Éditeur(s) : HAL CCSD American Association for the Advancement of Science
Résumé :  
Amazon forests are a key but poorly understood component of the global carbon cycle. If, as anticipated, they dry this century, they might accelerate climate change through carbon losses and changed surface energy balances. We used records from multiple long-term monitoring plots across Amazonia to assess forest responses to the intense 2005 drought, a possible analog of future events. Affected forest lost biomass, reversing a large long-term carbon sink, with the greatest impacts observed where the dry season was unusually intense. Relative to pre-2005 conditions, forest subjected to a 100-millimeter increase in water deficit lost 5.3 megagrams of aboveground biomass of carbon per hectare. The drought had a total biomass carbon impact of 1.2 to 1.6 petagrams (1.2 × 1015 to 1.6 × 1015 grams). Amazon forests therefore appear vulnerable to increasing moisture stress, with the potential for large carbon losses to exert feedback on climate change.
ISSN: 0036-8075

hal-01032111
https://hal.archives-ouvertes.fr/hal-01032111
DOI : 10.1126/science.1164033

Éditeur(s) : HAL CCSD Czech Entomological Society
Résumé : International audience
ISSN: 1210-5759

hal-01091213
https://hal-agroparistech.archives-ouvertes.fr/hal-01091213

Éditeur(s) : HAL CCSD Elsevier
Résumé : DNA metabarcoding on soil samples is increasingly used for large-scale and multi-taxa biodiversity studies. However, DNA extraction may be a major bottleneck for such wide uses. It should be cost/time effective and allow dealing with large sample volumes so as to maximise the representativeness of both micro- and macro-organisms diversity. Here, we compared the performances of a fast and cheap extracellular DNA extraction protocol with a total DNA extraction method in retrieving bacterial, eukaryotic and plant diversity from tropical soil samples of ca. 10 g. The total DNA extraction protocol yielded more high-quality DNA. Yet, the extracellular DNA protocol provided similar diversity assessments although it presented some differences in clades relative abundance and undersampling biases. We argue that extracellular DNA is a good compromise between cost, labor, and accuracy for high throughput DNA metabarcoding studies of soil biodiversity.
ISSN: 0038-0717

hal-01532638
https://hal.archives-ouvertes.fr/hal-01532638
DOI : 10.1016/j.soilbio.2016.01.008
PRODINRA : 384522

Éditeur(s) : HAL CCSD Linnean Society of London
Résumé :  
absent
ISSN: 0024-4066

hal-01032089
https://hal.archives-ouvertes.fr/hal-01032089

Éditeur(s) : HAL CCSD Wiley
Résumé : 1. Niche theory proposes that species differences underlie both coexistence within communities and the differentiation in species composition among communities via limiting similarity and environmental filtering. However, it has been difficult to extend niche theory to species-rich communities because of the empirical challenge of quantifying niches for many species. This has motivated the development of functional and phylogeny-based approaches in community ecology, which represent two different means of approximating niche attributes. 2. Here, we assess the utility of plant functional traits and phylogenetic relationships in predicting community assembly processes using the largest trait and phylogenetic data base to date for any set of species-rich communities. 3. We measured 17 functional traits for all 4672 individuals of 668 tree species co-occurring in nine tropical rain forest plots in French Guiana. Trait variation was summarized into two ordination axes that reflect species niche overlap. 4. We also generated a dated molecular phylogenetic tree based on DNA sequencing of two plastid loci (rbcL and matK) comprising 97% of the individuals and 91% of the species in the plots. 5. We found that, on average, co-occurring species had greater functional and, to a lesser extent, phylogenetic similarity than expected by chance. 6. We also found that functional traits and their ordination loadings showed significant, albeit weak, phylogenetic signal, suggesting that phylogenetic distance provides pertinent information on niche overlap in tropical tree communities. 7. Synthesis. We provide the most comprehensive examination to date of the relative importance of environmental filtering and limiting similarity in structuring tropical tree communities. Our results confirm that environmental filtering is the overriding influence on community assembly in these species-rich systems.
ISSN: 0141-6707

hal-01032423
https://hal.archives-ouvertes.fr/hal-01032423
DOI : 10.1111/j.1365-2745.2012.01966.x

Éditeur(s) : HAL CCSD Wiley/Blackwell
Résumé : Whole genome sequencing is helping generate robust phylogenetic hypotheses for a range of taxonomic groups that were previously recalcitrant to classical molecular phylogenetic approaches. As a case study, we performed a shallow shotgun sequencing of eight species in the tropical tree family Chrysobalanaceae to retrieve large fragments of high-copy number DNA regions and test the potential of these regions for phylogeny reconstruction. We were able to assemble the nuclear ribosomal cluster (nrDNA), the complete plastid genome (ptDNA) and a large fraction of the mitochondrial genome (mtDNA) with approximately 1000x, 450x and 120x sequencing depth respectively. The phylogenetic tree obtained with ptDNA resolved five of the seven internal nodes. In contrast, the tree obtained with mtDNA and nrDNA data were largely unresolved. This study demonstrates that genome skimming is a cost-effective approach and shows potential in plant molecular systematics within Chrysobalanaceae and other under-studied groups.
ISSN: 1755-098X

hal-01204217
https://hal.archives-ouvertes.fr/hal-01204217
DOI : 10.1111/1755-0998.12246
PRODINRA : 283530

Éditeur(s) : HAL CCSD Wiley
Résumé : Negative density dependence (NDD) and environmental filtering (EF) shape community assembly, but their relative importance is poorly understood. Recent studies have shown that seedlings mortality risk is positively related to the phylogenetic relatedness of neighbours. However, natural enemies, whose depredations often cause NDD, respond to functional traits of hosts rather than phylogenetic relatedness per se. To understand the roles of NDD and EF in community assembly, we assessed the effects on seedling mortality of functional similarity, phylogenetic relatedness and stem density of neighbouring seedlings and adults in a species-rich tropical forest. Mortality risks increased for common species when their functional traits departed substantially from the neighbourhood mean, and for all species when surrounded by close relatives. This indicates that NDD affects community assembly more broadly than does EF, and leads to the tentative conclusion that natural enemies respond to phylogenetically correlated traits. Our results affirm the prominence of NDD in structuring species-rich communities.
ISSN: 1461-023X

hal-01032429
https://hal.archives-ouvertes.fr/hal-01032429
DOI : 10.1111/j.1461-0248.2011.01705.x

Éditeur(s) : HAL CCSD Springer Verlag
Résumé :  
In studying the ant genus Azteca, a Neotropical group of arboreal species, we aimed to determine the extent to which the ants use predation and/or aggressiveness to protect their host plants from defoliating insects. We compared a territorially dominant, carton-nester, Azteca chartifex, and three plant-ant species. Azteca alfari and Azteca ovaticeps are associated with the myrmecophyte Cecropia (Cecropiaceae) and their colonies shelter in its hollow branches; whereas Azteca bequaerti is associated with Tococa guianensis (Melastomataceae) and its colonies shelter in leaf pouches situated at the base of the laminas. Whereas A. bequaerti workers react to the vibrations transmitted by the lamina when an alien insect lands on a leaf making it unnecessary for them to patrol their plant, the workers of the three other species rather discover prey by contact. The workers of all four species use a predatory behaviour involving spread-eagling alien insects after recruiting nestmates at short range, and, in some cases, at long range. Because A. alfari and A. ovaticeps discard part of the insects they kill, we deduced that the workers' predatory behaviour and territorial aggressiveness combine in the biotic defence of their host tree.
ISSN: 0028-1042

hal-01032079
https://hal.archives-ouvertes.fr/hal-01032079
DOI : 10.1007/s00114-008-0448-y

Éditeur(s) : HAL CCSD Wiley
Résumé :  
The complex structure of tree bark reflects its many functions, which include structural support as well as defence against fire, pests and pathogens. Thick bark, however, might limit respiration by the living tissues of the trunk. Nevertheless, little research has addressed community-level variation in bark thickness, and to the best of our knowledge, no one has tested multiple hypotheses to explain variation in bark thickness. We conducted an extensive survey of bark thickness within and among species of trees in the tropical rain forests of French Guiana. Trunk bark thickness increased by 1.2 mm per 10 cm increase in stem diameter, and varied widely at all taxonomic levels. Mean trunk bark thickness was 4.5 mm (range: 0.5-29 mm), which was less that found in two Amazonian rain forests in previous studies. This survey of bark thickness should be of use for forest management since tree survival through fire is strongly predicted by bark thickness. We combined the survey data with multiple datasets to test several functional hypotheses proposed to explain variation in bark thickness. We found bark to provide an average of 10% of the flexural rigidity of tree stems, which was substantially less than that found in the only other study of bark stiffness. Bark thickness was uncorrelated with species' association with fire-prone habitats, suggesting that the influence of fire on bark thickness does not extend into moist Forests. There was also little evidence that bark thickness is affected by its function as a defence against herbivory. Nor was there evidence that thick bark limits trunk respiration. A re-analysis of previously collected anatomical data indicated that variation in rhytidome (non-conducting outer bark) thickness explains much of the variation in overall bark thickness. As rhytidome is primarily involved in protecting the living tissues of the trunk, we suggest that bark thickness is driven mostly by its defensive function. Functional explanations for the variation in bark thickness were not clear-cut. Nevertheless, this study provides a foundation for further investigation of the functional bases of bark in tropical trees.
ISSN: 0269-8463

hal-01032124
https://hal.archives-ouvertes.fr/hal-01032124
DOI : 10.1111/j.1365-2435.2010.01736.x

Éditeur(s) : HAL CCSD Elsevier
Résumé : Volatile terpenes are among the most diverse class of defensive compounds in plants, and they are implicated in both direct and indirect defense against herbivores. In terpenes, both the quantity and the diversity of compounds appear to increase the efficiency of defense as a diverse blend of compounds provides a more efficient protection against a broader range of herbivores and limits the chances that an enemy evolves resistance. Theory predicts that plant defensive compounds should be allocated differentially among tissues according to the value of the tissue, its cost of construction and the herbivore pressure on it. We collected volatile terpenes from bark and leaves of 178 individual tree belonging to 55 angiosperm species in French Guiana and compare the kind, amount, and diversity of compounds in these tissues. We hypothesized that in woody plants, the outermost part of the trunk should hold a more diverse blend of volatile terpenes. Additionally, as herbivore communities associated with the leaves is different to the one associated with the bark, we also hypothesized that terpene blends should be distinct in the bark vs. the leaves of a given species. We found that the mixture of volatile terpenes released by bark is different and more diverse than that released by leaves, both in monoterpenes and sesquiterpenes. This supports our hypothesis and further suggests that the emission of terpenes by the bark should be more important for trunk defense than previously thought. (c) 2012 Elsevier Ltd. All rights reserved.
ISSN: 0031-9422

hal-01032417
https://hal.archives-ouvertes.fr/hal-01032417
DOI : 10.1016/j.phytochem.2012.07.003

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : Characterizing the trophic relationships between large herbivores and the outstanding plant diversity in rainforest is a major challenge because of their elusiveness. This is crucial to understand the role of these herbivores in the functioning of the rainforest ecosystems. We tested a non-invasive approach based on the high-throughput sequencing of environmental samples using small plant plastid sequences (the trnL P6 loop) and ribosomal ITS1 primers, referred to as DNA metabarcoding, to investigate the diet of the largest neotropical herbivore, the lowland tapir. Sequencing was performed on plant DNA extracted from tapir faeces collected at the Nouragues station, a protected area of French Guiana. In spite of a limited sampling, our approach reliably provided information about the lowland tapir's diet at this site. Indeed, 95.1% and 74.4% of the plant families and genera identified thanks to the trnL P6 loop, respectively, matched with taxa already known to be consumed by tapirs. With this approach we were able to show that two families and eight new genera are also consumed by the lowland tapir. The taxonomic resolution of this method is limited to the plant family and genera. Complementary barcodes, such as a small portion of ITS1, can be used to efficiently narrow identifications down to the species in some problematic families. We will discuss the remaining limitations of this approach and how useful it is at this stage to unravel the diet of elusive rainforest herbivores and better understand their role as engineers of the ecosystem.
ISSN: 1932-6203

hal-01190578
https://hal.archives-ouvertes.fr/hal-01190578
PRODINRA : 209109
PUBMED : 23560107
DOI : 10.1371/journal.pone.0060799