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Food & Soil Health

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Food security is a major concern in the face of climate change, population growth, and planetary boundaries. Healthy soils are foundational to sustainable (and safe) food production. To ensure sustainable food production and human health, we study contaminant and nutrient cycling in agricultural soils in urban and rural environments. We study a wide variety of crops with sizable effort directed toward sustainable rice production. Contaminants of interest include metals (and metalloids) such as lead, arsenic, and cadmium and excess nutrients such as nitrogen. One overarching objective is to evaluate land management decisions with the aim to mitigate greenhouse gas emissions including methane, carbon dioxide, and nitrous oxide. We are interested in the intersection between food production, soil health, and human health. And we are particularly interested in communities most impacted by climate change, food insecurity, and environmental pollution. Within our work, we use interdisciplinary approaches to tackle these environmental justice issues. 

Our three research areas include:

  1. Metal toxicity in urban gardens
  2. Building soil health and promoting carbon storage in agricultural soils
  3. Coupled climate change and soil metal(oid) cycling impacts on rice production

Metal toxicity in urban gardens 

Project lead: Alexis Wilson

Urban agriculture is defined as areas within cities used for growing crops or raising small livestock, either for personal consumption or sale. Urban gardens are important to communities of color and low-income communities in particular because they are spaces for building and sustaining communities and increasing food security. However, since these sites exist in urban areas, there is a risk that garden soils may be contaminated with heavy metal(loid)s such as lead, cadmium, chromium, and arsenic.  These are common soil contaminants due to anthropogenic activities and pose a health risk to those exposed.

The combination of urban food insecurity and soil contamination becomes an Environmental Justice issue because communities of color and low-income communities disproportionately face food insecurity and exposure to environmental pollution. While patterns of soil contamination have frequently been broadly characterized  in urban areas, levels of metal contamination and exposure threats are still lacking for urban agricultural spaces. As such, the overall goal of this research is to use an interdisciplinary approach that emphasizesEnvironmental Justice and Community-Based Participatory Research as foundational frameworks to advance our understanding of the threat of soil contamination to urban gardens across the San Francisco Bay Area, specifically focusing on marginalized communities. The results of this work will contribute to a better understanding of heavy metal contamination in urban gardens, the health risk associated with exposure, and techniques for mitigating heavy metals in garden soils.  Overall, the goal of this research is to ensure that all communities can safely participate in urban agriculture and enjoy its many benefits.

Projects Include:

  • Assessing heavy metal contamination in urban school garden soils in Northern California 
  • Assessing urban gardener’s knowledge and concern of soil contamination in Palo Alto and East Palo Alto, California 

Building soil health and promoting carbon storage in agricultural soils

Project lead: Anna Gomes

In order to simultaneously reduce nitrogen pollution, mitigate climate change, and improve on-farm water use efficiency, crop production needs to be circular and regenerative. Amidst ongoing concerns around surface and groundwater quality, drought conditions, which are expected to increase in frequency and intensity, and the urgency to decarbonize food production, farmers need crop fertilizer strategies that can both ensure yields and soil quality while reducing global net greenhouse gas (GHG) emissions. Globally, food production is responsible for two-thirds of anthropogenic nitrous oxide (N2O) (a potent GHG emissions. Due to the asynchronous timing of nitrogen supply and demand, often from rapidly-released synthetic nitrogen fertilizer, agricultural soils have low nitrogen use efficiency leading to excess soil nitrogen left to pollute our environment and exacerbate climate change. The production and use of synthetic fertilizers represents about 2.4% of global emissions and is heavily reliant on natural gas as a feedstock. Meanwhile, human, animal, crop, and urban waste are full of critical crop nutrients including nitrogen, phosphorus, and potassium which could be collected, processed,  and applied as organic fertilizer. Integrated nutrient management, or meeting crop nutrient requirements with both synthetic and organic sources, might allow for improved nitrogen use efficiency and building healthier soils. 

Projects Include: 

  • Carbon and nitrogen mineralization dynamics of compost and recovered waste mineral nitrogen fertilizer for Salinas Valley cool season vegetable crops (lab incubation and greenhouse plant pot experiments)
  • Cover crop mineralization rates to inform Ag Order 4.0 Policy (lab incubation and field study)
  • Quantifying ‘wasted’ nutrients in California’s Salinas Valley rural and urban environments (quantitative study with plant pot experiment)
  • Quantifying the water and nutrient holding capacity increases with compost application type and rate studying sites with long-term compost amendments in California  (field measurements)

Current interns:

  • Diego Gutierrez, Stanford Undergraduate, Earth Systems
  • Pete Muhitch, Stanford Undergraduate, Earth Systems

Coupled climate change and soil metal(oid) cycling impacts on rice production

Project leads: Aria Hamann Duncan 
Current interns: Celine Heck, The Nueva School, San Mateo

Our focus on rice stems from it being a global staple crop, with more than 50% of the global population consuming rice daily. Unfortunately, global rice yields are already falling behind population growth. Toxic metals and metalloids within soils (including those of Asia and the U.S.) contribute to decreasing rice yields and an increase in grain contamination. The primary metal(loid) contaminants include arsenic and cadmium, which can decrease yields and are known human carcinogens whose long-term exposure adversely impacts human development and health. Our recent study (Muehe et al., 2019) revealed that the combined threat of climate change and soil arsenic will increase arsenic bioavailability in the soil, and subsequently decrease rice productivity and increase grain arsenic levels more than currently anticipated. With more than half of the world’s population relying on rice, decreased rice yields and grain quality will have a devastating impact on humanity. We are presently seeking to understand the biogeochemical processes affecting the uptake of contaminants by rice, their accumulation in grain, and their effects on rice yields and grain quality under current and future climatic conditions. By understanding the processes governing metal uptake, we hope to provide predictive information on yields and grain quality, while also helping to devise mitigation strategies that maximize yields and minimize metal(oid) content in the grain. We primarily base our research on growth chamber experiments to simulate field conditions, laboratory experiments, field trial and measurement, and predictive modeling.

Projects include:

  • Unraveling the impact and developing predictive models of soil arsenic concentrations on rice yields and grain chemistry under current and future climates
  • Examining the impacts of alternate wetting and drying irrigation on root structure and rhizosphere biogeochemistry  under future climate conditions

Past researchers:

a. Postdocs:

  • Kristin Boye [link]
  • E. Marie Muehe [link]
  • Angelia Seyfferth [link]

b. PhD Students:

c. Interns:

  • Natalia Armenta (SESUR 2023)
  • Frida Daniela Garcia-Ledezma (SURGE 2023)
  • Hussam Algallaf (Earth Systems Undergraduate)
  • Drew Nagesh (Palo Alto High School)
  • Jasmine Adriana Lizardo(Earth Systems Undergraduate, 2022)
  • Rachel Iweka (SURGE 2022)
  • Cali Ordas (SESUR 2022)
  • Alisha Jain (2022 Stanford Earth Young Investigators)
  • Emily Zhao (ES Undergraduate)
  • Sofia Epifantseva (Stanford King Center RA)
  • Lilia Barragan (2016 SURGE)
  • Mariejo Plaganas (2016 SURGE)
  • Aria Hamann (2017 SURGE)
  • Oliver Lewis (2017 MUIR)
  • Sindhu Goli (2017&2018 Stanford Earth Young Investigators)
  • Hyunseok (Jacob) Hwang (2018 SESUR)
  • Marcus Hill (2018 SURGE)
  • Olivia Kline (2019 SESUR)
  • Valeria Nava (2019 SURGE)
  • Rishi Jain (2019 Stanford Earth Young Investigators) [spotlights link]


  • Muehe, E. M.; Wang, T.; Kerl, C. F.; Planer-Friedrich, B.; Fendorf, S. Rice Production Threatened by Coupled Stresses of Climate and Soil Arsenic. Nat. Commun. 2019, 10 (1), 1–10. [Stanford news link]
  • Boye, K.; Lezama-Pacheco, J.; Fendorf, S. Relevance of Reactive Fe:S Ratios for Sulfur Impacts on Arsenic Uptake by Rice. Soils 2017, 1 (1), 1.
  • Seyfferth, A. L.; McCurdy, S.; Schaefer, M. V.; Fendorf, S., Arsenic concentrations in paddy soil and rice and health implications for major rice-growing regions of cambodia. Environmental Science & Technology 2014, 48, (9), 4699-4706.
  • Seyfferth, A. L.; Fendorf, S., Silicate mineral impacts on the uptake and storage of arsenic and plant nutrients in rice (Oryza sativa L.). Environmental Science & Technology 2012, 46, (24), 13176-13183.
  • Seyfferth, A. L.; Webb, S. M.; Andrews, J. C.; Fendorf, S., Defining the distribution of arsenic species and plant nutrients in rice (Oryza sativa L.) from the root to the grain. Geochimica et Cosmochimica Acta 2011, 75, (21), 6655-6671.
  • Seyfferth, A. L.; Webb, S. M.; Andrews, J. C.; Fendorf, S., Arsenic localization, speciation, and co-occurrence with iron on rice (Oryza sativa L.) roots having variable Fe coatings. Environmental Science & Technology 2010, 44, (21), 8108-8113.