Soil Biogeochemistry & Biogeophysics

Phytoremediation of arsenic contaminated soils


We are working with a community partnership to investigate sustainable arsenic remediation at a field site in south Berkeley. When planning for a community orchard, gardeners discovered arsenic contamination (20-100 mg/kg) in the soil of the Santa Fe Right-of-Way, a former railroad grade now vacant.

We are conducting phytoremediation field trials using the brake fern, Pteris vittata L. Phytoremediation is the use of plants to remediate the soil, in this case by extracting the contaminant from the soil and translocating it to above-ground parts. P. vittata is an arsenic hyperaccumulator; arsenic concentrations in P. vittata fronds can reach 1000-7500 mg/kg. By harvesting the fronds, arsenic is removed from the site while leaving valuable topsoil in place. We are currently investigating use of organic and inorganic slow-release fertilizers to enhance arsenic accumulation in fern fronds. These field trials are a springboard for work quantifying the effects of soil characteristics, climate, and the presence of multiple contaminants on the remediation efficiency of P. vittata. We thus study fundamental biogeochemical cycling of arsenic and metals in soil, through a remediation lens. We hope to contribute to the development of affordable, low-waste, broadly applicable soil remediation methods.

Community partners at the Santa Fe Right-of-Way include Berkeley Partners for Parks, the Berkeley Community Gardening Collaborative, the Ecology Center, and Spiral Gardens Community Food Security Project.

soil sampling slide hammer cropped-1
fern close up
lab work-sample preparation-1

Effects of increasing salinity and redox oscillation on selenium cycling and phylogenetic diversity in littoral sediments of the Salton Sea


The Salton Sea, located in the desert area of southeastern California, is the largest lake in the state. It is a shallow, eutrophic and hypersaline lake whose shoreline is currently at an elevation of more than 70 m below sea level. Because the Salton Sea has no outlets and is located in an arid region of high evaporation, it has been accumulating soluble salts in its water and insoluble constituents in its bottom sediment for nearly 100 years, reaching a current salinity a third higher than seawater. Selenium (Se) is among the constituents that, in addition to water salinity, threaten the health of the Salton Sea.

The Salton Sea is an ecological disaster that may not attract the attention and investment needed to avoid catastrophic impacts to public health and to the millions of birds the lake supports (Cohen, 2008). The Salton Sea will change dramatically in the near future, whether or not officials take action on its behalf. The various restoration actions proposed, including the “no-action alternative” (Cohen and Huyn, 2006) would all results in similar changes at the Salton Sea. Salinity will increase and the surface of the lake will drop, due to a decrease in inflows to the lake. The uptake and bioaccumulation of Se by primary producers would likely increase because of higher Se concentrations entering the system from tributaries and drains (U.S. Department of Interior, 2007). Bottom sediment from medium water depths is higher in Se than from shallower depths, and this sediment would be exposed to more oxic conditions than generally prevail at shallower depths, increasing the possible oxidation, and consequently remobilization, of Se. The objectives of our research are to characterize selenium cycling at the sediment-water interface under conditions of increasing salinities, and switch from anoxic/suboxic to oxic conditions and to correlate the geochemistry of selenium with the changes observed in microbial community structure to identify the particular taxonomic groups driving Se geochemistry.


Coupled sulfur and iron cycling in Pescadero estuary: A multi-disciplinary investigation into an annual fish kill

The largest coastal watershed between the Golden Gate Bridge in San Francisco and Santa Cruz, CA, Pescadero is a critical, complex habitat and intermittent estuary for a diversity of animals; however, fish kill events have been occurring at Pescadero since 1995. In recent years, these events have been more severe and regular than in nearby intermittent estuaries in California and are strongly tied to sulfur redox cycling. With connections to deteriorating water quality, this research focuses on microbial sulfate reduction to hydrogen sulfide and sulfide oxidation from reduced iron sulfides in order to develop an integrated and comprehensive understanding of the geochemical and biological interactions in the Pescadero Estuary. (Collaboration with S. Carlson and M. Stacey, UC Berkeley)  

Iron cycling in subalpine wetlands: Impact on fate and transport of dissolved organic carbon

Soils comprise the largest pool of terrestrial carbon (C) and are thus strongly susceptible to climate change, with important implications for greenhouse gas production and surface water quality. Wetlands are especially important players in the global C cycle since they contain about one-third of the planet’s soil C stock. Carbon cycling in soils is partly controlled by their chemistry, especially by the environmental chemistry of iron (Fe), due to the interactions between Fe mineral phases and organic matter. It is consequently crucial to develop a better mechanistic and kinetic understanding of the role that Fe-oxides play in the fate and transport of dissolved organic carbon (DOC) in wetland ecosystems. We are engaged in a multi-scale environmental chemistry study that integrates field-measurements, soil column experiments and molecular measurements to study the influence of climatic parameters, redox conditions, and chemical conditions on the fate and transport of DOC in wetland ecosystems. (Collaboration with T. Borch & E. Kelly, Colorado State University and C. Rhoades,US Forest Service)


Elucidating the effects of molecular-scale physico-chemical processes on the fate and transport of engineered nanoparticles in soils

Recent progress in nanotechnology has led to the development of engineered nanoparticles (NPs), small size materials that exhibit specific physico-chemical properties. Due to their high reactivity, NPs have been incorporated in a number of common products and have been increasingly used in many different industrial fields over the last ten years. However, this recent enthusiasm has simultaneously raised serious concerns relative to the potential release of engineered NPs into natural environments, and to their potential negative effects on humans and ecosystems. It has been suggested that NPs can constitute a new class of micro-pollutants, and consequently their “life cycle” in natural environments including aquatic systems and soils needs to be understood to evaluate their potential impacts on living organisms.

Among the NPs, quantum dots (QDs) are widely used in electronic devices and biomedicine for in vivo imaging. Many studies have recently focused on direct exposure of model organisms (bacteria, algae) to QDs but only few of them were devoted to their transfer to aquatic systems, and no clear information is available regarding their fate in soils. In natural settings, QDs residence time may range from months to years, but critical information regarding the physico-chemical processes controlling QDs distribution, transformation and toxicity is still missing, highlighting the importance of molecular-scale characterization of QDs to accurately predict their fate in natural environments. The overarching goal of this project is to decipher how molecular-scale physico-chemical processes promoted by mineral surfaces and organic ligands, affect the transport, reactivity and dissolution of CdSe QDs soils. (Collaboration with A. Gélabert and M. Benedetti, Paris University)

Impacts of aggregate-scale heterogeneity of transport and biogeochemical processes on selenium mobility in soil


For redox active contaminants, such as selenium, reductive transformations are particularly critical in natural and accelerated attenuation owing to the higher mobility and toxicity of their oxidized states. Reduction of Se is largely controlled by microbial processes. Reducing conditions are therefore important for immobilizing selenium at contaminated sites throughout the San Joaquin Valley (CA). However, the subsurface is physically complex and the resulting redox (micro)environments, and associated metabolic processes, are heterogeneously distributed in both space and time. A qualitative and quantitative understanding of variations in the redox processes operating at the microscale will therefore be critical in developing comprehensive and predictive models describing the dynamics of biogeochemical systems.

The present research project proposes to examine spatial heterogeneity of selenium reduction within physically complex systems representative of natural environments, with structural complexity that integrate, rather than segregate, biological, geochemical, and physical processes. The overall objective is to determine what key physical and biogeochemical factors determine the extent and location of selenium reduction and the transport between compartments at the soil aggregate scale. The focus will be on (1) understanding how localized biogeochemical environments are controlled by the intrinsic microbial activity and dynamics versus mass transfer limitations, (2) identifying the key environmental determinants that control Se-reducers diversity, and (3) establishing how Se-reducers community structure and biogeochemical (micro-)heterogeneity affect the transformation rates of selenium in the subsurface.


Comparing the effects of chemical and organic fertilization on soil quality, plant productivity and insect pest incidence in tomato cropping systems

tomato 2

Non efficient use of chemical fertilizers can increase the susceptibility of plants to insect pests, cause groundwater contamination due to nitrate leaching, and result in emissions of nitrous oxide, a potent greenhouse gas. On the other hand, organic fertilization practices add organic matter to the soil, improving its structure, aeration and water retention, and promoting soil microbial activity and a slow release of nutrient. As a result organically-fertilized fields show reduced pest populations compared to conventionally-fertilized ones.

The overall goal of this project is to understand how soil fertility management may affect soil quality as well as plant health and may therefore affect insect pest abundance, using tomato as a teste crop in the coastal area of northern California. We are particularly interested in comparing the short-term and long-term effects of chemical versus organic fertilization (composts and compost teas) on soil physico-chemical characteristics, soil microorganisms, plant quality, crop yield and densities of several insect pests and in determining the relationships between soil fertility, crop nutritional status and insect pest incidence. The proposed research will benefit vegetable growers interested in implementing ecologically-based pest management strategies, which will allow them to reduce fertilizer use and costs while keeping high yields, maintaining soil health and fertility as well as minimizing environmental impacts. (Collaboration with M. Altieri, UC Berkeley)

tomato 1

Kinetics and rates of organic matter degradation coupled to nitrate, iron and sulfate reduction in wetland soils and littoral sediments



Carbon and nutrients cycles in natural porous media, such as soils or sediments, are strongly determined by the activity of the resident microbial populations since many environmentally relevant reactions are mediated by microorganisms. To predict the evolution of biogeochemical cycles, mathematical expressions that describe the rates at which chemical constituents are consumed and produced are necessary. The present research investigates how biogeochemical transformation rates relate to environmental factors and to the physical structure and hydrology of the local environment. Organic matter degradation plays an important role in nutrient cycling in sediments and soils. Coupled to organic matter oxidation, a sequential reduction of electron acceptors with depth generally proceeds on the basis of theoretical thermodynamic energy yields to microorganisms. We are currently working on testing the hypothesis that potential rates of terminal electron acceptor utilization during anaerobic organic carbon oxidation not only reflect the reactivity of the sedimentary organic matter being degraded but also the nature of the terminal electron acceptor.

Experimental work includes flow-through experiments, with which reaction rates are measured under steady-state conditions. In such systems, the physical integrity of the soil/sediment is preserved and solute flow is controlled, therefore mass-transfer limitations will occur the same way as in natural environments. An application of a reactive transport model allows for recovering kinetic parameters for biogeochemical reactions.


Space agriculture: Effects of low gravity on water flow, nitrogen cycling, and microbial biomass dynamics in a soil-based cropping unit

In the hypothesis that Mars can be inhabited by a six-people crew by 2050, bioregenerative agriculture has being considered as a mean to recycle water, produce food, sequester CO2, produce O2, and decompose organic wastes. However, Mars gravitational acceleration (0.38g) has unknown consequences on most physical and biogeochemical processes within the root zone, where adequate supply of water, nutrients and O2 is required by plants and microorganisms. On Mars, gravitational advection would be substantially different than on Earth, but it is not clear whether this would hinder, maintain or facilitate nutrient accessibility. As pore wetting in reduced gravity would be more likely to nucleate air pockets, the unsaturated hydraulic conductivity would be much lower, and air pockets could entrap gases (e.g., O2) and dissolved nutrients (e.g., NH4+ and NO3ˉ), not available to roots and microorganisms at the rates they would on Earth.

We investigate the feedback that low gravity has on water flow, and its effects on the soil-nutrient-biomass dynamics in a soil-based agricultural plot on Mars using a mechanistic soil reactive transport model. We demonstrated that under a 0.38g Martian gravity, leaching of water, N and C decrease by 50-70% as compared to Earth, but emissions of N2O, N2 and CO2 gases increase respectively by 150%, 350%, and 20% relative to Earth. Martian soil-based agriculture would require 50-70% less irrigation water volume, and about 50% less net N supply (e.g., fertilizers) as compared to on Earth. Ideally, low water and nutrient footprint would make soil-based cropping an attractive option to support life on Mars. (Collaboration with F. Maggi, Sydney University)