<p>Fungal pathogens likely play an important role in regulating populations of tree seedlings and preserving forest diversity, due to their ubiquitous presence and differential effects on survival. Host-specific mortality from natural enemies is one of the most widely tested hypotheses in community ecology to explain the high biodiversity of forests. The effects of fungal pathogens on seedling survival are usually discussed under the framework of the Janzen-Connell (JC) hypothesis, which posits that seedlings are more likely to survive when dispersed far from the parent tree or at low densities due to pressure from host-specific pathogens (Janzen 1970, Connell 1971). One of the key challenges to assessing the importance of JC effects has been to identify and quantify the effects of the large numbers of potential pathogens required to maintain host diversity. The primary objectives of this research were to (1) characterize the fungi associated with seedling disease and mortality for a number of important southeastern US forest tree species; and (2) determine if these associations are consistent with the Janzen-Connell hypothesis in terms of differential effects on seedling survival.<br></p><p>Culture-based methods and ribosomal DNA (rDNA) sequencing were used to characterize the fungal community in recently dead and live seedlings of thirteen common tree species in a temperate mixed hardwood forest (North Carolina, USA), with the goal of identifying putative seedling pathogens. Cultures were initially classified and grouped into 130 operational taxonomic units (OTUs) using 96% internal transcribed spacer (ITS) sequence similarity; 46% of all OTUs were found only once. Using rarefaction, it was concluded that the richness of the system was not fully sampled and likely included over 200 taxa (based on non-parametric richness estimators). Species richness did not differ between sampling sites or among the five most common hosts sampled. The large ribosomal subunit (LSU) region of rDNA was then sequenced for representative samples of common OTUs and refined identifications using a constrained maximum likelihood phylogenetic analysis. Phylogenetic placement verified strong BLAST classifications, and allowed for placement of unknown taxa to the order level, with many of these unknowns placed in the Leotiomycetes and Xylariales (Sordariomycetes).<br> </p><p>Next, a hierarchical Bayesian model was developed to predict the effects of multiple putative fungal pathogens on individual seedling survival, without forcing the effects of multiple fungi to be additive. The process of disease was partitioned into a chain of events including incidence, infection, detection, and survival, and conditional probabilities were used to quantify each component individually, but in the context of one another. The use of this modeling approach was illustrated by examining the effects of two putative fungal pathogens, <italics>Colletotrichum acutatum</italics> and <italics>Cylindrocarpon</italics> sp. A, an undescribed species of <italics>Cylindrocarpon</italics>, on the survival of five seedling hosts in both a maximum likelihood and Bayesian framework.<br> </p><p>Finally, the model was used to assess the impacts of these fungi on seedling survival, alone and in combination, using data on five potential fungal pathogens and five hosts. Multi-host fungi had differential effects on seedling survival depending on host identity, and multiple infections may impact survival even when single infections do not. Evaluating these interactions among multiple plant and fungal species generates a set of targeted hypotheses of specific plant-fungal combinations that could help us better understand pathogen-driven diversity maintenance at larger scales than previously possible. Building on these results, some recommendations are provided as to how the Janzen-Connell hypothesis can be re-evaluated with respect to host specificity, pathogen distribution, and environmental context.</p> / Dissertation

Natural enemies are ubiquitous in nature. In many communities, natural enemies have a major effect on the diversity of their prey. Their effects are very diverse: they can promote or undermine the ability of their prey to coexist through a variety of mechanisms. As such, an important step in understanding how diversity is maintained will be to understand how different forms of predator behavior affect prey coexistence. In this dissertation, I study how two major types of predators affect plant coexistence in two different communities. First, I study natural enemies in tropical forests, using both theory and empirical work. In tropical forests, most natural enemies are thought have a narrow host range, and be distance-responsive (i.e., mainly harm seeds and seedlings that are near adults of their main host). Previous theoretical work has shown that specialized natural enemies can maintain diversity of their prey, whether or not they are distance-responsive. However, it is unknown whether specialist natural enemies are more or less able to promote prey coexistence if they are distance-responsive. Using theoretical models, I show that distance-responsive predators are less able to maintain diversity. Additionally, I show that habitat partitioning does not interfere with the ability of distance-responsive predators to maintain diversity, even if it causes seedling survival to be highest near conspecific adults. From an empirical aspect, I studied the host range of seed-associated fungi. Soilborne microbes, such as fungi, are thought to play an important role in maintaining diversity in tropical forests. However, the microbial community itself is often treated as a black box, and little is known about which microbes are causing major effects, or how 8 specialized seed-microbe associations are. Here I use experimental inoculations to examine the host range and effect of a guild of seed-associated fungi that are thought to be mainly pathogens. I show that fungal species are differentially able to colonize different seed species, and have species-specific effects on seed germination. I show that in many cases, plant phylogeny, and to a lesser extent fungus phylogeny, are good predictors of colonization. Finally, I study how an optimally foraging granivore can promote (or undermine) coexistence amongst annual plants, using theory. Optimal foraging theory is one of the major theories for how predators behave; despite this, little is known about whether an optimally foraging predator could promote coexistence amongst a diverse community of prey. Previous models have shown than two species can coexist due to optimal foraging, but did not test whether multiple prey can coexist, nor if the effect is altered by environmental variation. Here, I show that if the predators specialize on different prey at different times, the predators can allow multiple prey species to coexist. In this case, environmental variation has little effect on the ability of predators to maintain diversity. If the predators are generalists, they cannot maintain diversity. Additionally, I show that generalist predators will create a negative storage effect, undermining coexistence.

No description available.

Les mécanismes expliquant le maintien de la diversité végétale dans les forêts tropicales sont mal connus. Une hypothèse particulièrement étudiée est l’hypothèse Janzen-Connell qui postule que ces mécanismes sont essentiellement causés par les interactions entre les plantes et leurs ennemis naturels, en particulier les organismes pathogènes. Dans cette thèse, nous nous sommes donc intéressés aux agents pathogènes présents dans les sols d’une forêt guyanaise et à leur lien de spécificité avec les plantes. Dans le cas où l’hypothèse Janzen-Connell serait vérifiée, on peut s’attendre à ce que les plantes structurent les communautés de micro-organismes pathogènes. Nos travaux se sont focalisés sur les Oomycètes et en particulier les Phytophthora, pathogènes des arbres très importants, mais nous nous sommes aussi intéressés aux champignons pathogènes. Ainsi, nous avons développé et comparé des jeux d’amorces PCR spécifiques des Phytophthora et des Péronosporomycètes afin d’étudier ces organismes par metabarcoding. Ces amorces ont ensuite servi à étudier la diversité des communautés de Phytophthora dans des échantillons de sols de deux sites forestiers de Guyane Française prélevés au pied d’arbres appartenant à 10 familles végétales. Une faible diversité a été retrouvée, avec seulement 8 taxons en tout, et la très large dominance d’un complexe d’espèces Phytophthora heveae. La structuration par la plante-hôte de ces communautés est plutôt faible. Dans une étude complémentaire, nous avons analysé la diversité des Oomycètes et des champignons pathogènes dans les sols et les litières de six plantations monospécifiques et au sein d’une forêt naturelle de Guyane. La structuration par l’hôte s’est avérée nulle pour les Oomycètes et faible pour les champignons pathogènes. Enfin, nous n’avons pas réussi à déclencher expérimentalement des mortalités ou dépérissements par des Oomycètes sur le wacapou, une espèce d’arbre guyanaise, via des inoculations de sols de forêt. Au final, les résultats de cette thèse ne supportent pas l’hypothèse selon laquelle les Oomycètes seraient d’importants acteurs du maintien de la diversité végétale dans les forêts tropicales. Par ailleurs, ils nous interrogent sur la faible diversité de ce groupe de microorganismes dans les sols et litières dans un hotspot de diversité végétale. / The mecanisms implied in the maintenance of plant diversity in tropical forests are still poorly known. One particularly studied hypothesis is the Janzen-Connell hypothesis, which posits that these mecanisms are essentially caused by the interactions between plant and their natural enemies, including pathogenic organisms. In this thesis, we looked at the pathogenic organisms present in the soils of a Guyanese forest, and the specificity of their interactions withplants. In the case where the Janzen-Connell hypothesis would be verified, we could expect that pathogenic micro-organisms communities would be structured by plants. Our works focused on Oomycetes and especially the Phytophthora, which are very important pathogens of trees, but we also took an interest on pathogenic Fungi. Thus, we developed PCR primer sets specific of the Phytophthora and Peronosporomycete groups, in order to study these organismsthroughmetabarcoding. These primers were then used to investigate the community of Phytophthora in soils sampled from two French Guiana sites, near trees belonging to 10 families. A low diversity was described, with a total of only 8 taxas, and the overwhelming dominance of the species complex P. heveae. A weak host effect was detected. In a complementary study, we looked at the diversity of Oomycetes and Fungi in soils and litters of six monospecific tree plantations and a Guianese natural forest. Structuration by host appeared to be null for Oomycetes and weak for pathogenic Fungi. Finally, we did not success in trying to experimentally provoke, through forest soil inoculations, Janzen-Connell mortalities due to Oomycetes on the Wacapou, a Guianese tree species. In the end, the results of this thesis do not support the hypothesis that Oomycetes may be important agents of the maintenance of tree diversity in tropical forests. Moreover, they bring some questions about the low diversity of this group of micro-organisms in a tree diversity hotspot.

Made available in DSpace on 2016-06-02T19:26:21Z (GMT). No. of bitstreams: 1 MEIGA_Ana_2012.pdf: 1469449 bytes, checksum: 04e1e39246304f63a7f5b2af105d0d8a (MD5) Previous issue date: 2012-05-30 / Animals may influence the spatial distribution and survivorship of plants with which they interact. For instance, the Janzen-Connell model predict that the probability of seed and seedling survivorship is reduced around the parental plant because of the intense seed predation and herbivory in this place, which suggests the role of seed dispersal in plant regeneration. The hunting and habitat fragmentation threaten the regeneration of many plant species that depend on large animals to disperse their seeds. In this study I investigated the relationship between seed dispersion, predation and the spatial distribution and survival of seedlings of the palm Attalea dubia in native forest preserved, evaluating the importance of mammals for plant regeneration. In a second part I compared the pre-dispersal seed predation of A. dubia in three habitats: a continuous forest area, a forest fragment and a pasture. This study was undertaken in Parque Estadual Carlos Botelho , and adjacent areas in south-west of São Paulo State. The flowering and fruiting phenology of the palm was observed during a year (October 2010 to November 2011). Focal observations of fruiting palms and cameras traps allowed us to verify which species of mammals included fruits or seeds of A. dubia in the diet. Seed predation and removal experiments combined with the mapping of the spatial distribution of seedling and adult plants were taken to evaluate the importance of mammals in regeneration and test the Janzen-Connell hypothesis. Fruiting of Attalea dubia occurs throughout the year. The mammal species recorded interacting with A. dubia fruits and seeds were: Cebus nigritus, Guerlinguetus ingrami, Philander frenatus and sigmodontineous rodents. Seeds away from the parent palm were more likely to survive than seeds around the parent palm. The spatial distribution seedlings and juveniles also agree with the Janzen-Connell hypothesis. Small mammals removed most seeds to short distances, around 4 meters. Seed predation by rodents was higher in the fragment than in continuous forest and much reduced in the pasture. Predation by invertebrates was reduced in continuous forest and higher in the fragment. There was no compensation of the seed predation: seed predation by invertebrates did not increase in the absence of rodents. Mammals seems to be not essential to the palm regeneration, but they may be important for the spatial distribution of A. dubia. I suggest that the importance of small mammals, such as squirrels, to seed dispersal and plant regeneration of large-seeded plants has been underestimated. Changes in seed predation among habitats may lead to the dominance of some plant species, reducing plant diversity in the long term. The increase in abundance of A. dubia that occurs in highly disturbed areas and edges of fragments can be the result of the lower seed predation in these areas. / A sobrevivência, distribuição espacial e densidade das plantas podem ser mediadas pelas interações entre animais e plantas. Alguns modelos (como de Janzen-Connell) assumem que a probabilidade de sobrevivência de sementes e plântulas é menor ao redor da planta-mãe devido à intensa predação de sementes e herbivoria, sugerindo que a dispersão de sementes tenha um papel fundamental na regeneração. Os mamíferos de grande porte são reconhecidos por desenvolverem um importante papel na dispersão de sementes. A caça e fragmentação de hábitats ameaça a regeneração de muitas espécies de plantas que dependem de animais de grande porte para dispersar suas sementes. O presente estudo foi dividido em dois capítulos, a primeira parte desse trabalho é dedicada a investigar a relação entre a dispersão e predação de sementes, mortalidade de plântulas e a distância de plantas adultas, de forma a verificar o papel de mamíferos dispersores de sementes na regeneração e distribuição espacial da palmeira Attalea dubia em floresta nativa preservada. O segundo capítulo é uma comparação entre predação de sementes não dispersas de A. dubia em três contextos ambientais: em uma área contínua, uma área fragmentada e uma pastagem. O estudo foi realizado no Parque Estadual Carlos Botelho, região sudoeste do Estado de São Paulo e em seu entorno. Foi observada a fenologia de floração e frutificação da palmeira pelo período de um ano (outubro de 2010 a setembro de 2011). Observações focais de plantas, complementadas com o uso de armadilhas fotográficas, permitiram registrar quais mamíferos consomem seus frutos. Informações sobre predação de sementes e experimentos de remoção, combinadas com observações da distribuição espacial de plântulas e palmeiras adultas, foram realizados para uma melhor compreensão sobre o papel de animais na regeneração da espécie e o teste da hipótese de Janzen-Connell. Para comparar a predação de sementes em diferentes contextos ambientais foram coletadas sementes sob a copa da planta-mãe. Sementes predadas foram classificadas de acordo com o agente de predação (roedores ou insetos). A frutificação de A. dubia ocorreu ao longo de todo o ano com diferentes estágios de maturação. As seguintes espécies de mamíferos foram visualizadas interagindo com frutos/sementes de A. dubia: Cebus nigritus, Guerlinguetus ingrami, Philander frenatus e roedores sigmodontíneos não identificados. A distância da remoção de sementes e frutos de A. dubia por pequenos mamíferos foi baixa (4 metros), sendo que a maioria das sementes não foi removida. Sementes distantes da planta-mãe permaneceram mais intactas que sementes ao redor da mesma, corroborando a hipótese de Janzen-Connell. No segundo capítulo, a predação por roedores foi maior no fragmento que na floresta contínua e bem reduzida no pasto. A predação por invertebrados foi reduzida na floresta contínua frente ao fragmento. Não houve compensação na predação de sementes, de forma que a predação por invertebrados não aumentou na ausência de roedores. É possível que os mamíferos desempenhem um papel importante para a dinâmica populacional da palmeira Attalea dubia. Embora eles não sejam essenciais para a sobrevivência da palmeira, uma vez que a planta recruta mesmo em locais com ausência de mamíferos de maior porte, a atividade de mamíferos de pequeno porte parece ser suficiente para explicar a distribuição espacial da palmeira no Parque Estadual Carlos Botelho. Assim pode-se inferir que a importância dos mamíferos de pequeno porte em relação à eficiência no processo da dispersão de sementes está sendo subestimada. Alterações na predação de sementes podem levar à dominância de algumas espécies vegetais, reduzindo a diversidade vegetal em longo prazo. Invertebrados em fragmentos e na pastagem não parecem compensar a predação de sementes de Attalea dubia efetuada principalmente por roedores na floresta contínua. O aumento na abundância de A. dubia verificado em áreas muito perturbadas e bordas de fragmentos pode ser decorrente da menor predação de sementes nestas áreas.

Les adultes conspécifiques (ou évolutivement proches) réduisent le recrutement des graines/plantules à leur proximité, à cause d’une forte pression de prédation par des ennemis spécialistes ou peu mobiles (Hypothèse de Janzen-Connell). Cependant, l’importance de l’effet Janzen-Connell reste controversé, suggérant que les interactions entre adultes et plantules ne se restreignent pas aux adultes conspécifiques proches, ni aux ennemis spécialistes : les adultes hétérospécifiques, la taille des adultes et la représentation de leur lignée dans la canopée pourraient aussi contrôler le recrutement des plantules. De plus, les effets des adultes sur les graines/plantules pourraient être médiés par des ennemis généralistes et très mobiles, par des champignons mutualistes et par certaines conditions micro-environnementales. Nous avons étudié les effets des arbres adultes sur le recrutement des graines/plantules de chêne, via les ennemis mobiles, les champignons mutualistes et enfin les conditions micro-environnementales. Nos résultats démontrent que : (i) un adulte conspécifique empêche le recrutement des plantules à proximité, via une accumulation des décomposeurs spécialistes qui augmentent la qualité nutritionnelle des plantules, attirant ainsi les ennemis. De plus, un adulte de grande taille attire des herbivores mollusques ; (ii) un adulte hétérospécifique favorise le recrutement des plantules à sa proximité, en réduisant l’herbivorie et en améliorant le microenvironnement ; (iii) une canopée évolutivement proche favorise le recrutement des graines et plantules, en rassasiant les prédateurs de graines et en augmentant le soutien par les mycorhizes, respectivement. Ainsi, nos résultats permettent d’identifier les structures forestières optimales pour le recrutement du chêne. De plus, nos résultats suggèrent que le recrutement maintient les chênes proches de leurs espèces apparentées et donc dans leur niche ancestrale. / Conspecific (or closely related) adults reduce seed/seedling recruitment in their proximity, due to high pressure from specialized or little mobile enemies (Janzen-Connell Hypothesis). However, the importance of the Janzen-Connell effect remains controversial, suggesting that interactions between adults and seedlings are not restricted to close conspecific adults, nor to specialized enemies: heterospecific adults, size of adults and dominance of their lineage in the canopy may also control seed/seedling recruitment. Moreover, effects of adults on seeds/seedlings may be mediated by generalist or mobile enemies, fungal mutualists, and microenvironmental conditions. We studied the effect of adult trees on recruitment of oak seeds/seedlings, via mobile enemies, fungal mutualists, and finally microenvironmental conditions. Our results demonstrated that (i) a conspecific adult impedes recruitment of proximate seedlings by accumulating specialist decomposers that favor nutritional quality of seedlings and thereby attract herbivores. Moreover, a large adult attracts mollusk herbivores; (ii) a heterospecific adult favors recruitment of proximate seedlings, by reducing herbivory and improving the micro-environment; (iii) a closely related canopy favors seeds and seedlings recruitment, by oversaturating seed predators and increasing mycorrhizal support, respectively. Hence, our results permit to identify forest structures that are optimal for oak recruitment. Moreover, our results suggest that recruitment maintain oaks close to related species, in their ancestral niche.