Showing papers by "Wageningen University and Research Centre published in 2007"

Adapting Agriculture to Climate Change

Abstract: The strong trends in climate change already evident, the likelihood of further changes occurring, and the increasing scale of potential climate impacts give urgency to addressing agricultural adaptation more coherently. There are many potential adaptation options available for marginal change of existing agricultural systems, often variations of existing climate risk management. We show that implementation of these options is likely to have substantial benefits under moderate climate change for some cropping systems. However, there are limits to their effectiveness under more severe climate changes. Hence, more systemic changes in resource allocation need to be considered, such as targeted diversification of production systems and livelihoods. We argue that achieving increased adaptation action will necessitate integration of climate change-related issues with other risk factors, such as climate variability and market risk, and with other policy domains, such as sustainable development. Dealing with the many barriers to effective adaptation will require a comprehensive and dynamic policy approach covering a range of scales and issues, for example, from the understanding by farmers of change in risk profiles to the establishment of efficient markets that facilitate response strategies. Science, too, has to adapt. Multidisciplinary problems require multidisciplinary solutions, i.e., a focus on integrated rather than disciplinary science and a strengthening of the interface with decision makers. A crucial component of this approach is the implementation of adaptation assessment frameworks that are relevant, robust, and easily operated by all stakeholders, practitioners, policymakers, and scientists.

Botrytis cinerea: the cause of grey mould disease

Abstract: Introduction: Botrytis cinerea (teleomorph: Botryotinia fuckeliana) is an airborne plant pathogen with a necrotrophic lifestyle attacking over 200 crop hosts worldwide. Although there are fungicides for its control, many classes of fungicides have failed due to its genetic plasticity. It has become an important model for molecular study of necrotrophic fungi. Taxonomy: Kingdom: Fungi, phylum: Ascomycota, subphylum: Pezizomycotina, class: Leotiomycetes, order: Helotiales, family: Sclerotiniaceae, genus: Botryotinia. Host range and symptoms: Over 200 mainly dicotyledonous plant species, including important protein, oil, fibre and horticultural crops, are affected in temperate and subtropical regions. It can cause soft rotting of all aerial plant parts, and rotting of vegetables, fruits and flowers post-harvest to produce prolific grey conidiophores and (macro)conidia typical of the disease. Pathogenicity: B. cinerea produces a range of cell-wall-degrading enzymes, toxins and other low-molecular-weight compounds such as oxalic acid. New evidence suggests that the pathogen triggers the host to induce programmed cell death as an attack strategy. Resistance: There are few examples of robust genetic host resistance, but recent work has identified quantitative trait loci in tomato that offer new approaches for stable polygenic resistance in future.

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88

Abstract: The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid. We sequenced the 33.9-megabase genome of A. niger CBS 513.88, the ancestor of currently used enzyme production strains. A high level of synteny was observed with other aspergilli sequenced. Strong function predictions were made for 6,506 of the 14,165 open reading frames identified. A detailed description of the components of the protein secretion pathway was made and striking differences in the hydrolytic enzyme spectra of aspergilli were observed. A reconstructed metabolic network comprising 1,069 unique reactions illustrates the versatile metabolism of A. niger. Noteworthy is the large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors, and the presence of putative gene clusters for fumonisin and ochratoxin A synthesis.

Mycorrhizal responses to biochar in soil – concepts and mechanisms

Abstract: Experiments suggest that biomass-derived black carbon (biochar) affects microbial populations and soil biogeochemistry. Both biochar and mycor- rhizal associations, ubiquitous symbioses in terrestrial ecosystems, are potentially important in various ecosystem services provided by soils, contributing to sustainable plant production, ecosystem restoration, and soil carbon sequestration and hence mitigation of global climate change. As both biochar and mycor- rhizal associations are subject to management, under- standing and exploiting interactions between them could be advantageous. Here we focus on biochar effects on mycorrhizal associations. After reviewing the experimental evidence for such effects, we critically examine hypotheses pertaining to four mechanisms by which biochar could influence mycorrhizal abundance and/or functioning. These mechanisms are (in decreas- ing order of currently available evidence supporting them): (a) alteration of soil physico-chemical proper- ties; (b) indirect effects on mycorrhizae through effects on other soil microbes; (c) plant-fungus signaling interference and detoxification of allelochemicals on biochar; and (d) provision of refugia from fungal grazers. We provide a roadmap for research aimed at testing these mechanistic hypotheses.

CO2 balance of boreal, temperate, and tropical forests derived from a global database

Abstract: Terrestrial ecosystems sequester 2.1 Pg of atmospheric carbon annually. A large amount of the terrestrial sink is realized by forests. However, considerable uncertainties remain regarding the fate of this carbon over both short and long timescales. Relevant data to address these uncertainties are being collected at many sites around the world, but syntheses of these data are still sparse. To facilitate future synthesis activities, we have assembled a comprehensive global database for forest ecosystems, which includes carbon budget variables (fluxes and stocks), ecosystem traits (e.g. leaf area index, age), as well as ancillary site information such as management regime, climate, and soil characteristics. This publicly available database can be used to quantify global, regional or biome-specific carbon budgets; to re-examine established relationships; to test emerging hypotheses about ecosystem functioning [e.g. a constant net ecosystem production (NEP) to gross primary production (GPP) ratio]; and as benchmarks for model evaluations. In this paper, we present the first analysis of this database. We discuss the climatic influences on GPP, net primary production (NPP) and NEP and present the CO2 balances for boreal, temperate, and tropical forest biomes based on micrometeorological, ecophysiological, and biometric flux and inventory estimates. Globally, GPP of forests benefited from higher temperatures and precipitation whereas NPP saturated above either a threshold of 1500 mm precipitation or a mean annual temperature of 10 degrees C. The global pattern in NEP was insensitive to climate and is hypothesized to be mainly determined by nonclimatic conditions such as successional stage, management, site history, and site disturbance. In all biomes, closing the CO2 balance required the introduction of substantial biome-specific closure terms. Nonclosure was taken as an indication that respiratory processes, advection, and non-CO2 carbon fluxes are not presently being adequately accounted for.

Spatial vegetation patterns and imminent desertification in Mediterranean arid ecosystems

Abstract: Arid ecosystems cover about 40% of Earth's land area and are home to over two billion people, yet they remain vulnerable to climate change and human actions. Using numerical simulations, and data from Mediterranean ecosystems in Spain, Morocco and Greece, Kefi et al. show that patch-size distribution of vegetation follows a power law. As grazing pressure increases, patch size deviates from the power law close to the transition to desert conditions. So patch-size distribution may be a useful early warning of desertification. The cover shows an arid landscape (top) in the El Planeron nature reserve in Belchite, Spain, and the lower panels show degradation in this landscape. In a separate paper, Scanlon et al. use satellite imagery to show that the size distribution of tree clusters in the Kalahari basin also follows a scale-free power law. This can be explained by positive feedback associated with preferential environments near existing trees. In News & Views Ricard Sole discusses both papers. COVER IMAGE Sonia & Michael Kefi/ Yolanda Pueyo/ Santiago Begueria Portugues This paper describes and models the effect of grazing on vegetation patchiness in three arid Mediterranean ecosystems. The patch size distribution of the vegetation in these ecosystems follows a power law, which can be explained by invoking local positive interactions among plants. Deviations from power laws occur when grazing pressure is high, and may be a harbinger of imminent desertification. Humans and climate affect ecosystems and their services1, which may involve continuous and discontinuous transitions from one stable state to another2. Discontinuous transitions are abrupt, irreversible and among the most catastrophic changes of ecosystems identified1. For terrestrial ecosystems, it has been hypothesized that vegetation patchiness could be used as a signature of imminent transitions3,4. Here, we analyse how vegetation patchiness changes in arid ecosystems with different grazing pressures, using both field data and a modelling approach. In the modelling approach, we extrapolated our analysis to even higher grazing pressures to investigate the vegetation patchiness when desertification is imminent. In three arid Mediterranean ecosystems in Spain, Greece and Morocco, we found that the patch-size distribution of the vegetation follows a power law. Using a stochastic cellular automaton model, we show that local positive interactions among plants can explain such power-law distributions. Furthermore, with increasing grazing pressure, the field data revealed consistent deviations from power laws. Increased grazing pressure leads to similar deviations in the model. When grazing was further increased in the model, we found that these deviations always and only occurred close to transition to desert, independent of the type of transition, and regardless of the vegetation cover. Therefore, we propose that patch-size distributions may be a warning signal for the onset of desertification.

Economic effects of bovine mastitis and mastitis management: a review.

Abstract: Several studies have been published since 1990 on the economics of mastitis and mastitis management However, hardly any of these studies has discussed the consistency of results with other studies In the present paper, the economic factors associated with mastitis are explained, providing a framework for economic analysis As a second step calculations of the costs of mastitis and the costs in relation to the benefits of mastitis management published since 1990 in peer-reviewed journals are extensively reviewed and analysed The result shows a large variation in the calculated costs and benefits of mastitis and mastitis management between the different studies Moreover, it is clear that important factors were ignored in some of the studies The framework provided in this paper can provide a basis for analysis for future studies on the economics of mastitis and mastitis management

The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization

Abstract: We sequenced and annotated the genome of the filamentous fungus Fusarium graminearum, a major pathogen of cultivated cereals. Very few repetitive sequences were detected, and the process of repeat-induced point mutation, in which duplicated sequences are subject to extensive mutation, may partially account for the reduced repeat content and apparent low number of paralogous (ancestrally duplicated) genes. A second strain of F. graminearum contained more than 10,000 single-nucleotide polymorphisms, which were frequently located near telomeres and within other discrete chromosomal segments. Many highly polymorphic regions contained sets of genes implicated in plant-fungus interactions and were unusually divergent, with higher rates of recombination. These regions of genome innovation may result from selection due to interactions of F. graminearum with its plant hosts.

Identification of a mechanism of photoprotective energy dissipation in higher plants

Abstract: Under conditions of excess sunlight the efficient light-harvesting antenna found in the chloroplast membranes of plants is rapidly and reversibly switched into a photoprotected quenched state in which potentially harmful absorbed energy is dissipated as heat, a process measured as the non-photochemical quenching of chlorophyll fluorescence or qE. Although the biological significance of qE is established, the molecular mechanisms involved are not. LHCII, the main light-harvesting complex, has an inbuilt capability to undergo transformation into a dissipative state by conformational change and it was suggested that this provides a molecular basis for qE, but it is not known if such events occur in vivo or how energy is dissipated in this state. The transition into the dissipative state is associated with a twist in the configuration of the LHCII-bound carotenoid neoxanthin, identified using resonance Raman spectroscopy. Applying this technique to study isolated chloroplasts and whole leaves, we show here that the same change in neoxanthin configuration occurs in vivo, to an extent consistent with the magnitude of energy dissipation. Femtosecond transient absorption spectroscopy, performed on purified LHCII in the dissipative state, shows that energy is transferred from chlorophyll a to a low-lying carotenoid excited state, identified as one of the two luteins (lutein 1) in LHCII. Hence, it is experimentally demonstrated that a change in conformation of LHCII occurs in vivo, which opens a channel for energy dissipation by transfer to a bound carotenoid. We suggest that this is the principal mechanism of photoprotection.

Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry

Abstract: Untargeted metabolomics aims to gather information on as many metabolites as possible in biological systems by taking into account all information present in the data sets. Here we describe a detailed protocol for large-scale untargeted metabolomics of plant tissues, based on reversed phase liquid chromatography coupled to high-resolution mass spectrometry (LC-QTOF MS) of aqueous methanol extracts. Dedicated software, MetAlign, is used for automated baseline correction and alignment of all extracted mass peaks across all samples, producing detailed information on the relative abundance of thousands of mass signals representing hundreds of metabolites. Subsequent statistics and bioinformatics tools can be used to provide a detailed view on the differences and similarities between (groups of) samples or to link metabolomics data to other systems biology information, genetic markers and/or specific quality parameters. The complete procedure from metabolite extraction to assembly of a data matrix with aligned mass signal intensities takes about 6 days for 50 samples.

Properties, production, and applications of camelid single-domain antibody fragments

Abstract: Camelids produce functional antibodies devoid of light chains of which the single N-terminal domain is fully capable of antigen binding. These single-domain antibody fragments (VHHs or Nanobodies®) have several advantages for biotechnological applications. They are well expressed in microorganisms and have a high stability and solubility. Furthermore, they are well suited for construction of larger molecules and selection systems such as phage, yeast, or ribosome display. This minireview offers an overview of (1) their properties as compared to conventional antibodies, (2) their production in microorganisms, with a focus on yeasts, and (3) their therapeutic applications.

Preference for Nature in Urbanized Societies: Stress, Restoration, and the Pursuit of Sustainability

Abstract: Urbanicity presents a challenge for the pursuit of sustainability. High settlement density may offer some environmental, economic, and social advantages, but it can impose psychological demands that people find excessive. These demands of urban life have stimulated a desire for contact with nature through suburban residence, leading to planning and transportation practices that have profound implications for the pursuit of sustainability. Some might dismiss people's desire for contact with nature as the result of an anti-urban bias in conjunction with a romantic view of nature. However, research in environmental psychology suggests that people's desire for contact with nature serves an important adaptive function, namely, psychological restoration. Based on this insight, we offer a perspective on an underlying practical challenge: designing communities that balance settlement density with satisfactory access to nature experience. We discuss research on four issues: how people tend to believe that nature is restorative; how restoration needs and beliefs shape environmental preferences; how well people actually achieve restoration in urban and natural environments; and how contact with nature can promote health. In closing, we consider urban nature as a design option that promotes urban sustainability.

Indicators for biodiversity in agricultural landscapes: a pan‐European study

Abstract: Summary 1. In many European agricultural landscapes, species richness is declining considerably. Studies performed at a very large spatial scale are helpful in understanding the reasons for this decline and as a basis for guiding policy. In a unique, large-scale study of 25 agricultural landscapes in seven European countries, we investigated relationships between species richness in several taxa, and the links between biodiversity and landscape structure and management. 2. We estimated the total species richness of vascular plants, birds and five arthropod groups in each 16-km 2 landscape, and recorded various measures of both landscape structure and intensity of agricultural land use. We studied correlations between taxonomic groups and the effects of landscape and land-use parameters on the number of species in different taxonomic groups. Our statistical approach also accounted for regional variation in species richness unrelated to landscape or land-use factors. 3. The results reveal strong geographical trends in species richness in all taxonomic groups. No single species group emerged as a good predictor of all other species groups. Species richness of all groups increased with the area of semi-natural habitats in the landscape. Species richness of birds and vascular plants was negatively associated with fertilizer use. 4. Synthesis and applications. We conclude that indicator taxa are unlikely to provide an effective means of predicting biodiversity at a large spatial scale, especially where there is large biogeographical variation in species richness. However, a small list of landscape and land-use parameters can be used in agricultural landscapes to infer large-scale patterns of species richness. Our results suggest that to halt the loss of biodiversity in these landscapes, it is important to preserve and, if possible, increase the area of semi-natural habitat.

Shallow lakes theory revisited: various alternative regimes driven by climate, nutrients, depth and lake size

Abstract: Shallow lakes have become the archetypical example of ecosystems with alternative stable states. However, since the early conception of that theory, the image of ecosystem stability has been elaborated for shallow lakes far beyond the simple original model. After discussing how spatial heterogeneity and fluctuation of environmental conditions may affect the stability of lakes, we review work demonstrating that the critical nutrient level for lakes to become turbid is higher for smaller lakes, and seems likely to be affected by climatic change too. We then show how the image of just two contrasting states has been elaborated. Different groups of primary producers may dominate shallow lakes, and such states dominated by a particular group may often represent alternative stable states. In tropical lakes, or small stagnant temperate waters, free-floating plants may represent an alternative stable state. Temperate shallow lakes may be dominated alternatively by charophytes, submerged angiosperms, green algae or cyanobacteria. The change of the lake communities along a gradient of eutrophication may therefore be seen as a continuum in which gradual species replacements are interrupted at critical points by more dramatic shifts to a contrasting alternative regime dominated by different species. The originally identified shift between a clear and a turbid state remains one of the more dramatic examples, but is surely not the only discontinuity that can be observed in the response of these ecosystems to environmental change.

Ecology: managing evolving fish stocks.

Abstract: Evolutionary impact assessment is a framework for quantifying the effects of harvest-induced evolution on the utility generated by fish stocks

Diversity of the human gastrointestinal tract microbiota revisited.

Abstract: Since the early days of microbiology, more than a century ago, representatives of over 400 different microbial species have been isolated and fully characterized from human gastrointestinal samples. However, during the past decade molecular ecological studies based on ribosomal RNA (rRNA) sequences have revealed that cultivation has been able only to access a small fraction of the microbial diversity within the gastrointestinal tract. The increasing number of deposited rRNA sequences calls for the setting up a curated database that allows handling of the excessive degree of redundancy that threatens the usability of public databases. The integration of data from cultivation-based studies and molecular inventories of small subunit (SSU) rRNA diversity, presented here for the first time, provides a systematic framework of the microbial diversity in the human gastrointestinal tract of more than 1000 different species-level phylogenetic types (phylotypes). Such knowledge is essential for the design of high-throughput approaches such as phylogenetic DNA microarrays for the comprehensive analysis of gastrointestinal tract microbiota at multiple levels of taxonomic resolution. Development of such approaches is likely to be pivotal to generating novel insights in microbiota functionality in health and disease.

Intestinal Integrity and Akkermansia muciniphila, a Mucin-Degrading Member of the Intestinal Microbiota Present in Infants, Adults, and the Elderly

Abstract: Fluorescence in situ hybridization and real-time PCR analysis targeting the 16S rRNA gene of Akkermansia muciniphila were performed to determine its presence in the human intestinal tract. These techniques revealed that an A. muciniphila-like bacterium is a common member of the human intestinal tract and that its colonization starts in early life and develops within a year to a level close to that observed in adults (10(8) cells/g) but decreases (P < 0.05) in the elderly.