The processes that determine the structure of plant communities are of considerable practical and theoretical interest. Natural enemies such as herbivores, seed predators and pathogens provide one potentially important influence on plant diversity. I investigated the effects of natural enemies on plant diversity in two contrasting, species-rich plant communities (tropical forests in Panama and temperate grasslands in the UK), focusing on pre-dispersal seed predation by insects, and the mortality of seeds and seedlings caused by soil fungi. In Panama I found that pre-dispersal insect seed predators generate significant levels of mortality in multiple tropical tree species, with high heterogeneity in predation rates among individuals and at different forest sites. Insect seed predators were highly host-specific, consistent with a role in enhancing plant diversity. At Upper Seeds, a calcareous grassland site in the UK, I used manipulative experiments to show that soil fungi increase the diversity of plants propagating from soil seed banks. A parallel experiment in Panama, mimicking germination under light gap conditions, revealed differential effects of fungi among sites, with fungicide treatment appearing to increase the diversity of propagated seedlings at some sites but reducing it at others. These results suggest that the influence of soil fungi on pre-emergence mortality can alter plant diversity, even when post-emergence mortality from fungal pathogens is limited. In Panama, I also tested whether enemy-mediated mortality increases with rainfall, potentially contributing to the positive regional correlations widely observed between precipitation and plant diversity. In contrast to predictions, neither pre-dispersal insect seed predation nor the influence of soil fungi on seedling recruitment were affected significantly by site humidity, or (for soil fungi) with experimentally manipulated soil moisture levels. Overall, my results provide evidence that pre-dispersal seed predators and soil fungi can affect plant recruitment and diversity at early life stages, with potential consequences for the community structure of adult plants.

Les espèces exotiques envahissantes végétales sont des plantes introduites et naturalisées hors de leur aire de répartition native et capables de maintenir et d’accroitre leur population. Certaines sont considérées comme transformatrices de par leur effet sur les écosystèmes : leur structure, leur fonctionnement ainsi que leur communauté végétale et animale. Ces transformations peuvent rendre certaines de ces espèces nuisibles de par leurs impacts écologiques et économiques important. Les travaux réalisés dans le cadre de cette thèse et présentés ici ont pour objectif d’approfondir les connaissances sur l’impact des invasions biologiques. La faune du sol, la végétation native et leur substrat ainsi que son fonctionnement ont été étudiés à différentes échelles spatiales. Deux espèces exotiques, envahissantes en Europe, ont été considérées comme modèles pour ces travaux : le robinier faux-acacia (Robinia pseudoacacia) et la renouée du japon (Reynoutria japonica). Premièrement, une méta-analyse globale a permis de démontrer l’effet positif des invasions biologiques végétales sur l’abondance de certains groupes de la faune du sol, notamment les consommateurs primaires, en fonction de la structure de l’habitat (ouvert ou fermé). Ensuite, une étude à large échelle sur le robinier faux-acacia a permis d’illustrer les différences qui peuvent exister dans la réponse des écosystèmes forestiers aux invasions le long d’un gradient latitudinal. Ce gradient, composé de quatre régions distinctes en Europe de l’Ouest présente des différences de climat et de végétation dominante, ces différences modifiant l’impact du robinier faux-acacia. Une étude approfondie sur le robinier faux-acacia en Normandie a permis de mieux comprendre l’effet du robinier faux-acacia sur les communautés animales et végétales ainsi que sur le fonctionnement des écosystèmes par comparaison avec deux essences natives dominantes. Finalement, une manipulation expérimentale en laboratoire a démontré l’impact des composés allélopathiques de la renouée du Japon sur une partie de la faune du sol. Cette étude a montré que certaines espèces exotiques envahissantes sont susceptibles d’influencer la faune, et les réseaux trophiques, du sol par leur métabolisme secondaire. Ces travaux illustrent l’intérêt, dans le contexte des invasions biologiques végétales, de l’étude simultanée des compartiments aériens et souterrains à différentes échelles spatiales. / Invasive alien plants are species introduced and naturalized outside of their native distribution range and which have the capacity to maintain and expand their population. Some of these species are considered to be ecosystem transformers by altering their structure, functioning as well as resident animal and plant communities. These induced alterations make some of these species undesirable through their ecological and economical impacts. The work presented in this thesis aimed at a better understanding of the impact of biological invasions by alien plants. The soil fauna, native vegetation and their substrate, as well as ecosystem functioning, were studied at different spatial scales. Two exotic alien species, invasive in Europe, were considered as biological models for this work: the black locust (Robinia pseudoacacia) and the Japanese knotweed (Reynoutria japonica). Firstly, a global meta-analysis demonstrated the positive impact that plant invasions can exert on the abundance of some groups within the soil fauna, notably primary consumers, within different types of habitats (open or closed). Then, a large-scale study on the black locust revealed the differences that can can occur in the response of forest ecosystems to invasions along a latitudinal gradient. Study sites along this gradient, distributed amog four distinct regions in western Europe, exhibit differences in climate and dominant native vegetation which can alter the impact of the black locust. A detailed study on black locust impact in Normandy demonstrated the impact of R. pseudoacacia on native plant and soil fauna communities, as well as some ecosystem functions, in comparison to two native tree species. Finally, a laboraty experiment demonstrated the impact that allelopathic compounds extracted from Japanese knotweed rhizomes can have on some organisms within the soil fauna. This study showed that some invasive alient plants can influence the soil fauna, and soil food webs, through their secondary metabolism. This thesis illustrates that simultaneous study of both aboveground and belowground ecosystem compartments at different spatial scales is of interest in the context of biological invasions.

<p>Benthic diatoms are valuable tools for biological monitoring and paleo-ecological reconstruction of past environmental conditions. This thesis aims at describing size-related properties of benthic diatoms and suggests that data assessment for community analysis can be improved by considering the importance of scale. It investigates which environmental factors structure epilithic diatom communities on the coast of the Gulf of Bothnia and identifies environmental factors correlated with phytobenthic biomass. It also contributes to the floristic knowledge of the Baltic Sea. </p><p>Diatom species show large variation in size. The responses of large species (≥1000 μm3) in diatom communities to environmental factors are underestimated if solely measured as relative abundance, as is the common practice. However, relative abundance gives the best gradient resolution, as compared to surface area and biovolume, if species are counted separately in two biovolume classes. Small and large species in the same community may respond differently to the same environmental factors. </p><p>To assess the principal environmental factors structuring diatom communities in the Gulf of Bothnia, 270 quantitative samples were collected from submerged stones. Sampling was carried out in spring in four areas of the Bothnian Bay, characterized by a stable north-south salinity gradient (0.4-3.3 psu), and in three areas of the Bothnian Sea which has a rather uniform salinity of ca. 5 psu. Canonical correspondence analysis (CCA) identified salinity and exposure to wave action as the principal factors structuring the diatom communities of the Bothnian Bay, whereas exposure to wave action was the principal factor in the Bothnian Sea. Measurements of relative ignition loss suggested that the cover of macroalgae, and thereby the higher abundance of epiphytic diatoms in the epilithic samples, was positively correlated with salinity in the Bothnian Bay and with water movement in the Bothnian Sea. </p><p>Two new brackish water species are described, <i>Navicula sjoersii</i> S. Busse & Snoeijs and <i>N. bossvikensis</i> S. Busse & Snoeijs. The new species are compared with <i>N. perminuta</i> Grunow, a common brackish-water species.</p>

The effects of fire on vernal herbs of the mesic forests of eastern North America are poorly understood. I studied the influence of prescribed fire on species richness, abundance of rare and common species, and density of exotics in the vernal herbaceous layer. To determine these effects, three sites in central Kentucky were surveyed prior to and following one of three treatments: spring burn, winter burn, or negative control. I conducted low-intensity spring burns in April 2010 and winter burns in February 2011. I used chi square analyses to test for changes in species richness, abundance of rare species, abundance of common species, and abundance of Glechoma hederacea, an exotic herb. I used multiple logistic regressions to test for the effect of burn severity on the abundance of two of the most common herbs, Erythronium americanum and Viola sororia sensu lato. The abundance of rare species increased significantly after fire treatment, with a 2% greater increase on burned plots than control plots (p < 0.05), and showed a 40% greater increase in plots burned in winter than plots burned in spring. However, there was no significant difference in overall species richness due to fire or to the season in which the prescribed fire was conducted. There were no significant differences in the density of common species or Glechoma hederacea due to fire treatment or due to fire season. There were also no significant differences in the abundances of Erythronium americanum or Viola sororia sensu lato due to burn severity. Changes in the abundance of rare species due to fire might suggest that prescribed burns may slightly increase the diversity of vernal herbs in eastern mesic forests. Changes in the abundance of rare species due to fire season might suggest that prescribed fires conducted prior to emergence may further increase the diversity of vernal herbs in the eastern mesic forest.

El estudio de los microorganismos en cultivo puro ha propiciado el desarrollo de la genética, la bioquímica y la biotecnología. Sin embargo, la ecología ha permanecido reticente a incorporar a los microorganismos en su acervo teórico y experimental, principalmente debido a las dificultades metodológicas para observar a los microbios en la naturaleza, y como resultado de los caminos divergentes que han trazado las disciplinas de la microbiología y la ecología general. Esta tesis trata de demostrar que los patrones ecológicos de comunidades microbianas son susceptibles de ser analizados mediante la combinación de técnicas filogenéticas y herramientas de estadística multivariante. El uso de técnicas filogenéticas permite solventar, o al menos paliar, el hecho de la no independencia de los organismos vivos debido a la ascendencia común. Con la información ambiental adicional (como reflejo del determinismo abiótico) y la información espacial (como amalgama de eventos históricos y de dispersión), es posible explorar los posibles mecanismos que subyacen a la estructura y a la diversidad de las comunidades microbianas. / The study of microorganisms in pure laboratory culture has delivered fruitful insights into genetics, biochemistry and biotechnology. However, ecology has remained reluctant to incorporate microorganisms in its experimental and theoretical underpinnings mainly due to methodological difficulties in observing microorganisms in nature, and as a result of the different paths followed by the disciplines of microbiology and general ecology. In this dissertation, I argue that novel insights into microbial community patterns arise when phylogenetic relatedness are used in conjunction with multivariate statistical techniques in the context of broad scales of description.

Benthic diatoms are valuable tools for biological monitoring and paleo-ecological reconstruction of past environmental conditions. This thesis aims at describing size-related properties of benthic diatoms and suggests that data assessment for community analysis can be improved by considering the importance of scale. It investigates which environmental factors structure epilithic diatom communities on the coast of the Gulf of Bothnia and identifies environmental factors correlated with phytobenthic biomass. It also contributes to the floristic knowledge of the Baltic Sea. Diatom species show large variation in size. The responses of large species (≥1000 μm3) in diatom communities to environmental factors are underestimated if solely measured as relative abundance, as is the common practice. However, relative abundance gives the best gradient resolution, as compared to surface area and biovolume, if species are counted separately in two biovolume classes. Small and large species in the same community may respond differently to the same environmental factors. To assess the principal environmental factors structuring diatom communities in the Gulf of Bothnia, 270 quantitative samples were collected from submerged stones. Sampling was carried out in spring in four areas of the Bothnian Bay, characterized by a stable north-south salinity gradient (0.4-3.3 psu), and in three areas of the Bothnian Sea which has a rather uniform salinity of ca. 5 psu. Canonical correspondence analysis (CCA) identified salinity and exposure to wave action as the principal factors structuring the diatom communities of the Bothnian Bay, whereas exposure to wave action was the principal factor in the Bothnian Sea. Measurements of relative ignition loss suggested that the cover of macroalgae, and thereby the higher abundance of epiphytic diatoms in the epilithic samples, was positively correlated with salinity in the Bothnian Bay and with water movement in the Bothnian Sea. Two new brackish water species are described, Navicula sjoersii S. Busse &amp; Snoeijs and N. bossvikensis S. Busse &amp; Snoeijs. The new species are compared with N. perminuta Grunow, a common brackish-water species.

[Truncated abstract] This study investigated the organisational role of environmental stability on the fish communities that inhabit the Fortescue River, an intermittent and variable system in north-Western Australia. It did so by examining the relationships between pool stability (measured by persistence of water through time, and variation in maximum pool depth through time) and the number and type of species within pools, temporal fluctuations in total fish abundance and intra-specific abundance, population size frequency distributions, and growth rate. It also examined the association between life history traits and the stability of the environments occupied within the river, and the stability of the river at large. The results indicated that environmental stability was the major factor structuring the fish communities. Among-pool comparisons revealed that unstable pools contained fewer species, a greater fraction of juvenile size classes, and underwent greater fluctuations in total and intra-specific numerical abundance through time, than stable pools . . . Stability affected community structure by determining (or describing) the probability that a pool would undergo periods of extreme shrinkage, that is, the likelihood that fish will be exposed to extreme physico-chemical fluctuations and complete eradication. While the physical environment (acting through stability) primarily structured the fish communities of the Fortescue River there was indirect evidence that even within this variable river system, biological interactions played a role, albeit minor. Future investigations into the role of environmental stability will benefit from the use of accepted and quantitative methods by all stream ecologists.

Les patrons de diversité caractérisent la structure de la diversité des communautés, c'est-à-dire sa valeur, sa distribution et son changement dans l'espace et le temps. Leur étude peut amener des informations importantes sur les processus écologiques qui en sont à l'origine. Cependant de nombreuses hypothèses de travail sont faites lors de leur analyse. L'idée générale de cette thèse est qu'en remettant en cause ces hypothèses, un certain nombre de développements liés aux indices de diversité et aux modèles nuls deviennent possibles et permettent de mieux comprendre les processus écologiques à l'origine des patrons de diversité fonctionnelle ou phylogénétique. Le premier chapitre est consacré à l'étude des patrons de diversité fonctionnelle des communautés végétales alpines à de multiples échelles spatiales et organisationnelles. Le second chapitre s'intéresse aux perspectives méthodologiques amenés par les nombres de Hill. Dans le dernier chapitre, on s'intéresse aux enjeux méthodologiques d'un nouveau type de données de communautés : l'ADN environnemental. / Patterns of community diversity refers to the structure of diversity, i.e. its quantification, its distribution and its turnover in space and time. Its study is likely to shed the light on the assembly rules that determined the structure of communities. However, numerous ecological assumptions are often made when studying diversity patterns. What motivated the work was the perspective that by relaxing these assumptions, a number of developments linked to diversity indices and null models are possible and can help to understand the impact of multiple ecological processes on phylogenetic and functional diversity patterns. In a first part we studied the pattern of functional diversity of alpine plant communities as a function of spatial and organizational scales. In the second part, we studied the methodological perspectives brought by the Hill numbers. In a third part, we addressed the main methodological issues of a new type of community data: environmental DNA.

L’urbanisation aboutit à une grande diversité environnementale, paysagère, historique des espaces verts en ville, avec également des pratiques de gestion très variées, qui, peuvent affecter la biodiversité qu’ils abritent. Or, la composante du sol reste très peu étudiée et les communautés de Collemboles présentes dans les parcs urbains constitue une thématique de recherche jusqu’à présent relativement ignorée. Si ces Arthropodes sont de petite taille (de l’ordre du millimètre), ils sont en effet très nombreux dans les sols et aujourd’hui reconnus comme de bons indicateurs pour le monitoring des sols.Les effets de différents filtres abiotiques ont été testés en appliquant à la fois une approche taxonomique et fonctionnelle des communautés de Collemboles dans les parcs urbains de Naples et de Montpellier. La thèse se développe alors en trois axes correspondant à l’étude des effets:- de la composition et fragmentation de la mosaïque urbaine proche- des dynamiques temporelles propres aux parcs- des pratiques de gestion courantesL’analyse conduite à Montpellier a permis de mettre en évidence l’existence de plusieurs groupes homogènes de paysages auxquels étaient associées des structures de communautés différentes. En effet, les paysages urbains les plus hétérogènes favorisent le développement et le maintien de communautés mieux structurées et plus riches en espèces.Par ailleurs, l’étude menée à Naples a montré que le maintien d’un couvert végétal spécifique et principalement boisé, conjointement à la présence de litière au sol, apparaissent comme les facteurs les plus importants pour permettre l’établissement de communautés mieux structurées et plus riches en espèces. Dans une moindre mesure, l’âge des parcs et le précédant usage du sol étaient également déterminants.Enfin, une analyse fonctionnelle (étude de traits morphologiques et préférences de microhabitats) a été envisagée pour évaluer l’intensification de la gestion du sous-bois au sein des habitats boisés des parcs des deux villes. Un gradient abiotique clair a été observé. En revanche, contrairement aux hypothèses énoncées et à la littérature récente sur le sujet, les communautés de Collemboles étaient mieux discriminées du point de vue taxonomique que du point de vue fonctionnel. Il semblerait donc que l’intensification de la gestion du sous-bois ne soit pas un filtre environnemental imposant des changements dans les patterns de traits des espèces présentes.Si d’un côté les études développées dans cette thèse apportent des connaissances fondamentales sur l’écologie des Collemboles présents dans les parcs urbains, de l’autre elle vise à intégrer ces résultats pour un développement plus durable en termes d’aménagement et de gestion des espaces verts urbains. / Urbanization causes a huge diversity in landscapes, environmental conditions and green spaces history. This phenomena also induces different vegetation management practices, which may affect urban fauna. However, scarce attention has been paid to belowground communities in cities and Collembola hosted by soils of urban parks represent a neglected research topic. These taxa are very common in most soils and have been recognized as proper indicators for soil monitoring programs.The effects of diverse abiotic filters on Collembola in Naples and Montpellier public parks has been studied from both taxonomic and functional points of view. In particular, the PhD work was developed based on three principal axes, aiming to test the effects of:- the neighboring landscape context,- the park historical dynamics,- the current park management.The analyses carried out in Montpellier showed different neighboring landscape patterns to which belonged diverse species communities. Indeed, more heterogeneous landscape patterns guarantee the richest and most structured species communities.The study conducted in Naples highlighted that maintaining a specific land cover, especially a canopy cover, jointly to a litter layer on soils are the main factors assuring more structured species communities. To a less extent, park age and the previous land use of the area were also important drivers in modelling species assemblages.Finally, a functional analysis (i.e. morphological traits and microhabitat preferences) was applied to evaluate the brushwood management intensification in woody areas of both cities parks. A clear abiotic gradient was observed. By contrast, functional responses of Collembola communities to brushwood management intensification contradicted our research hypothesis based on the recent literature. Thus, it seems that brushwood removal does not cause shifts in species trait patterns in urban parks.This PhD work increased fundamental knowledge on urban park Collembola ecology, and it strives to integrate these findings in a more suitable landscaping and management of urban green spaces.

O conjunto de alterações causadas pela poluição atmosférica é considerado uma fonte importante de estresse ambiental. A poluição é hoje uma das maiores preocupações ambientais do mundo, pois afeta todas as fontes de recursos naturais que as populações humanas utilizam para a sobrevivência. Agravando esse quadro, somam-se as modificações na paisagem, que intensificam ainda mais os efeitos da poluição. As comunidades de liquens, entre as mais sensíveis em nível de ecossistema, são capazes de demonstrar sinais precoces como resposta às mudanças ambientais e ser úteis como biondicadoras e biomonitoras dessas mudanças. Avaliações em nível de indivíduos e de comunidades de liquens podem ser ferramentas de monitoramento ambiental, assim como uma abordagem com base na estrutura funcional dessas comunidades. Ainda, o uso de atributos funcionais pode permitir compreender como os liquens são capazes de se adaptar funcionalmente à forte pressão ambiental da poluição, além de servir como nova ferramenta para o biomonitoramento da qualidade do ar. Assim sendo, o objetivo geral desta tese foi avaliar os efeitos da poluição atmosférica e da paisagem (como descritora de poluição) na estrutura e na resposta funcional das comunidades de liquens. A partir dos resultados obtidos demonstramos que os liquens de áreas urbanas têm clara influência da poluição atmosférica e das mudanças na paisagem como estresse ambiental, tanto em nível estrutural quanto funcional. No primeiro artigo, avaliamos a qualidade do ar em cada um dos municípios amostrados, contribuindo para a gestão destas áreas com informações relevantes em nível de saúde pública e ambiental. No segundo, demonstramos que tanto a riqueza, cobertura e composição de espécies, além da vitalidade dos liquens, são afetadas pela poluição atmosférica e pelas mudanças da paisagem, sendo a vitalidade e a composição de espécies os melhores indicadores para avaliar os efeitos de múltiplos distúrbios ambientais neste tipo de áreas urbanas. No terceiro artigo, verificamos que alguns atributos funcionais de liquens podem ser bons indicadores da qualidade do ar, relacionados ao tipo de alga, tipo de crescimento, estratégia reprodutiva e à presença de proteção no talo. Fechamos a tese com a descrição de uma nova espécie encontrada, até o momento, somente em áreas pouco urbanizadas. Portanto, novas formas de se utilizar os liquens como bioindicadores e biomonitores de qualidade do ar foram propostas, ampliando ainda mais a aplicação prática desses organismos. / The set of changes caused by air pollution is an important source of environmental stress. Pollution is one of the greatest environmental concerns worldwide in the present days, since it affects all natural resources that people need to survive. Worsening this panorama, there are serious changes in land cover intensifying the effects of pollution. Lichens, which are among the most sensitive organisms in the ecosystem, are able to show early signs as responses to environmental changes. Besides, they can also be useful as bioindicators and biomonitors of such changes. Evaluations using single lichen species and/or lichen communities can be tools of environmental monitoring, as well as an approach based on the functional structure of these communities. The use of functional traits may allow the understanding of how lichens are able to functionally adapt to the strong pressure of pollution. Furthermore, this is also a promising method to be used as a new tool for air quality biomonitoring. Therefore, the main objective of this thesis was to evaluate the effects of air pollution and land cover changes (as surrogates of this pollution) on lichen communities structure and functional response. From the results found, we could demonstrate that lichens from urban areas have clear influence of atmospheric pollution and land cover changes as environmental stresses. The effects are both in structure and function of these communities. In the first paper, we evaluated the air quality in each of the studied cities, contributing to the environmental management of these areas with relevant information for public and environmental health. In the second, we demonstrated that lichen species richness, cover and composition, besides thallus vitality, are affected by air pollution and land cover changes. Among these parameters, we showed that vitality and species composition are the best indicators to evaluate multiple disturbances in this type of urban environment. In the third paper, we verified that some functional traits can be good indicators of air quality, namely the ones related to the type of lichen algae, growing form, reproduction strategy and the presence of any protection (physical or chemical) in the thallus. We ended the thesis with the description of a new species which is so far only found in low urbanized areas. Thus, new means of using lichens as bioindicators and biomonitors of air quality were proposed, helping to expand the application of these organisms in environmental studies and actions.