No description available.

The aim of this study was to assess how the plant community and its species diversity are affected by establishment methods and warming. Priority effects, i.e., the order of species arrival in plant establishment, are an important subject when invasive species become more common, and the biodiversity decreases as the global temperature continues to increase. A field experiment was carried out to investigate the effect of establishment methods and temperature on plant communities by using four different establishment methods. The plants were divided into two groups (fast and slow germinating) and sown at two occasions, one earlier than the other. Half of the study plots were then treated with OTC (Open Top Chambers) and the other half were used as control. There was a difference in temperature between the OTC blocks and the control blocks. OTC had no effect on the number of species or the Shannon diversity index but affected the proportion fast germinating, slow germinating, and naturally established species. There was a significant effect of the establishment events on the plant community. There was also a significant interaction between OTC treatment and establishment, only present for the proportion of fast germinating species. The temperature differences can provide information on plant responses to global warming and the results can mostly be explained by priority effects such as numerical superiority and competition in combination with germination rate are. The results of this study can be used to better understand how warming and priority effects may affect plant communities in the future.

京都大学 / 新制・課程博士 / 博士(生命科学) / 甲第23332号 / 生博第450号 / 新制||生||60(附属図書館) / 京都大学大学院生命科学研究科統合生命科学専攻 / (主査)教授 片山 高嶺, 教授 永尾 雅哉, 教授 上村 匡 / 学位規則第4条第1項該当 / Doctor of Philosophy in Life Sciences / Kyoto University / DFAM

Communities are a critical link that impact how species-level population dynamics translate into ecosystem functions, and thus, understanding community assembly is an important goal of ecology. Variation in the relative importance of the four processes of drift, selection, speciation, and dispersal likely govern much of the variation that is observed in community structure across landscapes. Microbial communities provide critical functions across an array of environments, but only recently have technological advances in DNA sequencing allowed us to study these communities with higher resolution. My dissertation research has investigated community assembly in host-associated microbial communities, with a focus on understanding how stochasticity in dispersal that leads to priority affects can impact bacterial community assembly in amphibian embryos. In chapter 1, I experimentally show that priority effects resulting from stochastic dispersal can be observed in the microbiome of newly-hatched hourglass treefrog (Dendropsophus ebraccatus) tadpoles. Changes in microbiome composition due to priority effects could be observed in a simple two bacteria system and when the inoculation by the initial bacteria is followed by a more diverse community inoculum. Outcomes of my two taxa system in co-culture do not strictly mirror those observed in treefrog embryos, highlighting that priority effect outcomes are context dependent. Additionally, these results provide support that priority effects do not benefit all bacterial species equally and the magnitude of these effects will be dependent on the traits of individual colonists. In chapter 2 I demonstrate that priority effects are not unique to the hourglass treefrog system but can be observed in spring peeper (Pseudacris crucifer) tadpoles as well. This study demonstrates the applicability of priority effects in increasing the abundance of target probiotic taxa; a benefit to amphibian populations facing threats by a lethal fungal pathogen. By treating embryos with a priority inoculation of Janthinobacterium lividum, a bacterial species known to inhibit fungal pathogen growth, I increased the relative abundance of J. lividum on newly hatched tadpoles. I also provide evidence that closely-related species of bacteria can effectively co-exist regardless of priority inoculation. An understanding of variation in the amphibian microbiome across life stages in the wild is required to better understand the long-term impacts of priority effects in embryos. My final chapter, therefore, examined compositional changes in the microbiomes of locally occurring amphibians in Virginia across the egg, tadpole, and juvenile developmental stages. In this study, I show characterize the initial egg microbiome across amphibian species and demonstrate that egg microbiomes, are distinct between species but are more similar across species than tadpole or juvenile microbiomes. Additionally, I show that minor differences in host environment can lead to differences in the microbiome structure of conspecific tadpoles. Overall, my dissertation empirically demonstrates the role of dispersal, and more specifically priority effects, in the assembly of the vertebrate microbiome. / Doctor of Philosophy / An ecological community is a set of species that occur at a given site. Communities have been a fundamental focus of ecological research, as communities serve to link the population dynamics of individual species to ecosystem level processes provided by species. Microbial communities, in particular, are of interest because of the wide range of important functions they provide across a variety of systems, yet relatively little is known about how these communities initially come together and are maintained. This is particularly true for the microbial communities that live in and on plants and animals, which are called "host-associated" communities. Host-associated microbial communities contribute many important functions to their hosts, including guiding host development, assisting with nutrient assimilation, and providing disease resistance. Four processes are thought to govern how ecological communities assemble across landscapes at local sites or habitat patches: selection, dispersal, speciation, and drift. Variation in the relative importance of these processes is thought to drive the variation in community composition across sites, or in the case of host-associated microbial communities, across hosts. Selection occurs at a local level when environmental variables or the presence of other species impact where a species occurs. Dispersal of individuals among habitat patches can also impact what species occur at a local site, and speciation gives rise to new species in communities over time. Drift is the stochastic, or random, element of species abundance that is driven by variation in the birth and death rates of a population at a site. I have investigated the assembly of host-associated microbial communities using amphibians as a study system. In chapter 1, I experimentally demonstrate that stochasticity in dispersal that impacts which species arrive first to a site (priority effects) can be observed in the host-associated bacterial communities of newly-hatched treefrog (Dendropsophus ebraccatus) tadpoles. This can be observed in a simplified system where only two bacterial species are used, and also when a single bacterial species arrives and is followed by a more diverse community of bacteria. However, not every bacterial species is able to take advantage of priority, and these results seem to be context dependent, as the outcomes in treefrog embryos do not exactly mirror the outcomes when the bacteria are grown in a nutrient broth together. In chapter 2, I show that priority effects are not unique to the hourglass treefrog system; priority effects can also be observed in spring peeper (Pseudacris crucifer) tadpoles. In this study, I also demonstrated that we may be able to apply our knowledge of priority effects to benefit amphibian populations threatened by a potentially lethal fungal pathogen by manipulating the abundances of bacteria on the skin during development. Priority treatment of embryos with Janthinobacterium lividum, a bacterial species known for its ability to inhibit growth of this fungal pathogen, resulted in increased relative abundance of J. lividum in the tadpoles following hatching. Additionally, I found that even closely-related bacterial species can have differing abilities to take advantage of priority effects and can co-exist on tadpoles. To determine long-term impacts of priority effects in embryos requires an understanding of the variation associated with amphibians in the wild across different life stages. My final chapter, therefore, focused on examining changes in the bacterial communities associated with locally occurring amphibians in Virginia across the egg, tadpole, and juvenile stages of development. Specifically, I characterize the initial communities associated with eggs across different species, including predicted associations with algal symbionts, and examine patterns of host-associated communities among species and across development. Overall, my dissertation showcases the role that dispersal, but more specifically priority effects, can play in the development of the vertebrate microbiome.

<p>Elucidating the mechanisms structuring communities has been a challenge for community ecology since its beginnings. One theory argues that assembly rules structure communities by means of deterministic mechanisms arising from biological interactions. Another view maintains that patterns seen in community composition and species abundance result from stochastic processes such as migration and extinction. The dilemma has yet not been resolved unambiguously. The main issue is that communities shaped by deterministic mechanisms can produce stochastic patterns via priority effects. The main goal of this study was to determine whether assembly rules structure communities. My strategy was to minimize priority effects by controlling timing of colonization. To do this I used a null community by combining communities of 17 rock pools. This null community was later divided among experimental communities. I conducted three experiments: (1) Experimental communities were exposed to the same external conditions. (2) Communities were exposed to different environments, disturbance, dispersal and habitat heterogeneity. (3) Replicated null communities were connected to allow inter-replicate dispersal. After 4 months, communities (experiment 1) formed alternative states, suggesting the lack of assembly rules control in community structure. The second experiment showed that adding factors results in more alternative states. The increasing number of alternative states among replicate communities indicates that diversified environment and migration are needed to reproduce qualitative patterns observed in nature. The last experiment (3) showed that patterns observed among connected replicate communities resemble patterns that emerged in the presence of biological interactions in unconnected communities. Similarity of patterns between connected and unconnected groups of communities suggest that local biological interactions can be sufficient to structure communities to a considerable degree. Nevertheless, the regional processes appear necessary in their role of supplying species for local communities.</p> / Doctor of Philosophy (PhD)

Understanding mechanisms regulating the assembly of ecological communities is a major goal of community ecology. I combined experimental and theoretical approaches to investigate the influences of various ecological factors on the assembly of protist communities. My research included three experimental studies and one theoretical study. Two experimental studies used freshwater heterotrophic ciliated protists as model organisms to examine how species dispersal across local communities and functional and phylogenetic diversity of the species pool influence historical contingency of the assembled communities, respectively. The results of the first experiment showed that the differences in species colonization history led to alternative community states that substantially differed in species composition and abundances, regardless of the level of species dispersal. The results of the second experiment showed that historical contingency, measured by beta diversity and the strength of inhibitive priority effects decreased as phylogenetic and functional diversity of the species pool increased. In the third experimental study, I used the same model system and observed positive relationships between phylogenetic diversity and temporal stability of community biomass. These positive relationships are likely due to the reduced competition among species and increased asynchronous species responses to environmental changes under higher phylogenetic diversity. The theoretical study explored how phytoplankton and zooplankton coevolution drives species diversity patterns along productivity gradients in a mathematical model system. I explored the conditions for evolutionary divergence in phytoplankton and zooplankton and the consequent productivity-diversity relationships (PDR) using the theory of adaptive dynamics and numerical simulations. The results of numerical simulations showed that the coevolutionary dynamics of phytoplankton and zooplankton can generate transient unimodal or positive PDRs, and positive PDRs when the systems reach steady states. The findings of my research suggest an important role of traits and species ecological difference in understanding causes and consequences of biodiversity in community ecology.

No description available.

Les modèles d'occupation de niche au sein des communautés locales, la variabilité spatiale de la biodiversité le long des gradients environnementaux du stress et des perturbations, et les processus de succession végétale sont plusieurs sujets fondamentaux en écologie. Récemment, l'approche basée sur les traits est apparue comme un moyen prometteur de comprendre les processus structurant les communautés végétales et cette approche a même été proposée comme méthode pour reconstruire l'écologie communautaire en fonction des traits fonctionnels. Par conséquent, lier ces thèmes fondamentaux en utilisant une lentille fonctionnelle devrait nous donner un aperçu de certaines questions fondamentales en écologie et sera l'objectif principal de ma thèse. En général, mon projet de doctorat vise à étudier les structures de l'occupation de l'espace fonctionnel dans les gradients spatio-temporels. Plus précisément, l'objectif du chapitre 2 est (i) d'étudier les modèles d'occupation de la niche fonctionnelle en calculant trois métriques clés de niche (le volume total de niche fonctionnelle , le chevauchement des niches fonctionnelles et le volume de niche fonctionnel moyen) des communautés pauvres en espèces aux communautés riches en espèces et (ii) de déterminer le principal facteur de la structure observée de l'occupation de la niche fonctionnelle dans les communautés végétales du monde entier. Dans le chapitre 3, je vise à prédire et à expliquer la variation de la richesse en espèces selon les gradients de stress et de perturbation, en reliant le modèle d'équilibre dynamique et l'occupation de la niche fonctionnelle en fonction du cadre développé au chapitre 2. L'objectif du chapitre 4 est de tester expérimentalement l’application d'une méthode d'ordination CSR évaluée globalement en fonction de trois traits de feuilles (surface foliaire, teneur en matière sèche des feuilles et surface foliaire spécifique) dans les études locales. Enfin, l'objectif du chapitre 5 est de tester expérimentalement les hypothèses qui concilient les points de vue déterministes et historiquement contingents de la succession végétale, en étudiant la variation des divergences taxonomiques et fonctionnelles entre les communautés selon des gradients de stress et de perturbation. L'étude globale (chapitre 2) est basée sur une collection de 21 jeux de données, couvrant les biomes tropicaux et tempérés, et se compose de 313 communautés végétales représentant différentes formes de croissance. Les études locales (chapitre 3, 4 et 5) sont basées sur le même système expérimental constitué de 24 mésocosmes présentant différents niveaux de stress et de perturbation. L'expérience a commencé en 2009 avec le même mélange de graines de 30 espèces herbacées semées sur les 24 mésocosmes et s'est terminée en 2016. Nous avons permis la colonisation naturelle de graines de la banque commune de graines de sol et de l'environnement pendant la succession de sept ans. Dix traits ont été mesurés sur cinq individus (échantillonnés directement à partir des mésocosmes) par espèce par mésocosme en 2014 (chapitre 3 et 4). Un autre ensemble de traits (16 traits, y compris certains traits qui ne pouvaient pas être mesurés directement dans les mésocosmes), ont été mesurés au niveau de l'espèce (valeurs moyennes des traits) pour les 34 espèces les plus abondantes (certaines espèces disparues dans les mésocosmes) au cours des sept Ans, en les regroupant séparément pour une saison de croissance. Au chapitre 2, nous avons constaté que les communautés étaient plus diverses en termes fonctionnels (une augmentation du volume fonctionnel total) dans les communautés riches en espèces et que les espèces se chevauchaient davantage au sein de la communauté (augmentation du chevauchement fonctionnel), mais ne divisaient pas plus finement l'espace fonctionnel (aucune réduction du volume fonctionnel moyen). En outre, le filtrage de l'habitat est un processus répandu qui conduit à la caractérisation de l'occupation de niche fonctionnelle dans les communautés végétales. Dans le chapitre 3, nous avons trouvé un modèle similaire d'occupation de niche fonctionnelle sur un système expérimental avec une taille spatiale communautaire constante et un effort d'échantillonnage des traits, qui, avec le chapitre 2, nous a fourni une image plus complète et plus solide de l'occupation de niche fonctionnelle dans les communautés végétales. De plus, nous avons réussi à relier le modèle de l'occupation de la niche fonctionnelle et le modèle d'équilibre dynamique et avons constaté que le filtrage concurrentiel était le processus dominant qui détermine le mode d'occupation de la niche fonctionnelle et la richesse des espèces le long du stress et de la perturbation des gradients. Au chapitre 4, nous fournissons un soutien empirique à une méthode d'ordination CSR calibrée globalement en montrant une relation entre l'abondance relative d'espèces en croissance dans les mésocosmes ayant différents niveaux de fertilité du sol et mortalité indépendante de la densité et leur classification CSR. Au chapitre 5, nous avons montré que la succession d'installations au cours de sept ans dans ces mésocosmes était plus déterministe d'un point de vue fonctionnel, mais plus historiquement contingent d'un point de vue taxonomique et que l'importance relative de la contingence historique a diminué à mesure que l'environnement devenait plus stressé ou perturbé. En conclusion, les structures de l'occupation de l'espace fonctionnel dans (le volume fonctionnel total, le chevauchement fonctionnel et le volume fonctionnel moyen, les Chapitre 2 et 3) ou entre les communautés locales (dissimilarité fonctionnelle, chapitre 5) sont déterministes plutôt que neutres (ou contingence historique ). Les espèces tolératrices de stress sont plus avantagées dans les mésocosmes moins fertiles tandis que les espèces rudérales sont plus avantagées dans les mésocosmes avec plus de mortalité indépendante de la densité. / Abstract : The patterns of niche occupancy within local communities, the spatial variability of biodiversity along environmental gradients of stress and disturbance, and the processes of plant succession are several fundamental topics in ecology. Recently, the trait-based approach has emerged as a promising way to understand the processes structuring plant communities and has even been proposed as a method to rebuild community ecology based on functional traits. Therefore, linking these fundamental themes through a functional lens should give us more insight into some basic questions in ecology and will be the main objective of my thesis. Generally, my PhD project is to investigate the structures of functional space occupancy along both spatial and temporal gradients. Specifically, the objective of Chapter 2 is to investigate the patterns of functional niche occupancy by calculating three key niche metrics (the total functional niche volume, the functional niche overlap and the average functional niche volume) from speciespoor communities to species-rich communities and to determine the main driver of the observed pattern of functional niche occupancy across plant communities worldwide. In Chapter 3, I aim to predict and explain the variation of species richness along gradients of stress and disturbance, by linking the dynamic equilibrium model and functional niche occupancy based on the framework developed in Chapter 2. The objective of Chapter 4 is to experimentally test the application of a globally calibrated CSR ordination method based on three leaf traits (leaf area, leaf dry matter content and specific leaf area) in local studies. Finally, the aim of Chapter 5 is to experimentally test the hypotheses reconciling the deterministic and historically contingent views of plant succession, by investigating the variation of taxonomic and functional dissimilarities between communities along gradients of stress and disturbance. The global study (Chapter 2) is based on a collection 21 trait datasets, spanning tropical to temperate biomes, and consisting of 313 plant communities representing different growth forms. The local studies (Chapter 3, 4 and 5) are based on the same experimental system consisting of 24 mesocosms experiencing different levels of stress and disturbance. The experiment started in 2009 with the same seed mixture of 30 herbaceous species broadcast over the 24 mesocosms and ended in 2016. We allowed natural colonization of seeds from the common soil seed bank and from the surroundings during the seven-year succession. Ten traits were measured on five individuals (sampled directly from the mesocosms) per species per mesocosms in 2014 (Chapter 3 and 4). Another set of traits (16 traits including some traits that were not able to measured directly in the mesocosms) were measured at the species level (species mean traits values) for the 34 most abundant species (some species disappeared in the mesocosms) over the seven years, by regrowing them separately for one growing season. In Chapter 2, we found communities were more functionally diverse (an increase in total functional volume) in species-rich communities, and species overlapped more within the community (an increase in functional overlap) but did not more finely divide the functional space (no decline in average functional volume). Moreover, habitat filtering is a widespread process driving the pattern of functional niche occupancy across plant communities. In Chapter 3, we found a similar pattern of functional niche occupancy on an experimental system with a constant community spatial size and trait-sampling effort, which together with Chapter 2 provided us a more comprehensive and robust picture of functional niche occupancy across plant communities. In addition, we succeeded in linking the pattern of functional niche occupancy and the dynamic equilibrium model and found that habitat filtering was the dominant process determining the pattern of functional niche occupancy and species richness along the gradients stress and disturbance. In Chapter 4, we provide empirical support for a globally calibrated CSR ordination method by showing a relationship between the relative abundance of species growing in mesocosms having different levels of soil fertility and density-independent mortality and their CSR classification. In Chapter 5, we showed that plant succession over seven years in these mesocosms was more deterministic from a functional perspective but more historically contingent from a taxonomic perspective, and that the relative importance of historical contingency decreased as the environment became more stressed or disturbed. In conclusion, the structures of functional space occupancy within (the total functional volume, the functional overlap and the average functional volume; Chapter 2 and 3) or between local communities (functional dissimilarity, Chapter 5) are deterministic rather than neutral (or historical contingency). Stress-tolerators were more favored in high stress communities, while ruderals are more favored in high disturbed mesocosms (Chapter 4).