Fungal communities associated with roots play a key role in nutrient uptake and in mitigating the abiotic and biotic stress of their host. In this study, we characterized the roots mycobiome of wild and cultivated pearl millet [Pennisetum glaucum (L.) R. Br., synonym: Cenchrus americanus (L.) Morrone] in three agro-ecological areas of Senegal following a rainfall gradient. We hypothesized that wild pearl millet could serve as a reservoir of endophytes for cultivated pearl millet. We therefore analyzed the soil factors influencing fungal community structure and whether cultivated and wild millet shared the same fungal communities. The fungal communities associated with pearl millet were significantly structured according to sites and plant type (wild vs cultivated). Besides, soil pH and phosphorus were the main factors influencing the fungal community structure. We observed a higher fungal diversity in cultivated compared to wild pearl millet. Interestingly, we detected higher relative abundance of putative pathotrophs, especially plant pathogen, in cultivated than in wild millet in semi-arid and semi-humid zones, and higher relative abundance of saprotrophs in wild millet in arid and semi-humid zones. A network analysis based on taxa co-occurrence patterns in the core mycobiome revealed that cultivated millet and wild relatives had dissimilar groups of hub taxa. The identification of the core mycobiome and hub taxa of cultivated and wild pearl millet could be an important step in developing microbiome engineering approaches for more sustainable management practices in pearl millet agroecosystems.

Rhizosphere microbial communities are important components of the soil-plant-atmosphere continuum in paddy field ecosystems where they contribute to nutrient cycling and rice productivity. However, the rhizosphere microbial sensitivity to anthropic soil disturbance across plant growth stages remains little investigated. Here, we tracked the effects of long-term (> 25 years) N and NPK-fertilization on bacterial and archaeal community inhabiting the rice rhizosphere at three growth stages (tillering, panicle initiation and booting). Our results reveal that the effect of long-term inorganic fertilization on rhizosphere microbial communities varied with growth stage and that the bacterial and archaeal community differed in their response to N and NPK-fertilization. The microbial communities inhabiting the rice rhizosphere at the panicle initiation appear to be more sensitive to long-term inorganic fertilization than those at the tillering and booting stage. However, the effect of growth stage on microbial sensitivity to long-term inorganic fertilization was more strongly pronounced for bacterial than archaeal community. Furthermore, our results reveal dynamics of bacteria and archaea co-occurrence patterns in the rice rhizosphere, with differentiated bacterial and archaeal pivotal roles in the microbial inter-kingdom networks across growth stages. Hence, our study brings new insights on rhizosphere bacteria and archaea co-occurrence and sensitivity to long-term inorganic fertilization across growth stages in field-grown rice. By identifying one of the critical rice growth stages during which rhizosphere microbial communities are highly sensitive to inorganic fertilization, our results open new avenues for developing appropriate strategies in microbiome engineering to mitigate biotic and abiotic stress and improve crop yields.