Plantecophys - An R Package for Analysing and Modelling Leaf Gas Exchange Data

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Abstract

Here I present the R package 'plantecophys', a toolkit to analyse and model leaf gas exchange data. Measurements of leaf photosynthesis and transpiration are routinely collected with portable gas exchange instruments, and analysed with a few key models. These models include the Farquhar-von Caemmerer-Berry (FvCB) model of leaf photosynthesis, the Ball-Berry models of stomatal conductance, and the coupled leaf gas exchange model which combines the supply and demand functions for CO ₂ in the leaf. The 'plantecophys' R package includes functions for fitting these models to measurements, as well as simulating from the fitted models to aid in interpreting experimental data. Here I describe the functionality and implementation of the new package, and give some examples of its use. I briefly describe functions for fitting the FvCB model of photosynthesis to measurements of photosynthesis-CO ₂ response curves ('A-C _i curves'), fitting Ball-Berry type models, modelling C3 photosynthesis with the coupled photosynthesis-stomatal conductance model, modelling C4 photosynthesis, numerical solution of optimal stomatal behaviour, and energy balance calculations using the Penman-Monteith equation. This open-source package makes technically challenging calculations easily accessible for many users and is freely available on CRAN.

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Most cited references 10

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A biochemical model of photosynthetic CO2 assimilation in leaves of C 3 species.

G D Farquhar, S. von Caemmerer, J A Berry (1980)

Various aspects of the biochemistry of photosynthetic carbon assimilation in C3 plants are integrated into a form compatible with studies of gas exchange in leaves. These aspects include the kinetic properties of ribulose bisphosphate carboxylase-oxygenase; the requirements of the photosynthetic carbon reduction and photorespiratory carbon oxidation cycles for reduced pyridine nucleotides; the dependence of electron transport on photon flux and the presence of a temperature dependent upper limit to electron transport. The measurements of gas exchange with which the model outputs may be compared include those of the temperature and partial pressure of CO2(p(CO2)) dependencies of quantum yield, the variation of compensation point with temperature and partial pressure of O2(p(O2)), the dependence of net CO2 assimilation rate on p(CO2) and irradiance, and the influence of p(CO2) and irradiance on the temperature dependence of assimilation rate.

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Some relationships between the biochemistry of photosynthesis and the gas exchange of leaves.

S. von Caemmerer, G Farquhar (1981)

A series of experiments is presented investigating short term and long term changes of the nature of the response of rate of CO2 assimilation to intercellular p(CO2). The relationships between CO2 assimilation rate and biochemical components of leaf photosynthesis, such as ribulose-bisphosphate (RuP2) carboxylase-oxygenase activity and electron transport capacity are examined and related to current theory of CO2 assimilation in leaves of C3 species. It was found that the response of the rate of CO2 assimilation to irradiance, partial pressure of O2, p(O2), and temperature was different at low and high intercellular p(CO2), suggesting that CO2 assimilation rate is governed by different processes at low and high intercellular p(CO2). In longer term changes in CO2 assimilation rate, induced by different growth conditions, the initial slope of the response of CO2 assimilation rate to intercellular p(CO2) could be correlated to in vitro measurements of RuP2 carboxylase activity. Also, CO2 assimilation rate at high p(CO2) could be correlated to in vitro measurements of electron transport rate. These results are consistent with the hypothesis that CO2 assimilation rate is limited by the RuP2 saturated rate of the RuP2 carboxylase-oxygenase at low intercellular p(CO2) and by the rate allowed by RuP2 regeneration capacity at high intercellular p(CO2).

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Modeling the Exchanges of Energy, Water, and Carbon Between Continents and the Atmosphere

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Atmospheric general circulation models used for climate simulation and weather forecasting require the fluxes of radiation, heat, water vapor, and momentum across the land-atmosphere interface to be specified. These fluxes are calculated by submodels called land surface parameterizations. Over the last 20 years, these parameterizations have evolved from simple, unrealistic schemes into credible representations of the global soil-vegetation-atmosphere transfer system as advances in plant physiological and hydrological research, advances in satellite data interpretation, and the results of large-scale field experiments have been exploited. Some modern schemes incorporate biogeochemical and ecological knowledge and, when coupled with advanced climate and ocean models, will be capable of modeling the biological and physical responses of the Earth system to global change, for example, increasing atmospheric carbon dioxide.

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Author and article information

Contributors

Paul C. Struik: Role: Editor

Journal

Journal ID (nlm-ta): PLoS One

Journal ID (iso-abbrev): PLoS ONE

Journal ID (publisher-id): plos

Journal ID (pmc): plosone

Title: PLoS ONE

Publisher: Public Library of Science (San Francisco, CA USA )

ISSN (Electronic): 1932-6203

Publication date (Electronic): 18 November 2015

Publication date Collection: 2015

Volume: 10

Issue: 11

Electronic Location Identifier: e0143346

Affiliations

[001]Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia

Wageningen University, NETHERLANDS

Author notes

Competing Interests: The author has declared that no competing interests exist.

Analyzed the data: RAD. Wrote the paper: RAD.

* E-mail: r.duursma@ 123456westernsydney.edu.au

Article

Publisher ID: PONE-D-15-30031

DOI: 10.1371/journal.pone.0143346

PMC ID: 4651500

PubMed ID: 26581080

SO-VID: a83f3d8b-cf98-444f-9dda-fbb77ea55a61

License:

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

History

Date received : 9 July 2015

Date accepted : 2 November 2015

Page count

Figures: 5, Tables: 1, Pages: 13

Funding

The author has no support or funding to report.

Custom metadata

Data Availability The software presented in this paper is available from an online repository ( http://www.bitbucket.org/remkoduursma/plantecophys), and the example code in another repository ( http://www.github.com/remkoduursma/duursma2015plosone).

Plantecophys - An R Package for Analysing and Modelling Leaf Gas Exchange Data

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