The degree to which biotic interactions influence invasion success may partly depend on the evolutionary relationship between invaders and native species. In particular, since host-use by enemies such as invertebrate herbivores and fungal pathogens tends to be phylogenetically conserved, exotic plants that have close native relatives in the invaded range should be more likely to interact with enemies. In this thesis, I explore this idea using a series of experiments and field surveys at nested taxonomic levels. My results indicate that exotics from multiple plant families experience lower damage if their average phylogenetic distance from locally co-occurring native family members is higher. I then demonstrate that within the Asteraceae, foliar and capitular damage are lower on exotic compared to native species. Both damage types had a relatively large phylogenetic component, but did not decline with phylogenetic distance to native or exotic confamilials. Finally, I show that communities with versus without close relatives are unlikely to differ in resistance to the novel invader, Solidago virgaurea: biotic resistance imposed by competitors, generalist vertebrates, and specialist invertebrates resulted in similar patterns of damage and mortality regardless of the presence of congeneric natives. In some cases, effects of biota were positive: growth of S. virgaurea seedlings in soils collected near congeneric natives was enhanced more than in soils from communities where congenerics were absent. Overall, these results suggest that biotic interactions between exotic and native species can be phylogenetically structured, although trends based on distance measures tend to be weak. In some cases, damage does decline with phylogenetic distance to native species; however this trend is unlikely to be a strong force limiting invasion or structuring plant communities. These results have significant implications for current theories of invasion biology including the "Enemy Release Hypothesis" and "Darwin's Naturalization Hypothesis", as well as for community phylogenetics.

In this thesis I describe fine-scale spatial patterns in rain forest termites, from the colony to the assemblage level, sampled from one hectare plots in Central African and South East Asian lowland rain forest. By so doing the ecological interactions that structure this functionally important and abundant soil community were identified. The African termite assemblage, dominated by soil-feeding termites, saturated the upper soil profile (collected from 90% of soil pits). In contrast termites were collected from <50% of soil pits in Asia, with this difference reflecting the lower species densities and abundances of soil-feeding termites in Asian forests. Territoriality and inter-specific competition was shown to be important between colonies of soil-feeding species in the African plot. The termite assemblages were spatially associated with several environmental properties. However these could not explain the spatial patterns in the functional components of the assemblages. Wood-feeding termites were highly patchily distributed, due to the heterogeneous nature of their food material, but also due to possible competitive interactions for this. Humus-feeding termites were homogenously structured, due to the continuous nature of soil as their feeding and nesting material. True soil-feeding termites, unique to the African assemblage, were heterogeneously distributed despite the equally continuous nature of their feeding and nesting material. This structure may arise from facilitative interactions, such as co-operative defence against ant predation which may be intense in African systems, or through the transfer of soil material at different stages of decomposition. Competition for space is apparent in both regions, both at the colony level among soil-feeding genera, and between aggregations of functional groups. Positive and negative biotic interactions, operating at various spatial and functional scales, appear to be important in influencing how assemblage composition is spatially structured. If indeed facilitation is important in maintaining the taxonomic and functional diversity in termite assemblages, it would be valuable to confirm the mechanism(s) that drives this (i.e. predation and/or food transfer), as these may then influence ecosystem stability.

The distribution of species in space is determined by the species dispersal capacity, adaptation to environmental conditions, and response to predators and competitors. To determine the importance of dispersal limitation, environmental filtering, and species interactions on the distribution of species in the Brazilian Amazonian forest, I sampled termites in a large area of Brazil. I investigated patterns in species occurrence that could indicate competition and predation structuring termite communities, and analyzed the association of termite abundance and species richness with the density of ant predators. The spatial distribution of termites, and their association with climatic and edaphic conditions were also used to infer about the effects of dispersal limitation and environmental filtering. A total of 271 termite species and 4,389 colonies was found in the 148 transects sampled. Predator density was the strongest predictor of termite abundance and species richness at small spatial scales, but the turnover in termite species composition was mostly associated with measures of soil texture. At broad spatial scales, soil chemistry, climate, and isolation by distance were associated with termite abundance, species richness, and species composition. These results suggest that both species interactions, their association with the environment, and their dispersal capacity determine their distribution. Nevertheless, dispersal limitation seem to be stronger over large areas, whereas environmental filtering can act both at small and large geographic scales.

Natural habitat in the eastern United States has diminished over the past century because of the effects of invasive species. Both plant and animal invaders can alter habitat structure and may decrease survival of native species. The degree to which an invasive species alters ecosystem function depends on the functional characteristics of affected species and the resulting cascading effects. The loss of important native species, such as foundation species, can potentially influence the structure and distribution of animal communities because of the foundation species' unique ecosystem roles. The foundation species concept is relatively new to the terrestrial ecology and the impact on animal communities resulting in the loss of terrestrial foundation species is generally unknown. Eastern hemlock (Tsuga Canadensis), a foundation species in the eastern United States, is declining in abundance due to the invasive sap-sucking insect, hemlock woolly adelgid (Adelges tsugae, Annand). The loss of hemlock may impact the distribution and microhabitat associations of dependent species such as small mammals. I hypothesized that the distribution, population size, community composition, and microhabitat associations of small mammal species differ in response to canopy disturbance from the effects of logging and invasive species. In this dissertation, Chapter One provides an exploration of the past research conducted on 1) invasive species and how they affect habitat structure, 2) foundation species and how they affect ecosystem function, 3) small mammal habitat associations and population cycling, 4) occupancy modeling and its usefulness and limitations in the analysis of local occupancy, colonization rates, and extinction rates. Chapter Two presents a large-scale experiment on how the hemlock woolly adelgid impacts distribution and community assembly of small mammals. Chapter Three presents how forest disturbance, food resources, and habitat structure effects local colonization and extinction patterns of southern red-backed voles. Chapter Four presents how a paper published in 2005 brought the foundation species concept to terrestrial research and how the foundation species concept can be misleading in research.

Os afloramentos rochosos ferruginosos denominados bancadas lateríticas podem ser considerados uma paisagem peculiar no Centro-Oeste do Brasil, próximos às cidades de Corumbá e Ladário, MS. Embora situada em uma região populosa, próxima a fazendas e sítios urbanos, esta vegetação ainda é desconhecida. Neste estudo avaliamos a composição florística e a estrutura da comunidade, bem como suas relações florísticas com outros afloramentos rochosos. O levantamento foi conduzido em três locais - Banda Alta (19°08´S, 57°34´W, 85 m altitude); São Sebastião do Carandá (19°06´S, 57°31´W, 90 m) e Monjolinho (19°16´S, 57°31´W, 65-150 m). A vegetação encontrada nestes afloramentos rochosos ocorre como uma cobertura contínua sobre o substrato rochoso ou como ilhas de solo. Para o estrato contínuo, a vegetação foi amostrada em parcelas de 1 m² distribuídas aleatoriamente. A própria ilha de solo foi considerada uma unidade amostral. A composição de espécies e os valores de cobertura foram avaliados em cada parcela ou ilha de solo. Avaliaram-se 199 parcelas e 164 ilhas de solo neste estudo. Além da abundância das espécies o tamanho e outras características das ilhas de solo foram incluídas neste levantamento. Os dados foram explorados através de tabelas fitossociológicas e de técnicas estatísticas de classificação e ordenação. As relações florísticas foram exploradas nos níveis taxonômicos de famílias e gêneros pela comparação de listas de espécies publicadas de outros afloramentos. Foram amostradas 188 espécies pertencentes a 58 famílias nas três bancadas lateríticas. Deste total, 66 espécies foram encontradas nas parcelas e 181 nas ilhas de solo. A estrutura da comunidade é influenciada, principalmente, pela presença de fina camada de substrato e pela área insular. Processos envolvendo competição exclusiva e diferentes respostas ao regime hídrico aparentemente podem ser as maiores fontes da separação espacial e padrões de abundância. A flora das bancadas lateríticas mostrou similaridade com a flora de afloramentos graníticos da Caatinga, em nível de famílias e gêneros. Condições climáticas e outros fatores podem influenciar as disjunções florísticas observadas mas o substrato rochoso parece ser o fator determinante, com exceção das bancadas lateríticas. Esperava-se que as bancadas fossem similares a outros afloramentos ferruginosos mas isto não ocorreu, sugerindo um importante efeito da história paleoclimática da plataforma continental nos padrões de composição e abundância de espécies da comunidade vegetal das bancadas lateríticas. / The ironstone outcrops called bancadas lateríticas can be considered a peculiar feature of the Central Brazil landscape nearby the cities of Corumbá and Ladário (MS). Although situated in a populated region, near farmlands and cities, the vegetation occurring on these outcrops is completely unknown. In this work we aim to explore the species composition, the floristic relations with other rock outcrops and the community structure of the vegetation thriving on the ironstone surface of the bancadas. The survey was conducted in three outcrops - Banda Alta (19°08´S, 57°34´W, 85 m altitude); São Sebastião do Carandá (19°06´S, 57°31´W, 90 m) and Monjolinho (19°16´S, 57º31´W, 65-150 m). The vegetation found on the rock outcrops occurred as a continuous cover or in groups called soil-islands. In the continuous formation, the vegetation cover was sampled by random Quadrats of 1 m2. A single soil island was taken as a sample unit. The species composition and correspondent cover value was evaluated for each quadrat and soil island. A total of 199 random quadrats and 164 soil islands was used in this work. Along with the abundance of species, the size and other features of each soil islands were included in the survey. The data was explored by the construction of phytosociological tables and statistical classification and ordination techniques. The floristic relations were explored at the level of families and genera by comparisons with published species lists from other outcrops. We detected 188 species belonging to 58 plant families on the three Bancadas outcrops. From this total, 66 species were found in random quadrats and 181 in soil islands. The community structure is primarily influenced by the substrate thickness and the soil island area. Processes involving apparent species competitive exclusion and different responses to water regime can be major sources of the overall spatial disjunction and abundance patterns. The bancadas flora showed similarities with the flora of granite outcrops in the Caatinga formation at the level of genera and families. Climate and other factors can play a role in the floristic disjuntions observed but the rock substrate poses as a dominant factor with the exception of the Bancadas. The departure from the expected similarity with other ironstone outcrops suggests an important effect of Paleoclimatic history of the continental shelf in the patterns of species composition and abundance in the Bancadas plant community.

A caracterização da biodiversidade de comunidades bentônicas resume-se, no litoral brasileiro, a pouco mais de uma dezena de trabalhos estudando, na totalidade, uma área aproximada de apenas 3400 m2. Pretendeu-se aqui propor um novo método, inédito para comunidades marinhas de substrato consolidado, baseado na amostragem de unidades de heterogeneidade da paisagem, denominados povoamentos, visando um aumento na velocidade e abrangência das amostragens neste ambiente. Este estudo foi realizado em um trecho de 260m do costão leste da Praia do Presídio (Enseada das Palmas, P. Est. de Ilha Anchieta, Ubatuba, SP) e divididiu-se em quatro abordagens: 1) identificação e descrição dos povoamentos presentes e spécies neles dominantes; 2) mapeamento da repartição horizontal geo-referenciada de cada povoamento e determinação de sua amplitude vertical máxima; 3) quantificação de seus recobrimentos percentuais médios a partir de imagens; 4) avaliação da composição específica e da variação espacial de povoamentos selecionados. Trinta povoamentos, incluídos nas categorias Banco, Colônia, Crosta e Tapete, além de um atributo não-biológico incluído na categoria Região, foram identificados e descritos e as informações serão disponibilizadas em um banco de dados na internet. O mapeamento foi realizado em apenas 6 mergulhos, em cada estação, de 50 a 80 minutos. A maior parte os povoamentos ocorreu pontualmente. O número de povoamentos e a repartição horizontal dos mesmos praticamente não se alteraram entre verão e inverno. A análise da freqüência relativa dos povoamentos evidenciou que Banco de Sargassum (BSG) apresentou maior valor no verão (25,3%) e Tapete de Amphiroa e Jania (TAJ), no inverno (21,3%). Quanto à distribuição vertical, foram delimitadas quatro principais zonas baseadas na freqüência relativa: uma mais rasa definida por BSG, outra intermediária superior definida por TAJ, outra intermediária inferior definida por Tapete de Ectoprocta (TEC) e uma mais funda definida por povoamentos variáveis com a estação. Foram obtidos 84 elementos amostrais fotográficos no verão e 100 no inverno, os quais evidenciaram 26 e 28 povoamentos, respectivamente. Foram realizadas análises de repartição espacial nos modos R e Q e avaliação de heterogeneidade dos agrupamentos formados. BSG apresentou maior valor de recobrimento percentual médio tanto no período de verão (26,1%) quanto de inverno (32,0%), seguido de TEC (19,7% no verão e 24,2% no inverno), significativamente maior que a maioria dos demais povoamentos (p<0,05). Os povoamentos fitobentônicos foram mais representativos na área (62,2% de recobrimento médio no verão e 61,8% no inverno). Quando consideradas as categorias de povoamentos, os bancos fitobentônicos foram mais representativos (31,2% no verão e 37,0% no inverno). Se somados animais e algas, a categoria ?tapete? foi a mais representada (46,3% no verão e 41,4% no inverno), com grande contribuição dos povoamentos TAJ e TEC, indicando uma possível influência da sedimentação na área. A análise de repartição espacial em Modo R evidenciou a existência de seis grupos no verão e cinco no inverno, sugerindo povoamentos com as mesmas exigências ecológicas. Já em Modo Q observou-se que a comunidade da área é bastante heterogênea, apresentando um padrão em manchas, sendo os povoamentos BSG, Região de Substrato Inconsolidado, TAJ, TEC (e algumas de suas variações) e Tapete de Gelidiopsis e Hypnea (TGH) os responsáveis pela formação dos grupos com o Índice de Similaridade de Morisita-Horn. A análise da composição específica dos povoamentos BSG, TAJ, TEC e TGH evidenciou que os mesmos podem ser considerados homogêneos ou apresentam-se na forma de fácies na área de estudo, podendo ser utilizados como unidades operacionais de forma consistente. Entretanto, estudos em outras áreas são necessários para fornecer suporte aos dados obtidos, principalmente em relação aos dois últimos povoamentos, que carecem de estudos ecológicos. A análise espectral evidenciou suficiência amostral para todos os povoamentos em relação aos pontos Calleja adotados. Os espectros de riqueza foram diagonais e os de diversidade foram retangulares. Para os quatro povoamentos, o Índice de Diversidade de Shannon ficou entre 1,6 e 2,2 e o de Diversidade de Simpson, entre 2,6 e 5,7. O povoamento TGH foi o mais rico e o mais diverso. A comunidade estudada no presente estudo pode ser considerada característica da região sudeste do Brasil. O método dos povoamentos, tanto a partir da Abordagem 2 quanto da 3, possibilitou a caracterização estrutural da comunidade de forma rápida. A análise da micro-heterogeneidade de 4 povoamentos evidenciou que podem ser utilizados como unidades ecológicas consistentes. / The biodiversity characterization of benthic communities in the Brazilian coast is limited to a few works, which studied an area of about 3,400 m2. The objective of this study was to propose a new method, unprecedented in hard bottom marine communities, based in the sampling of landscape heterogeneity units, named physiognomies and settlements, aiming at an increase in sampling speed and covering in this environment. This study was performed in a 260 m infralittoral stretch of Presidio Beach eastern coast (Palmas Bay, Anchieta Island State Park, Ubatuba, SP) and was divided in four approaches: 1) identification e description of settlements and their dominant species; 2) georeferenced spatial repartition mapping of each settlement and determination of maximum vertical amplitude; 3) mean percent cover quantification from digital images; 4) evaluation of specific composition and spatial variation of selected settlements. Thirty settlements, included in Bed, Colony, Crust and Turf categories, besides a non-biological attribute included in Region category, were identified and described and the information will be available in a database in the internet. Mapping was performed in only 6 dives of 50 to 80 minutes in each season. The major part of the settlements occurred punctually. Settlements number and horizontal repartition practically did not change between summer and winter. Sargassum Bed (SGB) was more frequent in the summer (25.3%) and Amphiroa and Jania Turf (AJT) in the winter (21.3%). In relation to vertical repartition, four main zones were delimited based in relative frequencies: a shallower one defined by SGB, another upper intermediary defined by AJT, another lower intermediary defined by Ectoprocta Turf (ECT) and a last one, deeper, defined by variable settlements according to season. Eighty four sampling units were obtained in summer and 100 in winter, from which 26 and 28 settlements could be recognized, respectively. Cluster analysis in R and Q modes and heterogeneity evaluation of the obtained groups were made. SGB showed the highest mean percent cover as much in summer (26.1%) as in winter (32.0%), followed by ECT (19.7% in summer and 24.2% in winter), significantly higher than most of the other settlements (p<0.05). Phytobenthic settlements were the most representative in the area (62.2% of mean cover in summer and 61.8% in winter). When settlements categories were considered, phytobenthic beds were the most representative (31.2% in summer and 37.0% in winter). With animals and algae altogether, the category ?turf? was the most represented (46.3% in summer and 41.4% in winter), with great contribution of AJT and ECT, indicating a possible sedimentation influence in the area. The cluster analysis in R Mode showed the existence of six groups in summer and five in winter, suggesting settlements with the same ecological exigencies. In Q Mode a highly heterogeneous community could be evidenced, showing a patchy pattern. The settlements SGB, Unconsolidated Substrate Region, AJT, ECT (and some of its variations) and Gelidiopsis and Hypnea Turf (GHT) were the responsible for group formation with the use of Morisita-Horn Similarity Index. Specific composition analysis of SGB, AJT, ECT and GHT showed that these settlements can be considered homogeneous or present themselves as facies in the study area and can be consistently used as operational units. However, studies in other areas are necessary in order to give support to the obtained data, mainly regarding ECT and GHT, which lack ecological studies. Spectral analysis made evident sampling sufficiency for all settlements in relation to Calleja points adopted. Richness spectra were diagonal and diversity spectra were rectangular. For the four settlements, Shannon?s Diversity Index was between 1.6 and 2.2 and Simpson?s Dominance Index, between 2.6 and 5.7. GHT was the richest and most diverse settlement. The community studied in the present work can be considered typical of Brazilian south eastern region. Settlements method, through approaches 2 and 3, facilitated community structural characterization in a fast way. Micro-heterogeneity evaluation of four settlements showed that they can be used as consistent ecological units.

Tropical ecosystems are some of the most diverse and productive ecosystems on the planet. These ecosystems are also some of the most threatened worldwide and this is largely driven by agricultural expansion. Predicting biotic responses to such forms of environmental change is a challenge that requires an increased understanding of the factors structuring these communities in both pristine environments as well as environments that are undergoing environmental change. Studying patterns in the spatial structure of communities can provide important insights into ecological and evolutionary processes structuring communities. Combining such approaches with analyses of the distribution of activity and the genomic content of communities can help us better understand relationships between community structure and function. I explore the topics of microbial spatial scaling, activity, and gene content in both pristine tropical rainforest environments as well as tropical regions undergoing agricultural conversion. I first pose a fundamental question in microbial spatial ecology, i.e. why do microorganisms tend to show weaker spatial patterns than macro-organisms? I show that trees and soil microorganisms differ in the rates at which their communities change over space. I test the hypothesis that low rates of spatial turnover in microbial communities are an artifact of how we assess the community structure of microbial communities and show that sampling extent is likely the main driver of these differences. Next, I examine a Central Africa ecosystem that is undergoing conversion to agriculture. I show that there are numerous indications of biotic homogenization in these soil microbial communities and that the active fraction of the community shows a more pronounced response to environmental change. Finally, I examine two microbial processes in the Amazon Basin that have been reported to change following conversion to agriculture: methane production and methane consumption. I investigate changes to the genes and taxa involved in these processes and propose a new conceptual framework for how these processes might be changing. Work in this thesis contributes to a broader understanding of the spatial and functional ecology of tropical microorganisms and offers perspectives useful for those interested in predicting and mitigating the impacts of environmental change on these communities. / 2019-02-17

Made available in DSpace on 2015-03-05T16:19:35Z (GMT). No. of bitstreams: 0 Previous issue date: 30 / Nenhuma / As planárias terrestres são consideradas potenciais bons indicadores do grau de antropização e conservação de seus hábitats e de áreas de alta biodiversidade geral. Para o Rio Grande do Sul, há registros de espécies que podem ser utilizadas como indicadoras de áreas preservadas ou alteradas, mas os trabalhos anteriores têm se concentrado em unidades de conservação, contendo áreas relativamente extensas de floresta nativa. O presente trabalho buscou analisar a estrutura e a composição, ao longo de um ciclo anual, da comunidade de tricladidos terrestres em áreas de mata secundária e áreas ajardinadas do Campus da Universidade do Vale do Rio dos Sinos - UNISINOS, em São Leopoldo, RS. Foram selecionadas quatro áreas de mata secundária e quatro ajardinadas, onde se realizaram 12 amostragens. Para cada área foram demarcados dois transectos de 100m de comprimento, sendo selecionados aleatoriamente dez pontos ao longo de cada transecto. Em cada ponto, foi utilizada uma parcela de 4m², com esforço amostral de 10 minut / Land planarians are bioindicators of the degree of anthropization and preservation of their habitats and areas of high general biodiversity. Some species which occur in Rio Grande do Sul could be used as bioindicators of preserved or altered areas, but the studies have been restricted to legally protected areas showing relatively large fragments of native forest. This paper aims at analysing the structure and composition of land planarian community in areas of secondary forests and grassland of the Universidade do Vale do Rio dos Sinos Campus - UNISINOS, in São Leopoldo, RS along an annual cycle. Four areas of secondary forest and four grassland areas were selected, where 12 samplings were carried out. For each area two 100m-long transects had their boundaries set, where ten points along each transect were randomly chosen. At each point a 4m² plot was used, with a 10-minute sampling effort. 78 specimens were recorded, which belong to nine species of two Terricola families (Geoplanidae e Rhynchodemidae). Only

Je vous propose à travers la lecture de cette thèse d'entreprendre un voyage épistémologique, un déplacement hors de votre lieu de résidence (et de recherche) habituel, un passage du "comment", donc de la résolution de questions pragmatiques, au "pourquoi", à la définition des finalités de la recherche scientifique. Ce voyage doit être vécu comme une aventure, une tentative difficile et périlleuse au cours de laquelle vous serez amené à défier l'autorité d'un Grand Partage régnant sur les mers épistémologiques, légitimant la connaissance vraie et justifiée au détriment de la croyance et de l'opinion. Ce départage opposera au réalisme une posture constructiviste et relativiste affirmationniste concevant la recherche scientifique non comme un progrès dans la découverte du réel ou vers une vérité universelle mais comme la confrontation de points de vue donnant lieu à des définitions communes, des représentations partagées. S'en suivra une escale sur l'île de l'écologie des communautés, où l'étude des prédictions produites par les écologues illustrera deux types de recherche : l'une, qualifiée d'analytique, vise à fournir des explications du réel par la décomposition et la simplification ; l'autre, qualifiée de synthétique, veut la compréhension par la mise en lien. Alors que la première utilise un langage exclusif, engendrant un double mouvement d'exclusion et d'esquive de certaines questions, la seconde discute par le biais d'un langage coélitaire, créant de la complexité, de l'épaississement pour reconfigurer notre connaissance du monde afin de susciter des questions subjectivement neuves. Ce voyage aboutira à la proposition d'une nouvelle architecture pour la maison écologie alors engagée dans une recherche synthétique. / With this thesis, I propose that you undertake an epistemological travel to move outside your usual place of residence (and of research), a transition from the “how”, so from the resolution of practical issues, to the “why” and the definition of the purposes of scientific research. This travel must be experienced as an adventure, a difficult and dangerous attempt during which you will defy the authority of a Grand Partage prevailing on the epistemological seas, legitimizing a true and justified knowledge to the detriment of belief and opinion. This will oppose a realist position to a constructivist and relativist affirmationist position seeing scientific research not as one step in the discovery of the real or of a universal truth but as the confrontation of points of view leading to common definitions and shared representations. Will follow a stopover on the island of community ecology, where the study of different kinds of predictions produced by ecologists is used to illustrate two types of research: one is called “analytical” and aims to provide explanations of reality by decomposition and simplification; the other one, called “synthetical” intends to understand by setting links. While the first uses an exclusive language, generating a double movement of exclusion and avoidance of some questions, the second discusses through a coélitaire language, creating complexity and thickening to reconfigure our knowledge of the world to generate questions that are subjectively new. This travel will finally lead to the proposal of a new architecture for the home of ecology engaged in a synthetical research.

Bacteria are ubiquitous to marine living surfaces, taking on a broad spectrum of roles from mutualistic to pathogenic. Despite their universality, much remains unknown about their basic ecology and interactions with higher organisms. To address this gap, this thesis firstly examines the bacterial communities associated with three co-occurring marine eukaryote hosts from temperate Australia: the demosponge Cymbastela concentrica, the subtidal red macroalga Delisea pulchra and the intertidal green macroalga Ulva australis. Molecular characterisation of the bacterial communities was undertaken using 16S rRNA gene library analysis to compare within-host (alpha) and between-host (beta) diversity for the three microbial communities. This study highlights the potentially substantial contribution host-associated microorganisms could have on marine microbial diversity. The remaining focus for this thesis was on the bacterial community associated with D. pulchra. This alga produces a suite of biologically active secondary metabolites (furanones) that non-toxically inhibit acyl homoserine lactone (AHL)-driven quorum sensing in bacteria, affecting a range of phenotypes including colonisation and virulence traits. The ecology of D. pulchra???s epiphytic bacteria was investigated using a mechanistic approach to explain bacterial colonisation patterns. In particular, concepts and models of ecological succession founded in eukaryote ecology were investigated. The thesis concludes with a study investigating the effect of furanones and elevated temperature on bacteria-induced disease and thallus bleaching of D. pulchra. In the presence of furanones colonisation and infection of two Roseobacter isolates from D. pulchra???s epiphytic bacterial community were inhibited. Ruegeria strain R11 was demonstrated to have temperature regulated virulence, which caused thallus bleaching in furanone-free algae. The implications of elevated sea temperatures resulting from global warming for algal health are discussed.