Special Issues

Nutrient Sensing & Signalling

Peptide Signalling

Plant Biomechanics & Mechanobiology

Techniques in Ecophysiology
& Evolution of Physiological Processes

Improving Photosynthesis

Resource Allocation & Growth/
Roots & Rhizosphere Processes

Organellar Signalling

Exploiting the Engine of C4 Photosynthesis

Plant Membrane Biology

Special Issues Archive



Preface Leegood & Long

Photorespiratory bypasses: how can they work? Peterhansel et al.

Rubisco activity and regulation as targets for crop improvement. Parry et al.

Chloroplast transformation for engineering of photosynthesis. Hanson et al.

Engineering photosynthesis in plants and synthetic microorganisms. Maurino and Weber

The cyanobacterial CCM as a source of genes for improving photosynthetic CO2 fixation in crop species. Dean Price et al.

Origins and diversity of eukaryotic carbon concentrating mechanisms: lessons for the future. Meyer and Griffiths

Cyanobacterial-based approaches to improving photosynthesis in plants. Zarzycki et al.

Nonenzymic carotenoid oxidation and photooxidative stress signalling in plants. Ramel et al.

Leaf rolling allows quantification of mRNA abundance in mesophyll cells of sorghum. Covshoff et al.


Maximizing root/rhizosphere efficiency for improving crop productivity and nutrient use efficiency in intense agriculture of China. Fusuo Zhang

The objectives of this paper are to summarize the principles of root/rhizosphere management and provide an overview of some successful case studies on how to exploit the biological potential of root system and rhizosphere processes to improve crop productivity and nutrient use efficiency.

Contributions of roots and rootstocks to sustainable, intensified crop production. Gregory et al.

The purpose of this review is to explore some of the ways in which understanding root systems and their interactions with soils could contribute to the development of more sustainable systems of intensive production. Physical interactions with soil particles limit root growth if soils are dense, but root–soil contact is essential for optimal growth and uptake of water and nutrients.

Apoplastic hydrogen peroxide in the growth zone of the maize primary root under water stress. I. Increased levels are specific to the apical region of growth maintenance. Voothuluru and Sharp

To gain an understanding of how apoplastic ROS levels change under water stress, cerium chloride staining was used in conjunction with transmission electron microscopy to examine the spatial distribution of apoplastic H2O2. The results revealed that apoplastic H2O2 levels increased specifically in the apical region of the growth zone under water stress, correlating spatially with the maintenance of cell elongation.

Soil conditions and cereal root system architecture: review and considerations for linking Darwin and Weaver Rich & Watt

Here we review how soil conditions influence root system architecture; focusing on cereals. Cereals provide half of human calories, and their root systems differ from those of dicotyledons. We find that few controlled-environment studies combine more than one soil stimulus and, those that do, highlight the complexity of responses.


On the move: Induced resistance in monocots. Balmer et al.

Although plants possess an arsenal of constitutive defences such as structural barriers and preformed antimicrobial defences, many attackers are able to overcome the pre-existing defence layers. In this review, current facts and trends concerning basal immunity, and systemic acquired/induced systemic resistance in the defence of monocots against pathogens and herbivores will be summarized.

Microbial recognition and evasion of host immunity. Pel and Pieterse

Evasion of host immune recognition is less well studied but is emerging as another important strategy. Escape from recognition by the host’s immune system can be caused by alterations in the structure of the recognized MAMPs, or by active intervention of ligand-receptor recognition. This paper reviews the structure and recognition of common MAMPs and the ways that plant-associated microbes have evolved to prevent detection by their host.

Soil abiotic factors influence interactions between below ground herbivores and plant roots. Erb and Lu

Root herbivores are important ecosystem drivers and agricultural pests, and, possibly as a consequence, plants protect their roots using a variety of defensive strategies. One aspect that distinguishes belowground from aboveground plant–insect interactions is that roots are constantly exposed to a set of soil-specific abiotic factors. These factors can profoundly influence root resistance, and, consequently, the outcome of the interaction with belowground feeders. In this review, we synthesize the current literature on the impact of soil moisture, nutrients, and texture on root–herbivore interactions.

Controlling crop diseases using induced resistance: challenges for the future. Walters et al.

Since induced resistance is a host response, its expression under field conditions is likely to be influenced by a number of factors, including the environment, genotype, crop nutrition and the extent to which plants are already induced. Although research in this area has increased over the last few years, our understanding of the impact of these influences on the expression of induced resistance is still poor.

Towards establishing broad-spectrum disease resistance in plants: silicon leads the way. Van Bockhaven et al.

Priming of plant immune responses, alterations in phytohormone homeostasis, regulation of iron homeostasis, silicon-driven photorespiration and interaction with defence signalling components all are potential mechanisms involved in regulating silicon-triggered resistance responses. Further elucidating how silicon exerts its beneficial properties may create new avenues for developing plants that are better able to withstand multiple attackers.


The molecular architecture of the plant nuclear pore complex. Tamura and Hara-Nishimura

The nucleus contains the cell’s genetic material, which directs cellular activity via gene regulation. In this review, we summarize the current knowledge regarding the plant NPC proteome and address structural and functional aspects of plant nucleoporins, which support the fundamental cellular machinery.

Assessing the function of the plant nuclear pore complex and the search for specificity. Geraint Parry

The plant nuclear pore complex (NPC) is a critical controlling element in this nucleocytoplasmic movement of protein and RNA. The NPC is comprised of approximately 30 nucleoporin proteins arranged in radial symmetry around the central pore. Here is presented an overview as to how the members of the plant NPC affect signalling pathways, highlighting the progress and difficulties within this research area.


Auxin biosynthesis and storage forms. DA Korasick, TA Enders & L Strader

This review discusses the many ways auxin levels are regulated through biosynthesis, storage forms, and inactivation, and the potential roles modified auxins play in regulating the bioactive pool of auxin to affect plant growth and development.

Tuning the auxin transcriptional response Pierre-Jerome, Moss & Nemhauser

How does auxin provoke such a diverse array of responses? We review what is currently known about differences between family members of the components that make up the auxin response complex, as well as areas of potential differences in their interactions outside of the core module

Auxin: simply complicated M Sauer, S Robert, & J Kleine-Vehn

Auxin is a plant hormone involved in an extraordinarily broad variety of biological mechanisms. These range from basic cellular processes, such as endocytosis, cell polarity and cell cycle control over localized responses like cell elongation and differential growth, to macroscopic phenomena such as embryogenesis, tissue patterning and de novo formation of organs. This review gives an overview of these rather recent and emerging areas of auxin research, and tries to formulate some of the open questions.

Auxin and self-organization at the shoot apical meristem. M Sassi & T Vernoux

This review discusses both the experimental and theoretical evidence for the implication of auxin in the control of organogenesis and self organization of the shoot apical meristem.

The role of auxin in shaping shoot architecture Andrea Gallavotti

Recent advances in deciphering the molecular mechanisms that regulate auxin function have produced several tools to investigate how auxin affects the establishment and plasticity of plant morphology. Here the extensive evidence that connects auxin and its biology with the determination of plant shoot architecture is reviewed, with particular emphasis on the most recent discoveries in two well-studied model plant systems, the dicotyledonous Arabidopsis and the monocot maize.

Lateral root initiation is a probabilistic event whose frequency is set by fluctuating levels of auxin response MJ Laskoswski

This review assesses the sequence of molecular events that lead to lateral root formation in relation to the locations in which they occur, addresses how nutrients regulate the response generally though not exclusively by altering sensitivity to auxin, and finally considers the factors that control auxin levels.

Auxin and the Arabidopsis thaliana gynoecium. E Larsson, RG Franks & E Sundberg

This review summarizes recent advances in our understanding of how auxin biosynthesis, transport and responses together generate specific gynoecial domains. It also highlights areas where future research endeavors are likely to provide additional insight into the homeostatic molecular mechanisms by which auxin regulates gynoecium development

Evidence of oxidative attenuation of auxin signalling WA Peer, Y Chen & AS Murphy

This report summarizes previously published data and show additional data regarding oxIAA is generation in planta, oxIAA as a substrate in transport assays, and oxIAA as a signalling molecule in auxin-mediate responses. It then examine the relationship between IAA and ROS generation, and oxIAA levels in ROS scavenging mutants.

PLANT BIOMECHANICS Edited by Bruno Moulia

Plant biomechanics and mechanobiology are convergent paths to flourishing interdisciplinary research B Moulia

Plant micro and nanomechanics. I Burgert & T Keplinger

This paper reviews the most common micro- and nanomechanical approaches that are utilized to study primary and secondary cell walls from a biomechanics perspective. A significant part of the article is devoted to an overview of the methodological aspects of the mechanical characterization techniques with a particular focus on new developments and advancements in the field of nanomechanics.

Shrinking the hammer: micromechanical approaches to morphogenesis P Milani, SA Braybrook & A Boudaoud

Shape is imposed by the structural elements of the organism, and the translation of cellular activity into morphogenesis must go through these elements. Many methods have been recently developed to quantify at cellular resolution the properties of the main structural element in plants, the cell wall. As plant cell growth is restrained by the cell wall and powered by turgor pressure. These different micromechanical approaches are reviewed here, with a critical assessment of their strengths and weaknesses, and a discussion of how they can help us understand the regulation of growth and morphogenesis.

A force of nature: molecular mechanisms of mechanoperception in plants. GB Monshausen & ES Haswell

Here, we describe recent progress in the identification and characterization of two classes of putative mechanoreceptors, ion channels and receptor-like kinases. We also discuss how the secondary messenger Ca2+ operates at the centre of many of these mechanical signal transduction pathways.

Modes of deformation of walled cells Jacques Dumais

In this review, I attempt a first classification of the different modes of surface deformation used by walled cells. The two most restrictive modes - inextensional and equi-area deformations - are embodied in the exine of pollen grains and the wall-like pellicle of euglenoids, respectively. The greatest morphogenetic power is reached with the processive intussusception and chemorheological growth mechanisms that underlie the expansive growth of walled cells. A comparison of these two growth mechanisms suggests a possible way to tackle the complexity behind wall growth.

On the role of stress anisotropy in the growth of stems TI Baskin & OE Jensen

Efforts to quantify stress anisotropy in the stem have found that it is predominantly axial, and large enough in principle to explain the elongation of the epidermis despite its axial microfibrils. That the epidermis experiences a stress deriving from the inner tissue, the so-called “tissue stress”, has been widely recognized; however, the origin of the dominant axial direction remains obscure. We suggest that understanding the role of stress anisotropy in plant growth requires a deeper understanding of the nature of stress in hierarchical, organic structures.

The cellular mechanics of an invasive life style. AA Nezhad & A Geitmann

Mechanical control of morphogenesis at the shoot apex. Robinson et al.

Morphogenesis does not just require the correct expression of patterning genes; these genes must induce the precise mechanical changes necessary to produce a new form. Here we overview the current understanding of the mechanical dynamics and its influence on cellular and developmental processes in the shoot apex. We are only starting to uncover the mechanical basis underlying morphogenesis, and many exciting questions remain to be answered.

Slow, fast and furious: understanding the physics of plant movements Yoël Forterre

This review summarizes the main physical mechanisms plants use to achieve motility, highlighting recent work at the frontier of biology and physics on rapid movements. Emphasis is given to presenting in a single framework pioneering biological studies of water transport and growth with more recent physics research on poroelasticity and mechanical instabilities.

How do roots elongate in a structured soil?. Jin et al.

Methods for measuring plant vulnerability to cavitation: a critical review Cochard et al.

Xylem cavitation resistance has profound implications for plant physiology and ecology. This process is characterized by a vulnerability curve showing the variation of the percentage of cavitation as a function of xylem pressure potential. In this review, we provide a panorama of the techniques that have been used to generate such a curve. The techniques differ by 1) the way cavitation is induced, 2) the way cavitation is measured and we propose a nomenclature based on these two entries.

Integrative biomechanics for tree ecology: beyond wood density and strength Fournier et al.

In this paper, we propose concepts and methods that make it possible to better integrate, from an ecological point of view, the way trees mechanically explore their aerial environment “without muscle”. We propose a new view of biomechanical performance, describing the biomechanical framework for studying “motricity”. The way this biomechanical framework has been and could be used in tree ecology at species and community levels is reviewed and discussed.

Biophysical and size-dependent perspectives on plant evolution. Karl J. Niklas

Although organisms cannot obviate the effects of physical laws and processes, the consequences of these effects can be altered by ontogenetic or phylogenetic alterations in geometry, shape, or orientation as well as in body size. This examination shows how physical laws limit phenotypic expression, but how they also simultaneously provide alternative, potentially adaptive possibilities.


Will C3 crops enhanced with the C4-CCM live up to their full potential (yield)? Driever & Kromdijk

In this review, we assess possible positive or negative effects of the introduction of a carbon concentrating mechanism in C3 crop species on crop potential productivity and yield robustness.

Thermography to explore plant-environment interactions Costa et al.

This review presents and discusses the advantages of thermal imaging applications to plant science, agriculture, and ecology, as well as its limitations and possible approaches to minimize them, by highlighting examples from previous and ongoing research.

Measurement of the matric potential of soil water in the rhizosphere Whalley, Ober & Jenkins

In this review, the relationship between matric potential and soil water content is explored. It is shown that for any given soil type, this relationship is not unique and therefore both soil water content and matric potential need to be measured for the soil water status to be fully described.

Leaf mesophyll conductance and leaf hydraulic conductance: an introduction to their measurement and coordination Flexas et al.

Chlorophyll fluorescence analysis: a guide to good practice and understanding some new applications EH Murchie & T Lawson

In this review, we recognize the requirements for the use of this technique in the fields of ecology and agriculture and especially where measurements must be rapid. In addition, the development of new equipment such as monitoring fluorometers which are intended for automated long-term assessment of photosynthesis and chlorophyll fluorescence imaging for phenotypic screening has offered new opportunities.

Crawling leaves: photosynthesis in sacoglossan sea slugs Cruz et al.

The state of knowledge on autotrophy as a nutritional source for sacoglossans and the strategies they have developed to avoid excessive light, with emphasis to the behavioural and physiological mechanisms suggested to be involved in the photoprotection of kleptoplasts is reviewed.

Metabolomics in plant environmental physiology Brunetti et al.

This review examines the main techniques used in situ within field sites with particular reference to sampling and processing, and those more appropriate for use in laboratory-based settings with emphasis on secondary metabolite analysis.


The evolution of autotrophy in relation to phosphorus requirement J Raven

This review begins with a consideration of the origin of life and whether autotrophy is an ancestral trait. There is then a consideration of the roles of phosphorus in organisms, and of elemental stoichiometries in food webs, starting from autotrophs and proceeding to phago- and osmo-chemo-organotrophs.

Is it easy to move and easy to evolve? Evolutionary accessibility and adaptation Edwards & Donoghue

How do leaf veins influence the worldwide leaf economic spectrum? Review and synthesis Sack et al.

Uncorrelated evolution of leaf and petal venation patterns across the angiosperm phylogeny Roddy et al.

Ontogeny strongly and differentially alters leaf economic and other key traits in three diverse Helianthus species Mason

Did greater burial depth increase the seed size of domesticated legumes? Kluyver et al.

We tested the hypothesis that human cultivation buried seeds deeper than natural dispersal, exerting unconscious selection favouring larger seeds with greater reserves. Using a comparative approach, we sampled accessions of eight grain legumes, originating from independent domestication centres across several continents.


Maturing peptides open for communication R Aalen

Gated communities: apoplastic and symplastic signals converge at plasmodesmata to control cell fates Stahl and Simon

Take a deep breath: peptide signalling in stomatal patterning and differentiation Richardson & Torii

IDA a peptide ligand regulating cell separation processes in plants M Butenko

GOLVEN peptide signaling controls different developmental processes in the root A Fernandez, P Hilson & T Beeckman

Peptides as triggers of plant defence M Albert

Message in a bottle: small signalling peptide outputs during growth and development Czyzewicz et al.

Mining the genome of Arabidopsis thaliana as a basis for the identification of novel bioactive peptides involved in oxidative stress tolerance De Coninck et al.

The family of Peps and their precursors in Arabidopsis: differential expression and localization but similar induction of pattern-triggered immune responses Bartels et al.

Regulation of floral patterning and organ identity by Arabidopsis ERECTA-family receptor kinase genes Bemis et al.

Regulation of plant vascular stem cells by endodermis-derived EPFL-family peptide hormones and phloem-expressed ERECTA-family receptor kinases N Uchida & M Tasaka

NEVERSHED and INFLORESCENCE DEFICIENT IN ABSCISSION are differentially required for cell expansion and cell separation during floral organ abscission in Arabidopsis thaliana Liu et al.

A CLE-WOX signalling module regulates root meristem maintenance and vascular tissue development in rice Chu et al.

The CEP family in land plants: evolutionary analyses, expressionstudies and role in Arabidopsis shoot development Roberts et al.

CEP genes regulate root and shoot development in response to environmental cues and are specific to seed plants Delay, Imin, Djordjevic

The peptide encoding MtCEP1 gene modulates lateral root and nodule numbers in Medicago truncatula Imin et al.


Genetic engineering to improve plant performance under drought: physiological evaluation of achievements, limitations and possibilities DW Lawlor

Taking transgenic rice drought screening to the field Gaudin et al.

Salt stress or salt shock: which genes are we studying? Y Shavrukov

The role of l-ascorbic acid recycling in responding to environmental stress and in promoting plant growth DR Gallie

Sensing the environment: key roles of membrane-localized kinases in plant perception and response to abiotic stress Osakabe et al.

The molecular architecture of the plant nuclear pore complex Tamura & Hara-Nishimura

Assessing the function of the plant nuclear pore complex and the search for specificity G Parry

The significance of CP29 reversible phosphorylation in thylakoids of higher plants under environmental stresses Chen et al.

In this review, we discuss recent advancements in CP29 phosphorylation and dephosphorylation studies and its physiological significance under environmental stresses in higher plants, especially in the monocotyledonous crops

What controls fleshy fruit acidity? A review of malate and citrate accumulation in fruit cells Etienne et al.

This review combines analyses of transcriptomic, metabolomic, and proteomic data, and fruit process-based simulation models of the accumulation of citric and malic acids, to further our understanding of the physiological mechanisms likely to control the accumulation of these two acids during fruit development.

Sweet immunity in the plant circadian regulatory network Bolouri Moghaddam & Van den Ende
This review focuses on the emerging connections between sugar metabolism, sugar signalling, hormone signalling, and the circadian clock, with repercussions on plant innate immunity, uncovering the possible integrated network among these components.

Emerging roles of microRNAs in the mediation of drought stress response in plants Y Ding, Y Tao, and C Zhu

Drought is a major environmental stress factor that limits agricultural production worldwide. This review summarizes recent molecular studies on the miRNAs involved in the regulation of drought-responsive genes, with emphasis on miRNA-associated regulatory networks involved in drought stress response.

Photo-oxidative stress in emerging and senescing leaves: a mirror image? M Juvany, M Müller, and S Munné-Bosch

This review focuses on the role of photo-oxidative stress both at early stages of leaf growth and during leaf senescence. We consider early leaf growth to be the stages at which the leaf is photosynthetically active but still depends on imported photoassimilates for net growth. During leaf senescence, we focus on the processes involved in the initiation, re-organization and terminal phases. Furthermore, we aim at characterizing such processes beyond the information gathered in the model plant Arabidopsis thaliana and include recent literature on the topic obtained in perennials.

Global calcium transducer P-type Ca2+-ATPases open new avenues for agriculture by regulating stress signalling Kamrul Huda et al.

The key roles of Ca2+-ATPases in transport systems and stress signalling in cellular homeostasis are addressed in this review. A complete understanding of plant defence mechanisms under stress will allow bioengineering of improved crop plants, which will be crucial for food security currently observed worldwide in the context of global climate changes. Overall, this article covers classification, evolution, structural aspects of Ca2+-ATPases, and their emerging roles in plant stress signalling.

Can prolonged exposure to low VPD disturb the ABA signalling in stomatal guard cells?

This review discusses changes in the normal pattern of signal transduction that could account for disruption of guard cell signalling after long-term exposure to some environmental conditions, with special emphasis on long-term low vapour pressure deficit (VPD).

Making open data work for plant scientists Leonelli et al.

Here we highlight some of the challenges encountered by plant researchers at the bench when generating, interpreting and attempting to disseminate their data. We review the difficulties involved in sharing sequencing, transcriptomics, proteomics and metabolomics data. We then identify and assess the benefits and drawbacks of three data sharing venues currently available to plant scientists: (1) journal publication; (2) university repositories; and (3) community and project-specific databases.

A criticism of the value of midparent in polyploidization Alberto Gianinetti

Genetic additivity occurs when the effects of different alleles, or different genes, add up in the resulting phenotype. Non-additive effects (genetic interactions) are typically measured as deviations from MPV. Recently, however, the use of MPV has been directly transposed to the study of genetic additivity in newly synthesized plant polyploids, assuming that they should as well display mid-parent expression patterns for additive traits. Here, it is shown that this direct transposition is incorrect.

Hybrid breeding in wheat: technologies to improve hybrid wheat seed production Whitford et al.

This review outlines the problems with existing hybrid wheat breeding systems and explores molecular-based technologies that could improve the hybrid production system to reduce hybrid seed production costs, a pre-requisite for a commercial hybrid wheat system.