Université Paul-Valéry Montpellier

Fungi are an understudied, biotechnologically valuable group of organisms. Due to the immense range of habitats that fungi inhabit, and the consequent need to compete against a diverse array of other fungi, bacteria, and animals, fungi have developed numerous survival mechanisms. The unique attributes of fungi thus herald great promise for their application in biotechnology and industry. Moreover, fungi can be grown with relative ease, making production at scale viable. The search for fungal biodiversity, and the construction of a living fungi collection, both have incredible economic potential in locating organisms with novel industrial uses that will lead to novel products. This manuscript reviews fifty ways in which fungi can potentially be utilized as biotechnology. We provide notes and examples for each potential exploitation and give examples from our own work and the work of other notable researchers. We also provide a flow chart that can be used to convince funding bodies of the importance of fungi for biotechnological research and as potential products. Fungi have provided the world with penicillin, lovastatin, and other globally significant medicines, and they remain an untapped resource with enormous industrial potential.

Understanding, modeling, and predicting the impact of global change on ecosystem functioning across biogeographical gradients can benefit from enhanced capacity to represent biota as a continuous distribution of traits. However, this is a challenge for the field of biogeography historically grounded on the species concept. Here we focus on the newly emergent field of functional biogeography: the study of the geographic distribution of trait diversity across organizational levels. We show how functional biogeography bridges species-based biogeography and earth science to provide ideas and tools to help explain gradients in multifaceted diversity (including species, functional, and phylogenetic diversities), predict ecosystem functioning and services worldwide, and infuse regional and global conservation programs with a functional basis. Although much recent progress has been made possible because of the rising of multiple data streams, new developments in ecoinformatics, and new methodological advances, future directions should provide a theoretical and comprehensive framework for the scaling of biotic interactions across trophic levels and its ecological implications.

Abstract Biological coloration presents a canvas for the study of ecological and evolutionary processes. Enduring interest in colour‐based phenotypes has driven, and been driven by, improved techniques for quantifying colour patterns in ever‐more relevant ways, yet the need for flexible, open frameworks for data processing and analysis persists. Here we introduce pavo 2 , the latest iteration of the r package pavo . This release represents the extensive refinement and expansion of existing methods, as well as a suite of new tools for the cohesive analysis of the spectral and (now) spatial structure of colour patterns and perception. At its core, the package retains a broad focus on (a) the organization and processing of spectral and spatial data, and tools for the alternating (b) visualization, and (c) analysis of data. Significantly, pavo 2 introduces image‐analysis capabilities, providing a cohesive workflow for the comprehensive analysis of colour patterns. We demonstrate the utility of pavo with a brief example centred on mimicry in Heliconius butterflies. Drawing on visual modelling, adjacency, and boundary strength analyses, we show that the combined spectral (colour and luminance) and spatial (pattern element distribution and boundary salience) features of putative models and mimics are closely aligned. pavo 2 offers a flexible and reproducible environment for the analysis of colour, with renewed potential to assist researchers in answering fundamental questions in sensory ecology and evolution.

Biological responses to climate change have been widely documented across taxa and regions, but it remains unclear whether species are maintaining a good match between phenotype and environment, i.e. whether observed trait changes are adaptive. Here we reviewed 10,090 abstracts and extracted data from 71 studies reported in 58 relevant publications, to assess quantitatively whether phenotypic trait changes associated with climate change are adaptive in animals. A meta-analysis focussing on birds, the taxon best represented in our dataset, suggests that global warming has not systematically affected morphological traits, but has advanced phenological traits. We demonstrate that these advances are adaptive for some species, but imperfect as evidenced by the observed consistent selection for earlier timing. Application of a theoretical model indicates that the evolutionary load imposed by incomplete adaptive responses to ongoing climate change may already be threatening the persistence of species.

Abstract. Biomass burning impacts vegetation dynamics, biogeochemical cycling, atmospheric chemistry, and climate, with sometimes deleterious socio-economic impacts. Under future climate projections it is often expected that the risk of wildfires will increase. Our ability to predict the magnitude and geographic pattern of future fire impacts rests on our ability to model fire regimes, using either well-founded empirical relationships or process-based models with good predictive skill. While a large variety of models exist today, it is still unclear which type of model or degree of complexity is required to model fire adequately at regional to global scales. This is the central question underpinning the creation of the Fire Model Intercomparison Project (FireMIP), an international initiative to compare and evaluate existing global fire models against benchmark data sets for present-day and historical conditions. In this paper we review how fires have been represented in fire-enabled dynamic global vegetation models (DGVMs) and give an overview of the current state of the art in fire-regime modelling. We indicate which challenges still remain in global fire modelling and stress the need for a comprehensive model evaluation and outline what lessons may be learned from FireMIP.

The processes causing the latitudinal gradient in species richness remain elusive. Ecological theories for the origin of biodiversity gradients, such as competitive exclusion, neutral dynamics, and environmental filtering, make predictions for how functional diversity should vary at the alpha (within local assemblages), beta (among assemblages), and gamma (regional pool) scales. We test these predictions by quantifying hypervolumes constructed from functional traits representing major axes of plant strategy variation (specific leaf area, plant height, and seed mass) in tree assemblages spanning the temperate and tropical New World. Alpha-scale trait volume decreases with absolute latitude and is often lower than sampling expectation, consistent with environmental filtering theory. Beta-scale overlap decays with geographic distance fastest in the temperate zone, again consistent with environmental filtering theory. In contrast, gamma-scale trait space shows a hump-shaped relationship with absolute latitude, consistent with no theory. Furthermore, the overall temperate trait hypervolume was larger than the overall tropical hypervolume, indicating that the temperate zone permits a wider range of trait combinations or that niche packing is stronger in the tropical zone. Although there are limitations in the data, our analyses suggest that multiple processes have shaped trait diversity in trees, reflecting no consistent support for any one theory.

Plant adaptation to drought has been extensively studied at many scales from ecology to molecular biology across a large range of model species. However, the conceptual frameworks underpinning the definition of plant strategies, and the terminology used across the different disciplines and scales are not analogous. 'Drought resistance' for instance refers to plant responses as different as the maintenance of growth and productivity in crops, to the survival and recovery in perennial woody or grassland species. Therefore, this paper aims to propose a unified conceptual framework of plant adaptive strategies to drought based on a revised terminology in order to enhance comparative studies. Ecological strategies encapsulate plant adaptation to multidimensional variation in resource variability but cannot account for the dynamic and short-term responses to fluctuations in water availability. Conversely, several plant physiological strategies have been identified along the mono-dimensional gradient of water availability in a given environment. According to a revised terminology, dehydration escape, dehydration avoidance, dehydration tolerance, dormancy, and desiccation tolerance are clearly distinguishable. Their sequential expression is expressed as water deficit increases while cavitation tolerance is proposed here to be a major hydraulic strategy underpinning adaptive responses to drought of vascular plants. This continuum of physiological strategies can be interpreted in the context of the ecological trade-off between water-acquisition vs. water-conservation, since growth maintenance is associated with fast water use under moderate drought while plant survival after growth cessation is associated with slow water use under severe drought. Consequently, the distinction between 'drought resistance' and 'drought survival', is emphasized as crucial to ensure a correct interpretation of plant strategies since 'knowing when not to grow' does not confer 'drought resistance' but may well enhance 'drought survival'. This framework proposal should improve cross-fertilization between disciplines to help tackle the increasing worldwide challenges that drought poses to plant adaptation.

Plants respond to resource stress by changing multiple aspects of their biomass allocation, morphology, physiology and architecture. To date, we lack an integrated view of the relative importance of these plastic responses in alleviating resource stress and of the consistency/variability of these responses among species. We subjected nine species (legumes, forbs and graminoids) to nitrogen and/or light shortages and measured 11 above-ground and below-ground trait adjustments critical in the alleviation of these stresses (plus several underlying traits). Nine traits out of 11 showed adjustments that improved plants' potential capacity to acquire the limiting resource at a given time. Above ground, aspects of plasticity in allocation, morphology, physiology and architecture all appeared important in improving light capture, whereas below ground, plasticity in allocation and physiology were most critical to improving nitrogen acquisition. Six traits out of 11 showed substantial heterogeneity in species plasticity, with little structuration of these differences within trait covariation syndromes. Such comprehensive assessment of the complex nature of phenotypic responses of plants to multiple stress factors, and the comparison of plant responses across multiple species, makes a clear case for the high (but largely overlooked) diversity of potential plastic responses of plants, and for the need to explore the potential rules structuring them.

The Routledge Handbook of Research Methods for Social-Ecological Systems provides a synthetic guide to the range of methods that can be employed in social-ecological systems (SES) research.\nThe book is primarily targeted at graduate students, lecturers and researchers working on SES, and has been written in a style that is accessible to readers entering the field from a variety of different disciplinary backgrounds. Each chapter discusses the types of SES questions to which the particular methods are suited and the potential resources and skills required for their implementation, and provides practical examples of the application of the methods. In addition, the book contains a conceptual and practical introduction to SES research, a discussion of key gaps and frontiers in SES research methods, and a glossary of key terms in SES research. Contributions from 97 different authors, situated at SES research hubs in 16 countries around the world, including South Africa, Sweden, Germany and Australia, bring a wealth of expertise and experience to this book.\nThe first book to provide a guide and introduction specifically focused on methods for studying SES, this book will be of great interest to students and scholars of sustainability science, environmental management, global environmental change studies and environmental governance. The book will also be of interest to upper-level undergraduates and professionals working at the science–policy interface in the environmental arena.

Polar ice core records attest to a colossal volcanic eruption that took place ca. A.D. 1257 or 1258, most probably in the tropics. Estimates based on sulfate deposition in these records suggest that it yielded the largest volcanic sulfur release to the stratosphere of the past 7,000 y. Tree rings, medieval chronicles, and computational models corroborate the expected worldwide atmospheric and climatic effects of this eruption. However, until now there has been no convincing candidate for the mid-13th century "mystery eruption." Drawing upon compelling evidence from stratigraphic and geomorphic data, physical volcanology, radiocarbon dating, tephra geochemistry, and chronicles, we argue the source of this long-sought eruption is the Samalas volcano, adjacent to Mount Rinjani on Lombok Island, Indonesia. At least 40 km(3) (dense-rock equivalent) of tephra were deposited and the eruption column reached an altitude of up to 43 km. Three principal pumice fallout deposits mantle the region and thick pyroclastic flow deposits are found at the coast, 25 km from source. With an estimated magnitude of 7, this event ranks among the largest Holocene explosive eruptions. Radiocarbon dates on charcoal are consistent with a mid-13th century eruption. In addition, glass geochemistry of the associated pumice deposits matches that of shards found in both Arctic and Antarctic ice cores, providing compelling evidence to link the prominent A.D. 1258/1259 ice core sulfate spike to Samalas. We further constrain the timing of the mystery eruption based on tephra dispersal and historical records, suggesting it occurred between May and October A.D. 1257.

Summary In a rapidly changing world, ecology has the potential to move from empirical and conceptual stages to application and management issues. It is now possible to make large‐scale predictions up to continental or global scales, ranging from the future distribution of biological diversity to changes in ecosystem functioning and services. With these recent developments, ecology has a historical opportunity to become a major actor in the development of a sustainable human society. With this opportunity, however, also comes an important responsibility in developing appropriate predictive models, correctly interpreting their outcomes and communicating their limitations. There is also a danger that predictions grow faster than our understanding of ecological systems, resulting in a gap between the scientists generating the predictions and stakeholders using them (conservation biologists, environmental managers, journalists, policymakers). Here, we use the context provided by the current surge of ecological predictions on the future of biodiversity to clarify what prediction means, and to pinpoint the challenges that should be addressed in order to improve predictive ecological models and the way they are understood and used. Synthesis and applications . Ecologists face several challenges to ensure the healthy development of an operational predictive ecological science: (i) clarity on the distinction between explanatory and anticipatory predictions; (ii) developing new theories at the interface between explanatory and anticipatory predictions; (iii) open data to test and validate predictions; (iv) making predictions operational; and (v) developing a genuine ethics of prediction.

There is considerable evidence that biodiversity promotes multiple ecosystem functions (multifunctionality), thus ensuring the delivery of ecosystem services important for human well-being. However, the mechanisms underlying this relationship are poorly understood, especially in natural ecosystems. We develop a novel approach to partition biodiversity effects on multifunctionality into three mechanisms and apply this to European forest data. We show that throughout Europe, tree diversity is positively related with multifunctionality when moderate levels of functioning are required, but negatively when very high function levels are desired. For two well-known mechanisms, 'complementarity' and 'selection', we detect only minor effects on multifunctionality. Instead a third, so far overlooked mechanism, the 'jack-of-all-trades' effect, caused by the averaging of individual species effects on function, drives observed patterns. Simulations demonstrate that jack-of-all-trades effects occur whenever species effects on different functions are not perfectly correlated, meaning they may contribute to diversity-multifunctionality relationships in many of the world's ecosystems.

Abstract. This paper presents a new global burned area (BA) product, generated from the Moderate Resolution Imaging Spectroradiometer (MODIS) red (R) and near-infrared (NIR) reflectances and thermal anomaly data, thus providing the highest spatial resolution (approx. 250 m) among the existing global BA datasets. The product includes the full times series (2001–2016) of the Terra-MODIS archive. The BA detection algorithm was based on monthly composites of daily images, using temporal and spatial distance to active fires. The algorithm has two steps, the first one aiming to reduce commission errors by selecting the most clearly burned pixels (seeds), and the second one targeting to reduce omission errors by applying contextual analysis around the seed pixels. This product was developed within the European Space Agency's (ESA) Climate Change Initiative (CCI) programme, under the Fire Disturbance project (Fire_cci). The final output includes two types of BA files: monthly full-resolution continental tiles and biweekly global grid files at a degraded resolution of 0.25∘. Each set of products includes several auxiliary variables that were defined by the climate users to facilitate the ingestion of the product into global dynamic vegetation and atmospheric emission models. Average annual burned area from this product was 3.81 Mkm2, with maximum burning in 2011 (4.1 Mkm2) and minimum in 2013 (3.24 Mkm2). The validation was based on a stratified random sample of 1200 pairs of Landsat images, covering the whole globe from 2003 to 2014. The validation indicates an overall accuracy of 0.9972, with much higher errors for the burned than the unburned category (global omission error of BA was estimated as 0.7090 and global commission as 0.5123). These error values are similar to other global BA products, but slightly higher than the NASA BA product (named MCD64A1, which is produced at 500 m resolution). However, commission and omission errors are better compensated in our product, with a tendency towards BA underestimation (relative bias −0.4033), as most existing global BA products. To understand the value of this product in detecting small fire patches (<100 ha), an additional validation sample of 52 Sentinel-2 scenes was generated specifically over Africa. Analysis of these results indicates a better detection accuracy of this product for small fire patches (<100 ha) than the equivalent 500 m MCD64A1 product, although both have high errors for these small fires. Examples of potential applications of this dataset to fire modelling based on burned patches analysis are included in this paper. The datasets are freely downloadable from the Fire_cci website (https://www.esa-fire-cci.org/, last access: 10 November 2018) and their repositories (pixel at full resolution: https://doi.org/cpk7, and grid: https://doi.org/gcx9gf).

Abstract Aims Vegetation‐plot records provide information on the presence and cover or abundance of plants co‐occurring in the same community. Vegetation‐plot data are spread across research groups, environmental agencies and biodiversity research centers and, thus, are rarely accessible at continental or global scales. Here we present the sPlot database, which collates vegetation plots worldwide to allow for the exploration of global patterns in taxonomic, functional and phylogenetic diversity at the plant community level. Results sPlot version 2.1 contains records from 1,121,244 vegetation plots, which comprise 23,586,216 records of plant species and their relative cover or abundance in plots collected worldwide between 1885 and 2015. We complemented the information for each plot by retrieving climate and soil conditions and the biogeographic context (e.g., biomes) from external sources, and by calculating community‐weighted means and variances of traits using gap‐filled data from the global plant trait database TRY. Moreover, we created a phylogenetic tree for 50,167 out of the 54,519 species identified in the plots. We present the first maps of global patterns of community richness and community‐weighted means of key traits. Conclusions The availability of vegetation plot data in sPlot offers new avenues for vegetation analysis at the global scale.

Increasing evidence-synthesized in this paper-shows that economic growth contributes to biodiversity loss via greater resource consumption and higher emissions. Nonetheless, a review of international biodiversity and sustainability policies shows that the majority advocate economic growth. Since improvements in resource use efficiency have so far not allowed for absolute global reductions in resource use and pollution, we question the support for economic growth in these policies, where inadequate attention is paid to the question of how growth can be decoupled from biodiversity loss. Drawing on the literature about alternatives to economic growth, we explore this contradiction and suggest ways forward to halt global biodiversity decline. These include policy proposals to move beyond the growth paradigm while enhancing overall prosperity, which can be implemented by combining top-down and bottom-up governance across scales. Finally, we call the attention of researchers and policy makers to two immediate steps: acknowledge the conflict between economic growth and biodiversity conservation in future policies; and explore socioeconomic trajectories beyond economic growth in the next generation of biodiversity scenarios.

Dispersal is a process of central importance for the ecological and evolutionary dynamics of populations and communities, because of its diverse consequences for gene flow and demography. It is subject to evolutionary change, which begs the question, what is the genetic basis of this potentially complex trait? To address this question, we (i) review the empirical literature on the genetic basis of dispersal, (ii) explore how theoretical investigations of the evolution of dispersal have represented the genetics of dispersal, and (iii) discuss how the genetic basis of dispersal influences theoretical predictions of the evolution of dispersal and potential consequences. Dispersal has a detectable genetic basis in many organisms, from bacteria to plants and animals. Generally, there is evidence for significant genetic variation for dispersal or dispersal-related phenotypes or evidence for the micro-evolution of dispersal in natural populations. Dispersal is typically the outcome of several interacting traits, and this complexity is reflected in its genetic architecture: while some genes of moderate to large effect can influence certain aspects of dispersal, dispersal traits are typically polygenic. Correlations among dispersal traits as well as between dispersal traits and other traits under selection are common, and the genetic basis of dispersal can be highly environment-dependent. By contrast, models have historically considered a highly simplified genetic architecture of dispersal. It is only recently that models have started to consider multiple loci influencing dispersal, as well as non-additive effects such as dominance and epistasis, showing that the genetic basis of dispersal can influence evolutionary rates and outcomes, especially under non-equilibrium conditions. For example, the number of loci controlling dispersal can influence projected rates of dispersal evolution during range shifts and corresponding demographic impacts. Incorporating more realism in the genetic architecture of dispersal is thus necessary to enable models to move beyond the purely theoretical towards making more useful predictions of evolutionary and ecological dynamics under current and future environmental conditions. To inform these advances, empirical studies need to answer outstanding questions concerning whether specific genes underlie dispersal variation, the genetic architecture of context-dependent dispersal phenotypes and behaviours, and correlations among dispersal and other traits.

The canonical model of sex-chromosome evolution predicts that, as recombination is suppressed along sex chromosomes, gametologs will progressively differentiate, eventually becoming heteromorphic. However, there are numerous examples of homomorphic sex chromosomes across the tree of life. This homomorphy has been suggested to result from frequent sex-chromosome turnovers, yet we know little about which forces drive them. Here, we describe an extremely fast rate of turnover among 28 species of Ranidae. Transitions are not random, but converge on several chromosomes, potentially due to genes they harbour. Transitions also preserve the ancestral pattern of male heterogamety, in line with the 'hot-potato' model of sex-chromosome transitions, suggesting a key role for mutation-load accumulation in non-recombining genomic regions. The importance of mutation-load selection in frogs might result from the extreme heterochiasmy they exhibit, making frog sex chromosomes differentiate immediately from emergence and across their entire length.

Integrating scientific and local knowledge within disaster risk reduction (DRR) using methods that encourage knowledge exchange and two‐way dialogue is a difficult yet important task. This article shows how participatory mapping can help in fostering integrative DRR through the involvement of a large range of stakeholders. It draws on a project conducted in the municipality of Masantol, Philippines that is regularly affected by flooding and other natural hazards. Participatory 3‐Dimensional Mapping, or P3DM, has been used for both risk assessment and DRR planning. P3DM facilitates the interpretation, assimilation and understanding of geo‐referenced data by making them visible and tangible to everyone. Given that maps are scaled and geo‐referenced, P3DM also helps in incorporating both local and scientific knowledge through a two‐way dialogue in DRR.

This article is based on a long consideration of the concept of small business after 30 years of conceptual development. Most, if not all, researchers in small business have accepted the idea that small business is specific (the preponderant role of the owner-manager, low level of functional breakdown, intuitive strategy, etc.). However, the somewhat excessive assertion of this idea may suggest that all small firms adopt a specific management method, with the result that management specificity becomes a universal principle. If we allow that small business management can be specific, we must also allow the corollary of this statement, namely the possibility of denaturing (loss of specificity). In other words, a small-sized firm does not necessarily have to adhere to the classical management method. The authors of this article advocate a contingency approach to small business managerial specificity that would allow for the definition of a validity framework for the thesis of small business managerial specificity.

In invertebrates, defensins were found in arthropods and in the mussels. Here, we report for the first time the identification and characterization of a defensin (Cg-Def) from an oyster. Cg-def mRNA was isolated from Crassostrea gigas mantle using an expressed sequence tag approach. To gain insight into potential roles of Cg-Def in oyster immunity, we produced the recombinant peptide in Escherichia coli, characterized its antimicrobial activities, determined its solution structure by NMR spectroscopy, and quantified its gene expression in vivo following bacterial challenge of oysters. Recombinant Cg-Def was active in vitro against Gram-positive bacteria but showed no or limited activities against Gram-negative bacteria and fungi. The activity of Cg-Def was retained in vitro at a salt concentration similar to that of seawater. The Cg-Def structure shares the so-called cystine-stabilized α-β motif (CS-αβ) with arthropod defensins but is characterized by the presence of an additional disulfide bond, as previously observed in the mussel defensin (MGD-1). Nevertheless, despite a similar global fold, the Cg-Def and MGD-1 structures mainly differ by the size of their loops and by the presence of two aspartic residues in Cg-Def. Distribution of Cg-def mRNA in various oyster tissues revealed that Cg-def is mainly expressed in mantle edge where it was detected by mass spectrometry analyses. Furthermore, we observed that the Cg-def messenger concentration was unchanged after bacterial challenge. Our results suggest that Cg-def gene is continuously expressed in the mantle and would play a key role in oyster by providing a first line of defense against pathogen colonization. In invertebrates, defensins were found in arthropods and in the mussels. Here, we report for the first time the identification and characterization of a defensin (Cg-Def) from an oyster. Cg-def mRNA was isolated from Crassostrea gigas mantle using an expressed sequence tag approach. To gain insight into potential roles of Cg-Def in oyster immunity, we produced the recombinant peptide in Escherichia coli, characterized its antimicrobial activities, determined its solution structure by NMR spectroscopy, and quantified its gene expression in vivo following bacterial challenge of oysters. Recombinant Cg-Def was active in vitro against Gram-positive bacteria but showed no or limited activities against Gram-negative bacteria and fungi. The activity of Cg-Def was retained in vitro at a salt concentration similar to that of seawater. The Cg-Def structure shares the so-called cystine-stabilized α-β motif (CS-αβ) with arthropod defensins but is characterized by the presence of an additional disulfide bond, as previously observed in the mussel defensin (MGD-1). Nevertheless, despite a similar global fold, the Cg-Def and MGD-1 structures mainly differ by the size of their loops and by the presence of two aspartic residues in Cg-Def. Distribution of Cg-def mRNA in various oyster tissues revealed that Cg-def is mainly expressed in mantle edge where it was detected by mass spectrometry analyses. Furthermore, we observed that the Cg-def messenger concentration was unchanged after bacterial challenge. Our results suggest that Cg-def gene is continuously expressed in the mantle and would play a key role in oyster by providing a first line of defense against pathogen colonization. Antimicrobial peptides (AMPs) 5The abbreviations used are: AMPantimicrobial peptideCg-DefC. gigas defensinDGdistance geometryDQF-COSYtwo-dimensional double-quantum filter correlation spectroscopyMALDI-TOF MSmatrix-assisted laser desorption/ionization time of flight mass spectrometryESI-MSelectrospray ionization mass spectrometryNOEnuclear Overhauser effectNOESYtwo-dimensional nuclear Overhauser effect spectroscopyRP-HPLCreversed-phase high performance liquid chromatographyr.m.s.d.root mean square deviationTOCSYtotal correlation spectroscopyRTreverse transcriptaseGAPDHglyceraldehyde-3-phosphate dehydrogenaseMICminimum inhibitory concentrationEFelongation factorIfremerInstitut Francais de Recherche pour l'Exploitation de la MerCFUcolony forming units.5The abbreviations used are: AMPantimicrobial peptideCg-DefC. gigas defensinDGdistance geometryDQF-COSYtwo-dimensional double-quantum filter correlation spectroscopyMALDI-TOF MSmatrix-assisted laser desorption/ionization time of flight mass spectrometryESI-MSelectrospray ionization mass spectrometryNOEnuclear Overhauser effectNOESYtwo-dimensional nuclear Overhauser effect spectroscopyRP-HPLCreversed-phase high performance liquid chromatographyr.m.s.d.root mean square deviationTOCSYtotal correlation spectroscopyRTreverse transcriptaseGAPDHglyceraldehyde-3-phosphate dehydrogenaseMICminimum inhibitory concentrationEFelongation factorIfremerInstitut Francais de Recherche pour l'Exploitation de la MerCFUcolony forming units. are important components of the innate immune system that have been conserved during evolution (1Yang D. Biragyn A. Kwak L.W. Oppenheim J.J. Trends Immunol. 2002; 23: 291-296Abstract Full Text Full Text PDF PubMed Scopus (614) Google Scholar). They constitute a first line of host defense against pathogens in plants and animals (2Bulet P. Stocklin R. Menin L. Immunol. Rev. 2004; 198: 169-184Crossref PubMed Scopus (849) Google Scholar, 3Boman H.G. J. Intern. Med. 2003; 254: 197-215Crossref PubMed Scopus (868) Google Scholar). We estimate that more than 1000 antimicrobial peptides have been described at the level of their primary structure (2Bulet P. Stocklin R. Menin L. Immunol. Rev. 2004; 198: 169-184Crossref PubMed Scopus (849) Google Scholar). They are gathered in the Antimicrobial Sequence Database (www.bbc-m.units.it/∼tossi/amsdb.html). AMPs can be classified into three major groups: (i) linear peptides that form amphipathic α-helices, (ii) cyclic peptides containing cysteine-residue engaged in disulfide bonds, and (iii) peptides with an overrepresentation in certain amino acids (proline, arginine, glycine, or histidine). Despite their great diversity in terms of size, primary structure, amino acid composition, and mode of action, most AMPs are characterized by the preponderance in cationic and hydrophobic amino acids (2Bulet P. Stocklin R. Menin L. Immunol. Rev. 2004; 198: 169-184Crossref PubMed Scopus (849) Google Scholar). In most of the cases, this amphipathic character is considered as crucial for the interaction of the effective peptide with the membrane of sensitive microorganisms. This first interaction seems to be essential whatever the exact mode of action: (i) through disruption of their negatively charged cytoplasmic membranes or (ii) through killing following translocation into the bacteria without membrane lyses and binding to a specific target protein (4Brogden K.A. Nat. Rev. Microbiol. 2005; 3: 238-250Crossref PubMed Scopus (4314) Google Scholar). Depending on their tissue distribution, AMPs ensure either a systemic or a local protection of the organism against pathogens. antimicrobial peptide C. gigas defensin distance geometry two-dimensional double-quantum filter correlation spectroscopy matrix-assisted laser desorption/ionization time of flight mass spectrometry electrospray ionization mass spectrometry nuclear Overhauser effect two-dimensional nuclear Overhauser effect spectroscopy high performance liquid mean square correlation spectroscopy inhibitory concentration Francais de Recherche pour l'Exploitation de la forming units. antimicrobial peptide C. gigas defensin distance geometry two-dimensional double-quantum filter correlation spectroscopy matrix-assisted laser desorption/ionization time of flight mass spectrometry electrospray ionization mass spectrometry nuclear Overhauser effect two-dimensional nuclear Overhauser effect spectroscopy high performance liquid mean square correlation spectroscopy inhibitory concentration Francais de Recherche pour l'Exploitation de la forming units. the defensins an important peptide They are and in and tissues that are in host defense against are cationic in size, containing three or disulfide and are active against a of bacteria and C. P. R. L. L. R. P. 2004; PubMed Scopus Google Scholar). The defensins can be into three the and are on the of the of their and more the cyclic J. J. J. Full Text Full Text PDF PubMed Scopus Google Scholar). The are produced and in of animals and in have been in and were to be or expressed H.G. J. Intern. Med. 2003; 254: 197-215Crossref PubMed Scopus (868) Google Scholar, A. J. 2005; Full Text Full Text PDF PubMed Scopus Google Scholar, Microbiol. 2002; PubMed Google Scholar). In from their antimicrobial activities, defensins play an important role in and of specific P. Microbiol. 2003; PubMed Scopus Google Scholar). In with the of the on their structure, the in of the defensins is on their (2Bulet P. Stocklin R. Menin L. Immunol. Rev. 2004; 198: 169-184Crossref PubMed Scopus (849) Google Scholar). The defensins differ from the defensins by their disulfide P. C. PubMed Scopus Google Scholar). are the most of and defensins have been isolated in arthropods and and (2Bulet P. Stocklin R. Menin L. Immunol. Rev. 2004; 198: 169-184Crossref PubMed Scopus (849) Google Scholar). of the defensins were isolated from the of in and defensins are in of animals (2Bulet P. Stocklin R. Menin L. Immunol. Rev. 2004; 198: 169-184Crossref PubMed Scopus (849) Google Scholar). In AMPs have been in as in the C. P. J. Full Text Full Text PDF PubMed Scopus Google and P. PubMed Scopus Google Scholar). defensins from the have been found to sequence to defensins from to in antimicrobial activities have been detected in the of AMPs have been characterized despite to from and by using de J. J. Immunol. Rev. 2004; 198: PubMed Scopus Google Scholar). In the we report the characterization of the first in oyster. The Crassostrea gigas defensin (Cg-Def) mRNA been isolated from mantle edge using the expressed sequence tag approach. 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R. 2003; PubMed Scopus Google Scholar). Recombinant Cg-Def was expressed in with the The were at to in of of and of with of was with at for bacterial were by and at The were by bacteria in in by at for using a The was by in a at for at to protein and of Recombinant Cg-Def protein was by by with acid at a of in for at were with two of against acid in membranes and The at the Cg-Def was to by the in of to and of the for in the at The was by of by and the peptide was in at in the presence of The was to using a high performance liquid and the of were The peptide was with a at a of on a The of the Cg-Def was at in at during the Cg-Def was to using an additional using the and as the peptide was at in a solution containing and and in the presence of and R. J. 2003; PubMed Scopus Google Scholar). the Cg-Def was to by using a as described was by and the peptide concentration was by amino acid and at on the of the of the peptides were determined using matrix-assisted laser ionization mode mass spectrometry and electrospray ionization mass spectrometry Antimicrobial activity of recombinant Cg-Def was against the Gram-positive the Gram-negative and The activity of the peptide was against the following and inhibitory were determined in by the liquid on the described by and C. P. in Scholar). was used for and was used for was in at with was at on a or effect was by following a at was with of at a concentration the was with of an of at a of in and at of were after and of on The of was after a at a the bacterial was with NMR of Cg-Def were either in a or in to a The was to the by of or and at with a They are for the were with to to the NMR were on a with a and were in the of In the was at the of the at the spectroscopy PubMed Scopus Google Scholar, J. spectroscopy A. J. Scholar, J. and nuclear Overhauser effect spectroscopy D. J. were in the mode using the D. R. A. J. Scholar). in the was by the J. PubMed Scopus Google for the where a was The were with a time of and with of and were by using the The was using the described by NMR of and Google Scholar). To the the was in at and first a and an was for their and were from two at and with a time of and into to their and were into and distance The were from the and the were from the of the and To the distance and were used as in the that with in P. C. J. PubMed Scopus Google Scholar). In the first of the an of structures was from a structure with and In disulfide was used as were considered as the distance was than and the was than to the Cg-Def structure, and the of the and the disulfide were used as of was and the structures with a of of were with The was with R. J. PubMed Scopus Google and the of the structure and the were determined with D. P. 23: PubMed Scopus Google Scholar). The and of Cg-Def are in the and the of C. gigas by and tissue from C. gigas was with liquid and to the mantle was in using an and at for were at for at and the was by on with with peptides were with containing The was in and a high performance liquid on an and was using a at a of were in of and for antimicrobial the active were in a by on a using a at a of The were by and of Cg-def C. gigas were by with bacteria The was with three bacterial and The bacterial were in at for and in for were by and in concentration was from the at of to tissue were at two and and in into and at in of were following and with The were in to at were used in for was using of with in a containing and in were with the in the presence of with the following and as and The gene the was used as the and were and were the following of and expression level the were determined for using the of was on and The of was determined as the mean of three The expression of Cg-def was on the of of from oyster the and expressed in to the gene The expression of Cg-Def was on the for expression results PubMed Scopus Google Scholar). Cg-def and of C. gigas defensin (Cg-Def) was by of on a C. gigas mantle edge as described The oyster Cg-def a of a containing a sequence at of the and a The a acid The amino acid sequence with a and the for is most after the the in as by Cg-Def is as a with a an as observed with the mussel or the The amino acid sequence of the peptide was with defensins from the defensin in and that defensins from and and observed for the mussel defensins MGD-1 and Cg-Def is an of this to the presence of two Cg-Def shares of with MGD-1 from but a of at the of the was with defensin from the and the The of the defensin to the so-called defensin a high of with Cg-Def and the mussel defensins Trends 2003; Full Text Full Text PDF PubMed Scopus Google Scholar). a acid with to the arthropod and defensins been isolated from the and of the gene a the The of Cg-def is similar to that of the mussel and defensin Trends 2003; Full Text Full Text PDF PubMed Scopus Google Scholar). the of the arthropod and defensin that a (i) the the defensin is by (ii) the the the defensin for a level of Trends 2003; Full Text Full Text PDF PubMed Scopus Google Scholar). of the sequence from the for observed in of expressed during and and and and and and expressed in a and and of Recombinant of Cg-Def for of its activity and its structure, Cg-Def was expressed in with the Recombinant protein was by from the bacteria with and Cg-Def was by and its was by and mass spectrometry and The of Cg-Def was two after with Cg-Def was during at in the presence of a The was by at an additional more hydrophobic this hydrophobic was found to a with a mass of The by is in with the mass of This that the recombinant Cg-Def its residues as described by R. J. 2003; PubMed Scopus Google the of and was to the of Cg-Def this the recombinant Cg-Def was found to have a mass by that is in to the mass The peptide was to antimicrobial and NMR spectroscopy Antimicrobial of antimicrobial activity of the recombinant Cg-Def was determined against a of Gram-positive and Gram-negative bacteria and fungi. The are in The peptide was active at concentration against most of the Gram-positive bacteria and the bacteria and Cg-Def was active at against Cg-Def showed no activity at against the Gram-negative bacteria and concentration the peptide was active against Cg-Def activity against at high were to the of Cg-Def. The activity of the peptide was by and the of was after at Cg-Def against the Gram-positive bacteria was with Cg-Def at concentration than the bacteria were in activity of recombinant effect of P. in a of killing of Cg-Def on of in a To the high of the the of Cg-Def in the effect of the peptide on bacterial was in vitro at from to Cg-Def is active against and at a concentration to the in seawater. the is unchanged the concentration for and for in the and a bacterial can be observed for the bacteria In to most Cg-Def seems to its activity at a high salt concentration C. C. P. J. 2004; Full Text Full Text PDF PubMed Scopus Google Scholar, A. R. J. 2004; Full Text Full Text PDF PubMed Scopus Google of on Cg-Def antimicrobial concentration in in after in the without concentration to the in bacterial in the concentration to the in bacterial in the in a NMR two-dimensional NMR and of Cg-Def were at from to The identification of the of Cg-Def was by and of and to the described by NMR of and Google Scholar). Nevertheless, we that the two-dimensional for of the two This a for this to from the to the and The sequence been to the for the through the J. 2005; Full Text Full Text PDF PubMed Scopus Google Scholar). a is to and primary structure, and solution as and A. 2002; PubMed Scopus Google Scholar). The two were to the and to the two similar were by at in the to the ionization of the The system sensitive to the ionization was to The in this was to a of the was was detected in the but characterized in the of the recombinant Cg-Def are in the as and were in a of and were with the of and of were by and The of is by the two for and for the of suggest a structure, in with the presence of the disulfide This is by as for the and for of and were of and were observed for of and The of the and the of and in a for and that to of the of and were to that observed for a The showed and that the a and a the and the of the a for the the found in of were and the The of and residues were found in of of a of Cg-Def is in The global structure of Cg-Def was and the motif that of an structure and two by three disulfide C. 3: Full Text Full Text PDF PubMed Scopus Google and by a disulfide P. R. A. PubMed Scopus Google Scholar, D. L. 2003; PubMed Scopus Google Scholar, A. P. A. PubMed Scopus Google Scholar). The of the were for the residues in a of and for the and The of residues for the and of the that were in the most and the additional and in the of of the residues were found in the of structure that the Cg-Def structure mainly of a two and and three loops and for loops and and were in and and and and a was found for the is to that the the the global is by the and disulfide The Cg-Def an character with a hydrophobic to the hydrophobic of the and a to the and Nevertheless, the and hydrophobic residues are The hydrophobic mainly the disulfide bonds, the and is to the and hydrophobic loops and the and and negatively charged and residues are The Cg-Def structure was with that of MGD-1 structure was previously determined A. P. A. PubMed Scopus Google Scholar). showed that the and were conserved Cg-def mRNA and the tissue of Cg-def we by mRNA in various oyster or no Cg-def mRNA was in most of the and a high mRNA to the level in the was detected in mantle In C. gigas the mantle as the tissue Cg-def To the presence of Cg-Def in an of this tissue was first to and to activity of the from oyster revealed the presence of two with antimicrobial two were to mass by To the mass the recombinant Cg-Def was used as of was observed the mass by and the by in The hydrophobic a with a mass at to that by for the recombinant Cg-Def. This peptide with antimicrobial activity against to the form of Cg-Def. the active that been showed a but mass of in of Cg-def after the expression of Cg-def during bacterial two of were In the first were by with bacteria and in the were used as were with from mantle at two challenge and were observed for Cg-def expression and bacteria at the revealed that Cg-def mRNA are in C. gigas oyster and that the level of was by the host defense are to to are In innate and are In and defense against pathogens through that are of the innate The of AMPs in to is by their in in and at the at the and its In antimicrobial activities have been detected in the of Scopus Google no been characterized despite to by from and tissues de J. J. Immunol. Rev. 2004; 198: PubMed Scopus Google Scholar). In this and for the first time in an we the characterization of an isolated from mantle a of the defensin is in and was three disulfide this defensin The amino acid sequence of the C. gigas defensin with defensins from the the as observed with the defensins and from Cg-Def disulfide This additional was to the peptide more in high as in A. P. A. PubMed Scopus Google Scholar). this is to the mussel defensins this additional disulfide C. P. J. Full Text Full Text PDF PubMed Scopus Google Scholar). Cg-Def an to be a sequence for translocation to the of the but a an as observed in the mussel or the P. P. Immunol. PubMed Scopus Google Scholar). This would suggest a of for the oyster To its Cg-Def was produced in and in This recombinant was of peptide of for and for the of Cg-Def in was the presence of residues in the the of with disulfide is a by the of in a that the of and in a bacterial host system J. J. J. Full Text Full Text PDF PubMed Scopus Google Scholar). described the of and in J. J. J. Full Text Full Text PDF PubMed Scopus Google Scholar, J. Full Text Full Text PDF PubMed Scopus Google Scholar). We report for the first time the in a bacterial host of an with that can be in The activity of the recombinant Cg-Def was against a of bacteria and fungi. with on defensins (2Bulet P. Stocklin R. Menin L. Immunol. Rev. 2004; 198: 169-184Crossref PubMed Scopus (849) Google Cg-Def was active in vitro against Gram-positive bacteria but showed no or limited activities against Gram-negative bacteria and fungi. Cg-Def its in the presence of high to This the that Cg-Def its activity in in vivo and would play a role in the antimicrobial defense of the oyster C. Cg-Def a of for to a to of bacteria in a C. PubMed Google Scholar). This is for for it been that the primary the salt of the antimicrobial Full Text Full Text PDF PubMed Scopus Google Scholar, J. Med. 2002; PubMed Scopus Google Scholar). from the disulfide the global of Cg-Def the motif observed in the defensins isolated from A. P. A. PubMed Scopus Google C. 3: Full Text Full Text PDF PubMed Scopus Google and plants P. L. P. A. 2003; PubMed Scopus Google Scholar). The Cg-Def and MGD-1 were and their structures were and This revealed of residues with three P. J. PubMed Google Scholar). Cg-Def and MGD-1 the disulfide that to the and to the of their The residues were mainly gathered in and their sequence the Cg-Def structure was with that of MGD-1 A. P. A. PubMed Scopus Google Scholar). showed that the and were conserved and the was for the of the residues and of Cg-Def with residues and of MGD-1 of was for the the two structures the and a similar disulfide Nevertheless, were observed for the disulfide and for the of the three the three disulfide and for Cg-Def and and for the for Cg-Def and for is mainly to the of by the of the This is to the the and the first The is a of this disulfide that on the of the Cg-Def and in MGD-1 as in the and loops of Cg-Def additional the of the the are conserved the of the loops are This is more hydrophobic for than that of MGD-1 that two charged Nevertheless, to the in the sequence the for Cg-Def and at the for it that have with to the In the were it been that the of MGD-1 is for a of the activity P. C. J. 2003; PubMed Scopus Google this is is that the of hydrophobic and in AMPs is essential for their antimicrobial The showed that of and and were conserved and the two antimicrobial mainly differ by the presence of two aspartic residues and and by the of a peptide and at the the Cg-Def and MGD-1 mainly to the two aspartic the hydrophobic by the of the disulfide bonds, hydrophobic and charged residues and are at the to a of hydrophobic and Our results showed that in the mantle as the tissue Cg-Def. we were to by of defensin from the we detected its presence by mass spectrometry of mantle tissue The results are in with for the In the AMPs are produced in where are and following bacterial P. J. PubMed Google Scholar). In the AMPs are produced in the of and into the in to a the systemic in the expression of peptides is in the of tissues P. D. Full Text Full Text PDF PubMed Scopus Google as observed for the expression of peptides in defensin is expressed in the and in the and a and P. Immunol. 2005; PubMed Scopus Google in AMPs are produced by Immunol. PubMed Scopus Google Scholar). from most of the AMPs in the of have been isolated from de J. J. Immunol. Rev. 2004; 198: PubMed Scopus Google Scholar). Our results would suggest that Cg-Def is continuously expressed in the oyster at that this an important in host protection against in the mantle is a of to that a for bacterial and potential pathogens. more of Cg-def gene expression in to various be to gain insight into the role of Cg-Def in oyster In AMPs and characterization be from oyster on AMPs are of great to the oyster immune system with the and it to pathogens. We are to A. J. for during defensin recombinant We J. de and for and