Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes

<p>Abstract</p> <p>Background</p> <p>Comparative genomics has emerged as a promising means of unravelling the molecular networks underlying complex traits such as drought tolerance. Here we assess the genotype-dependent component of the drought-induced transcriptome response in two poplar genotypes differing in drought tolerance. Drought-induced responses were analysed in leaves and root apices and were compared with available transcriptome data from other <it>Populus </it>species.</p> <p>Results</p> <p>Using a multi-species designed microarray, a genomic DNA-based selection of probesets provided an unambiguous between-genotype comparison. Analyses of functional group enrichment enabled the extraction of processes physiologically relevant to drought response. The drought-driven changes in gene expression occurring in root apices were consistent across treatments and genotypes. For mature leaves, the transcriptome response varied weakly but in accordance with the duration of water deficit. A differential clustering algorithm revealed similar and divergent gene co-expression patterns among the two genotypes. Since moderate stress levels induced similar physiological responses in both genotypes, the genotype-dependent transcriptional responses could be considered as intrinsic divergences in genome functioning. Our meta-analysis detected several candidate genes and processes that are differentially regulated in root and leaf, potentially under developmental control, and preferentially involved in early and long-term responses to drought.</p> <p>Conclusions</p> <p>In poplar, the well-known drought-induced activation of sensing and signalling cascades was specific to the early response in leaves but was found to be general in root apices. Comparing our results to what is known in arabidopsis, we found that transcriptional remodelling included signalling and a response to energy deficit in roots in parallel with transcriptional indices of hampered assimilation in leaves, particularly in the drought-sensitive poplar genotype.</p

La ressource forestière française en chênes rouvre et pédonculé. Analyse et explication historique

Le chêne pédonculé et le chêne sessile couvrent 31 % de la surface boisée de production. Par le passé, pour faire face à la pénurie de bois, le besoin s'est fait sentir de réglementer l'exploitation des forêts, le mode d'exploitation du «tire et aire» entériné par le premier code forestier de 1376, ressemblait à nos aménagements en taillis sous futaie et taillis simple. Les donnée ; de l'Inventaire forestier national montrent qu'aujourd'hui encore les taillis et taillis scus futaie sont largement majoritaires (fig 1). Ainsi, l'exemple donné, en forêt domaniale, de la conversion en futaie régulière, souvent mise à mal puisque dans leur majorité les futaies ont moins de 120 ans (fig 4), n'a pas eu les effets escomptés sur les principaux propriétaires de la chênaie que sont les privés et les collectivités publiques (fig 2). L'excellente qualité technologique des grumes de taillis sous futaie (fig 6) est un des éléments explicatifs du maintien de ce régime.The French forest resource of sessile and pedunculate oak; an analysis in the light of past history. Pedunculate oak and sessile oak cover 31% of the forested area used for yield. In the past, because of wood shortage, it was necessary to regulate forestry harvesting; the "tire and aire" forestry harvesting was ratified by the first forestry code of 1376 and was similar to the present management as coppice with standards and simple coppice systems. The IFN (National Forestry Inventory) data show that nowadays both coppices and coppices with standards are largely dominant (fig 1). Hence the example given of a state forest its conversion into an even-aged forest, is often difficult since the majority of high forests are < 120 yr old (fig 4) and has the expected effects on the main oak-wood owners: ie private owners and local communities. The excellent technological quality of the tree trunks from coppice with standards (fig 6) is one reason why the use of such a system has been maintained

Concurrence des rameaux latéraux vis-à-vis de la pousse terminale chez le frêne (Fraxinus excelsior L.) : relation avec les défauts de branchaison et de fourchaison

International audienc

Enseignement d’un parcours militant [entretien avec Moustafa Mansour ; entretien conduit par Haoues Seniguer], Confluences Méditerranée, n°95, 2015

Mansour Moustafa, « Enseignement d’un parcours militant [entretien avec Moustafa Mansour ; entretien conduit par Haoues Seniguer], Confluences Méditerranée, n°95, 2015 ».Mansour Moustafa, « Enseignement d’un parcours militant [entretien avec Moustafa Mansour ; entretien conduit par Haoues Seniguer], Confluences Méditerranée, n°95, 2015 ».<br>Dans l’entretien accordé à « Confluences Méditerranée », Moustafa Mansour revient sur un engagement actif de vingt-cinq ans contre les discriminations raciales et les inégalités de classe. Ses multiples expériences, sa connaissance du terrain et ses responsabilités associatives (en particulier au sein du CRI : « Coordination contre le racisme et l’islamophobie ») lui permettent avec le recul de porter des critiques fortes sur de nombreux sujets : les instrumentalisations politiques, le positionnement de diverses associations ayant pignon sur rue, les formes de lutte contre l’islamophobie, l’élitisme d’une certaine intelligentsia musulmane... La déception ayant été au bout de tous les dialogues classiques comme des promesses d’intégration, une démarche radicalement autonome s’imposerait désormais en privilégiant l’auto-organisation de tous les mouvements de libération de l’immigration postcoloniale et des quartiers populaires

Réponse des assemblages de collemboles à la manipulation expérimentale de la densité des arbres le long d'un gradient d'âge de peuplements de chêne sessile

National audienceDe nouvelles contraintes exercées par le réchauffement climatique font actuellement pressions sur les écosystèmes forestiers et vont imposer une adaptation de leur gestion sylvicole pour préserver leur santé. Ainsi le plan forestier national incite maintenant les gestionnaires forestiers à appliquer un régime d’éclaircie plus intensif afin de réduire la densité des peuplements forestiers. Ceci devrait permettre d’atténuer le risque de stress hydrique accru par des sécheresses estivales qui s’annoncent plus fréquentes à l’avenir. Cependant, peu d'études ont encore évalué l'impact potentiel de cette dynamisation de la gestion forestière sur la biodiversité du sol. Les collemboles représentent une communauté emblématique des sols forestiers. En effet, on les trouve en forte abondance au sein de l’épisolum humifère et ils jouent un rôle essentiel dans la régulation des populations fongiques décomposeurs de litière. De plus, les collemboles ont des sensibilités contrastées aux changements de conditions de milieux provoqués par les pratiques de gestion suivant les espèces. Ils sont ainsi de bons indicateurs biologiques de la qualité des sols forestiers. L’objectif de notre étude a été d’évaluer à échelle nationale la réponse des assemblages de collemboles à la manipulation de la densité en arbres en futaie régulière de chêne sessile

Les interactions entre plantes comme levier de la plasticité des traits et de la décomposition des litières foliaires de Quercus petraea le long d'un gradient d'abondance : conséquences en termes de turnover du sol et du stockage de carbone

International audienceNew adaptation and mitigation strategies are needed to manage temperate forests in the context of climate change with more frequent droughts. Thinning intensification has been proposed as an adaptation strategy to improve forest resistance to drought. Partial cutting of forest stands by thinning operations mimics the natural disturbance by treefall events and can affects tree leaf litter traits by altering interactions among forest plants. The importance of plant litter traits and decomposability for C and nutrient cycling processes has been largely emphasized. However, the role of biotic interactions as drivers of intraspecific variability in litter traits remains surprisingly little studied. In this study, we used a large-scale, multi-site network of long-term tree removal experiments manipulating the abundance of a foundation tree species, i.e. Quercus petraea, to assess how plant interactions control intraspecific variation in oak leaf litter traits and decomposability. We studied 19 plots across eight experimental sites covering a large gradient of oak abundance, stand age and local abiotic context. Oak leaf litter quality strongly declined with tree removal in early forest successional stage. Litter became poorer in nutrients such as N and Mg and richer in secondary metabolites such as lignin and condensed tannins. Variance partitioning indicated that oak abundance explained as much variation in oak leaf litter traits as oak age and twice as much as soil inherent fertility. Confirmatory path analysis revealed that the decline of oak leaf litter quality induced by tree removal was most likely driven by a shift in understory plant species composition. This response pattern could reflect the plasticity of oak leaf litter traits to the shortage of nutrient supply related to the development of understory plants competitors with higher nutrient capture and retention ability. Our data also give consistent but weaker support that the decrease in oak leaf litter quality with tree removal could be driven by alleviated competition for light among canopy trees and subsequent enhanced crown exposure to light. This plasticity in oak leaf litter traits had important consequences for ecosystem functioning. The decline of oak leaf litter quality in turn slowed its decomposition and induced a decline of the forest floor turnover. This slower forest floor dynamics largely mitigated forest floor C loss associated to reduced litterfall caused by tree removal, resulting in a weak net forest floor C loss. Interestingly, the decline of oak leaf litter quality also induced a shift of litter N loss from N release to N immobilization. Overall, our study provides evidence that biotic factors such as plant interactions are major drivers of plasticity in leaf litter traits and decomposability. This finding contributes to the emerging view that phenotypic plasticity is fundamentally related to biotic interactions for sessile organisms, especially for long-lived and large plant species such as trees. Further, we demonstrated that this plasticity shaped by plant interactions can be a major driver of ecosystem processes. Taking this source of functional diversity into account could help us to better understand how changing biodiversity affects ecosystem functioning in the context of global change

La communauté des plantes forestières comme pilote de la diversité du sol - une évaluation à large échelle des assemblages de collemboles à partir de la manipulation de la densité des peuplements

International audiencePlant-soil interactions are increasingly recognized to play a major role for terrestrial ecosystems functioning. However, few studies to date have focused on long-term dynamic ecosystems such as forests. Indeed, forest ecosystems are vertically stratified by multiple vegetation strata and the canopy cover manipulation through contrasted stand density management strategies could alter the overall architecture of forest plant community. Very little is known about the cascading effect on soil biodiversity and ecosystem function such as litter decomposition. The aim of this study was to assess the response of a major group of soil fauna, namely collembola, to oak stand density experimental manipulation. A total of 33 stands distributed over a large geographic area were studied covering a wide gradient of stand density, i.e. stand basal area from 2.5 to 43.7 m2.ha-1, stand age, i.e. 18 to 171-year-old, and pedoclimatic context conditions. Our results shown that the response of collembolan assemblages to stand density was highly dependent on stand age. Indeed, collembolan abundance and diversity tend to decrease with stand density reduction in young stands while no response was observed in old stands. Further, a substantial shift of collembolan species composition was observed within young stands and this was strongly associated with contrasted responses among functional groups. Hemiedaphic and euedaphic species abundance and diversity were strongly depleted by stand density reduction whereas epedaphic abundance was unaffected. In contrast, epedaphic diversity tended to be enhanced by stand density reduction. Patterns of collembolan assemblages response to stand density was consistent among pedoclimatic contexts, i.e. mull vs moder. Exploratory analysis using causal diagrams, i.e. path analyses, highlights that those changes were mainly related to understorey vegetation, microclimatic and soil pH condition alterations. These changes of collembolan assemblages could have important functional implications, especially on microbial respiration process through their grazing activities

Les communautés végétales comme pilote de la biodiversité du sol : évidences expérimentales des assemblages de collemboles par une manipulation de long terme de l'ouverture de la canopée à large échelle

International audiencePlant-soil interactions are increasingly recognized to play a major role in terrestrial ecosystems functioning. However, few studies to date have focused on slow dynamic ecosystems such as forests. As they are vertically stratified by multiple vegetation strata, tree removal could alter forest plant community through tree canopy opening. Very little is known about cascading effect on soil biodiversity. We conducted a large-scale, multi-site assessment of collembolan assemblage response to long-term experimental manipulation of tree canopy opening in oak temperate forests. A total of 33 experimental plots were studied covering a large gradient of tree canopy basal area, stand age and local abiotic contexts. Collembolan abundance strongly declined with tree canopy opening in early forest successional stage and this was mediated by a shift in understory plant community composition. Collembolan functional groups had contrasting response patterns, which were mediated by different ecological factors. Epedaphic abundance and species richness increased with tree canopy opening in relation with the increase in understory plant species richness. In contrast, euedaphic abundance and species richness declined in early forest successional stage in relation with changes in understory plant community composition and species richness, as well as microclimatic conditions. Overall, our study provides experimental evidence that forest plant community can be a strong driver of collembolan assemblages. It also emphasizes the role of trees as foundation species of forest ecosystems that can shape soil biodiversity through their regulation of understory plant community and ecosystem abiotic conditions

Les interactions entre plantes comme levier de la plasticité des traits et de la décomposition des litières foliaires de Quercus petraea le long d'un gradient d'abondance : conséquences en termes de turnover du sol et du stockage de carbone

International audienceNew adaptation and mitigation strategies are needed to manage temperate forests in the context of climate change with more frequent droughts. Thinning intensification has been proposed as an adaptation strategy to improve forest resistance to drought. Partial cutting of forest stands by thinning operations mimics the natural disturbance by treefall events and can affects tree leaf litter traits by altering interactions among forest plants. The importance of plant litter traits and decomposability for C and nutrient cycling processes has been largely emphasized. However, the role of biotic interactions as drivers of intraspecific variability in litter traits remains surprisingly little studied. In this study, we used a large-scale, multi-site network of long-term tree removal experiments manipulating the abundance of a foundation tree species, i.e. Quercus petraea, to assess how plant interactions control intraspecific variation in oak leaf litter traits and decomposability. We studied 19 plots across eight experimental sites covering a large gradient of oak abundance, stand age and local abiotic context. Oak leaf litter quality strongly declined with tree removal in early forest successional stage. Litter became poorer in nutrients such as N and Mg and richer in secondary metabolites such as lignin and condensed tannins. Variance partitioning indicated that oak abundance explained as much variation in oak leaf litter traits as oak age and twice as much as soil inherent fertility. Confirmatory path analysis revealed that the decline of oak leaf litter quality induced by tree removal was most likely driven by a shift in understory plant species composition. This response pattern could reflect the plasticity of oak leaf litter traits to the shortage of nutrient supply related to the development of understory plants competitors with higher nutrient capture and retention ability. Our data also give consistent but weaker support that the decrease in oak leaf litter quality with tree removal could be driven by alleviated competition for light among canopy trees and subsequent enhanced crown exposure to light. This plasticity in oak leaf litter traits had important consequences for ecosystem functioning. The decline of oak leaf litter quality in turn slowed its decomposition and induced a decline of the forest floor turnover. This slower forest floor dynamics largely mitigated forest floor C loss associated to reduced litterfall caused by tree removal, resulting in a weak net forest floor C loss. Interestingly, the decline of oak leaf litter quality also induced a shift of litter N loss from N release to N immobilization. Overall, our study provides evidence that biotic factors such as plant interactions are major drivers of plasticity in leaf litter traits and decomposability. This finding contributes to the emerging view that phenotypic plasticity is fundamentally related to biotic interactions for sessile organisms, especially for long-lived and large plant species such as trees. Further, we demonstrated that this plasticity shaped by plant interactions can be a major driver of ecosystem processes. Taking this source of functional diversity into account could help us to better understand how changing biodiversity affects ecosystem functioning in the context of global change