Éditeur(s) : HAL CCSD Society for Range Management
Résumé : Grasslands and agroecosystems occupy one-third of the terrestrial area, but their contribution to the global carbon cycle remains uncertain. We used a set of 316 site-years of CO(2) exchange measurements to quantify gross primary productivity, respiration, and light-response parameters of grasslands, shrublands/savanna, wetlands, and cropland ecosystems worldwide. We analyzed data from 72 global flux-tower sites partitioned into gross photosynthesis and ecosystem respiration with the use of the light-response method (Gilmanov, T. G., D. A. Johnson, and N. Z. Saliendra. 2003. Growing season CO(2) fluxes in a sagebrushsteppe ecosystem in Idaho: Bowen ratio/energy balance measurements and modeling. Basic and Applied Ecology 4:167-183) from the RANGEFLUX and WORLDGRASSAGRIFLUX data sets supplemented by 46 sites from the FLUXNET La Thuile data set partitioned with the use of the temperature-response method (Reichstein, M., E. Falge, D. Baldocchi, D. Papale, R. Valentini, M. Aubinet, P. Berbigier, C. Bernhofer, N. Buchmann, M. Falk, T. Gilmanov, A. Granier, T. Grunwald, K. Havrankova, D. Janous, A. Knohl, T. Laurela, A. Lohila, D. Loustau, G. Matteucci, T. Meyers, F. Miglietta, J.M. Ourcival, D. Perrin, J. Pumpanen, S. Rambal, E. Rotenberg, M. Sanz, J. Tenhunen, G. Seufert, F. Vaccari, T. Vesala, and D. Yakir. 2005. On the separation of net ecosystem exchange into assimilation and ecosystem respiration: review and improved algorithm. Global Change Biology 11: 1.424-1439). Maximum values of the quantum yield (alpha = 75 mmol.mol(-1)), photosynthetic capacity (A(max) = 3.4 mg CO(2) . m(-2).s-1), gross photosynthesis (P(g,max) = 1.16 g CO(2) . m(-2).d(-1)), and ecological light-use efficiency (epsilon(ecol) = 59 mmol . mol(-1)) of managed grasslands and high-production croplands exceeded those of most forest ecosystems, indicating the potential of nonforest ecosystems for uptake of atmospheric CO(2). Maximum values of gross primary production (8 600 g CO(2) . m(-2).yr(-1)), total ecosystem respiration (7 900 g CO(2) . m(-2).yr(-1)), and net CO(2) exchange (2 400 g CO(2) . m(-2).yr(-1)) were observed for intensively managed grasslands and high-yield crops, and are comparable to or higher than those for forest ecosystems, excluding some tropical forests. On average, 80% of the nonforest sites were apparent sinks for atmospheric CO(2), with mean net uptake of 700 g CO(2) . m(-2).yr(-1) for intensive grasslands and 933 g CO(2) . m(-2).d(-1) for croplands. However, part of these apparent sinks is accumulated in crops and forage, which are carbon pools that are harvested, transported, and decomposed off site. Therefore, although agricultural fields may be predominantly sinks for atmospheric CO(2), this does not imply that they are necessarily increasing their carbon stock.
ISSN: 1550-7424

hal-01190754
https://hal.archives-ouvertes.fr/hal-01190754
DOI : 10.2111/rem-d-09-00072.1
PRODINRA : 214043

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : While Amazonian forests are extraordinarily diverse, the abundance of trees is skewed strongly towards relatively few 'hyperdominant' species. In addition to their diversity, Amazonian trees are a key component of the global carbon cycle, assimilating and storing more carbon than any other ecosystem on Earth. Here we ask, using a unique data set of 530 forest plots, if the functions of storing and producing woody carbon are concentrated in a small number of tree species, whether the most abundant species also dominate carbon cycling, and whether dominant species are characterized by specific functional traits. We find that dominance of forest function is even more concentrated in a few species than is dominance of tree abundance, with only ≈1% of Amazon tree species responsible for 50% of carbon storage and productivity. Although those species that contribute most to biomass and productivity are often abundant, species maximum size is also influential, while the identity and ranking of dominant species varies by function and by region.
ISSN: 2041-1723

hal-01204225
https://hal.archives-ouvertes.fr/hal-01204225
DOI : 10.1038/ncomms7857
PRODINRA : 305614
PUBMED : 25919449

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Aim To examine variation in the phylogenetic diversity (PD) of tree communities across geographical and environmental gradients in Amazonia.Location Two hundred and eighty-three c.1ha forest inventory plots from across Amazonia.Methods We evaluated PD as the total phylogenetic branch length across species in each plot (PDss), the mean pairwise phylogenetic distance between species (MPD), the mean nearest taxon distance (MNTD) and their equivalents standardized for species richness (ses.PDss, ses.MPD, ses.MNTD). We compared PD of tree communities growing (1) on substrates of varying geological age; and (2) in environments with varying ecophysiological barriers to growth and survival.Results PDss is strongly positively correlated with species richness (SR), whereas MNTD has a negative correlation. Communities on geologically young- and intermediate-aged substrates (western and central Amazonia respectively) have the highest SR, and therefore the highest PDss and the lowest MNTD. We find that the youngest and oldest substrates (the latter on the Brazilian and Guiana Shields) have the highest ses.PDss and ses.MNTD. MPD and ses.MPD are strongly correlated with how evenly taxa are distributed among the three principal angiosperm clades and are both highest in western Amazonia. Meanwhile, seasonally dry tropical forest (SDTF) and forests on white sands have low PD, as evaluated by any metric.Main conclusions High ses.PDss and ses.MNTD reflect greater lineage diversity in communities. We suggest that high ses.PDss and ses.MNTD in western Amazonia results from its favourable, easy-to-colonize environment, whereas high values in the Brazilian and Guianan Shields may be due to accumulation of lineages over a longer period of time. White-sand forests and SDTF are dominated by close relatives from fewer lineages, perhaps reflecting ecophysiological barriers that are difficult to surmount evolutionarily. Because MPD and ses.MPD do not reflect lineage diversity per se, we suggest that PDss, ses.PDss and ses.MNTD may be the most useful diversity metrics for setting large-scale conservation priorities.
ISSN: 1366-9516

hal-01557462
https://hal.univ-lorraine.fr/hal-01557462
DOI : 10.1111/ddi.12357

Éditeur(s) : HAL CCSD Wiley
Résumé : [b]1.[/b] Plant functional traits, in particular specific leaf area (SLA), wood density and seed mass, are often good predictors of individual tree growth rates within communities. Individuals and species with high SLA, low wood density and small seeds tend to have faster growth rates.[br/][br/][b]2.[/b] If community-level relationships between traits and growth have general predictive value, then similar relationships should also be observed in analyses that integrate across taxa, biogeographic regions and environments. Such global consistency would imply that traits could serve as valuable proxies for the complex suite of factors that determine growth rate, and, therefore, could underpin a new generation of robust dynamic vegetation models. Alternatively, growth rates may depend more strongly on the local environment or growth–trait relationships may vary along environmental gradients.[br/][br/][b]3.[/b] We tested these alternative hypotheses using data on 27 352 juvenile trees, representing 278 species from 27 sites on all forested continents, and extensive functional trait data, 38% of which were obtained at the same sites at which growth was assessed. Data on potential evapotranspiration (PET), which summarizes the joint ecological effects of temperature and precipitation, were obtained from a global data base.[br/][br/][b]4.[/b] We estimated size-standardized relative height growth rates (SGR) for all species, then related them to functional traits and PET using mixed-effect models for the fastest growing species and for all species together.[br/][br/][b]5.[/b] Both the mean and 95th percentile SGR were more strongly associated with functional traits than with PET. PET was unrelated to SGR at the global scale. SGR increased with increasing SLA and decreased with increasing wood density and seed mass, but these traits explained only 3.1% of the variation in SGR. SGR–trait relationships were consistently weak across families and biogeographic zones, and over a range of tree statures. Thus, the most widely studied functional traits in plant ecology were poor predictors of tree growth over large scales.[br/][br/][b]6.[/b] Synthesis. We conclude that these functional traits alone may be unsuitable for predicting growth of trees over broad scales. Determining the functional traits that predict vital rates under specific environmental conditions may generate more insight than a monolithic global relationship can offer.
ISSN: 0022-0477

hal-01204226
https://hal.archives-ouvertes.fr/hal-01204226
DOI : 10.1111/1365-2745.12401
PRODINRA : 307144

Éditeur(s) : HAL CCSD Wiley
Résumé : 1. Functional traits are posited to explain interspecific differences in performance, but these relationships are difficult to describe for long-lived organisms such as trees, which exhibit strong ontogenetic changes in demographic rates. Here, we use a size-dependent model of tree growth to test the extent to which of 17 functional traits related to leaf and stem economics, adult stature and seed size predict the ontogenetic trajectory of tree growth.[br/] 2. We used a Bayesian modelling framework to parameterize and contrast three size-dependent diameter growth models using 16 years of census data from 5524 individuals of 50 rain forest tree species: a size-dependent model, a size-dependent model with species-specific parameters and a size-dependent model based on functional traits.[br/] 3. Most species showed clear hump-shaped ontogenetic growth trajectories and, across species, maximum growth rate varied nearly tenfold, from 0.58 to 5.51 mm year(-1). Most species attained their maximum growth at 60% of their maximum size, whereas the magnitude of ontogenetic changes in growth rate varied widely among species.[br/] 4. The Trait-Model provided the best compromise between explained variance and model parsimony and needed considerably fewer parameters than the model with species terms.[br/] 5. Stem economics and adult stature largely explained interspecific differences in growth strategy. Maximum absolute diameter growth rates increased with increasing adult stature and leaf delta(13)C and decreased with increasing wood density. Species with light wood had the greatest potential to modulate their growth, resulting in hump-shaped ontogenetic growth curves. Seed size and leaf economics, generally thought to be of paramount importance for plant performance, had no significant relationships with the growth parameters.[br/] 6. Synthesis. Our modelling approach offers a promising way to link demographic parameters to their functional determinants and hence to predict growth trajectories in species-rich communities with little parameter inflation, bridging the gap between functional ecology and population demography.
ISSN: 0022-0477

hal-01032387
https://hal.archives-ouvertes.fr/hal-01032387
DOI : 10.1111/j.1365-2745.2011.01883.x

Éditeur(s) : HAL CCSD
Résumé : International audience
Cumulative human impacts have led to the degradation of marine ecosystems and thedecline of biodiversity in the European and contiguous seas. Effective conservationmeasures are urgently needed to reverse these trends. Conservation must entail societalchoices, underpinned by human values and worldviews that differ between the countriesbordering these seas. Social, economic and political heterogeneity adds to the challenge ofbalancing conservation with sustainable use of the seas. Comprehensive macro-regionalcoordination is needed to ensure effective conservation of marine ecosystems andbiodiversity of this region. Under the European Union Horizon 2020 framework programme,the MarCons COST action aims to promote collaborative research to support marinemanagement, conservation planning and policy development. This will be achieved bydeveloping novel methods and tools to close knowledge gaps and advance marineconservation science. This action will provide support for the development of macro-regional and national policies through six key actions: to develop tools to analysecumulative human impacts; to identify critical scientific and technical gaps in conservationefforts; to improve the resilience of the marine environment to global change and biologicalinvasions; to develop frameworks for integrated conservation planning across terrestrial,freshwater, and marine environments; to coordinate marine conservation policy acrossnational boundaries; and to identify effective governance approaches for marine protectedarea management. Achieving the objectives of these actions will facilitate the integration ofmarine conservation policy into macro-regional maritime spatial planning agendas for theEuropean and contiguous seas, thereby offsetting the loss of biodiversity and ecosystemservices in this region.
Research Ideas and Outcomes

hal-01474085
https://hal-univ-perp.archives-ouvertes.fr/hal-01474085
https://hal-univ-perp.archives-ouvertes.fr/hal-01474085/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01474085/file/RIO_article_11884.pdf
DOI : 10.3897/rio.3.e11884

Éditeur(s) : HAL CCSD
Résumé : Atmospheric carbon dioxide records indicate that the land surface has acted as a strong global carbon sink over recent decades, with a substantial fraction of this sink probably located in the tropics, particularly in the Amazon. Nevertheless, it is unclear how the terrestrial carbon sink will evolve as climate and atmospheric composition continue to change. Here we analyse the historical evolution of the biomass dynamics of the Amazon rainforest over three decades using a distributed network of 321 plots. While this analysis confirms that Amazon forests have acted as a long-term net biomass sink, we find a long-term decreasing trend of carbon accumulation. Rates of net increase in above-ground biomass declined by one-third during the past decade compared to the 1990s. This is a consequence of growth rate increases levelling off recently, while biomass mortality persistently increased throughout, leading to a shortening of carbon residence times. Potential drivers for the mortality increase include greater climate variability, and feedbacks of faster growth on mortality, resulting in shortened tree longevity. The observed decline of the Amazon sink diverges markedly from the recent increase in terrestrial carbon uptake at the global scale, and is contrary to expectations based on models.
ISSN: 1476-4687

hal-01204223
https://hal.archives-ouvertes.fr/hal-01204223
DOI : 10.1038/nature14283
PRODINRA : 294797
PUBMED : 25788097

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699
Spontaneous gene flow between wild and cultivated chicory, Cichorium intybus L., may have implications for the genetic structure and evolution of populations and varieties. One aspect of this crop-wild gene flow is the dispersal of transgenes from genetically modified varieties, e.g. gene flow from GM chicory to natural chicory could have unwanted consequences. With the purpose to identify and quantify crop-wild gene flow in chicory, we analysed introgression in 19 wild chicory populations and 16 accessions of chicory varieties and landraces distributed across Northern, Central and Mediterranean Europe. The analysis used 281 AFLP markers and 75 SSAP markers giving a total of 356 polymorphic markers. Results from model based assignments with the program STRUCTURE indicated many incidents of recent gene flow. Gene flow was observed both between cultivars and wild populations, between landraces and wild populations, between different wild populations as well as between cultivars. Population structure visualized by distance-based clustering showed a North-South geographical structuring of the wild populations, and a general grouping of the cultivars corresponding to known origin. The results indicated, however, that the structuring between the two groups of wild and cultivated types was weak. As crop and wild recipients are genetically close and genes are transferred between the two types rather frequently, focus on mitigating crop-wild gene flow should be increased, before transgenic varieties are cultivated openly.
ISSN: 0925-9864

hal-01032184
https://hal.archives-ouvertes.fr/hal-01032184
DOI : 10.1007/s10722-008-9375-1

Éditeur(s) : HAL CCSD European Geosciences Union
Résumé : International audience
The seasonal climate drivers of the carbon cycle in tropical forests remain poorly known, although these forests account for more carbon assimilation and storage than any other terrestrial ecosystem. Based on a unique combination of seasonal pan-tropical data sets from 89 experimental sites (68 include aboveground wood productivity measurements and 35 litter productivity measurements), their associated canopy photosynthetic capacity (enhanced vegetation index, EVI) and climate, we ask how carbon assimilation and aboveground allocation are related to climate seasonality in tropical forests and how they interact in the seasonal carbon cycle. We found that canopy photosynthetic capacity seasonality responds positively to precipitation when rainfall is < 2000 mm yr(-1) (water-limited forests) and to radiation otherwise (light-limited forests). On the other hand, independent of climate limitations, wood productivity and litterfall are driven by seasonal variation in precipitation and evapotranspiration, respectively. Consequently, light-limited forests present an asynchronism between canopy photosynthetic capacity and wood productivity. First-order control by precipitation likely indicates a decrease in tropical forest productivity in a drier climate in water-limited forest, and in current light-limited forest with future rainfall < 2000 mm yr(-1).
ISSN: 1726-4170

hal-01557759
https://hal.univ-lorraine.fr/hal-01557759
https://hal.univ-lorraine.fr/hal-01557759/document
https://hal.univ-lorraine.fr/hal-01557759/file/bg-13-2537-2016.pdf
DOI : 10.5194/bg-13-2537-2016

Éditeur(s) : HAL CCSD American Association for the Advancement of Science
Résumé : The biodiversity-productivity relationship (BPR) is foundational to our understanding of the global extinction crisis and its impacts on ecosystem functioning. Understanding BPR is critical for the accurate valuation and effective conservation of biodiversity. Using ground-sourced data from 777,126 permanent plots, spanning 44 countries and most terrestrial biomes, we reveal a globally consistent positive concave-down BPR, showing that continued biodiversity loss would result in an accelerating decline in forest productivity worldwide. The value of biodiversity in maintaining commercial forest productivity alone-US$166 billion to 490 billion per year according to our estimation-is more than twice what it would cost to implement effective global conservation. This highlights the need for a worldwide reassessment of biodiversity values, forest management strategies, and conservation priorities.
ISSN: 0036-8075

hal-01607784
https://hal.archives-ouvertes.fr/hal-01607784
DOI : 10.1126/science.aaf8957
PRODINRA : 389856

Éditeur(s) : HAL CCSD Wiley
Résumé : While attention on logging in the tropics has been increasing, studies on the long-term effects of silviculture on forest dynamics and ecology remain scare and spatially limited. Indeed, most of our knowledge on tropical forests arises from studies carried out in undisturbed tropical forests. This bias is problematic given that logged and disturbed tropical forests are now covering a larger area than the so-called primary forests. A new network of permanent sample plots in logged forests, the Tropical managed Forests Observatory (TmFO), aims to fill this gap by providing unprecedented opportunities to examine long-term data on the resilience of logged tropical forests at regional and global scales. TmFO currently includes 24 experimental sites distributed across three tropical regions, with a total of 490 permanent plots and 921ha of forest inventories.
ISSN: 1402-2001

hal-01204230
https://hal.archives-ouvertes.fr/hal-01204230
DOI : 10.1111/avsc.12125
PRODINRA : 323838

Éditeur(s) : HAL CCSD Royal Society, The
Résumé : International audience
Although many coral reefs have shifted from coral-to-algal dominance, the consequence of such a transition for coral–algal interactions and their underlying mechanisms remain poorly understood. At the microscale, it is unclear how diffusive boundary layers (DBLs) and surface oxygen concentrations at the coral–algal interface vary with algal competitors and competitiveness. Using field observations and microsensor measurements in a flow chamber, we show that coral (massive Porites) interfaces with thick turf algae, macroalgae, and cyanobacteria, which are successful competitors against coral in the field, are characterized by a thick DBL and hypoxia at night. In contrast, coral interfaces with crustose coralline algae, conspecifics, and thin turf algae, which are poorer competitors, have a thin DBL and low hypoxia at night. Furthermore, DBL thickness and hypoxia at the interface with turf decreased with increasing flow speed, but not when thick turf was upstream. Our results support the importance of water-mediated transport mechanisms in coral–algal interactions. Shifts towards algal dominance, particularly dense assemblages, may lead to thicker DBLs, higher hypoxia, and higher concentrations of harmful metabolites and pathogens along coral borders, which in turn may facilitate algal overgrowth of live corals. These effects may be mediated by flow speed and orientation.
ISSN: 0962-8452

hal-01359387
https://hal-univ-perp.archives-ouvertes.fr/hal-01359387
DOI : 10.1098/rspb.2016.1137

Éditeur(s) : HAL CCSD Portland Press
Résumé : International audience
For cellular fitness and survival, gene expression levels need to be regulated in response to a wealth of cellular and environmental signals. TFs (transcription factors) execute a large part of this regulation by interacting with the basal transcription machinery at promoter regions. Archaea are characterized by a simplified eukaryote-like basal transcription machinery and bacteria-type TFs, which convert sequence information into a gene expression output according to cis-regulatory rules. In the present review, we discuss the current state of knowledge about these rules in archaeal systems, ranging from DNA-binding specificities and operator architecture to regulatory mechanisms.
ISSN: 0300-5127

hal-01542965
http://hal.upmc.fr/hal-01542965
DOI : 10.1042/BST20120312

Éditeur(s) : HAL CCSD eLife Sciences Publication
Résumé : When 2 Mha of Amazonian forests are disturbed by selective logging each year, more than 90 Tg of carbon (C) is emitted to the atmosphere. Emissions are then counterbalanced by forest regrowth. With an original modelling approach, calibrated on a network of 133 permanent forest plots (175 ha total) across Amazonia, we link regional differences in climate, soil and initial biomass with survivors' and recruits' C fluxes to provide Amazon-wide predictions of post-logging C recovery. We show that net aboveground C recovery over 10 years is higher in the Guiana Shield and in the west (21 +/- 3 Mg C ha(-1)) than in the south (12 +/- 3 Mg C ha(-1)) where environmental stress is high (low rainfall, high seasonality). We highlight the key role of survivors in the forest regrowth and elaborate a comprehensive map of post-disturbance C recovery potential in Amazonia.
ISSN: 2050-084X

hal-01606806
https://hal.archives-ouvertes.fr/hal-01606806
DOI : 10.7554/eLife.21394
PRODINRA : 389858

Éditeur(s) : HAL CCSD Ecological Society of America
Résumé : CABI:20153174020
Understanding how plants are constructed - i.e., how key size dimensions and the amount of mass invested in different tissues varies among individuals - is essential for modeling plant growth, carbon stocks, and energy fluxes in the terrestrial biosphere. Allocation patterns can differ through ontogeny, but also among coexisting species and among species adapted to different environments. While a variety of models dealing with biomass allocation exist, we lack a synthetic understanding of the underlying processes. This is partly due to the lack of suitable data sets for validating and parameterizing models. To that end, we present the Biomass And Allometry Database (BAAD) for woody plants. The BAAD contains 259634 measurements collected in 176 different studies, from 21084 individuals across 678 species. Most of these data come from existing publications. However, raw data were rarely made public at the time of publication. Thus, the BAAD contains data from different studies, transformed into standard units and variable names. The transformations were achieved using a common workflow for all raw data files. Other features that distinguish the BAAD are: (i) measurements were for individual plants rather than stand averages; (ii) individuals spanning a range of sizes were measured; (iii) plants from 0.01-100 m in height were included; and (iv) biomass was estimated directly, i.e., not indirectly via allometric equations (except in very large trees where biomass was estimated from detailed sub-sampling). We included both wild and artificially grown plants. The data set contains the following size metrics: total leaf area; area of stem cross-section including sapwood, heartwood, and bark; height of plant and crown base, crown area, and surface area; and the dry mass of leaf, stem, branches, sapwood, heartwood, bark, coarse roots, and fine root tissues. We also report other properties of individuals (age, leaf size, leaf mass per area, wood density, nitrogen content of leaves and wood), as well as information about the growing environment (location, light, experimental treatment, vegetation type) where available. It is our hope that making these data available will improve our ability to understand plant growth, ecosystem dynamics, and carbon cycling in the world's vegetation.
ISSN: 0012-9658

hal-01535227
https://hal.archives-ouvertes.fr/hal-01535227
DOI : 10.1890/14-1889.1
PRODINRA : 306122