabolomic profiling of crops, and (iv) the analysis of the rhizosphere microbiota in fields. The project involves a multidisciplinary consortium of 6 partners in 3 countries, ranging from prominent academic research groups to field extension specialists to facilitate outreach to the farming community and other stakeholders. This project is expected to generate new knowledge on phytoprotection and the importance of biodiversity in suppressiveness. This knowledge will be important to develop novel biodiversity indicators of soil quality, and to define management strategies to improve crop health in soils with poor or no suppressiveness properties and facing the challenge of global change.

El Hamico designs and validates an innovative, low-cost, on-site, and ecological bioremediation solution, suitable to sewer pipes, artificial channels and streams, and thus at improving the security and the quality of degraded urban river while lowering the bioremediation costs. El Hamico proposes a new electrochemical way of controlling and directing microbial functioning toward some goals expected by human, by the management of anode potential. Additionally, it not only will pave a new way to new bio-remediation technologies and will develop innovative tools and methods of the water management and effluent, its management concept of microbial populations and activities may be extended to all processes requiring control of anaerobic microbial functioning. To have an operational objective allowing directing our project towards real applications, El Hamico focuses on environmental applications: the management of microbes involved in the biodegradation; but it could have applications in the food and health fields, wherever the selection and monitoring of microbial populations and their functioning are needed.