The SIPSM workshop will comprise six technical sessions over a span of six days. The technical sessions and their details are provided below:
Session 1 : Field measurements to study photosynthesis
In this session, we will delve into the fundamentals of A-Ci (CO2 response) and A-Q (light response) curves, which are fundamental to the study of active photosynthesis [1], exploring various parameters derived from these curves. Our focus will be on understanding the significance of these parameters in assessing the impact of climate change on plants. Additionally, we will gain insights into the intricacies of the instruments employed for measuring leaf gas exchange. Through practical application, students will have the opportunity to utilize our LiCor 6800 instrument to construct these curves and analyze data collected in the field, uncovering biophysical trait parameters associated with photosynthesis.
Session 2 : Modeling photosynthesis using kinetic modeling
In this session, we will introduce the concept of modeling metabolism using kinetic models, and discuss how the approach can be used to both study photosynthesis[2] and develop engineering strategies to enhance photosynthesis[3]. In the practical session, students will learn how to use both simple and complex kinetic models (Farquhar[4] and ePhotosynthesis[5] models) to simulate photosynthesis under different environmental conditions. Information gathered from field measurement (previous session) will be used to reparametrize the kinetic model so that it can be used to predict photosynthesis rates for our plant specimens in different climatic conditions including high atmospheric CO2 conditions likely to be experienced in the future.
Session 3 : Coupled leaf level model for mass and energy exchange
In this session, students will be introduced to the bio-physical and bio-chemical processes that determine mass and energy exchange between the leaf and its surrounding micro-environment. This will include models for photosynthesis, stomatal conductance, boundary layer conductance, and leaf energy balance. Using these models, we will be able to predict the photosynthetic carbon flux, transpiratory water loss flux, and its associated latent heat energy loss. The energy balance model accounts for radiation balance at the leaf level and predicts leaf temperature and the associated sensible heat loss. These processes are coupled since leaf temperature affects the rates of biochemical reactions. In the hands on session, students will be able to use MLCan[13] and BioCro[12] models to simulate leaf level responses to changing micro-environmental conditions.
Session 4 : Measuring plant performance using chlorophyll fluorescence
This session will introduce students to the concepts of Chlorophyll fluorescence, a non-invasive measurement of photosystem II (PSII) activity which can act as a probe to monitor photosynthetic processes and assess plant health [10]. The technique is no longer restricted to the leaf level, but also applicable at the canopy and landscape levels due to recent advancements in the remote sensing platforms. The theory session will also include an introduction to the LiCor Modulated PAM fluorometer, and basics of data handling and analysis. In the hands-on practical session, we will focus on instrument set up and operation for plant leaves. A wide range of plant types will be used including C3 and C4 crop models and a set of evergreen and deciduous tree seedlings. We will demonstrate both survey type measurements for rapid monitoring and screening of plant performance as well as more complex measurements of leaf chlorophyll fluorescence for deeper understanding of photosynthetic processes. Participants will also be divided into small groups and assigned plants grown under different conditions (such as high and low light, heat and cold stress, drought and salinity stress). Measurements of photosynthetic performance will be analyzed and observed photosynthetic stress responses will be discussed.
Session 5 : Modeling metabolism in source and sink tissue using flux balance analysis
In this session, students will be introduced to the concept of flux balance analysis (FBA), a constraint-based modeling approach that can be used to study qualitative properties of steady-state metabolism without the need for any information on metabolite concentrations, enzyme concentration and kinetic parameters [6]. Students will learn of the strengths and limitations of the approach, and additionally of extensions of FBA developed to overcome many of its limitations. In the practical session students will use the PlantCoreMetabolism v2.1 model [7] and the cobrapy modeling framework [8] to simulate heterotrophic and autotrophic metabolism in a plant tissue culture setting. Students will also build models of C3, C4 and CAM leaves and use a diel FBA approach [9] to predict steady-state metabolic fluxes in line with the experimentally determined behavior in these systems.
Session 6 : Studying plant physiology and structure using Functional Structural Plant Models
The focus of the final session of the workshop is to scale leaf level processes to the canopy level through functional structural plant models or FSPMs. FSPMs are plant models capable of describing the development of the plant 3D structure and select physiological functions over time in response to environmental conditions[11]. In the theory session students will learn about how this can be possible using multi-layer canopy radiation models and multi-layer scalar mixing models. The former accounts for the effect of attenuation of photosynthetic active radiation (PAR) and near infrared radiation (NIR), leaf shading and leaf zenith angles within each canopy layer. The latter on the other hand resolves vertical variation in canopy scalar fluxes of CO2 , water vapor and heat and helps in the determination of canopy microenvironmental variables such as CO2 concentrations, vapor pressure density and air temperature. Understanding how these FSPMs are built, trained on phenotyping data and operate will help students understand the potential applications of these powerful models. The hands-on session will introduce students to (a) BioCro, a semi-mechanistic dynamic crop growth modeling framework[12], and (b) MLCan, a multilayer canopy-soil-root system model[13]. The exercise will end with an example of parameterizing an FSPM model using measured phenotyping data.
References:
Sharkey, Thomas D. 2016. “What Gas Exchange Data Can Tell Us about Photosynthesis.” Plant Cell and Environment 39 (6): 1161–63. https://doi.org/10.1111/pce.12641.
Caemmerer, S. von. 2000. Biochemical Models of Leaf Photosynthesis. Biochemical Models of Leaf Photosynthesis. Collingwood, Australia: CSIRO Publishing.
South, Paul F., Amanda P. Cavanagh, Helen W. Liu, and Donald R. Ort. 2019. “Synthetic Glycolate Metabolism Pathways Stimulate Crop Growth and Productivity in the Field.” Science 363 (6422): eaat9077. https://doi.org/10.1126/SCIENCE.AAT9077.
Wu, Alex, Graeme L. Hammer, Al Doherty, Susanne von Caemmerer, and Graham D. Farquhar. 2019. “Quantifying Impacts of Enhancing Photosynthesis on Crop Yield.” Nature Plants 5 (4): 380–88. https://doi.org/10.1038/s41477-019-0398-8.
Zhu, Xin-Guang, Yu Wang, Donald R. Ort, and Stephen P. Long. 2013. “E -Photosynthesis: A Comprehensive Dynamic Mechanistic Model of C3 Photosynthesis: From Light Capture to Sucrose Synthesis.” Plant, Cell & Environment 36 (9): 1711–27. https://doi.org/10.1111/pce.12025.
Sweetlove, Lee J., and R. George Ratcliffe. 2011. “Flux-Balance Modeling of Plant Metabolism.” Frontiers in Plant Science 2 (August): 38. https://doi.org/10.3389/fpls.2011.00038.
Shameer, Sanu, Yu Wang, Pedro Bota, R. George Ratcliffe, Stephen P. Long, and Lee J. Sweetlove. 2022. “A Hybrid Kinetic and Constraint‐based Model of Leaf Metabolism Allows Predictions of Metabolic Fluxes in Different Environments.” The Plant Journal 109 (1): 295–313. https://doi.org/10.1111/tpj.15551.
Ebrahim, Ali, Joshua A Lerman, Bernhard O Palsson, and Daniel R Hyduke. 2013. “COBRApy: COnstraints-Based Reconstruction and Analysis for Python.” BMC Systems Biology 7 (1): 74. https://doi.org/10.1186/1752-0509-7-74.
Cheung, C Y Maurice, Mark G Poolman, David A Fell, R George Ratcliffe, and Lee J Sweetlove. 2014. “A Diel Flux Balance Model Captures Interactions between Light and Dark Metabolism during Day-Night Cycles in C3 and Crassulacean Acid Metabolism Leaves.” Plant Physiology 165 (2): 917–29. https://doi.org/10.1104/pp.113.234468.
Maxwell, Kate & Johnson, Giles. (2000). Chlorophyll fluorescence---a practical guide. J Exp Bot. 51. 10.1093/jxb/51.345.659.
Vos, J., J. B. Evers, G. H. Buck-Sorlin, B. Andrieu, M. Chelle, and P H B de Visser. 2010. “Functional-Structural Plant Modelling: A New Versatile Tool in Crop Science.” Journal of Experimental Botany 61 (8): 2101–15. https://doi.org/10.1093/jxb/erp345.
Migue, Fernando E., Matthew Maughan, Germán A. Bollero, and Stephen P. Long. 2012. “Modeling Spatial and Dynamic Variation in Growth, Yield, and Yield Stability of the Bioenergy Crops Miscanthus × Giganteus and Panicum Virgatum across the Conterminous United States.” GCB Bioenergy 4 (5): 509–20. https://doi.org/10.1111/j.1757-1707.2011.01150.x.
Le, Phong V.V., Praveen Kumar, Darren T. Drewry, and Juan C. Quijano. 2012. “A Graphical User Interface for Numerical Modeling of Acclimation Responses of Vegetation to Climate Change.” Computers & Geosciences 49 (December): 91–101. https://doi.org/10.1016/j.cageo.2012.07.007.