Czech Agrifood Research Center

Life on Earth is sustained by a small volume of soil surrounding roots, called the rhizosphere. The soil is where most of the biodiversity on Earth exists, and the rhizosphere probably represents the most dynamic habitat on Earth; and certainly is the most important zone in terms of defining the quality and quantity of the Human terrestrial food resource. Despite its central importance to all life, we know very little about rhizosphere functioning, and have an extraordinary ignorance about how best we can manipulate it to our advantage. A major issue in research on rhizosphere processes is the intimate connection between the biology, physics and chemistry of the system which exhibits astonishing spatial and temporal heterogeneities. This review considers the unique biophysical and biogeochemical properties of the rhizosphere and draws some connections between them. Particular emphasis is put on how underlying processes affect rhizosphere ecology, to generate highly heterogeneous microenvironments. Rhizosphere ecology is driven by a combination of the physical architecture of the soil matrix, coupled with the spatial and temporal distribution of rhizodeposits, protons, gases, and the role of roots as sinks for water and nutrients. Consequences for plant growth and whole-system ecology are considered. The first sections address the physical architecture and soil strength of the rhizosphere, drawing their relationship with key functions such as the movement and storage of elements and water as well as the ability of roots to explore the soil and the definition of diverse habitats for soil microorganisms. The distribution of water and its accessibility in the rhizosphere is considered in detail, with a special emphasis on spatial and temporal dynamics and heterogeneities. The physical architecture and water content play a key role in determining the biogeochemical ambience of the rhizosphere, via their effect on partial pressures of O2 and CO2, and thereby on redox potential and pH of the rhizosphere, respectively. We address the various mechanisms by which roots and associated microorganisms alter these major drivers of soil biogeochemistry. Finally, we consider the distribution of nutrients, their accessibility in the rhizosphere, and their functional relevance for plant and microbial ecology. Gradients of nutrients in the rhizosphere, and their spatial patterns or temporal dynamics are discussed in the light of current knowledge of rhizosphere biophysics and biogeochemistry. Priorities for future research are identified as well as new methodological developments which might help to advance a comprehensive understanding of the co-occurring processes in the rhizosphere.

Root elongation in drying soil is generally limited by a combination of mechanical impedance and water stress. Relationships between root elongation rate, water stress (matric potential), and mechanical impedance (penetration resistance) are reviewed, detailing the interactions between these closely related stresses. Root elongation is typically halved in repacked soils with penetrometer resistances >0.8-2 MPa, in the absence of water stress. Root elongation is halved by matric potentials drier than about -0.5 MPa in the absence of mechanical impedance. The likelihood of each stress limiting root elongation is discussed in relation to the soil strength characteristics of arable soils. A survey of 19 soils, with textures ranging from loamy sand to silty clay loam, found that ∼10% of penetration resistances were >2 MPa at a matric potential of -10 kPa, rising to nearly 50% >2 MPa at - 200 kPa. This suggests that mechanical impedance is often a major limitation to root elongation in these soils even under moderately wet conditions, and is important to consider in breeding programmes for drought-resistant crops. Root tip traits that may improve root penetration are considered with respect to overcoming the external (soil) and internal (cell wall) pressures resisting elongation. The potential role of root hairs in mechanically anchoring root tips is considered theoretically, and is judged particularly relevant to roots growing in biopores or from a loose seed bed into a compacted layer of soil.

Retrotransposons are mobile genetic elements that transpose through reverse transcription of an RNA intermediate. Retrotransposons are ubiquitous in plants and play a major role in plant gene and genome evolution. In many cases, retrotransposons comprise over 50% of nuclear DNA content, a situation that can arise in just a few million years. Plant retrotransposons are structurally and functionally similar to the retrotransposons and retroviruses that are found in other eukaryotic organisms. However, there are important differences in the genomic organization of retrotransposons in plants compared to some other eukaryotes, including their often-high copy numbers, their extensively heterogeneous populations, and their chromosomal dispersion patterns. Recent studies are providing valuable insights into the mechanisms involved in regulating the expression and transposition of retrotransposons. This review describes the structure, genomic organization, expression, regulation, and evolution of retrotransposons, and discusses both their contributions to plant genome evolution and their use as genetic tools in plant biology.

Summary Plants are subject to a wide range of abiotic stresses, and their cuticular wax layer provides a protective barrier, which consists predominantly of long‐chain hydrocarbon compounds, including alkanes, primary alcohols, aldehydes, secondary alcohols, ketones, esters and other derived compounds. This article discusses current knowledge relating to the effects of stress on cuticular waxes and the ways in which the wax provides protection against the deleterious effects of light, temperature, osmotic stress, physical damage, altitude and pollution. Topics covered here include biosynthesis, morphology, composition and function of cuticular waxes in relation to the effects of stress, and some recent findings concerning the effects of stress on regulation of wax biosynthesis are described. Contents Summary 469 I Introduction 470 II Biosynthesis of cuticular wax 470 III Deposition and crystalline morphology of cuticular wax 474 IV Cuticular wax as a photoprotective layer 475 V Effects of irradiation and temperature on cuticular wax composition 478 VI Contact angles and wettability 481 VII Humidity effects 482 VIII Water, salinity and cold stress 482 IX Mechanical stress 485 X Altitude 486 XI Pollution 486 XII Genetic and environmental control of cuticular wax production 488 XIII Conclusions 493 Acknowledgements 493 References 493

Soils of coniferous forest ecosystems are important for the global carbon cycle, and the identification of active microbial decomposers is essential for understanding organic matter transformation in these ecosystems. By the independent analysis of DNA and RNA, whole communities of bacteria and fungi and its active members were compared in topsoil of a Picea abies forest during a period of organic matter decomposition. Fungi quantitatively dominate the microbial community in the litter horizon, while the organic horizon shows comparable amount of fungal and bacterial biomasses. Active microbial populations obtained by RNA analysis exhibit similar diversity as DNA-derived populations, but significantly differ in the composition of microbial taxa. Several highly active taxa, especially fungal ones, show low abundance or even absence in the DNA pool. Bacteria and especially fungi are often distinctly associated with a particular soil horizon. Fungal communities are less even than bacterial ones and show higher relative abundances of dominant species. While dominant bacterial species are distributed across the studied ecosystem, distribution of dominant fungi is often spatially restricted as they are only recovered at some locations. The sequences of cbhI gene encoding for cellobiohydrolase (exocellulase), an essential enzyme for cellulose decomposition, were compared in soil metagenome and metatranscriptome and assigned to their producers. Litter horizon exhibits higher diversity and higher proportion of expressed sequences than organic horizon. Cellulose decomposition is mediated by highly diverse fungal populations largely distinct between soil horizons. The results indicate that low-abundance species make an important contribution to decomposition processes in soils.

Powdery mildew fungi are obligate biotrophic pathogens that only grow on living hosts and cause damage in thousands of plant species. Despite their agronomical importance, little direct functional evidence for genes of pathogenicity and virulence is currently available because mutagenesis and transformation protocols are lacking. Here, we show that the accumulation in barley (Hordeum vulgare) and wheat (Triticum aestivum) of double-stranded or antisense RNA targeting fungal transcripts affects the development of the powdery mildew fungus Blumeria graminis. Proof of concept for host-induced gene silencing was obtained by silencing the effector gene Avra10, which resulted in reduced fungal development in the absence, but not in the presence, of the matching resistance gene Mla10. The fungus could be rescued from the silencing of Avra10 by the transient expression of a synthetic gene that was resistant to RNA interference (RNAi) due to silent point mutations. The results suggest traffic of RNA molecules from host plants into B. graminis and may lead to an RNAi-based crop protection strategy against fungal pathogens.

Abstract In this article, using data from a survey of 218 consumers across two samples, we propose a measurement scale for word of mouth (e‐WOM scale) in the context of electronic service. A battery of statistical tests reveals that the WOM construct encompasses four dimensions: WOM intensity, positive valence WOM, negative valence WOM, and WOM content. Our proposed e‐WOM scale can be used as a strategic tool for business managers aiming to improve their word‐of‐mouth marketing strategies. Copyright © 2010 ASAC. Published by John Wiley & Sons, Ltd.

Demand for organic foods is partially driven by consumers' perceptions that they are more nutritious. However, scientific opinion is divided on whether there are significant nutritional differences between organic and non-organic foods, and two recent reviews have concluded that there are no differences. In the present study, we carried out meta-analyses based on 343 peer-reviewed publications that indicate statistically significant and meaningful differences in composition between organic and non-organic crops/crop-based foods. Most importantly, the concentrations of a range of antioxidants such as polyphenolics were found to be substantially higher in organic crops/crop-based foods, with those of phenolic acids, flavanones, stilbenes, flavones, flavonols and anthocyanins being an estimated 19 (95 % CI 5, 33) %, 69 (95 % CI 13, 125) %, 28 (95 % CI 12, 44) %, 26 (95 % CI 3, 48) %, 50 (95 % CI 28, 72) % and 51 (95 % CI 17, 86) % higher, respectively. Many of these compounds have previously been linked to a reduced risk of chronic diseases, including CVD and neurodegenerative diseases and certain cancers, in dietary intervention and epidemiological studies. Additionally, the frequency of occurrence of pesticide residues was found to be four times higher in conventional crops, which also contained significantly higher concentrations of the toxic metal Cd. Significant differences were also detected for some other (e.g. minerals and vitamins) compounds. There is evidence that higher antioxidant concentrations and lower Cd concentrations are linked to specific agronomic practices (e.g. non-use of mineral N and P fertilisers, respectively) prescribed in organic farming systems. In conclusion, organic crops, on average, have higher concentrations of antioxidants, lower concentrations of Cd and a lower incidence of pesticide residues than the non-organic comparators across regions and production seasons.

As sessile organisms, plants are unable to escape from the many abiotic and biotic factors that cause a departure from optimal conditions of growth and development. Low temperature represents one of the most harmful abiotic stresses affecting temperate plants. These species have adapted to seasonal variations in temperature by adjusting their metabolism during autumn, increasing their content of a range of cryo-protective compounds to maximise their cold tolerance. Some of these molecules are synthesised de novo. The down-regulation of some gene products represents an additional important regulatory mechanism. Ways in which plants cope with cold stress are described, and the current state of the art with respect to both the model plant Arabidopsis thaliana and crop plants in the area of gene expression and metabolic pathways during low-temperature stress are discussed.

A total of 568 new simple sequence repeat (SSR)-based markers for barley have been developed from a combination of database sequences and small insert genomic libraries enriched for a range of short simple sequence repeats. Analysis of the SSRs on 16 barley cultivars revealed variable levels of informativeness but no obvious correlation was found with SSR repeat length, motif type, or map position. Of the 568 SSRs developed, 242 were genetically mapped, 216 with 37 previously published SSRs in a single doubled-haploid population derived from the F(1) of an interspecific cross between the cultivar Lina and Hordeum spontaneum Canada Park and 26 SSRs in two other mapping populations. A total of 27 SSRs amplified multiple loci. Centromeric clustering of markers was observed in the main mapping population; however, the clustering severity was reduced in intraspecific crosses, supporting the notion that the observed marker distribution was largely a genetical effect. The mapped SSRs provide a framework for rapidly assigning chromosomal designations and polarity in future mapping programs in barley and a convenient alternative to RFLP for aligning information derived from different populations. A list of the 242 primer pairs that amplify mapped SSRs from total barley genomic DNA is presented.

SUMMARY Mechanical impedance to root growth is one of the most important factors determining root elongation and proliferation within a soil profile. Penetrometers overestimate resistance to root growth in soil by a factor of between two and eight and, although they remain the most convenient method for predicting root resistance, careful interpretation of results and choice of penetrometer design are essential if improved estimates of soil resistance to root elongation are to be obtained. Resistance to root growth through pressurized cells containing ballotini considerably exceeds the confining pressure applied externally to these cells. Results from this work are reappraised. Existing models of soil penetration by roots and penetrometers are reviewed together with the factors influencing penetration resistance. The interpretation of results from mechanical impedance experiments is examined in some detail and root responses, including possible mechanisms of response, are discussed.

Most apomictic root-knot nematodes (RKN; Meloidogyne spp.) have host ranges that encompass the majority of flowering plants, and M. incognita is possibly the world's most damaging crop pathogen. The ancestors, age, and origins of the polyphagous RKN are obscure, but there is increasing evidence that M. incognita, M. javanica, and M. arenaria are closely related, heterogeneous species with a recent, hybrid (reticulate) origin. If so, they must owe much of their current worldwide distributions to spread by agriculture. Host resistance appears to be generally durable in the field, but laboratory studies suggest that apomixis does not prevent evolution in response to selection by a parasitic bacterium (Pasteuria penetrans) and host resistance. Maintaining general fitness may be the evolutionary priority for most populations of polyphagous RKN, and a wide host range, important in the field but not in the laboratory, may be conserved by apomixis. Several factors may help confer a wide host range, including suppression of host resistance, perhaps as a consequence of the strength of the induced susceptible response. Resistance genes effective against RKN appear not to have resulted from coevolution. Rates of juvenile invasion and/or development are low in many wild and some crop plants, with the result that they are both poor hosts and sustain less damage. Overall, it is suggested that greater coordination, particularly of fundamental research, is required.

The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.

This paper (i) reviews temperature/development rate relationships in plants and poikilothermic invertebrates, (ii) argues that the relationship is often linear over much of the range up to the thermal optimum (To) and provides a possible mechanism, (iii) provides evidence of a trade-off between the base temperature (Tb) and the thermal constant (DD) that enables each species to adapt to its thermal environment, and (iv) indicates some of the practical and ecological implications. Where a linear relationship has been characterised it is possible to estimate the base temperature for development (Tb, expressed in °C) and the thermal constant for development (DD, the reciprocal of the temperature coefficient (a), expressed in degree [°C] days accumulated above Tb). A possible basis for the linear relationship between rate and temperature is proposed based on the Arrhenius and Sharpe-Schoolfield equations involving activation enthalpy and progressive inactivation of the reactant molecules at both low and high temperatures. Knowledge of Tb and DD enables rates of development of organisms/processes to be calculated and compared at any given temperature between Tb and To. An analysis of published results for differentiation processes (differentiation = a change of state) in species of insects, Collembola, spiders, nematodes and plants showed that Tb tended to vary with the temperature of the niche to which the organism is adapted, and that there was a trade-off between Tb and DD. Tropical species had higher values of Tb than temperate and DD decreased as Tb increased (and vice versa). This conferred a competitive advantage on each species in the thermal environment to which it was adapted. The decrease in DD tended to be relatively greater than the increase in Tb, further favouring a high Tb in tropical species. A mechanism for the trade-off is suggested whereby DD and Tb were shown to be correlated (P < 0.01) with the activation enthalpy (HA) of an assumed, rate-limiting enzyme. Thermal time can also be applied to processes involving growth (= an increase in dry weight) when the DD requirement for development to maturity is the sum of the requirements for differentiation and growth. Rates of both differentiation and growth can vary greatly between species, depending upon the niche they inhabit, and the implications of such differences for resource requirements are considered. In insects and nematodes, but not in annual plants, development is usually coupled to growth. Consequently, when resources are inadequate, mature size in these animals varies less than in plants. Thermal time is shown to provide insight into the life strategies of species within their communities and to have practical implications.

BACKGROUND: Recent studies of ancestral maize populations indicate that linkage disequilibrium tends to dissipate rapidly, sometimes within 100 bp. We set out to examine the linkage disequilibrium and diversity in maize elite inbred lines, which have been subject to population bottlenecks and intense selection by breeders. Such population events are expected to increase the amount of linkage disequilibrium, but reduce diversity. The results of this study will inform the design of genetic association studies. RESULTS: We examined the frequency and distribution of DNA polymorphisms at 18 maize genes in 36 maize inbreds, chosen to represent most of the genetic diversity in U.S. elite maize breeding pool. The frequency of nucleotide changes is high, on average one polymorphism per 31 bp in non-coding regions and 1 polymorphism per 124 bp in coding regions. Insertions and deletions are frequent in non-coding regions (1 per 85 bp), but rare in coding regions. A small number (2-8) of distinct and highly diverse haplotypes can be distinguished at all loci examined. Within genes, SNP loci comprising the haplotypes are in linkage disequilibrium with each other. CONCLUSIONS: No decline of linkage disequilibrium within a few hundred base pairs was found in the elite maize germplasm. This finding, as well as the small number of haplotypes, relative to neutral expectation, is consistent with the effects of breeding-induced bottlenecks and selection on the elite germplasm pool. The genetic distance between haplotypes is large, indicative of an ancient gene pool and of possible interspecific hybridization events in maize ancestry.

Botanical insecticides keep attracting more attention from environmental and small farmers worldwide as they are considered as a suitable alternative to synthetic insecticides. The use of secondary metabolites in a defensive manner isolated from plants is a tradition more than 3000 years old. However, despite current intensive research, the assortment of suitable commercial products is very limited and insufficient in view of the global rise in the demand for biopesticides. Farm products as well as new basic substances offer an important perspective of being widely used in the protection against harmful insects due to their multiple undoubted benefits. These benefits, which are also drawbacks of botanical insecticides, as well as their history in addition to their presence and perspective are critically reviewed in this paper.

Dickeya species (formerly Erwinia chrysanthemi ) cause diseases on numerous crop and ornamental plants world‐wide. Dickeya spp. (probably D. dianthicola ) were first reported on potato in the Netherlands in the 1970s and have since been detected in many other European countries. However, since 2004–5 a new pathogen, with the proposed name ‘ D. solani ’, has been spreading across Europe via trade in seed tubers and is causing increasing economic losses. Although disease symptoms are often indistinguishable from those of the more established blackleg pathogen Pectobacterium spp., Dickeya spp. can initiate disease from lower inoculum levels, have a greater ability to spread through the plant’s vascular tissue, are considerably more aggressive, and have higher optimal temperatures for disease development (the latter potentially leading to increased disease problems as Europe’s climate warms). However, they also appear to be less hardy than Pectobacterium spp. in soil and other environments outside the plant. Scotland is currently the only country in Europe to enforce zero tolerance for Dickeya spp. in its potato crop in an attempt to keep its seed tuber industry free from disease. However, there are a number of other ways to control the disease, including seed tuber certification, on‐farm methods and the use of diagnostics. For diagnostics, new genomics‐based approaches are now being employed to develop D. dianthicola ‐ and ‘ D. solani ’‐specific PCR‐based tests for rapid detection and identification. It is hoped that these diagnostics, together with other aspects of ongoing research, will provide invaluable tools and information for controlling this serious threat to potato production.

In‐season determination of corn ( Zea mays L.) N requirements via remote sensing may help optimize N application decisions and improve profit, fertilizer use efficiency, and environmental quality. The objective of this study was to use aerial color‐infrared (CIR) photography as a remote‐sensing technique for predicting in‐season N requirements for corn at the V7 growth stage. Field studies were conducted for 2 yr at three locations, each with and without irrigation, in the North Carolina Coastal Plain. Experimental treatments were a complete factorial of four N rates at planting (N PL ) and five N rates at V7 (N V7 ). Aerial CIR photographs were taken at each of the locations at V7 before N application. Optimum N V7 ranged from 0 to 207 kg N ha −1 with a mean of 67 kg N ha −1 . Significant but weak correlations were observed between optimum N V7 rates and the band combinations relative green, Relative Green Difference Vegetation Index, and Relative Difference Vegetation Index as measured in CIR photos. High proportions of soil reflectance in the images early in the corn growing season (V7) likely confounded our attempts to relate spectral information to optimum N V7 rates. The primary obstacles to applying this technique early in the season are the use of relative digital counts or indices that require high‐N reference strips in the field and strong background reflectance from the soil. When the N PL treatments that were nonresponsive to N V7 (i.e., optimum N V7 = 0) were removed from the analysis, the normalized near infrared, the Green Difference Vegetation Index, the Green Ratio Vegetation Index, and the Green Normalized Difference Vegetation Index were the best predictors of optimum N V7 rate ( r 2 = 0.33).

Synopsis Plot error variances were large for lint yield, bolls per plant, seed per boll, and boll weight; small for lint percentage, seed and tint index, and fiber length, strength and fineness. Genotype x environment interaction variances were generally small for all traits except yield and bolls per plant. Lint yield was highly positively correlated with lint percentage and bolls per plant and negatively correlated with seed index and weight per boll.

The eukaryotic nucleolus is involved in ribosome biogenesis and a wide range of other RNA metabolism and cellular functions. An important step in the functional analysis of the nucleolus is to determine the complement of proteins of this nuclear compartment. Here, we describe the first proteomic analysis of plant (Arabidopsis thaliana) nucleoli, in which we have identified 217 proteins. This allows a direct comparison of the proteomes of an important nuclear structure between two widely divergent species: human and Arabidopsis. The comparison identified many common proteins, plant-specific proteins, proteins of unknown function found in both proteomes, and proteins that were nucleolar in plants but nonnucleolar in human. Seventy-two proteins were expressed as GFP fusions and 87% showed nucleolar or nucleolar-associated localization. In a striking and unexpected finding, we have identified six components of the postsplicing exon-junction complex (EJC) involved in mRNA export and nonsense-mediated decay (NMD)/mRNA surveillance. This association was confirmed by GFP-fusion protein localization. These results raise the possibility that in plants, nucleoli may have additional functions in mRNA export or surveillance.