Toxicity of triclosan, penconazole and metalaxyl on Caulobacter crescentus and a freshwater microbial community as assessed by flow cytometry.

Biocides are widely used for domestic hygiene, agricultural and industrial applications. Their widespread use has resulted in their introduction into the environment and raised concerns about potential deleterious effects on aquatic ecosystems. In this study, the toxicity of the biocides triclosan, penconazole and metalaxyl were evaluated with the freshwater bacterium Caulobacter crescentus and with a freshwater microbial community using a combination of single- and double-stain flow cytometric assays. Growth of C.  crescentus and the freshwater community were repressed by triclosan but not by penconazole or metalaxyl at concentrations up to 250 μM. The repressive effect of triclosan was dependent on culture conditions. Caulobacter crescentus was more sensitive to triclosan when grown with high glucose at high cell density than when grown directly in sterilized lake water at low cell density. This suggests that the use of conventional growth conditions may overestimate biocide toxicity. Additional experiments showed that the freshwater community was more sensitive to triclosan than C.  crescentus, with 10 nM of triclosan being sufficient to repress growth and change the phylogenetic composition of the community. These results demonstrate that isolate-based assays may underestimate biocide toxicity and highlight the importance of assessing toxicity directly on natural microbial communities. Because 10 nM of triclosan is within the range of concentrations observed in freshwater systems, these results also raise concerns about the risk of introducing triclosan into the environment.

Spatial predictions of land-use transitions and associated threats to biodiversity: the case of forest regrowth in mountain grasslands

Question Can we predict where forest regrowth caused by abandonment of agricultural activities is likely to occur? Can we assess how it may conflict with grassland diversity hotspots? Location Western Swiss Alps (4003210m a.s.l.). Methods We used statistical models to predict the location of land abandonment by farmers that is followed by forest regrowth in semi-natural grasslands of the Western Swiss Alps. Six modelling methods (GAM, GBM, GLM, RF, MDA, MARS) allowing binomial distribution were tested on two successive transitions occurring between three time periods. Models were calibrated using data on land-use change occurring between 1979 and 1992 as response, and environmental, accessibility and socio-economic variables as predictors, and these were validated for their capacity to predict the changes observed from 1992 to 2004. Projected probabilities of land-use change from an ensemble forecast of the six models were combined with a model of plant species richness based on a field inventory, allowing identification of critical grassland areas for the preservation of biodiversity. Results Models calibrated over the first land-use transition period predicted the second transition with reasonable accuracy. Forest regrowth occurs where cultivation costs are high and yield potential is low, i.e. on steeper slopes and at higher elevations. Overlaying species richness with land-use change predictions, we identified priority areas for the management and conservation of biodiversity at intermediate elevations. Conclusions Combining land-use change and biodiversity projections, we propose applied management measures for targeted/identified locations to limit the loss of biodiversity that could otherwise occur through loss of open habitats. The same approach could be applied to other types of land-use changes occurring in other ecosystems.

The future of terrestrial mammals in the Mediterranean basin under climate change.

The Mediterranean basin is considered a hotspot of biological diversity with a long history of modification of natural ecosystems by human activities, and is one of the regions that will face extensive changes in climate. For 181 terrestrial mammals (68% of all Mediterranean mammals), we used an ensemble forecasting approach to model the future (approx. 2100) potential distribution under climate change considering five climate change model outputs for two climate scenarios. Overall, a substantial number of Mediterranean mammals will be severely threatened by future climate change, particularly endemic species. Moreover, we found important changes in potential species richness owing to climate change, with some areas (e.g. montane region in central Italy) gaining species, while most of the region will be losing species (mainly Spain and North Africa). Existing protected areas (PAs) will probably be strongly influenced by climate change, with most PAs in Africa, the Middle East and Spain losing a substantial number of species, and those PAs gaining species (e.g. central Italy and southern France) will experience a substantial shift in species composition.

Making better biogeographical predictions of species' distributions

1. Biogeographical models of species' distributions are essential tools for assessing impacts of changing environmental conditions on natural communities and ecosystems. Practitioners need more reliable predictions to integrate into conservation planning (e.g. reserve design and management). 2. Most models still largely ignore or inappropriately take into account important features of species' distributions, such as spatial autocorrelation, dispersal and migration, biotic and environmental interactions. Whether distributions of natural communities or ecosystems are better modelled by assembling individual species' predictions in a bottom-up approach or modelled as collective entities is another important issue. An international workshop was organized to address these issues. 3. We discuss more specifically six issues in a methodological framework for generalized regression: (i) links with ecological theory; (ii) optimal use of existing data and artificially generated data; (iii) incorporating spatial context; (iv) integrating ecological and environmental interactions; (v) assessing prediction errors and uncertainties; and (vi) predicting distributions of communities or collective properties of biodiversity. 4. Synthesis and applications. Better predictions of the effects of impacts on biological communities and ecosystems can emerge only from more robust species' distribution models and better documentation of the uncertainty associated with these models. An improved understanding of causes of species' distributions, especially at their range limits, as well as of ecological assembly rules and ecosystem functioning, is necessary if further progress is to be made. A better collaborative effort between theoretical and functional ecologists, ecological modellers and statisticians is required to reach these goals.

Plutonium and americium isotopes as alternative chronostratigraphic markers in tropical regions: An application in the Havana Bay (Cuba)

The low 137Cs activity observed in marine sediments of tropical regions often precludes its use as chronostratigraphic marker. Here we present a study on the use of Pu and Am radioisotopes as alternative markers to constrain the 210Pb ages in a sediment core of the Havana Bay (Cuba). Mean activity ratios of 238Pu/239,240Pu, 241Am/239,240Pu and 241Pu/239,240Pu indicated that the nuclear weapon tests fallout is the main source of the anthropogenic radionuclides. While the inventory of 137Cs in the sediments is lower than the expected fallout inventory, 239,240Pu accumulates in the sediments with inventories higher than the expected fallout inventory. The high fluxes of 239,240Pu are nevertheless corroborated here through use of 210Pb, and confirm that focusing of solid particles is of great importance in the investigated site. 239,240Pu showed to be a useful time tracer in marine sites where the 137Cs signal is very low.

Simulation of stromatolite growth using diffusion-limited aggregation and a discrete model of biogeochemical exchanges in microbial mat

Resume : Mieux comprendre les stromatolithes et les tapis microbiens est un sujet important en biogéosciences puisque cela aide à l'étude des premières formes de vie sur Terre, a mieux cerner l'écologie des communautés microbiennes et la contribution des microorganismes a la biominéralisation, et même à poser certains fondements dans les recherches en exobiologie. D'autre part, la modélisation est un outil puissant utilisé dans les sciences naturelles pour appréhender différents phénomènes de façon théorique. Les modèles sont généralement construits sur un système d'équations différentielles et les résultats sont obtenus en résolvant ce système. Les logiciels disponibles pour implémenter les modèles incluent les logiciels mathématiques et les logiciels généraux de simulation. L'objectif principal de cette thèse est de développer des modèles et des logiciels pour aider a comprendre, via la simulation, le fonctionnement des stromatolithes et des tapis microbiens. Ces logiciels ont été développés en C++ en ne partant d'aucun pré-requis de façon a privilégier performance et flexibilité maximales. Cette démarche permet de construire des modèles bien plus spécifiques et plus appropriés aux phénomènes a modéliser. Premièrement, nous avons étudié la croissance et la morphologie des stromatolithes. Nous avons construit un modèle tridimensionnel fondé sur l'agrégation par diffusion limitée. Le modèle a été implémenté en deux applications C++: un moteur de simulation capable d'exécuter un batch de simulations et de produire des fichiers de résultats, et un outil de visualisation qui permet d'analyser les résultats en trois dimensions. Après avoir vérifié que ce modèle peut en effet reproduire la croissance et la morphologie de plusieurs types de stromatolithes, nous avons introduit un processus de sédimentation comme facteur externe. Ceci nous a mené a des résultats intéressants, et permis de soutenir l'hypothèse que la morphologie des stromatolithes pourrait être le résultat de facteurs externes autant que de facteurs internes. Ceci est important car la classification des stromatolithes est généralement fondée sur leur morphologie, imposant que la forme d'un stromatolithe est dépendante de facteurs internes uniquement (c'est-à-dire les tapis microbiens). Les résultats avancés dans ce mémoire contredisent donc ces assertions communément admises. Ensuite, nous avons décidé de mener des recherches plus en profondeur sur les aspects fonctionnels des tapis microbiens. Nous avons construit un modèle bidimensionnel de réaction-diffusion fondé sur la simulation discrète. Ce modèle a été implémenté dans une application C++ qui permet de paramétrer et exécuter des simulations. Nous avons ensuite pu comparer les résultats de simulation avec des données du monde réel et vérifier que le modèle peut en effet imiter le comportement de certains tapis microbiens. Ainsi, nous avons pu émettre et vérifier des hypothèses sur le fonctionnement de certains tapis microbiens pour nous aider à mieux en comprendre certains aspects, comme la dynamique des éléments, en particulier le soufre et l'oxygène. En conclusion, ce travail a abouti à l'écriture de logiciels dédiés à la simulation de tapis microbiens d'un point de vue tant morphologique que fonctionnel, suivant deux approches différentes, l'une holistique, l'autre plus analytique. Ces logiciels sont gratuits et diffusés sous licence GPL (General Public License). Abstract : Better understanding of stromatolites and microbial mats is an important topic in biogeosciences as it helps studying the early forms of life on Earth, provides clues re- garding the ecology of microbial ecosystems and their contribution to biomineralization, and gives basis to a new science, exobiology. On the other hand, modelling is a powerful tool used in natural sciences for the theoretical approach of various phenomena. Models are usually built on a system of differential equations and results are obtained by solving that system. Available software to implement models includes mathematical solvers and general simulation software. The main objective of this thesis is to develop models and software able to help to understand the functioning of stromatolites and microbial mats. Software was developed in C++ from scratch for maximum performance and flexibility. This allows to build models much more specific to a phenomenon rather than general software. First, we studied stromatolite growth and morphology. We built a three-dimensional model based on diffusion-limited aggregation. The model was implemented in two C++ applications: a simulator engine, which can run a batch of simulations and produce result files, and a Visualization tool, which allows results to be analysed in three dimensions. After verifying that our model can indeed reproduce the growth and morphology of several types of stromatolites, we introduced a sedimentation process as an external factor. This lead to interesting results, and allowed to emit the hypothesis that stromatolite morphology may be the result of external factors as much as internal factors. This is important as stromatolite classification is usually based on their morphology, imposing that a stromatolite shape is dependant on internal factors only (i.e. the microbial mat). This statement is contradicted by our findings, Second, we decided to investigate deeper the functioning of microbial mats, We built a two-dimensional reaction-diffusion model based on discrete simulation, The model was implemented in a C++ application that allows setting and running simulations. We could then compare simulation results with real world data and verify that our model can indeed mimic the behaviour of some microbial mats. Thus, we have proposed and verified hypotheses regarding microbial mats functioning in order to help to better understand them, e.g. the cycle of some elements such as oxygen or sulfur. ln conclusion, this PhD provides a simulation software, dealing with two different approaches. This software is free and available under a GPL licence.

Assessing catchment-scale erosion and yields of suspended solids from improved temperate grassland.

This paper quantifies the yields of suspended solids (SS) from a headwater catchment managed as improved temperate grassland, providing the first direct, catchment-scale evidence of the rates of erosion from this land-use in the UK and assessing the threat posed to aquatic ecosystems. High-resolution monitoring of catchment hydrology and the concentrations of SS and volatile organic matter (VOM) were carried out in the first-order channel of the Den Brook headwater catchment in Devon (UK) during the 2006-2007 hydrological season. The widely used 'rating curve' (discharge-concentration) approach was employed to estimate yields of SS, but as demonstrated by previous researchers, this study showed that discharge is a poor predictor of SS concentrations and therefore any yields estimated from this technique are likely to be highly uncertain. Nevertheless, for the purpose of providing estimates of yields that are comparable to previous studies on other land uses/sources, this technique was adopted albeit in an uncertainty-based framework. The findings suggest that contrary to the common perception, grasslands can be erosive landscapes with SS yields from this catchment estimated to be between 0.54 and 1.21 t ha(-1) y(-1). In terms of on-site erosion problems, this rate of erosion does not significantly exceed the commonly used 'tolerable' threshold in the UK ( approximately 1 t ha(-1) y(-1)). In terms of off-site erosion problems, it is argued here that the conventional expression of SS yield as a bulk annual figure has little relevance to the water quality and ecological status of surface waters and therefore an alternative technique (the concentration-frequency curve) is developed within this paper for the specific purpose of assessing the ecological threat posed by the delivery of SS into surface waters. This technique illustrates that concentrations of SS recorded at the catchment outlet frequently exceed the water quality guidelines, such as those of the EU Freshwater Fisheries Directive (78/659/EC), and pose a serious threat to aquatic organisms. It is suggested that failure to recognise improved temperate grasslands as a potential source of particulate material could result in the non-compliance of surface waters to water quality guidelines, deterioration of ecological status and failure of water quality remediation measures.

Self-Organising Maps and Correlation Analysis as a Tool to Explore Patterns in Excitation-Emission Matrix Data Sets and to Discriminate Dissolved Organic Matter Fluorescence Components

Dissolved organic matter (DOM) is a complex mixture of organic compounds, ubiquitous in marine and freshwater systems. Fluorescence spectroscopy, by means of Excitation-Emission Matrices (EEM), has become an indispensable tool to study DOM sources, transport and fate in aquatic ecosystems. However the statistical treatment of large and heterogeneous EEM data sets still represents an important challenge for biogeochemists. Recently, Self-Organising Maps (SOM) has been proposed as a tool to explore patterns in large EEM data sets. SOM is a pattern recognition method which clusterizes and reduces the dimensionality of input EEMs without relying on any assumption about the data structure. In this paper, we show how SOM, coupled with a correlation analysis of the component planes, can be used both to explore patterns among samples, as well as to identify individual fluorescence components. We analysed a large and heterogeneous EEM data set, including samples from a river catchment collected under a range of hydrological conditions, along a 60-km downstream gradient, and under the influence of different degrees of anthropogenic impact. According to our results, chemical industry effluents appeared to have unique and distinctive spectral characteristics. On the other hand, river samples collected under flash flood conditions showed homogeneous EEM shapes. The correlation analysis of the component planes suggested the presence of four fluorescence components, consistent with DOM components previously described in the literature. A remarkable strength of this methodology was that outlier samples appeared naturally integrated in the analysis. We conclude that SOM coupled with a correlation analysis procedure is a promising tool for studying large and heterogeneous EEM data sets.

A Monte Carlo approach to the inverse problem of diffuse pollution risk in agricultural catchments

The hydrological and biogeochemical processes that operate in catchments influence the ecological quality of freshwater systems through delivery of fine sediment, nutrients and organic matter. Most models that seek to characterise the delivery of diffuse pollutants from land to water are reductionist. The multitude of processes that are parameterised in such models to ensure generic applicability make them complex and difficult to test on available data. Here, we outline an alternative - data-driven - inverse approach. We apply SCIMAP, a parsimonious risk based model that has an explicit treatment of hydrological connectivity. we take a Bayesian approach to the inverse problem of determining the risk that must be assigned to different land uses in a catchment in order to explain the spatial patterns of measured in-stream nutrient concentrations. We apply the model to identify the key sources of nitrogen (N) and phosphorus (P) diffuse pollution risk in eleven UK catchments covering a range of landscapes. The model results show that: 1) some land use generates a consistently high or low risk of diffuse nutrient pollution; but 2) the risks associated with different land uses vary both between catchments and between nutrients; and 3) that the dominant sources of P and N risk in the catchment are often a function of the spatial configuration of land uses. Taken on a case-by-case basis, this type of inverse approach may be used to help prioritise the focus of interventions to reduce diffuse pollution risk for freshwater ecosystems. (C) 2012 Elsevier B.V. All rights reserved.

El poblament prehistòric i tardoromà al paratge de Montcortès i Pla de Corts: una síntesi

L’estancament que han patit històricament les comarques dels Pallars (Jussà i Sobirà) tant a nivell humà com econòmic, ha ajudat, fins fa pocs anys, a conservar fossilitzades estructures socials, religioses i humanes de diferents períodes, alhora que a nivell científic, aquest estancament té com a conseqüència la marginació quant al gruix de les investigacions que es fan a la resta del país. Es proposa en aquest treball de síntesi una anàlisi i contrastació de les dades que ens ofereix la historiografia quant al poblament i la seva evolució des de la Prehistòria fins al període tardoromà al Paratge de Montcortès i Pla de Corts (Baix Pallars, Pallars Sobirà), amb l’aportació de les darreres investigacions, encara sense publicar, que ens proporcionen, alhora que noves dades quantitatives, informació qualitativa sobre el funcionament d’aquests grups humans, és a dir, una nova perspectiva biofísica sobre la coevolució dels nous sistemes socioeconòmics amb els ecosistemes naturals en aquest territori.

Facing the broader dimensions of biological invasions

Invasive species are an excellent opportunity to think about the nature society desires, particularly in the face of global changes. Nature and human views of nature are rapidly evolving; our approach to bio- logical invasions through biosecurity institutions and land management policies must evolve in tandem with these changes. We review three dimensions that are insufficiently addressed. First, biological inva- sions are culturally shaped and interpreted. Humans play a major role in the movement and nurturing of alien life, and esthetics, perception, and emotion are deeply implicated in the management of invasive species. What people fear or regret with invasive species are not their effects on nature per se, but their effects on a particular desired nature, and policymaking must reflect this. Second, biological invasions are not restricted to negative impacts. Invasions take place in landscapes where many natural condi- tions have been altered, so policy tools must recognize that invasive species are a functional, structural, and compositional part of transformed ecosystems. In some cases, native species benefit from changes in resource availability caused by invasions or from protections provided by an invasive plant. Finally, invasive species can help ecosystems and people to adapt to global change by maintaining ecosystem processes such as productivity, carbon storage, and nutrient cycling in a context of climate change or land cover transformations. While recognition is growing among ecologists that novel, invaded ecosystems have value, and while the on-the-ground application of biosecurity policies has of necessity adjusted to local contexts and other agendas, invasion biology could aid policymaking by better addressing the three complexities inherent in the three dimensions highlighted above.

Modelling bird species richness with neural networks for forest landscape management in NE Spain

Para preservar la biodiversidad de los ecosistemas forestales de la Europa mediterránea en escenarios actuales y futuros de cambio global mediante una gestión forestal sostenible es necesario determinar cómo influye el medio ambiente y las propias características de los bosques sobre la biodiversidad que éstos albergan. Con este propósito, se analizó la influencia de diferentes factores ambientales y de estructura y composición del bosque sobre la riqueza de aves forestales a escala 1 × 1 km en Cataluña (NE de España). Se construyeron modelos univariantes y multivariantes de redes neuronales para respectivamente explorar la respuesta individual a las variables y obtener un modelo parsimonioso (ecológicamente interpretable) y preciso. La superficie de bosque (con una fracción de cabida cubierta superior a 5%), la fracción de cabida cubierta media, la temperatura anual y la precipitación estival medias fueron los mejores predictores de la riqueza de aves forestales. La red neuronal multivariante obtenida tuvo una buena capacidad de generalización salvo en las localidades con una mayor riqueza. Además, los bosques con diferentes grados de apertura del dosel arbóreo, más maduros y más diversos en cuanto a su composición de especies arbóreas se asociaron de forma positiva con una mayor riqueza de aves forestales. Finalmente, se proporcionan directrices de gestión para la planificación forestal que permitan promover la diversidad ornítica en esta región de la Europa mediterránea.

Defining ecological strategies in neuroprosthetics.

Neurological disorders disrupt the equilibrium within the brain and spinal cord ecosystems. Ecology reuses, recycles, and reduces to help maintain the balance across ecosystems. Likewise, neuroprosthetics can help the brain help itself with ecoprosthetic designs that integrate the principles of the "three 'R's."

Multi-scale effects of nestling diet on breeding performance in a terrestrial top predator inferred from stable isotope analysis

Inter-individual diet variation within populations is likely to have important ecological and evolutionary implications. The diet-fitness relationships at the individual level and the emerging population processes are, however, poorly understood for most avian predators inhabiting complex terrestrial ecosystems. In this study, we use an isotopic approach to assess the trophic ecology of nestlings in a long-lived raptor, the Bonelli"s eagle Aquila fasciata, and investigate whether nestling dietary breath and main prey consumption can affect the species" reproductive performance at two spatial scales: territories within populations and populations over a large geographic area. At the territory level, those breeding pairs whose nestlings consumed similar diets to the overall population (i.e. moderate consumption of preferred prey, but complemented by alternative prey categories) or those disproportionally consuming preferred prey were more likely to fledge two chicks. An increase in the diet diversity, however, related negatively with productivity. The age and replacements of breeding pair members had also an influence on productivity, with more fledglings associated to adult pairs with few replacements, as expected in long-lived species. At the population level, mean productivity was higher in those population-years with lower dietary breadth and higher diet similarity among territories, which was related to an overall higher consumption of preferred prey. Thus, we revealed a correspondence in diet-fitness relationships at two spatial scales: territories and populations. We suggest that stable isotope analyses may be a powerful tool to monitor the diet of terrestrial avian predators on large spatio-temporal scales, which could serve to detect potential changes in the availability of those prey on which predators depend for breeding. We encourage ecologists and evolutionary and conservation biologists concerned with the multi-scale fitness consequences of inter-individual variation in resource use to employ similar stable isotope-based approaches, which can be successfully applied to complex ecosystems such as the Mediterranean.

A wolf in sheep"s clothing: carnivory in dominant sea urchins in the Mediterranean

Arbacia lixula and Paracentrotus lividus are the dominant sea urchins in the Mediterranean sublittoral, where they are key structuring species due to their grazing activity. It has been commonly accepted that competition between both species is minimized by specializing in different algal foods. A. lixula is considered to feed mainly on encrusting coralline algae, while P. lividus prefers fleshy macroalgae. We used stable isotope analysis to test if these species occupy different trophic positions at 3 locations in the western Mediterranean and one in Macaronesia. Our results show unambiguously that A. lixula always occupies a higher trophic level than P. lividus, with a δ15N comparable in some locations to strict carnivores such as Actinia schmidti or Marthasterias glacialis. A temporal monitoring at one locality showed that this signature of a higher trophic level is consistent throughout the year. These results are incompatible with the current belief of an herbivorous diet for A. lixula and suggest that it must be considered an omnivore tending to carnivory in Mediterranean ecosystems, feeding at least partially on sessile animals such as Cirripedia, Hydrozoa or Bryozoa. A parallel analysis of gut contents showed a predominance of vegetal items in both species, although A. lixula consistently had a higher abundance of animal components than P. lividus. Our results challenge the validity of using gut content observations alone for characterizing the trophic behaviour of omnivorous marine invertebrates that feed on a variety of food sources with different digestibility.