In the understanding of the molecular interaction between plants and their microbiome, a key point is to identify simplified models of the microbiome including relevant bacterial and fungal partners which could also be effective in plant growth promotion. Here, as proof-of-concept, we aim to identify the possible interactions between symbiotic nitrogen-fixing rhizobia and soil fungi (Trichoderma spp.), hence shed light on synergistic roles rhizospheric fungi could have in the symbiotic nitrogen fixation with host plants. We selected 4 strains of the model rhizobium Sinorhizobium meliloti and 4 Trichoderma species (T. velutinum, T. tomentosum, T. gamsii and T. harzianum). In an experimental scheme of 4 x 4 strains x species combinations, we investigated the rhizobia physiological and transcriptomic responses elicited by fungal spent media, as well as spent media effects on rhizobia-host legume plant (alfalfa, Medicago sativa L.) symbiosis. Fungal spent media had large effects on rhizobia, specific for each fungal species and rhizobial strains combination, indicating a general rhizobia genotype x fungal genotype interaction. Differential expression of a high number of genes was shown in rhizobia strains. Moreover, changes in rhizobia exopolysaccharide and auxin production were identified in response to fungal spent media. Different rhizobium-fungus combinations were also shown to have synergistic effects on alfalfa symbiotic phenotypes. Our results provide a first insight into interactions involving nitrogen-fixing rhizobia and rhizospheric fungi, highlighting the panoply of genes and genotypic interactions (fungus, rhizobium, host plant) which may concur to plant symbiosis.

Arbuscular mycorrhizal fungi (AMF), the mutualistic symbionts with most crops, constitute a research system of human-associated fungi whose relative simplicity and synchrony are conducive to experimental ecology. However, little is known about the shifts in adaptive strategies of sorghum associated AMFs where strong AMF succession replaces initially ruderal species with competitive ones and where the strongest plant response to drought is to manage these AMF. First, we hypothesize that, when irrigation is stopped to mimic drought, competitive AMF species should be replaced by AMF species tolerant to drought stress. We then, for the first time, correlate AMF abundance and host plant transcription to test two novel hypotheses about the mechanisms behind the shift from ruderal to competitive AMF. Surprisingly, despite imposing drought stress, we found no stress tolerant AMF. Remarkably, we found strong and differential correlation between the successional shift from ruderal to competitive AMF and sorghum genes whose products (i) produce and release strigolactone signals, (ii) perceive mycorrhizal-lipochitinoligosaccharide (Myc-LCO) signals, (iii) provide plant lipid and sugar to AMF and, (iv) import minerals and water provided by AMF. These novel insights into host gene expression and succession of AMF show adaptive strategies evolved by AMF and their hosts and provide a rationale for selecting AMF to reduce inputs and maximize yield in commercial agriculture. Future research opportunities include testing the specifics and generality of our hypotheses by employing genetically modified host plants, and exploring additional genes underlying the adaptive strategies in natural succession.

Rapid environmental change forces long-lived plants like trees to immigrate into zones still occupied by phylogenetically distantly related species. Does such phylogenetic isolation (PI) change the trees’ ecosystem functioning such as litter decomposition? We studied oaks (Quercus petraea) of low and high PI, reciprocally transplanting their litters to identify effect of aboveground litter quality and belowground decomposer biota. Across 8 and 14 months we quantified decomposition (mass loss, C-loss and N-loss), decomposer biota (Acari, Collembola, microbes) and 13C/12C ratio. Across 14 months, aboveground PI retarded decomposition (mass and C loss). Across 8 and 14 months, above- and belowground PI extensively altered relationships between decomposition and abundances/diversities of different soil biota, reduced microbial activity and 13C/12C ratios. Overall, coexistence of trees with distant relatives impedes and severely re-organizes C and N recycling. Such negative ecosystem feedback might prevent trees from tracking and conserving abiotic niches under environmental change.