Showing papers in "New Phytologist in 2005"

What have we learned from 15 years of free-air CO2 enrichment (FACE)? A meta-analytic review of the responses of photosynthesis, canopy properties and plant production to rising CO2.

Abstract: Contents Summary 1 I. What is FACE? 2 II. Materials and methods 2 III. Photosynthetic carbon uptake 3 IV. Acclimation of photosynthesis 6 V. Growth, above-ground production and yield 8 VI. So, what have we learned? 10 Acknowledgements 11 References 11 Appendix 1. References included in the database for meta-analyses 14 Appendix 2. Results of the meta-analysis of FACE effects 18 Summary Free-air CO2 enrichment (FACE) experiments allow study of the effects of elevated [CO2] on plants and ecosystems grown under natural conditions without enclosure. Data from 120 primary, peer-reviewed articles describing physiology and production in the 12 large-scale FACE experiments (475–600 ppm) were collected and summarized using meta-analytic techniques. The results confirm some results from previous chamber experiments: light-saturated carbon uptake, diurnal C assimilation, growth and above-ground production increased, while specific leaf area and stomatal conductance decreased in elevated [CO2]. There were differences in FACE. Trees were more responsive than herbaceous species to elevated [CO2]. Grain crop yields increased far less than anticipated from prior enclosure studies. The broad direction of change in photosynthesis and production in elevated [CO2] may be similar in FACE and enclosure studies, but there are major quantitative differences: trees were more responsive than other functional types; C4 species showed little response; and the reduction in plant nitrogen was small and largely accounted for by decreased Rubisco. The results from this review may provide the most plausible estimates of how plants in their native environments and field-grown crops will respond to rising atmospheric [CO2]; but even with FACE there are limitations, which are also discussed.

Genes and salt tolerance: bringing them together.

Abstract: Salinity tolerance comes from genes that limit the rate of salt uptake from the soil and the transport of salt throughout the plant, adjust the ionic and osmotic balance of cells in roots and shoots, and regulate leaf development and the onset of senescence. This review lists some candidate genes for salinity tolerance, and draws together hypotheses about the functions of these genes and the specific tissues in which they might operate. Little has been revealed by gene expression studies so far, perhaps because the studies are not tissue-specific, and because the treatments are often traumatic and unnatural. Suggestions are made to increase the value of molecular studies in identifying genes that are important for salinity tolerance.

The global distribution of ecosystems in a world without fire

Abstract: This paper is the first global study of the extent to which fire determines global vegetation patterns by preventing ecosystems from achieving the potential height, biomass and dominant functional types expected under the ambient climate (climate potential). To determine climate potential, we simulated vegetation without fire using a dynamic global-vegetation model. Model results were tested against fire exclusion studies from different parts of the world. Simulated dominant growth forms and tree cover were compared with satellite-derived land- and tree-cover maps. Simulations were generally consistent with results of fire exclusion studies in southern Africa and elsewhere. Comparison of global 'fire off' simulations with landcover and treecover maps show that vast areas of humid C(4) grasslands and savannas, especially in South America and Africa, have the climate potential to form forests. These are the most frequently burnt ecosystems in the world. Without fire, closed forests would double from 27% to 56% of vegetated grid cells, mostly at the expense of C(4) plants but also of C(3) shrubs and grasses in cooler climates. C(4) grasses began spreading 6-8 Ma, long before human influence on fire regimes. Our results suggest that fire was a major factor in their spread into forested regions, splitting biotas into fire tolerant and intolerant taxa.

Assessing the generality of global leaf trait relationships

Abstract: Summary • Global-scale quantification of relationships between plant traits gives insight into the evolution of the world’s vegetation, and is crucial for parameterizing vegetation‐ climate models. • A database was compiled, comprising data for hundreds to thousands of species for the core ‘leaf economics’ traits leaf lifespan, leaf mass per area, photosynthetic capacity, dark respiration, and leaf nitrogen and phosphorus concentrations, as well as leaf potassium, photosynthetic N-use efficiency (PNUE), and leaf N : P ratio. • While mean trait values differed between plant functional types, the range found within groups was often larger than differences among them. Future vegetation‐ climate models could incorporate this knowledge. • The core leaf traits were intercorrelated, both globally and within plant functional types, forming a ‘leaf economics spectrum’. While these relationships are very general, they are not universal, as significant heterogeneity exists between relationships fitted to individual sites. Much, but not all, heterogeneity can be explained by variation in sample size alone. PNUE can also be considered as part of this trait spectrum, whereas leaf K and N : P ratios are only loosely related.

Proanthocyanidins--a final frontier in flavonoid research?

Abstract: Proanthocyanidins are oligomeric and polymeric end products of the flavonoid biosynthetic pathway. They are present in the fruits, bark, leaves and seeds of many plants, where they provide protection against predation. At the same time they give flavor and astringency to beverages such as wine, fruit juices and teas, and are increasingly recognized as having beneficial effects on human health. The presence of proanthocyanidins is also a major quality factor for forage crops. The past 2 years have seen important breakthroughs in our understanding of the biosynthesis of the building blocks of proanthocyanidins, the flavan-3-ols (+)-catechin and (-)-epicatechin. However, virtually nothing is known about the ways in which these units are assembled into the corresponding oligomers in vivo. Molecular genetic approaches are leading to an understanding of the regulatory genes that control proanthocyanidin biosynthesis, and this information, together with increased knowledge of the enzymes specific for the pathway, will facilitate the genetic engineering of plants for introduction of value-added nutraceutical and forage quality traits.

Anatomical and chemical defenses of conifer bark against bark beetles and other pests.

Abstract: Conifers are long-lived organisms, and part of their success is due to their potent defense mechanisms. This review focuses on bark defenses, a front line against organisms trying to reach the nutrient-rich phloem. A major breach of the bark can lead to tree death, as evidenced by the millions of trees killed every year by specialized bark-invading insects. Different defense strategies have arisen in conifer lineages, but the general strategy is one of overlapping constitutive mechanical and chemical defenses overlaid with the capacity to up-regulate additional defenses. The defense strategy incorporates a graded response from 'repel', through 'defend' and 'kill', to 'compartmentalize', depending upon the advance of the invading organism. Using a combination of toxic and polymer chemistry, anatomical structures and their placement, and inducible defenses, conifers have evolved bark defense mechanisms that work against a variety of pests. However, these can be overcome by strategies including aggregation pheromones of bark beetles and introduction of virulent phytopathogens. The defense structures and chemicals in conifer bark are reviewed and questions about their coevolution with bark beetles are discussed.

UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi

Abstract: Identification of ectomycorrhizal (ECM) fungi is often achieved through comparisons of ribosomal DNA internal transcribed spacer (ITS) sequences with accessioned sequences deposited in public databases. A major problem encountered is that annotation of the sequences in these databases is not always complete or trustworthy. In order to overcome this deficiency, we report on UNITE, an open-access database. • UNITE comprises well annotated fungal ITS sequences from well defined herbarium specimens that include full herbarium reference identification data, collector/source and ecological data. At present UNITE contains 758 ITS sequences from 455 species and 67 genera of ECM fungi. • UNITE can be searched by taxon name, via sequence similarity using blastn, and via phylogenetic sequence identification using galaxie. Following implementation, galaxie performs a phylogenetic analysis of the query sequence after alignment either to pre-existing generic alignments, or to matches retrieved from a blast search on the UNITE data. It should be noted that the current version of UNITE is dedicated to the reliable identification of ECM fungi. • The UNITE database is accessible through the URL http://unite.zbi.ee

Leaf nitrogen and phosphorus stoichiometry across 753 terrestrial plant species in China

Abstract: Leaf nitrogen and phosphorus stoichiometry of Chinese terrestrial plants was studied based on a national data set including 753 species across the country. Geometric means were calculated for functional groups based on life form, phylogeny and photosynthetic pathway, as well as for all 753 species. The relationships between leaf N and P stoichiometric traits and latitude (and temperature) were analysed. The geometric means of leaf N, P, and N : P ratio for the 753 species were 18.6 and 1.21 mg g(-1) and 14.4, respectively. With increasing latitude (decreasing mean annual temperature, MAT), leaf N and P increased, but the N : P ratio did not show significant changes. Although patterns of leaf N, P and N : P ratios across the functional groups were generally consistent with those reported previously, the overall N : P ratio of China's flora was considerably higher than the global averages, probably caused by a greater shortage of soil P in China than elsewhere. The relationships between leaf N, P and N : P ratio and latitude (and MAT) also suggested the existence of broad biogeographical patterns of these leaf traits in Chinese flora.

Constraints on the evolution of adaptive phenotypic plasticity in plants

Abstract: The high potential fitness benefit of phenotypic plasticity tempts us to expect phenotypic plasticity as a frequent adaptation to environmental heterogeneity. Examples of proven adaptive plasticity in plants, however, are scarce and most plastic responses actually may be 'passive' rather than adaptive. This suggests that frequently requirements for the evolution of adaptive plasticity are not met or that such evolution is impeded by constraints. Here we outline requirements and potential constraints for the evolution of adaptive phenotypic plasticity, identify open questions, and propose new research approaches. Important open questions concern the genetic background of plasticity, genetic variation in plasticity, selection for plasticity in natural habitats, and the nature and occurrence of costs and limits of plasticity. Especially promising tools to address these questions are selection gradient analysis, meta-analysis of studies on genotype-by-environment interactions, QTL analysis, cDNA-microarray scanning and quantitative PCR to quantify gene expression, and two-dimensional gel electrophoresis to quantify protein expression. Studying plasticity along the pathway from gene expression to the phenotype and its relationship with fitness will help us to better understand why adaptive plasticity is not more universal, and to more realistically predict the evolution of plastic responses to environmental change.

The control of stomata by water balance.

Abstract: It is clear that stomata play a critical role in regulating water loss from terrestrial vegetation. What is not clear is how this regulation is achieved. Stomata appear to respond to perturbations of many aspects of the soil-plant-atmosphere hydraulic continuum, but there is little agreement regarding the mechanism (or mechanisms) by which stomata sense such perturbations. This review discusses feedback and feedforward mechanisms by which hydraulic perturbations are putatively transduced into stomatal movements, in relation to generic empirical features of those responses. It is argued that a metabolically mediated feedback response of stomatal guard cells to the water status in their immediate vicinity ('hydro-active local feedback') remains the best explanation for many well-known features of hydraulically related stomatal behaviour, such as transient 'wrong-way' responses and the equivalence of hydraulic supply and demand as stomatal effectors. Furthermore, many curious phenomena that appear inconsistent with feedback, such as 'apparent feedforward' humidity responses and 'isohydric' behaviour (water potential homeostasis), are in fact expected to emerge from the juxtaposition of hydro-active local feedback and the well-known hysteretic and threshold-like effect of water potential on xylem hydraulic resistance.

In touch: plant responses to mechanical stimuli

Abstract: Perception and response to mechanical stimuli are likely essential at the cellular and organismal levels. Elaborate and impressive touch responses of plants capture the imagination as such behaviors are unexpected in otherwise often quiescent creatures. Touch responses can turn plants into aggressors against animals, trapping and devouring them, and enable flowers to be active in ensuring crosspollination and shoots to climb to sunlit heights. Morphogenesis is also influenced by mechanical perturbations, including both dynamic environmental stimuli, such as wind, and constant forces, such as gravity. Even individual cells must sense turgor and wall integrity, and subcellular organelles can translocate in response to mechanical perturbations. Signaling molecules and hormones, including intracellular calcium, reactive oxygen species, octadecanoids and ethylene, have been implicated in touch responses. Remarkably, touch-induced gene expression is widespread; more than 2.5% of Arabidopsis genes are rapidly up-regulated in touch-stimulated plants. Many of these genes encode calcium-binding, cell wall modifying, defense, transcription factor and kinase proteins. With these genes as tools, molecular genetic methods may enable elucidation of mechanisms of touch perception, signal transduction and response regulation.

Rhizosphere geometry and heterogeneity arising from root‐mediated physical and chemical processes

Abstract: The rhizosphere differs from the bulk soil in a range of biochemical, chemical and physical processes that occur as a consequence of root growth, water and nutrient uptake, respiration and rhizodeposition. These processes also affect microbial ecology and plant physiology to a considerable extent. This review concentrates on two features of this unique environment: rhizosphere geometry and heterogeneity in both space and time. Although it is often depicted as a soil cylinder of a given radius around the root, drawing a boundary between the rhizosphere and bulk soil is an impossible task because rhizosphere processes result in gradients of different sizes. For instance, because of diffusional constraints, root uptake can result in a depletion zone extending <1 mm for phosphate to several centimetres for nitrate, while respiration may affect the bulk of the soil. Rhizosphere processes are responsible for spatial and temporal heterogeneities in the soil, although these are sometimes difficult to distinguish from intrinsic soil heterogeneity. A further complexity is that these processes are regulated by plants, microbial communities and soil constituents, and their many interactions. Novel in situ techniques and modelling will help in providing a holistic view of rhizosphere functioning, which is a prerequisite for its management and manipulation.

In the light of stomatal opening: new insights into ‘the Watergate’

Abstract: Stomata can be regarded as hydraulically driven valves in the leaf surface, which open to allow CO2 uptake and close to prevent excessive loss of water. Movement of these 'Watergates' is regulated by environmental conditions, such as light, CO2 and humidity. Guard cells can sense environmental conditions and function as motor cells within the stomatal complex. Stomatal movement results from the transport of K+ salts across the guard cell membranes. In this review, we discuss the biophysical principles and mechanisms of stomatal movement and relate these to ion transport at the plasma membrane and vacuolar membrane. Studies with isolated guard cells, combined with recordings on single guard cells in intact plants, revealed that light stimulates stomatal opening via blue light-specific and photosynthetic-active radiation-dependent pathways. In addition, guard cells sense changes in air humidity and the water status of distant tissues via the stress hormone abscisic acid (ABA). Guard cells thus provide an excellent system to study cross-talk, as multiple signaling pathways induce both short- and long-term responses in these sensory cells.

Linking leaf and root trait syndromes among 39 grassland and savannah species

Abstract: Summary • Here, we tested hypothesized relationships among leaf and fine root traits of grass, forb, legume, and woody plant species of a savannah community. • CO 2 exchange rates, structural traits, chemistry, and longevity were measured in tissues of 39 species grown in long-term monocultures. • Across species, respiration rates of leaves and fine roots exhibited a common regression relationship with tissue nitrogen (N) concentration, although legumes had lower rates at comparable N concentrations. Respiration rates and N concentration declined with increasing longevity of leaves and roots. Species rankings of leaf and fine-root N and longevity were correlated, but not specific leaf area and specific root length. The C 3 and C 4 grasses had lower N concentrations than forbs and legumes, but higher photosynthesis rates across a similar range of leaf N. • Despite contrasting photosynthetic pathways and N 2 -fixing ability among these species, concordance in above- and below-ground traits was evident in comparable rankings in leaf and root longevity, N and respiration rates, which is evidence of a common leaf and root trait syndrome linking traits to effects on plant and ecosystem processes.

Nutrient availability and management in the rhizosphere: exploiting genotypic differences

Abstract: Crop nutrition is frequently inadequate as a result of the expansion of cropping into marginal lands, elevated crop yields placing increasing demands on soil nutrient reserves, and environmental and economic concerns about applying fertilizers. Plants exposed to nutrient deficiency activate a range of mechanisms that result in increased nutrient availability in the rhizosphere compared with the bulk soil. Plants may change their root morphology, increase the affinity of nutrient transporters in the plasma membrane and exude organic compounds (carboxylates, phenolics, carbohydrates, enzymes, etc.) and protons. Chemical changes in the rhizosphere result in altered abundance and composition of microbial communities. Nutrient-efficient genotypes are adapted to environments with low nutrient availability. Nutrient efficiency can be enhanced by targeted breeding through pyramiding efficiency mechanisms in a desirable genotype as well as by gene transfer and manipulation. Rhizosphere microorganisms influence nutrient availability; adding beneficial microorganisms may result in enhanced availability of nutrients to crops. Understanding the role of plant-microbe-soil interactions in governing nutrient availability in the rhizosphere will enhance the economic and environmental sustainability of crop production.

Impacts of parasitic plants on natural communities.

Abstract: Parasitic plants have profound effects on the ecosystems in which they occur. They are represented by some 4000 species and can be found in most major biomes. They acquire some or all of their water, carbon and nutrients via the vascular tissue of the host's roots or shoots. Parasitism has major impacts on host growth, allometry and reproduction, which lead to changes in competitive balances between host and nonhost species and therefore affect community structure, vegetation zonation and population dynamics. Impacts on hosts may further affect herbivores, pollinators and seed vectors, and the behaviour and diversity of these is often closely linked to the presence and abundance of parasitic plants. Parasitic plants can therefore be considered as keystone species. Community impacts are mediated by the host range of the parasite (the diversity of species that can potentially act as hosts) and by their preference and selection of particular host species. Parasitic plants can also alter the physical environment around them--including soil water and nutrients, atmospheric CO2 and temperature--and so may also be considered as ecosystem engineers. Such impacts can have further consequences in altering the resource supply to and behaviour of other organisms within parasitic plant communities.

A modular concept of phenotypic plasticity in plants

Abstract: Based on empirical evidence from the literature we propose that, in nature, phenotypic plasticity in plants is usually expressed at a subindividual level. While reaction norms (i.e. the type and the degree of plant responses to environmental variation) are a property of genotypes, they are expressed at the level of modular subunits in most plants. We thus contend that phenotypic plasticity is not a whole-plant response, but a property of individual meristems, leaves, branches and roots, triggered by local environmental conditions. Communication and behavioural integration of interconnected modules can change the local responses in different ways: it may enhance or diminish local plastic effects, thereby increasing or decreasing the differences between integrated modules exposed to different conditions. Modular integration can also induce qualitatively different responses, which are not expressed if all modules experience the same conditions. We propose that the response of a plant to its environment is the sum of all modular responses to their local conditions plus all interaction effects that are due to integration. The local response rules to environmental variation, and the modular interaction rules may be seen as evolving traits targeted by natural selection. Following this notion, whole-plant reaction norms are an integrative by-product of modular plasticity, which has far-reaching methodological, ecological and evolutionary implications.

Using L-systems for modeling source-sink interactions, architecture and physiology of growing trees: the L-PEACH model.

Abstract: Functional-structural plant models simulate the development of plant structure, taking into account plant physiology and environmental factors. The L-PEACH model is based on the development of peach trees. It demonstrates the usefulness of L-systems in constructing functional-structural models. L-PEACH uses L-systems both to simulate the development of tree structure and to solve differential equations for carbohydrate flow and allocation. New L-system-based algorithms are devised for simulating the behavior of dynamically changing structures made of hundreds of interacting, time-varying, nonlinear components. L-PEACH incorporates a carbon-allocation model driven by source-sink interactions between tree components. Storage and mobilization of carbohydrates during the annual life cycle of a tree are taken into account. Carbohydrate production in the leaves is simulated based on the availability of water and light. Apices, internodes, leaves and fruit grow according to the resulting local carbohydrate supply. L-PEACH outputs an animated three-dimensional visual representation of the growing tree and user-specified statistics that characterize selected stages of plant development. The model is applied to simulate a tree's response to fruit thinning and changes in water stress. L-PEACH may be used to assist in horticultural decision-making processes after being calibrated to specific trees.

Leaf hydraulic capacity in ferns, conifers and angiosperms: impacts on photosynthetic maxima

Abstract: The hydraulic plumbing of vascular plant leaves varies considerably between major plant groups both in the spatial organization of veins, as well as their anatomical structure. Five conifers, three ferns and 12 angiosperm trees were selected from tropical and temperate forests to investigate whether the profound differences in foliar morphology of these groups lead to correspondingly profound differences in leaf hydraulic efficiency. We found that angiosperm leaves spanned a range of leaf hydraulic conductance from 3.9 to 36 mmol m 2 s − 1 MPa − 1 , whereas ferns (5.9–11.4 mmol m − 2 s − 1 MPa − 1 ) and conifers (1.6–9.0 mmol m − 2 s − 1 MPa − 1 ) were uniformly less conductive to liquid water. Leaf hydraulic conductance (K leaf ) correlated strongly with stomatal conductance indicating an internal leaf-level regulation of liquid and vapour conductances. Photosynthetic capacity also increased with K leaf , however, it became saturated at values of K leaf over 20 mmol m − 2 s − 1 MPa − 1 . The data suggest that vessels in the leaves of the angiosperms studied provide them with the flexibility to produce highly conductive leaves with correspondingly high photosynthetic capacities relative to tracheid-bearing species. .

Epigenetics and plant evolution

Abstract: A fundamental precept of evolutionary biology is that natural selection acts on phenotypes determined by DNA sequence variation within natural populations. Recent advances in our understanding of gene regulation, however, have elucidated a spectrum of epigenetic molecular phenomena capable of altering the temporal, spatial, and abundance patterns of gene expression. These modifications may have morphological, physiological, and ecological consequences, and are heritable across generations, suggesting they are important in evolution. A corollary is that genetic variation per se is not always a prerequisite to evolutionary change. Here, we provide an introduction to epigenetic mechanisms in plants, and highlight some of the empirical studies illustrative of the possible connections between evolution and epigenetically mediated alterations in gene expression and morphology.

Community structure of arbuscular mycorrhizal fungi at different soil depths in extensively and intensively managed agroecosystems

Abstract: Summary • The vertical distribution of spores of arbuscular mycorrhizal fungi (AMF) was investigated in soil profiles of extensively and intensively managed agroecosystems, including two permanent grasslands, a vineyard and two continuously mono-cropped maize fields. • The number of AMF spores decreased with increasing soil depth – most drastically in the grasslands and the vineyard – but there was a large diversity of AMF species even in the deepest soil layers (50–70 cm). This was particularly striking in the maize fields where the highest species numbers were found below ploughing depth. Some species sporulated mainly, or exclusively, in the deep soil layers, others mainly in the top layers. • Soil samples were used to inoculate trap cultures. Up to 18 months after inoculation, there was no conspicuous difference in the species composition among the trap cultures representing different soil depths, and only a weak match to the species composition determined by analysis of field samples. • Our results indicate that the AMF communities in deep soil layers are surprisingly diverse and different from the topsoil. Thus, deep soil layers should be included in studies to get a complete picture of AMF diversity.

Is plant performance limited by abundance of arbuscular mycorrhizal fungi? A meta-analysis of studies published between 1988 and 2003

Abstract: Summary • We conducted meta-analyses of 290 published field and glasshouse trials to determine the effects of various agricultural practices on mycorrhizal colonization in nonsterile soils, and the consequence of those effects on yield, biomass, and phosphorus (P) concentration. • Mycorrhizal colonization was increased most by inoculation (29% increase), followed by shortened fallow (20%) and reduced soil disturbance (7%). The effect of crop rotation depended on whether the crop was mycorrhizal. Increased colonization resulted in a yield increase in the field of 23% across all management practices. • Biomass at harvest and shoot P concentration in early season were increased by inoculation (57 and 33%, respectively) and shortened fallow (55 and 24%). Reduced disturbance increased shoot P concentration by 27%, but biomass was not significantly affected. Biomass was significantly reduced in 2% of all trials in which there was a significant increase in colonization. • Irrespective of management practice, an increased mycorrhizal colonization was less likely to increase biomass if either soil P or indigenous inoculum potential was high.

Maternal effects provide phenotypic adaptation to local environmental conditions

Abstract: In outcrossing plants, seed dispersal distance is often less than pollen movement. If the scale of environmental heterogeneity within a population is greater than typical seed dispersal distances but less than pollen movement, an individual's environment will be similar to that of its mother but not necessarily its father. Under these conditions, environmental maternal effects may evolve as a source of adaptive plasticity between generations, enhancing offspring fitness in the environment that they are likely to experience. This idea is illustrated using Campanula americana, an herb that grows in understory and light-gap habitats. Estimates of seed dispersal suggest that offspring typically experience the same light environment as their mother. In a field experiment testing the effect of open vs understory maternal light environments, maternal light directly influenced offspring germination rate and season, and indirectly affected germination season by altering maternal flowering time. Results to date indicate that these maternal effects are adaptive; further experimental tests are ongoing. Evaluating maternal environmental effects in an ecological context demonstrates that they may provide phenotypic adaptation to local environmental conditions.

Duplication and DNA segmental loss in the rice genome: implications for diploidization.

Abstract: Large-scale duplication events have been recently uncovered in the rice genome, but different interpretations were proposed regarding the extent of the duplications. Through analysing the 370 AAb genome sequences assembled into 12 chromosomes of Oryza sativa subspecies indica, we detected 10 duplicated blocks on all 12 chromosomes that contained 47% of the total predicted genes. Based on the phylogenetic analysis, we inferred that this was a result of a genome duplication that occurred c. 70 million years ago, supporting the polyploidy origin of the rice genome. In addition, a segmental duplication was also identified involving chromosomes 11 and 12, which occurred c. 5 million years ago. Following the duplications, there have been large-scale chromosomal rearrangements and deletions. About 30-65% of duplicated genes were lost shortly after the duplications, leading to a rapid diploidization. Together with other lines of evidence, we propose that polyploidzation is still an ongoing process in grasses of polyploidy origins.

Forest fragmentation effects on patch occupancy and population viability of herbaceous plant species

Abstract: Habitat fragmentation is one of the major threats to species diversity. In this review, we discuss how the genetic and demographic structure of fragmented populations of herbaceous forest plant species is affected by increased genetic drift and inbreeding, reduced mate availability, altered interactions with pollinators, and changed environmental conditions through edge effects. Reported changes in population genetic and demographic structure of fragmented plant populations have, however, not resulted in large-scale extinction of forest plants. The main reason for this is very likely the long-term persistence of small and isolated forest plant populations due to prolonged clonal growth and long generation times. Consequently, the persistence of small forest plant populations in a changing landscape may have resulted in an extinction debt, that is, in a distribution of forest plant species reflecting the historical landscape configuration rather than the present one. In some cases, fragmentation appears to affect ecosystem integrity rather than short-term population viability due to the opposition of different fragmentation-induced ecological effects. We finally discuss extinction and colonization dynamics of forest plant species at the regional scale and suggest that the use of the metapopulation concept, both because of its heuristic power and conservation applications, may be fruitful.

Managing the manganese: molecular mechanisms of manganese transport and homeostasis.

Abstract: Manganese (Mn) is an essential metal nutrient for plants. Recently, some of the genes responsible for transition metal transport in plants have been identified; however, only relatively recently have Mn2+ transport pathways begun to be identified at the molecular level. These include transporters responsible for Mn accumulation into the cell and release from various organelles, and for active sequestration into endomembrane compartments, particularly the vacuole and the endoplasmic reticulum. Several transporter gene families have been implicated in Mn2+ transport, including cation/H+ antiporters, natural resistance-associated macrophage protein (Nramp) transporters, zinc-regulated transporter/iron-regulated transporter (ZRT/IRT1)-related protein (ZIP) transporters, the cation diffusion facilitator (CDF) transporter family, and P-type ATPases. The identification of mutants with altered Mn phenotypes can allow the identification of novel components in Mn homeostasis. In addition, the characterization of Mn hyperaccumulator plants can increase our understanding of how plants can adapt to excess Mn, and ultimately allow the identification of genes that confer this stress tolerance. The identification of genes responsible for Mn2+ transport has substantially improved our understanding of plant Mn homeostasis.

Inheritance and recombination of mitochondrial genomes in plants, fungi and animals.

Abstract: Summary It is generally assumed that mitochondrial genomes are uniparentally transmitted, homoplasmic and nonrecombining. However, these assumptions draw largely from early studies on animal mitochondrial DNA (mtDNA). In this review, we show that plants, animals and fungi are all characterized by episodes of biparental inheritance, recombination among genetically distinct partners, and selfish elements within the mitochondrial genome, but that the extent of these phenomena may vary substantially across taxa. We argue that occasional biparental mitochondrial transmission may allow organisms to achieve the best of both worlds by facilitating mutational clearance but continuing to restrict the spread of selfish genetic elements. We also show that methodological biases and disproportionately allocated study effort are likely to have influenced current estimates of the extent of biparental inheritance, heteroplasmy and recombination in mitochondrial genomes from different taxa. Despite these complications, there do seem to be discernible similarities and differences in transmission dynamics and likelihood of recombination of mtDNA in plant, animal and fungal taxa that should provide an excellent opportunity for comparative investigation of the evolution of mitochondrial genome dynamics.

Legume nodule senescence: roles for redox and hormone signalling in the orchestration of the natural aging process.

Abstract: Research on legume nodule development has contributed greatly to our current understanding of plant-microbe interactions. However, the factors that orchestrate root nodule senescence have received relatively little attention. Accumulating evidence suggests that redox signals contribute to the establishment of symbiosis and senescence. Although degenerative in nature, nodule senescence is an active process programmed in development in which reactive oxygen species (ROS), antioxidants, hormones and proteinases have key roles. Nodules have high levels of the redox buffers, ascorbate and glutathione, which are important in the nodulation process and in senescence. These metabolites decline with N-fixation as the nodule ages but the resultant decrease in redox buffering capacity does not necessarily lead to enhanced ROS or oxidative stress. We propose models by which ROS and antioxidants interact with hormones such as abscisic acid in the orchestration of nodule senescence.

Uptake, translocation and transformation of arsenate and arsenite in sunflower (Helianthus annuus): formation of arsenic-phytochelatin complexes during exposure to high arsenic concentrations.

Abstract: Summary • The aim of the study was to determine the time-dependent formation of arsenic–phytochelatin (As–PC) complexes in the roots, stems and leaves of an arsenic-nontolerant plant (Helianthus annuus) during exposure to 66 mol l−1 arsenite (As(III)) or arsenate (As(V)). • We used our previously developed method of simultaneous element-specific (inductively coupled plasma mass spectrometry, ICP-MS) and molecular-specific (electrospray-ionization mass spectrometry, ES-MS) detection systems interfaced with a suitable chromatographic column and eluent conditions, which enabled us to identify and quantify As–PC complexes directly. • Roots of As-exposed H. annuus contained up to 14 different arsenic species, including the complex of arsenite with two (γ-Glu-Cys)2-Gly molecules [As(III)–(PC2)2], the newly identified monomethylarsonic phytochelatin-2 or (γ-Glu-Cys)2-Gly CH3As (MA(III)–PC2) and at least eight not yet identified species. The complex of arsenite with (γ-Glu-Cys)3-Gly (As(III)–PC3) and the complex of arsenite with glutathione (GSH) and (γ-Glu-Cys)2-Gly (GS–As(III)–PC2) were present in all samples (roots, stems and leaves) taken from plants exposed to As. The GS–As(III)–PC2 complex was the dominant complex after 1 h of exposure. As(III)–PC3 became the predominant As–PC complex after 3 h, binding up to 40% of the As present in the exposed plants. • No As–PC complexes were found in sap (mainly xylem sap from the root system), in contrast to roots, stems and leaves, which is unequivocal evidence that As–PC complexes are not involved in the translocation of As from root to leaves of H. annuus.

Functional-structural plant modelling.

Abstract: In the last decade, many research teams throughout the world initiated a new approach in plant science by developing computer models of plant functioning and growth. The intention of this approach was to understand the complex interactions between plant architecture and the physical and biological processes that drive the plant development at several spatial and temporal scales, using so-called functional-structural plant models (FSPMs). Explicitly taking into account the spatial distribution of plant organs has multiple consequences: (i) FSPMs are usually associated with 3D plant models where plant architecture is represented as a collection of interconnected plant components, which are distributed in the 3D below- and above-ground space; (ii) FSPMs usually deal with the spatial distribution of both environmental and biological processes; (iii) FSPMs are usually based on scaling up, mostly from the organ to the plant, but also from tissue to organ or from plant to stand; and (iv) to deal with the system complexity owing to the high number of plant constituents, and to deal with the potentially high numbers of interacting processes, FSPMs must develop adequate computational methods. To discuss these questions, in 1996 the FSPM series of workshops (http://amap.cirad.fr/workshop/FSPM04/index.html) was established to assemble regularly from all over the world scientists who integrate 3D representations of plants, physiological models, environmental models, computer science and mathematics into their approach. The general aim of this community is to understand better, through the use of 3D representations, the importance of taking into account the spatialisation of processes in plant functioning and morpho-genesis. The FSPM community contributes to unravelling these integrated plant functioning mechanisms and in this issue of New Phytologistwe feature a set of papers that address the different aspects and questions raised (Godin et al, 2005), so highlighting the current advances and future directions required. (Resume d'auteur)