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Brassinosteroids (BRs) are key regulators in plant growth and development. The main BR perceiving receptor in Arabidopsis is Brassinosteroid Insensitive 1 (BRI1). Seedling root growth and hypocotyl elongation can be accurately predicted using a model for BRI1 receptor activity. Genetic evidence shows that non ligand-binding co-receptors of the Somatic Embryogenesis Receptor-like Kinase (SERK) family are essential for BRI1 signal transduction. A relatively simple biochemical model based on the properties of SERK loss-of-function alleles explains complex physiological responses of the BRI1 mediated BR pathway. The model uses BRI1-BR occupancy as the central estimated parameter and includes BRI1-SERK interaction based on mass action kinetics and accurately describes wild type root growth and hypocotyl elongation. Simulation studies suggest that the SERK co-receptors primarily act to increase the magnitude of the BRI1 signal. The model predicts that only a small number of active BRI1-SERK complexes are required to carry out BR signaling at physiological ligand concentration. Finally, when calibrated with single mutants, the model predicts that roots of the serk1serk3 double mutant are almost completely BL-insensitive, while the double mutant hypocotyls remain sensitive. This points to residual BRI1 signaling or to a different co-receptor requirement in shoots.

Nitrogen fertilization increases crop yield but excessive nitrate use can be a major environmental problem due to soil leaching or greenhouse gas emission. Root traits have been seldom considered as selection criteria to improve Nitrogen Use Efficiency of crops, due to the difficulty of measuring root traits under field conditions. Nonetheless, learning about mechanisms of lateral root (LR) growth stimulation or repression by nitrate availability could help to redesign root system architecture (RSA), a strategy aimed at developing plants with a dense and profound root system and with higher N uptake efficiency. Here, we explored the genetic diversity provided by natural populations of the model species Arabidopsis thaliana to identify potentially adaptive differences in biomass production and root morphology in response to nitrate availability. A core collection of 24 accessions that maximizes the genetic diversity within the species and Col-0 ( the reference accession) were grown vertically on agar medium at moderate (N+) nitrate level for 6 days and then transferred to the same condition or to low (N-) nitrate concentration for 7 days. There was a major nutritional effect on the shoot biomass and root to shoot biomass ratio. The variation of the root biomass and RSA traits (primary root length, LRs number, LR mean length, total LRs length and LR densities) was primarily genetically determined. Differences in RSA traits between accessions were somewhat more pronounced at N-. Some accessions produced almost no visible LRs (Pyl-1, N13) at N-, while other produced up to a dozen (Kn-0). Taken together our data illustrate that natural variation exists within Arabidopsis for the studied traits. The identification of RSA ideotypes in the N response will facilitate further analysis of quantitative traits for root morphology. Crown copyright (c) 2012 Published by Elsevier Ireland Ltd. All rights reserved.

Biodiversity is responsible for the provision of many ecosystem services; human well-being is based on these services, and consequently on biodiversity. In soil, earthworms represent the largest component of the animal biomass and are commonly termed ecosystem engineers'. This review considers the contribution of earthworms to ecosystem services through pedogenesis, development of soil structure, water regulation, nutrient cycling, primary production, climate regulation, pollution remediation and cultural services. Although there has been much research into the role of earthworms in soil ecology, this review demonstrates substantial gaps in our knowledge related in particular to difficulties in identifying the effects of species, land use and climate. The review aims to assist people involved in all aspects of land management, including conservation, agriculture, mining or other industries, to obtain a broad knowledge of earthworms and ecosystem services.

For the last 150 years many studies have shown the importance of earthworms for plant growth, but the exact mechanisms involved in the process are still poorly understood. Many important functions required for plant growth can be performed by soil microbes in the rhizosphere. To investigate earthworm influence on the rhizosphere microbial community, we performed a macrocosm experiment with and without Pontoscolex corethrurus (EW+ and EW−, respectively) and followed various soil and rhizosphere processes for 217 days with sugarcane. In EW+ treatments, N2O concentrations belowground (15 cm depth) and relative abundances of nitrous oxide genes (nosZ) were higher in bulk soil and rhizosphere, suggesting that soil microbes were able to consume earthworm-induced N2O. Shotgun sequencing (total DNA) revealed that around 70 microbial functions in bulk soil and rhizosphere differed between EW+ and EW− treatments. Overall, genes indicative of biosynthetic pathways and cell proliferation processes were enriched in EW+ treatments, suggesting a positive influence of worms. In EW+ rhizosphere, functions associated with plant-microbe symbiosis were enriched relative to EW− rhizosphere. Ecological networks inferred from the datasets revealed decreased niche diversification and increased keystone functions as an earthworm-derived effect. Plant biomass was improved in EW+ and worm population proliferated.

A inoculação em milho com Rizobactérias Promotoras de Crescimento em Plantas (Plant-Growth-Promoting Rhizobacteria - PGPR) pode melhorar o crescimento desse cultivar, diminuir o uso de fertilizantes nitrogenados e os custos da produção, além de diminuir os impactos negativos ao meio ambiente. Além disso, a produção de pigmentos, tais como a melanina, por essas bactérias pode ter aplicações comerciais promissoras em indústrias de alimentos, produtos farmacêuticos, cosméticos e têxteis. O objetivo geral desse trabalho foi realizar um estudo de caracterização genética e bioquímica de 20 bactérias endofíticas isoladas de milho (Zea mays L.) cultivado no Cerrado goiano para observar a diversidade genética, identificar bactérias que possam ser utilizadas como inoculantes e verificar a produção de pigmentos tipo melanina (melanina-like) por essas bactérias. Para o estudo de diversidade foi realizada análise com os marcadores moleculares: região espaçadora intergênica 16S-23S rRNA; regiões palindrômicas extragênicas repetidas (REP); genes atpD, glnII e 16S rRNA; restrição do gene 16S rRNA; gene melA. Foi realizado também o sequenciamento parcial do gene 16S rRNA para identificar os isolados de milho. Para observar a produção de pigmentos melaninalike, as bactérias foram cultivadas em meio de cultura batata líquido, com Ltriptofano e sulfato de cobre, e posteriormente foi identificada a produção de pigmentos melanina-like através do pico de absorbância em espectrofotômetro nos comprimentos de onda de 300, 350 e 400 nm. A concentração de pigmentos melanina-like foi calculada por uma reta padrão, obtida das leituras com melanina sintética em diferentes concentrações a 400 nm. Pela análise de similaridade utilizando os marcadores moleculares foi possível observar grande diversidade genética das bactérias estudadas que foi confirmada pelo sequenciamento parcial do gene 16S rRNA, pois foram identificadas bactérias de diferentes gêneros: Agrobacterium, Burkholderia e Cedecea. Essas bactérias identificadas poderão ser utilizadas na formulação de inoculantes para as variedades de milho cultivadas no Brasil. Quanto à produção de pigmentos, o isolado de milho MT45 apresentou alta produção de melanina-like e poderá ser utilizado na obtenção de bioprodutos. Inoculation of maize with Plant-Growth-Promoting Rhizobacteria (PGPR) can improve the growth of this cultivar, reduce the use of nitrogenous fertilizers and the costs of production, and reduce the negative impacts to the environment. Moreover, the production of pigments, such as melanin, by these bacteria might have promising commercial applications in food industries, pharmaceutical, cosmetics and textiles products. The general objective of this work was to study genetic and biochemical characterization of 20 endophytic bacteria isolated from maize (Zea mays L.) grown in the Cerrado Goiás to observe the genetic diversity, identify bacteria that can be used as inoculants and check production melanin-like pigment by these bacteria. For the diversity study, analysis was performed with molecular markers: 16S-23S rRNA intergenic spacer sequences, dispersed repetitive extragenic palindromic DNA sequences (REP), genes atpD, glnII e 16S rRNA, 16S rRNA gene restriction; gene melA. It was also performed the partial 16S rRNA gene sequencing to identify isolated from maize. To observe the production of pigments melanin-like, bacteria were grown on potato liquid culture media, with L-tryptophan and copper sulfate, and was subsequently identified the production of melanin-like pigments over the peak of absorbance in a spectrophotometer at wavelengths of 300, 350 and 400 nm. The concentration of melanin-like pigments was calculated from a standard line, from the readings obtained using synthetic melanin at different concentrations at 400 nm. By the similarity analysis using molecular markers was observed great genetic diversity of bacteria studied which was confirmed by partial sequencing of the 16S rRNA gene, because were identified bacteria of Agrobacterium, Burkholderia and Cedecea genera. These identified bacteria may be used in the inoculants formulation for maize varieties grown in Brazil. For pigment production, the maize isolated MT45 showed high production of melanin-like and may be used to obtain bioproducts. Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES

The perennial grasses are considered as a rich source of lignocellulosic biomass, making it a second generation alternative energy source and can diminish the use of fossil fuels. In this work, four perennial grasses Saccharum arundinaceum, Panicum antidotale, Thysanolaena latifolia and Neyraudia reynaudiana were selected to verify their potential as a substrate to produce hydrolytic enzymes and to evaluate them as second generation energy biomass. Here, cellulase and hemi-cellulase producing three endophytic bacteria (Burkholderia cepacia BPS-GB3, Alcaligenes faecalis BPS-GB5 and Enterobacter hormaechei BPS-GB8) recovered from N. reynaudiana and S. arundinaceum were selected to develop a triculture (CC3) consortium. During 12 days of submerged cultivation, a 55-70% loss in dry weight was observed and the maximum activity of β-glucosidase (5.36 to 12.34 IU) and Xylanase (4.33 to 10.91 IU) were observed on 2nd and 6th day respectively, whereas FPase (0.26 to 0.53 IU) and CMCase (2.31 to 4.65 IU) showed maximum activity on 4th day. Around 15-30% more enzyme activity was produced in CC3 as compared to monoculture (CC1) and coculture (CC2) treatments, suggested synergetic interaction among the selected three bacterial strains. Further, the biomass was assessed using Fourier-transform infrared spectroscopy (FTIR) and Scanning electron microscopy (SEM). The FTIR analysis provides important insights into the reduction of cellulose and hemicellulose moieties in CC3 treated biomass and SEM studies shed light into the disruption of surface structure leading to access of cellulose or hemicelluloses microtubules. The hydrolytic potential of the CC3 system was further enhanced due to reduction in lignin as evidenced by 1-4% lignin reduction in biomass compositional analysis. Additionally, laccase gene was detected from A. faecalis and E. hormaechei which further shows the laccase production potential of the isolates. To our knowledge, first time we develop an effective endophytic endogenous bacterial triculture system having potential for the production of extracellular enzymes utilizing S. arundinaceum and N. reynaudiana as lignocellulosic feedstock.

Ammonium nutrition often represents an important growth-limiting stress in plants. Some of the symptoms that plants present under ammonium nutrition have been associated with pH deregulation, in fact external medium pH control is known to improve plants ammonium tolerance. However, the way plant cell metabolism adjusts to these changes is not completely understood. Thus, in this work we focused on how Arabidopsis thaliana shoot and root respond to different nutritional regimes by varying the nitrogen source (NO3 and NH4), concentration (2 and 10 mM) and pH of the external medium (5.7 and 6.7) to gain a deeper understanding of cell metabolic adaptation upon altering these environmental factors. The results obtained evidence changes in the response of ammonium assimilation machinery and of the anaplerotic enzymes associated to Tricarboxylic Acids (TCA) cycle in function of the plant organ, the nitrogen source and the degree of ammonium stress. A greater stress severity at pH 5.7 was related to NH4 accumulation; this could not be circumvented in spite of the stimulation of glutamine synthetase, glutamate dehydrogenase, and TCA cycle anaplerotic enzymes. Moreover, this study suggests specific functions for different gin and gdh isoforms based on the nutritional regime. Overall, NH4 accumulation triggering ammonium stress appears to bear no relation to nitrogen assimilation impairment. AS is holder of a Ph.D. grant from the Basque Government. This research was financially supported by the Basque Government (IT932-16), the University of the Basque Country (EHUA14/14), the Spanish Ministry of Economy and Competitiveness (BIO2014-56271-R co-funded by FEDER) and the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement number 334019. We are also grateful to Dr. J. F. Moran and Dr. K. A. Roubelakis-Angelakis for lending CS and GDH antibodies, respectively.

International audience; Sucrose transport between source and sink tissues is supposed to be a key-step for an efficient regrowth of perennial rye-grass after defoliation and might be altered by light conditions. we assessed the effect of different light regimes (high vs low light applied before or after defoliation) on growth, fructans and sucrose mobilization, as well as on sucrose transporter expression during 14 days of regrowth. Our results reported that defoliation led to a mobilization of C reserves (first sucrose and then fructans), which was parallel to an induction of LpSUT1 sucrose transporter expression in source and sink tissues (i.e. leaf sheaths and elongating leaf bases, respectively) irrespective to light conditions. Light regime (high or low light) had little effects on regrowth and on C reserves mobilization during the first 48 h of regrowth after defoliation. Thereafter, low light conditions, delaying the recovery of photosynthetic capacities, had a negative effect on C reserves re-accumulation (especially sucrose). Surprisingly, high light did not enhance sucrose transporter expression. Indeed, while light conditions had no effect on LpSUT1 expression, LpSUT2 transcripts levels were enhanced for low light grown plants. These results indicate that two sucrose transporter currently identified in Lolium perenne L are differentially regulated by light and sucrose. (C) 2012 Elsevier Masson SAS. All rights reserved.

The metabolic theory of ecology (MTE) predicts the effects of body size and temperature on metabolism through considerations of vascular distribution networks and biochemical kinetics. MTE has also been extended to characterise processes from cellular to global levels. MTE has generated both enthusiasm and controversy across a broad range of research areas. However, most efforts that claim to validate or invalidate MTE have focused on testing predictions. We argue that critical evaluation of MTE also requires strong tests of both its theoretical foundations and simplifying assumptions. To this end, we synthesise available information and find that MTE's original derivations require additional assumptions to obtain the full scope of attendant predictions. Moreover, although some of MTE's simplifying assumptions are well supported by data, others are inconsistent with empirical tests and even more remain untested. Further, although many predictions are empirically supported on average, work remains to explain the often large variability in data. We suggest that greater effort be focused on evaluating MTE's underlying theory and simplifying assumptions to help delineate the scope of MTE, generate new theory and shed light on fundamental aspects of biological form and function.

The metabolic theory of ecology (MTE) predicts the effects of body size and temperature on metabolism through considerations of vascular distribution networks and biochemical kinetics. MTE has also been extended to characterise processes from cellular to global levels. MTE has generated both enthusiasm and controversy across a broad range of research areas. However, most efforts that claim to validate or invalidate MTE have focused on testing predictions. We argue that critical evaluation of MTE also requires strong tests of both its theoretical foundations and simplifying assumptions. To this end, we synthesise available information and find that MTE's original derivations require additional assumptions to obtain the full scope of attendant predictions. Moreover, although some of MTE's simplifying assumptions are well supported by data, others are inconsistent with empirical tests and even more remain untested. Further, although many predictions are empirically supported on average, work remains to explain the often large variability in data. We suggest that greater effort be focused on evaluating MTE's underlying theory and simplifying assumptions to help delineate the scope of MTE, generate new theory and shed light on fundamental aspects of biological form and function.

We investigated the ecological strategies exerted by the soil bacterium Burkholderia terrae BS001 at the hyphae of the soil saprotrophic fungus Lyophyllum sp. strain Karsten. Recently, this bacterium has been reported to form biofilms around, and to comigrate with, growing hyphae of Lyophyllum sp. strain Karsten. In addition, it was found to be able to utilize fungal metabolites. Here, we extend this work to shed some light on the interactions between the bacterial and fungal partner which allow ecological success for the former. In standing liquid microcosms inoculated with Lyophyllum sp. strain Karsten, we detected, upon prolonged incubation, the formation of a mycelial mat at the liquid-air interface. From this mat, primordia were formed after 4-6 weeks, which eventually resulted in mushrooms. However, upon addition of strain BS001 to the bulk liquid, mushroom formation from the fungal mat was clearly inhibited, as evidenced by (1) the formation of significantly lower numbers of primordia and (2) a delay of the onset of primordia formation. Moreover and importantly, the presence of strain BS001 caused the fungus to secrete large amounts of exudates at the mycelial mat, whereas such exudation was absent from control (uninoculated) or Escherichia coli K12- or Variovorax paradoxus BS64-inoculated microcosms. In the exudates, glycerol was the main carbonaceous component, and this compound could be easily utilized by strain BS001. Thus, in different experimental set-ups with the fungal partner, strain BS001 was shown to grow in the fungal exudates on the mat. The two fungal-interactive phenotypes were specific for B. terrae strain BS001, as the other bacteria used in our study, i.e. E. coli K12 and V. paradoxus BS64, did not exhibit any of these phenomena.

TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR1 (TCP) transcription factors control developmental processes in plants. The 24 TCP transcription factors encoded in the Arabidopsis (Arabidopsis thaliana) genome are divided into two classes, class I and class II TCPs, which are proposed to act antagonistically. We performed a detailed phenotypic analysis of the class I tcp20 mutant, showing an increase in leaf pavement cell sizes in 10-d-old seedlings. Subsequently, a glucocorticoid receptor induction assay was performed, aiming to identify potential target genes of the TCP20 protein during leaf development. The LIPOXYGENASE2 (LOX2) and class I TCP9 genes were identified as TCP20 targets, and binding of TCP20 to their regulatory sequences could be confirmed by chromatin immunoprecipitation analyses. LOX2 encodes for a jasmonate biosynthesis gene, which is also targeted by class II TCP proteins that are under the control of the microRNA JAGGED AND WAVY (JAW), although in an antagonistic manner. Mutation of TCP9, the second identified TCP20 target, resulted in increased pavement cell sizes during early leaf developmental stages. Analysis of senescence in the single tcp9 and tcp20 mutants and the tcp9tcp20 double mutants showed an earlier onset of this process in comparison with wild-type control plants in the double mutant only. Both the cell size and senescence phenotypes are opposite to the known class II TCP mutant phenotype in JAW plants. Altogether, these results point to an antagonistic function of class I and class II TCP proteins in the control of leaf development via the jasmonate signaling pathway.

International audience; Despite its high capacity to take up nitrate from soil, winter rapeseed (Brassica napus) is characterized by a low N recovery in seeds. Thus, to maintain yield, rapeseed requires a high fertilization rate. Increasing nutrient use efficiency in rapeseed by addition of a biostimulant could help improve its agroenvironmental balance. The effects of marine brown seaweed Ascophyllum nodosum on plant growth have been well described physiologically. However, to our knowledge, no study has focused on transcriptomic analyses to determine metabolic targets of these extracts. A preliminary screening of different extracts revealed a significant effect of one of them (AZAL5) on rapeseed root (+102 %) and shoot ( 23 %) growth. Microarray analysis was then used on AZAL5-treated or nontreated plants to characterize changes in gene expression that were further supported by physiological evidence. Stimulation of nitrogen uptake (+21 and +115 % in shoots and roots, respectively) and assimilation was increased in a similar manner to growth, whereas sulfate content (+63 and +133 % in shoots and roots, respectively) was more strongly stimulated leading to sulfate accumulation. Among the identified genes whose expression was affected by AZAL5, MinE, a plastid division regulator, was the most strongly affected. Its effect was supported by microscopic analysis showing an enhancement of chloroplast number per cell and starch content but without a significant difference in net photosynthetic rate. In conclusion, it is suggested that AZAL5, which promotes plant growth and nutrient uptake, could be used as a supplementary tool to improve rapeseed agroenvironmental balance.

Brassinosteroid (BR) signaling is essential for plant growth and development. In Arabidopsis (Arabidopsis thaliana), BRs are perceived by the BRASSINOSTEROID INSENSITIVE1 (BRI1) receptor. Root growth and hypocotyl elongation are convenient downstream physiological outputs of BR signaling. A computational approach was employed to predict root growth solely on the basis of BRI1 receptor activity. The developed mathematical model predicts that during normal root growth, few receptors are occupied with ligand. The model faithfully predicts root growth, as observed in bri1 loss-of-function mutants. For roots, it incorporates one stimulatory and two inhibitory modules, while for hypocotyls, a single inhibitory module is sufficient. Root growth as observed when BRI1 is overexpressed can only be predicted assuming that a decrease occurred in the BRI1 half-maximum response values. Root growth appears highly sensitive to variation in BR concentration and much less to reduction in BRI1 receptor level, suggesting that regulation occurs primarily by ligand availability and biochemical activity.

Contents Summary 30 I. Allocation in perspective 31 II. Topics of this review 32 III. Methodology 32 IV. Environmental effects 33 V. Ontogeny 36 VI. Differences between species 40 VII. Physiology and molecular regulation 41 VIII. Ecological aspects 42 IX. Perspectives 45 Acknowledgements 45 References 45 Appendices A1–A4 49 Summary We quantified the biomass allocation patterns to leaves, stems and roots in vegetative plants, and how this is influenced by the growth environment, plant size, evolutionary history and competition. Dose–response curves of allocation were constructed by means of a meta-analysis from a wide array of experimental data. They show that the fraction of whole-plant mass represented by leaves (LMF) increases most strongly with nutrients and decreases most strongly with light. Correction for size-induced allocation patterns diminishes the LMF-response to light, but makes the effect of temperature on LMF more apparent. There is a clear phylogenetic effect on allocation, as eudicots invest relatively more than monocots in leaves, as do gymnosperms compared with woody angiosperms. Plants grown at high densities show a clear increase in the stem fraction. However, in most comparisons across species groups or environmental factors, the variation in LMF is smaller than the variation in one of the other components of the growth analysis equation: the leaf area : leaf mass ratio (SLA). In competitive situations, the stem mass fraction increases to a smaller extent than the specific stem length (stem length : stem mass). Thus, we conclude that plants generally are less able to adjust allocation than to alter organ morphology.

International audience; This study focuses on the chemotaxis, colonization and rice growth promoting ability of indole acetic acid (IAA) and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase-producing rhizobacteria Rhizobium leguminosarum bv. trifolii SN10, previously isolated from root nodules of Trifolium alexandrium L. We show here that R. leguminosarum bv. trifolii SN10 promote the growth of four different rice varieties grown in India in terms of biomass, root branching and N content. In addition, using scanning electron microscopy and viable cell counts, we provide evidence that the bacteria successfully colonize the root surface of the rice variety which showed maximum growth promotion upon inoculation. Not only this, R. leguminosarum bv. trifolii SN10 exhibit a strong chemotaxis response towards the rice seed and root exudates despite the presence of a bacteriostatic phenolic compound, 7-hydroxycoumarin (umbelliferone). Further, R. leguminosarum bv. trifolii SN10 secretion of phytohormones such as IAA and ACC deaminase suggest the potential of the plant growth promoting rhizobacteria to be used as biofertilizer to enhance rice crop production in the subcontinent.

In this study, the effects of plant genotype, soil type and nutrient use efficiency on the composition of different bacterial communities associated with rice roots were investigated. Thus, total bacteria, Alpha- and Betaproteobacteria, Pseudomonas and Actinobacteria were studied using PCR, followed by denaturing gradient gel electrophoresis (PCR-DGGE). Rice genotype determined, to a large extent, the composition of the different bacterial communities across cultivars. Several cultivars belonging to Oryza sativa ssp. indica tended to select similar bacterial communities, whereas those belonging to subspecies japonica and aromatica selected ones with divergent community structures. An effect of soil type was pronounced for the Actinobacteria communities, while a small effect of 'improved' and 'traditional' plants was noted for all communities analyzed. A few dominant bands in PCR-DGGE, affiliated with Rhizobium radiobacter, Dickeya zeae, Mycobacterium bolletii and with members of the Rhizobiales, Rhodospirillaceae and Paenibacillaceae, were spread across cultivars. In contrast, a majority of bands (e.g. affiliated with Enterobacter cloacae or Burkholderia kururiensis) was only present in particular cultivars or was erratically distributed among rice replicates. These findings suggested that both bacterial adaptation and plant genotype contribute to the shaping of the dynamic bacterial communities associated with roots of rice plants.

Background, aim and scope: Phytoremediation does exploit natural plant physiological processes and can be used to decontaminate agricultural soils, industrial sites, brownfields, sediments and water containing inorganic and organic pollutants or to improve food chain safety by phytostabilisation of toxic elements. It is a low-cost and environment friendly technology targetting removal, degradation or immobilisation of contaminants. The aim of the present review is to highlight some recent advances in phytoremediation in the Alpine context. Main features: Case studies are presented where phytoremediation has been or can be successfully applied in Alpine areas to: (1) clean-up industrial wastewater containing sulphonated aromatic xenobiotics released by dye and textile industries; (2) remediate agricultural soils polluted by petroleum hydrocarbons; (3) improve food chain safety in soils contaminated with toxic trace elements (As, Co, Cr and Pb); and (4) treat soils impacted by modern agricultural activities with a special emphasis on phosphate fertilisation. Conclusions, recommendations and perspectives: Worlwide, including in Alpine areas, the controlled use of appropriate plants is destined to play a major role for remediation and restoration of polluted and degraded ecosystems, monitoring and assessment of environmental quality, prevention of landscape degradation and immobilisation of trace elements. Phytotechnologies do already offer promising approaches towards environmental remediation, human health, food safety and sustainable development for the 21st century in Alpine areas and elsewhere all over the world

Deficiency in mycorrhizal inoculum in soils due to land use types (LUT) can be alleviated by inoculum addition. Inoculum effects may depend both on quantity and on quality of inoculum applied. A greenhouse bioassay was carried out to determine the effect of host soil mycorrhizal inoculum on mycorrhizal colonization, carbon allocation and partitioning of seedlings of two native timber species of Cameroon humid forest, raised on surface soils (0-20 cm) collected from early secondary forests, LUT derived from slash-and-burn agriculture and selective logging. Host soil mycorrhizal inoculum was collected from the root zones of con-specific tree species. Mycorrhizal inoculation effect (MIE) was estimated as percent difference of average total biomass between seedlings grown on inoculated and non-inoculated soils. Six months-old seedlings of Pterocarpus soyauxii and Lophira alata were mainly colonized by members of the Glomaceae and Gigasporaceae, respectively, as shown by molecular typing. They generally performed poorly in soils with indigenous inoculum. But addition of soil inoculum from P. soyauxii trees favored nodulation, significantly increased mycorrhizal colonization and total biomass but decreased root-to-shoot ratios, resulting in large and positive MIE, irrespective of LUT. ln contrast, host soil inoculum of L. alata did not affect fractional mycorrhizal colonization but significantly increased total biomass, resulted in high carbon allocation to roots, in low and sometimes negative MIE. Therefore, seedlings' responses to mycorrhizal inoculum depend on host soil inoculum and that could be critical for successful rejuvenation of tropical trees.Key words. Arbuscular mycorrhiza-host soil inoculum-Iand use types-Pterocarpus soyauxii-Lophira alata-Cameroon

The large variation in the relationships between environmental factors and plant traits observed in natural communities exemplifies the alternative solutions that plants have developed in response to the same environmental limitations. Qualitative attributes, such as growth form, woodiness, and leaf habit can be used to approximate these alternative solutions. Here, we quantified the extent to which these attributes affect leaf trait values at a given resource supply level, using measured plant traits from 105 different species (254 observations) distributed across 50 sites in mesic to wet plant communities in The Netherlands. For each site, soil total N, soil total P, and water supply estimates were obtained by field measurements and modeling. Effects of growth forms, woodiness, and leaf habit on relations between leaf traits (SLA, specific leaf area; LNC, leaf nitrogen concentration; and LPC, leaf phosphorus concentration) vs. nutrient and water supply were quantified using maximum-likelihood methods and Bonferroni post hoc tests. The qualitative attributes explained 8-23% of the variance within sites in leaf traits vs. soil fertility relationships, and therefore they can potentially be used to make better predictions of global patterns of leaf traits in relation to nutrient supply. However, at a given soil fertility, the strength of the effect of each qualitative attribute was not the same for all leaf traits. These differences may imply a differential regulation of the leaf economy traits at a given nutrient supply, in which SLA and LPC seem to be regulated in accordance to changes in plant size and architecture while LNC seems to be primarily regulated at the leaf level by factors related to leaf longevity.

Biotic soil parameters have so far seldom played a role in practical soil assessment and management of grasslands. However, the ongoing reduction of external inputs in agriculture would imply an increasing reliance on ecosystem self-regulating processes. Since soil biota play an important role in these processes and in the provision of ecosystem services, biological soil parameters should be an integral part of soil assessment. The general objective of the current study is to investigate to what extent biotic soil parameters provide additional value in soil quality assessment of grassland on sandy soils. We measured abiotic and biotic soil parameters together with process parameters underlying ecosystem services in 20 permanent production grasslands. Cross-validated stepwise regression was used to identify abiotic and biotic soil parameters that explained the soil ecosystem services soil structure maintenance, water regulation, supply of nutrients, and grassland production, respectively. Process parameters underlying the ecosystem service soil structure maintenance such as bulk density and the percentage of sub-angular blocky elements were mainly influenced by SOM and its qualities. The correlations between penetration resistance at 0–10 cm and the percentage of soil crumbs with earthworms suggested a relationship to earthworm activity. Parameters underlying the service of water regulation showed no clear relationship to biotic soil parameters. Water infiltration rate in the field was explained by the penetration resistance at 10–20 cm. Process parameters underlying the service of nutrients’ supply such as the potentially mineralizable C and N were mainly determined by soil total N. The potential C and N mineralization were more related to biotic soil parameters, whereby each parameter was the other’s antithesis. The grassland production without N fertilization viz. the nitrogen supply capacity of the soil measured as N yield, was mainly explained by soil organic matter (SOM) and soil moisture, and to a lesser extent by soil total N. One gram of SOM per kg of dry soil corresponded to 3.21 kg N yield ha −1 , on top of a constant of 15.4 kg N ha −1 . The currently applied calculations in the Dutch grassland fertilization recommendation, underestimated in 85% of the production grasslands, the measured nitrogen supply capacity of the soil by on average 42 kg N ha −1 (31%). This legitimizes additional research to improve the currently applied recommendations for sandy soils. The response of N yield to N fertilization ranged from 35 to 102%. This wide range emphasizes the importance of a better recommendation base to target N fertilizer. The response of N yield to N fertilization was predicted by the total number of enchytraeids, the underlying mechanism of which needs further investigation on different soil types. This knowledge can be important for the optimal use of fertilizer and its consequences for environmental quality.

Leaf area index (LAI) is an important variable for modelling canopy photosynthesis and crop water use. In many crop simulation models, prediction of LAI is very sensitive to errors in the value of parameter “specific leaf area” (SLA), which often relies on destructive measurements to determine. In this study, we present a model for predicting LAI of greenhouse crops based on the quantification of easily measured morphological traits as affected by temperature and radiation. Our model predicts LAI based on canopy light interception as a function of node development rate along with specific leaf size and elongation rates characteristics defined on a leaf number basis. Growth studies with five greenhouse crops (cucumber, sweet pepper, chrysanthemum, tulip and lilium) were conducted in different greenhouses and different sites during 2003 to 2009. The model was evaluated, in comparison with two commonly used methods for predicting LAI – the growing degree days (GDD) based model and SLA based model, using independent data from other experiments. The coefficient of determination (r2) and the root mean squared error (RMSE) between the predicted and measured values using our photothermal method are 0.99 and 0.95 (r2, RMSE) for leaf number, 0.98 and 0.01 m for specific leaf length, and 0.98 and 0.13 m2 m−2 for canopy LAI. For the GDD-based model, the r2 and RMSE are 0.93 and 4.23, 0.82 and 0.04 m, 0.87 and 0.48 m2 m−2 for the three traits, respectively. For the SLA-based model, the r2 and RMSE for canopy LAI is 0.81 and 1.24 m2 m−2 when using the estimated SLA data as input or 0.94 and 0.25 m2 m−2 when using the measured SLA data as input. So, our model better predicts LAI for greenhouse crops at different latitudes and a range of planting densities and pruning systems. Although calibrations for specific light regime, pruning practices and cultivars are needed, the fact that production conditions in commercial greenhouse production are often well controlled and production practices are often rather standardized implies a general applicability of our model.

The rhizosphere environment selects a particular microbial community that arises from the one present in bulk soil due to the release of particular compounds in exudates and different opportunities for microbial colonization. During plant-microorganism coevolution, microbial functions supporting plant health and productivity have developed, of which most are described in cultured plant-associated bacteria. This review discusses the state of the art concerning the ecology of the hitherto-uncultured bacteria of the rhizosphere environment, focusing on Acidobacteria, Verrucomicrobia and Planctomycetes. Furthermore, a strategy is proposed to recover bacterial isolates from these taxa from the rhizosphere environment.

Pseudomonas putida strain P9 is a novel competent endophyte from potato. P9 causes cultivar-dependent suppression of Phytophthora infestans . Colonization of the rhizoplane and endosphere of potato plants by P9 and its rifampin-resistant derivative P9R was studied. The purposes of this work were to follow the fate of P9 inside growing potato plants and to establish its effect on associated microbial communities. The effects of P9 and P9R inoculation were studied in two separate experiments. The roots of transplants of three different cultivars of potato were dipped in suspensions of P9 or P9R cells, and the plants were planted in soil. The fate of both strains was followed by examining colony growth and by performing PCR-denaturing gradient gel electrophoresis (PCR-DGGE). Colonies of both strains were recovered from rhizoplane and endosphere samples of all three cultivars at two growth stages. A conspicuous band, representing P9 and P9R, was found in all Pseudomonas PCR-DGGE fingerprints for treated plants. The numbers of P9R CFU and the P9R-specific band intensities for the different replicate samples were positively correlated, as determined by linear regression analysis. The effects of plant growth stage, genotype, and the presence of P9R on associated microbial communities were examined by multivariate and unweighted-pair group method with arithmetic mean cluster analyses of PCR-DGGE fingerprints. The presence of strain P9R had an effect on bacterial groups identified as Pseudomonas azotoformans , Pseudomonas veronii , and Pseudomonas syringae. In conclusion, strain P9 is an avid colonizer of potato plants, competing with microbial populations indigenous to the potato phytosphere. Bacterization with a biocontrol agent has an important and previously unexplored effect on plant-associated communities.

The dense hyphal network directly underneath the fruiting bodies of ectomycorrhizal fungi might exert strong influences on the bacterial community of soil. Such fruiting bodies might serve as hot spots for bacterial activity, for instance by providing nutrients and colonization sites in soil. Here, we assessed the putative selection of specific members of the Sphingomonadaceae family at the bases of the fruiting bodies of the ectomycorrhizal fungi Laccaria proxima and Russula exalbicans in comparison to the adjacent bulk soil. To do so, we used a previously designed Sphingomonadaceae -specific PCR-denaturing gradient gel electrophoresis (DGGE) system and complemented this with analyses of sequences from a Sphingomonadaceae -specific clone library. The analyses showed clear selective effects of the fruiting bodies of both fungi on the Sphingomonadaceae community structures. The effect was especially prevalent with R. exalbicans . Strikingly, similar fungi sampled approximately 100 m apart showed similar DGGE patterns, while corresponding bulk soil-derived patterns differed from each other. However, the mycospheres of L. proxima and R. exalbicans still revealed divergent community structures, indicating that different fungi select for different members of the Sphingomonadaceae family. Excision of specific bands from the DGGE patterns, as well as analyses of the clone libraries generated from both habitats, revealed fruiting body-specific Sphingomonadaceae types. It further showed that major groups from the mycospheres of R. exalbicans and L. proxima did not cluster with known bacteria from the database, indicating new groups within the family of Sphingomonadaceae present in these environments.

The bacterial communities in the Laccaria proxima mycosphere (soil from beneath fruiting bodies) and the corresponding bulk soil were compared by cultivation-dependent and cultivation-independent methods. To assess the distribution of type III secretion systems (TTSS), a PCR-based system for the broad detection of a highly conserved gene involved in TTSS, that is hrcR, was developed and used to assay the cultured bacteria from the L. proxima mycosphere and surrounding bulk soil. PCR-DGGE based on the 16S ribosomal RNA gene showed the selection of presumably mycosphere-specific bacterial groups in the mycosphere of L. proxima compared to the bulk soil in 3 sampling years. Moreover, plate counts revealed that the numbers of culturable heterotrophic bacteria were increased in the mycosphere as compared to the bulk soil. Strikingly, the percentage of randomly picked isolates that carried the hrcR gene showed a significant increase, from 2.8 in the bulk to 13.4 in the mycosphere soil. The increase could be mainly attributed to the emergence of a hrcR positive Pseudomonas fluorescens, denoted BS053, which constituted the most dominant species in the culturable mycosphere communities. This organism was, together with a hrcR-positive Burkholderia terrae BS110, exclusively found in mycosphere soil. Direct detection of hrcR genes using a cultivation-independent approach showed the selection of several hrcR gene types uniquely in the mycosphere, indicating the selection of several TTSS-harboring bacterial species. Thus, different bacteria were found to be enriched in the L. proxima mycosphere and TTSS can be involved in some of the interactions with the fungal host.

BFP - Equipe OrFE; Plant growth and crop yield are negatively affected by a reduction in water availability. However, a clear understanding of how growth is regulated under nonlethal drought conditions is lacking. Recent advances in genomics, phenomics, and transcriptomics allow in-depth analysis of natural variation. In this study, we conducted a detailed screening of leaf growth responses to mild drought in a worldwide collection of Arabidopsis thaliana accessions. The genetic architecture of the growth responses upon mild drought was investigated by subjecting the different leaf growth phenotypes to genome-wide association mapping and by characterizing the transcriptome of young developing leaves. Although no major effect locus was found to be associated with growth in mild drought, the transcriptome analysis delivered further insight into the natural variation of transcriptional responses to mild drought in a specific tissue. Coexpression analysis indicated the presence of gene clusters that co-vary over different genetic backgrounds, among others a cluster of genes with important regulatory functions in the growth response to osmotic stress. It was found that the occurrence of a mild drought stress response in leaves can be inferred with high accuracy across accessions based on the expression profile of 283 genes. A genome-wide association study on the expression data revealed that trans regulation seems to be more important than cis regulation in the transcriptional response to environmental perturbations.

The floating treatment wetland (FTW) is an innovative hydroponic device which can be installed on the surface of a stormwater retention pond to improve its pollutant removal efficiency. Limited full-scale experiments have been published, and no design or maintenance guidelines have been developed to date to promote their use. This paper presents implementation and maintenance considerations developed based on the monitoring of three full-scale ponds retrofitted with FTWs. Results suggest that the size and relative surface cover of the FTW, the relative root depth, and the capability of the plants to tolerate periodic anaerobic conditions are crucial factors to promote good removal across a spectrum of pollutants. Special attention to the location and anchorage of the FTW are thought to promote good performance and facilitate FTW maintenance. While zinc and copper sediment concentrations were unlikely to cause undue aquatic impacts after 2 years of operation, more frequent sediment removal will be ...

Physical damage can strongly affect plant growth, reducing the biomass of developing organs situated at a distance from wounds. These effects, previously studied in leaves, require the activation of jasmonate (JA) signalling. Using a novel assay involving repetitive cotyledon wounding in Arabidopsis seedlings, we uncovered a function of JA in suppressing cell division and elongation in roots. Regulatory JA signalling components were then manipulated to delineate their relative impacts on root growth. The new transcription factor mutant myc2-322B was isolated. In vitro transcription assays and whole-plant approaches revealed that myc2-322B is a dosage-dependent gain-of-function mutant that can amplify JA growth responses. Moreover, myc2-322B displayed extreme hypersensitivity to JA that totally suppressed root elongation. The mutation weakly reduced root growth in undamaged plants but, when the upstream negative regulator NINJA was genetically removed, myc2-322B powerfully repressed root growth through its effects on cell division and cell elongation. Furthermore, in a JA-deficient mutant background, ninja1 myc2-322B still repressed root elongation, indicating that it is possible to generate JA-responses in the absence of JA. We show that NINJA forms a broadly expressed regulatory layer that is required to inhibit JA signalling in the apex of roots grown under basal conditions. By contrast, MYC2, MYC3 and MYC4 displayed cell layer-specific localisations and MYC3 and MYC4 were expressed in mutually exclusive regions. In nature, growing roots are likely subjected to constant mechanical stress during soil penetration that could lead to JA production and subsequent detrimental effects on growth. Our data reveal how distinct negative regulatory layers, including both NINJA-dependent and -independent mechanisms, restrain JA responses to allow normal root growth. Mechanistic insights from this work underline the importance of mapping JA signalling components to specific cell types in order to understand and potentially engineer the growth reduction that follows physical damage., Author Summary The study of plant development is generally carried out in the absence of physical injury. However, damage to plant organs through biotic and abiotic insult is common in nature. Under these conditions the jasmonate pathway that has a low activity in unstressed vegetative tissues imposes its activity on cell division and elongation. Such jasmonate-dependent growth restriction can strongly impact plant productivity. Taking roots as a model, we show that it is possible to manipulate regulatory layers in jasmonate signalling such that cell division and cell elongation can be constrained differently. This approach may lead to future strategies to alter organ growth. Moreover, during this study we identified a novel mutant in a key regulator of the jasmonate pathway. This mutant generated a positive regulator of jasmonate signalling that was so active that we were able to show that hormone synthesis can be completely uncoupled from hormone responses, suggesting ways to modify traits of potential agronomic importance.

This work determines the ffects of long-term anoxia conditions--21 days--on Strategy I responses to iron (Fe) deficiency in Citrus and its impact on Fe uptake and distribution. The study was carried out in Citrus aurantium L. seedlings grown under flooding conditions (S) and in both the presence (+Fe) and absence of Fe (-Fe) in nutritive solution. The results revealed a strong down-regulation (more than 65%) of genes HA1 and FRO2 coding for enzymes proton-ATPase and Ferric-Chelate Reductase (FC-R), respectively, in -FeS plants when compared with -Fe ones. H+-extrusion and FC-R activity analyses confirmed the genetic results, indicating that flooding stress markedly repressed acidification and reduction responses to Fe deficiency (3.1- and 2.0-fold, respectively). Waterlogging reduced by half Fe concentration in +FeS roots, which led to 30% up-regulation of Fe transporter IRT1, although this effect was unable to improve Fe absorption. Consequently, flooding inhibited 57Fe uptake in +Fe and -Fe seedlings (29.8 and 66.2%, respectively) and 57Fe distribution to aerial part (30.6 and 72.3%, respectively). This evidences that the synergistic action of both enzymes H+-ATPase and FC-R is the preferential regulator of the Fe acquisition system under flooding conditions and, hence, their inactivation implies a limiting factor of citrus in their Fe-deficiency tolerance in waterlogged soils.

It has previously been reported that endophytic diazotrophic bacteria contribute significantly to the nitrogen budgets of some graminaceous species. In this study the contribution of biological nitrogen fixation to the N-budget of a South African sugarcane cultivar was evaluated using 15N natural abundance, acetylene reduction and 15N incorporation. Plants were also screened for the presence of endophytic diazotrophic bacteria using acetylene reduction and nifH-gene targeted PCR with the pure bacterial strains. 15N natural abundance studies on field-grown sugarcane indicated that the plants did not rely extensively on biological nitrogen fixation. Furthermore, no evidence was found for significant N2-fixation or nitrogenase activity in field-grown or glasshouse-grown plants using 15N incorporation measurements and acetylene reduction assays. Seven endophytic bacterial strains were isolated from glasshouse-grown and field-grown plants and cultured on N-free medium. The diazotrophic character of these seven strains could not be confirmed using acetylene reduction and PCR screening for nifH. Thus, although biological nitrogen fixation may occur in South African sugarcane varieties, the contribution of this N-source in the tested cultivar was not significant.

Despite the intensive research effort directed at predicting the effects of climate change on plants in the Arctic, the impact of environmental change on species' distributions remains difficult to quantify. Predictive habitat distribution models provide a tool to predict the geographical distribution of a species based on the ecological gradients that determine it, and to estimate how the distribution of a species might respond to environmental change. Here, we present a model of the distribution of the dwarf shrub Dryas octopetala L. around the fjord Kongsfjorden, Svalbard. The model was built from field observations, an Advanced Space-borne Thermal Emission and Reflection Radiometer (ASTER) image, a GIs database containing environmental data at a spatial resolution of 20 m, and relied on generalized linear models (GLMs). We used a logistic GLM to predict the occurrence of the species and a Gaussian GLM to predict its abundance at the sites where it occurred. Temperature and topographical exposure and inclination of a site appeared to promote both the occurrence and the abundance of D. octopetala. The occurrence of the species was additionally negatively influenced by snow and water cover and topographical exposure towards the north, whereas the abundance of the species appeared lower on calciferous substrates. Validation of the model using independent data and the resulting distribution map showed that they successfully recover the distribution of D. octopetala in the study area (kappa = 0.46, AUC =0.81 for the logistic GLM [n - 200], r(2) = 0.29 for the Gaussian GLM [n - 36]). The results further highlight that models predicting the local distribution of plant species in an Arctic environment would greatly benefit from data on the distribution and duration of snow cover. Furthermore, such data are necessary to make quantitative estimates for the impact of changes in temperature and winter precipitation on the distribution of plants in the Arctic. (C) 2005 Elsevier Inc. All rights reserved.

Pseudomonas putida strain angstrom 313, a deleterious rhizosphere bacterium, reduced pea nitrogen content when inoculated alone or in combination with Rhizobium leguminosarum bv. viceae on plants in the presence of soil under greenhouse conditions. When plants were grown gnotobiotically in liquid media, mixed inocula of angstrom 313 and rhizobia gave a higher proportion of small evenly distributed nodules when compared with a single rhizobial inoculation. In addition, the rhizobial root establishment was reduced by angstrom 313 irrespective of inoculum, density, indicating that angstrom 313 has the capacity to interact with the early rhizobial infection process. When pea seedlings were simultaneously inoculated with angstrom 313 and rhizobia, angstrom 313 colonised the root hairs to the same extent as the rhizobia, according to analysis by immunofluorescence microscopy. This suggests that the root hair colonisation trait of P. putida interferes with the onset of the symbiotic process. (c) 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.

This paper compares responses to environmental stress of the ecophysiological traits of organisms in the detrital soil food webs of grasslands in the Netherlands, using the relationship between average body mass M and numerical abundance N. The microbial biomass and biodiversity of belowground fauna were measured in 110 grasslands on sand, 85 of them farmed under organic, conventional and intensive management. Bacterial cell volume and abundance and electrophoretic DNA bands as well as bacterial activity in the form of either metabolic quotient (qCO2) or microbial quotient (Cmic/Corg) predicted the response of microorganisms to stress. For soil fauna, the logarithm of body mass log(M) was approximately linearly related to the logarithm of numerical abundance log(N) with slope near -1, and the regression slope and the proportion of predatory species were lower in intensive agroecosystems (more reduced substrates with higher energy content). Linear regression of log(N) on log(M) had slope not far from -3/4. The approach to monitoring data illustrated in this paper could be useful in assessing land-use quality.

Two species of Pseudomonas chromosomally tagged with gfp, which had shown antagonistic activity against the tomato pathogen Ralstonia solanacearum in a previous study, were assessed for their impact in the rhizosphere of maize. Plant growth characteristics, numbers of indigenous heterotrophic bacteria, changes in the bacterial community structure according to the r/K strategy concept, and shifts in MIDI-FAME profiles of culturable bacterial fractions as well as total rhizosphere microbial communities were determined in relation to seed and soil treatment with the exogenous pseudomonads. The maize rhizosphere proved to be a suitable habitat for the introduced P. chlororaphis IDV1 and P. putida RA2, which showed good survival after introduction. However, both inoculants showed a small growth-reducing effect towards maize, which might have been caused by the high densities of inoculants used (i.e. competition for nutrients and action of metabolites produced) and/or changes in microbial community structure (both culturable bacterial fraction and the total microflora). Probably, an altered balance among the indigenous maize rhizosphere populations occurred. Thus, the culturable bacteria, as well as the total microflora in the rhizosphere, changed in response to the introduced pseudomonads, and their development was dependent on the growth stage of the plant. The FAME analyses showed that these microbial communities comprised different populations, and were separated according to, first, the method used (direct versus cultivation-based), second, sampling time, and, finally, inoculation level. (C) 2004 Elsevier Ltd. All rights reserved.

Along the east Atlantic migratory flyway, goose and swan species rely on the availability of suitable coastal habitats as staging sites during migration and for breeding. Especially for the Russian part of the flyway, detailed descriptions of these habitats in relation to use by herbivores are lacking. We report on salt-marsh characteristics and habitat use by barnacle geese in a recently established breeding site, near the village Tobseda at Kolokolkova Bay in the Pechora Delta, Russia. A classification of plant communities was made and both vegetation and soil properties were measured. Goose visitation was assessed by counting droppings. From the bay towards the dunes there was a gradient of decreasing salinity, along with a gradual shift in plant communities from salt marshes to freshwater bogs, tundra and dunes. Barnacle geese visited salt-marsh communities of the low and middle marsh more than the high marsh and non-saline communities. Two low marsh communities were preferred. Both had high tiller densities and low canopy heights and were dominated by Carex subspathacea, a species with high forage quality. Those characteristics are selected by geese, but might be maintained through grazing. The salt marsh at our site bears similarities to other marshes at similar latitudes along the Russian coast and in Canada. We discuss whether processes like grazing facilitation and habitat degeneration through overgrazing occur on our site.

An object-oriented simulation model was developed to integrate detailed analyses of perennial ryegrass (Lolium perenne) plant part dimensions, and their mass, cell wall content (CWC) and cell wall digestibility (CWD). The model was validated against data from two field experiments, carried out in The Netherlands (52degreesN) and Norway (67degreesN). In the experiments, the effects of temperature x daylength interactions on development, growth and digestibility were determined. Three cultivars differing in heading date were used, and undisturbed growth and regrowth after early (only in The Netherlands) and late cutting were studied. The sensitivity of the model was tested for changes in parameters determining morphological development. A grass plant was modelled as an aggregation of shoot objects. A shoot is an aggregation of phytomers, plus an inflorescence in the reproductive development stage. A phytomer consists of a leaf blade, a leaf sheath, a stem internode and a root. Each phytomer has an axillary bud, which can develop into a new shoot. Morphological development, organic matter (OM) growth and composition were simulated well by the model. Only for regrowing crops in The Netherlands CWC was lower and CWD was higher in the simulations than observed in the field, whereas the differences increased when stem development was more advanced at the moment of cutting. This was attributed to residual stems in the stubble after cutting due to difficulties with machine cutting of lodged crops on the experimental plots. The model can be considered as sufficiently accurate to simulate OM yield and composition of grass cultivars differing in heading date and growing under strongly contrasting temperature and daylength conditions. When the leaf appearance rate, width or length of the leaf blade were increased in the sensitivity analysis, OM yield enhanced, but composition and digestibility of the reproductive grass crops were not systematically affected. (C) 2004 Elsevier B.V. All rights reserved.

The rate and scale of human-driven changes can exert profound impacts on ecosystems, the species that make them up and the services they provide that sustain humanity. Given the speed at which these changes are occurring, one of society's major challenges is to coexist within ecosystems and to manage ecosystem services in a sustainable way. The effect of possible scenarios of global change on ecosystem services can be explored using ecosystem models. Such models should adequately represent ecosystem processes above and below the soil surface (aboveground and belowground) and the interactions between them. We explore possibilities to include such interactions into ecosystem models at scales that range from global to local. At the regional to global scale we suggest to expand the plant functional type concept (aggregating plants into groups according to their physiological attributes) to include functional types of aboveground–belowground interactions. At the scale of discrete plant communities, process-based and organism-oriented models could be combined into “hybrid approaches” that include organism-oriented mechanistic representation of a limited number of trophic interactions in an otherwise process-oriented approach. Under global change the density and activity of organisms determining the processes may change non-linearly and therefore explicit knowledge of the organisms and their responses should ideally be included. At the individual plant scale a common organism-based conceptual model of aboveground–belowground interactions has emerged. This conceptual model facilitates the formulation of research questions to guide experiments aiming to identify patterns that are common within, but differ between, ecosystem types and biomes. Such experiments inform modelling approaches at larger scales. Future ecosystem models should better include this evolving knowledge of common patterns of aboveground–belowground interactions. Improved ecosystem models are necessary tools to reduce the uncertainty in the information that assists us in the sustainable management of our environment in a changing world. [KEYWORDS: Models; Interaction; Aboveground–belowground; Global change; Soil organisms; Vegetation; Processes; Ecosystem services; Food web; Process-oriented; Organism-oriented]

Seeds of melon cultivars “Hasanbey” and “Kirkagac” were primed (P) with 18 dS m −1 NaCl solution for 3 days at 20 °C. After priming, non-primed (NP) and P seeds were sown in germination boxes containing sphagnum peat. The germination boxes were placed in an unheated greenhouse and watered with five different NaCl solutions (0.3 (control), 4.5, 9.0, 13.5 and 18.0 dS m −1 ), for a period of 4 weeks. Total emergence and dry weight were higher in melon seedlings derived from P seeds and they emerged earlier than NP seeds. Moreover, seeds from NP groups could tolerate up to 9.0 dS m −1 NaCl salinity, while the total emergence values of P groups in cvs. “Hasanbey” and “Kirkagac” did not decrease below 50% at 13.5 and 18.0 dS m −1 , respectively. NaCl priming enhanced total sugar and proline accumulation and prevented toxic and nutrient deficiency effects of salinity because less Na but more K and especially Ca was accumulated in melon seedlings. As a matter of fact, Na:Ca balances of seedlings derived from P seeds were significantly lower than those of NP seeds under similar salinity levels. These results suggest that NaCl priming of melon seeds increased salt tolerance of seedlings by promoting K and Ca accumulation, besides inducing osmoregulation by the accumulation of organic solutes.

Deep-rooting trees in agroforestry systems may promote distribution of spores of arbuscular mycorrhizal fungi (AMF) at deeper soil levels. We investigated the vertical distribution of AMF spores in Oxisols under agroforestry and monocultural (unshaded) coffee systems in on-farm experiments ( Brazil). The number of AMF spores was considered as an indicator of mycorrhiza incidence in soil. Spores were extracted from 0-1, 2-3, 5-7.5, 10-15, 20-30, 40-60 cm soil-depths in agroforestry and monocultural coffee systems, of three different age groups (young, medium-aged and old), using centrifugation methods, and counted. Fine roots were collected and dry-weighed from 0-30 cm in young and old systems and from several depths in medium-aged systems. Soils were characterised with respect to texture, pH, organic matter, calcium, magnesium, phosphorus and potassium. Agroforestry had a higher percentage of spores (12-21% of the total number of spores) and roots (on average 1.5 g L-1 soil) in deeper layers (20-60 cm), and a lower percentage (79-88%) closer to the surface (0-15 cm) than the monocultural fields (respectively 3-12%, 0.6 g L-1 soil and 88-97%). Greater numbers of spores in the deeper soil layers may be explained by greater amounts of roots and may be an indicator of greater incidence of mycorrhiza in agroforestry than in monocultural coffee systems. Greater mycorrhizal incidence at deeper soil layers in the agroforestry system may change the dynamics of phosphorus cycling in soil, making this nutrient more available to plants.

The effect of slash-and-burn agriculture on earthworm surface cast deposition was assessed in 4-5 year old Chromolaena odorata (CHR) and young forest (YFOR). fallow (12-15 years) in the humid forest zone of southern Cameroon. In the villages Ngoungoumou (56.8% forest cover), Metet (39.5% forest cover), and Nkometou (24.9% forest cover), plots were established in both fallow types and half were slashed, burned,and cropped in 2000, the rest maintained,as undisturbed controls. In 2001, cropped plots were split,one half abandoned to fallow, the other cropped a second time as in 2000. Casts were collected weekly from April to December in 2000 and 2001. In 2000, surface cast deposition was different between villages, in both fallow types and land-uses. At Nkometou casting was lowest and no effects of fallow type. or land-use were found. At Metet and Ngoungoumou, more casts were deposited in undisturbed fallow (22.5 and 3.0 Mg ha(-1), respectively) than in the cropped treatment (7.1 and 0.6 Mg ha-1, respectively). Cropping reduced cast deposit ion in both fallow types, yet more so in CHR than in YFOR. In 2001, as in 2000, no differences were found at Nkometou. At Metet and Ngoungoumou, more casts were deposited in undisturbed controls than in the other treatments. Cast deposition was higher in plots in the first year of fallow. after cropping than in double cropped plots, indicating an immediate recovery after cropping. Cast production was not correlated with soil chemical properties across villages. Earthworm species assemblages were different between villages, with large bodied, endogeic and anecic species most abundant at Metet. Earthworm species assemblage is likely to be the main factor determining surface cast deposition and thus differences between villages.

Supplementary lighting is frequently applied in the winter season for crop production in greenhouses. The effect of supplementary lighting on plant growth depends on the balance between assimilate production in source leaves and the overall capacity of the plants to use assimilates. This study aims at quantifying the source-sink balance and carbohydrate content of three tomato cultivars differing in fruit size, and to investigate to what extent the source/sink ratio correlates with the potential fruit size. Cultivars Komeet (large size), Capricia (medium size), and Sunstream (small size, cherry tomato) were grown from 16 August to 21 November, at similar crop management as in commercial practice. Supplementary lighting (High Pressure Sodium lamps, photosynthetic active radiation at 1 m below lamps was 162 μmol photons m(-2) s(-1); maximum 10 h per day depending on solar irradiance level) was applied from 19 September onward. Source strength was estimated from total plant growth rate using periodic destructive plant harvests in combination with the crop growth model TOMSIM. Sink strength was estimated from potential fruit growth rate which was determined from non-destructively measuring the fruit growth rate at non-limiting assimilate supply, growing only one fruit on each truss. Carbohydrate content in leaves and stems were periodically determined. During the early growth stage, 'Komeet' and 'Capricia' showed sink limitation and 'Sunstream' was close to sink limitation. During this stage reproductive organs had hardly formed or were still small and natural irradiance was high (early September) compared to winter months. Subsequently, during the fully fruiting stage all three cultivars were strongly source-limited as indicated by the low source/sink ratio (average source/sink ratio from 50 days after planting onward was 0.17, 0.22, and 0.33 for 'Komeet,' 'Capricia,' and 'Sunstream,' respectively). This was further confirmed by the fact that pruning half of the fruits hardly influenced net leaf photosynthesis rates. Carbohydrate content in leaves and stems increased linearly with the source/sink ratio. We conclude that during the early growth stage under high irradiance, tomato plants are sink-limited and that the level of sink limitation differs between cultivars but it is not correlated with their potential fruit size. During the fully fruiting stage tomato plants are source-limited and the extent of source limitation of a cultivar is positively correlated with its potential fruit size.

Eyespot is a major fungal disease of winter wheat, mostly affecting the base of the stem. The development of biological control approaches, using organisms such as earthworms, represents a potential alternative strategy for eyespot control. In a greenhouse experiment, we analyzed the response of two wheat cultivars (Soissons and Aubusson) to the presence of the pathogenic fungus Oculimacula yallundae and the anecic earthworm Lumbricus terrestris, alone and in combination. We assessed necrosis frequency, necrosis severity, wheat biomass, resource allocation and soil mineral concentrations. Disease incidence was lower in the presence of earthworms: the frequency of necrosis was 44% lower for Soissons and 70% lower for Aubusson. Necrosis severity was also lower for both cultivars (50% lower for Soissons and 80% lower for Aubusson) in the presence of earthworms. Earthworms had no detectable effect on the shoot and root biomasses of plants exposed to the fungus, but they modified resource allocation between plant organs and nutrient translocation within the plant. Our results suggest that earthworms are a potentially effective biocontrol agent for eyespot, and we discuss the possible underlying mechanisms. (C) 2015 Elsevier B.V. All rights reserved.

Highlight Growth curve modelling and GWA mapping are combined to unravel the dynamic regulation of plant growth., Growth is a complex trait determined by the interplay between many genes, some of which play a role at a specific moment during development whereas others play a more general role. To identify the genetic basis of growth, natural variation in Arabidopsis rosette growth was followed in 324 accessions by a combination of top-view imaging, high-throughput image analysis, modelling of growth dynamics, and end-point fresh weight determination. Genome-wide association (GWA) mapping of the temporal growth data resulted in the detection of time-specific quantitative trait loci (QTLs), whereas mapping of model parameters resulted in another set of QTLs related to the whole growth curve. The positive correlation between projected leaf area (PLA) at different time points during the course of the experiment suggested the existence of general growth factors with a function in multiple developmental stages or with prolonged downstream effects. Many QTLs could not be identified when growth was evaluated only at a single time point. Eleven candidate genes were identified, which were annotated to be involved in the determination of cell number and size, seed germination, embryo development, developmental phase transition, or senescence. For eight of these, a mutant or overexpression phenotype related to growth has been reported, supporting the identification of true positives. In addition, the detection of QTLs without obvious candidate genes implies the annotation of novel functions for underlying genes.

Soil N availability is constrained by the breakdown of N-containing polymers such as proteins to oligopeptides and amino acids that can be taken up by plants and microorganisms. Excess N is released from microbial cells as ammonium (N mineralization), which in turn can serve as substrate for nitrification. According to stoichiometric theory, N mineralization and nitrification are expected to increase in relation to protein depolymerization with decreasing N limitation, and thus from higher to lower latitudes and from topsoils to subsoils. To test these hypotheses, we compared gross rates of protein depolymerization, N mineralization and nitrification (determined using 15N pool dilution assays) in organic topsoil, mineral topsoil, and mineral subsoil of seven ecosystems along a latitudinal transect in western Siberia, from tundra (67°N) to steppe (54°N). The investigated ecosystems differed strongly in N transformation rates, with highest protein depolymerization and N mineralization rates in middle and southern taiga. All N transformation rates decreased with soil depth following the decrease in organic matter content. Related to protein depolymerization, N mineralization and nitrification were significantly higher in mineral than in organic horizons, supporting a decrease in microbial N limitation with depth. In contrast, we did not find indications for a decrease in microbial N limitation from arctic to temperate ecosystems along the transect. Our findings thus challenge the perception of ubiquitous N limitation at high latitudes, but suggest a transition from N to C limitation of microorganisms with soil depth, even in high-latitude systems such as tundra and boreal forest. Key Points We compared soil N dynamics of seven ecosystems along a latitudinal transectShifts in N dynamics suggest a decrease in microbial N limitation with depthWe found no decrease in microbial N limitation from arctic to temperate zones

International audience; Because they are tethered in space, plants have to make the most of their local growth environment. In order to grow in an ever-changing environment, plants constantly remodel their shapes. This adaptive attribute requires the orchestration of complex environmental signals at the cellular and organismal levels. A battery of small molecules, classically known as phytohormones, allows plants to change their body plan by using highly integrated signaling networks and transcriptional cascades. Amongst these hormones, brassinosteroids (BRs), the polyhydroxylated steroid of plants, influence plant responsiveness to the local environment and exquisitely promote, or interfere with, many aspects of plant development. The molecular circuits that wire steroid signals at the cell surface to the promoters of thousands of genes in the nucleus have been defined in the past decade. This review recapitulates how the transduction of BR signals impacts the temporally unfolding programs of plant growth. First, we summarize the paradigmatic BR signaling pathway acting primarily in cellular expansion. Secondly, we describe the current wiring diagram and the temporal dynamics of the BR signal transduction network. And finally we provide an overview of how key players in BR signaling act as molecular gates to transduce BR signals onto other signaling pathways.

International audience; Intensive agriculture is often criticized for negative impacts on environment and human health. This issue may be solved by a better management of organisms living in crop fields. Here, we review the benefits of earthworms for crops, and we present techniques to increase earthworm abundance. The major points are the following: (1) Earthworms usually improve soil structural stability and soil porosity and reduce runoff. (2) Earthworms modify soil organic matter (SOM) and nutrient cycling. Specifically, earthworms stabilize SOM fractions within their casts, and they also increase the mineralization of organic matter in the short term by altering physical protection within aggregates and enhancing microbial activity. (3) The positive correlation between earthworm abundance and crop production is not systematic, and contrasting effects on yields have been observed. Earthworms induce the production of hormone-like substances that improve plant growth and health. (4) Direct drilling increases earthworm abundance and species diversity, but the beneficial effect of reduced tillage depends upon the species present and tillage intensity. (5) Organic amendments enhance earthworm abundance. (6) Earthworms feeding at soil surface are the most exposed to pesticides and other agrochemicals. Finally, we discuss how to combine management practices, including inoculation, to increase the earthworm services. We conclude that using earthworm services in cropping systems has potential to boost agricultural sustainability.