Endophytic Fungus Drives Nodulation and N ₂ Fixation Attributable to Specific Root Exudates

Abstract

Endophytic fungi play important roles in the modification of ecosystem productivity; however, the underlying mechanisms are only partly understood. A 2-year field plot experiment verified that the endophytic fungus <i>Phomopsis liquidambaris</i> increased peanut (<i>Arachis hypogaea</i> L.) yields and significantly increased nodulation and N₂ fixation regardless of whether N fertilizers were added. Root exudates collected from <i>P. liquidambaris</i>-colonized plants significantly improved nodulation and N₂ fixation. Rhizosphere stimulation experiments further showed that colonized root exudates had significantly decreased soil nitrate (NO₃^-) concentrations, with decreased abundance and diversity of ammonia oxidizing archaea (AOA). In contrast, the abundance and diversity of diazotrophs significantly increased, and most diazotrophs identified were peanut nodulation-related strains (<i>Bradyrhizobium</i> sp.). <i>P. liquidambaris</i> symbiosis increased the expression of phenolic and flavonoid synthesis-related genes, and the derived phenolics and flavonoids could effectively increase the chemotaxis, biofilm formation, and <i>nodC</i> gene expression (nodulation-related biological processes) of the <i>Bradyrhizobium</i> strain. Metabolic pattern analysis showed that phenolics and flavonoids are more likely to accumulate to higher levels in the rhizosphere soil of peanuts colonized with <i>P. liquidambaris</i> Finally, a synthetic root exudate experiment further confirmed the underlying mechanisms for the <i>P. liquidambaris</i>-induced improvement in nodulation and N₂ fixation, i.e., that the specific root exudates derived from <i>P. liquidambaris</i> colonization decrease nitrate concentration and increase the population and biological activities of peanut nodulation-related <i>Bradyrhizobium</i> species, which beneficially enhance peanut-<i>Bradyrhizobium</i> interactions. Therefore, this study is the first to provide new insight into a positive relationship between an exotic endophytic fungus, crop nodulation, and N₂ fixation increase.<b>IMPORTANCE</b> Endophytic fungi play an important role in balancing the ecosystem and boosting host growth; however, the underpinning mechanisms remain poorly understood. Here, we found that endophytic fungal colonization with <i>P. liquidambaris</i> significantly increased the productivity, nodulation, and N₂ fixation of peanuts through the secretion of specific root exudates. We provide a reasonable mechanism explaining how <i>P. liquidambaris</i> promotes peanut nodulation and N₂ fixation, whereby the specific root exudates produced by <i>P. liquidambaris</i> colonization decrease rhizosphere soil nitrate (NO3^-) and increase the population and biological activities of peanut-nodulating-related <i>Bradyrhizobium</i> strains, which is beneficial to enhancing the peanut-<i>Bradyrhizobium</i> symbiotic interaction. Our study provides reliable empirical evidence to show the mechanism of how an exotic endophytic fungus drives an increase in nodulation and N₂ fixation, which will be helpful in erecting a resource-efficient and sustainable agricultural system.