Our current understanding suggests that nutrient management strategies applied to agricultural soils over multiple years are required to cause major and stable shifts in soil microbial communities. However, some studies suggest that agricultural soils can benefit even from sporadic, single additions of organic matter. Here we investigate how single additions of high-quality organic matter can cause significant shifts in microbial soil communities over multiple cropping cycles. We grew radishes in a tropical Oxisol soil for six crop cycles after a single application of a high-nitrogen compost or urea. At planting and before biomass harvest, we sampled soils influenced by the radish rhizosphere and sequenced bacterial and archaeal 16S and fungal ITS rDNA marker genes. We measured microbial richness and diversity, community composition and structure, and constructed correlation networks to predict cross-domain microbial interactions. We found that a single application of compost, compared to urea or control, resulted in a persistent improved plant biomass response and led to sustained changes in the soil microbial community throughout the duration of the 227-day study. Compost altered the structure of both the fungal and prokaryotic microbial communities, introduced new microorganisms that persisted in the resident soil system, and altered soil microbial correlation network structure and hub taxa. In contrast, fertilization with urea did not significantly alter the structure of soil microbial communities compared to the control but reduced network complexity and altered hub taxa. This study highlights the significant impacts that high-quality organic matter fertilization can exert on agricultural soil microbiomes and adds to the growing body of knowledge on using organic fertilizers as a way to steer the soil microbiome toward a healthier soil.

Environmental indicators for nitrogen (N) use efficiency (NUE) based only on N inputs and N removal are becoming widely used in science, policy, and commercial supply chains to track the sustainability of food production. However, these indicators do not reflect the contribution of inherent soil productivity, which can supply half of crop demand and is therefore a core principle in determining how much fertilizer is needed and the corresponding risk of N losses. Using a global dataset of optimal N rates for crop production, we evaluated the performance of conventional (N recovery efficiency) and simplified NUE indicators to understand their relationship and respective limitations, helping inform policy efforts for simultaneously meeting food production and sustainability goals. A key finding is that conventional agronomic approaches designed to optimize crop productivity and profit related to N fertilizer inputs have tradeoffs for environmental performance, with only 35 and 31 % of observations (n=448) falling within sustainable ranges for NUE. Meanwhile, simplified NUE indicators such as N balance or the ratio of N outputs to inputs were unable to detect sites with inherently low N recovery efficiency and high risk of N losses, highlighting a weakness of neglecting soil N supply in their calculations. Together these results suggest the need for a combined approach that merges insights from locally available agronomic data on N recovery efficiency with global environmental thresholds for NUE. Using our findings as a case study, we propose new steps forward for evaluating NUE in different cropping systems and regions to enhance food security while mitigating N pollution.

Nitrogen (N) is an essential but generally limiting nutrient for biological systems. Development of the Haber-Bosch industrial process for ammonia synthesis helped to relieve N limitation of agricultural production, fueling the Green Revolution and reducing hunger. However, the massive use of industrial N fertilizer has doubled the N moving through the global N cycle with dramatic environmental consequences that threaten planetary health. Thus, there is an urgent need to reduce losses of reactive N from agriculture, while ensuring sufficient N inputs for food security. Here we review current knowledge related to N use efficiency (NUE) in agriculture and identify research opportunities in the areas of agronomy, plant breeding, biological N fixation (BNF), soil N cycling, and modeling to achieve responsible, sustainable use of N in agriculture. Amongst these opportunities, improved agricultural practices that synchronize crop N demand with soil N availability are low-hanging fruit. Crop breeding that targets root and shoot physiological processes will likely increase N uptake and utilization of soil N, while breeding for BNF effectiveness in legumes will enhance overall system NUE. Likewise, engineering of novel N-fixing symbioses in non-legumes could reduce the need for chemical fertilizers in agroecosystems but is a much longer-term goal. The use of simulation modeling to conceptualize the complex, interwoven processes that affect agroecosystem NUE, along with multi-objective optimization, will also accelerate NUE gains.