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International audience; Shifts in the frequency and magnitude of rain events (precipitation patterns) associated with climate change may impact ecosystem nitrogen and carbon cycling through effects on plant physiology and soil microbial activity. Here, we determined how the combination of temporal irrigation distribution and N supply affects plant-microbial C and N dynamics in microcosms with winter wheat. First, we investigated legacy effect of 12 weeks of contrasting irrigation distribution (frequent and small versus infrequent and large water inputs) and N inputs (high versus low) on plant biomass, organic and inorganic N pools, and potential nitrification and denitrification rates. Second, we investigated legacy effects of these treatments on C and N fluxes in plants and microbes over 29 h after a rewetting event, using 13C-CO2 and 15N-NH4 labeling. We found that irrigation distribution and N input led to significant differences in plant responses and soil C input, setting the scene for the rewetting response. Immediately after rewetting, microorganisms outcompeted plants for soil mineral N. However, over time, the net outcome of competition improved for plants regardless of water or N input history. Further, we found that a history of frequent irrigation led to more productive plants (biomass and rate of photosynthesis) and increased their net competitiveness for N over microorganisms. This suggests that the shift toward more extreme fluctuations in soil moisture predicted by climate forecasts for most temperate zones may have negative implications for plant productivity due to altered N dynamics between plants and soil microorganisms.

International audience; Plant-plant associations, notably cereal-legume intercropping, have been proposed in agroecology to better value resources and thus reduce the use of chemical inputs in agriculture. Wheat-pea intercropping allows to decreasing the use of nitrogen fertilization through ecological processes such as niche complementarity and facilitation. Rhizosphere microbial communities may account for these processes, since they play a major role in biogeochemical cycles and impact plant nutrition. Still, knowledge on the effect of intecropping on the rhizosphere microbiota remains scarce. Especially, it is an open question whether rhizosphere microbial communities in cereal-legume intercropping are the sum or not of the microbiota of each plant species cultivated in sole cropping. In the present study, we assessed the impact of wheat and pea in IC on the diversity and structure of their respective rhizosphere microbiota. For this purpose, several cultivars of wheat and pea were cultivated in sole and intercropping. Roots of wheat and pea were collected separately in intercropping for microbiota analyses to allow deciphering the effect of IC on the bacterial community of each plant species/cultivar tested. Our data confirmed the well-known specificity of the rhizosphere effect and further stress the differentiation of bacterial communities between pea genotypes (Hr and hr). As regards the intercropping effect, diversity and structure of the rhizosphere microbiota were comparable to sole cropping. However, a specific co-occurrence pattern in each crop rhizosphere due to intercropping was revealed through network analysis. Bacterial co-occurrence network of wheat rhizosphere in IC was dominated by OTUs belonging to Alphaproteobacteria, Bacteroidetes and Gammaproteobacteria. We also evidenced a common network found in both rhizosphere under IC, indicating the interaction between the plant species; this common network was dominated by Acidobacteria, Alphaproteobacteria, and Bacteroidetes, with three OTUs belonging to Acidobacteria, Betaproteobacteria and Chloroflexi that were identified as keystone taxa. These findings indicate more complex rhizosphere bacterial networks in intercropping. Possible implications of these conclusions are discussed in relation with the functioning of rhizosphere microbiota in intercropping accounting for its beneficial effects.

International audience; Healthy 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.

SPE EA BIOmE GESTAD INRA SUPDAT; International audience; How plant species associations affect the rhizosphere microbiota, in comparison to each plant species, has been overlooked. Here we investigated how bi-species plant associations affect total bacterial and N-cycling microbial communities (nitrate reducers and ammonia-oxidizers), as an example of functional communities, at low and high soil N levels. At low N level, the total bacterial abundance in the rhizosphere of the bi-species associations was significantly higher than that of either plant on its own for half of the bi-species associations. For the other associations, the bacterial abundance was not different from the corresponding mono-species cultures. The abundance of several N-cycling guilds was also enhanced by some of the bi-species associations with increases of up to 125% and no negative effects were recorded, which highlights the importance of plant diversity in agro-ecosystems.

International audience; The root-knot nematode (RKN) Meloidogyne mayaguensis is considered as one of the most damaging RKN species because of its extremely wide host range. Recent surveys have shown the rapid spread of this parasite in agro-ecosytems, often making crop cultivation not viable in the heavily infested areas. Here, we report the identification, molecular cloning, genomic organisation and sequence analysis of a new satellite DNA (satDNA) family from M. mayaguensis (named pMmPet). It is comprised of two groups of A+T rich, tandemly repeated units of 174 and 180 bp, respectively. Using these sequences as targets, hybridisation and PCR experiments performed on a wide collection of 44 populations belonging to 15 RKN species showed that the pMmPet family could only be detected in the 16 M. mayaguensis populations tested. In addition, because of their repetitive nature, positive detection of pMmPet sequences was achieved in single individual nematodes. Therefore, the repeated sequence described here possesses features that make it an excellent candidate for use as a specific and extremely sensitive tool for the accurate detection and identification of this invasive pest on a routine basis. Clearly, monitoring the occurrence and spread of M. mayaguensis at the domestic and international levels are needed to avoid wholesale loss of agricultural resources in the infested regions.

Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the assembled sequence of this asexually reproducing nematode, totaling 86 Mb, exists in pairs of homologous but divergent segments. This suggests that ancient allelic regions in M. incognita are evolving toward effective haploidy, permitting new mechanisms of adaptation. The number and diversity of plant cell wall-degrading enzymes in M. incognita is unprecedented in any animal for which a genome sequence is available, and may derive from multiple horizontal gene transfers from bacterial sources. Our results provide insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategies

International audience; Plant species are important drivers of soil microbial communities. However, how plant functional traits are shaping these communities has received less attention though linking plant and microbial traits is crucial for better understanding plant-microbe interactions. Our objective was to determine how plant-microbe interactions were affected by plant traits. Specifically we analyzed how interactions between plant species and microbes involved in nitrogen cycling were affected by plant traits related to nitrogen nutrition in interaction with soil nitrogen availability. Eleven plant species, selected along an oligotrophic-nitrophilic gradient, were grown individually in a nitrogen-poor soil with two levels of nitrate availability. Plant traits for both carbon and nitrogen nutrition were measured and the genetic structure and abundance of rhizosphere microbial communities, in particular the ammonia oxidizer and nitrate reducer guilds, were analyzed. The structure of the bacterial community in the rhizosphere differed significantly between plant species and these differences depended on nitrogen availability. The results suggest that the rate of nitrogen uptake per unit of root biomass and per day is a key plant trait, explaining why the effect of nitrogen availability on the structure of the bacterial community depends on the plant species. We also showed that the abundance of nitrate reducing bacteria always decreased with increasing nitrogen uptake per unit of root biomass per day, indicating that there was competition for nitrate between plants and nitrate reducing bacteria. This study demonstrates that nitrate-reducing microorganisms may be adversely affected by plants with a high nitrogen uptake rate. Our work puts forward the role of traits related to nitrogen in plant-microbe interactions, whereas carbon is commonly considered as the main driver. It also suggests that plant traits related to ecophysiological processes, such as nitrogen uptake rates, are more relevant for understanding plant-microbe interactions than composite traits, such as nitrophily, which are related to a number of ecophysiological processes.