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Author |
Donald, J.; Maxfield, P.; Leroy, C.; Ellwood, M.D.F. |
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Title |
Epiphytic suspended soils from Borneo and Amazonia differ in their microbial community composition |
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Journal Article |
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Year |
2020 |
Publication |
Acta Oecologica |
Abbreviated Journal |
Acta Oecol. |
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Volume |
106 |
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Keywords |
Asplenium; Bacteria; Borneo; Bromeliaceae; Canopy; French Guiana; Fungi; Plfa; Rainforest; bacterium; community composition; epiphyte; fungus; microbial community; niche; relative abundance; soil microorganism; species diversity; tropical forest; Amazonia; Borneo; Danum Valley; East Malaysia; French Guiana; Malaysia; Nouragues; Sabah; Asplenium; Asplenium nidus; Aves; Bacteria (microorganisms); Bromeliaceae; Fungi |
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Microbial organisms support the high species diversity associated with tropical forests, and likely drive functional processes, but microorganisms found in rainforest canopies are not well understood. We quantified the microbial diversity of suspended soils from two classical epiphytic model systems (bromeliads & bird's nest ferns) across two localities: the Nouragues Reserve in French Guiana and Danum Valley in Malaysian Borneo. Non-epiphytic suspended soils were also collected as controls at the Nouragues Reserve. Effects of epiphyte type and sample location on microbial community composition were determined using Phospholipid Fatty Acid (PLFA) analysis. Total microbial biomass remained constant across the suspended soil types, but PLFA peaks denoting the relative abundance of different microbes varied between bromeliads, bird's nest ferns and non-epiphytic control soils. Suspended soils associated with bird's nest ferns from Borneo contained a microbial community significantly different in composition from those of congeneric bird's nest ferns from Amazonia, due to shifts in the relative abundance of fungi and bacteria. Our findings reveal that epiphytes create convergent niches for microorganisms in tropical canopies, while highlighting the sensitive nature of suspended soil microbial communities. © 2020 Elsevier Masson SAS |
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20 Baily Place, Cheswick, Bristol, BS16 1BG, United Kingdom |
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Elsevier B.V. |
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1146609x (Issn) |
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EcoFoG @ webmaster @ |
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959 |
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Schimann, H.; Joffre, R.; Roggy, J.C.; Lensi, R.; Domenach, A.M. |
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Title |
Evaluation of the recovery of microbial functions during soil restoration using near-infrared spectroscopy |
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Journal Article |
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Year |
2007 |
Publication |
Applied Soil Ecology |
Abbreviated Journal |
Appl. Soil Ecol. |
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Volume |
37 |
Issue |
3 |
Pages |
223-232 |
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NIRS; microbial activities; respiration; denitrification; carbon; nitrogen; soil functioning; restoration |
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Microbial-based indicators, such as C and N contents or microbial functions involved in C and N cycles, are currently used to describe the status of soils in disturbed areas. Microbial functions are more accurate indicators but their measurement for studies at the ecosystem level remains problematical because of the huge spatial variability of these processes and, consequently, of the large number of soil samples which must be analyzed. Our goal was to test the capacity of near-infrared reflectance spectroscopy (NIRS) to predict respiration and denitrification but also carbon and nitrogen contents of soils submitted to various procedures of restoration. To achieve this objective, we took advantage of an experiment conducted on a reforestation system established after open-cast gold mining in French Guiana. In this experimental station, plantations of various ages and various soil textures were at our disposal. Our results showed that both plantations and soil texture had a strong impact on the recovery of soil functioning: carbon and nitrogen contents, respiration and denitrification increased with age of plantation and clay content. Calibrations were performed between spectral data and microbial-based indicators using partial least squares regression (PLS). The results showed that C and N contents were accurately predicted. Microbial functions were less precisely predicted with results more accurate on clayey soils than on sandy soils. In clayey soils, perturbed or restored soils and the year of plantation were discriminated very efficiently through principal component analyses of spectral signatures (over 80% of variance explained on the first two axes). Near-infrared spectroscopy may thus be extended to the prediction of functional soil parameters, but the capacity of this method must be strengthened by expending the databases with other soils in other contexts. The possibility of using NIRS provides many opportunities for understanding both the temporal dynamics and the spatial variability of the recovery of key microbial functions during soil restoration. (c) 2007 Elsevier B.V. All rights reserved. |
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UMR EcoFoG, Kourou 97387, French Guiana, Email: heidy.schimann@cirad.fr |
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ELSEVIER SCIENCE BV |
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0929-1393 |
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ISI:000250668000006 |
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EcoFoG @ eric.marcon @ |
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154 |
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van Gorsel, E.; Delpierre, N.; Leuning, R.; Black, A.; Munger, J.W.; Wofsy, S.; Aubinet, M.; Feigenwinter, C.; Beringer, J.; Bonal, D.; Chen, B.Z.; Chen, J.Q.; Clement, R.; Davis, K.J.; Desai, A.R.; Dragoni, D.; Etzold, S.; Grunwald, T.; Gu, L.H.; Heinesch, B.; Hutyra, L.R.; Jans, W.W.P.; Kutsch, W.; Law, B.E.; Leclerc, M.Y.; Mammarella, I.; Montagnani, L.; Noormets, A.; Rebmann, C.; Wharton, S. |
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Title |
Estimating nocturnal ecosystem respiration from the vertical turbulent flux and change in storage of CO2 |
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Journal Article |
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Year |
2009 |
Publication |
Agricultural and Forest Meteorology |
Abbreviated Journal |
Agric. For. Meteorol. |
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Volume |
149 |
Issue |
11 |
Pages |
1919-1930 |
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Keywords |
Ecosystem respiration; Micrometeorology; Advection; u-star correction; Eddy covariance; Chamber; Process-based modelling |
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Micrometeorological measurements of night time ecosystem respiration can be systematically biased when stable atmospheric conditions lead to drainage flows associated with decoupling of air flow above and within plant canopies. The associated horizontal and vertical advective fluxes cannot be measured using instrumentation on the single towers typically used at micrometeorological sites. A common approach to minimize bias is to use a threshold in friction velocity, u*, to exclude periods when advection is assumed to be important, but this is problematic in situations when in-canopy flows are decoupled from the flow above. Using data from 25 flux stations in a wide variety of forest ecosystems globally, we examine the generality of a novel approach to estimating nocturnal respiration developed by van Gorsel et al. (van Gorsel, E., Leuning, R., Cleugh, H.A., Keith, H., Suni, T., 2007. Nocturnal carbon efflux: reconciliation of eddy covariance and chamber measurements using an alternative to the u*-threshold filtering technique. Tellus 59B, 397-403, Tellus, 59B, 307-403). The approach is based on the assumption that advection is small relative to the vertical turbulent flux (F-C) and change in storage (F-S) of CO2 in the few hours after sundown. The sum of F-C and F-S reach a maximum during this period which is used to derive a temperature response function for ecosystem respiration. Measured hourly soil temperatures are then used with this function to estimate respiration R-Rmax. The new approach yielded excellent agreement with (1) independent measurements using respiration chambers, (2) with estimates using ecosystem light-response curves of F-c + F-s extrapolated to zero light, R-LRC, and (3) with a detailed process-based forest ecosystem model, R-cast. At most sites respiration rates estimated using the u*-filter, R-ust, were smaller than R-Rmax, and R-LRC. Agreement of our approach with independent measurements indicates that R-Rmax, provides an excellent estimate of nighttime ecosystem respiration. (C) 2009 Elsevier B.V. All rights reserved. |
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[van Gorsel, Eva; Leuning, Ray] CSIRO Marine & Atmospher Res, Canberra, ACT 2061, Australia, Email: Eva.vangorsel@csiro.au |
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ELSEVIER SCIENCE BV |
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0168-1923 |
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ISI:000270640300013 |
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EcoFoG @ eric.marcon @ |
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102 |
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Millet, J.; Pascal, J.P.; Kiet, L.C. |
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Title |
Effects of Disturbance Over 60 Years on a Lowland Forest in Southern Vietnam |
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Journal Article |
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Year |
2010 |
Publication |
Journal of Tropical Forest Science |
Abbreviated Journal |
J. Trop. For. Sci. |
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Volume |
22 |
Issue |
3 |
Pages |
237-246 |
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Keywords |
Lowland tropical forest; disturbance impact; floristic composition; forest structure; Tan Phu forest |
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MILLET J, PASCAL JP & MET LC. 2010. Effects of disturbance over 60 years on a lowland forest in southern Vietnam. Tropical lowland forests are some of the most threatened in the world and this is particularly the case in Vietnam. This study aimed to identify changes in species composition and forest structure in the Tan Phu lowland forest resulting from disturbance over a 60 year period. Analysis of forest composition and structure rely on data from 25 plots of 0.5-ha size established in a lowland secondary forest. The five forest stands described differed greatly from the three forest stand types described in 1943. Some long-lived shade-tolerant species had been replaced by pioneer species, such as Cratoxylon formosum and Shorea roxburghii. In addition to altering composition, forest disturbances had resulted in large changes in forest structure. While in the past, forest stands had a large number of exploitable trees, current forest stands have few trees in the diameter class > 50 cm and sometimes no trees in the diameter class > 80 cm. This paper provides notable results on forest tree ecology, forest dynamics and on the state of secondary forests in Vietnam. This is particularly important as future goods and services will increasingly have to come from such forests. |
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[Millet, J.] Univ Lyon 1, F-69622 Villeurbanne, France, Email: jerome.millet@ird.if |
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FOREST RESEARCH INST MALAYSIA |
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0128-1283 |
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ISI:000280653200003 |
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EcoFoG @ webmaster @ |
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283 |
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Wagner, F.; Herault, B.; Stahl, C.; Bonal, D.; Rossi, V. |
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Title |
Modeling water availability for trees in tropical forests |
Type |
Journal Article |
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Year |
2011 |
Publication |
Agricultural and Forest Meteorology |
Abbreviated Journal |
Agric. For. Meteorol. |
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Volume |
151 |
Issue |
9 |
Pages |
1202-1213 |
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Keywords |
Water balance model; Amazonian rainforest; Time domain reflectometer; Bayesian inference; Tree drought stress |
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Modeling soil water availability for tropical trees is a prerequisite to predicting the future impact of climate change on tropical forests. In this paper we develop a discrete-time deterministic water balance model adapted to tropical rainforest climates, and we validate it on a large dataset that includes micrometeorological and soil parameters along a topographic gradient in a lowland forest of French Guiana. The model computes daily water fluxes (rainfall interception, drainage, tree transpiration and soil plus understorey evapotranspiration) and soil water content using three input variables: daily precipitation, potential evapotranspiration and solar radiation. A novel statistical approach is employed that uses Time Domain Reflectometer (TDR) soil moisture data to estimate water content at permanent wilting point and at field capacity, and root distribution. Inaccuracy of the TDR probes and other sources of uncertainty are taken into account by model calibration through a Bayesian framework. Model daily output includes relative extractable water, REW, i.e. the daily available water standardized by potential available water. The model succeeds in capturing temporal variations in REW regardless of topographic context. The low Root Mean Square Error of Predictions suggests that the model captures the most important drivers of soil water dynamics, i.e. water refilling and root water extraction. Our model thus provides a useful tool to explore the response of tropical forests to climate scenarios of changing rainfall regime and intensity. (C) 2011 Elsevier B.V. All rights reserved. |
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[Wagner, F; Herault, B] Univ Antilles Guyane, UMR Ecol Forets Guyane, F-97387 Kourou, France, Email: fabien.wagner@ecofog.gf |
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Elsevier Science Bv |
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0168-1923 |
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WOS:000294032000005 |
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EcoFoG @ webmaster @ |
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337 |
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Flores, O.; Rossi, V.; Mortier, F. |
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Title |
Autocorrelation offsets zero-inflation in models of tropical saplings density |
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Journal Article |
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2009 |
Publication |
Ecological Modelling |
Abbreviated Journal |
Ecol. Model. |
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Volume |
220 |
Issue |
15 |
Pages |
1797-1809 |
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Hierarchical Bayesian Modelling; Conditional Auto-Regressive model; Variable selection; Zero-Inflated Poisson; Posterior predictive; Paracou; French Guiana |
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Modelling the local density of tropical saplings can provide insights into the ecological processes that drive species regeneration and thereby help predict population recovery after disturbance. Yet, few studies have addressed the challenging issues in autocorrelation and zero-inflation of local density. This paper presents Hierarchical Bayesian Modelling (HBM) of sapling density that includes these two features. Special attention is devoted to variable selection, model estimation and comparison. We developed a Zero-Inflated Poisson (ZIP) model with a latent correlated spatial structure and compared it with non-spatial ZIP and Poisson models that were either autocorrelated (Spatial Generalized Linear Mixed, SGLM) or not (generalized linear models, GLM). In our spatial models, local density autocorrelation was modeled by a Conditional Auto-Regressive (CAR) process. 13 explicative variables described ecological conditions with respect to topography, disturbance, stand structure and intraspecific processes. Models were applied to six tropical tree species with differing biological attributes: Oxandra asbeckii, Eperua falcata, Eperua grandiflora, Dicorynia guianensis, Qualea rosea, and Tachigali melinonii. We built species-specific models using a simple method of variable selection based on a latent binary indicator. Our spatial models showed a close correlation between observed and estimated densities with site spatial structure being correctly reproduced. By contrast, the non-spatial models showed poor fits. Variable selection highlighted species-specific requirements and susceptibility to local conditions. Model comparison overall showed that the SGLM was the most accurate explanatory and predictive model. Surprisingly, zero-inflated models performed less well. Although the SZIP model was relevant with respect to data distribution, and more flexible with respect to response curves, its model complexity caused marked variability in parameter estimates. In the SUM, the spatial process alone accounted for zero-inflation in the data. A refinement of the hypotheses employed at the process level could compensate for distribution flaws at the data level. This study emphasized the importance of the HBM framework in improving the modelling of density-environment relationships. (C) 2008 Elsevier B.V. All rights reserved. |
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[Flores, O.] CNRS, Ctr Ecol Fonct & Evolut, UMR 5175, F-34293 Montpellier 5, France, Email: olivierflores@free.fr |
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ELSEVIER SCIENCE BV |
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0304-3800 |
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ISI:000267585400007 |
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EcoFoG @ eric.marcon @ |
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201 |
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Grabchak, M.; Marcon, E.; Lang, G.; Zhang, Z. |
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Title |
The generalized Simpson’s entropy is a measure of biodiversity |
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Journal Article |
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2017 |
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Plos One |
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Plos One |
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12 |
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3 |
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e0173305 |
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Modern measures of diversity satisfy reasonable axioms, are parameterized to produce diversity profiles, can be expressed as an effective number of species to simplify their interpretation, and come with estimators that allow one to apply them to real-world data. We introduce the generalized Simpson’s entropy as a measure of diversity and investigate its properties. We show that it has many useful features and can be used as a measure of biodiversity. Moreover, unlike most commonly used diversity indices, it has unbiased estimators, which allow for sound estimation of the diversity of poorly sampled, rich communities. |
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Public Library of Science |
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EcoFoG @ webmaster @ |
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742 |
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Fu, T.; Houel, E.; Amusant, N.; Touboul, D.; Genta-Jouve, G.; Della-Negra, S.; Fisher, G.L.; Brunelle, A.; Duplais, C. |
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Biosynthetic investigation of γ-lactones in Sextonia rubra wood using in situ TOF-SIMS MS/MS imaging to localize and characterize biosynthetic intermediates |
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Journal Article |
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2019 |
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Scientific Reports |
Abbreviated Journal |
Sci. Rep. |
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9 |
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1928 |
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Molecular analysis by parallel tandem mass spectrometry (MS/MS) imaging contributes to the in situ characterization of biosynthetic intermediates which is crucial for deciphering the metabolic pathways in living organisms. We report the first use of TOF-SIMS MS/MS imaging for the cellular localization and characterization of biosynthetic intermediates of bioactive γ-lactones rubrynolide and rubrenolide in the Amazonian tree Sextonia rubra (Lauraceae). Five γ-lactones, including previously reported rubrynolide and rubrenolide, were isolated using a conventional approach and their structural characterization and localization at a lateral resolution of ~400 nm was later achieved using TOF-SIMS MS/MS imaging analysis. 2D/3D MS imaging at subcellular level reveals that putative biosynthetic γ-lactones intermediates are localized in the same cell types (ray parenchyma cells and oil cells) as rubrynolide and rubrenolide. Consequently, a revised metabolic pathway of rubrynolide was proposed, which involves the reaction between 2-hydroxysuccinic acid and 3-oxotetradecanoic acid, contrary to previous studies suggesting a single polyketide precursor. Our results provide insights into plant metabolite production in wood tissues and, overall, demonstrate that combining high spatial resolution TOF-SIMS imaging and MS/MS structural characterization offers new opportunities for studying molecular and cellular biochemistry in plants. © 2019, The Author(s). |
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Physical Electronics, Chanhassen, MN 55317, United States |
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Nature Publishing Group |
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20452322 (Issn) |
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EcoFoG @ webmaster @ |
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866 |
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Corbara, B.; Carpenter, J.M.; Cereghino, R.; Leponce, M.; Gibernau, M.; Dejean, A. |
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Diversity and nest site selection of social wasps along Guianese forest edges: assessing the influence of arboreal ants |
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Journal Article |
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Year |
2009 |
Publication |
Comptes Rendus Biologies |
Abbreviated Journal |
C. R. Biol. |
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332 |
Issue |
5 |
Pages |
470-479 |
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Polistinae; Diversity; Nest site selection; Ant-wasp-plant interactions; French Guiana |
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monitored), and estimate that we recorded up to 73% of the local social wasp fauna. This baseline study was complemented by a long-term survey of the same area and the examination of isolated trees (permitting us to record two additional species, resulting in a total of 63 wasp species). Our results form a continuum from species avoiding nesting on any plant (6.5% of the wasp species) to species nesting on plants but avoiding those sheltering ant nests (82%), to, finally, wasps nesting in association with arboreal ants known to divert army ant raids (11.5%). Consequently, this study documents that most wasp species select plants possibly repulsive to arboreal ants, while associations with arboreal ants, although confirmed here, have been overrepresented in the literature. To cite this article: B. Corbara et al., C. R. Biologies 332 (2009). (C) 2009 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved. |
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[Dejean, Alain] CNRS Guyane, UPS 2561, F-97300 Cayenne, France, Email: bruno.corbara@univ-bpclermont.fr |
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ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER |
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1631-0691 |
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ISI:000266021400007 |
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EcoFoG @ eric.marcon @ |
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113 |
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Gond, V.; Bartholome, E.; Ouattara, F.; Nonguierma, A.; Bado, L. |
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Monitoring and mapping of waters and wetlands in arid regions using the SPOT-4 VEGETATION imaging system |
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Journal Article |
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2004 |
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International Journal of Remote Sensing |
Abbreviated Journal |
Int. J. Remote Sens. |
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25 |
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5 |
Pages |
987-1004 |
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Abstract |
Monitoring the state of small waterbodies and wetlands is very useful in dry regions, because their existence is entirely controlled by the rhythm of local rainfall. On VEGETATION image colour composites, waterbodies and marshy vegetation show up clearly. Yet simple image classification does not yield sufficiently good results because 'spectral signatures' vary significantly together with the ecological conditions of these surfaces. A robust contextual procedure taking into account local contrast was successfully developed and tested. A systematic validation was carried out and a map of waterbodies and wetlands was produced for Burkina Faso and neighbouring regions. |
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Ctr Commun Rech, I-21020 Ispra, VA, Italy, Email: valery.gond@cirad.fr |
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TAYLOR & FRANCIS LTD |
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0143-1161 |
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ISI:000187996500007 |
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EcoFoG @ eric.marcon @ |
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266 |
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