About

Dr. Christopher Simmons is the Department Chair and a Professor in the Department of Food Science and Technology at the University of California, Davis. He holds a Ph.D. from UC Davis, earned in 2011. His research focuses on improving energy and water use efficiency in food processing by reclaiming energy from waste biomass streams and developing strategies for wastewater treatment and recycling. Specifically, he utilizes high-throughput, massively parallel sequencing and bioinformatics approaches to characterize microbial communities capable of deconstructing waste biomass into fermentable sugars under industrial conditions. These data are used to discover enzymes and molecular pathways that enhance industrial bioconversion of waste biomass into biofuels. Additionally, Dr. Simmons studies the microbial ecology of plant-soil systems exposed to food processing effluents to develop strategies for recycling food processing wastewater to agriculture. His contributions have been recognized through awards such as the 2018 California Department of Pesticide Regulation - Integrated Pest Management Achievement Award, the 2019 UC Davis Chancellor's Fellow, and the 2023 UC Davis Academic Senate Distinguished Teaching Award for Graduate and Professional Education.

Research topics

• Ecology
• Agronomy
• Biology
• Botany
• Horticulture
• Food science
• Pulp and paper industry
• Chemistry
• Biochemistry

Selected publications

• Biochemical pesticides and soil changes resulting from biosolarization with cover crop amendments

  Journal of Agriculture and Food Research · 2026-03-19 · 1 citations

  articleOpen accessSenior authorCorresponding

  Biosolarization is an agricultural pest management technique that uses organic matter amendments and plastic mulch to control soil pests in a variety of cropping systems without harmful chemical fumigants. Biosolarization involves amending soil with organic matter, irrigating, and covering the surface with a clear tarp to suppress pests, combining stressors from increased temperature, reduced oxygen, and biochemical pesticide production. In particular, cover crops present a convenient, in situ amendment source for biosolarization. However, research is needed to evaluate the effectiveness of cover crops as soil amendments for biosolarization prior to large-scale applications. This study uses Brassica juncea (brown mustard) cover crop residues as biosolarization amendments to determine changes in soil properties contributing to pest suppression and crop growth. Specifically, a field trial was employed to quantify soil organic acid biochemical pesticide production, residual phytotoxicity, moisture content, pH, and electrical conductivity with B. juncea monoculture and B. juncea-Vicia villosa (hairy vetch) mixture cover crop amendments. Additionally, a simulated laboratory study evaluated changes in soil isothiocyanate biochemical pesticide concentrations during biosolarization with B. juncea cover crop amendments. Treatments were compared to non-biosolarized soil amended with cover crop residues, non-amended soil treated with solarization, and non-amended unheated soil controls. Results show biosolarization with cover crop residues increase the cumulative exposure to fermentative organic acid and plant-derived isothiocyanate compounds in soil by 314% and 28%, respectively, without causing persistent phytotoxicity. These findings highlight the potential for biosolarization with cover crop amendments to control soil pests without negatively impacting the growth of subsequent crops. • Biochemical pesticides were quantified from cover crop residue soil amendments • Cover crop soil amendments were studied with and without biosolarization treatments • Biosolarization with cover crop residues increased soil biochemical pesticides • Phytotoxicity from biosolarized soils was alleviated within eight days • Combining biosolarization with cover cropping practices may enhance pest control

  PublisherDOI

• Extreme-throughput multimodal optical-sectioning structured illumination microscopy for large-area imaging

  2026-03-04

  article

  We present a high-speed, multimodal optical-sectioning structured illumination microscopy (OS-SIM) system for large-area surface microscopy. The system supports both reflectance and multiband fluorescence imaging with area-throughput up to ~190 cm²/min at 1.1 μm resolution. A low magnification objective and time-delay-integration (TDI) strip scanning sensor enable continuous imaging over a 16 mm-wide field-of-view. Inclusive of full sample automation and real-time image processing and display, the system achieves a space-bandwidth-time product of ~667 megapixels/sec for surface area imaging.

  PublisherDOI

• Biosolarization as an alternative method to inhibit parasitic Phelipanche ramosa germination

  Frontiers in Agronomy · 2026-03-10 · 1 citations

  articleOpen accessSenior author

  Phelipanche ramosa , or branched broomrape, is a parasitic weed that attaches to the roots of host plants and can cause great agricultural losses, from reduced yield to crop termination without harvest. Conventional approaches to manage broomrape infestations include fumigation with toxic compounds, such as methyl bromide. Solarization has been used as well, but can leave a field out of service for entire seasons. Biosolarization is an alternative pest management strategy with a shorter timeframe that can reduce the need for fumigants and preplant herbicides by amending soil with organic matter, covering with a clear tarp, and irrigating. Weed seeds subjected to biosolarization experience a variety of stresses –including biocidal organic acids, high temperatures, and low oxygen– that can prevent future germination. This study evaluated the application of biosolarization with two different amendments, three amendment rates, and three temperatures for reduction of P. ramosa germinability. Simulated biosolarization was carried out in anaerobic bioreactors of wetted and amended soil with seeds incorporated. Tomato pomace and spent mushroom substrate were used as the organic matter amendments. Soil pH, electrical conductivity, and production of biocidal organic acids were evaluated before and after biosolarization, alongside germination capacity of P. ramosa seeds. Soil metrics of biosolarization treatments were compared to unamended, solarized soil and seed germination capacity was compared to that of untreated, control seeds. Broomrape germination is triggered by strigolactone, a plant hormone released into the rhizosphere. Therefore, a strigolactone analog was used to test the germinability of the treated seeds in absence of a host. To isolate the effects of biocidal organic acid exposure on broomrape germinability, seeds were also exposed to the acids produced during biosolarization, but without the added thermal and low oxygen stresses. The results suggest that biosolarization is an effective method to reduce P. ramosa germinability by >99% with amendment rates as low as 1.0% by dry weight and temperatures of 35 °C, which can inform future validation in field studies. Use of biosolarization may help protect the production of host plants on an infested field, while reducing the need for toxic compounds or lengthy treatments.

  PublisherOA PDFDOI

• Optical-sectioning structured illumination microscopy using high-brightness, high-resolution micro-LED displays

  2026-03-04

  article

  Structured illumination microscopy (SIM) enables real-time, optically sectioned fluorescence imaging, but its adoption has been limited by the complexity and limitations of pattern generation systems. We present a novel OS-SIM system using a commercial 4K micro-LED (μLED) display, which uniquely combines high brightness, fine pixel pitch, and large active area in a single, integrated light source and pattern generator. With a pixel pitch of 9.306 μm, brightness of ~2 million nits, and frame rates up to 100 fps, our μLED-based system supports fast and efficient OS-SIM. We achieved a spatial modulation frequency of 35.8 line pairs/mm over a ~4 cm² field—more than double previously reported values for μLED-driven microscopy. This work demonstrates the transformative potential of μLED displays for compact, high-performance SIM systems.

  PublisherDOI

• Effect of Cover Cropping and Biosolarization on Eggplant Growth, Soil Pests, and Soil Nitrogen

  SSRN Electronic Journal · 2025-01-01

  preprintOpen accessSenior author
  PublisherDOI

• Effect of cover cropping and biosolarization on eggplant growth, soil pests, and soil nitrogen

  Journal of Agriculture and Food Research · 2025-07-15 · 3 citations

  articleOpen accessSenior authorCorresponding

  Cover cropping and biosolarization are agricultural practices capable of controlling soil pests, enhancing soil health, and improving crop yields. Biosolarization utilizes solar heating and biochemical pesticide production from organic matter amendments to control agricultural pests. This study evaluates the effects of using cover crop residues from Brassica juncea monocultures and mixtures with Vicia villosa as biosolarization amendments on subsequent eggplant production, soil nitrogen, and soil pests, including weeds and fungal crown rot. These treatments were compared to non-biosolarized soil amended with the same cover crop monocultures and mixtures, non-amended soil treated with solarization, and non-amended, untreated soil controls. Results indicate the cover crop amendments improve eggplant fruit yield by 154 %, while decreasing fungal crown rot disease relative to untreated controls (P < 0.05). Additionally, employing biosolarization with these amendments reduced subsequent weed mass relative to cover cropped, solarized, and untreated controls (P < 0.05). Biosolarization also increased soil nitrate concentrations compared to cover crop-amended soil without biosolarization (P < 0.05). These findings exhibit the additive potential of cover cropping and biosolarization practices to be implemented in agriculture to control soil pests without chemical fumigants, while enhancing soil health and crop productivity. • Soil amendments were studied for effects on eggplant health and productivity. • B. juncea and V. villosa residues were used alone or in tandem with biosolarization. • Cover crop residues in soil increased eggplant growth rate and yield. • Biosolarization with cover crop residue amendments decreased weed density. • Soil nitrate increased in biosolarized soils relative to cover crops controls.

  PublisherDOI

• Assessment of spent mushroom substrate recycling via soil biosolarization

  Waste Management Bulletin · 2025-11-17 · 2 citations

  articleOpen accessSenior authorCorresponding

  • Gas evolution, pH, phytotoxicity, biocidal organic acids and nitrogen were analyzed. • Spent mushroom substrate biosolarization induces conditions known to be pesticidal. • Spent mushroom substrate composition affects pest suppression potential. • Biosolarization increases soil total nitrogen compared to solarization. • Spent mushroom substrate and cover crops can interact to influence phytotoxicity. Biosolarization is an alternative to pesticides for soil pest management that utilizes food industry organic matter byproducts as soil amendments to create conditions conducive to pest suppression. Spent mushroom substrate (SMS) is the main byproduct of mushroom cultivation. New uses are needed for this waste stream as its production continues to increase. This study evaluated two types of SMS as sole amendments and as co-amendments with cover crop biomass for biosolarization. SMS consisted of rice bran with hardwood sawdust (BS SMS) and soybean hulls with oak sawdust (SO SMS). Cover crop biomass was a mix of Secale cereale and Trifolium incarnatum . Gas evolution, pH, biocidal organic acid (BOA) production, phytotoxicity, and soil nitrogen were tracked during and/or after simulated biosolarization. SMS and cover crop treatments were compared to rice bran-amended soil and unamended, solarized soil. Results indicate that SO SMS treatments can produce BOA concentrations and phytotoxic conditions comparable to rice bran-amended soil, with BOA content correlating to radish seed germination indices with a coefficient of determination of 0.683. The pH of treatments including cover crop biomass, whether as a sole or co-amendment, significantly decreased during biosolarization, but were higher than pH of rice bran controls. SO SMS and cover crop biomass as sole amendments significantly increased total nitrogen content compared to solarized soil (P < 0.05), likely due to the addition of nitrogen-containing organic matter, but not mineral nitrogen. These findings suggest that certain SMS compositions may be valuable amendments for agricultural pest control via biosolarization.

  PublisherDOI

• Circular urban agriculture: Food waste-derived fertilizers lead to comparable yields in a tomato greenhouse experiment

  Journal of Agriculture and Food Research · 2025-09-01 · 1 citations

  articleOpen access

  Urban agriculture could promote sustainable food systems by localizing food production and consumption and increasing climate resilience. This study investigated the use of liquid food waste-derived digestate (FWDD) as biofertilizer in community learning gardens. Tomato plants (Solanum lycopersicum L.) were grown in a greenhouse in either potting medium alone (1) or amended with synthetic mineral fertilizer (2), compost (3), or a compost-FWDD blend (4). The control amended with mineral fertilizer and the compost-FWDD blend exhibited similar plant height and aboveground biomass area. While the positive control produced the highest total fruit yield, the total edible fruit yield and total fruit weight were similar in the compost-FWDD blend, which yielded the largest average fruit weight. Compost and compost-FWDD treatments produced lighter, tarter, but not more acidic tomatoes. No detrimental soil effects of FWDD amendment were observed. FWDD may increase the circularity and social resilience of historically underserved urban communities, although further research is needed to assess social perceptions and to quantify the life cycle impacts of FWDD in this context.

  PublisherDOI

• Food Waste Derived Digestate Greenhouse Experimental Design v1

  2025-10-31

  articleOpen access

  This document outlines the protocol to follow to demonstrate the use of pasteurized food waste derived digestate (FWDD) as liquid fertilizer in community learning gardens, as a means of promoting sustainable urban agriculture and social resilience. This method was developed for a trial using tomatoes, as part of a publication in the Journal of Agriculture and Food Research.

  PublisherOA PDFDOI

• Techno-economic evaluation of synergistic pasteurization of apple juice using UV-A light and olive byproduct extract

  Food and Bioproducts Processing · 2025-12-31 · 1 citations

  article
  PublisherDOI

Frequent coauthors

• Jean S. VanderGheynst

  69 shared

• Blake A. Simmons

  49 shared

• Steven W. Singer

  Joint BioEnergy Institute

  44 shared

• James J. Stapleton

  40 shared

• Yigal Achmon

  27 shared

• Amitha P. Reddy

  25 shared

• Jesús D. Fernández-Bayo

  Universidad de Granada

  24 shared

• Joshua T. Claypool

  14 shared

Awards & honors

• 2018: California Department of Pesticide Regulation - Integr…
• 2019: UC Davis - Chancellor's Fellow
• 2023: UC Davis Academic Senate - Distinguished Teaching Awar…