Showing papers by "Agrocampus Ouest published in 2013"

A decade of Predictions in Ungauged Basins (PUB)—a review

Abstract: The Prediction in Ungauged Basins (PUB) initiative of the International Association of Hydrological Sciences (IAHS), launched in 2003 and concluded by the PUB Symposium 2012 held in Delft (23–25 October 2012), set out to shift the scientific culture of hydrology towards improved scientific understanding of hydrological processes, as well as associated uncertainties and the development of models with increasing realism and predictive power. This paper reviews the work that has been done under the six science themes of the PUB Decade and outlines the challenges ahead for the hydrological sciences community.Editor D. KoutsoyiannisCitation Hrachowitz, M., Savenije, H.H.G., Bloschl, G., McDonnell, J.J., Sivapalan, M., Pomeroy, J.W., Arheimer, B., Blume, T., Clark, M.P., Ehret, U., Fenicia, F., Freer, J.E., Gelfan, A., Gupta, H.V., Hughes, D.A., Hut, R.W., Montanari, A., Pande, S., Tetzlaff, D., Troch, P.A., Uhlenbrook, S., Wagener, T., Winsemius, H.C., Woods, R.A., Zehe, E., and Cudennec, C., 2013. A d...

“Panta Rhei—Everything Flows”: Change in hydrology and society—The IAHS Scientific Decade 2013–2022

Abstract: The new Scientific Decade 2013-2022 of IAHS, entitled Panta RheiEverything Flows, is dedicated to research activities on change in hydrology and society. The purpose of Panta Rhei is to reach an improved interpretation of the processes governing the water cycle by focusing on their changing dynamics in connection with rapidly changing human systems. The practical aim is to improve our capability to make predictions of water resources dynamics to support sustainable societal development in a changing environment. The concept implies a focus on hydrological systems as a changing interface between environment and society, whose dynamics are essential to determine water security, human safety and development, and to set priorities for environmental management. The Scientific Decade 2013-2022 will devise innovative theoretical blueprints for the representation of processes including change and will focus on advanced monitoring and data analysis techniques. Interdisciplinarity will be sought by increased efforts to connect with the socio-economic sciences and geosciences in general. This paper presents a summary of the Science Plan of Panta Rhei, its targets, research questions and expected outcomes.

Towards a climate-dependent paradigm of ammonia emission and deposition

Abstract: Existing descriptions of bi-directional ammonia (NH3) land-atmosphere exchange incorporate temperature and moisture controls, and are beginning to be used in regional chemical transport models. However, such models have typically applied simpler emission factors to upscale the main NH3 emission terms. While this approach has successfully simulated the main spatial patterns on local to global scales, it fails to address the environment- and climate-dependence of emissions. To handle these issues, we outline the basis for a new modelling paradigm where both NH3 emissions and deposition are calculated online according to diurnal, seasonal and spatial differences in meteorology. We show how measurements reveal a strong, but complex pattern of climatic dependence, which is increasingly being characterized using ground-based NH3 monitoring and satellite observations, while advances in process-based modelling are illustrated for agricultural and natural sources, including a global application for seabird colonies. A future architecture for NH3 emission-deposition modelling is proposed that integrates the spatio-temporal interactions, and provides the necessary foundation to assess the consequences of climate change. Based on available measurements, a first empirical estimate suggests that 5°C warming would increase emissions by 42 per cent (28-67%). Together with increased anthropogenic activity, global NH3 emissions may increase from 65 (45-85) Tg N in 2008 to reach 132 (89-179) Tg by 2100.

Bio++: Efficient Extensible Libraries and Tools for Computational Molecular Evolution

Abstract: Efficient algorithms and programs for the analysis of the ever-growing amount of biological sequence data are strongly needed in the genomics era. The pace at which new data and methodologies are generated calls for the use of pre-existing, optimized-yet extensible-code, typically distributed as libraries or packages. This motivated the Bio++ project, aiming at developing a set of C++ libraries for sequence analysis, phylogenetics, population genetics, and molecular evolution. The main attractiveness of Bio++ is the extensibility and reusability of its components through its object-oriented design, without compromising the computer-efficiency of the underlying methods. We present here the second major release of the libraries, which provides an extended set of classes and methods. These extensions notably provide built-in access to sequence databases and new data structures for handling and manipulating sequences from the omics era, such as multiple genome alignments and sequencing reads libraries. More complex models of sequence evolution, such as mixture models and generic n-tuples alphabets, are also included.

A regulatory network-based approach dissects late maturation processes related to the acquisition of desiccation tolerance and longevity of Medicago truncatula seeds.

Abstract: In seeds, desiccation tolerance (DT) and the ability to survive the dry state for prolonged periods of time (longevity) are two essential traits for seed quality that are consecutively acquired during maturation. Using transcriptomic and metabolomic profiling together with a conditional-dependent network of global transcription interactions, we dissected the maturation events from the end of seed filling to final maturation drying during the last 3 weeks of seed development in Medicago truncatula. The network revealed distinct coexpression modules related to the acquisition of DT, longevity, and pod abscission. The acquisition of DT and dormancy module was associated with abiotic stress response genes, including late embryogenesis abundant (LEA) genes. The longevity module was enriched in genes involved in RNA processing and translation. Concomitantly, LEA polypeptides accumulated, displaying an 18-d delayed accumulation compared with transcripts. During maturation, gulose and stachyose levels increased and correlated with longevity. A seed-specific network identified known and putative transcriptional regulators of DT, including ABSCISIC ACID-INSENSITIVE3 (MtABI3), MtABI4, MtABI5, and APETALA2/ ETHYLENE RESPONSE ELEMENT BINDING PROTEIN (AtAP2/EREBP) transcription factor as major hubs. These transcriptional activators were highly connected to LEA genes. Longevity genes were highly connected to two MtAP2/EREBP and two basic leucine zipper transcription factors. A heat shock factor was found at the transition of DT and longevity modules, connecting to both gene sets. Gain- and loss-of-function approaches of MtABI3 confirmed 80% of its predicted targets, thereby experimentally validating the network. This study captures the coordinated regulation of seed maturation and identifies distinct regulatory networks underlying the preparation for the dry and quiescent states.

High throughput quantitative phenotyping of plant resistance using chlorophyll fluorescence image analysis.

Abstract: In order to select for quantitative plant resistance to pathogens, high throughput approaches that can precisely quantify disease severity are needed. Automation and use of calibrated image analysis should provide more accurate, objective and faster analyses than visual assessments. In contrast to conventional visible imaging, chlorophyll fluorescence imaging is not sensitive to environmental light variations and provides single-channel images prone to a segmentation analysis by simple thresholding approaches. Among the various parameters used in chlorophyll fluorescence imaging, the maximum quantum yield of photosystem II photochemistry (Fv/Fm) is well adapted to phenotyping disease severity. Fv/Fm is an indicator of plant stress that displays a robust contrast between infected and healthy tissues. In the present paper, we aimed at the segmentation of Fv/Fm images to quantify disease severity. Based on the Fv/Fm values of each pixel of the image, a thresholding approach was developed to delimit diseased areas. A first step consisted in setting up thresholds to reproduce visual observations by trained raters of symptoms caused by Xanthomonas fuscans subsp. fuscans (Xff) CFBP4834-R on Phaseolus vulgaris cv. Flavert. In order to develop a thresholding approach valuable on any cultivars or species, a second step was based on modeling pixel-wise Fv/Fm-distributions as mixtures of Gaussian distributions. Such a modeling may discriminate various stages of the symptom development but over-weights artifacts that can occur on mock-inoculated samples. Therefore, we developed a thresholding approach based on the probability of misclassification of a healthy pixel. Then, a clustering step is performed on the diseased areas to discriminate between various stages of alteration of plant tissues. Notably, the use of chlorophyll fluorescence imaging could detect pre-symptomatic area. The interest of this image analysis procedure for assessing the levels of quantitative resistance is illustrated with the quantitation of disease severity on five commercial varieties of bean inoculated with Xff CFBP4834-R. In this paper, we describe an image analysis procedure for quantifying the leaf area impacted by the pathogen. In a perspective of high throughput phenotyping, the procedure was automated with the software R downloadable at http://www.r-project.org/ . The R script is available at http://lisa.univ-angers.fr/PHENOTIC/telechargements.html .

LEA polypeptide profiling of recalcitrant and orthodox legume seeds reveals ABI3-regulated LEA protein abundance linked to desiccation tolerance

Abstract: In contrast to orthodox seeds that acquire desiccation tolerance during maturation, recalcitrant seeds are unable to survive drying. These desiccation-sensitive seeds constitute an interesting model for comparative analysis with phylogenetically close species that are desiccation tolerant. Considering the importance of LEA (late embryogenesis abundant) proteins as protective molecules both in drought and in desiccation tolerance, the heat-stable proteome was characterized in cotyledons of the legume Castanospermum australe and it was compared with that of the orthodox model legume Medicago truncatula. RNA sequencing identified transcripts of 16 homologues out of 17 LEA genes for which polypeptides are detected in M. truncatula seeds. It is shown that for 12 LEA genes, polypeptides were either absent or strongly reduced in C. australe cotyledons compared with M. truncatula seeds. Instead, osmotically responsive, non-seed-specific dehydrins accumulated to high levels in the recalcitrant cotyledons compared with orthodox seeds. Next, M. truncatula mutants of the ABSCISIC ACID INSENSITIVE3 (ABI3) gene were characterized. Mature Mtabi3 seeds were found to be desiccation sensitive when dried below a critical water content of 0.4 g H2O g DW –1 . Characterization of the LEA proteome of the Mtabi3 seeds revealed a subset of LEA proteins with severely reduced abundance that were also found to be reduced or absent in C. australe cotyledons. Transcripts of these genes were indeed shown to be ABI3 responsive. The results highlight those LEA proteins that are critical to desiccation tolerance and suggest that comparable regulatory pathways responsible for their accumulation are missing in both desiccationsensitive genotypes, revealing new insights into the mechanistic basis of the recalcitrant trait in seeds.

Advances in understanding, models and parameterizations of biosphere-atmosphere ammonia exchange

Abstract: Atmospheric ammonia (NH3) dominates global emissions of total reactive nitrogen (Nr), while emissions from agricultural production systems contribute about two-thirds of global NH3 emissions; the remaining third emanates from oceans, natural vegetation, humans, wild animals and biomass burning. On land, NH3 emitted from the various sources eventually returns to the biosphere by dry deposition to sink areas, predominantly semi-natural vegetation, and by wet and dry deposition as ammonium \( \left({\text{NH}}_{4}^{ + }\right) \) to all surfaces. However, the land/atmosphere exchange of gaseous NH3 is in fact bi-directional over unfertilized as well as fertilized ecosystems, with periods and areas of emission and deposition alternating in time (diurnal, seasonal) and space (patchwork landscapes). The exchange is controlled by a range of environmental factors, including meteorology, surface layer turbulence, thermodynamics, air and surface heterogeneous-phase chemistry, canopy geometry, plant development stage, leaf age, organic matter decomposition, soil microbial turnover, and, in agricultural systems, by fertilizer application rate, fertilizer type, soil type, crop type, and agricultural management practices. We review the range of processes controlling NH3 emission and uptake in the different parts of the soil-canopy-atmosphere continuum, with NH3 emission potentials defined at the substrate and leaf levels by different \( \left[{\text{NH}}_{4}^{ + }\right] \)/[H+] ratios (Γ). Surface/atmosphere exchange models for NH3 are necessary to compute the temporal and spatial patterns of emissions and deposition at the soil, plant, field, landscape, regional and global scales, in order to assess the multiple environmental impacts of airborne and deposited NH3 and \( {\text{NH}}_{4}^{ + } \). Models of soil/vegetation/atmosphere NH3 exchange are reviewed from the substrate and leaf scales to the global scale. They range from simple steady-state, “big leaf” canopy resistance models, to dynamic, multi-layer, multi-process, multi-chemical species schemes. Their level of complexity depends on their purpose, the spatial scale at which they are applied, the current level of parameterization, and the availability of the input data they require. State-of-the-art solutions for determining the emission/sink Γ potentials through the soil/canopy system include coupled, interactive chemical transport models (CTM) and soil/ecosystem modelling at the regional scale. However, it remains a matter for debate to what extent realistic options for future regional and global models should be based on process-based mechanistic versus empirical and regression-type models. Further discussion is needed on the extent and timescale by which new approaches can be used, such as integration with ecosystem models and satellite observations.

Manure management for greenhouse gas mitigation.

Abstract: Ongoing intensification and specialisation of livestock production lead to increasing volumes of manure to be managed, which are a source of the greenhouse gases (GHGs) methane (CH4) and nitrous oxide (N2O). Net emissions of CH4 and N2O result from a multitude of microbial activities in the manure environment. Their relative importance depends not only on manure composition and local management practices with respect to treatment, storage and field application, but also on ambient climatic conditions. The diversity of livestock production systems, and their associated manure management, is discussed on the basis of four regional cases (Sub-Saharan Africa, Southeast Asia, China and Europe) with increasing levels of intensification and priorities with respect to nutrient management and environmental regulation. GHG mitigation options for production systems based on solid and liquid manure management are then presented, and potentials for positive and negative interactions between pollutants, and between management practices, are discussed. The diversity of manure properties and environmental conditions necessitate a modelling approach for improving estimates of GHG emissions, and for predicting effects of management changes for GHG mitigation, and requirements for such a model are discussed. Finally, we briefly discuss drivers for, and barriers against, introduction of GHG mitigation measures for livestock production. There is no conflict between efforts to improve food and feed production, and efforts to reduce GHG emissions from manure management. Growth in livestock populations are projected to occur mainly in intensive production systems where, for this and other reasons, the largest potentials for GHG mitigation may be found.

Can fisheries-induced evolution shift reference points for fisheries management?

Abstract: Biological reference points are important tools for fisheries management. Reference points are not static, but may change when a population's environment or the population itself changes. Fisheries-induced evolution is one mechanism that can alter population characteristics, leading to "shifting" reference points by modifying the underlying biological processes or by changing the perception of a fishery system. The former causes changes in "true" reference points, whereas the latter is caused by changes in the yardsticks used to quantify a system's status. Unaccounted shifts of either kind imply that reference points gradually lose their intended meaning. This can lead to increased precaution, which is safe, but potentially costly. Shifts can also occur in more perilous directions, such that actual risks are greater than anticipated. Our qualitative analysis suggests that all commonly used reference points are susceptible to shifting through fisheries-induced evolution, including the limit and "precautionary" reference points for spawning-stock biomass, B_lim and B_pa, and the target reference point for fishing mortality, F_0.1. Our findings call for increased awareness of fisheries-induced changes and highlight the value of always basing reference points on adequately updated information, to capture all changes in the biological processes that drive fish population dynamics.

Inhibition of Staphylococcus aureus Invasion into Bovine Mammary Epithelial Cells by Contact with Live Lactobacillus casei

Abstract: Staphylococcus aureus is a major pathogen that is responsible for mastitis in dairy herds. S. aureus mastitis is difficult to treat and prone to recurrence despite antibiotic treatment. The ability of S. aureus to invade bovine mammary epithelial cells (bMEC) is evoked to explain this chronicity. One sustainable alternative to treat or prevent mastitis is the use of lactic acid bacteria (LAB) as mammary probiotics. In this study, we tested the ability of Lactobacillus casei strains to prevent invasion of bMEC by two S. aureus bovine strains, RF122 and Newbould305, which reproducibly induce acute and moderate mastitis, respectively. L. casei strains affected adhesion and/or internalization of S. aureus in a strain-dependent manner. Interestingly, L. casei CIRM-BIA 667 reduced S. aureus Newbould305 and RF122 internalization by 60 to 80%, and this inhibition was confirmed for two other L. casei strains, including one isolated from bovine teat canal. The protective effect occurred without affecting bMEC morphology and viability. Once internalized, the fate of S. aureus was not affected by L. casei. It should be noted that L. casei was internalized at a low rate but survived in bMEC cells with a better efficiency than that of S. aureus RF122. Inhibition of S. aureus adhesion was maintained with heat-killed L. casei, whereas contact between live L. casei and S. aureus or bMEC was required to prevent S. aureus internalization. This first study of the antagonism of LAB toward S. aureus in a mammary context opens avenues for the development of novel control strategies against this major pathogen.

Evidence for participation of the methionine sulfoxide reductase repair system in plant seed longevity

Abstract: Seeds are in a natural oxidative context leading to protein oxidation. Although inevitable for proper progression from maturation to germination, protein oxidation at high levels is detrimental and associated with seed aging. Oxidation of methionine to methionine sulfoxide is a common form of damage observed during aging in all organisms. This damage is reversible through the action of methionine sulfoxide reductases (MSRs), which play key roles in lifespan control in yeast and animal cells. To investigate the relationship between MSR capacity and longevity in plant seeds, we first used two Medicago truncatula genotypes with contrasting seed quality. After characterizing the MSR family in this species, we analyzed gene expression and enzymatic activity in immature and mature seeds exhibiting distinct quality levels. We found a very strong correlation between the initial MSR capacities in different lots of mature seeds of the two genotypes and the time to a drop in viability to 50% after controlled deterioration. We then analyzed seed longevity in Arabidopsis thaliana lines, in which MSR gene expression has been genetically altered, and observed a positive correlation between MSR capacity and longevity in these seeds as well. Based on our data, we propose that the MSR repair system plays a decisive role in the establishment and preservation of longevity in plant seeds.

Effects of high fiber intake during late pregnancy on sow physiology, colostrum production, and piglet performance

Abstract: Dietary fiber given during pregnancy may influence sow endocrinology and increase piglet BW gain during early lactation. The aim of the current study was to determine whether dietary fiber given to sows during late pregnancy induces endocrine changes that could modulate sow colostrum production and, thus, piglet performance. From d 106 of pregnancy until parturition, 29 Landrace×Large White nulliparous sows were fed gestation diets containing 23.4 [high fiber (HF); n=15] or 13.3% total dietary fiber [low fiber (LF); n=14]. In the HF diet, wheat and barley were partly replaced by soybean hulls, wheat bran, sunflower meal (undecorticated), and sugar beet pulp. After parturition, sows were fed a standard lactation diet. Colostrum production was estimated during 24 h, starting at the onset of parturition (T0) and ending at 24 h after parturition (T24) based on piglet weight gains. Jugular blood samples were collected from sows on d 101 of pregnancy, daily from d 111 of gestation to d 3 of lactation, and then on d 7 and 21 of lactation (d 0 being the day of parturition). Postprandial kinetics of plasma glucose and insulin concentrations were determined on d 112 of pregnancy. The feeding treatment did not influence sow colostrum yield (3.9±0.2 kg) or piglet weight gain during the first day postpartum to d 21 of lactation. Colostrum intake of low birth weight piglets (<900 g) was greater in litters from HF sows than from LF sows (216±24 vs. 137±22 g; P=0.02). Preweaning mortality was lower in HF than LF litters (6.2 vs. 14.7%; P=0.01). Circulating concentrations of progesterone, prolactin, estradiol-17β, and cortisol were not influenced by the treatment. Sows fed the HF diet had greater postprandial insulin concentrations than LF sows (P=0.02) whereas the postprandial glucose peak was similar. At T24, colostrum produced by HF sows contained 29% more lipid than colostrum produced by LF sows (P=0.04). Immunoglobulin A concentrations in colostrum were lower at T0 and T24 (P=0.02) in HF than LF sows (at T0: 8.6±1.1 vs. 11.9±1.1 mg/mL; at T24: 2.5±0.7 vs. 4.8±0.7 mg/mL). In conclusion, dietary fiber in late pregnancy affected sow colostrum composition but not colostrum yield, increased colostrum intake of low birth weight piglets, and decreased preweaning mortality, but these effects were not related to changes in peripartum concentrations of the main hormones involved in lactogenesis.

A novel bioactive peptide from yoghurts modulates expression of the gel-forming MUC2 mucin as well as population of goblet cells and Paneth cells along the small intestine☆

Abstract: Several studies demonstrated that fermented milks may provide a large number of bioactive peptides into the gastrointestinal tract. We previously showed that beta-casomorphin-7, an opioid-like peptide produced from bovine β-casein, strongly stimulates intestinal mucin production in ex vivo and in vitro models, suggesting the potential benefit of milk bioactive peptides on intestinal protection. In the present study, we tested the hypothesis that the total peptide pool (TPP) from a fermented milk (yoghurt) may act on human intestinal mucus-producing cells (HT29-MTX) to induce mucin expression. Our aim was then to identify the peptide(s) carrying the biological activity and to study its impact in vivo on factors involved in gut protection after oral administration to rat pups (once a day, 9 consecutive days). TPP stimulated MUC2 and MUC4 gene expression as well as mucin secretion in HT29-MTX cells. Among the four peptide fractions that were separated by preparative reversed-phase high-performance liquid chromatography, only the C2 fraction was able to mimic the in vitro effect of TPP. Interestingly, the sequence [94-123] of β-casein, present only in C2 fraction, also regulated mucin production in HT29-MTX cells. Oral administration of this peptide to rat pups enhanced the number of goblet cells and Paneth cells along the small intestine. These effects were associated with a higher expression of intestinal mucins (Muc2 and Muc4) and of antibacterial factors (lysozyme, rdefa5). We conclude that the peptide β-CN(94-123) present in yoghurts may maintain or restore intestinal homeostasis and could play an important role in protection against damaging agents of the intestinal lumen.

Genetics of residual feed intake in growing pigs: Relationships with production traits, and nitrogen and phosphorus excretion traits

Abstract: Residual feed intake (RFI) is defined as the difference between the observed ADFI and the ADFI predicted from production and maintenance requirements. The objectives of this study were to evaluate RFI as a selection criterion to improve feed efficiency and its potential to reduce N and P excretion in 4 pig breeds. Data were collected between 2000 and 2009 in French central test stations for 2 dam breeds [French Landrace (LR) and Large White (LWD)], and 2 sire breeds [Large White (LWS) and Pietrain (PP)]. Numbers of recorded pigs were 6407, 10,694, 2342, and 2448 for the LR, LWD, LWS, and PP breeds, respectively. All PP animals were genotyped for the halothane mutation. This data set was used to calculate RFI equations for each of the 4 breeds, and to estimate genetic parameters for RFI together with growth, carcass, and meat quality traits, and N and P excretion during the test period (35 to 110 kg BW). The RFI explained 20.1% in PP, 26.5% in LWS, 27.6% in LWD, and 29.5% in LR of the phenotypic variability of ADFI. The PP breed differed from the others in this respect, probably due to a lower impact of the variation of body composition on ADFI. Heritability estimates of RFI ranged from 0.21 ± 0.03 (LWD) to 0.33 ± 0.06 (PP) depending on the breed. Heritabilities of N and P excretion traits ranged from 0.29 ± 0.06 to 0.40 ± 0.06. The RFI showed positive genetic correlations with feed conversion ratio (FCR) and excretion traits, these correlations being greater in the sire breeds (from 0.57 to 0.86) than in the dam breeds (from 0.38 to 0.53). Compared with FCR, RFI had weaker genetic correlations with carcass composition, growth rate, and excretion traits. Estimates of genetic correlations between FCR and excretion traits were very close to 1 for all breeds. Finally, excretion traits were, at the genetic level, correlated positively with ADFI, negatively with growth rate and carcass leanness, whereas the halothane n mutation in PP was shown to reduce N and P excretion levels. To conclude, new selection indexes including RFI can be envisaged to efficiently disentangle the responses to selection on growth rate and body composition from those on feed efficiency, with favorable impacts on N and P excretions, particularly in sire pig breeds. However, the switch from FCR to RFI in selection indexes should not resolve the genetic antagonism between feed efficiency and meat quality.

Solute transport dynamics in small, shallow groundwater-dominated agricultural catchments: insights from a high-frequency, multisolute 10 yr-long monitoring study

Abstract: . High-frequency, long-term and multisolute measurements are required to assess the impact of human pressures on water quality due to (i) the high temporal and spatial variability of climate and human activity and (ii) the fact that chemical solutes combine short- and long-term dynamics. Such data series are scarce. This study, based on an original and unpublished time series from the Kervidy-Naizin headwater catchment (Brittany, France), aims to determine solute transfer processes and dynamics that characterise this strongly human-impacted catchment. The Kervidy-Naizin catchment is a temperate, intensive agricultural catchment, hydrologically controlled by shallow groundwater. Over 10 yr, five solutes (nitrate, sulphate, chloride, and dissolved organic and inorganic carbon) were monitored daily at the catchment outlet and roughly every four months in the shallow groundwater. The concentrations of all five solutes showed seasonal variations but the patterns of the variations differed from one solute to another. Nitrate and chloride exhibit rather smooth variations. In contrast, sulphate as well as organic and inorganic carbon is dominated by flood flushes. The observed nitrate and chloride patterns are typical of an intensive agricultural catchment hydrologically controlled by shallow groundwater. Nitrate and chloride originating mainly from organic fertilisers accumulated over several years in the shallow groundwater. They are seasonally exported when upland groundwater connects with the stream during the wet season. Conversely, sulphate as well as organic and inorganic carbon patterns are not specific to agricultural catchments. These solutes do not come from fertilisers and do not accumulate in soil or shallow groundwater; instead, they are biogeochemically produced in the catchment. The results allowed development of a generic classification system based on the specific temporal patterns and source locations of each solute. It also considers the stocking period and the dominant process that limits transport to the stream, i.e. the connectivity of the stocking compartment. This mechanistic classification can be applied to any chemical solute to help assess its origin, storage or production location and transfer mechanism in similar catchments.

A success story: water primroses, aquatic plant pests

Abstract: Aquatic ecosystems are currently invaded by non-indigenous aquatic plants. A major challenge for biological invasion research is to develop the ability to predict the spread of species. Throughout the world, Ludwigia peploides subsp. montevidensis and Ludwigia grandiflora subsp. hexapetala are now considered to be two of the most invasive aquatic plants. This paper reviews the scientific knowledge about these species, their ecological and socio-economic impacts and methods of management. Water primrose possesses some advantageous biological traits, such as rapid growth rate, efficient reproductive capacity, high plasticity in growth response, broad ecological tolerance and allelopathic compounds which might explain its expansion and colonization of numerous ecosystems. Much attention must be paid to Ludwigia grandiflora subsp. hexapetala and Ludwigia peploides subsp. montevidensis. According to climatic models, global warming will further increase the spread of these species in Europe. Copyright © 2013 John Wiley & Sons, Ltd.

Evolutionary History of the Plant Pathogenic Bacterium Xanthomonas axonopodis

Abstract: Deciphering mechanisms shaping bacterial diversity should help to build tools to predict the emergence of infectious diseases. Xanthomonads are plant pathogenic bacteria found worldwide. Xanthomonas axonopodis is a genetically heterogeneous species clustering, into six groups, strains that are collectively pathogenic on a large number of plants. However, each strain displays a narrow host range. We address the question of the nature of the evolutionary processes – geographical and ecological speciation – that shaped this diversity. We assembled a large collection of X. axonopodis strains that were isolated over a long period, over continents, and from various hosts. Based on the sequence analysis of seven housekeeping genes, we found that recombination occurred as frequently as point mutation in the evolutionary history of X. axonopodis. However, the impact of recombination was about three times greater than the impact of mutation on the diversity observed in the whole dataset. We then reconstructed the clonal genealogy of the strains using coalescent and genealogy approaches and we studied the diversification of the pathogen using a model of divergence with migration. The suggested scenario involves a first step of generalist diversification that spanned over the last 25 000 years. A second step of ecology-driven specialization occurred during the past two centuries. Eventually, secondary contacts between host-specialized strains probably occurred as a result of agricultural development and intensification, allowing genetic exchanges of virulence-associated genes. These transfers may have favored the emergence of novel pathotypes. Finally, we argue that the largest ecological entity within X. axonopodis is the pathovar.

1d-SAX: A Novel Symbolic Representation for Time Series

Abstract: SAX Symbolic Aggregate approXimation is one of the main symbolization techniques for time series. A well-known limitation of SAX is that trends are not taken into account in the symbolization. This paper proposes 1d-SAX a method to represent a time series as a sequence of symbols that each contain information about the average and the trend of the series on a segment. We compare the efficiency of SAX and 1d-SAX in terms of goodness-of-fit, retrieval and classification performance for querying a time series database with an asymmetric scheme. The results show that 1d-SAX improves performance using equal quantity of information, especially when the compression rate increases.

Risk assessment of herbicides and booster biocides along estuarine continuums in the Bay of Vilaine area (Brittany, France).

Abstract: A 2-year study was implemented to characterize the contamination of estuarine continuums in the Bay of Vilaine area (NW Atlantic Coast, Southern Brittany, France) by 30 pesticide and biocide active substances and metabolites. Among these, 11 triazines (ametryn, atrazine, desethylatrazine, desethylterbuthylazine, desisopropyl atrazine, Irgarol 1051, prometryn, propazine, simazine, terbuthylazine, and terbutryn), 10 phenylureas (chlortoluron, diuron, 1-(3,4-dichlorophenyl)-3-methylurea, fenuron, isoproturon, 1-(4-isopropylphenyl)-3-methylurea, 1-(4-isopropylphenyl)-urea, linuron, metoxuron, and monuron), and 4 chloroacetanilides (acetochlor, alachlor, metolachlor, and metazachlor) were detected at least once. The objectives were to assess the corresponding risk for aquatic primary producers and to provide exposure information for connected studies on the responses of biological parameters in invertebrate sentinel species. The risk associated with contaminants was assessed using risk quotients based on the comparison of measured concentrations with original species sensitivity distribution-derived hazardous concentration values. For EU Water Framework Directive priority substances, results of monitoring were also compared with regulatory Environmental Quality Standards. The highest residue concentrations and risks for primary producers were recorded for diuron and Irgarol 1051 in Arzal reservoir, close to a marina. Diuron was present during almost the all survey periods, whereas Irgarol 1051 exhibited a clear seasonal pattern, with highest concentrations recorded in June and July. These results suggest that the use of antifouling biocides is responsible for a major part of the contamination of the lower part of the Vilaine River course for Irgarol 1051. For diuron, agricultural sources may also be involved. The presence of isoproturon and chloroacetanilide herbicides on some dates indicated a significant contribution of the use of plant protection products in agriculture to the contamination of Vilaine River. Concentration levels and associated risk were always lower in estuarine sites than in the reservoir, suggesting that Arzal dam reduces downstream transfer of contaminants and favors their degradation in the freshwater part of the estuary. Results of the additional monitoring of two tidal streams located downstream of Arzal dam suggested that, although some compounds may be transferred to the estuary, their impact was probably very low. Dilution by marine water associated with tidal current was also a major factor of concentration reduction. It is concluded that the highest risks associated to herbicides and booster biocides concerned the freshwater part of the estuary and that its brackish/saltwater part was exposed to a moderate risk, although some substances may sometimes exhibit high concentration but mainly at low tide and on an irregular basis.

Hydrologically driven seasonal changes in the sources and production mechanisms of dissolved organic carbon in a small lowland catchment

Abstract: [1] To obtain better constraints on the control of seasonal hydrological variations on dissolved organic carbon (DOC) dynamics in headwater catchments, we combined hydrometric monitoring with high-frequency analyses of DOC concentration and DOC chemical composition (specific UV adsorption, δ13C) in soil and stream waters during one complete hydrological cycle in a small lowland catchment of western France. We observed a succession of four hydrological periods, each corresponding to specific DOC signatures. In particular, the rise of the upland water table at the end of the rewetting period yielded to a strong increase of the specific UV absorbance (from 2.5 to 4.0 L mg C−1 m−1) and of the δ13C values (from −29 to −27‰) of the soil DOC. Another striking feature was the release of large amounts of DOC during reduction of soil Fe-oxyhydroxides at the end of the high-flow period. Comparison of hydrometric data with DOC composition metrics showed that soils from the upland domains were rapidly DOC depleted after the rise of the water table in these domains, whereas wetland soils acted as quasi-infinite DOC sources. Results from this study showed that the composition and ultimate source of the DOC exported to the stream will depend on the period within the annual hydrological cycle. However, we found that the aromatic DOC component identified during the high-flow period will likely represent the dominant DOC component in stream waters on an annual basis, because most of the annual stream DOC flux is exported during such periods.

Effect of thermal heat stress on energy utilization in two lines of pigs divergently selected for residual feed intake.

Abstract: Castrated males from 2 lines of purebred French Large White obtained from a divergent selection experiment for their residual feed intake (RFI) over 7 generations were measured for their energy utilization during thermal acclimation to increased ambient temperature. The RFI(+) line consumed more feed than predicted from its performance, whereas the RFI- line consumed less feed. Each pig was exposed to 24°C for 7 d (P0) and thereafter to a constant temperature of 32°C for 3 consecutive periods of 7 d (P1, P2, P3). Feed intake, feeding behavior parameters, digestibility, components of heat production (HP; measured by indirect calorimetry in respiration chambers), and energy, nitrogen, fat, and water balance were measured in pigs offered feed and water ad libitum and individually housed in respiratory chambers. Two identical respiratory chambers were simultaneously used, and 5 pigs of each line were measured successively. Whatever the trait, the interaction between line and period was not significant (P > 0.10). On average, ADFI was greater in the RFI+ than in the RFI- line (1,945 vs. 1,639 g/d; P = 0.051) in relation to an increase of the mean size of each feeding bout (128 vs. 82 g/visit; P < 0.001). There was no line effect on nutrient and energy digestibility. Total HP tended to be greater in RFI+ than in RFI- lines (1,279 vs. 1,137 kJ·kg BW-0.60·d-1; P = 0.065), which tended to retain more energy (968 vs. 798 kJ·kg BW-0.60·d-1; P = 0.050). The sensible heat loss was greater in RFI+ compared with the RFI- line (644 vs. 560 kJ·kg BW-0.60·d-1; P = 0.020). The RFI+ pigs consumed more water (+981 vs. 657 g·kg BW-0.60·d-1; P = 0.085) and produced more urine (589 vs. 292 g·kg BW-0.60·d-1; P < 0.001) than RFI- pigs, whereas water evaporation was similar for both lines. On average, ME intake and HP declined by about 38% and 20%, respectively, from P0 to P1 (P < 0.001). In contrast to ME intake, HP gradually decreased (P < 0.05) from P1 to P3 in connection with a reduction of the activity related HP. The evaporative heat loss represented 30% on the total heat loss on P0, and this proportion significantly increased on P1 (61%; P < 0.001) and remained constant thereafter. In conclusion, our results suggest that thermal heat acclimation in pigs is mainly related to a biphasic reduction of HP rather than a change in the ability of losing heat, and it did not significantly differ between RFI+ and RFI- lines despite a decreased HP in the latter ones.

Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids

Abstract: We have used new generation sequencing (NGS) technologies to identify single nucleotide polymorphism (SNP) markers from three European pear (Pyrus communis L.) cultivars and subsequently developed a subset of 1096 pear SNPs into high throughput markers by combining them with the set of 7692 apple SNPs on the IRSC apple Infinium® II 8K array. We then evaluated this apple and pear Infinium® II 9K SNP array for large-scale genotyping in pear across several species, using both pear and apple SNPs. The segregating populations employed for array validation included a segregating population of European pear (‘Old Home’בLouise Bon Jersey’) and four interspecific breeding families derived from Asian (P. pyrifolia Nakai and P. bretschneideri Rehd.) and European pear pedigrees. In total, we mapped 857 polymorphic pear markers to construct the first SNP-based genetic maps for pear, comprising 78% of the total pear SNPs included in the array. In addition, 1031 SNP markers derived from apple (13% of the total apple SNPs included in the array) were polymorphic and were mapped in one or more of the pear populations. These results are the first to demonstrate SNP transferability across the genera Malus and Pyrus. Our construction of high density SNP-based and gene-based genetic maps in pear represents an important step towards the identification of chromosomal regions associated with a range of horticultural characters, such as pest and disease resistance, orchard yield and fruit quality.