Les écosystèmes forestiers constituent le principal réservoir à long terme de carbone. Toutefois, les dynamiques saisonnières de productions de cette biomasse ligneuse, en relation avec l'assimilation du carbone par l'écosystème et les déterminants environnementaux, restent peu étudiées, limitant notre compréhension du cycle du carbone et particulièrement sa sensibilité aux changements actuels du climat. Cette thèse a pour objectif de comprendre les relations entre le processus de séquestration du carbone dans le bois en formation, la physiologie de l’arbre, l’assimilation du carbone par le peuplement, et les conditions environnementales du site. L’étude porte sur trois sites instrumentés d’une tour à flux avec un peuplement constitué principalement par, respectivement l’épicéa à Tharandt en 2016, le hêtre à Hesse en 2015-2017, et le chêne à Barbeau en 2016. La formation du bois a été suivis par prélèvement hebdomadaire de microcarottes contenant, le phloème, le cambium et le xylème en formation sur des arbres dominants sélectionnés dans l’empreinte de mesure de la tour. La productivité primaire brute a été estimée par Eddy-Covariance, et les variables climatiques mesurés grâce aux dispositifs de la tour. En premier, nous avons mis au point une nouvelle approche histologique, plus rapide et plus précise que la méthode précédemment publiée sur les résineux, pour quantifier la dynamique intra-annuelle de la séquestration du carbone dans le bois en formation, basée sur des mesures répétées de la densité apparente du xylème, et applicable également aux angiospermes. Dans le 2nd chapitre, nous avons montré que l’occurrence en même temps du développement de la canopée et de la reprise de l’activité cambiale pouvait ralentir la croissance radiale du xylème, et favoriser la formation d’un xylème à porosité élevée mais rapidement fonctionnel. Dans le 3ème chapitre, nous avons démontré que le plan ligneux détermine la coordination temporelle entre la croissance en taille et en biomasse du tronc au cours de la saison de végétation, la séquestration du carbone dans le bois en formation étant toujours décalée derrière la croissance radiale du tronc due aux processus internes de la xylogenèse, avec une tendance croissance du décalage temporel pour l’épicéa et le hêtre, mais une tendance décroissante chez le chêne. Le 4ème chapitre démontre que indépendamment du peuplement, la dynamique d'assimilation du carbone présentait une courbe en cloche symétrique culminant en Juin, tandis que la dynamique saisonnière de la séquestration du carbone variait entre les 3 espèces. Le peuplement de hêtres a concentré la séquestration du carbone dans le tronc en Mai-Juillet, tandis que les peuplements d'épicéa et de chênes ont plutôt culminé en Juin-Août et ont concentré cette séquestration vers la 2ème partie de la saison de végétation. Dans le 5ème chapitre, grâce à un suivi de trois ans des flux de carbone, de la croissance des arbres, et des facteurs environnementaux dans le peuplement de hêtres matures, nous avons montré que le classement du bilan de carbone annuel n'était pas maintenu d'une année à l'autre, avec l’assimilation de carbone annuel la plus élevée en 2017, mais la production de biomasse ligneuse la plus élevée en 2016. Cela suggère que l'allocation du carbone de l'assimilation à la séquestration dans la tige ne suit pas une simple règle d’allométrie. Enfin, nous avons observé que, parallèlement à la formation d'un nouveau xylème, la teneur en amidon augmentait également durant la formation du bois. Cela suggère que le stockage de carbone et la croissance du tronc étaient étroitement liés, avec une proportion plus importante chez le chêne que chez l’épicéa et le hêtre. Ainsi, cette thèse a permis d'améliorer nos connaissances sur la dynamique de l'allocation du carbone dans l'arbre, de l'assimilation au niveau des feuilles à la séquestration à long terme dans le bois, et d'explorer leur sensibilité respective aux conditions climatiques. / Forest ecosystems are the major and most perennial terrestrial carbon pool. However, the seasonal dynamics of production of this woody biomass, in relation to the ecosystem carbon uptake remain poorly studied, limiting our understanding of the carbon cycle and particularly its sensitivity to current climate changes. This thesis aimed to better understand the underlying process of carbon sequestration within forming wood, as related to tree physiology, stand carbon assimilation and site environmental conditions. The study was conducted on three instrumented site with a flux tower, the stand is dominated respectively by spruce in Tharandt in 2016, by beech in Hesse in 2015-2017, and by oak in Barbeau in 2016. To monitor wood formation, wood samples containing phloem, cambial zone, and developing xylem were collected weekly on dominant trees within the tower footprint. Flux tower measurements were used to estimate the daily GPP of the stand, and record the climatic conditions. In the 1st chapter, we developed a novel histologic approach, to quantify the intra-annual dynamics of carbon sequestration in spruce forming wood. This approach, based on repeated measurements of xylem apparent density, is easier, faster, and more accurate than the previously available method, and is applicable also to angiosperm species. In the 2nd chapter, we showed that simultaneous occurrence of the canopy development and the resumption of cambial activity slowed down xylem radial growth, and might entail the formation of xylem with high porosity but functional at early growing season. In the 3rd chapter, we demonstrated that the tree-ring structure determined the temporal coordination between stem growth in size and in biomass along the growing season, with carbon sequestration in forming wood always lagging behind stem radial growth due to inner processes of xylogenesis. Indeed, we showed an increasing timelag ranging from ten days to nearly one month for spruce and beech, but a decreasing timelag from nearly three to one week for oak trees. In the 4th chapter, we observed that regardless of the stand, carbon assimilation followed a large and symmetric bell curve peaking in June, while seasonal dynamics of carbon sequestration differed among the three species. The beech trees concentrated carbon sequestration in stem in May-July, while the spruce and oak trees rather peaked in June-August, and completed stem growth towards the second part of the growing season. In the 5th chapter, based on a three-year monitoring of carbon fluxes, trees growth and environmental factors in the mature beech stand, we showed that ranking of annual carbon balance was not maintained from one year to another, with higher carbon assimilation during the hottest year, but higher woody biomass production in the wettest year. This suggests that allocation of carbon from assimilation to sequestration in stem is not following a simple allometric rule. In the last chapter, we observed that parallel to formation of a new xylem, starch content also increased in forming wood, suggesting that storage and stem growth were tightly connected along the growing season, with higher allocation to storage for sessile oak, compared to spruce and beech. This thesis has improved our knowledge about the dynamics of carbon allocation in the tree, from assimilation at the leaf level to long-term sequestration into the wood, and allowed to explore their respective sensitivity to climate conditions. A better quantification of the shift between stem growth in size and in biomass will require to disentangle the kinetics of cellulose and lignin deposition. However, our work contributed to a better understanding of the intra-annual dynamics of stem radial growth and carbon sequestration, which could help to improve modelling of forests net primary productivity, in the context of current global warming.

L'augmentation importante de la population mondiale, et par conséquent de ses besoins, exerce une pression de plus en plus importante sur les surfaces forestières. L'outil le mieux adapté au suivi des forêts, à l'échelle du globe, est la télédétection. C'est dans ce contexte que se situe ce travail de thèse, qui vise à améliorer l'estimation des paramètres biophysiques des arbres à partir de données de télédétection. L'originalité de ce travail a été d'étudier cette estimation des paramètres biophysiques en menant plusieurs études de sensibilité avec une démarche expérimentale sur des données expérimentales et sur des données simulées. Tout d'abord, l'étude s'est portée sur des séries temporelles de mesures de diffusiométrie radar obtenues sur deux sites : l'un constitué d'un cèdre en zone tempérée et l'autre d'une parcelle de forêt tropicale. Puis, cette étude de sensibilité a été poursuivie en imageant, avec une résolution élevée, plusieurs parcelles aux configurations différentes à l'intérieur d'une forêt de pin. Enfin, des données optiques et radars simulées ont été fusionnés afin d'évaluer l'apport de la fusion de données optique et radar dans l'inversion des paramètres biophysiques. / The significant increase of the world population, and therefore its needs, pushes increasingly high in forest areas. The best tool for monitoring forest across the globe is remote sensing. It is in this context that this thesis, which aims to improve the retrieval of biophysical parameters of trees from remote sensing data, takes place. The originality of this work was to study the estimation of biophysical parameters across multiple sensitivity studies on experimental data and simulated data. First, the study focused on the time series of radar scatterometry measurements obtained on two sites: one characterized by a cedar in the temperate zone and the other by a forest plot of rainforest. Then, the sensitivity analysis was continued by imaging with high resolution, several forest plots with different configurations within a pine forest. Finally, simulated radar and optical data were combined to evaluate the contribution of optical and radar data fusion in the inversion of biophysical parameters.

The impacts of climate change on temperate forests are predicted to accelerate, with widespread implications for forest biodiversity and function. Remote sensing has provided insights into regional patterns of vegetation dynamics, and experimental studies have demonstrated impacts of specific changes on individual species. However, forests are diverse and complex ecosystems. To understand how different species in different forests respond to interacting environmental pressures, widespread ground-based monitoring is needed. The only practical way to achieve this is through the involvement of non-professional researchers, i.e., with citizen science. However, many techniques used to identify subtle changes in forests require expensive equipment and professional expertise. This thesis aimed to identify practical methods for citizen scientists to collect useful data on forest ecosystem dynamics in relation to climate change. Methods for monitoring tree phenology and canopy-understorey interactions were the main focus, as tree phenology exerts strong control on understorey light and forest biodiversity, and is already responding to climate change. The response of understorey vegetation to canopy closure in four woodlands from a single region of England (Devon) was examined in detail. These geographically close woodlands differed considerably in their composition and seasonal dynamics. The spring period was particularly important for herb-layer development, and small variations in canopy openness had important effects on herb-layer cover and composition. This work highlights the need to monitor a range of different woodlands at the regional scale, with sufficient resolution to pick up small but crucial differences through time. Citizen scientists could help to collect such data by monitoring herb-layer cover and changes in the abundance of key species, alongside monitoring the overstorey canopy. The spring leaf phenology of four canopy trees (ash, beech, oak and sycamore) were monitored intensively in one woodland using a range of methods: counts, percentage estimates and photography. First budburst and leaf expansion dates were compared with estimates of leaf expansion timing and rate, derived from time-series data using logistic growth models. Frequently used first-event dates were potentially misleading due to high variation in leaf development rates within and between species. Percentage estimates and counts produced similar estimates of leaf expansion timing and rate. A photo-derived greenness index produced similar estimates of timing, but not rate, and was compromised by practical issues of photographing individual crowns in closed canopy woodland. Citizen science should collect time-series data instead of frequently-used first event dates―visual observations offer the most practical way to do this, but further work is needed to test reliability with citizen scientists. Given high intra- and inter-species variation in tree phenology, whole forest canopies need to be monitored to infer canopy closure timing. Canopy openness was assessed using sophisticated hemispherical photography and a range of low-cost alternatives, across four Devon woodlands over a year. Visual estimates and ordinary photography were too coarse to identify fine-scale variation in canopies. Smartphone fisheye photography analysed with free software was identified as a reliable surrogate for estimating relative, though not absolute, canopy openness. The method has high potential as a citizen science tool, as different phone models and users gave similar canopy openness estimates. In a detailed follow-up study, smartphone fisheye photography, hemispherical photography and visual observations of leaf expansion were used every other day to characterise spring canopy development. Logistic growth models estimated canopy closure timing and rate. Visual observations identified much earlier canopy development than either photographic method. Smartphone fisheye photography performed comparably to hemispherical photography. There is good potential for practical application of smartphone fisheye photography, as similar canopy closure estimates were gained from photos taken once every two weeks. The research in this thesis identifies a range of methods suitable for widespread monitoring of forest ecosystem dynamics in relation to climate change. Developing a smartphone app for automatic analysis and submission of canopy images will be an important next step to enabling widespread use. A pilot project is underway to begin testing methods with citizen scientists. Further research into data quality with citizen scientists is needed before the methods can be rolled out widely with confidence.

La formation du bois (xylogénèse) produit une large partie de la biomasse de la planète et une ressource essentielle pour l'Homme. Les cellules du bois sont produites par division dans le cambium puis s'élargissent, forment une paroi épaisse lignifiée et meurent. Pendant l'année, ces processus sont définis par des dates, durées et vitesses qui caractérisent la dynamique intra-annuelle de la xylogénèse. Cette dynamique reste peu explorée alors que c'est un aspect clé, car c'est elle qui détermine la quantité et la qualité du bois produit et c'est sur elle que les facteurs de régulation agissent. Ce travail vise à améliorer nos connaissances sur la dynamique intra-annuelle de la xylogénèse. Pendant trois ans (2007-2009), la xylogénèse a été suivie pour 45 arbres de trois espèces de conifères (sapin pectiné, épicéa commun et pin sylvestre) dans les Vosges. Pour ça, des petits échantillons de bois ont été prélevés chaque semaine sur le tronc des arbres sélectionnés. Les échantillons ont été préparés au laboratoire, puis des sections anatomiques ont été réalisées pour observer la xylogénèse au microscope. Cette thèse a permis d'améliorer notre connaissance du fonctionnement de la xylogénèse, un système biologique d'une fascinante complexité. Nous avons caractérisé - grâce à l'innovation d'une méthode statistique performante - les aspects méconnus de la dynamique de différenciation des cellules du bois. Nous avons alors pu dévoiler les mécanismes par lesquels la dynamique de la xylogénèse donne forme à la structure du cerne, établir la dynamique intra-annuelle de l'accumulation du carbone dans le bois et évaluer les mécanismes de l'influence du climat sur la xylogénèse / Wood formation (xylogenesis) produces a large part of the biomass of this planet and provides a crucial resource to Mankind. Wood cells are produced by division in the cambium, after what they enlarge, build a lignified thick wall and die. During a year, these processes take place at certain dates, last for certain durations and go at certain rates. These dates, durations and rates characterize the intra-annual dynamics of xylogenesis. This dynamics remains poorly explored whereas it is a key aspect as it determines the quantity and quality of the produced wood and conveys the influence of intrinsic (gene, hormone) and extrinsic (environment) regulatory factors. This work aims to improve our knowledge on the intra-annual dynamics of xylogenesis. During three years (2007-2009), xylogenesis was monitored for 45 trees of three conifer species (silver fir, Norway spruce, and Scots pine) in northeast France. For that, small wood samples were collected weekly on tree stem. Samples were prepared at the laboratory, and anatomical sections were cut to observe xylogenesis under a light microscope. This thesis has improved our knowledge on the functioning of xylogenesis, a biological system of a fascinating complexity. We characterized - thanks to the development of an efficient statistical method - the little known aspects of wood cell differentiation dynamics. Based on this characterization, we eluded the mechanisms by which xylogenesis dynamics shapes tree ring structure, we established the intra-annual dynamics of carbon accumulation in wood and we evaluated the mechanisms of the climate influence on xylogenesis

Forests play an important role in the net ecosystem exchange of CO2 in terrestrial ecosystems. Soil respiration is often the major source of CO2 in forests and is greatly influenced by climatic variability and management practices. Spatial and temporal variations of soil respiration have been examined in a chronosequence (60, 30, 15, and 1 year-old) of temperate, afforested, white pine (Pinus strobus) forest stands in Southern Ontario, Canada, in order to investigate any age related differences. Spatial and temporal variations of soil respiration in a 74 year-old boreal, mixed-wood forest in Central Ontario, was also studied and compared with results from the 60 year-old, temperate, white pine, forest stand, in order to investigate any climate related differences. Soil CO2 flux, temperature, and moisture were measured for one year (June 2003 to May 2004, inclusive, for the chronosequence study, and August 2003 to July 2004, inclusive, for the boreal-temperate study). In all stands, temporal variability of soil respiration followed the seasonal pattern of soil temperature, reaching a minimum in winter and maximum in summer. Temporal variability of soil temperature was able to explain 80 to 96% of the temporal variability in soil respiration at all stands. Spatial variability in soil respiration was also observed at all stands and the degree of this variability was seasonal, following the seasonal trend of mean daily soil respiration. Spatial variability of some soil chemical properties was highly correlated with the spatial variability of soil respiration, while litter thickness was not. The location of soil respiration measurement with respect to tree trunks may also help to explain some of the spatial variability in soil respiration. Across the chronosequence, the highest mean daily CO2 efflux was observed during the growing season for the 15 year-old-stand (5.2 ± 1.3 to 0.4 ± 0.2 μmol CO2 m^-2 s^-1), which was comparable to the 60 year-old-stand (4.9 ± 1.3 to 0.2 ±0.1 μmol CO2 m^-2 s^-1), but higher than the 30 year (3.8 ± 0.9 to 0.2 ± 0.0 μmol CO2 m^-2 s^-1) and 1 year (2.9 ± 0.9 to 0.3 ± 0.3 μmol CO2 m^-2 s^-1) old stands. From boreal-temperate comparison, it was observed that mean daily soil respiration rates for the boreal stand (6.9 ± 1.7 to 0.5 ±0.1 μmol CO2 m^-2 s^-1) were higher during the growing season compared to the 60 year-old temperate forest stand. Understanding temporal and spatial variability of soil respiration and how it is controlled is essential to improving forest ecosystem carbon budget assessments, and subsequently, the global carbon budget. This study will contribute direct observations necessary for improving and validating forest ecosystem CO2 exchange models. / Thesis / Master of Science (MSc)

La compréhension des processus écologiques qui sous-tendent l’assemblage des communautés végétales et la coexistence des espèces est un objectif central en écologie. Ces processus sont potentiellement nombreux et de natures contrastées. Ainsi, la composition d’une communauté de plantes dépend de processus déterministes liés aux conditions environnementales abiotiques (climat, conditions physiques et chimiques du sol, lumière) et d’interactions biotiques complexes, positives (facilitation, symbioses) comme négatives (compétition, prédation, pathogènes). En outre, les communautés sont influencées par des processus stochastiques (capacité de dispersion limitée, dérive écologique). Si les mécanismes à l’origine de ces processus sont très différents, ils ont néanmoins en commun la génération de motifs (patterns) spatiaux de distribution d’espèces dans les communautés. L’analyse de la structure spatiale des communautés permet ainsi une étude indirecte des processus régissant les communautés. La nature complexe de ces patterns spatiaux a mené au développement de nombreuses méthodes statistiques de détection et de description de patterns. Les méthodes basées sur des vecteurs propres spatiaux sont parmi les plus puissantes et précises pour détecter des patterns complexes et multi-échelles. Ces vecteurs propres, utilisés comme prédicteurs spatiaux, peuvent être combinés à un ensemble de variables environnementales dans un cadre de partition de variation. Celui-ci permet, en théorie, de démêler les effets uniques et l’effet conjoint des variables environnementales et spatiales sur la variation de composition d’une communauté. Il mène ainsi à une quantification de l’action des processus déterministes et des processus stochastiques sur l’assemblage de la communauté. Néanmoins, je montre dans cette thèse qu’un certain flou méthodologique concernant deux étapes déterminantes des analyses basées sur les vecteurs propres spatiaux a mené une proportion élevée d’études à utiliser ces méthodes de manière sous-optimale, voire fortement biaisée. Ceci compromet la fiabilité des patterns spatiaux détectés et des processus écologiques inférés. Une autre limitation de ce cadre d’analyse concerne la fraction de la partition de variation décrivant l’effet environnemental spatialement structurés qu’aucune méthode ne permet de tester.Cette thèse présente des solutions non biaisées, puissantes et précises à ces différentes limitations méthodologiques et permet d’élargir le cadre de l’inférence de processus écologique à partir de patterns spatiaux de communautés. Les différentes étapes d’amélioration de ces méthodes ont également été illustrées dans la thèse au travers de trois cas d’études fournis par deux communautés d’arbres tropicale et tempérée et une communauté de champignons symbiotiques des arbres. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

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Forests affect climate by absorbing CO₂ but also by altering albedo, latent heat flux, and sensible heat flux. In this study we used the Community Earth System Model to assess the biophysical effect of North American temperate forests on climate and how this effect changes with location, tree type, and forest management. We calculated the change in annual temperature and energy balance associated with afforestation with either needle leaf evergreen trees (NET) or broadleaf deciduous trees (BDT) and between forests with high and low leaf-area indices (LAI). Afforestation from crops to forests resulted in lower albedo and higher sensible heat flux but no consistent difference in latent heat flux. Forests were consistently warmer than crops at high latitudes and colder at lower latitudes. In North America, the temperature response from afforestation shifted from warming to cooling between 34° N and 40° N for ground temperature and between 21° N and 25° N for near surface air temperature. NET tended to have lower albedo, higher sensible heat flux and warmer temperatures than BDT. The effect of tree PFT was larger than the effect of afforestation in the south and in the mid-Atlantic. Increasing LAI, a proxy for increased management intensity, caused a cooling effect in both tree types, but NET responded more strongly and albedo decreased while albedo increased for BDT. Our results show that forests' location, tree type, and management intensity can have nearly equal biophysical effects on temperature. A forest will have maximum biophysical cooling effect if it is in the south, composed of broadleaf PFT, and is managed to maximize leaf area index. / Master of Science

Vegetation changes in Czech lowland forests over the past decades Martin Kopecký ABSTRACT To explore decadal changes in plant species diversity and composition of typical lowland forests in the Czech Republic, I compared vegetation on plots sampled decades ago with vegetation on the same plots sampled recently. First I evaluated the robustness of the approach used in my thesis. In Chapter 1, we provided the first direct test of the effect of uncertainty in original plot location on results from vegetation resurvey. We found that temporal trends in vegetation diversity and composition were comparable between exactly relocated permanent and only approximately relocated semi-permanent plots. Therefore, we conclude that the resurvey of semi-permanent plots is robust to the uncertainty in original plot location. Then, we showed that vegetation in lowland oak forest shifted from species-rich communities of thermophilous forest toward species poorer communities of mesic forest (Chapter 2). The species typical for thermophilous oak forests and nationally endangered species suffered the most significant decline. We identified as the main driver behind these changes shift from traditional coppicing toward high forest management after WWII. Further, we explored the processes behind temporal shifts in species diversity...