Plants constantly interact with the microbes that surround them, engaging in a spectrum of relationships ranging from beneficial to pathogenic. These relationships include mutualisms, where both partners benefit; pathogenic interactions, which harm the plant host; and commensal associations, which have a neutral effect. Among mutualisms, two fundamental forms of plant–microbe interactions are the plant-mycorrhizal symbiosis and the legume-rhizobium symbiosis. Evidence from fossils suggests that the mycorrhizal symbiosis evolved concurrently with plant terrestrialization [1]. The legume-rhizobium symbiosis, in turn, is thought to have evolved from plant-mycorrhizal symbiosis [2]. Mycorrhizal and rhizobial symbioses promote plant uptake of nutrients such as phosphorus and nitrogen; in exchange, plants provide photosynthesis-derived carbon to their microbial partners [3], [4]. These symbiotic relationships not only benefit plant fitness and productivity, but also act as key drivers of biodiversity, ecosystem protection, and agricultural sustainability [1], [5]. It is estimated that plants allocate more than 13 Gt of CO2 equivalent annually to mycorrhizal fungi, significantly influencing global soil carbon sequestration [6]. Despite the recognized importance of plant–microbe symbioses, the molecular mechanisms underlying their initiation and maintenance remain largely elusive.

The recognition of mycorrhizal fungi-derived Myc factors by plants is crucial for establishing symbiosis. However, mutualistic and pathogenic microbes coexist in soil, and fungal pathogens produce molecules similar to Myc factors that can trigger plant immune responses [7]. How plants discriminate between microbial friends and foes to selectively activate symbiosis or immunity is yet to be resolved. Plants also interact with a myriad of commensal microbes in the rhizosphere, sustaining them through nutrients present in root exudates [8]. These commensals can enhance plant growth and health through direct mechanisms such as hormone production, nitrogen fixation, and phosphorus mobilization, as well as indirectly by interacting with other mutualistic or pathogenic microbes, thereby collectively influencing plant fitness [9], [10]. Thus, elucidating the continuous spectrum of the plant–microbe holobiont—from mutualism to commensalism to pathogenesis—has become a significant interdisciplinary frontier, offering new insights for both fundamental biology and translational agriculture.

Modern agriculture relies heavily on chemical fertilizers and pesticides. The harnessing of plant–microbe symbioses offers a promising pathway toward more sustainable agricultural practices with a reduced environmental footprint. Since 2013, our group has been dedicated to unveiling the molecular mechanisms of plant–microbe symbioses and advancing their applications in agriculture. Our work focuses on addressing the following key questions: (1) How are nutrient exchange and regulation sustained in the mycorrhizal symbiosis? (2) How do plants discriminate between beneficial and pathogenic microbes? (3) Why are legume plants able to form root nodules for nitrogen fixation? In the following sections, I will retrospect the progress made in addressing these questions, discuss current applications, and outline future research directions to enable successful field applications.