Résumé
Premise In the Amazon basin, seasonally flooded (SF) forests offer varying water constraints, providing an excellent way to investigate the role of habitat selection on microbial communities within plants. However, variations in the microbial community among host plants cannot solely be attributed to environmental factors, and how plant traits contribute to microbial assemblages remains an open question. Methods We described leaf- and root-associated microbial communities using ITS2 and 16 S high-throughput sequencing and investigated the stochastic-deterministic balance shaping these community assemblies using two null models. Plant ecophysiological functioning was evaluated by focusing on 10 leaf and root traits in 72 seedlings, belonging to seven tropical SF tree species in French Guiana. We then analyzed how root and leaf traits drove the assembly of endophytic communities. Results While both stochastic and deterministic processes governed the endophyte assembly in the leaves and roots, stochasticity prevailed. Discrepancies were found between fungi and bacteria, highlighting that these microorganisms have distinct ecological strategies within plants. Traits, especially leaf traits, host species and spatial predictors better explained diversity than composition, but they were modest predictors overall. Conclusions This study widens our knowledge about tree species in SF forests, a habitat sensitive to climate change, through the combined analyses of their associated microbial communities with functional traits. We emphasize the need to investigate other plant traits to better disentangle the drivers of the relationship between seedlings and their associated microbiomes, ultimately enhancing their adaptive capacities to climate change.
Auteurs, date et publication :
Auteurs Marion Boisseaux , Valérie Troispoux , Alice Bordes , Jocelyn Cazal , Saint-Omer Cazal , Sabrina Coste , Clément Stahl , Heidy Schimann
Publication : American Journal of Botany
Date : 2025
Volume : 111
Issue : 12
Pages : e16366
Catégorie(s)
#CIRAD #FORET ParacouRésumé
Forest dynamic models predict the current and future states of ecosystems and are a nexus between physiological processes and empirical data, forest plot inventories and remote-sensing information. The problem of biodiversity representation in these models has long been an impediment to a detailed understanding of ecosystem processes. This challenge is amplified in species-rich and high-carbon tropical forests. Here we describe an individual-based and spatially explicit forest growth simulator, TROLL, that integrates recent advances in plant physiology. Processes (carbon assimilation, allocation, reproduction, and mortality) are linked to species-specific functional traits, and the model was parameterized for an Amazonian tropical rainforest. We simulated a forest regeneration experiment from bare soil, and we validated it against observations at our sites. Simulated forest regeneration compared well with observations for stem densities, gross primary productivity, aboveground biomass, and floristic composition. After 500years of regrowth, the simulated forest displayed structural characteristics similar to observations (e.g., leaf area index and trunk diameter distribution). We then assessed the model's sensitivity to a number of key model parameters: light extinction coefficient and carbon quantum yield, and to a lesser extent mortality rate, and carbon allocation, all influenced ecosystem features. To illustrate the potential of the approach, we tested whether variation in species richness and composition influenced ecosystem properties. Overall, species richness had a positive effect on ecosystem processes, but this effect was controlled by the identity of species rather by richness per se. Also, functional trait community means had a stronger effect than functional diversity on ecosystem processes. TROLL should be applicable to many tropical forests sites, and data requirement is tailored to ongoing trait collection efforts. Such a model should foster the dialogue between ecology and the vegetation modeling community, help improve the predictive power of models, and eventually better inform policy choices.
Auteurs, date et publication :
Auteurs Isabelle Marechaux , Jerome Chave
Publication : ECOLOGICAL MONOGRAPHS
Date : 2017
Volume : 87
Issue : 4
Pages : 632-664
Catégorie(s)
#ANR-Citation #CIRAD #CNRS #FORET NouraguesRésumé
Tropical forests are a major component of the global carbon cycle and home to two-thirds of terrestrial species. Upper-canopy trees store the majority of forest carbon and can be vulnerable to drought events and storms. Monitoring their growth and mortality is essential to understanding forest resilience to climate change, but in the context of forest carbon storage, large trees are underrepresented in traditional field surveys, so estimates are poorly constrained. Aerial photographs provide spectral and textural information to discriminate between tree crowns in diverse, complex tropical canopies, potentially opening the door to landscape monitoring of large trees. Here we describe a new deep convolutional neural network method, Detectree2, which builds on the Mask R-CNN computer vision framework to recognize the irregular edges of individual tree crowns from airborne RGB imagery. We trained and evaluated this model with 3797 manually delineated tree crowns at three sites in Malaysian Borneo and one site in French Guiana. As an example application, we combined the delineations with repeat lidar surveys (taken between 3 and 6 years apart) of the four sites to estimate the growth and mortality of upper-canopy trees. Detectree2 delineated 65 000 upper-canopy trees across 14 km2 of aerial images. The skill of the automatic method in delineating unseen test trees was good (F1 score = 0.64) and for the tallest category of trees was excellent (F1 score = 0.74). As predicted from previous field studies, we found that growth rate declined with tree height and tall trees had higher mortality rates than intermediate-size trees. Our approach demonstrates that deep learning methods can automatically segment trees in widely accessible RGB imagery. This tool (provided as an open-source Python package) has many potential applications in forest ecology and conservation, from estimating carbon stocks to monitoring forest phenology and restoration. Python package available to install at https://github.com/PatBall1/Detectree2.
Auteurs, date et publication :
Auteurs James G.C. Ball , Sebastian H.M. Hickman , Tobias D. Jackson , Xian Jing Koay , James Hirst , William Jay , Matthew Archer , Mélaine Aubry-Kientz , Grégoire Vincent , David A. Coomes
Publication : Remote Sensing in Ecology and Conservation
Date : 2025
Pages : 1–14
Catégorie(s)
#CIRAD #FORET ParacouRésumé
Every year, logging in the world's largest tropical forest, located within the Amazon biome, continues unabated. Although it is a preferred alternative to deforestation, the residual stand and site are impacted by logging. The objective of this review was to determine and assess the current state of research throughout Amazonia on the subject of logging impacts. To achieve this goal, a systematic approach was utilized to gather, assess and categorize research articles conducted in the Amazon biome over the last decade. Eligibility for inclusion of articles required demonstration of a direct impact from logging operations. A total of 121 articles were determined to meet the eligibility requirements and were included in this review. Articles were subdivided into three environmental categories: forest (n = 85), wildlife (n = 24) and streams (n = 12). The results of this review demonstrated that impacts from logging activities to the forest site were a direct result of the logging cycle (e.g., how often logging occurs) or logging intensity (e.g., how many trees are felled). The impacts to wildlife varied dependent on species, whereas impacts to streams were affected more by the logging system. Overall, research suggested that to attain sustainability and diminish the impacts from logging, a lower logging intensity of 10–15 m3 ha−1 and a longer logging cycle of 40–60 years would be essential for the long-term viability of forest management in Amazonia.
Auteurs, date et publication :
Auteurs Daniel DeArmond , Fabiano Emmert , Alberto C.M. Pinto , Adriano J.N. Lima , Niro Higuchi
Date : 2023
Catégorie(s)
#CIRAD #FORET ParacouRésumé
Wood production in fast-growing Eucalyptus grandis trees is highly dependent on both potassium (K) fertilization and water availability but the molecular processes underlying wood formation in response to the combined effects of these two limiting factors remain unknown. E. grandis trees were submitted to four combinations of K-fertilization and water supply. Weighted gene co-expression network analysis and MixOmics-based co-regulation networks were used to integrate xylem transcriptome, metabolome and complex wood traits. Functional characterization of a candidate gene was performed in transgenic E. grandis hairy roots. This integrated network-based approach enabled us to identify meaningful biological processes and regulators impacted by K-fertilization and/or water limitation. It revealed that modules of co-regulated genes and metabolites strongly correlated to wood complex traits are in the heart of a complex trade-off between biomass production and stress responses. Nested in these modules, potential new cell-wall regulators were identified, as further confirmed by the functional characterization of EgMYB137. These findings provide new insights into the regulatory mechanisms of wood formation under stressful conditions, pointing out both known and new regulators co-opted by K-fertilization and/or water limitation that may potentially promote adaptive wood traits.
Auteurs, date et publication :
Auteurs Raphael Ployet , Monica T. Veneziano Labate , Thais Regiani Cataldi , Mathias Christina , Marie Morel , Helene San Clemente , Marie Denis , Benedicte Favreau , Mario Tomazello Filho , Jean-Paul Laclau , Carlos Alberto Labate , Gilles Chaix , Jacqueline Grima-Pettenati , Fabien Mounet
Publication : NEW PHYTOLOGIST
Date : 2019
Volume : 223
Issue : 2
Pages : 766-782
Catégorie(s)
#ANR-Citation #CIRAD #FORET ItatingaRésumé
Key message Inventory and seasonal variation of terpene emissions from tropical trees in French Guiana: implications for environmental and ecological roles. Abstract A limited understanding of foliar terpene emissions from different tree species is prominent in diverse tropical forests. We conducted a study in French Guiana, screening BVOC emissions from 36 tropical woody species. We focused on 32 species in the dry season and 33 in the wet season, documenting terpene emissions for the first time in some of these tree species. Our findings show that 93.8% emitted terpenes in the dry season, while only 33.3% did so in the wet season. Terpene emissions ranged from 0.01 to 80.9 μg g−1 h−1 in the dry season and 0 to 11.7 μg g−1 h−1 in the wet season, consistent with previous reports. We identified and quantified 23 terpene compounds, including 19 monoterpenes and 4 sesquiterpenes. Additionally, 2 non-terpenoid compounds were detected: 2,2,4,6,6-pentamethylheptane (with no detected emissions in the dry season) and toluene. Among the monoterpenes, the most abundant were α-terpinolene, limonene, α-pinene, β-ocimene, and sabinene. As for sesquiterpenes, β-caryophyllene, α-caryophyllene, and α-copaene were observed during the dry season, while during the wet season, α-terpinolene predominated, followed by limonene, α-pinene, sabinene, β-caryophyllene, and α-copaene. Isoprene was detected in most of the species studied in both seasons. Sesquiterpene emissions displayed a notable phylogenetic pattern, whereas total terpenes and monoterpenes did not; however, total terpenes and monoterpenes exhibited a significant seasonal influence. Our study demonstrates that seasonality strongly influences BVOC production in tropical trees, with higher emissions in the dry season. These findings imply that various factors and conditions influence tree emissions in this tropical forest, affecting their ecological, environmental, and climatic roles, as well as the implementation of atmospheric chemistry models.
Auteurs, date et publication :
Auteurs Joan Llusià , Dolores Asensio , Jordi Sardans , Iolanda Filella , Guille Peguero , Oriol Grau , Romà Ogaya , Ifigenia Urbina , Albert Gargallo-Garriga , Lore T. Verryckt , Leandro Van Langenhove , Laëtitia M. Brechet , Elodie Courtois , Clément Stahl , Ivan A. Janssens , Josep Peñuelas
Publication : Trees
Date : 2025
Volume : 38
Issue : 4
Pages : 997-1012
Catégorie(s)
#CIRAD #CNRS #FORET Nouragues #FORET ParacouAuteurs, date et publication :
Auteurs Sébastien Fontaine , Clément Stahl , Katja Klumpp , Catherine Picon‐Cochard , Marcia M. Grise , Camille Dezécache , Lise Ponchant , Vincent Freycon , Lilian Blanc , Damien Bonal , Benoit Burban , Jean‐François Soussana , Vincent Blanfort , Gaël Alvarez
Publication : Global Change Biology
Date : 2018
Volume : 24
Issue : 3
Pages : e732–e733
Catégorie(s)
#CIRAD #FORET ParacouRésumé
Knowledge of the physiological mechanisms underlying species vulnerability to drought is critical for better understanding patterns of tree mortality. Investigating plant adaptive strategies to drought should thus help to fill this knowledge gap, especially in tropical rainforests exhibiting high functional diversity. In a semi-controlled drought experiment using 12 rainforest tree species, we investigated the diversity in hydraulic strategies and whether they determined the ability of saplings to use stored non-structural carbohydrates during an extreme imposed drought. We further explored the importance of water- and carbon-use strategies in relation to drought survival through a modelling approach. Hydraulic strategies varied considerably across species with a continuum between dehydration tolerance and avoidance. During dehydration leading to hydraulic failure and irrespective of hydraulic strategies, species showed strong declines in whole-plant starch concentrations and maintenance, or even increases in soluble sugar concentrations, potentially favouring osmotic adjustments. Residual water losses mediated the trade-off between time to hydraulic failure and growth, indicating that dehydration avoidance is an effective drought-survival strategy linked to the ‘fast–slow’ continuum of plant performance at the sapling stage. Further investigations on residual water losses may be key to understanding the response of tropical rainforest tree communities to climate change.
Auteurs, date et publication :
Auteurs Camille Ziegler , Hervé Cochard , Clément Stahl , Louis Foltzer , Bastien Gérard , Jean-Yves Goret , Patrick Heuret , Sébastien Levionnois , Pascale Maillard , Damien Bonal , Sabrina Coste , Menachem Moshelion
Publication : Journal of Experimental Botany
Date : 2024
Pages : erae159
Catégorie(s)
#CIRAD #FORET ParacouRésumé
Forest biomass retrieval using P-band synthetic aperture radar (SAR) data has been studied during the past two decades. However, much progress remains necessary to recover biomass for tropical dense forests, where above-ground biomass (AGB) values are often found between 250 and 400 t/ha. In this high range, the sensitivity of radar backscatter to AGB is small and can be obscured by disturbing effects. These are related to measurement errors, forest characteristics, and environment variations, but the most important is the underlying topography. In this work, we develop a new backscatter coefficient called t0 in order to minimize topography effects, based on 1) the medium nonreflection symmetry related to azimuth slopes and 2) the change in backscatter angular variation coming with the change in scattering mechanisms due to slopes. The method is tested on TropiSAR campaign data acquired over tropical forest plots in French Guiana. Using power laws between AGB and the backscattering coefficients, results based on the correlation analysis demonstrate the relevance of the proposed method.
Auteurs, date et publication :
Auteurs Ludovic Villard , Thuy Le Toan
Publication : IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing
Date : 2015
Volume : 8
Issue : 1
Pages : 214–223
Catégorie(s)
#CIRAD #FORET ParacouAuteurs, date et publication :
Auteurs Dinh Ho Tong Minh , Thuy Le Toan , Fabio Rocca , Stefano Tebaldini , Mauro Mariotti d'Alessandro , Ludovic Villard
Publication : IEEE Transactions on Geoscience and Remote Sensing
Date : 2025
Volume : 52
Issue : 2
Pages : 967-979