Interactions between oak and cervids during the process of forest regeneration - the case study of plain temperate oak stands (Quercus robur et Q. petraea)

Les cervidés ont vu leur abondance et leur distribution spatiale augmenter fortement depuis les dernières décennies, en France, et plus généralement à l’échelle de l’hémisphère Nord. Si ces espèces jouent un rôle clé dans le fonctionnement des écosystèmes forestiers, le niveau actuel des populations compromet le processus de régénération forestière de certaines essences cruciales pour la filière sylvicole telles que les chênes sessile et pédonculé (Quercus robur et Q. petraea). L’objectif de cette thèse est de quantifier et décrire les mécanismes sous-jacent de la contrainte exercée par les cervidés sur la régénération et d’identifier dans quelle mesure certaines opérations sylvicoles (coupe, dégagement et pose d’enclos) influencent cette contrainte. L’analyses de la composition de panses de cerf et de chevreuil sur le site de La Petite Pierre (Vosges) a permis de montrer que les glands de chêne représentaient une ressource significative dans le régime alimentaire de ces deux espèces, mais que leur consommation de gland saturait les années de forte fructification. Par des approches expérimentales, nous avons mis en évidence que l’abroutissement de la pousse apicale réduisait toujours la croissance en hauteur des semis que ce soit en condition de terrain, ou en pépinière, et que ce phénomène s’expliquait par une faible plasticité d’allocation des ressources pour compenser la perte de tissu. L’analyse d’un résultats d’un réseau d’enclos-exclos répartis sur plusieurs sites en France et en Suède a permis de montrer que la coupe d’arbre adulte pour augmenter l’ouverture de la canopée accentuait l’effet négatif des cervidés sur la croissance et la survie de jeunes semis de chêne, via une plus forte fréquentation des cervidés dans les patches de régénération ouverts. Enfin, suite à l’implémentant du processus d’herbivorie dans un modèle de dynamique forestière (bibliothèque Régénération de CAPSIS), j’ai effectué des simulations suggérant que sous une forte pression d’herbivorie, des opérations de dégagement moins fréquentes et maintenant des espèces accompagnatrices appétentes comme le charme permettrait de réduire l’influence négative des cervidés sur la croissance du chêne. En conclusion, les résultats de cette thèse étayent l’hypothèse que les cervidés représentent une contrainte significative pour le processus de régénération du chêne, mais suggère qu’une gestion de la végétation de sous-bois adaptée permettrait de réduire cette contrainte et de se rapprocher d’un équilibre plus durable entre faune sauvage et activités sylvicoles.The abundance and spatial distribution of cervids have drastically increased in France, and more generally in the Northern hemisphere over the last decades. These species play a crucial part in the functioning of forest ecosystems, but the current level of their populations compromises the process of forest regeneration for many tree species of crucial importance such as pedunculate and sessile oak (Quercus robur et Q. petraea). The objectives of this thesis are to quantify and unravel the mechanisms underlying the constraint exerted by cervids on oak regeneration through the consumption of acorns, of oak saplings and of admixed understory species, and (ii) to identify how specific forest management operations (i.e. fencing, felling, and clearing) can limit or enhance this constraint. The analysis of a long-term dataset of red and roe deer rumen content sampled in the study site of La Petite Pierre (Northeastern France) showed that acorns represented a significant resource in the diet of these two species, but that their acorn consumption saturated years of high fructification. Using experimental approaches, we showed that simulated deer browsing on the apical shoot systematically reduced oak sapling height growth both in situ and ex situ, and this was explained by a relatively poor plasticity in resource allocation following browsing to compensate for the loss of tissues. The analysis of a network of fenced-unfenced plots located in several sites in France and in Sweden showed that felling to increase canopy openness enhanced the negative effect of cervids on oak sapling growth and survival through a higher frequentation of cervids under open canopies. Lastly, after implementing the process of herbivory in a forest dynamic model (i.e. Regeneration library of CAPSIS modelling tool), I conducted simulations that suggested that under a high browsing pressure, less frequent clearing operations maintaining highly palatable sapling species such as hornbeam could reduce the negative influence of cervids on oak regeneration. To conclude, this thesis results confirm that cervids exert a significant constraint on the process of oak regeneration, but also suggest that adapted management of the understory vegetation could reduce this constraint and contribute to restore a balance between wildlife and silvicultural activities

Interactions entre chêne et cervidés durant le processus de renouvellement - cas des peuplements forestiers tempérés de plaine (Quercus robur et Q. petraea)

The abundance and spatial distribution of cervids have drastically increased in France, and more generally in the Northern hemisphere over the last decades. These species play a crucial part in the functioning of forest ecosystems, but the current level of their populations compromises the process of forest regeneration for many tree species of crucial importance such as pedunculate and sessile oak (Quercus robur et Q. petraea). The objectives of this thesis are to quantify and unravel the mechanisms underlying the constraint exerted by cervids on oak regeneration through the consumption of acorns, of oak saplings and of admixed understory species, and (ii) to identify how specific forest management operations (i.e. fencing, felling, and clearing) can limit or enhance this constraint. The analysis of a long-term dataset of red and roe deer rumen content sampled in the study site of La Petite Pierre (Northeastern France) showed that acorns represented a significant resource in the diet of these two species, but that their acorn consumption saturated years of high fructification. Using experimental approaches, we showed that simulated deer browsing on the apical shoot systematically reduced oak sapling height growth both in situ and ex situ, and this was explained by a relatively poor plasticity in resource allocation following browsing to compensate for the loss of tissues. The analysis of a network of fenced-unfenced plots located in several sites in France and in Sweden showed that felling to increase canopy openness enhanced the negative effect of cervids on oak sapling growth and survival through a higher frequentation of cervids under open canopies. Lastly, after implementing the process of herbivory in a forest dynamic model (i.e. Regeneration library of CAPSIS modelling tool), I conducted simulations that suggested that under a high browsing pressure, less frequent clearing operations maintaining highly palatable sapling species such as hornbeam could reduce the negative influence of cervids on oak regeneration. To conclude, this thesis results confirm that cervids exert a significant constraint on the process of oak regeneration, but also suggest that adapted management of the understory vegetation could reduce this constraint and contribute to restore a balance between wildlife and silvicultural activities.Les cervidés ont vu leur abondance et leur distribution spatiale augmenter fortement depuis les dernières décennies, en France, et plus généralement à l’échelle de l’hémisphère Nord. Si ces espèces jouent un rôle clé dans le fonctionnement des écosystèmes forestiers, le niveau actuel des populations compromet le processus de régénération forestière de certaines essences cruciales pour la filière sylvicole telles que les chênes sessile et pédonculé (Quercus robur et Q. petraea). L’objectif de cette thèse est de quantifier et décrire les mécanismes sous-jacent de la contrainte exercée par les cervidés sur la régénération et d’identifier dans quelle mesure certaines opérations sylvicoles (coupe, dégagement et pose d’enclos) influencent cette contrainte. L’analyses de la composition de panses de cerf et de chevreuil sur le site de La Petite Pierre (Vosges) a permis de montrer que les glands de chêne représentaient une ressource significative dans le régime alimentaire de ces deux espèces, mais que leur consommation de gland saturait les années de forte fructification. Par des approches expérimentales, nous avons mis en évidence que l’abroutissement de la pousse apicale réduisait toujours la croissance en hauteur des semis que ce soit en condition de terrain, ou en pépinière, et que ce phénomène s’expliquait par une faible plasticité d’allocation des ressources pour compenser la perte de tissu. L’analyse d’un résultats d’un réseau d’enclos-exclos répartis sur plusieurs sites en France et en Suède a permis de montrer que la coupe d’arbre adulte pour augmenter l’ouverture de la canopée accentuait l’effet négatif des cervidés sur la croissance et la survie de jeunes semis de chêne, via une plus forte fréquentation des cervidés dans les patches de régénération ouverts. Enfin, suite à l’implémentant du processus d’herbivorie dans un modèle de dynamique forestière (bibliothèque Régénération de CAPSIS), j’ai effectué des simulations suggérant que sous une forte pression d’herbivorie, des opérations de dégagement moins fréquentes et maintenant des espèces accompagnatrices appétentes comme le charme permettrait de réduire l’influence négative des cervidés sur la croissance du chêne. En conclusion, les résultats de cette thèse étayent l’hypothèse que les cervidés représentent une contrainte significative pour le processus de régénération du chêne, mais suggère qu’une gestion de la végétation de sous-bois adaptée permettrait de réduire cette contrainte et de se rapprocher d’un équilibre plus durable entre faune sauvage et activités sylvicoles

The influence of fencing on seedling establishment during reforestation of oak stands: a comparison of artificial and natural regeneration techniques including costs

In temperate Europe, oak-dominated forests are widespread, supporting high biodiversity and providing important ecosystem services. Insufficient natural regeneration has, however, been a concern for over a century. The objective of this study was to gain insights into differences in regeneration success using artificial and natural regeneration techniques for reforestation of oak (Quercus robur L.) stands. We monitored seedlings following planting, direct seeding and natural regeneration over five years in a randomized block experiment in southern Sweden with fenced and non-fenced plots. Fencing had a strong positive effect on height growth, especially for planted seedlings that were taller than the other seedlings and more frequently browsed in non-fenced plots. In contrast, there was little effect of fencing on survival, establishment rate and recruitment rate of seedlings. Due to aboveground damage on seedlings from voles, protection of acorns did not improve establishment rate following direct seeding. Under current circumstances at the site with a sparse shelterwood of old oaks, we conclude that natural regeneration was the most cost-efficient regeneration method. It resulted in the most seedlings at the lowest cost. However, regeneration success was heavily influenced by interference from herbaceous vegetation. With a small additional investment in vegetation control, the results might have been improved for planting and direct seeding

Strength of species interactions determines biodiversity and stability in microbial communities

Organisms—especially microbes—tend to live together in ecosystems. While some of these ecosystems are very biodiverse, others are not, and while some are very stable over time, others undergo strong temporal fluctuations. Despite a long history of research and a plethora of data, it is not fully understood what determines the biodiversity and stability of ecosystems. Theory and experiments suggest a connection between species interaction, biodiversity and the stability of ecosystems, where an increase in ecosystem stability with biodiversity could be observed in several cases. However, what causes these connections remains unclear. Here, we show in microbial ecosystems in the laboratory that the concentrations of available nutrients can set the strength of interactions between bacteria. High nutrient concentrations allowed the bacteria to strongly alter the chemical environment, causing on average more negative interactions between species. These stronger interactions excluded more species from the community, resulting in a loss of biodiversity. At the same time, the stronger interactions also decreased the stability of the microbial communities, providing a mechanistic link between species interaction, biodiversity and stability in microbial ecosystems.NIH (Grant R01-GM102311

A Methodology and Tool for Mapping the Risk of Cumulative Effects on Benthic Habitats

The implementation of the European integrated marine policy poses many scientific challenges. Among them, the knowledge and understanding of interactions between anthropogenic pressures and ecological components is an important issue, particularly to help define Good Environmental Status, environmental targets and monitoring programs of the Marine Strategy Framework Directive (2008, MSFD). Assessment of cumulative effects of different pressures is a particularly complex issue requiring modeling tools and methods, as well as accurate data sets on human activities, anthropogenic pressures and ecological components. The results of these assessments are also uncertain and highly dependent on the calculation methods and assumptions, as well as on the data sets used. Within this context, we developed a technical and methodological approach to map the risk of cumulative effects of different pressures on benthic habitats. These developments were initiated as part of the implementation of the MSFD in France to contribute to the diagnosis of the marine environment. Here we provide a demonstrator to illustrate the feasibility for mapping the risk of cumulative effects of different pressures on benthic habitats, as well as the confidence index and the variability associated with this analysis. The method is based on a spatial analysis using a mapping of benthic habitats and their sensitivity to pressures, as well as the distribution and intensity of human activities and associated pressures. We collected and prepared relatively accurate and consistent data sets to describe human activities and benthic habitats. Data sets are embedded into a grid that facilitates the management and analysis of the data and exploitation of the results. The demonstrator consists of a relational database using the Spatial Query Language (SQL) language as well as data analysis scripts using the R language. The first demonstrator operations validated the main methodological and technical choices and helped to identify future developments needed to facilitate the appropriation and integration of these approaches in the implementation of public policies for the management of the marine environment

Vermicompost significantly affects plant growth. A meta-analysis

International audienceFood production and waste management are two increasing issues ensuing from the growing world population. Recycling organic residues into amendment for food production seems to appear as an opportunity to partially solve this double challenge. Vermicomposting is a process whereby earthworms transform organic residues into compost that can be used as a substrate for plant growth. Many studies have evaluated the effect of vermicompost on plant growth, but a quantitative summary of these studies is still missing. This is the first meta-analysis providing a quantitative summary of the effect size of vermicompost on plant growth. We found that vermicompost brought about average increases of 26% in commercial yield, 13% in total biomass, 78% in shoot biomass, and 57% in root biomass. The positive effect of vermicompost on plant growth reached a maximum when vermicompost represented 30 to 50% of the soil volume. The best original material to be used for vermicompost production was cattle manure. The effect was stronger when no fertilizer was added, and lower when the standard Metro-Mix 360 substratum recommended by some authors was used as a growing medium in greenhouse or climatic chambers. Herbs (especially Cucurbitaceae and Asteraceae) and legumes exhibited the largest biomass increase in the presence of vermicompost. These results are discussed through an analysis of potential publication biases showing an over-representation of studies with a high effect size. We finally recommend authors of primary research to provide a minimum set of statistical parameters, output variables, and experimental condition parameters to make it easier to include their work in meta-analyses. Overall, our study provides synthetic information on the beneficial effects of vermicompost for plant growth, which could help bring waste management and agriculture together towards a society with a more circular economy

The cost of deer to trees: changes in resource allocation from growth-related traits and phenolic content to structural defence

International audienceBackground and aims-Plants may use various defence mechanisms to protect their tissues against deer browsing and the allocation of resources to defence may trade-off with plants' growth. In a context of increasing deer populations in European forests, understanding the resource allocation strategies of trees is critical to better assess their ability to face an increasing browsing pressure. The aim of this study was to determine how deer removal affects the resource allocation to both defensive and growth-related traits in field conditions for three tree species (Abies alba, Picea abies and Fagus sylvatica). Methods-We compared eight pairs of fenced-unfenced plots to contrast plots with and without browsing pressure. The pairs were set up in 2005 and 2014 to compare different fencing duration. We measured leaf and shoot traits related to the defence against herbivores (phenolic content, structural resistance, C:N ratio) and to the investment in plants' growth and productivity (specific leaf area and nutrient content). Key results-For the three species, the structural resistance of leaves and shoots was negatively correlated with SLA, nutrient content and phenolic content. For Abies alba, exclusion of deer decreased shoot structural resistance in favour of higher nutrient content, SLA and phenolic content. The fencing duration had no effect on the different measured traits. Conclusions-Our results support the assumption of a trade-off between structural defence and growth-related traits at the intraspecific scale for the three studied species. We also confirmed the hypothesis that exposure to deer browsing is involved in the resource allocation of woody species. For Abies alba, fencing led to a change in resource allocation from structural defence to growth-related traits and chemical defence

Modular Assembly of Polysaccharide-Degrading Marine Microbial Communities

Understanding the principles that govern the assembly of microbial communities across earth’s biomes is a major challenge in modern microbial ecology. This pursuit is complicated by the difficulties of mapping functional roles and interactions onto communities with immense taxonomic diversity and of identifying the scale at which microbes interact [1]. To address this challenge, here, we focused on the bacterial communities that colonize and degrade particulate organic matter in the ocean [2, 3, 4]. We show that the assembly of these communities can be simplified as a linear combination of functional modules. Using synthetic polysaccharide particles immersed in natural bacterioplankton assemblages [1, 5], we showed that successional particle colonization dynamics are driven by the interaction of two types of modules: a first type made of narrowly specialized primary degraders, whose dynamics are controlled by particle polysaccharide composition, and a second type containing substrate-independent taxa whose dynamics are controlled by interspecific interactions—in particular, cross-feeding via organic acids, amino acids, and other metabolic byproducts. We show that, as a consequence of this trophic structure, communities can assemble modularly—i.e., by a simple sum of substrate-specific primary degrader modules, one for each complex polysaccharide in the particle, connected to a single broad-niche range consumer module. Consistent with this model, a linear combination of the communities on single-polysaccharide particles accurately predicts community composition on mixed-polysaccharide particles. Our results suggest that the assembly of heterotrophic communities that degrade complex organic materials follows simple design principles that could be exploited to engineer heterotrophic microbiomes.ISSN:0960-9822ISSN:1879-044

Do trait responses to simulated browsing in Quercus robur saplings affect their attractiveness to Capreolus capreolus the following year?

International audienceWith the rise of large herbivore populations in most northern hemisphere forests, browsing is becoming an increasingly important driver of forest regeneration dynamics. Among other processes affecting the regeneration, the concept of plant-herbivore feedback loops holds that browsed saplings are more subject to subsequent herbivory. This phenomenon is interpreted as a consequence of compensatory growth following browsing since fast growth is generally associated with higher digestibility and lower defense against herbivores. However, studies linking browsing-induced trait variations to subsequent attractiveness to herbivores are still lacking, especially in the forest context. In this study, we experimentally examine the existence of a feedback loop between oak (Quercus robur L.) and roe deer (Capreolus capreolus) and investigate its underlying morphological and chemical traits. We simulated single and repeated roe deer browsing on nursery-grown oak saplings and measured the changes in sapling height growth, lateral branching, leaf traits and winter shoot traits over two years. We conducted winter feeding trials with tame roe deer one year after the first treatment to test the effect of simulated browsing on sapling attractiveness. Simulated browsing reduced sapling height growth but had no effect on branching. Simulated browsing had no effect on leaf traits after half a year, but decreased the phenolic content and increased the fiber content of winter shoots the following winter. Contrary to our predictions, roe deer preferentially browsed control saplings over saplings previously browsed. After two years, repeated browsing promoted fast carbon acquisition leaf traits (high chlorophyll, high specific leaf area and low fiber content), reduced leaf phenolic content and increased leaf digestibility. We showed that a reduction in 1-year-old oak sapling height growth following browsing, combined with increased structural defense at the expense of chemical defense in winter shoots the following winter, was correlated with reduced browsing pressure, thereby challenging the feedback loop hypothesis. However, we also demonstrated that repeated browsing promoted fast carbon acquisition leaf traits in 2.5-year-old saplings, which tend to support the existence of a feedback loop on older and more intensively browsed saplings. As such, our study provides empirical evidence that morphological and physiological trait responses to browsing influence oak sapling attractiveness, but that the direction and magnitude of this effect depend on the ontogenic stage of the sapling and on the number of browsing events

Oak regeneration facing deer browsing: Can competition between saplings offset the diversion effect? A simulation experiment

peer reviewedThe constraint caused by wild ungulates on forest regeneration is increasing worldwide. Hypotheses for plant association effects predict that species susceptible to herbivory can gain protection from other neighbouring plant species. In theory, such interactions could help limit the impact of browsing on the regeneration of specific tree species. However, the presence of neighbouring species can also result in increasing competition for resources between species. The resultant effects on forest regeneration of these interactions, both positive (protection against herbivores) and negative (inter-specific competition) are still unclear. To gain insight, we coupled models of browsing by roe deer (Capreolus capreolus) and of forest dynamics to simulate trajectories of oak (Quercus petraea (Matt.) Liebl.) regeneration admixed with species of contrasted palatability and growth rate under different scenarios of browsing pressure and initial sapling density. We also investigated how releasing oak saplings from all or specific neighbours during the simulation affect regeneration. We found that admixed species composition had a relatively weak effect on the density of oak recruits, but a strong effect on the duration of the regeneration phase. Oak regenerated faster when admixed with species of intermediate growth and low palatability (Fagus sylvatica) than with species of fast growth and high palatability (Carpinus betulus L.), except at intermediate sapling density and high browsing pressure where we found the opposite. Releasing oak from all competitors was most effective in promoting oak regeneration when admixed with both species together, although the benefit of competition release was much weaker at high browsing pressure. Lastly, we found that at low initial sapling density (i.e., 10 saplings/m ), oak regeneration was driven only by browsing and the effect of admixing species became negligible. Our study showed that admixing oak with palatable neighbours impedes rather than improves oak regeneration due to increased competition for resources. As such, we suggest that the benefits of herbivore diversion can be off-set by increased inter-specific competition