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.

"More than half of the world population is now living in cities. Few reports have addressed issues regarding the microbiological quality of urban surfaces and their potential role as vectors of bacterial pathogens. Here, we present an original PRME proposal exploring the functioning of urban surface microbiomes, and the selective forces that can favor increases in Human bacterial pathogens over city surfaces and impact their virulence properties. We propose a field based project that will explore urban microbiomes of three sites (in France) previously found to harbor hazardous actinobacteria like Nocardia cyriacigeorgica but also Pseudomonas cells including highly cytotoxic P. aeruginosa. The relationships between socio-urbanistic parameters of the city, pollutants and biological components of urban surface sediments (made of dusts, plant debris, various wastes), and synurbic bacterial taxa will be studied. Global ""-omics"" approaches based on DNA and RNA will be implemented to decipher the urban surface microbiome and define the main selective pressures impacting these organizations. The defined tasks will imply studying: (i) the interactions between the triad (termed BFP) bacteria, fungi and photosynthetic organisms (such as microalgae and bryophytes), and certain chemical pollutants observable in urban surface sediments, in order to identify the key parameters (e. g. protective barriers conferred by microalgae, functional synergies) explaining the success of certain bacterial pathogens in these environments; (ii) the loads of bacterial virulence genes in urban sediments defined by PCR assays, and meta-genomic and meta-transcriptomic analyses, in order to specify the hazards for Human health; and (iii) the pathogenomic innovations observed in synurbic pathogenic bacteria, and the assessment of the risks generated for Human health in the contexts of lung and intestinal exposures (through Human cell lines). These data will shed new light on the health risks associated with urban surface microbiomes."

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.

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.

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.