About

Matthew Edmund Gilbert is an Associate Professor in the Department of Plant Sciences at UC Davis. He holds a Ph.D. in Botany from Rhodes University, obtained in 2008, and a B.Sc. (Honors) in Botany as well as a B.Sc. in Botany and Microbiology from Rhodes University. His research focuses on the mechanisms by which leaf photosynthesis and water loss respond to environmental factors. He investigates stomatal responses to light, CO2, and plant water relations within the context of environmental and ecological problems, often at a larger scale than individual leaves. His work aims to improve Land Surface Models by incorporating physiological stress responses to heat, water deficit, and light, and explores whether crop water use can be modestly reduced through breeding plants with altered stomatal characteristics, assessing the physiological consequences in the field. Gilbert's research includes field experiments on diverse crop genotypes to predict and evaluate the costs of altered water use, and to develop screening techniques for breeders. His current projects involve collaborations with various organizations, including the Almond Board of California, the California Department of Food and Agriculture, and the International Wheat Yield Partnership, focusing on water use evaluation, physiological adaptation to high pH soils, and drought response screening in beans. He teaches courses such as Metabolic Processes of Cultivated Plants, Field Techniques in Plant Physiology, and other segments of plant physiology and ecology graduate courses. His outreach work emphasizes solving practical agricultural problems through basic plant physiology research, with many projects funded by Californian, national, and international groups related to specific crops.

Research topics

• Biology
• Botany
• Agroforestry
• Cell biology
• Soil science
• Biophysics
• Biochemistry
• Physics
• Ecology
• Agronomy
• Environmental science

Selected publications

• <scp> TinyCO ₂ </scp> : High‐performance, low‐cost <scp> CO ₂ </scp> enrichment for field‐grown plants

  Methods in Ecology and Evolution · 2025-06-02 · 1 citations

  articleOpen access

  Abstract Rising atmospheric CO 2 levels place terrestrial ecosystems under novel environmental conditions, and research in field settings is key to understanding how real plant communities will respond. Despite decades of progress in elevated CO 2 (eCO 2 ) experiments, major gaps persist in our knowledge of plant responses to interacting influences of climate change, especially in areas outside North America and Western Europe. With a goal to expand access to field‐based eCO 2 research, we designed, built, and tested TinyCO 2 , a low‐cost field experiment for climate change research on plants. TinyCO 2 features sixteen 0.62‐m 2 plot areas, half with ambient and half with elevated (+200 ppm) CO 2 concentrations, and is suitable for short‐stature plants (≤0.5 m in height). Using a proportional‐integral control algorithm and constant sampling of air within the plots, TinyCO 2 achieves consistent elevation of [CO 2 ] averaging +196.9 ppm. During testing, 95.1% of measured CO 2 concentrations fell within 20% of the setpoint (ambient CO 2 + 200 ppm). A streamlined design and efficient use of instrumentation reduced the cost of the system to roughly one‐fifth of the cost of similar experiments from the past 30 years ($13.68 vs. $64.65 ppm −1 m −2 , adjusted to 2024 USD). Our results demonstrate a system capable of precise and accurate field‐based CO 2 elevation for significantly reduced cost. We envision the TinyCO 2 design being implemented in a multitude of field‐based eCO 2 studies, perhaps as part of a globally distributed collaborative network experiment.

  PublisherOA PDFDOI

• Author response for "TinyCO&lt;sub&gt;2 &lt;/sub&gt;: High-performance, low-cost CO&lt;sub&gt;2&lt;/sub&gt; enrichment for field-grown plants"

  2025-03-28

  peer-review
  PublisherDOI

• Covariation MS uncovers a protein that controls cysteine catabolism

  Nature · 2025-09-17 · 5 citations

  articleOpen access

  Abstract The regulation of metabolic processes by proteins is fundamental to biology and yet is incompletely understood. Here we develop a mass spectrometry (MS)-based approach that leverages genetic diversity to nominate functional relationships between 285 metabolites and 11,868 proteins in living tissues. This method recapitulates protein–metabolite functional relationships mediated by direct physical interactions and local metabolic pathway regulation while nominating 3,542 previously undescribed relationships. With this foundation, we identify a mechanism of regulation over liver cysteine utilization and cholesterol handling, regulated by the poorly characterized protein LRRC58. We show that LRRC58 is the substrate adaptor of an E3 ubiquitin ligase that mediates proteasomal degradation of CDO1, the rate-limiting enzyme of the catabolic shunt of cysteine to taurine 1 . Cysteine abundance regulates LRRC58-mediated CDO1 degradation, and depletion of LRRC58 is sufficient to stabilize CDO1 to drive consumption of cysteine to produce taurine. Taurine has a central role in cholesterol handling, promoting its excretion from the liver 2 , and we show that depletion of LRRC58 in hepatocytes increases cysteine flux to taurine and lowers hepatic cholesterol in mice. Uncovering the mechanism of LRRC58 control over cysteine catabolism exemplifies the utility of covariation MS to identify modes of protein regulation of metabolic processes.

  PublisherDOI

• <i>Vitis vinifera</i> L. varieties (cv. Cabernet Sauvignon and Chardonnay) vary in leaf water flux in response to elevated CO2 growing conditions and a gradual water deficit

  AoB Plants · 2025-02-01 · 1 citations

  articleOpen access

  Abstract Grapevine (Vitis vinifera L.) stomata are highly sensitive to atmospheric changes and influence the tradeoff between water and carbon, as estimated by intrinsic water use efficiency (iWUE). The aim of this study was to examine how elevated CO2 concentrations and water deficit affect the iWUE and whole plant evapotranspiration of two grapevine varieties (cv. Cabernet Sauvignon and cv. Chardonnay). Dormant cuttings were collected from a vineyard in Temecula Valley, CA, and were grown in a growth chamber under one of two CO2 treatments: near ambient (410 ppm) or elevated (700 ppm). After 8 weeks of vegetative growth, grapevines were subjected to a well-watered (25% soil water content [SWC]) or gradual water-deficit treatment implemented over 12 days. We measured leaf gas exchange, including photosynthesis (Anet), stomatal conductance (gs), intercellular carbon (Ci), and calculated iWUE (Anet/gs), as well as daily cumulative evapotranspiration per unit leaf area (g cm−2 day−1). Vines were harvested to determine total dry weight, root mass fraction, and nitrogen content. We found that elevated CO2 and water deficit interactively increased the iWUE for both varieties, with Cabernet Sauvignon having 20% greater iWUE than Chardonnay at ~5% SWC. Chardonnay exhibited greater maximum conductance, and 43% more water transpired than Cabernet Sauvignon under a well-watered treatment. Chardonnay plants were also more impacted by elevated CO2 and water-deficit treatment than Cabernet Sauvignon, exhibiting greater stomatal sensitivity under these treatments. At ambient CO2, water deficit negatively impacted Chardonnay’s photosynthesis than Cabernet Sauvignon. However, this effect was not observed at elevated CO2. This study elucidates the intraspecific differences in stomatal behaviour, productivity, and water use of two V. vinifera L. genotypes (Cabernet Sauvignon and Chardonnay), under elevated CO2 concentrations and short-term water deficit.

  PublisherOA PDFDOI

• Author response for "TinyCO&lt;sub&gt;2 &lt;/sub&gt;: High-performance, low-cost CO&lt;sub&gt;2&lt;/sub&gt; enrichment for field-grown plants"

  2025-05-05

  peer-review
  PublisherDOI

• Diversity in stomatal and hydraulic responses to terminal drought in common bean ( Phaseolus vulgaris ) and tepary bean ( P. acutifolius )

  2024-08-23

  preprintOpen accessSenior author

  Plants differ widely in how soil drying affects stomatal conductance ( g s ) and leaf water potential ( ψ leaf ), and in the underlying physiological controls. Efforts to breed crops for drought resilience would benefit from a better understanding of these mechanisms and their diversity. We grew 12 diverse genotypes of common bean ( Phaseolus vulgaris L.) and four of tepary bean ( P. acutifolius; a highly drought resilient species) in the field under irrigation and terminal drought, and quantified responses of g s and ψ leaf , and their controls (soil water potential [ ψ soil ], evaporative demand [Δ w ] and plant hydraulic conductance [ K ]). We hypothesized that (i) common beans would be more ”isohydric” (i.e., exhibit strong stomatal closure in drought, minimizing ψ leaf decline) than tepary beans, and that genotypes with larger ψ leaf decline (more ”anisohydric”) would exhibit (ii) smaller increases in Δ w , due to less suppression of evaporative cooling by stomatal closure and hence less canopy warming, but (iii) larger K declines due to ψ leaf decline. Contrary to our hypotheses, we found that half of the common bean genotypes were similarly anisohydric to most tepary beans; that isohydric genotypes experienced less canopy warming and hence smaller increases in Δ w in drought, and similar declines in K ; and that stomatal closure was similar in isohydric and anisohydric genotypes. g s and ψ leaf were virtually insensitive to drought in one tepary genotype (G40068). Our results highlight the potential importance of non-stomatal mechanisms for leaf cooling, and the variability in drought resilience traits among closely related crop legumes.

  PublisherOA PDFDOI

• Diversity in stomatal and hydraulic responses to post‐flowering drought in common (<i>Phaseolus vulgaris</i>) and tepary (<i>P. acutifolius</i>) beans

  Plant Cell & Environment · 2024-09-04 · 10 citations

  articleSenior author

  Abstract Plants differ widely in how soil drying affects stomatal conductance ( g s ) and leaf water potential ( ψ leaf ), and in the underlying physiological controls. Efforts to breed crops for drought resilience would benefit from a better understanding of these mechanisms and their diversity. We grew 12 diverse genotypes of common bean ( Phaseolus vulgaris L.) and four of tepary bean ( P. acutifolius; a highly drought resilient species) in the field under irrigation and post‐flowering drought, and quantified responses of g s and ψ leaf , and their controls (soil water potential [ ψ soil ], evaporative demand [Δ w ] and plant hydraulic conductance [ K ]). We hypothesised that (i) common beans would be more “isohydric” (i.e., exhibit strong stomatal closure in drought, minimising ψ leaf decline) than tepary beans, and that genotypes with larger ψ leaf decline (more “anisohydric”) would exhibit (ii) smaller increases in Δ w , due to less suppression of evaporative cooling by stomatal closure and hence less canopy warming, but (iii) larger K declines due to ψ leaf decline. Contrary to our hypotheses, we found that half of the common bean genotypes were similarly anisohydric to most tepary beans; canopy temperature was cooler in isohydric genotypes leading to smaller increases in Δ w in drought; and that stomatal closure and K decline were similar in isohydric and anisohydric genotypes. g s and ψ leaf were virtually insensitive to drought in one tepary genotype (G40068). Our results highlight the potential importance of non‐stomatal mechanisms for leaf cooling, and the variability in drought resilience traits among closely related crop legumes.

  PublisherDOI

• Author response for "TinyCO&lt;sub&gt;2 &lt;/sub&gt;: High-performance, low-cost CO&lt;sub&gt;2&lt;/sub&gt; enrichment for field-grown plants"

  2024-12-29

  peer-review
  PublisherDOI

• TSWIFT: Tower Spectrometer on Wheels for Investigating Frequent Timeseries for high-throughput phenotyping of vegetation physiology

  Plant Methods · 2023-03-28 · 17 citations

  articleOpen access

  BACKGROUND: Remote sensing instruments enable high-throughput phenotyping of plant traits and stress resilience across scale. Spatial (handheld devices, towers, drones, airborne, and satellites) and temporal (continuous or intermittent) tradeoffs can enable or constrain plant science applications. Here, we describe the technical details of TSWIFT (Tower Spectrometer on Wheels for Investigating Frequent Timeseries), a mobile tower-based hyperspectral remote sensing system for continuous monitoring of spectral reflectance across visible-near infrared regions with the capacity to resolve solar-induced fluorescence (SIF). RESULTS: We demonstrate potential applications for monitoring short-term (diurnal) and long-term (seasonal) variation of vegetation for high-throughput phenotyping applications. We deployed TSWIFT in a field experiment of 300 common bean genotypes in two treatments: control (irrigated) and drought (terminal drought). We evaluated the normalized difference vegetation index (NDVI), photochemical reflectance index (PRI), and SIF, as well as the coefficient of variation (CV) across the visible-near infrared spectral range (400 to 900 nm). NDVI tracked structural variation early in the growing season, following initial plant growth and development. PRI and SIF were more dynamic, exhibiting variation diurnally and seasonally, enabling quantification of genotypic variation in physiological response to drought conditions. Beyond vegetation indices, CV of hyperspectral reflectance showed the most variability across genotypes, treatment, and time in the visible and red-edge spectral regions. CONCLUSIONS: TSWIFT enables continuous and automated monitoring of hyperspectral reflectance for assessing variation in plant structure and function at high spatial and temporal resolutions for high-throughput phenotyping. Mobile, tower-based systems like this can provide short- and long-term datasets to assess genotypic and/or management responses to the environment, and ultimately enable the spectral prediction of resource-use efficiency, stress resilience, productivity and yield.

  PublisherOA PDFDOI

• METHODS FOR FINDING THE LOCATION OF HISTORICAL PHOTOGRAPHS FOR REPEAT PHOTOGRAPHY

  Madroño · 2023-01-11 · 1 citations

  article1st authorCorresponding

  Historical photographs are windows into the past. By comparing historical and modern photographs we can measure change; but how do we find the original camera location to repeat a photograph? Historical, geographic, topographic, and other clues may be used, but we lack a numerical method suitable for any user to find the general location of a historical photograph. We derive a geometric method that can be applied in the field or prior. The method uses measurements of at least three points of reference (POR) in the historical photograph and corresponding geographic locations measured via a compass or on a map. rePhoto, an open-source R package that applies the method and outputs spatial KML files for use with Google Earth, is provided. The geometric method was tested on 20 photographs with known locations and validated by independent users. The effectiveness of the method varied among users, but overall predicted a search area containing the original camera location 70% of the time (the prediction accuracy) and typically predicted search areas 99.5% smaller than the total region evaluated by the method. The method was robust regardless of whether three or four POR were used, and worked well even when POR were more than 30 km away. The proposed method only works for photographs with at least three identifiable geographic POR, thus other methods are illustrated for use more generally. California and the western USA have numerous iconic historical photographs, for which many locations could be found and re-photographed using methods described here.

  PublisherDOI

Frequent coauthors

• Thomas N. Buckley

  Plant (United States)

  38 shared

• Andrew J. McElrone

  University of California, Davis

  25 shared

• Guillaume Théroux‐Rancourt

  Biopterre

  15 shared

• Paul Gepts

  University of California, Davis

  12 shared

• Brad S. Ripley

  Rhodes University

  12 shared

• J. Mason Earles

  12 shared

• Craig R. Brodersen

  Yale University

  11 shared

• Antonia Palkovic

  Plant (United States)

  11 shared

Awards & honors

• Gilbert honored for graduate advising (2022)