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Houel, E.; Gonzalez, G.; Bessière, J.-M.; Odonne, G.; Eparvier, V.; Deharo, E.; Stien, D. |
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Title |
Therapeutic switching: From antidermatophytic essential oils to new leishmanicidal products |
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Journal Article |
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2015 |
Publication  |
Memorias do Inst. Oswaldo Cruz |
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110 |
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1 |
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106-113 |
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Antifungal agents; Antiparasitic agents; Leishmania; Peritoneal macrophages – sesquiterpenes; Therapeutic switching |
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This study examined whether the antidermatophytic activity of essential oils (EOs) can be used as an indicator for the discovery of active natural products against Leishmania amazonensis. The aerial parts of seven plants were hydrodistilled. Using broth microdilution techniques, the obtained EOs were tested against three strains of dermatophytes (Trichophyton mentagrophytes, Microsporum gypseum and Microsporum canis). To compare the EOs antifungal and antiparasitic effects, the EOs activities against axenic amastigotes of L. amazonensis were concurrently evaluated. For the most promising EOs, their antileishmanial activities against parasites infecting peritoneal macrophages of BALB/c mice were measured. The most interesting antifungal candidates were the EOs from Cymbopogon citratus, Otacanthus azureus and Protium heptaphyllum, whereas O. azureus, Piper hispidum and P. heptaphyllum EOs exhibited the lowest 50% inhibitory concentration (IC50) values against axenic amastigotes, thus revealing a certain correspondence between both activities. The P. hispidum EO was identified as the most promising product in the results from the infected macrophages model (IC50: 4.7 μg/mL, safety index: 8). The most abundant compounds found in this EO were sesquiterpenes, notably curzerene and furanodiene. Eventually, the evaluation of the antidermatophytic activity of EOs appears to be an efficient method for identifying new potential drugs for the treatment of L. amazonensis. |
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Export Date: 17 March 2015 |
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EcoFoG @ webmaster @ |
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587 |
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Gargallo-Garriga, Albert ; Sardans, Jordi ; Alrefaei, Abdulwahed Fahad ; Klem, Karel ; Fuchslueger, Lucia ; Ramirez-Rojas, Irène ; Donald, Julian ; Leroy, Celine ; Van Langenhove, Leandro ; Verbruggen, Erik ; Janssens, Ivan A. ; Urban, Otmar ; Penuelas, Josep |
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Tree Species and Epiphyte Taxa Determine the “Metabolomic niche” of Canopy Suspended Soils in a Species-Rich Lowland Tropical Rainforest |
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Journal Article |
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2021 |
Publication |
Metabolites |
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11 |
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11 |
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Bacteria, Canopy soils, Epiphyte, French Guiana, Metabolomics |
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Tropical forests are biodiversity hotspots, but it is not well understood how this diversity is structured and maintained. One hypothesis rests on the generation of a range of metabolic niches, with varied composition, supporting a high species diversity. Characterizing soil metabolomes can reveal fine-scale differences in composition and potentially help explain variation across these habitats. In particular, little is known about canopy soils, which are unique habitats that are likely to be sources of additional biodiversity and biogeochemical cycling in tropical forests. We studied the effects of diverse tree species and epiphytes on soil metabolomic profiles of forest floor and canopy suspended soils in a French Guianese rainforest. We found that the metabolomic profiles of canopy suspended soils were distinct from those of forest floor soils, differing between epiphyte-associated and non-epiphyte suspended soils, and the metabolomic profiles of suspended soils varied with host tree species, regardless of association with epiphyte. Thus, tree species is a key driver of rainforest suspended soil metabolomics. We found greater abundance of metabolites in suspended soils, particularly in groups associated with plants, such as phenolic compounds, and with metabolic pathways related to amino acids, nucleotides, and energy metabolism, due to the greater relative proportion of tree and epiphyte organic material derived from litter and root exudates, indicating a strong legacy of parent biological material. Our study provides evidence for the role of tree and epiphyte species in canopy soil metabolomic composition and in maintaining the high levels of soil metabolome diversity in this tropical rainforest. It is likely that a wide array of canopy microsite-level environmental conditions, which reflect interactions between trees and epiphytes, increase the microscale diversity in suspended soil metabolomes |
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MDPI |
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EcoFoG @ webmaster @ |
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1041 |
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Molto, Q.; Rossi, V.; Blanc, L. |
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Title |
Error propagation in biomass estimation in tropical forests |
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Journal Article |
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2013 |
Publication |
Methods in Ecology and Evolution |
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4 |
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2 |
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175-183 |
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Bayesian framework; Modelling; Redd; Uncertainty propagation |
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Reliable above-ground biomass (AGB) estimates are required for studies of carbon fluxes and stocks. However, there is a huge lack of knowledge concerning the precision of AGB estimates and the sources of this uncertainty. At the tree level, the tree height is predicted using the tree diameter at breast height (DBH) and a height sub-model. The wood-specific gravity (WSG) is predicted with taxonomic information and a WSG sub-model. The tree mass is predicted using the predicted height, the predicted WSG and the biomass sub-model. Our models were inferred with Bayesian methods and the uncertainty propagated with a Monte Carlo scheme. The uncertainties in the predictions of tree height, tree WSG and tree mass were neglected sequentially to quantify their contributions to the uncertainty in AGB. The study was conducted in French Guiana where long-term research on forest ecosystems provided an outstanding data collection on tree height, tree dynamics, tree mass and species WSG. We found that the uncertainty in the AGB estimates was found to derive primarily from the biomass sub-model. The models used to predict the tree heights and WSG contributed negligible uncertainty to the final estimate. Considering our results, a poor knowledge of WSG and the height-diameter relationship does not increase the uncertainty in AGB estimates. However, it could lead to bias. Therefore, models and databases should be used with care. This study provides a methodological framework that can be broadly used by foresters and plant ecologist. It provides the accurate confidence intervals associated with forest AGB estimates made from inventory data. When estimating region-scale AGB values (through spatial interpolation, spatial modelling or satellite signal treatment), the uncertainty of the forest AGB value in the reference forest plots has to be taken in account. We believe that in the light of the Reducing Emissions from Deforestation and Degradation debate, our method is a crucial step in monitoring carbon stocks and their spatio-temporal evolution. © 2012 The Authors. Methods in Ecology and Evolution © 2012 British Ecological Society. |
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CIRAD, UMR 'Ecologie des Forêts de Guyane', Kourou Cedex, 97 379, France |
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Export Date: 21 February 2013; Source: Scopus |
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EcoFoG @ webmaster @ |
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470 |
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Mortier, F.; Rossi, V.; Guillot, G.; Gourlet-Fleury, S.; Picard, N. |
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Population dynamics of species-rich ecosystems: The mixture of matrix population models approach |
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Journal Article |
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2013 |
Publication |
Methods in Ecology and Evolution |
Abbreviated Journal |
Methods Ecol. Evol. |
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4 |
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4 |
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316-326 |
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Bayesian; Clustering; Mixture models; Population dynamics; Reversible jump Markov chain Monte Carlo; Species-rich ecosystems; Tropical rain forests |
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Matrix population models are widely used to predict population dynamics, but when applied to species-rich ecosystems with many rare species, the small population sample sizes hinder a good fit of species-specific models. This issue can be overcome by assigning species to groups to increase the size of the calibration data sets. However, the species classification is often disconnected from the matrix modelling and from the estimation of matrix parameters, thus bringing species groups that may not be optimal with respect to the predicted community dynamics. We proposed here a method that jointly classified species into groups and fit the matrix models in an integrated way. The model was a special case of mixture with unknown number of components and was cast in a Bayesian framework. An MCMC algorithm was developed to infer the unknown parameters: the number of groups, the group of each species and the dynamics parameters. We applied the method to simulated data and showed that the algorithm efficiently recovered the model parameters. We applied the method to a data set from a tropical rain forest in French Guiana. The mixture matrix model classified tree species into well-differentiated groups with clear ecological interpretations. It also accurately predicted the forest dynamics over the 16-year observation period. Our model and algorithm can straightforwardly be adapted to any type of matrix model, using the life cycle diagram. It can be used as an unsupervised classification technique to group species with similar population dynamics. © 2012 The Authors. Methods in Ecology and Evolution © 2012 British Ecological Society. |
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Statistics Section IMM, Technical University of Denmark, Copenhagen, Denmark |
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2041210x (Issn) |
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Export Date: 16 April 2013; Source: Scopus; :doi 10.1111/2041-210x.12019; Language of Original Document: English; Correspondence Address: Mortier, F.; CIRAD, UPR Bsef, Montpellier, 34398, France; email: frederic.mortier@cirad.fr |
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EcoFoG @ webmaster @ |
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480 |
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Marcon, E.; Herault, B. |
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Decomposing phylodiversity |
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Journal Article |
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2015 |
Publication |
Methods in Ecology and Evolution |
Abbreviated Journal |
Methods in Ecology and Evolution |
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6 |
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3 |
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333-339 |
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Biodiversity; Entropy; Functional diversity; Phylogenetic diversity |
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Measuring functional or phylogenetic diversity is the object of an active literature. The main issues to address are relating measures to a clear conceptual framework, allowing unavoidable estimation-bias correction and decomposing diversity along spatial scales. We provide a general mathematical framework to decompose measures of species-neutral, phylogenetic or functional diversity into α and β components. We first unify the definitions of phylogenetic and functional entropy and diversity as a generalization of HCDT entropy and Hill numbers when an ultrametric tree is considered. We then derive the decomposition of diversity. We propose a bias correction of the estimates allowing meaningful computation from real, often undersampled communities. Entropy can be transformed into true diversity, that is an effective number of species or communities. Estimators of α- and β-entropy, phylogenetic and functional entropy are provided. Proper definition and estimation of diversity is the first step towards better understanding its underlying ecological and evolutionary mechanisms. © 2015 British Ecological Society. |
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Cirad, UMR EcoFoG, BP 709Kourou, French Guiana |
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Export Date: 31 March 2015 |
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EcoFoG @ webmaster @ |
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590 |
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Pavoine, S.; Marcon, E.; Ricotta, C. |
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‘Equivalent numbers’ for species, phylogenetic or functional diversity in a nested hierarchy of multiple scales |
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Journal Article |
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2016 |
Publication |
Methods in Ecology and Evolution |
Abbreviated Journal |
Methods in Ecology and Evolution |
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7 |
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10 |
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1152-1163 |
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alpha diversity; beta diversity; biodiversity; community ecology; community phylogenetics; diversity apportionment; gamma diversity; quadratic entropy |
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Many recent studies have searched to integrate species’ functions and phylogenies in the measurement of biodiversity. To obtain easily interpretable measures, some researchers recommended diversity indices expressed in terms of equivalent numbers of species: the number of equally likely and maximally dissimilar species needed to produce the given value of diversity. Then, biodiversity is often calculated at three scales: within communities (α diversity), among communities (β diversity) and in a region (γ diversity). These three scales are, however, insufficient to tackle the organization of biodiversity in space because, for most organisms, there is a nested hierarchy of multiple scales characterized by different patterns and processes, from the small neighbourhood to the biosphere. We developed methodologies for analysing species, functional, taxonomic or phylogenetic diversity in a hierarchy of multiple scales using equivalent numbers of species. As an example, we analysed the taxonomic and functional diversity of macroinvertebrate assemblages in the Loire River, France, at four levels: within sites (α diversity), among sites within geological regions (β1 diversity), among geological regions (β2 diversity) and at the river scale (γ diversity). The new hierarchical approaches of biodiversity revealed very low differences among sites within regions and among regions in terms of taxonomy and functional traits (size and diet), despite moderate, significant species turnover among geological regions. We compare our framework with those other authors have developed. We argue that different definitions of α, β, γ diversities are used in the literature reflecting different points of view on biodiversity. We make recommendations on how to normalize functional (or phylogenetic) dissimilarities among species to render sites and regions comparable, and discuss the pros and cons of our approach. The hierarchical approaches of biodiversity in terms of ‘equivalent numbers’ respond to current demands to obtain intuitive, easily interpretable components of biodiversity. The approaches we propose go beyond current developments by considering a hierarchy of spatial scales and unbalanced sampling design. They will provide powerful tools to detect the ecological and evolutionary processes that act differently at different scales. © 2016 The Authors. Methods in Ecology and Evolution © 2016 British Ecological Society |
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Department of Environmental Biology, University of Rome ‘La Sapienza’, Piazzale Aldo Moro 5, Rome, Italy |
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Export Date: 20 October 2016 |
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EcoFoG @ webmaster @ |
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697 |
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Perrot, T.; Guillaume, S.; Nadine, A.; Jacques, B.; Philippe, G.; Stéphane, D.; Rodnay, S.; Mélanie, M.-R.; Eric, G. |
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A reverse chemical ecology approach to explore wood natural durability |
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2020 |
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Microbial Biotechnology |
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Microb. Biotechnol. |
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13 |
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5 |
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1673-1677 |
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glutathione transferase; Article; biodegradation; data base; detoxification; ecology; enzyme activity; enzyme metabolism; forest; molecular dynamics; physical parameters; species identification; thermal analysis; Trametes versicolor; wood; wood durability |
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The natural durability of wood species, defined as their inherent resistance to wood-destroying agents, is a complex phenomenon depending on many biotic and abiotic factors. Besides the presence of recalcitrant polymers, the presence of compounds with antimicrobial properties is known to be important to explain wood durability. Based on the advancement in our understanding of fungal detoxification systems, a reverse chemical ecology approach was proposed to explore wood natural durability using fungal glutathione transferases. A set of six glutathione transferases from the white-rot Trametes versicolor were used as targets to test wood extracts from seventeen French Guiana neotropical species. Fluorescent thermal shift assays quantified interactions between fungal glutathione transferases and these extracts. From these data, a model combining this approach and wood density significantly predicts the wood natural durability of the species tested previously using long-term soil bed tests. Overall, our findings confirm that detoxification systems could be used to explore the chemical environment encountered by wood-decaying fungi and also wood natural durability. © 2020 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology. |
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Université de Lorraine, INRAE, LERMAB, Nancy, France |
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John Wiley and Sons Ltd |
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17517907 (Issn) |
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EcoFoG @ webmaster @ |
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955 |
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Schimann, H.; Bach, C.; Lengelle, J.; Louisanna, E.; Barantal, S.; Murat, C.; Buée, M. |
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Diversity and Structure of Fungal Communities in Neotropical Rainforest Soils: The Effect of Host Recurrence |
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2017 |
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Microbial Ecology |
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Microbial Ecology |
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73 |
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2 |
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310-320 |
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Amazonian forest; Fungal communities; Host recurrence; Litter; Second-generation sequencing; Soil |
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The patterns of the distribution of fungal species and their potential interactions with trees remain understudied in Neotropical rainforests, which harbor more than 16,000 tree species, mostly dominated by endomycorrhizal trees. Our hypothesis was that tree species shape the non-mycorrhizal fungal assemblages in soil and litter and that the diversity of fungal communities in these two compartments is partly dependent on the coverage of trees in the Neotropical rainforest. In French Guiana, a long-term plantation and a natural forest were selected to test this hypothesis. Fungal ITS1 regions were sequenced from soil and litter samples from within the vicinity of tree species. A broad range of fungal taxa was found, with 42 orders and 14 classes. Significant spatial heterogeneity in the fungal communities was found without strong variation in the species richness and evenness among the tree plots. However, tree species shaped the fungal assemblages in the soil and litter, explaining up to 18 % of the variation among the communities in the natural forest. These results demonstrate that vegetation cover has an important effect on the structure of fungal assemblages inhabiting the soil and litter in Amazonian forests, illustrating the relative impact of deterministic processes on fungal community structures in these highly diverse ecosystems. © 2016, Springer Science+Business Media New York. |
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Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche en Environnement et Matériaux, Université de Pau et Pays de l’Adour, Pau, France |
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Export Date: 19 February 2017 |
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EcoFoG @ webmaster @ |
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734 |
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Picard, N.; Gourlet-Fleury, S.; Sist, P. |
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Using process-dependent groups of species to model the dynamics of a tropical rainforest |
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2003 |
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Modelling Forest Systems |
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237-248 |
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The high tree species diversity in tropical forests is difficult to take into account in models. The usual solution consists of defining groups of species and then adjusting a set of parameters for each group. In this study, we address this issue by allowing a species to move from one species group to another, depending on the biological process that is concerned. We developed this approach with a matrix model of forest dynamics, for a tropical rainforest in French Guiana, at Paracou, focusing on the methodological aspects. The forest dynamics is split into three components: recruitment, growth and mortality. We then built five recruitment groups, five growth groups and five mortality groups. One species is characterized by a combination of the three groups, thus yielding in total 5 X 5 X 5 = 125 possibilities, out of which 43 are actually observed. The resulting matrix model provides a better view of the floristic composition of the forest, and does not have more parameters than it would have with five global species groups. However, its predictions are no more precise than those of the matrix model based on five global groups. |
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Cirad Foret, Montpellier, France |
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CABI PUBLISHING |
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ISI:000231866400021 |
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EcoFoG @ eric.marcon @ |
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249 |
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Strasburg, J.L.; Scotti-Saintagne, C.; Scotti, I.; Lai, Z.; Rieseberg, L.H. |
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Genomic Patterns of Adaptive Divergence between Chromosomally Differentiated Sunflower Species |
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Journal Article |
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2009 |
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Molecular Biology and Evolution |
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Mol. Biol. Evol. |
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26 |
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6 |
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1341-1355 |
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species boundaries; chromosomal rearrangements; positive selection; hybridization; sunflowers; Helianthus |
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Understanding the genetic mechanisms of speciation and basis of species differences is among the most important challenges in evolutionary biology. Two questions of particular interest are what roles divergent selection and chromosomal differentiation play in these processes. A number of recently proposed theories argue that chromosomal rearrangements can facilitate the development and maintenance of reproductive isolation and species differences by suppressing recombination within rearranged regions. Reduced recombination permits the accumulation of alleles contributing to isolation and adaptive differentiation and protects existing differences from the homogenizing effects of introgression between incipient species. Here, we examine patterns of genetic diversity and divergence in rearranged versus collinear regions in two widespread, extensively hybridizing sunflower species, Helianthus annuus and Helianthus petiolaris, using sequence data from 77 loci distributed throughout the genomes of the two species. We find weak evidence for increased genetic divergence near chromosomal break points but not within rearranged regions overall. We find no evidence for increased rates of adaptive divergence on rearranged chromosomes; in fact, collinear chromosomes show a far greater excess of fixed amino acid differences between the two species. A comparison with a third sunflower species indicates that much of the nonsynonymous divergence between H. annuus and H. petiolaris probably occurred during or soon after their formation. Our results suggest a limited role for chromosomal rearrangements in genetic divergence, but they do document substantial adaptive divergence and provide further evidence of how species integrity and genetic identity can be maintained at many loci in the face of extensive hybridization and gene flow. |
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Address |
[Strasburg, Jared L.; Scotti-Saintagne, Caroline; Rieseberg, Loren H.] Indiana Univ, Dept Biol, Bloomington, IN 47405 USA, Email: jstrasbu@indiana.edu |
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Publisher |
OXFORD UNIV PRESS |
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Edition |
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ISSN |
0737-4038 |
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Notes |
ISI:000266116500012 |
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no |
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Call Number |
EcoFoG @ eric.marcon @ |
Serial |
111 |
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