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Productivity benefits from diversity can arise when compatible pathogen hosts are buffered by unrelated neighbors, diluting pathogen impacts. However, the generality of pathogen dilution has been controversial and rarely tested within biodiversity manipulations. Here, we test whether soil pathogen dilution generates diversity- productivity relationships using a field biodiversity-manipulation experiment, greenhouse assays, and feedback modeling. We find that the accumulation of specialist pathogens in monocultures decreases host plant yields and that pathogen dilution predicts plant productivity gains derived from diversity. Pathogen specialization predicts the strength of the negative feedback between plant species in greenhouse assays. These feedbacks significantly predict the overyielding measured in the field the following year. This relationship strengthens when accounting for the expected dilution of pathogens in mixtures. Using a feedback model, we corroborate that pathogen dilution drives overyielding. Combined empirical and theoretical evidence indicate that specialist pathogen dilution generates overyielding and suggests that the risk of losing productivity benefits from diversity may be highest where environmental change decouples plant-microbe interactions.

To feed the world population while mitigating pressing nitrogen (N) pollution problems, tremendous efforts have been devoted to developing and implementing N‐efficient technologies in crop or livestock production, but limited progress has been made. The N management improvement on a farm does not necessarily translate to N pollution reduction on a broader scale due to complex responses of natural and human systems and lack of coordination among stakeholders. Consequently, it is imperative to develop an N management framework that encompasses the complex N dynamics across systems and spatial scales, yet simple enough to guide policies and actions of various stakeholders. Here, we propose a new framework,CAFE, that defines four N management systems (Cropping,Animal‐crop,Food, andEcosystem) in a hierarchical manner, and apply it to 13 representative countries to partition N surpluses across systems in a simple and consistent manner, thereby facilitating the identification and prioritization of systems‐based intervention strategies. Surprisingly, theCropping system contributes less than half of the total N surplus within itsEcosystem for most countries, highlighting the importance of N management beyond croplands. This framework reveals that the relevant priorities and key stakeholders for enhanced N management vary among countries, such as improving theCropping‐system efficiencies in China, adjusting the animal‐crop portfolio in the Netherlands, reducing food wastage in the U.S., and lowering crop storage losses and increasing overall production capacities in African countries. As N surplus increases along theCAFEhierarchy, systems‐based intervention strategies are revealed: (a) coupling chemical fertilizers with other N sources by maintaining half of the N from manure and biological N fixation; (b) coupling animal‐crop production by reducing animal density to lower than 1.2 livestock units per hectare, and increasing self‐sufficiency of animal feed to above 50%; (c) coupling food trade with domestic demand and production; and (d) coupling population needs for economic opportunities with environmental capacity of the region. This novel framework can help unpack the “wicked” N management challenges across systems to provide new insights and tools for improving N management on and beyond farms.

Although the importance of the soil microbiome in mediating plant community structures and functions has been increasingly emphasized in ecological studies, the biological processes driving crop diversity overyielding remain unexplained in agriculture. Based on the plant–soil feedback (PSF) theory and method, we quantified to what extent and how soil microbes contributed to intercropping overyielding.

Which processes drive the productivity benefits of biodiversity remain a critical, but unanswered question in ecology. We tested whether the soil microbiome mediates the diversity‐productivity relationships among late successional plant species. We found that productivity increased with plant richness in diverse soil communities, but not with low‐diversity mixtures of arbuscular mycorrhizal fungi or in pasteurised soils. Diversity‐interaction modelling revealed that pairwise interactions among species best explained the positive diversity‐productivity relationships, and that transgressive overyielding resulting from positive complementarity was only observed with the late successional soil microbiome, which was both the most diverse and exhibited the strongest community differentiation among plant species. We found evidence that both dilution/suppression from host‐specific pathogens and microbiome‐mediated resource partitioning contributed to positive diversity‐productivity relationships and overyielding. Our results suggest that re‐establishment of a diverse, late successional soil microbiome may be critical to the restoration of the functional benefits of plant diversity following anthropogenic disturbance.