Arnold J. Bloom’s research while affiliated with University of California, Davis and other places

Rubisco, the most prevalent protein on Earth, catalysers both a reaction that initiates C3 carbon fixation, and a reaction that initiates photorespiration, which stimulates protein synthesis. Regulation of the balance between these reactions under atmospheric CO2 fluctuations remains poorly understood. We have hypothesised that vascular plants maintain organic carbon‐to‐nitrogen homoeostasis by adjusting the relative activities of magnesium and manganese in chloroplasts to balance carbon fixation and nitrate assimilation rates. The following examined the influence of magnesium and manganese on carboxylation and oxygenation for rubisco purified from two ecotypes of Plantago lanceolata L.: one adapted to the elevated CO2 atmospheres that occur near a natural CO2 spring and the other adapted to more typical CO2 atmospheres that occur nearby. The plastid DNA coding for the large unit of rubisco was similar in both ecotypes. The kinetics of rubiscos from the two ecotypes differed more when associated with manganese than magnesium. Specificity for CO2 over O2 (Sc/o) for rubisco from both ecotypes was higher when the enzymes were bound to magnesium than manganese. Differences in the responses of rubisco from P. lanceolata to the metals may account for the adaptation of this species to different CO2 environments.

The behavior of many plant enzymes depends on the metals and other ligands to which they are bound. A previous study demonstrated that tobacco Rubisco binds almost equally to magnesium and manganese and rapidly exchanges one metal for the other. The present study characterizes the kinetics of Rubisco and the plastidial malic enzyme when bound to either metal. When Rubisco purified from five C3 species was bound to magnesium rather than manganese, the specificity for CO2 over O2, (Sc/o) increased by 25% and the ratio of the maximum velocities of carboxylation / oxygenation (Vcmax/Vomax) increased by 39%. For the recombinant plastidial malic enzyme, the forward reaction (malate decarboxylation) was 30% slower and the reverse reaction (pyruvate carboxylation) was three times faster when bound to manganese rather than magnesium. Adding 6‐phosphoglycerate and NADP⁺ inhibited carboxylation and oxygenation when Rubisco was bound to magnesium and stimulated oxygenation when it was bound to manganese. Conditions that favored RuBP oxygenation stimulated Rubisco to convert as much as 15% of the total RuBP consumed into pyruvate. These results are consistent with a stromal biochemical pathway in which (1) Rubisco when associated with manganese converts a substantial amount of RuBP into pyruvate, (2) malic enzyme when associated with manganese carboxylates a substantial portion of this pyruvate into malate, and (3) chloroplasts export additional malate into the cytoplasm where it generates NADH for assimilating nitrate into amino acids. Thus, plants may regulate the activities of magnesium and manganese in leaves to balance organic carbon and organic nitrogen as atmospheric CO2 fluctuates.

Rubisco, the most prevalent protein on the planet, initiates the conversion of CO2 into carbohydrates during photosynthesis. Responses of this process to atmospheric CO2 fluctuations daily, seasonally, and over millennia is still poorly understood. We have hypothesized that higher plants maintain carbon-to-nitrogen homeostasis by adjusting the balance of magnesium and manganese in chloroplasts to alter their relative carbon fixation and nitrogen assimilation rates. The following study examined the influence of magnesium and manganese on rubisco carboxylation and oxygenation in protein purified from two ecotypes of Plantago lanceolata: one adapted to the high atmospheric CO2 that occurs near a natural CO2 spring and the other adapted to more typical CO2 atmospheres that occur nearby. The plastid DNA coding for the large unit of rubisco were similar in both ecotypes. The kinetics of rubiscos from the two ecotypes differed more when they were associated with manganese than magnesium. Specificity for CO2 over O2 (Sc/o) for rubiscos from both ecotypes were higher when the enzymes were bound to magnesium than manganese. This disparity may account for the adaptation of this species to different CO2 environments.

Plants synthesize protein through assimilating inorganic nitrogen. Yet, the extent to which soil nitrogen sources alter crop responses to atmospheric CO 2 remains uncertain. We assessed wheat ( Triticum aestivum L.) biomass under CO 2 enrichment in genotypes that demonstrated a preference for ammonium (NH 4 ⁺ ) or nitrate (NO 3 ⁻ ), and contrasting degrees of NH 4 ⁺ tolerance. Nitrogen-form preference, but not NH 4 ⁺ tolerance, correlated with CO responses. Notably, NH 4 ⁺ -preferring genotypes maintained higher biomass and sustained grain nitrogen concentrations, thus avoiding CO 2 acclimation, the decline in biomass stimulation after prolonged exposure to CO 2 enrichment. Furthermore, NH 4 ⁺ nutrition accelerated flowering and increased spike biomass. Breeding for NH 4 ⁺ -adapted genotypes may not only improve climate resilience, but also potentially accelerate development and increase yield without any penalty on grain quality. Because wheat provides 20% of the protein and carbohydrate in the human diet, our study provided strategies to sustain food security under the atmospheric conditions anticipated in the future. Highlight Breeding for NH 4 ⁺ -adapted genotypes may not only improve climate resilience, but also potentially accelerate development and increase yield without any penalty on grain quality under elevated CO 2 atmospheres.

Rubisco (ribulose-1,5-bisphosphate carboxylase-oxygenase), the most prevalent protein on the planet 1,2 , catalyzes two competing chemical reactions. One reaction is the carboxylation of ribulose 1,5-bisphosphate (RuBP), which initiates plant carbohydrate synthesis. The other is the oxygenation of RuBP, which initiates photorespiration ³ . The common assumption is that photorespiration is a futile cycle that dissipates more than 25% of a plant’s energy as waste heat 4–6 , but inhibiting photorespiration decreases shoot protein synthesis 7–11 . Here is evidence for a previously unrecognized photorespiratory cycle in which rubisco converts RuBP into pyruvate, malic enzyme carboxylates pyruvate into malate, and malate dehydrogenase oxidizes malate, generating reductants that convert nitrate into amino acids (Fig. 1). This cycle becomes prominent only when rubisco or malic enzyme are associated with manganese, but prior experiments replaced the manganese bound to these enzymes with magnesium 3,12,13 . The proposed cycle coordinates photorespiration with several other processes including C 3 carbon fixation, pentose phosphate shunt, malate valve, and nitrogen metabolism. It thereby balances plant organic carbon and nitrogen as atmospheric CO 2 fluctuates daily, seasonally, and over millennia ¹⁴ . This carbon:nitrogen homeostasis improves photosynthetic efficiency ³ and explains why C 3 species, plants that photorespire at substantial rates, remain dominant in most habitats.

Premise: The agar-based culture of Arabidopsis seedlings is widely used for quantifying root traits. Shoot traits are generally overlooked in these studies, probably because the rosettes are often askew. A technique to assess the shoot surface area of seedlings grown inside agar culture dishes would facilitate simultaneous root and shoot phenotyping. Methods: We developed an image processing workflow in Python that estimates rosette area of Arabidopsis seedlings on agar culture dishes. We validated this method by comparing its output with other metrics of seedling growth. As part of a larger study on genetic variation in plant responses to nitrogen form and concentration, we measured the rosette areas from more than 2000 plate images. Results: The rosette area measured from plate images was strongly correlated with the rosette area measured from directly overhead and moderately correlated with seedling mass. Rosette area in the large image set was significantly influenced by genotype and nitrogen treatment. The broad-sense heritability of leaf area measured using this method was 0.28. Discussion: These results indicated that this approach for estimating rosette area produces accurate shoot phenotype data. It can be used with image sets for which other methods of leaf area quantification prove unsuitable.

Nitrogen is an essential element required for plant growth and productivity. Understanding the mechanisms and natural genetic variation underlying nitrogen use in plants will facilitate the engineering of plant nitrogen use to maximize crop productivity while minimizing environmental costs. To understand the scope of natural variation that may influence nitrogen use, we grew 1135 Arabidopsis thaliana natural genotypes on two nitrogen sources, nitrate and ammonium, and measured both developmental and defense metabolite traits. By using different environments and focusing on multiple traits, we identified a wide array of different nitrogen responses. These responses are associated with numerous genes, most of which were not previously associated with nitrogen responses. Only a small portion of these genes appear to be shared between environments or traits, while most are predominantly specific to a developmental or defense trait under a specific nitrogen source. Finally, by using a large population, we were able to identify unique nitrogen responses, such as preferring ammonium or nitrate, that appear to be generated by combinations of loci rather than a few large-effect loci. This suggests that it may be possible to obtain novel phenotypes in complex nitrogen responses by manipulating sets of genes with small effects rather than solely focusing on large-effect single gene manipulations.

Public understanding about complex issues such as climate change relies heavily on online resources. Yet the role that online instruction should assume in post-secondary science education remains contentious despite its near ubiquity during the COVID-19 pandemic. The objective here was to compare the performance of 1790 undergraduates taking either an online or face-to-face version of an introductory course on climate change. Both versions were taught by a single instructor, thus, minimizing instructor bias. Women, seniors, English language learners, and humanities majors disproportionately chose to enroll in the online version because of its ease of scheduling and accessibility. After correcting for performance-gaps among different demographic groups, the COVID-19 pandemic had no significant effect on online student performance and students in the online version scored 2% lower (on a scale of 0–100) than those in the face-to-face version, a penalty that may be a reasonable tradeoff for the ease of scheduling and accessibility that these students desire.

Premise: High-precision data acquisition (DAQ) is essential for developing new methods in the plant sciences. Commercial high-resolution DAQ systems are cost prohibitive, whereas the less expensive systems that are currently available lack the resolution and precision required for many physiological measurements. Methods and results: We developed the software libraries, called piadcs, and hardware design for a DAQ system based on an ultra-high-resolution analog-to-digital converter and a Raspberry Pi computer. We tested the system precision with and without a thermocouple attached and found the precision with the sensor to be better than ±0.01°C and the maximum possible system resolution to be 0.4 ppm. Conclusions: The ultra-high-resolution DAQ system described here is inexpensive, flexible enough to be used with many different sensors, and can be built by researchers with rudimentary electronic and computer skills. This system is most applicable in the development of new measurement techniques and the improvement of existing methods.

Nitrogen is an essential element required for plant growth and productivity. Understanding the mechanisms and natural genetic variation underlying nitrogen use in plants will facilitate engineering plant nitrogen use to maximize crop productivity while minimizing environmental costs. To understand the scope of natural variation that may influence nitrogen use, we grew 1135 Arabidopsis thaliana natural genotypes on two nitrogen sources, nitrate and ammonium, and measured both developmental and defense metabolite traits. By using different environments and focused on multiple traits, we identified a wide array of different nitrogen responses. These responses are associated with a large number of genes, most of them not previously associated with nitrogen responses. Only a small portion of these genes appear to be shared between environments or traits while most of the detected genes are predominantly specific to a developmental or defense trait under a specific nitrogen source. Finally, by using a large population we were able to identify unique nitrogen responses, like preferring ammonium or nitrate, that appear to be generated by combinations of loci rather than a few large effect loci. This suggests that it may be possible to obtain novel phenotypes in complex nitrogen responses by manipulating sets of genes with small effects rather than solely focusing on large effect single gene manipulations. One Sentence Summary Using a large collection of natural genotypes, and studying both developmental and metabolic responses, we found a large number of genes that are involved in the plants nitrogen response.