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'Stalagmiform' roots are here defined as dense, stalagmite-like aggregations of roots and rootlets which protrude from the sandy floor of certain limestone caves. Paper chromatography showed these structures were associated with large trees of Eucalyptus gomphocephala growing above the caves. They seem to form in response to localized abundance of water at sites beneath drip-points in the cave ceiling. The anatomy of ectomycorrhizal and non-infected stalagmiform rootlets was similar to that of Eucalypt rootlets. Non-pathogenic endophytes were also often present, giving many rootlets an endomycorrhizal character. This unusual combination of features places the stalagmiform root in a separate category from other specialized root structures. [ABSTRACT FROM AUTHOR]

A method for the combined estimation of caffeine, theophylline and theobromine in plant material is presented. The method involved a chloroform-ammonia extraction, separation of the bases in the chloroform extract by thin layer or paper chromatography and finally estimation of the eluted bases by spectrophotometry. Good recoveries of all three compounds were recorded. The method was used to estimate the level of these compounds in tea, coffee beans and cocoa cotyledons. [ABSTRACT FROM AUTHOR]

There is an urgent need to examine the range of ecosystems that is currently protected in national parks and reserves, to point out those examples that are unprotected and to establish a rational programme of priorities for protecting as complete a series as possible. The International Biological Programme has pioneered the field of large-scale survey work for the collection of data of relevance to this need and has contributed to the development of information retrieval techniques for handling the data. The first part of the paper discusses the rationale of the development of the data base and its modus operandi. The system is illustrated by two examples of retrieval and analysis for specific enquiries; the distribution of four species of Pinus, and the occurrence of grazing, logging and burning in national parks and equivalent reserves in the United States. The second part of the paper deals with system design, details of programming for the data base, and retrieval strategy. It is intended as an independent section which may be skipped if the reader has no interest in the finer points of the data base itself. [ABSTRACT FROM AUTHOR]

Globally, root production accounts for 33-67% of terrestrial net primary productivity and influences decomposition via root production and turnover, carbon (C) allocation to mycorrhizal fungi and root exudation. As recognized above ground, the timing of phenological events affects terrestrial C balance, yet there is no parallel understanding for below-ground phenology. In this paper we examine the phenology of root production and its relationship to temperature, soil moisture, and above-ground phenology. Synthesizing 87 observations of whole-plant phenology from 40 studies, we found that, on average, root growth occurs 25 ± 8 d after shoot growth but that the offset between the peak in root and shoot growth varies > 200 d across biomes (boreal, temperate, Mediterranean, and subtropical). Root and shoot growth are positively correlated with median monthly temperature and mean monthly precipitation in boreal, temperate, and subtropical biomes. However, a temperature hysteresis in these biomes leads to the hypothesis that internal controls over C allocation to roots are an equally, if not more, important driver of phenology. The specific mechanisms are as yet unclear but they are likely mediated by some combination of photoassimilate supply, hormonal signaling, and growth form. [ABSTRACT FROM AUTHOR]

Pollen grains are microscopic so their identification and quantification has, for decades, depended upon human observers using light microscopes: a labour-intensive approach. Modern improvements in computing and imaging hardware and software now bring automation of pollen analyses within reach. In this paper, we provide the first review in over 15 yr of progress towards automation of the part of palynology concerned with counting and classifying pollen, bringing together literature published from a wide spectrum of sources. We consider which attempts offer the most potential for an automated palynology system for universal application across all fields of research concerned with pollen classification and counting. We discuss what is required to make the datasets of these automated systems as acceptable as those produced by human palynologists, and present suggestions for how automation will generate novel approaches to counting and classifying pollen that have hitherto been unthinkable. [ABSTRACT FROM AUTHOR]

This paper examines the function of Arabidopsis thaliana At PTB1 and At PTB2 as plant splicing factors., The effect on splicing of overexpression of At PTB1 and At PTB2 was analysed in an in vivo protoplast transient expression system with a novel mini-exon splicing reporter. A range of mutations in pyrimidine-rich sequences were compared with and without At PTB and NpU2 AF65 overexpression. Splicing analyses of constructs in protoplasts and RNA from overexpression lines used high-resolution reverse transcription polymerase chain reaction ( RT- PCR)., At PTB1 and At PTB2 reduced inclusion/splicing of the potato invertase mini-exon splicing reporter, indicating that these proteins can repress plant intron splicing. Mutation of the polypyrimidine tract and closely associated Cytosine and Uracil-rich (CU-rich) sequences, upstream of the mini-exon, altered repression by At PTB1 and At PTB2. Coexpression of a plant orthologue of U2 AF65 alleviated the splicing repression of At PTB1. Mutation of a second CU-rich upstream of the mini-exon 3′ splice site led to a decline in mini-exon splicing, indicating the presence of a splicing enhancer sequence. Finally, RT- PCR of At PTB overexpression lines with c. 90 known alternative splicing ( AS) events showed that At PTBs significantly altered AS of over half the events., At PTB1 and At PTB2 are splicing factors that influence alternative splicing. This occurs in the potato invertase mini-exon via the polypyrimidine tract and associated pyrimidine-rich sequence. [ABSTRACT FROM AUTHOR]

The authors discuss the paper of Qi and colleagues which focuses on the response of relict genus Cercidiphyllum to climatic or geological changes using genetic information from chloroplast (cp) and nuclear DNAs. They mention that Qi and colleagues who used ecological niche modelling (ENM) estimated that the specie split from its sister lineage during late Cretaceous period based on cpDNA evidence. They state that the paper draws detailed pictured o the evolutionary history of Cercidiphyllum.

The article discusses several comments on paper of McCormack M.L. which is related to the redefining of fine roots which improves the understanding of contributions to terrestrial biosphere process. Topics discussed include how long-lived perennials are addressed to exclusion of crop series, how alfalfa plants and cuttings have different pattern of fine root development than second- and later-year plants, and monocots which does not develop secondary thickening.

Keywords: hydraulic efficiency; hydraulic safety; plant hydraulics; tradeoff; xylem EN hydraulic efficiency hydraulic safety plant hydraulics tradeoff xylem 1156 1158 3 04/19/21 20160915 NES 160915 We appreciate Bittencourt et al.'s (2016; in this issue of I New Phytologist i , pp. 1152-1155) constructive contributions following our paper, Gleason I et al i . Considering angiosperms, it is likely that nonvessel tissue fractions influence the safety-efficiency tradeoff indirectly (e.g. via their contribution to xylem capacitance, or whole-plant growth), rather than being forced by limited xylem space. On research priorities to advance understanding of the safety-efficiency tradeoff in xylem: A response to Bittencourt et al.'s (2016) comment 'On xylem hydraulic efficiencies, wood space-use and the safety-efficiency tradeoff' As such, vessel lumen fraction, vessel diameter, and vessel frequency are largely uncoupled from nonvessel tissue fractions across self-supporting angiosperm species (Zanne I et al i .,), and are therefore unlikely to trade off with mechanical safety and hydraulic efficiency (or safety). [Extracted from the article]

Plant regeneration from seed is largely governed by germinability and speed of germination. These fitness components have received considerably less attention in CO2 research relative to studies of vegetative or reproductive output responses. Moreover, the limited literature has not been rigorously examined for generalizable patterns of responses and/or potential mechanisms. We used a meta-analytic approach to summarize literature results of seed germination characteristics in response to parental CO2 enrichment ( e CO2). The direct effects of e CO2 on germination components were also analyzed. The data set came from 29 original research papers encompassing 64 species and 116 observations. Across all studies, parental e CO2 increased subsequent germination by 9%, but the responses varied among species by as much as 300%. The response was significantly higher in trees than in other life forms. With the exception of crops, parental e CO2 also increased germination rate in most life forms and functional groups. Despite a considerable interspecific variability, we found a positive correlation between germination success and seed mass responses to parental e CO2. Therefore, the observed diversity of regeneration success responses to parental e CO2 is partly controlled by the direction and magnitude of changes in seed mass. [ABSTRACT FROM AUTHOR]

Information about several papers discussed at the Plant Genome Dynamics Meeting held in Banyuls-sur-Mer, France on September 12-13, 2013 is presented. Topics include the whole genome duplication, evolutionary impact of transposable elements, and effect of genome architecture on distribution of genetic variation within species and populations. The meeting featured several speakers including Eric Schranz, Marie Mirouze, and Michael Purugganan.

The article focuses on the April 2014 issue of the journal related to the international plant science. It states that the issue features commentaries from authors, article reviews, and research papers related to plant science. It notes that the journal aims to offer rapid publication of high quality and original research in plant science. It mentions that the journal is available online at Wiley Online Library and on the website located at www.newphytologist.com.

As a result of the late Quaternary megafaunal extinctions (50 000-10 000 before present ( BP)), most continents today are depauperate of megaherbivores. These extinctions were time-transgressive, size- and taxonomically selective, and were caused by climate change, human hunting, or both. The surviving megaherbivores often act as ecological keystones, which was likely true in the past. In spite of this and extensive research on the causes of the Late Quaternary Extinctions, the long-term ecological consequences of the loss of the Pleistocene megafauna remained unknown until recently, due to difficulties in linking changes in flora and fauna in paleorecords. The quantification of Sporormiella and other dung fungi have recently allowed for explicit tests of the ecological consequences of megafaunal extirpations in the fossil pollen record. In this paper, I review the impacts of the loss of keystone megaherbivores on vegetation in several paleorecords. A growing number of studies support the hypothesis that the loss of the Pleistocene megafauna resulted in cascading effects on plant community composition, vegetation structure and ecosystem function, including increased fire activity, novel communities and shifts in biomes. Holocene biota thus exist outside the broader evolutionary context of the Cenozoic, and the Late Quaternary Extinctions represent a regime shift for surviving plant and animal species. [ABSTRACT FROM AUTHOR]

Ecologists, ecohydrologists, and biogeochemists need detailed insights into belowground properties and processes, including changes in water, salts, and other elements that can influence ecosystem productivity and functioning. Relying on traditional sampling and observation techniques for such insights can be costly, time consuming, and infeasible, especially if the spatial scales involved are large. Geophysical imaging provides an alternative or complement to traditional methods to gather subsurface variables across time and space. In this paper, we review aspects of geophysical imaging, particularly electrical and electromagnetic imaging, that may benefit ecologists seeking clearer understanding of the shallow subsurface. Using electrical resistivity imaging, for example, we have been able to successfully show the effect of land-use conversions to agriculture on salt mobilization and leaching across kilometer-long transects and to depths of tens of meters. Recent advances in ground-penetrating radar and other geophysical imaging methods currently provide opportunities for subsurface imaging with sufficient detail to locate small (≥5 cm diameter) animal burrows and plant roots, observe soil-water and vegetation spatial correlations in small watersheds, estuaries, and marshes, and quantify changes in groundwater storage at local to regional scales using geophysical data from ground- and space-based platforms. Ecologists should benefit from adopting these minimally invasive, scalable imaging technologies to explore the subsurface and advance our collective research. [ABSTRACT FROM AUTHOR]

Species discovery is a fundamental first step for all of biodiversity science. Recent research has claimed that the increasing number of authors associated with the description of new species represents an expanding workforce discovering the remaining new species from an ever-diminishing pool., Here, we present a comprehensive dataset from The International Plant Names Index ( IPNI) of new species of flowering plant published between 1970 and 2011., We show that, on average, 1855 new species have been described annually since 1970. We show that compared to other scientific disciplines the increased number of authors on taxonomic papers is relatively small and may reflect changes in scientific practice rather than an increase in taxonomic capacity., These data, alongside published results demonstrating a lag period of 35 yr between a specimen being collected and published as a new species, strongly suggest that the global taxonomic capacity to describe new species of flowering plant is stagnant at a time of unprecedented concern for conservation and extinction. [ABSTRACT FROM AUTHOR]

615I.615II.616III.618IV.622V.625VI.627VII.628628References628 Summary: Invasion science is a very active subdiscipline of ecology. However, some scientists contend that theoretical integration has been limited and that predictive power remains weak. This paper, focusing on plants, proposes a new multi‐pronged research strategy that builds on recent advances in invasion science. More intensive studies on particular model organisms and ecosystems are needed to improve our understanding of the full suite of interacting factors that influence invasions (‘model system research’). At the same time, comparative studies across many study systems are essential for unravelling the context‐dependencies of insights that emerge from particular studies (‘multi‐site studies’); and quantitative synthesis based on large datasets should be constrained to well‐defined theoretical domains (‘focused meta‐analysis’). We also suggest ways for better integration of information about species biology and ecosystem characteristics (‘invasion syndromes’). We expect that a resulting theory of invasions will need to be conceived as a somewhat heterogeneous conglomerate of elements of varying generality and predictive power: laws that apply to well‐specified domains, general concepts and theoretical frameworks that can guide thinking in research and management, and in‐depth knowledge about the drivers of particular invasions. [ABSTRACT FROM AUTHOR]

Featured paper: See also the Editorial by McDowell et al [ABSTRACT FROM AUTHOR]

This paper investigates the effects of cuticular wax on the release of strain and on the tensile properties of enzymatically isolated cuticular membranes ( CMs) taken from leaves of agave ( Agave americana), bush lily ( Clivia miniata), holly ( Ilex aquifolium), and ivy ( Hedera helix) and from fruit of apple ( Malus × domestica), pear ( Pyrus communis), and tomato ( Lycopersicon esculentum)., Biaxial strain release was quantified as the decrease in CM disc area following wax extraction. Stiffness, maximum strain and maximum force were determined in uniaxial tensile tests using strips of CM and dewaxed CMs ( DCMs)., Biaxial strain release, stiffness, and maximum strain, but not maximum force, were linearly related to the amount of wax extracted. Apple CM has the most wax and here the effect of wax extraction was substantially accounted for by the embedded cuticular wax. Heating apple CM to 80°C melted some wax constituents and produced an effect similar to, but smaller than, that resulting from wax extraction., Our results indicate that wax 'fixes' strain, effectively converting reversible elastic into irreversible plastic strain. A consequence of 'fixation' is increased cuticular stiffness. [ABSTRACT FROM AUTHOR]

Global warming may have profound effects on terrestrial ecosystems. However, a comprehensive evaluation of the effects of warming on ecosystem nitrogen (N) pools and dynamics is not available., Here, we compiled data of 528 observations from 51 papers and carried out a meta-analysis of experimental warming effects on 13 variables related to terrestrial N pools and dynamics., We found that, on average, net N mineralization and net nitrification rate were increased by 52.2 and 32.2%, respectively, under experimental warming treatment. N pools were also increased by warming, although the magnitude of this increase was less than that of N fluxes. Soil microbial N and N immobilization were not changed by warming, probably because microbes are limited by carbon sources. Grassland and shrubland/heathland were less responsive to warming than forest, probably because the reduction of soil moisture by warming offset the temperature effect in these areas. Soil heating cable and all-day treatment appeared to be the most effective method on N cycling among all treatment methods., Results of this meta-analysis are useful for better understanding the response of N cycling to global warming and the underlying mechanism of warming effects on plants and ecosystem functions. [ABSTRACT FROM AUTHOR]

The article presents information on various papers published by David J. Read, who was knighted in the 2007 Queen's Birthday Honours list for services to biological sciences. His research papers focus on the biology of mycorrhizas. His first paper dealt with Brunchorstia infection of Corsican pine. He also published a paper on the association of the ericoid mycorrhizal fungus Rhizoscyphus ericae with the Antarctic leafy liverwort Cephaloziella varians. Over the years, Read, with his students and postdoctoral colleagues, provided the basis for the current understanding of mycorrhizas and their central role in the ecology of heathland and boreal forest ecosystems.

The author comments on the significant research on trees published by the "New Phytologist" journal. Changes in tree ring width offer a composite picture of environmental influences on tree growth over extended periods. Periodic phenomena need long-term data to extract the characteristic periodicities and environmental impacts on masting. Meanwhile, papers in the unlabelled part of the relationship between time and space are characterized by relatively large areas of study and are basically field-based.

This article presents a commentary on a paper by B. P. Kemp and J. Doughty on the nature of the regions of S-receptor kinase (SRK). According to the authors, Kemp and Doughty present important data that move the story significantly forward. They claim that the paper shed light on the nature of the regions of SRK that are involved in haplotype-specific recognition. They also assert that the most novel aspect of the paper is the strategy of using a peptide array. The authors conclude that the significance of the work is potentially broader than providing a better understanding of SI receptor-ligand interactions.

Information about several papers discussed at the 6th New Phytologist Workshop called "Bridging Mycorrhizal Genomics, Metagenomics and Forest Ecology" held on November 15-16, 2012 in Nancy, France is presented. Topics at the meeting includes sequencing mycorrhizal fungal species, contributions of fungal genomics, and fungal ecology. The workshop featured several experts in fungal genomics including Alan Kuo, Jan Colpaert, and Dan Cullen.

Fungal symbionts that live asymptomatically inside plant tissues (endophytes) can influence plant-insect interactions. Recent work has shown that damage by leaf-cutting ants, a major Neotropical defoliator, is reduced to almost half in plants with high densities of endophytes. We investigated changes in the phenotype of leaves that could influence ants' behavior to result in the reduction of foliar damage., We produced cucumber seedlings with high and low densities of one common endophyte species, Colletotrichum tropicale. We used the leaves in bioassays and to compare chemical and physical leaf characteristics important for ants' food selection., Ants cut about one-third more area of cucumber leaves with lower densities of endophytes and removed c. 20% more paper disks impregnated with the extracts of those leaves compared with leaves and disks from plants hosting the fungus. Colletotrichum tropicale colonization did not cause detectable changes in the composition of volatile compounds, cuticular waxes, nutrients or leaf toughness., Our study shows that endophytes changed leaf chemistry and suggests that compounds with relative low volatility released after leaf wounding are a major factor influencing foraging decisions by ants when choosing between plants with low or high endophyte loads. [ABSTRACT FROM AUTHOR]

Information about several papers discussed at the 29th New Phytologist Symposium: Stomata in Manchester, England in July 2012 on the global impact of stomatic pores and guard cells is presented. Topics include stomatal development and evolution, climate models and improved crop production. Its logo is also provided which shows the role of such cells in regulating worldwide issues such as climate change and breeding of sustainable crop.

In this paper, we conducted a detailed analysis of the ZIP family transporter, NcZNT1, in the zinc (Zn)/cadmium (Cd) hyperaccumulating plant species, Noccaea caerulescens, formerly known as Thlaspi caerulescens. NcZNT1 was previously suggested to be the primary root Zn/Cd uptake transporter. Both a characterization of NcZNT1 transport function in planta and in heterologous systems, and an analysis of NcZNT1 gene expression and NcZNT1 protein localization were carried out., We show that NcZNT1 is not only expressed in the root epidermis, but also is highly expressed in the root and shoot vasculature, suggesting a role in long-distance metal transport. Also, NcZNT1 was found to be a plasma membrane transporter that mediates Zn but not Cd, iron (Fe), manganese (Mn) or copper (Cu) uptake into plant cells., Two novel regions of the NcZNT1 promoter were identified which may be involved in both the hyperexpression of NcZNT1 and its ability to be regulated by plant Zn status., In conclusion, we demonstrate here that NcZNT1 plays a role in Zn and not Cd uptake from the soil, and based on its strong expression in the root and shoot vasculature, could be involved in long-distance transport of Zn from the root to the shoot via the xylem. [ABSTRACT FROM AUTHOR]

This paper presents two models of carrier-dependent long-distance auxin transport in stems that represent the process at different scales. [ABSTRACT FROM AUTHOR]

Information about several papers discussed at a meeting held August 2011 sponsored by the Ecological Society of America on experiments which examine the effects of global change on carbon storage and exchange is presented. Topics include the comparison between autotrophic and heterotrophic respiration, temporal variation and non-linear responses, and the complexity of changes in the environment. The meeting featured several researchers including Vidya Suseela of Purdue University in the U.S.

Information about several papers discussed at a meeting held August 2011 sponsored by the Ecological Society of America on drought-induced forest mortality is presented. Topics include the patterns of mortality across landscapes, the involvement of tree stress and biotic agents such as pests and diseases, and investigations of physiological mechanisms of drought-induced tree mortality. The meeting featured several researchers including Henry Adams from University of Arizona in Tucson, Arizona.

Waterlogging affects large areas of agricultural land, resulting in severe economic penalties because of massive losses in crop production. Traditionally, plant breeding for waterlogging tolerance has been based on the field assessment of a range of agronomic and morphological characteristics. This review argues for a need to move towards more physiologically based approaches by targeting specific cellular mechanisms underling key components of waterlogging tolerance in plants. Also, while the main focus of researchers was predominantly on plant anoxia tolerance, less attention was given to plant tolerance to phytotoxins under waterlogged conditions. This paper reviews the production of major elemental and organic phytotoxins in waterlogged soils and describes their adverse effects on plant performance. The critical role of plasma membrane transporters in plant tolerance to secondary metabolite toxicity is highlighted, and ionic mechanisms mediating the this tolerance are discussed. A causal link between the secondary metabolite-induced disturbances to cell ionic homeostasis and programmed cell death is discussed, and a new ethylene-independent pathway for aerenchyma formation is put forward. It is concluded that plant breeding for waterlogging tolerance may significantly benefit from targeting mechanisms of tolerance to phytotoxins. [ABSTRACT FROM AUTHOR]

• Reduced lignin content in perennial crops has been sought as a means to improve biomass processability for paper and biofuels production, but it is unclear how this could affect wood properties and tree form. • Here, we studied a nontransgenic control and 14 transgenic events containing an antisense 4-coumarate:coenzyme A ligase (4CL) to discern the consequences of lignin reduction in poplar (Populus sp.). During the second year of growth, trees were grown either free-standing in a field trial or affixed to stakes in a glasshouse. • Reductions in lignin of up to 40% gave comparable losses in wood strength and stiffness. This occurred despite the fact that low-lignin trees had a similar wood density and up to three-fold more tension wood. In free-standing and staked trees, the control line had twice the height for a given diameter as did low-lignin trees. Staked trees had twice the height for a given diameter as free-standing trees in the field, but did not differ in wood stiffness. • Variation in tree morphogenesis appears to be governed by lignin × environment interactions mediated by stresses exerted on developing cells. Therefore our results underline the importance of field studies for assessing the performance of transgenic trees with modified wood properties. [ABSTRACT FROM AUTHOR]

• Anthropogenic nitrogen (N) addition may substantially alter the terrestrial N cycle. However, a comprehensive understanding of how the ecosystem N cycle responds to external N input remains elusive. • Here, we evaluated the central tendencies of the responses of 15 variables associated with the ecosystem N cycle to N addition, using data extracted from 206 peer-reviewed papers. • Our results showed that the largest changes in the ecosystem N cycle caused by N addition were increases in soil inorganic N leaching (461%), soil NO3- concentration (429%), nitrification (154%), nitrous oxide emission (134%), and denitrification (84%). N addition also substantially increased soil NH4+ concentration (47%), and the N content in belowground (53%) and aboveground (44%) plant pools, leaves (24%), litter (24%) and dissolved organic N (21%). Total N content in the organic horizon (6.1%) and mineral soil (6.2%) slightly increased in response to N addition. However, N addition induced a decrease in microbial biomass N by 5.8%. • The increases in N effluxes caused by N addition were much greater than those in plant and soil pools except soil NO3-, suggesting a leaky terrestrial N system. [ABSTRACT FROM AUTHOR]

•Lodging, the permanent displacement of crop plants from their vertical because of root or shoot failure, is a major yield constraint of the gluten free, panicle bearing cereal teff. The objective of this paper was to analyse the causes of lodging of teff by using, modifying and validating conventional biomechanical models. •The model parameters were obtained from a field trial with two contrasting teff cultivars, using novel in situ and laboratory measurements under wet and dry conditions. Cross-species model validation was done with rice ( Oryza sativa). •Teff is more susceptible to root lodging than to shoot lodging, although the data indicated that shoot strength is also insufficient. Hence, simultaneously breeding for both improved root anchorage and shoot strength is advocated. •The study showed that the lodging model, derived for the spike-bearing cereal wheat, needed modifications in order to be able to deal with panicle-bearing plants such as teff and rice. Water adhering to plants owing to rain or dew increased calculated lodging susceptibility. To prevent underestimation of lodging susceptibility, future lodging research should be done under completely wet conditions (water saturated soil and wetted shoots) [ABSTRACT FROM AUTHOR]

Agricultural weeds evolve in response to crop cultivation. Nevertheless, the central importance of evolutionary ecology for understanding weed invasion, persistence and management in agroecosystems is not widely acknowledged. This paper calls for more evolutionarily-enlightened weed management, in which management principles are informed by evolutionary biology to prevent or minimize weed adaptation and spread. As a first step, a greater knowledge of the extent, structure and significance of genetic variation within and between weed populations is required to fully assess the potential for weed adaptation. The evolution of resistance to herbicides is a classic example of weed adaptation. Even here, most research focuses on describing the physiological and molecular basis of resistance, rather than conducting studies to better understand the evolutionary dynamics of selection for resistance. We suggest approaches to increase the application of evolutionary-thinking to herbicide resistance research. Weed population dynamics models are increasingly important tools in weed management, yet these models often ignore intrapopulation and interpopulation variability, neglecting the potential for weed adaptation in response to management. Future agricultural weed management can benefit from greater integration of ecological and evolutionary principles to predict the long-term responses of weed populations to changing weed management, agricultural environments and global climate. [ABSTRACT FROM AUTHOR]

Contents Plant diseases induced by soil-borne plant pathogens are among the most difficult to control. In the absence of effective chemical control methods, there is renewed interest in biological control based on application of populations of antagonistic micro-organisms. In addition to Pseudomonas spp. and Trichoderma spp., which are the two most widely studied groups of biological control agents, the protective strains of Fusarium oxysporum represent an original model. These protective strains of F. oxysporum can be used to control wilt induced by pathogenic strains of the same species . Exploring the mechanisms involved in the protective capability of these strains is not only necessary for their development as commercial biocontrol agents but raises many basic questions related to the determinism of pathogenicity versus biocontrol capacity in the F. oxysporum species complex. In this paper, current knowledge regarding the interaction between the plant and the protective strains is reviewed in comparison with interactions between the plant and pathogenic strains. The success of biological control depends not only on plant–microbial interactions but also on the ecological fitness of the biological control agents. [ABSTRACT FROM AUTHOR]

Information about several papers discussed at the recent gathering of the International Parasitic Plant Society on the specialized anatomy and communication exhibited by parasitic plants is presented. Topics include the signalling molecule detected by some parasitic plants to locate their hosts which turned out to be a new plant hormone. The gathering featured several researchers including Jay Bolin, Kaori Yoneyama, and Anna Hoeniges.

In this article the authors discuss the papers published within the issue related to the use of pyrosequencing methods to characterize fungal communities. They examine the work of M. Öpik and colleagues which suggests that habitat preference may be a more important driver of host-fungus associations. Also investigated is the possibility that some of the unidentified sequences may represent described species that have not yet been subjected to molecular analysis.

Contents Summary 935 I. Introduction 936 II. Survey of genetic variation – sources and resources 936 III. Survey of molecular marker types 939 IV. Mapping approaches and tools 948 V. Survey of bioinformatics and computer resources 954 VI. Bringing it all together: stay-green gene case study 961 VII. The future of mapping 962 Acknowledgements 962 References 962 This paper is an update of our earlier review ( Jones et al., 1997 , Markers and mapping: we are all geneticists now. New Phytologist 137: 165–177), which dealt with the genetics of mapping, in terms of recombination as the basis of the procedure, and covered some of the first generation of markers, including restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), simple sequence repeats (SSRs) and quantitative trait loci (QTLs). In the intervening decade there have been numerous developments in marker science with many new systems becoming available, which are herein described: cleavage amplification polymorphism (CAP), sequence-specific amplification polymorphism (S-SAP), inter-simple sequence repeat (ISSR), sequence tagged site (STS), sequence characterized amplification region (SCAR), selective amplification of microsatellite polymorphic loci (SAMPL), single nucleotide polymorphism (SNP), expressed sequence tag (EST), sequence-related amplified polymorphism (SRAP), target region amplification polymorphism (TRAP), microarrays, diversity arrays technology (DArT), single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE) and methylation-sensitive PCR. In addition there has been an explosion of knowledge and databases in the area of genomics and bioinformatics. The number of flowering plant ESTs is c. 19 million and counting, with all the opportunity that this provides for gene-hunting, while the survey of bioinformatics and computer resources points to a rapid growth point for future activities in unravelling and applying the burst of new information on plant genomes. A case study is presented on tracking down a specific gene ( stay-green ( SGR), a post-transcriptional senescence regulator) using the full suite of mapping tools and comparative mapping resources. We end with a brief speculation on how genome analysis may progress into the future of this highly dynamic arena of plant science. [ABSTRACT FROM AUTHOR]

• The genetic control of carbon allocation and partitioning in woody perennial plants is poorly understood despite its importance for carbon sequestration, biofuels and other wood-based industries. It is also unclear how environmental cues, such as nitrogen availability, impact the genes that regulate growth, biomass allocation and wood composition in trees. • We phenotyped 396 clonally replicated genotypes of an interspecific pseudo-backcross pedigree of Populus for wood composition and biomass traits in above- and below-ground organs. The loci that regulate growth, carbon allocation and partitioning under two nitrogen conditions were identified, defining the contribution of environmental cues to their genetic control. • Sixty-three quantitative trait loci were identified for the 20 traits analyzed. The majority of quantitative trait loci are specific to one of the two nitrogen treatments, demonstrating significant nitrogen-dependent genetic control. A highly significant genetic correlation was observed between plant growth and lignin/cellulose composition, and quantitative trait loci co-localization identified the genomic position of potential pleiotropic regulators. • Pleiotropic loci linking higher growth rates to wood with less lignin are excellent targets to engineer tree germplasm improved for pulp, paper and cellulosic ethanol production. The causative genes are being identified with a genetical genomics approach. [ABSTRACT FROM AUTHOR]

The article discusses water transport in angiosperms and conifers, focusing on structural factors that influence a plant's resistance to xylem cavitation. Such cavitation increases resistance to water flow, places limits on gas exchange, and may lead to starvation or death of the plant. The paper describes the geometry, material components, and functions of the xylem. It notes that pit membranes facilitate water flow between cells, but restrict passage of gases and pathogens. The pit membranes also account for a large proportion of the hydraulic resistance exhibited by the xylem.

The article offers observations on a paper by Erik Lilleskov and colleagues in this issue about fruiting of mycorrhizal fungi in drought-stressed soil conditions. The results demonstrate the water-flow complexities where the soil, fungi, and plant meet. It discusses drought conditions in recent years and the lack of predictability of plant response. Mathematical modeling is conducted to make these predictions, but such predictions are difficult with unsaturated soil conditions. Tracer studies show that plants in arid areas extract water from fractured bedrock by developing deep root systems.

• Arbuscular mycorrhizas (AMs) contribute significantly to soil nutrient uptake in plants. As a consequence of the fungal colonization and of the deep reorganization shown by arbusculated cells, important impacts on root transcriptome are expected. • An Affymetrix GeneChip with 50 000 probe-sets and real-time RT-PCR allowed us to detect transcriptional changes triggered in Lotus japonicus by the AM fungus Gigaspora margarita, when arbuscules are at their maximum (28 d postinoculation (dpi)). An early time (4 dpi) was selected to differentiate genes potentially involved in signaling and/or in colonization of outer tissues. • A large number (75 out of 558) of mycorrhiza-induced genes code for proteins involved in protein turnover, membrane dynamics and cell wall synthesis, while many others are involved in transport (47) or transcription (24). Induction of a subset (24 genes) of these was tested and confirmed by qRT-PCR, and transcript location in arbusculated cells was demonstrated for seven genes using laser-dissected cells. • When compared with previously published papers, the transcript profiles indicate the presence of a core set of responsive genes (25) that seem to be conserved irrespective of the symbiotic partner identity. [ABSTRACT FROM AUTHOR]

Information about several papers discussed at a symposium titled "Crassulacean Acid Metabolism Plant Species as Markers of Global Climatic Change," within the Second National Ecology Meeting, and sponsered by the Mexican Scientific Society of Ecology is presented. Topics include discussions regarding the expansion of the range of crassulacean acid metabolism (CAM) plants due to climate change. The symposium featured several speakers including Drs. Louis S. Santiago and Erick De la Barrera.

The authors discuss how plants overcome abiotic stress through the help of their associations with symbionts and pathogens. They say the usual knowledge is that symbiotic associations are beneficial, while pathogen associations are harmful. The author reveals that reactive oxygen species (ROS) and reactive nitrogen species (RNS) are produced in both associations, meaning the plant and the microbe must be able to deal with ROS from both sides. They comment on a paper published within the issue about the beneficial aspect of plant-pathogen interactions.

• A previously published model of crop nitrogen (N) status based on intercepted photosynthetically active radiation ( Ri, mol per plant) suggested that plant organic N accumulation is related to Ri by a constant ratio, defined hereafter as the radiation use efficiency for N (NRUE). The aim of this paper was to compare the effects of N nutrition and CO2 enrichment on NRUE and RUE (radiation use efficiency for biomass accumulation). • In three unrelated glasshouse experiments, tomato plants ( Solanum lycopersicum) grown in hydroponics were fed for 28 d (exponential growth) with full solutions containing constant concentrations ([ ]) ranging from 0.05 to 15 mol m−3, both under ambient or CO2-enriched (1000 µl l−1) air. • Each experiment comprised five harvests. Low [ ] (< 0.3 mol m−3) limited growth via leaf area (LA) restriction and decreased light interception. CO2 enrichment enhanced dry weight and LA. RUE was not affected by [ ], but increased under CO2-enriched air. By contrast, NRUE was not affected by [ ] or CO2 enrichment. • It is suggested that the radiation efficiency for organic N acquisition (NRUE) did not depend on C or N nutrition for young plants grown under unstressed conditions. [ABSTRACT FROM AUTHOR]

• Striga is a parasitic weed attacking mainly maize, sorghum, millet and cowpea. Studying the interaction between rice and Striga is valuable since rice is a model monocot. In this paper, the susceptibility of different rice cultivars to S. hermonthica was tested and quantitative trait loci (QTL) for Striga tolerance mapped on the Bala × Azucena F6 population. • Seven rice cultivars were grown with and without S. hermonthica for 14 wk. For the mapping experiment, 115 recombinant inbred lines (RILs), along with Azucena and Bala, were grown with and without Striga for 11 wk. • Rice cultivars tested had different susceptibilities to Striga, ranging from highly susceptible to completely resistant. Azucena and Bala differed in the speed of Striga emergence and the impact on host growth. A genomic region between positions 139 and 166 cM on chromosome 1 was identified containing strong QTL (LOD = 4.9–15.7) for all traits measured. • This indicates that genes for Striga tolerance exist in rice germplasm and the mapped QTL can be further studied to promote understanding of the nature of resistance/tolerance and breeding for Striga-resistant crop plants. [ABSTRACT FROM AUTHOR]

• The outgrowth of tiller buds in Poaceae is influenced by the ratio of red to far-red light irradiance (R:FR). At each point in the plant canopy, R:FR is affected by light scattered by surrounding plant tissues. This paper presents a three-dimensional virtual plant modelling approach to simulate local effects of R:FR on tillering in spring wheat ( Triticum aestivum). • R:FR dependence of bud outgrowth was implemented in a wheat model, using three hypothetical responses of bud extension to R:FR (unit step, curvilinear and linear response). Bud break occurred when a threshold bud length was reached. Simulations were performed for three plant population densities. • In accordance with experimental observations, fewer tillers per plant were simulated for higher plant population densities. The linear and curvilinear responses caused a delay in the increase in tiller number compared with experimental data. The unit step response approached experimental results best. It is suggested that a model based on relatively simple relations can be used to simulate degree of tillering. • This study has shown that the virtual plant approach is a promising tool with which to address crop morphological and ecological research questions where the determining factors act at the level of the individual plant organ. [ABSTRACT FROM AUTHOR]

This article presents a commentary on a paper by K. Y. Lim. et al. which illustrates the power of viewing genome evolution from multiple perspectives within a phylogenetic framework. According to the authors, Lim et al. merged new data with prior knowledge to synthesize a timeline for polyploid genome evolution in the tobacco genus, Nicotiana. They claim that Lim et al. provide a global genomic view of polyploid evolution in Nicotiana by applying GISH to the genomes of four polyploid species of varying ages. In addition, the author applauds Lim et a. for interpreting prior work on Nicotiana polyploids in an evolutionary context.

• This paper presents the results of 2 yr of CO2 flux measurements on grassland communities of varying species richness, exposed to either the current or a warmer climate. • We grew experimental plant communities containing one, three or nine grassland species in 12 sunlit, climate-controlled chambers. Half of these chambers were exposed to ambient air temperatures, while the other half were warmed by 3°C. Equal amounts of water were added to heated and unheated communities, implying drier soils if warming increased evapotranspiration. Three main CO2 fluxes (gross photosynthesis, above-ground and below-ground respiration) were measured multiple times per year and reconstructed hourly or half-hourly by relating them to their most important environmental driver. • While CO2 outputs through respiration were largely unchanged under warming, CO2 inputs through photosynthesis were lowered, especially in summer, when heat and drought stress were higher. Above-ground CO2 fluxes were significantly increased in multispecies communities, as more complementary resource use stimulated productivity. Finally, effects of warming appeared to be smallest in monocultures. • This study shows that in a future warmer climate the CO2 sink capacity of temperate grasslands could decline, and that such adverse effects are not likely to be mitigated by efforts to maintain or increase species richness. [ABSTRACT FROM AUTHOR]

Information about several papers discussed at the Forestry Workshop of the Plant and Animal Genome XV Conference, held in January 2007 in San Diego, California is presented. The event focused on the genomics and evolution of forest trees, including topics on adaptive polymorphisms, quantitative trait locus analysis and tree life style. It featured presentations by Emanuele De Paoli, Gail Taylor and Gerald Tuskan.