Rothamsted Research

The aim of this review was to survey all fungal pathologists with an association with the journal Molecular Plant Pathology and ask them to nominate which fungal pathogens they would place in a 'Top 10' based on scientific/economic importance. The survey generated 495 votes from the international community, and resulted in the generation of a Top 10 fungal plant pathogen list for Molecular Plant Pathology. The Top 10 list includes, in rank order, (1) Magnaporthe oryzae; (2) Botrytis cinerea; (3) Puccinia spp.; (4) Fusarium graminearum; (5) Fusarium oxysporum; (6) Blumeria graminis; (7) Mycosphaerella graminicola; (8) Colletotrichum spp.; (9) Ustilago maydis; (10) Melampsora lini, with honourable mentions for fungi just missing out on the Top 10, including Phakopsora pachyrhizi and Rhizoctonia solani. This article presents a short resumé of each fungus in the Top 10 list and its importance, with the intent of initiating discussion and debate amongst the plant mycology community, as well as laying down a bench-mark. It will be interesting to see in future years how perceptions change and what fungi will comprise any future Top 10.

Soils collected across a long-term liming experiment (pH 4.0-8.3), in which variation in factors other than pH have been minimized, were used to investigate the direct influence of pH on the abundance and composition of the two major soil microbial taxa, fungi and bacteria. We hypothesized that bacterial communities would be more strongly influenced by pH than fungal communities. To determine the relative abundance of bacteria and fungi, we used quantitative PCR (qPCR), and to analyze the composition and diversity of the bacterial and fungal communities, we used a bar-coded pyrosequencing technique. Both the relative abundance and diversity of bacteria were positively related to pH, the latter nearly doubling between pH 4 and 8. In contrast, the relative abundance of fungi was unaffected by pH and fungal diversity was only weakly related with pH. The composition of the bacterial communities was closely defined by soil pH; there was as much variability in bacterial community composition across the 180-m distance of this liming experiment as across soils collected from a wide range of biomes in North and South America, emphasizing the dominance of pH in structuring bacterial communities. The apparent direct influence of pH on bacterial community composition is probably due to the narrow pH ranges for optimal growth of bacteria. Fungal community composition was less strongly affected by pH, which is consistent with pure culture studies, demonstrating that fungi generally exhibit wider pH ranges for optimal growth.

Cropland Acidification in China China is experiencing increasing problems with acid rain, groundwater pollution, and nitrous oxide emissions. Rapid development of industry and transportation has accelerated nitrate (N) emissions to the atmosphere. Consequently, soil degradation, water shortage, and pollution, in addition to atmospheric quality decline are becoming major public concerns across China. Since the 1990s, China has become both the largest consumer of chemical N fertilizers and the highest cereal producer in the world, which has consequences for arable soil acidification. Guo et al. (p. 1008 , published online 11 February) present a meta-analysis of a regional acidification phenomenon in Chinese arable soils that is largely associated with higher N fertilization and higher crop production. Such large-scale soil acidification is likely to threaten the sustainability of agriculture and affect the biogeochemical cycles of nutrients and also toxic elements in soils.

An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.

Low molecular weight antioxidants, such as ascorbate, glutathione, and tocopherol, are information-rich redox buffers that interact with numerous cellular components. In addition to crucial roles in defense and as enzyme cofactors, cellular antioxidants influence plant growth and development by modulating processes from mitosis and cell elongation to senescence and death (De Pinto and De Gara, 2004; Potters et al., 2004; Tokunaga et al., 2005). Most importantly, antioxidants provide essential information on cellular redox state, and they influence gene expression associated with biotic and abiotic stress responses to maximize defense. Growing evidence suggests a model for redox homeostasis in which the reactive oxygen species (ROS)–antioxidant interaction acts as a metabolic interface for signals derived from metabolism and from the environment. This interface modulates the appropriate induction of acclimation processes or, alternatively, execution of cell death programs. 

Abstract This review examines the direct effects of climate change on insect herbivores. Temperature is identified as the dominant abiotic factor directly affecting herbivorous insects. There is little evidence of any direct effects of CO 2 or UVB. Direct impacts of precipitation have been largely neglected in current research on climate change. Temperature directly affects development, survival, range and abundance. Species with a large geographical range will tend to be less affected. The main effect of temperature in temperate regions is to influence winter survival; at more northerly latitudes, higher temperatures extend the summer season, increasing the available thermal budget for growth and reproduction. Photoperiod is the dominant cue for the seasonal synchrony of temperate insects, but their thermal requirements may differ at different times of year. Interactions between photoperiod and temperature determine phenology; the two factors do not necessarily operate in tandem. Insect herbivores show a number of distinct life‐history strategies to exploit plants with different growth forms and strategies, which will be differentially affected by climate warming. There are still many challenges facing biologists in predicting and monitoring the impacts of climate change. Future research needs to consider insect herbivore phenotypic and genotypic flexibility, their responses to global change parameters operating in concert, and awareness that some patterns may only become apparent in the longer term.

Crop models are essential tools for assessing the threat of climate change to local and global food production. Present models used to predict wheat grain yield are highly uncertain when simulating how crops respond to temperature. Here we systematically tested 30 different wheat crop models of the Agricultural Model Intercomparison and Improvement Project against field experiments in which growing season mean temperatures ranged from 15 °C to 32 °C, including experiments with artificial heating. Many models simulated yields well, but were less accurate at higher temperatures. The model ensemble median was consistently more accurate in simulating the crop temperature response than any single model, regardless of the input information used. Extrapolating the model ensemble temperature response indicates that warming is already slowing yield gains at a majority of wheat-growing locations. Global wheat production is estimated to fall by 6% for each °C of further temperature increase and become more variable over space and time.

Summary The aim of this review was to undertake a survey of researchers working with plant‐parasitic nematodes in order to determine a ‘top 10’ list of these pathogens based on scientific and economic importance. Any such list will not be definitive as economic importance will vary depending on the region of the world in which a researcher is based. However, care was taken to include researchers from as many parts of the world as possible when carrying out the survey. The top 10 list emerging from the survey is composed of: (1) root‐knot nematodes ( M eloidogyne spp.); (2) cyst nematodes ( H eterodera and G lobodera spp.); (3) root lesion nematodes ( P ratylenchus spp.); (4) the burrowing nematode R adopholus similis ; (5) D itylenchus dipsaci ; (6) the pine wilt nematode B ursaphelenchus xylophilus ; (7) the reniform nematode R otylenchulus reniformis ; (8) X iphinema index (the only virus vector nematode to make the list); (9) N acobbus aberrans ; and (10) A phelenchoides besseyi . The biology of each nematode (or nematode group) is reviewed briefly.

Geographical information systems could be improved by adding procedures for geostatistical spatial analysis to existing facilities. Most traditional methods of interpolation are based on mathematical as distinct from stochastic models of spatial variation. Spatially distributed data behave more like random variables, however, and regionalized variable theory provides a set of stochastic methods for analysing them. Kriging is the method of interpolation deriving from regionalized variable theory. It depends on expressing spatial variation of the property in terms of the variogram, and it minimizes the prediction errors which are themselves estimated. We describe the procedures and the way we link them using standard operating systems. We illustrate them using examples from case studies, one involving the mapping and control of soil salinity in the Jordan Valley of Israel, the other in semi-arid Botswana where the herbaceous cover was estimated and mapped from aerial photographic survey.

The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term "microbiome." Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role. Video Abstract.

Experimental studies on CO2 assimilation of mesophytic C3 plants in relation to relative water content (RWC) are discussed. Decreasing RWC slows the actual rate of photosynthetic CO2 assimilation (A) and decreases the potential rate (Apot). Generally, as RWC falls from c. 100 to c. 75%, the stomatal conductance (gs) decreases, and with it A. However, there are two general types of relation of Apot to RWC, which are called Type 1 and Type 2. Type 1 has two main phases. As RWC decreases from 100 to c. 75%, Apot is unaffected, but decreasing stomatal conductance (gs) results in smaller A, and lower CO2 concentration inside the leaf (Ci) and in the chloroplast (Cc), the latter falling possibly to the compensation point. Down-regulation of electron transport occurs by energy quenching mechanisms, and changes in carbohydrate and nitrogen metabolism are considered acclimatory, caused by low Ci and reversible by elevated CO2. Below 75% RWC, there is metabolic inhibition of Apot, inhibition of A then being partly (but progressively less) reversible by elevated CO2; gs regulates A progressively less, and Ci and CO2 compensation point, Gamma rise. It is suggested that this is the true stress phase, where the decrease in Apot is caused by decreased ATP synthesis and a consequent decreased synthesis of RuBP. In the Type 2 response, Apot decreases progressively at RWC 100 to 75%, with A being progressively less restored to the unstressed value by elevated CO2. Decreased gs leads to a lower Ci and Cc but they probably do not reach compensation point: gs becomes progressively less important and metabolic limitations more important as RWC falls. The primary effect of low RWC on Apot is most probably caused by limited RuBP synthesis, as a result of decreased ATP synthesis, either through inhibition of Coupling Factor activity or amount due to increased ion concentration. Carbohydrate synthesis and accumulation decrease. Type 2 response is considered equivalent to Type 1 at RWC below c. 75%, with Apot inhibited by limited ATP and RuBP synthesis, respiratory metabolism dominates and Ci and Gamma rise. The importance of inhibited ATP synthesis as a primary cause of decreasing Apot is discussed. Factors determining the Type 1 and Type 2 responses are unknown. Electron transport is maintained (but down-regulated) in Types 1 and 2 over a wide range of RWC, and a large reduced/oxidized adenylate ratio results. Metabolic imbalance results in amino acid accumulation and decreased and altered protein synthesis. These conditions profoundly affect cell functions and ultimately cause cell death. Type 1 and 2 responses may reflect differences in gs and in sensitivity of metabolism to decreasing RWC.

1. The reliability of the Kjeldahl method for the determination of nitrogen in soils has been investigated using a range of soils containing from 0·03 to 2·7% nitrogen. 2. The same result was obtained when soil was analysed by a variety of Kjeldahl procedures which included methods known to recover various forms of nitrogen not determined by Kjeldahl procedures commonly employed for soil analysis. From this and other evidence presented it is concluded that very little, if any, of the nitrogen in the soils examined was in the form of highly refractory nitrogen compounds or of compounds containing N—N or N—O linkages. 3. Results by the method of determining nitrogen in soils recommended by the Association of Official Agricultural Chemists were 10–37% lower than those obtained by other methods tested. Satisfactory results were obtained by this method when the period of digestion recommended was increased. 4. Ammonium-N fixed by clay minerals is determined by the Kjeldahl method. 5. Selenium and mercury are considerably more effective than copper for catalysis of Kjeldahl digestion of soil. Conditions leading to loss of nitrogen using selenium are defined, and difficulties encountered using mercury are discussed. 6. The most important factor in Kjeldahl analysis is the temperature of digestion with sulphuric acid, which is controlled largely by the amount of potassium (or sodium) sulphate used for digestion. 7. The period of digestion required for Kjeldahl analysis of soil depends on the concentration of potassium sulphate in the digest. When the concentration is low (e.g. 0·3 g./ml. sulphuric acid) it is necessary to digest for several hours; when it is high (e.g. 1·0 g./ml. sulphuric acid) short periods of digestion are adequate. Catalysts greatly affect the rate of digestion when the salt concentration is low, but have little effect when the salt concentration is high. 8. Nitrogen is lost during Kjeldahl analysis when the temperature of digestion exceeds about 400° C. 9. Determinations of the amounts of sulphuric acid consumed by various mineral and organic soils during Kjeldahl digestion showed that there is little risk of loss of nitrogen under the conditions usually employed for Kjeldahl digestion of soil. Acid consumption values for various soil constituents are given, from which the amounts of sulphuric acid likely to be consumed during Kjeldahl digestion of different types of soil can be calculated. 10. Semi-micro Kjeldahl methods of determining soil nitrogen gave the same results as macro-Kjeldahl methods. 11. The use of the Hoskins apparatus for the determination of ammonium is described. 12. It is concluded that the Kjeldahl method is satisfactory for the determination of nitrogen in soils provided a few simple precautions are observed. The merits and defects of different Kjeldahl procedures are discussed.

ABSTRACT While the chemical nature of reactive oxygen species (ROS) dictates that they are potentially harmful to cells, recent genetic evidence suggests that in planta purely physicochemical damage may be much more limited than previously thought. The most potentially deleterious effect of ROS under most conditions is that at high concentrations they trigger genetically programmed cell suicide events. Moreover, because plants use ROS as second messengers in signal transduction cascades in processes as diverse as mitosis, tropisms and cell death, their accumulation is crucial to plant development as well as defence. Direct ROS signal transduction will ensue only if ROS escape destruction by antioxidants or are otherwise consumed in a ROS cascade. Thus, the major low molecular weight antioxidants determine the specificity of the signal. They are also themselves signal‐transducing molecules that can either signal independently or further transmit ROS signals. The moment has come to re‐evaluate the concept of oxidative stress. In contrast to this pejorative or negative term, implying a state to be avoided, we propose that the syndrome would be more usefully described as ‘oxidative signalling’, that is, an important and critical function associated with the mechanisms by which plant cells sense the environment and make appropriate adjustments to gene expression, metabolism and physiology.

A suction trap has been made in which the spores entering a narrow orifice, directed into the wind, are impacted on a Vaseline‐coated microscope slide moved across the orifice at 2 mm./hr. Estimates of spore content of the air can be made, with higher efficiency than by previous traps, at different times of day and thus be more closely correlated with variations in weather. Wind‐tunnel tests with spores of Lycopodium clavatum showed maximal and minimal efficiencies of 93.8 and 62.4% respectively, with a suction rate of 10.0 1./min., in the range of wind speeds from 1.5 to 9.3 m./sec.

The influence of pH on the relative importance of the two principal decomposer groups in soil, fungi and bacteria, was investigated along a continuous soil pH gradient at Hoosfield acid strip at Rothamsted Research in the United Kingdom. This experimental location provides a uniform pH gradient, ranging from pH 8.3 to 4.0, within 180 m in a silty loam soil on which barley has been continuously grown for more than 100 years. We estimated the importance of fungi and bacteria directly by measuring acetate incorporation into ergosterol to measure fungal growth and leucine and thymidine incorporation to measure bacterial growth. The growth-based measurements revealed a fivefold decrease in bacterial growth and a fivefold increase in fungal growth with lower pH. This resulted in an approximately 30-fold increase in fungal importance, as indicated by the fungal growth/bacterial growth ratio, from pH 8.3 to pH 4.5. In contrast, corresponding effects on biomass markers for fungi (ergosterol and phospholipid fatty acid [PLFA] 18:2omega6,9) and bacteria (bacterial PLFAs) showed only a two- to threefold difference in fungal importance in the same pH interval. The shift in fungal and bacterial importance along the pH gradient decreased the total carbon mineralization, measured as basal respiration, by only about one-third, possibly suggesting functional redundancy. Below pH 4.5 there was universal inhibition of all microbial variables, probably derived from increased inhibitory effects due to release of free aluminum or decreasing plant productivity. To investigate decomposer group importance, growth measurements provided significantly increased sensitivity compared with biomass-based measurements.

Global change will alter the supply of ecosystem services that are vital for human well-being. To investigate ecosystem service supply during the 21st century, we used a range of ecosystem models and scenarios of climate and land-use change to conduct a Europe-wide assessment. Large changes in climate and land use typically resulted in large changes in ecosystem service supply. Some of these trends may be positive (for example, increases in forest area and productivity) or offer opportunities (for example, "surplus land" for agricultural extensification and bioenergy production). However, many changes increase vulnerability as a result of a decreasing supply of ecosystem services (for example, declining soil fertility, declining water availability, increasing risk of forest fires), especially in the Mediterranean and mountain regions.

Many secondary metabolites found in plants have a role in defence against herbivores, pests and pathogens. In this review, a few examples are described and discussed, and some of the problems in determining the precise role(s) of such metabolites highlighted. The role of secondary metabolites in defence may involve deterrence/anti-feedant activity, toxicity or acting as precursors to physical defence systems. Many specialist herbivores and pathogens do not merely circumvent the deterrent or toxic effects of secondary metabolites but actually utilize these compounds as either host recognition cues or nutrients (or both). This is true of both cyanogenic glucosides and glucosinolates, which art discussed in detail as examples of defensive compounds. Their biochemistry is compared and contrasted. An enormous variety of secondary metabolites are derived from shikimic acid or aromatic amino acids, many of which have important roles in defence mechanisms. Several classes of secondary products are 'induced' by infection, wounding or herbivory, and examples of these are given. Genetic variation in the speed and extent of such induction may account, at least in part, for the difference between resistant and susceptible varieties. Both salicylates and jasmonates have been implicated as signals in such responses and in many other physiological processes, though their prescise roles and interactions in signalling and development are not fully understood. Contents Summary 617 I. Introduction 617 II. Cyanogenic glucosides 618 III. Glucosinolates 619 IV. Non-protein amino acids 621 V. Alkaloids 622 VI. Plant phenoiics 623 VII. Plant terpenes, sesquiterpenoids and sterols 626 VIII. Phytoalexins 626 IX. Salicylic acid and methyl jasnionate 627 X. Conclusions 628 References 629.

Abstract Mechanisms to mitigate global climate change by sequestering carbon ( C ) in different ‘sinks' have been proposed as at least temporary measures. Of the major global C pools, terrestrial ecosystems hold the potential to capture and store substantially increased volumes of C in soil organic matter ( SOM ) through changes in management that are also of benefit to the multitude of ecosystem services that soils provide. This potential can only be realized by determining the amount of SOM stored in soils now, with subsequent quantification of how this is affected by management strategies intended to increase SOM concentrations, and used in soil C models for the prediction of the roles of soils in future climate change. An apparently obvious method to increase C stocks in soils is to augment the soil C pools with the longest mean residence times ( MRT ). Computer simulation models of soil C dynamics, e.g. RothC and Century, partition these refractory constituents into slow and passive pools with MRT s of centuries to millennia. This partitioning is assumed to reflect: (i) the average biomolecular properties of SOM in the pools with reference to their source in plant litter, (ii) the accessibility of the SOM to decomposer organisms or catalytic enzymes, or (iii) constraints imposed on decomposition by environmental conditions, including soil moisture and temperature. However, contemporary analytical approaches suggest that the chemical composition of these pools is not necessarily predictable because, despite considerable progress with understanding decomposition processes and the role of decomposer organisms, along with refinements in simulation models, little progress has been made in reconciling biochemical properties with the kinetically defined pools. In this review, we will explore how advances in quantitative analytical techniques have redefined the new understanding of SOM dynamics and how this is affecting the development and application of new modelling approaches to soil C .

Push-pull strategies involve the behavioral manipulation of insect pests and their natural enemies via the integration of stimuli that act to make the protected resource unattractive or unsuitable to the pests (push) while luring them toward an attractive source (pull) from where the pests are subsequently removed. The push and pull components are generally nontoxic. Therefore, the strategies are usually integrated with methods for population reduction, preferably biological control. Push-pull strategies maximize efficacy of behavior-manipulating stimuli through the additive and synergistic effects of integrating their use. By orchestrating a predictable distribution of pests, efficiency of population-reducing components can also be increased. The strategy is a useful tool for integrated pest management programs reducing pesticide input. We describe the principles of the strategy, list the potential components, and present case studies reviewing work on the development and use of push-pull strategies in each of the major areas of pest control.

The recent rate of emergence of pathogenic fungi that are resistant to the limited number of commonly used antifungal agents is unprecedented. The azoles, for example, are used not only for human and animal health care and crop protection but also in antifouling coatings and timber preservation. The ubiquity and multiple uses of azoles have hastened the independent evolution of resistance in many environments. One consequence is an increasing risk in human health care from naturally occurring opportunistic fungal pathogens that have acquired resistance to this broad class of chemicals. To avoid a global collapse in our ability to control fungal infections and to avoid critical failures in medicine and food security, we must improve our stewardship of extant chemicals, promote new antifungal discovery, and leverage emerging technologies for alternative solutions.