Skip to main content Skip to secondary navigation

Rhizosphere Processes: Contaminant Impacts on Plants

Main content start

Rice is 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 of Asia and the U.S. contribute to decrease in yields, and similarly lower grain quality when contaminating this major food staple. The primary metal(loid) contaminants include arsenic, cadmium and lead, which are known human carcinogens and whose long-term exposure adversely impact human development and health. Our recent study 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 for substance, decreased rice yields and grain quality will have a devastating impact on humanity.

We seek to understand the biogeochemical processes affecting the uptake of these contaminants by rice, their accumulation in the grain, and their effects on rice yields and grain quality. Moreover, we strive to predict how these processes compare between 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 content in the grain. We primarily base our research on growth chamber experiments to simulate field conditions. We examine rice plant physiology, soil chemistry, and soil microbial communities under the different incubation conditions and thereby track the translocation of contaminants from soil to grain. In order to deduce mechanistic linkages between soil processes and plant productivity and grain quality, we combine advanced analytical techniques, including synchrotron-based X-ray analyses and soil microbial community analyses, with wet chemistry.

Project Leads

  • Aria Hamann Duncan
  • Tianmei Wang

Past Researchers

Postdoc fellows

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

Summer undergraduate and high school interns

  • 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.

Current Projects

Impacts of Climate Change

We are determining the impacts of climate change on rice yields and grain quality grown within metal(loid)-contaminated paddy soils

Fully climate-controlled growth chambers allowing the incubation of plants under current and future climate conditions (left). Within the growth chambers, rice plants are grown from seed in pots that contain soil with background or elevated arsenic concentrations. During growth, the pore water as well as the developmental stage of the rice plant is monitored continuously. Rice plants are harvested when the full biomass potential is reached (right) and analysed for the amount of accumulated arsenic in the different tissues. Furthermore, the soil geochemistry and microbial community is compared for the different incubation conditions.

Potential of alternate wetting and drying irrigation

We are exploring the potential of alternate wetting and drying irrigation to mitigate grain arsenic contamination, decrease paddy methane emissions, and reduce water use without compromising rice yields under a changing climate.

Soil profile
Design for upcoming experiment growing rice in root boxes (rhizotrons) with alternate wetting and drying under a future climate.

Past Projects

 Influence of sulphur on arsenic mobility in the rice rhizosphere

Adding charred harvest residues to paddy soil has the potential to decrease the concentration of arsenic in the following rice crop. Detailed investigations of the soil chemistry with synchrotron-based x-ray imaging techniques combined with close monitoring of the soil water chemistry helps us develop a mechanistic understanding of how these amendments influence the movement of arsenic in soil and plant.

Impact of silicate minerals on the uptake and storage of arsenic in rice

X-ray fluorescence images of Fe (a, c) and As (b, d) distributed within the rice root system. Images c and d represent magnified images of boxes in a and b, and the arrows represent areas where As is abundant while Fe is not. Image taken from Seyfferth et al., Environmental Science and Technology, 2010.