参考文献
Aganchich, B, S Wahbi, F Loreto, and M Centritto. 2009. “Partial Root Zone Drying: Regulation of Photosynthetic Limitations and Antioxidant Enzymatic Activities in Young Olive (Olea Europaea) Saplings.” Tree Physiology 29 (5): 685.
Ball, J. Timothy, Ian E. Woodrow, and Joseph A. Berry. 1987. A Model Predicting Stomatal Conductance and Its Contribution to the Control of Photosynthesis Under Different Environmental Conditions. Springer Netherlands.
Baly, EC. 1935. “The Kinetics of Photosynthesis.” Proceedings of the Royal Society of London Series B (Biological Sciences), no. 117: 218–39.
Bouvier, Annie, and Sylvie Huet. 1994. “Nls2 Nonlinear Regression by s PLUS Functions.” Computational Statistics & Data Analysis 18 (1): 187–90.
Buckley, T. N., S Martorell, A Diazespejo, M Tomàs, and H Medrano. 2014. “Is Stomatal Conductance Optimized over Both Time and Space in Plant Crowns? A Field Test in Grapevine Vitis Vinifera.” Plant Cell & Environment 37 (12): 2707.
Caemmerer, S. Von. 2000. “Biochemical Models of Leaf Photosynthesis.” Quarterly Review of Biology, 165.
Centritto, M, F Loreto, and K Chartzoulakis. 2003. “The Use of Low Co2 to Estimate Diffusional and Non-Diffusional Limitations of Photosynthetic Capacity of Salt-Stressed Olive Saplings.” Plant Cell and Environment 26 (4): 585–94.
Coursolle, Carole, Guillaume O. Prud’homme, Manuel Lamothe1, and Nathalie Isabel1. 2019. “Measuring Rapid a–Ci Curves in Boreal Conifers: Black Spruce and Balsam Fir.” Frontiers in Plant Science. https://doi.org/10.3389/fpls.2019.01276.
Cowan, I. R., and G. D. Farquhar. 1977. “Stomatal Function in Relation to Leaf Metabolism and Environment.” Symposia of the Society for Experimental Biology 31 (23): 471.
De Kauwe, Martin G, Yan Shih Lin, Ian J Wright, Belinda E Medlyn, Kristine Y Crous, David S Ellsworth, Vincent Maire, I Colin Prentice, Owen K Atkin, and Alistair Rogers. 2016. “A Test of the One Point Method for Estimating Maximum Carboxlation Capacity from Field Measured, Light Saturated Photosynthesis.” New Phytologist 210 (3): 1130.
Duursma, R. A., and B. E. Medlyn. 2012. “MAESPA: A Model to Study Interactions Between Water Limitation, Environmental Drivers and Vegetation Function at Tree and Stand Levels, with an Example Application to CO\(_2\) Drought Interactions.” Geoscientific Model Development Discussions 5 (4): 919–40.
Duursma, Remko A. 2015. “Plantecophys-an r Package for Analysing and Modelling Leaf Gas Exchange Data.” Plos One 10 (11): e0143346.
Duursma, Remko A., Paxton Payton, Michael P. Bange, Katrina J. Broughton, Renee A. Smith, Belinda E. Medlyn, and David T. Tissue. 2013. “Near-Optimal Response of Instantaneous Transpiration Efficiency to Vapour Pressure Deficit, Temperature and CO\(_2\) in Cotton (Gossypium Hirsutum l.).” Agricultural & Forest Meteorology 168 (1): 168–76.
Ellsworth, David S, Kristine Y Crous, Hans Lambers, and Julia Cooke. 2015. “Phosphorus Recycling in Photorespiration Maintains High Photosynthetic Capacity in Woody Species.” Plant Cell and Environment 38 (6): 1142–56.
Elzhov, Timur V., Katharine M. Mullen, Andrej Nikolai Spiess, and Ben Bolker. 2016. “Minpack.lm: R Interface to the Levenberg-Marquardt Nonlinear Least-Squares Algorithm Found in MINPACK, Plus Support for Bounds.”
Farquhar, G. D., S. Von Caemmerer, and J. A. Berry. 1980. “A Biochemical Model of Photosynthetic CO\(_2\) Assimilation in Leaves of C3 Species.” Planta 149 (1): 78–90.
Flexas J, Azespejo A, and Berry J A. 2007. “Analysis of Leakage in IRGA’s Leaf Chambers of Open Gas Exchange Systems: Quantification and Its Effects in Photosynthesis Parameterization.” Journal of Experimental Botany 58 (6): 1533.
Gu, Lianhong, Stephen G Pallardy, Kevin Tu, Beverly E Law, and Stan D Wullschleger. 2010. “Reliable Estimation of Biochemical Parameters from c-3 Leaf Photosynthesis-Intercellular Carbon Dioxide Response Curves.” Plant Cell & Environment 33 (11): 1852–74.
Haworth, Matthew, Dilek Killi, Alessandro Materassi, and Antonio Raschi. 2015. “Coordination of Stomatal Physiological Behavior and Morphology with Carbon Dioxide Determines Stomatal Control.” American Journal of Botany 102 (5): 677–88.
Haworth, Matthew, Giovanni Marino, and Mauro Centritto. 2018. “An Introductory Guide to Gas Exchange Analysis of Photosynthesis and Its Application to Plant Phenotyping and Precision Irrigation to Enhance Water Use Efficiency.” Journal of Water and Climate Change. https://doi.org/https://doi.org/10.2166/wcc.2018.152.
Heath, James R, Edward Ayres, Malcolm Possell, Richard D Bardgett, Helaina I J Black, Helen Grant, Phil Ineson, and Gerhard Kerstiens. 2005. “Rising Atmospheric Co2 Reduces Sequestration of Root-Derived Soil Carbon.” Science 309 (5741): 1711–13.
Hikosaka, K, K Ishikawa, A Borjigidai, O Muller, and Y Onoda. 2006. “Temperature Acclimation of Photosynthesis: Mechanisms Involved in the Changes in Temperature Dependence of Photosynthetic Rate.” Journal of Experimental Botany 57 (2): 291.
Huang, HY, XY Dou, PY Sun, B Deng, GJ Wu, and CL Peng. 2009. “Comparison of Photosynthetic Characteristics in Two Ecotypes of Jatropha Curcas in Summer.” Acta Ecologica Sinica, no. 29: 2861–67.
Jones, H. G. 1993. Plants and Microclimate. A Quantitative Approach to Environmental Plant Physiology. Cambridge University Press.
Joseph R., Stinziano, Adamson Rachael K., and Hanson David T. 2019. “Using Multirate Rapid ACi Curves as a Tool to Explore New Questions in the Photosynthetic Physiology of Plants.” New Phytologist. https://doi.org/10.1111/nph.15657.
Kemp, Freda. 2003. “Modern Applied Statistics with s.” Journal of The Royal Statistical Society Series D-the Statistician 52 (4): 704–5.
Knauer, Jürgen, Tarek S. El-Madany, Sönke Zaehle, and Mirco Migliavacca. 2018. “Bigleaf—An R Package for the Calculation of Physical and Physiological Ecosystem Properties from Eddy Covariance Data.” PLOS ONE 13 (8): e0201114. https://doi.org/10.1371/journal.pone.0201114.
Lauteri, Marco, Matthew Haworth, Rachid Serraj, Maria Cristina Monteverdi, and Mauro Centritto. 2014. “Photosynthetic Diffusional Constraints Affect Yield in Drought Stressed Rice Cultivars During Flowering.” PLOS ONE 9 (10).
Leuning, R. 1995. “A Critical Appraisal of a Combined Stomatal‐photosynthesis Model for C3 Plants.” Plant Cell and Environment 18 (4): 339–55.
Lobo, F. De A., M. P. De Barros, H. J. Dalmagro, Â. C. Dalmolin, W. E. Pereira, É. C. de Souza, G. L. Vourlitis, and C. E. Rodríguez Ortíz. 2013. “Fitting Net Photosynthetic Light-Response Curves with Microsoft Excel a Critical Look at the Models.” Photosynthetica 51 (3): 445–56.
Long, S. P., and C. J. Bernacchi. 2003. “Gas Exchange Measurements, What Can They Tell Us about the Underlying Limitations to Photosynthesis? Procedures and Sources of Error.” Journal of Experimental Botany 54 (392): 2393.
Marshall, B, and P V Biscoe. 1980. “A Model for C3 Leaves Describing the Dependence of Net Photosynthesis on Irradiance.” Journal of Experimental Botany 31 (1): 29–39.
Medlyn, B. E, E Dreyer, D Ellsworth, M Forstreuter, P. C Harley, M. U. F Kirschbaum, X Le Roux, P Montpied, J Strassemeyer, and A Walcroft. 2002. “Temperature Response of Parameters of a Biochemically Based Model of Photosynthesis. II. A Review of Experimental Data Review.” Plant Cell & Environment 25 (9): 1167–79.
Medlyn, Belinda E., Remko A. Duursma, Derek Eamus, David S. Ellsworth, I. Colin Prentice, Craig V. M. Barton, Kristine Y. Crous, Paolo De Angelis, Michael Freeman, and Lisa Wingate. 2011. “Reconciling the Optimal and Empirical Approaches to Modelling Stomatal Conductance.” Global Change Biology 17 (6): 2134–44.
Mejdová, Markéta, Jiří Dušek, Lenka Foltýnová, Lenka Macálková, and Hana Čížková. 2021. “Photosynthetic Parameters of a Sedge-Grass Marsh as a Big-Leaf: Effect of Plant Species Composition.” Scientific Reports 11 (1): 3723. https://doi.org/10.1038/s41598-021-82382-2.
Prado, C. H., and J. A. P. V. De Moraes. 1997. “Photosynthetic Capacity and Specific Leaf Mass in Twenty Woody Species of Cerrado Vegetation Under Field Conditions.” Photosynthetica 33 (1): 103–12.
Smith, Lindsay I. 2002. “A Tutorial on Principal Component Analysis.”
Stinziano, J. R., P. B. Morgan, D. J. Lynch, A. J. Saathoff, D. K. Mcdermitt, and D. T. Hanson. 2017. “The Rapid a-Ci Response: Photosynthesis in the Phenomic Era.” Plant Cell & Environment 40.
Stinziano, Joseph R, Dayle K Mcdermitt, Douglas J Lynch, Aaron J Saathoff, Patrick B Morgan, and David T Hanson. 2018. “The Rapid a/Ci Response: A Guide to Best Practices.” New Phytologist.
Stirbet, Alexandrina, and Govindjee. 2011. “On the Relation Between the Kautsky Effect (Chlorophyll a Fluorescence Induction) and Photosystem II: Basics and Applications of the OJIP Fluorescence Transient.” Journal of Photochemistry and Photobiology B: Biology, Special Issue on Recent Progress in the Studies of Structure and Function of Photosystem II, 104 (1): 236–57. https://doi.org/10.1016/j.jphotobiol.2010.12.010.
Stirbet, Alexandrina, and Govindjee. 2012. “Chlorophyll a Fluorescence Induction: A Personal Perspective of the Thermal Phase, the J–I–P Rise.” Photosynthesis Research 113 (1): 15–61. https://doi.org/10.1007/s11120-012-9754-5.
Thornley, J H M. 1976. “Mathematical Models in Plant Physiology.” London: Academic Press.
Tuzet, A, A Perrier, and R Leuning. 2003. “A Coupled Model of Stomatal Conductance, Photosynthesis and Transpiration.” Plant Cell and Environment 26 (7): 1097–1116.
Wullschleger, Stan D. 1993. “Biochemical Limitations to Carbon Assimilation in C3 Plants—a Retrospective Analysis of the a-Ci Curves from 109 Species.” Journal of Experimental Botany 44 (262): 907–20.
Yin, Xinyou, P C Struik, Pascual Romero, Jeremy Harbinson, Jochem B Evers, Peter E L Van Der Putten, and J Vos. 2009. “Using Combined Measurements of Gas Exchange and Chlorophyll Fluorescence to Estimate Parameters of a Biochemical C3 Photosynthesis Model: A Critical Appraisal and a New Integrated Approach Applied to Leaves in a Wheat (Triticum Aestivum) Canopy.” Plant Cell and Environment 32 (5): 448–64.
Zhang, XS, SH Shen, and J Song. 2009. “The Vertical Distribution of Cotton Leaf Nitrogen Content and Photosynthetic Characteristics in the North China Plain.” Acta Ecologica Sinica, no. 29: 1893–98.
ZiPiao, YE. 2010. “A Review on Modeling of Responses of Photosynthesis to Light and \(CO_2\).” Chinese Journal of Plant Ecology, no. 06.
实际上在Windows系统下安装的时候提供一个十分简陋的GUI。↩︎
特别注意,原始数据可以用文本编辑器打开,但为了方便使用这个软件包,准确输入与行号相关的参数,建议您使用带行号显示的软件,例如 windows 下的 notepad++↩︎
仅针对 C3 植物↩︎
具体参考 R 语言相关文档,为 R 语言最常用的数据格式↩︎
在 R 中,使用参数的值为默认值时可以不用填写该参数,例如使用默认选项分析 LI-6400 数据时,可只填写 data 项,具体参考 R 的相关入门手册↩︎
为Rubisco和RuBP限制的Ci转换点,物种间差异较大,可以通过预实验确定↩︎
若默认拟合方法失败,数据也无问题,那么是非线性拟合初始值设定的原因↩︎
即仅保留测量值,删除其他所有头文件、空行、 remark 等信息↩︎
首次使用安装,更换电脑或者升级 R 软件后,如果没有拷贝 library,也需要运行安装命令↩︎
需要注意,此时fitmethod一般推荐使用bilinear。↩︎
详细内容请参考原文↩︎
直角双曲线和非直角双曲线模型类似,如果测量时饱和光强之后光合速率不下降,则计算的P\(_{nmax}\)则远大于实测值。↩︎
例如本例的数据结果↩︎
有些时候结果并不理想,该方法并不是万无一失↩︎