From microbial dynamics to agroecosystem resilience: soil health responses to intensified and regenerative cropping systems in Kansas

Abstract

Sustaining agricultural production while preserving soil resources remains a central challenge for farming systems in rainfed agroecosystems in the face of climate variability, land degradation, and resource limitations. Soils are the foundations of agricultural systems, yet decades of intensive tillage management and monocropping have reduced soil organic matter levels, weakened soil structure, and disrupted microbial functioning across many dryland regions. These degradative trends are especially concerning in the U.S. Great Plains, where high variability in precipitation and frequent drought events constrain both crop yields and soil health stability. In this sense, regenerative agriculture (RA) practices, such as no-tillage, intensified crop rotations, and cover cropping, have gained recognition as a framework for improving soil function through the adoption of practices that enhance soil biological activity, increase organic matter inputs, and minimize soil disturbance. Understanding how these practices influence soil processes and the overall system’s productivity over time is essential for designing productive, resilient, and sustainable farming systems. This study investigates the interactions between soil biological processes, management intensity, and regenerative agriculture practices in rainfed cropping systems commonly used in Kansas. The overarching goal was to evaluate how management transitions toward greater crop intensification and diversification, reduced soil disturbance, and continuous soil cover influence soil health and overall performance at different spatial and temporal scales. Specifically, this research aimed to: i) examine the seasonal patterns in biological, chemical, and physical soil health indicators and identify the optimal sampling period for consistent soil health assessments; ii) assess the long-term effects of cropping systems intensification and diversification on chemical, physical, and biological dimensions of soil health; and iii) evaluate the impacts of cover crop adoption on crop yield and yield stability across multiple on-farm research environments. Across the integrated studies, soil microbial biomass, soil microbial community composition, extracellular enzyme activities, soil organic carbon (SOC), and soil aggregate stability were measured as indicators of soil health. Biological soil health indicators had strong temporal variability driven by crop growth stages, residue turnover, and climatic fluctuations. Soil microbial biomass and extracellular enzyme activities, especially [beta]-glucosidase, were on average 30-100% higher during active wheat growth and peaked at flowering compared to post-harvest periods. Additionally, soil temperature and moisture were also identified as drivers of this variability. Among the sampling times, the fall sampling around winter wheat planting provided the most consistent and representative assessment of soil health. Moreover, in the five-year study, the transition from conventional tillage to continuous no-tillage significantly increased soil organic carbon by 8-12% and soil microbial biomass by 15-25% at 0-5 cm depth across all treatments. Extracellular enzyme activities and soil aggregate stability also displayed significant improvements after five years, especially at 0-5 cm depth. However, differences between crop rotations varying in crop intensity and diversity were not yet statistically significant, thus suggesting that measurable benefits from increased crop intensification and diversification require longer timeframes in these situations. At the on-farm scale, cover crop adoption increased soil health. Notably, soil total microbial biomass and [beta]-glucosidase increased by up to 40% and 30%, respectively, across sites. Soil organic carbon also increased modestly (0.2 – 0.4 g kg⁻¹ yr⁻¹) in the cover crop treatments relative to the no cover crop treatments. Despite the improvements in soil health, crop yields of corn, soybean, and winter wheat were statistically similar between treatments across locations and years. Crop yield variability was attributed to precipitation patterns associated with each location, with the cover crop treatments exhibiting a neutral or slightly positive effect under drier conditions, thus indicating a role in buffering yield losses during low-rainfall years rather than increasing average absolute yields. Together, these findings demonstrate that biological soil health indicators are highly sensitive to short-term climatic and crop growth variation, and that improvements from regenerative agriculture practices accumulate progressively over time. The transition to continuous no-tillage systems rapidly enhances surface soil function, while the benefits of increased crop intensity and diversity, as well as cover cropping, emerge more gradually through sustained organic inputs and better soil function. Overall, this research provides a comprehensive, multi-scale assessment of soil health development under intensified, diversified, and regenerative cropping systems management. Through the link of seasonal microbial dynamics, long-term system evolution, and on-farm agronomic performance, this dissertation contributes to a deeper understanding of how soil processes modulate the resilience of rainfed agriculture in Kansas. These results highlight that the consistent application of regenerative agriculture practices and principles offers a viable pathway toward building more sustainable, profitable, efficient, and resilient farming systems in the U.S. Great Plains region.