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Protocols in ecological and environmental plant physiology


Functional Plant Biology publishes new and significant information on the functional biology of plants at all scales from the molecular through whole plant to community. More

Editor-in-Chief: Sergey Shabala


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Published online 26 March 2015
Comparative proteomic and physiological characterisation of two closely related rice genotypes with contrasting responses to salt stress 
Seyed Abdollah Hosseini, Javad Gharechahi, Manzar Heidari, Parisa Koobaz, Shapour Abdollahi, Mehdi Mirzaei, Babak Nakhoda and Ghasem Hosseini Salekdeh

According to a two-phase growth response concept, genotypes with differing susceptibility to salinity usually develop distinct responses when excess salt accumulates in their tissues. In this study, two rice genotypes (IR29 and FL478) were exposed to salt stress until they showed distinct growth. Their physiology and proteome responses were analysed. The sensitivity of IR29 to salinity may be due to its inability to exclude salt, compartmentalise excess ions or maintain its photosynthetic apparatus in a healthy state under salt stress.

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Published online 23 March 2015
Whole-plant respiration and its temperature sensitivity during progressive carbon starvation 
Martijn Slot and Kaoru Kitajima

Carbon release from plant respiration increases with temperature. Although it is thought that low sugar concentrations limit the rate of this increase, this has not been tested at the whole-plant level. When we sugar-starved Ardisia crenata plants, respiration decreased but, surprisingly, the sensitivity of respiration to warming increased. These results highlight the complexity of the controls over plant respiration, especially at the whole-plant level.

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Published online 20 March 2015
Impact of elevated atmospheric humidity on anatomical and hydraulic traits of xylem in hybrid aspen 
Anna Katarzyna Jasi?ska, Meeli Alber, Arvo Tullus, Märt Rahi and Arne Sellin

The Free Air Humidity Manipulation (FAHM) experiment offers unique possibilities to test trees’ acclimation capacity to increasing atmospheric humidity – a climate trend predicted for northern Europe. We investigated changes in wood anatomy and hydraulic conductivity in hybrid aspen; results showed moderate modifications in both the structure and functioning of xylem. Our results suggest that hybrid aspen is relatively insensitive to the changes in air humidity.

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Published online 17 March 2015
Leaf green-white variegation is advantageous under N deprivation in Pelargonium×hortorum 
Cyril Abadie, Marlène Lamothe, Caroline Mauve, Françoise Gilard and Guillaume Tcherkez

Growth and metabolism of green-white variegated and plain morphs of Pelargonium have been examined under nitrogen deficiency. Variegated plants performed better than non-variegated plants, owing to the remobilisation of nitrogenous compounds stored in leaf white areas. It is concluded that variegation is disadvantageous under non N-limited conditions due to the lower photosynthetic surface area, but is advantageous under nitrogen deprivation.

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Published online 06 March 2015
Novel chlorophylls and new directions in photosynthesis research 
Yaqiong Li and Min Chen

Chlorophylls d and f are red-shifted chlorophylls based on their significantly red-shifted absorption bands compared with chlorophyll a. Understanding the molecular mechanism of photosynthesis driven by red-shifted chlorophylls is of global importance and will contribute to cutting-edge photosynthetic research. The current research status in related to the red-shifted chlorophylls is reviewed in this review.

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Published online 24 February 2015
Towards a conceptual ABA ideotype in plant breeding for water limited environments 
Abraham Blum

ABA is a plant hormone produced in plants under drought stress. On one hand, it causes the plant to conserve its water status; on the other hand, it reduces growth and productivity. This opinion review examines the available data on ABA and attempts to resolve this conundrum by formulating an appropriate crop plant phenotypic ABA ideotype for breeders to pursue within different dryland stress environments.

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Published online 17 February 2015
Effects of different temperature regimes on flower development, microsporogenesis and fertility in bolting garlic (Allium sativum) 
Einat Shemesh Mayer, Tomer Ben-Michael, Sagie Kimhi, Itzhak Forer, Haim D. Rabinowitch and Rina Kamenetsky

Infertility prevents genetics research and conventional breeding in garlic. Recent achievement of fertility restoration enables extensive studies of garlic florogenesis and causes for male sterility. We report on temperature effects on flower development and pollen quality in fertile and male-sterile garlic, and on the vulnerable phases of pollen formation. It is concluded that under unstable climatic conditions, agro-management modifications will facilitate breeding and seed production in this important crop.

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Published online 02 December 2014
On the evaluation of methods for the recovery of plant root systems from X-ray computed tomography images 
Stefan Mairhofer, Craig Sturrock, Darren M. Wells, Malcolm J. Bennett, Sacha J. Mooney and Tony P. Pridmore

The evaluation of root system recovery methods for X-ray microcomputed tomography images is a challenging task. In this work, we aim to raise awareness of the evaluation problem and to propose experimental approaches that allow the performance of root extraction methods to be assessed. This should help users to better understand the strengths and limitations of each method and should allow a better comparison.

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Published online 26 November 2014
Image-based estimation of oat panicle development using local texture patterns 
Roger Boyle, Fiona Corke and Catherine Howarth

High-throughput phenotyping facilities provide opportunities for plant development observation and monitoring on new scales, but also present new problems in automatic image analysis. This paper presents a solution to one such problem by automating the detection of flowering in oats. This demonstrates the applicability of state-of-the-art computer vision algorithms to phenotyping, which may well be of value in similar atlas-based measurement.

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Published online 05 November 2014
Automatic estimation of wheat grain morphometry from computed tomography data 
Harry Strange, Reyer Zwiggelaar, Craig Sturrock, Sacha J. Mooney and John H. Doonan

Accurate and non-invasive measures of wheat grain morphometry can have impact on improvements in milling yield. An automated approach is presented to extract such measures from wheat CT data. The results show significant differences in measures between two disparate strains of wheat.

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Published online 23 September 2014
Surface reconstruction of wheat leaf morphology from three-dimensional scanned data 
Daryl M. Kempthorne, Ian W. Turner, John A. Belward, Scott W. McCue, Mark Barry, Joseph Young, Gary J. Dorr, Jim Hanan and Jerzy A. Zabkiewicz

Realistic virtual models of leaf surfaces are important for several applications in plant sciences, such as simulating agrichemical spray droplet motion on the leaf surface. Although there are effective approaches for reconstructing leaf surface from 3D scanned data, complications arise when dealing with wheat (Triticum aestivum) leaves, which tend to twist and bend. We present an algorithm that overcomes this topological difficulty, allowing significantly more leaf varieties to be modelled in this way.

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Published online 22 September 2014
Blobs and curves: object-based colocalisation for plant cells 
Carl J. Nelson, Patrick Duckney, Timothy J. Hawkins, Michael J. Deeks, P. Philippe Laissue, Patrick J. Hussey and Boguslaw Obara

Quantifying the colocalisation of labels is a major application of fluorescent microscopy in plant biology. Pixel-based quantification of colocalisation, such as Pearson’s correlation coefficient, gives limited information for further analysis. We show how applying bioimage informatics tools to a commonplace experiment allows further quantifiable results to be extracted. We use our object-based colocalisation technique to extract distance information, show temporal changes and demonstrate the advantages and pitfalls of using bioimage informatics for plant science.

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Published online 19 August 2014
Automated estimation of leaf area development in sweet pepper plants from image analysis 
Graham W. Horgan, Yu Song, Chris A. Glasbey, Gerie W. A. M. van der Heijden, Gerrit Polder, J. Anja Dieleman, Marco C. A. M. Bink and Fred A. van Eeuwijk

The total area of the leaves on a plant is important in horticulture, but manually measuring it is tedious and destructive. Getting a computer to recognise and count leaves is difficult, so we have used statistical methods to relate leaf area to the variations in colour in an image. This has potential to be a big help for scientists developing and testing new crop cultivars.

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blank image Functional Plant Biology
Volume 42 Number 4 2015

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Descriptive Table of Contents 
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Hydrogen peroxide promotes programmed cell death and salicylic acid accumulation during the induced production of sesquiterpenes in cultured cell suspensions of Aquilaria sinensis 
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Juan Liu , Yanhong Xu , Zheng Zhang and Jianhe Wei
pp. 337-346

We investigated the formation of agarwood, a substance believed to have interesting medicinal properties and that is produced only by certain plants when they are responding to an injury or infection. We evaluated the effects of hydrogen peroxide on cells of the plant Aquilaria sinensis; as we expected, the plant cells responded to this damaging chemical with specific changes in gene expression and the production of compounds known to be linked with toxicity and programmed cell death. Our results indicate that exposure to a reactive oxygen species, such as hydrogen peroxide, produces multiple cellular responses that culminate in an effective defensive reaction on the part of the plant (i.e. production of agarwood).


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Sufficient leaf transpiration and nonstructural carbohydrates are beneficial for high-temperature tolerance in three rice (Oryza sativa) cultivars and two nitrogen treatments 
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Dongliang Xiong , Tingting Yu , Xiaoxia Ling , Shah Fahad , Shaobing Peng , Yong Li and Jianliang Huang
pp. 347-356

Extreme high temperature can threaten rice (Oryza sativa L.) production by decreasing its seed setting percentage; however, sufficient nitrogen can alleviate this detrimental effect. Heat-tolerant cultivars show high leaf transpiration and nonstructural carbohydrates, and sufficient nitrogen can improve them. This suggests that sufficient leaf transpiration and nonstructural carbohydrates are beneficial for high-temperature tolerance in three rice cultivars and two N treatments.


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The variability in the xylem architecture of grapevine petiole and its contribution to hydraulic differences 
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Uri Hochberg , Asfaw Degu , Tanya Gendler , Aaron Fait and Shimon Rachmilevitch
pp. 357-365

Grapevine (Vitis vinifera) is known for its cultivar variability in response to deficit irrigation. A 3 year study, comparing Shiraz and Cabernet Sauvignon petioles anatomy, showed that Shiraz had larger vessels diameter that resulted in higher hydraulic conductivity and transpiration rates. These traits lead to lower water potentials and vulnerability to cavitation. Our results provide a link between xylem anatomy and plant performances.


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Plant hydraulic conductance adapts to shoot number but limits shoot vigour in grapevines 
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Markus Keller , Laura S. Deyermond and Bhaskar R. Bondada
pp. 366-375

This study sought to provide a biophysical basis for the common observation that shoot vigour in grapevines declines as the number of shoots per plant increases. We found that the plant’s capacity to supply water to its canopy adapts to the shoot number; however, limited adaptation, rather than competition with fruit growth, may constrain shoot growth and fruit growth. These findings may be used to optimise cultural practices that balance shoot and fruit growth for maximum quality.


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Ethylene is involved in high air humidity promoted stomatal opening of tomato (Lycopersicon esculentum) leaves 
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Louise E. Arve and Sissel Torre
pp. 376-386

Stomata movements are regulated by air humidity. The aim of this work was to study the role of ethylene and abscisic acid in air humidity stomatal responses. We show that both ethylene production and sensitivity play a role in high air humidity promoted stomatal opening and that high level of abscisic acid can inhibit the opening. The results indicate an interaction between ethylene and abscisic acid and provide novel insight into the role of plant hormones in air humidity regulated stomatal movements.

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Image based phenotyping during winter: a powerful tool to assess wheat genetic variation in growth response to temperature 
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Christoph Grieder , Andreas Hund and Achim Walter
pp. 387-396

Rates of plant growth and their reaction to main environmental factors such as temperature are difficult to determine under field conditions. By segmenting plant leaves from background in images taken from wheat plots, we were able to show significant variation among varieties for their response in canopy cover growth rates to changing temperatures. The developed approach is simple and fast and can be used to screen genetic mapping populations for growth response patterns to temperature and other environmental factors.


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Roles of gibberellins and cytokinins in regulation of morphological and physiological traits in Polygonum cuspidatum responding to light and nitrogen availabilities 
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Daisuke Sugiura , Koichiro Sawakami , Mikiko Kojima , Hitoshi Sakakibara , Ichiro Terashima and Masaki Tateno
pp. 397-409

The regulatory mechanisms of biomass allocation and the morphological and physiological traits of leaves in response to light and N availability are not fully understood. We found that both gibberellins and cytokinins are closely involved in the regulatory mechanisms in Polygonum cuspidatum. The results will help to further our understanding of plant morphogenesis in response to light and N availability.

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Nitrogen sharing and water source partitioning co-occur in estuarine wetlands 
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Lili Wei , David A. Lockington , Shen Yu and Catherine E. Lovelock
pp. 410-417

Co-existence mechanisms of different plant species in an ecosystem are one of the mysteries of nature. This field investigation in a natural estuarine ecosystem used isotopic fingerprints of water and nutrients to understand co-existing plant species in resource sharing or partitioning. Facilitation and competition were found co-occurring between two different plant pairs for water and nutrient in the estuarine wetlands.


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Histo-anatomical leaf variations related to depth in Posidonia oceanica 
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Silvia Nicastro , Anna M. Innocenti and Nicodemo G. Passalacqua
pp. 418-422

Neptune seagrass, (P. oceanica) plays an important biological and ecological role in marine ecosystems. We studied the acclimation capacity of P. oceanica at different depth and light regimes, finding that the inner structure of leaf cells changes in a way similar to that shown by phytoplankton cells to low light conditions. This result could offer new opportunities for understanding seagrass adaptations to the marine ecosystem.

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Interspecific variation in branch and leaf traits among three Syzygium tree species from different successional tropical forests 
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Shi-Dan Zhu , Ya-Jun Chen , Kun-Fang Cao and Qing Ye
pp. 423-432

Understanding how functional traits are associated with habitats is of great importance in plant biology. Through investigating a suite of branch and leaf functional traits of three Syzygium tree species in different successional tropical forests, we demonstrate that traits related to photosynthesis and/or hydraulics, rather than to drought tolerance, are key factors underlying the response and adaptation of these congeneric species to different environments.


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These articles have been peer reviewed and accepted for publication. They are still in production and have not been edited, so may differ from the final published form.

    FP15013  Accepted 22 March 2015
    Assessment of drought tolerance and its potential yield penalty in potato
    Heike Sprenger, Katharina Rudack, Christian Schudoma, Arne Neumann, Sylvia Seddig, Rolf Peters, Ellen Zuther, Joachim Kopka, Dirk Hincha, Dirk Walther, Karin Koehl

    FP14352  Accepted 13 March 2015
    Crosstalk among nitric oxide, calcium, and reactive oxygen species during triterpenoid biosynthesis in Betula platyphylla
    Fansuo Zeng, Kun Liu, Sida Li, Yaguang Zhan

    FP14336  Accepted 11 March 2015
    The role of oxidative stress in determining the level of viability of black poplar (Populus nigra L.) seeds stored at different temperatures
    Ewa Kalemba, Jan Suszka, Ewelina Ratajczak

    FP14152  Accepted 10 March 2015
    Dynamic carbon allocation into source and sink tissues determine within-plant differences in carbon isotope ratios
    Frederik Wegener, Wolfram Beyschlag, Christiane Werner

    FP14355  Accepted 08 March 2015
    Photosynthetic characteristics and light energy conversions under different light environments in five tree species occupying dominant status at different stages of subtropical forest succession
    Qiang Zhang, Tai-Jie Zhang, Wah Soon Chow, Xin Xie, Yuan-Jun Chen, Chang-Lian Peng

    FP14240  Accepted 02 March 2015
    In vivo epidermal UV-A-absorbance is induced by sunlight and protects Soldanella alpina leaves from photoinhibition
    Constance Laureau, Sylvie Meyer, Xavier Baudin, Christophe Huignard, Peter Streb

    FP14343  Accepted 28 February 2015
    Comparative expression profiling of three early inflorescence stages of oil palm indicates that vegetative to reproductive phase transition of meristem is regulated by sugar balance
    Walter Ajambang, Sintho Ardie, Hugo Volkaert, George Ngando-Ebongue, S. Sudarsono

    FP14134  Accepted 12 February 2015
    Temperature responses of photosynthesis and respiration by a sub-Antarctic megaherb from Heard Island
    Marcus Schortemeyer, John Evans, Dan Bruhn, Dana Bergstrom, Marilyn Ball


The Most Read ranking is based on the number of downloads from the CSIRO PUBLISHING website of articles published in the previous 12 months. Usage statistics are updated daily.

Rank Paper Details
1. Published 13 February 2015
The structure and activity of nodulation-suppressing CLE peptide hormones of legumes

April H. Hastwell, Peter M. Gresshoff and Brett J. Ferguson

2. Published 30 September 2014
Genomics for drought resistance – getting down to earth

Abraham Blum

3. Published 8 April 2014
Drought resistance and soil water extraction of a perennial C4 grass: contributions of root and rhizome traits

Yi Zhou, Christopher J. Lambrides and Shu Fukai

4. Published 14 August 2014
Crop yield components – photoassimilate supply- or utilisation limited-organ development?

John W. Patrick and Kim Colyvas

5. Published 7 May 2014
Variation in mesophyll conductance among Australian wheat genotypes

Eisrat Jahan, Jeffrey S. Amthor, Graham D. Farquhar, Richard Trethowan and Margaret M. Barbour

6. Published 14 July 2014
Photosynthesis–nitrogen relationships in tropical forest tree species as affected by soil phosphorus availability: a controlled environment study

Keith J. Bloomfield, Graham D. Farquhar and Jon Lloyd

7. Published 30 September 2014
Mucilage exudation facilitates root water uptake in dry soils

Mutez A. Ahmed, Eva Kroener, Maire Holz, Mohsen Zarebanadkouki and Andrea Carminati

8. Published 30 September 2014
Strategies to increase the yield and yield stability of crops under drought – are we making progress?

Neil C. Turner, Abraham Blum, Mehmet Cakir, Pasquale Steduto, Roberto Tuberosa and Neil Young

9. Published 14 August 2014
When smaller is better: leaf hydraulic conductance and drought vulnerability correlate to leaf size and venation density across four Coffea arabica genotypes

Andrea Nardini, Eele Õunapuu-Pikas and Tadeja Savi

10. Published 30 September 2014
Two potato (Solanum tuberosum) varieties differ in drought tolerance due to differences in root growth at depth

Jaime Puértolas, Carlos Ballester, E. David Elphinstone and Ian C. Dodd

11. Published 8 April 2014
Vapour pressure deficit aids the interpretation of cotton canopy temperature response to water deficit

Warren C. Conaty, James R. Mahan, James E. Neilsen and Greg A. Constable

12. Published 8 April 2014
Soil water availability influences the temperature response of photosynthesis and respiration in a grass and a woody shrub

Tony Joseph, David Whitehead and Matthew H. Turnbull

13. Published 8 April 2014
More fertile florets and grains per spike can be achieved at higher temperature in wheat lines with high spike biomass and sugar content at booting

M. Fernanda Dreccer, Kimberley B. Wockner, Jairo A. Palta, C. Lynne McIntyre, M. Gabriela Borgognone, Maryse Bourgault, Matthew Reynolds and Daniel J. Miralles

14. Published 8 April 2014
Photophysiological responses of marine diatoms to elevated CO2 and decreased pH: a review

Kunshan Gao and Douglas A. Campbell

15. Published 30 September 2014
Partial root zone drying exerts different physiological responses on field-grown grapevine (Vitis vinifera cv. Monastrell) in comparison to regulated deficit irrigation

Pascual Romero, Juan Gabriel Pérez-Pérez, Francisco M. del Amor, Adrián Martinez-Cutillas, Ian C. Dodd and Pablo Botía

16. Published 14 August 2014
Review on shape formation in epidermal pavement cells of the Arabidopsis leaf

Eveline Jacques, Jean-Pierre Verbelen and Kris Vissenberg

17. Published 7 May 2014
Spring barley shows dynamic compensatory root and shoot growth responses when exposed to localised soil compaction and fertilisation

Johannes Pfeifer, Marc Faget, Achim Walter, Stephan Blossfeld, Fabio Fiorani, Ulrich Schurr and Kerstin A. Nagel

18. Published 7 May 2014
Environmental stress activation of plant long-terminal repeat retrotransposons

Ahmed M. Alzohairy, Jamal S. M. Sabir, Gábor Gyulai, Rania A. A. Younis, Robert K. Jansen and Ahmed Bahieldin

19. Published 7 May 2014
Stomatal pore size and density in mangrove leaves and artificial leaves: effects on leaf water isotopic enrichment during transpiration

Leonel da Silveira Lobo Sternberg and Lynn M. Manganiello

20. Published 14 August 2014
Responses of rice to Fe2+ in aerated and stagnant conditions: growth, root porosity and radial oxygen loss barrier

Jenjira Mongon, Dennis Konnerup, Timothy D. Colmer and Benjavan Rerkasem

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