Stanford University

*** Ph.D. Thesis/ Oral Defense ***

Compost and Cover Crops for Nutrient Circularity

Anna Gomes

Wednesday, May 20, 2026, 9:30 AM

Turing Auditorium

Department of Earth System Science

Advisor: Dr. Scott Fendorf

Organic waste diversion policies and groundwater nitrate regulations are reshaping nutrient management in California agriculture, creating both new opportunities and new uncertainties for sustainable crop production. This dissertation examines how compost and non-legume cereal cover crops influence nitrogen (N) availability, nitrate-leaching risk, and soil health, with a focus on the “Salad Bowl of the World”, the Salinas Valley, California. Through laboratory incubations and field experiments, I evaluated whether these practices can improve N retention and recycling while remaining compatible with the agronomic and logistical constraints of high-value vegetable production. I investigated: (1) net N availability following co-application of compost and mineral fertilizer in soils differing in texture and fertility; (2) how cereal rye residue C/N ratio and temperature regulate N mineralization after fall incorporation; and (3) how fall versus over-winter cover crop systems affect soil moisture, soil temperature, and nitrate-leaching risk. A key contribution of this dissertation is challenging two common conceptions in nitrogen management: that compost has a predictable fixed N release, and that non-legume cover crops reliably reduce nitrate leaching no matter the management context. I also present the first Salinas Valley field trial focused on fall cover crops. 

In Chapter 1, I investigated whether compost can be spread at elevated rates without reducing short-term plant-available N when applied with fertilizer or applied to soil with high residual N. In an 84 d incubation across soils differing in texture and fertility, compost applied alone consistently caused net N immobilization, but co-application with ammonium sulfate offset this effect at moderate compost rates and often supported sustained net mineralization. These responses were strongly shaped by soil type and compost source, with compost N mineralization occurring as transient pulses rather than as a static low release rate. In Chapter 2, I examined how cereal rye residue quality and temperature regulate N release after soil incorporation. A 112 d incubation showed that low C/N rye residues readily mineralized N, whereas high C/N residues immobilized N under cooler conditions and shifted toward mineralization only as temperature increased, demonstrating that residue-derived N supply is highly sensitive to environmental conditions. 

For Chapters 3 and 4, I present results from field trials comparing short-duration fall cover crops with traditional over-winter cover crops. Our findings illustrate that fall cover crops can rapidly scavenge residual soil N and adapt more easily into intensive rotations, but their effects on nitrate-leaching risk were less consistent than over-winter cover crops. Timing of cover crop growth more consistently altered soil temperature than soil moisture, and nitrate outcomes depended on residue C/N, rainfall timing, weed pressure, soil type, and post-termination soil moisture and temperature. Overall, my dissertation shows that compost and non-legume cover crops can support improved N management in intensive vegetable systems, but their benefits depend on synchronizing N release with crop demand and hydrologic risk while accounting for soil type. These findings provide critical, data-driven guidance for growers and policymakers to refine nutrient management and cover crop timing, ultimately advancing both agricultural productivity and regional water quality objectives.