CAVIAR: an R package for checking, displaying and processing wood-formation-monitoring data

International audienceIn the last decade, the pervasive question of climate change impacts on forests has revived investigations on intra-annual dynamics of wood formation, involving disciplines such as plant ecology, tree physiology and dendrochronology. This resulted in the creation of many research groups working on this topic worldwide and a rapid increase in the number of studies and publications. Wood-formation-monitoring studies are generally based on a common conceptual model describing xylem cell formation as the succession of four differentiation phases (cell division, cell enlargement, cell wall thickening and mature cells). They generally use the same sampling techniques, sample preparation methods and anatomical criteria to separate between differentiation zones and discriminate and count forming xylem cells, resulting in very similar raw data. However, the way these raw data are then processed, producing the elaborated data on which statistical analyses are performed, still remains quite specific to each individual study. Thereby, despite very similar raw data, wood-formation-monitoring studies yield results that are still quite difficult to compare. CAVIAR-an R package specifically dedicated to the verification, visualization and manipulation of wood-formation-monitoring data-can help to improve this situation. Initially, CAVIAR was built to provide efficient algorithms to compute critical dates of wood formation phenology for conifers growing in temperate and cold environments. Recently, we developed it further to check, display and process wood-formation-monitoring data. Thanks to new and upgraded functions, raw data can now be consistently verified, standardized and modelled (using logistic regressions and Gompertz functions), in order to describe wood phenology and intra-annual dynamics of tree-ring formation. We believe that CAVIAR will help strengthening the science of wood formation dynamics by effectively contributing to the standardization of its concepts and methods, making thereby possible the comparison between data and results from different studies

Un scanner tomographique à rayons X pour l’analyse de la structure interne des arbres

Owner: motheAdded to JabRef: 2014.09.01Que vient faire un honnête scanner tomographique médical dans ce dossier sur ladendrométrie ? Médical ou pas, c’est un outil très performant pour analyser la structureinterne des arbres, et dont les applications sont nombreuses. Dans le cadre d’EMERGE, ila permis de « cartographier » les variations de densité et d’humidité dans l’arbre, ce quisera très utile pour affi ner les modèles de biomasse

Impact of compaction on two sensitive forest soils in Lorraine (France) assessed by the changes occurring in the perched water table

The mechanisation of forestry operations is too recent in France to have enough perspective and scientific knowledge of the effects on extensively managed soils.Two experimental sites on soils sensitive to compaction (silty acidic soils laying on top of a clayey subsoil) were set in Lorraine (France). A gentle and controlled compaction of these physically very analogous soils was carried out during spring 2007 at the Azerailles site (AZ) and during spring 2008 at the Clermont-en-Argonne site (CA). Immediate changes were observed for all ecosystem physical, chemical and biological functioning indicators.Soil restoration dynamics were followed using continuous monitoring of numerous parameters, including soil moisture and occurrence of a perched water table (PWT) (monitored at a daily time step) and PWT chemistry (monthly time step). Mid-term monitoring (7-8 years) results showed that both soils shifted towards a hydromorphic soil type attested by the increase in PWT frequency and duration, which invaded the soil upper layers, leading to characteristic Fe, Mn and S mobility and a change in organic compounds stability. Though soil types were very similar, the PWT characteristics varied notably between both sites. The mean residence time of the PWT was shown to be a major driver of its geochemistry, but with strong interaction with soil characteristics.A previous study made on both sites suggested that soil clay content and clay mineralogy controls the PWT dynamics through effects on aggregation. From a PWT perspective, seven years of monitoring were insufficient to observe any soil compaction recovery in the richer soil of AZ but a partial recovery was observed for the chemically poorer soil (CA).Compaction durably impacted the two studied soils and the probability that a new compaction event may occur before the complete recovery from the first disturbance must be considered in forest management

Improving the design of long-term monitoring experiments in forests: a new method for the assessment of local soil variability by combining infrared spectroscopy and dendrometric data

International audienceAbstractKey messageNear- and mid-infrared spectroscopy allows for the detection of local patterns of forest soil properties. In combination with dendrometric data, it may be used as a prospective tool for determining soil heterogeneity before setting up long-term forest monitoring experiments.ContextForest soils and stands generally exhibit higher spatial heterogeneity than other terrestrial ecosystems. This variability needs be taken into account before setting up long-term forest monitoring experiments to avoid multiple interactions between local heterogeneity and the factors tested in the experiment.AimsWe hypothesized that raw near- and mid-infrared spectra can be used as an integrated proxy of a large set of soil properties. The use of this method, in combination with dendrometric data, should provide a quick and cost-effective tool for optimizing the design of experimental forest sites.MethodsWe assessed the local soil heterogeneity at 11 experimental sites in oak and beech stands, which belong to a new forest long-term ecological research (LTER) network. We used near- and mid-infrared spectroscopy in soil and litter samples. The spectra were subjected to principal components analyses (PCA) to determine the intra-site variability of the soil and litter layers.ResultsBased on mapped PCA coordinates and basic dendrometric data, it was possible to design the experiment and minimize the interactions between the treatment layout and the tested variables. The method was validated with chemical analyses of the soil. No interaction was detected at the set-up of the experiment between the treatment layout and chemical soil properties (C, N, C/N ratio, pH, CEC, Al, Mg, P2O5, Fe, Mn, Na, and K).ConclusionNear-infrared (NIR) and mid-infrared (MIR) spectroscopy is a useful tool for characterizing the overall heterogeneity of soil chemical properties. It can be used without any preliminary calibration. In combination with dendrometric data, it provides a reliable method for optimizing LTER plots in different types of ecosystems

Mesures de volume, biomasse, minéralomasse : peut-on généraliser par groupes d'essences de même architecture et structure interne ?

Élaborer des tarifs génériques, valables pour toutes les essences de la ressource forestière,est une véritable gageure compte tenu de la masse de données nécessaire pour ajusterles modèles. Si l’information est largement disponible pour certaines essences, d’autressont peu (ou pas) renseignées. D’où l’idée de constituer des groupes d’essences de mêmearchitecture et structure interne, qui permettent de mutualiser l’information et proposerun modèle par groupe sinon par essence. Une opération structurante

Douglas fir stimulates nitrification in French forest soils

Douglas fir trees presumable stimulate nitrification in the soil. We studied in 21 French Douglas fir forests if and how nitrification is modulated by soil properties, past land use and current forest management. Soil (0–10 cm depth) was collected and initial concentrations of N-NH4+ and N-NO3−, potential net nitrogen mineralization (PNM) and net nitrification (PNN) rates and microbial biomass were measured. At 11 of the 21 sites, annual nitrate fluxes in the soil were measured using anion exchange resin bags. Soils contained between 2.3 to 29.4 mg N-NO3− kg soil−1. About 86% (±14%) of mineral N was nitrate. The proportion of nitrate increased to almost 100% during incubation. PNN varied from 0.10 mg N kg soil−1 day−1 to 1.05 mg N kg soil−1 day−1 (21 sites). Neither the initial nitrate concentration nor PNN was related to soil chemistry (pH, % C, %N, P, CEC), microbial biomass, texture, past land use or thinning. In situ net nitrate accumulation (NNA) estimated with resins beds varied from 4 to 100 kg N-NO3− ha−1 yr−1 (11 sites). It was positively correlated with base saturation, clay content, ELLENBERG N, temperature and negatively with soil organic N, C/N ratio and precipitation

Tree genotype and seasonal effects on soil properties and biogeochemical functioning in Mediterranean pine forests

International audienceIn forests, intraspecific genetic variation in trees can affect the entire ecosystem, which in turn depends on the different processes occurring through space and time in soil. We hypothesized that, in addition to the effect of the local site, tree genotype and season would have an effect on the properties and functions of the edaphic environment. We studied soils beneath different genotypes of Pinus pinaster Ait. (Atlantic, Mediterranean and African) in 45-year-old common gardens in spring and autumn. The pH, organic matter, nutrients and infrared spectroscopy, together with enzyme activities, were determined and used to evaluate the soil properties and biogeochemical functioning. In addition to strong site effects, tree genotype and seasonal effects were detected on soil properties and functions. Both were major controlling factors of microbially mediated functioning, especially processes related to the carbon (C) and nitrogen (N) cycles. In general, the soil environment beneath the Atlantic trees was different from that under the Mediterranean and African genotypes, with differences in raw infrared spectra and increased activities of enzymes involved in hemicellulose degradation and N mobilization. Regarding the season, the largest soil humidity (RH), electric conductivity (EC), and N and potassium (K) concentrations, coupled with the smallest phosphorus (P) concentration and C:N ratios, were detected in autumn. Degradation of C peaked in autumn, whereas P and N mobilization usually peaked in spring. Our results showed that, beyond local site effects, there were detectable effects of tree genotype and season in Mediterranean forest soils, which governed microbially mediated processes that might have relevant functional consequences at the ecosystem level

Within-stem maps of wood density and water content for characterization of species: a case study on three hardwood and two softwood species

Key message Variability and interrelations between wood density, water content, and related properties were analyzed by CT scanning of five species. Relative water content of lumens is proposed as the best complement to basic specific gravity for discrimination of species with respect to their functioning. Context X-ray computed tomography (CT) is an efficient tool for analysis of wood properties related to density and water content all along a tree stem. Basic specific gravity, an inherent property of the wood material, is well known and widely used in wood sciences. Aims The first aim of this study was to describe a method for mapping a set of wood properties within a tree stem. The second objective was to analyze the relations among these properties and to identify the one that offers the best information in addition to basic specific gravity for discrimination of species. Methods Wood discs were collected at various heights along a tree stem. We used a method consisting of comparing the CT images of the discs in the green state and after oven drying. Finally, 10 variables were computed for 115 trees of five temperate species: green, oven-dry, and basic specific gravities; moisture content; relative water content; relative water content of lumens; and fractions of air, water, free water, and cell walls. Results Maps of wood properties summarizing the radial and vertical variations were obtained, allowing us to highlight species-specific patterns. The five species were discriminated best when plotted in the plane defined by basic specific gravity and relative water content of lumens. Conclusion The proposed method is original and simple enough to process large samples. Because it correlated less with basic specific gravity than with moisture content, relative water content of lumens was selected for species characterization. This is the first study of such wood properties at this fine scale within a tree stem, simultaneously and for a substantial number of trees of five species including both hardwoods and softwoods

Patterns of within-stem variations in wood specific gravity and water content for five temperate tree species

• Key messageIntensive measurements of basic specific gravity and relative water content of lumens show that within-stem variations strongly depend on species and cannot be summarised through the typical patterns reported in the literature; breast height measurements are not always representative of the whole stem.• ContextKnowledge of the distribution of wood properties within the tree is essential for understanding tree physiology as well as for biomass estimations and for assessing the quality of wood products.• AimsThe radial and vertical variations of basic specific gravity (BSG) and relative water content of lumens (RWCL) were studied for five species: Quercus petraea/robur, Fagus sylvatica, Acer pseudoplatanus, Abies alba and Pseudotsuga menziesii. The observations were compared with typical patterns of variations reported in the literature.• MethodsWood discs were sampled regularly along tree stems and X-rayed in their fresh and oven-dry states.• ResultsAt breast height, BSG was found to clearly increase radially (pith to bark) for two species and to decrease for one species. For F. sylvatica and A. alba, the radial variations of BSG were rather U-shaped, with in particular inner wood areas showing respectively lower and higher BSG than the corresponding mature wood. RWCL increased generally from inner to outer area but wet sapwood was clearly distinguishable only for the coniferous species. Vertical variations of BSG and RWCL were strongly dependant on the species with usually non-linear patterns.• ConclusionThe observed variations of BSG were only partially in agreement with the reported typical radial patterns. Despite the vertical variations, the mean BSG of a cross-section at breast height appeared to be a good estimator of the mean BSG of the whole stem (although the difference was statistically significant for coniferous species), whereas breast height measurement of RWCL was not representative of the whole stem