UC Merced

This dissertation explores the impact of sustainable management practices, specifically the use of compost and cover crops, on soil health, soil organic carbon storage, and microbial communities in Californian nut orchard systems. This research addresses key questions surrounding the role of these practices in enhancing climate resilience and promoting long-term sustainability. Chapter 2 focuses on assessing soil organic carbon (SOC) stocks across conventionally managed almond, pistachio, peach, and walnut orchards, revealing significant variation in cumulative SOC ranging from 55 ± 5.2 Mg C ha⁻¹ to 109 ± 11.6 Mg C ha⁻¹. This variation is driven by factors such as orchard type, soil type, and irrigation methods. The chapter underscores the importance of deep soil sampling, as limiting sampling to surface soils would have underestimated SOC stocks by 60%. Method comparisons between the equivalent soil mass (ESM) and fixed depth (FD) approaches confirmed that ESM is preferable in systems where bulk density shifts are expected.Chapter 3 examines the effects of compost and cover crops on soil health indicators in almond and walnut orchards over three years. Experimental plots received annual applications of 19 Mg/ha of yard waste and manure compost, while cover crops were seeded at a rate of 13.8 kg/ha. Compost and cover crops significantly improved microbial biomass carbon (MBC) and nitrogen (MBN), with MBC increasing by 573 ± 98% in alleys and 307 ± 100% in berms, while MBN rose by 487 ± 95% in alleys and 55 ± 14% in berms. Additionally, permanganate oxidizable carbon (POXC) increased by 133 ± 23%, and short-term carbon mineralization rates were 70 ± 5% higher, indicating enhanced biological activity. Soil carbon content doubled, leading to an average SOC of 60.7 Mg C ha⁻¹ across sites by the end of the study, alongside improvements in wet aggregate stability and soil structure. Chapter 4 delves into the effects of these management practices on soil microbial diversity and structure, focusing on 16S and ITS sequencing of microbial communities in almond orchards. Soil samples were collected at four depth intervals (0-10 cm, 10-30 cm, 30-50 cm, and 50-100 cm) to assess how depth and management influence microbial communities. The results showed that compost and cover crops increased the abundance of beneficial bacterial and fungal phyla involved in organic matter decomposition and nutrient cycling. The study also emphasized that both soil depth and management practices must be considered to fully optimize microbial-plant interactions. Together, these findings highlight the critical role of compost amendments and the planting of cover crops in improving soil health, increasing carbon storage, and fostering resilient microbial communities in orchard systems. In conclusion, Chapter 5 discusses the feasibility of scaling these practices across California, limitations, and key takeaways to support management of these perennial systems for improved soil health, carbon storage, and agroecological resilience.