Harmful algal blooms (HABs) are becoming more prevalent throughout the world’s aquatic systems. These blooms have been the subjects of numerous studies because they can cause human health issues and economic impact through fish kills, contaminated shellfish and decreased tourism. Much research has focused on the “bottom-up” aspect of these blooms; namely, the potential role of increased nutrient input into coastal waters from anthropogenic sources causing increased growth in harmful algal species. However, there are also potential “top-down” controls affecting the rate at which harmful algal species are consumed by grazers. The aim of this project was to determine protozoan grazer population fluctuations and their grazing impact on HAB species through field monitoring and laboratory grazing experiments. Protozoan grazers were chosen because their growth rates could potentially keep up with those of HAB species. Declines in grazer populations before the onset of a bloom could be indicative of a release of the HAB from a “top-down” grazing control. Field samples taken during bloom and non-bloom events helped elucidate any microplankton community changes. After establishing that there appear to be changes to the grazer population before and after a bloom, ingestion experiments including direct epifluorescence microscopy and DNA analyses were conducted to determine if it is possible that a chosen protozoan grazer can ingest a HAB species. Finally, experiments were conducted to determine whether the HAB species was a favorable food source for the grazer. Population growth experiments in which grazers are fed a HAB species, 50:50 mixture, or normal culture food source were used to determine the survival and growth rate of the grazer. Although certain ciliates and heterotrophic dinoflagellates were found to feed on HAB species in the lab and in natural bloom samples, the HAB species as a food source produces lower grazer growth rates than on control food. Protozoan grazers may be a more effective control during bloom initiation than after the bloom has been established. / text

Phytoplankton succession and abundance in estuaries is known to be influenced by the relative strengths of various seasonally changing physical and chemical factors. Previous studies of Swan River Estuary phytoplankton biomass and composition have identified salinity, temperature, rainfall and nutrients as the most important controlling factors. These conclusions are generally based on analysis of data from river length transects and depth integrated day-time sampling. They describe influences ,affecting whole system phytoplankton abundance and succession. Many of the typical seasonal bloom that develop are ephemeral and only extend over relatively small areas. The focus of this study is a single site, Ron Courtney Island, considered typical of the upper estuary region. This region of the estuary was chosen as representative of the section of river most influenced by allochthonous nutrient input. It has been the region of most frequent and intense algal blooms over the past decade. The factors, physical, biological or physiological, that have the greatest influence on controlling phytoplankton biomass under various ambient conditions for this system are determined. While previous studies have recognised the importance of nitrogen to phytoplankton growth in the Swan River Estuary, they have focused on NO;, with only anecdotal reference to the importance of the alternative nitrogen source, NH4+. This is the first study to explore the influence of different nitrogen source fluxes on phytoplankton biomass in the upper Swan River Estuary. The roles of physiological adaptation to, and preferences for, 'new' (NO,), recycled (NH4+) and organic (urea) nitrogen sources in relation to ambient nutrient levels are explored. / Specific uptake rates (v), normalised to chlorophyll a, for NO;, NH4+ and urea were 0.2 ± 0.04 - 1831.1 ± 779.19, 0.5 ± 0.26 - 1731.6 ± 346.67 and 3.0 ± 0.60 - 2241.2 ± 252.56 ng N μg Chla-1 respectively. Urea concentration (14.8 - 117.7 μg urea-N 1-1) remained relatively constant over the 12 month study period. Measured ambient specific uptake rates for urea represent between 27.5% and 40.4% of total N uptake over the annual period February 1998 -January 1999. Seasonal nitrate uptake over the same period constituted only 11.3% (±10.77%, n=12) to 24.4% (± 13.02%, n=12) with the highest percentage during winter, when nitrate levels are elevated. It is suggested that urea provides a nutrient intermediary over the spring - summer period during transition from autotrophic to heterotrophic dominated communities. Grazing ,and nitrogen recycling are intricately connected by simultaneously providing top-down biomass control and bottom-up nutrient supply. Zooplankton (> 44 μm) grazing has been shown to reduce up to 40% of phytoplankton standing stock at times. Microheterotrophs (<300 pm) can reduce phytoplankton biomass production by up to 100% (potential production grazed, 11.1% day' - 99.6 % day-1) over an annual cycle. This correlated to mean seasonal day-time grazing loss of 80.47 ± 3.5 ngN μg Chla-1 in surface waters and 20.17 ± 9.7 ngN μg Chla-1 at depth (4.5m). Night time grazing for surface and bottom depths resulted in similar nitrogen loss rates (13.03 ± 4.84 ngN μg Chla-1). / Uptake rates for nitrate (r2 0.501) and urea (r2 0.512), doing with temperature (r2 0.605) were shown to have the greatest influence on phytoplankton distribution over depth and time. This research emphasises the need for more detailed investigations into the physiology of nutrient uptake and the effects of nutrient fluxes on phytoplankton biomass and distribution. Further research into the roles of organic nitrogen and pico and nanoplankton in this system is recommended.

There has been much interest in the last decade concerning the factors that influence diversity, especially how diversity and ecosystem processes may be linked. This study was based in small, cobble streams in South East Queensland. Its aim was to determine how the diversity and composition of consumers (the grazer guild) is influenced by both the production and composition of benthic algae, at different spatial scales. It also aimed to ascertain whether this response differs among grazer sub guilds with different dispersal capabilities. Ten sites in the Upper Brisbane and Mary catchments were sampled. The sites were selected to provide a range of productivity and composition. Grazers from these sites included snails and elmids, and larval mayflies, moths, and caddisflies. Grazer diversity and composition appeared to be structured by catchment scale influences, but environmental variables also affected which animals colonised patches and microhabitats (cobbles) within catchments. Primary productivity and algal composition could not be separated, with highly productive reaches also having a high cover of filamentous algal taxa. Grazer diversity displayed strongly positive, linear relationships with algal variables at the reach scale. It had a negative relationship with filamentous algae at the cobble scale, and a non-significant hump-shaped relationship with primary productivity. Survey data alone could not separate whether grazers were responding to habitat or food-related drivers, or to variations in productivity. Experimental manipulation of algal variables at the patch scale, using light and nutrients, also could not clearly uncouple the relationship between primary productivity and filamentous algal cover. Once reach scale variation was removed, grazer diversity displayed hump-shaped relationships with algal variables, including algal diversity. Much of this variation was due to patterns in mobile grazers, as sedentary grazers did not respond to algal variation at this scale. The density of the more mobile taxa showed similar patterns to those at the cobble scale (hump-shaped). A second field experiment was carried out in order to further investigate the responses of invertebrates to algal community composition at the cobble scale. Data from all three chapters suggested that as sites shifted to a dominance of filamentous algae, often with an associated increase in GPP, there was also a shift in the grazer community towards more sedentary grazers and away from the more mobile taxa. This also occurred at the cobble scale in the second experiment. The gut analysis and diet studies in the third chapter indicated that while many grazers consumed filamentous algae, it was not assimilated. This suggests that the preferences for sedentary taxa for cobbles and reaches dominated by filamentous algae are likely to be due to some other, possibly habitat-related, factor such as flow or predation refuge. The study provides a rare examination of relationships between primary productivity and consumer diversity in freshwater streams, and finds support for the pattern found in other systems of monotonic relationships of these two variables at large scales and hump-shaped relationships at smaller scales. It emphasises the importance of understanding other, potentially confounding, aspects of communities of producers, and investigates the possible roles of the most important of these (community composition) in structuring consumer communities in the small cobble streams of South-East Queensland.

This thesis discusses key conflicts in the Oostvaardersplassen. These conflicts include the contestation of the Oostvaardersplassen as wilderness, the debate on grazer mortality, and the debate on culling. Through Actor Network Theory, the actors involved in the Oostvaardersplassen are discussed. A number of documents are selected for the different actors to do a qualitative analysis of communication on the Oostvaardersplassen. The Oostvaardersplassen is a unique area, claimed from the sea and fully manmade, with a management philosophy with aspects from rewilding theories. Recurring themes in the actor documents are studied, such as the definitions of the terms ‘nature’ ‘wilderness’ and the use of interventions. In addition, the documents are analysed on their use of rhetoric tools and the way they discuss the general public in the Oostvaardersplassen debates. The nature of the Oostvaardersplassen as an experiment, the strong presence of emotions in the debates and the unclear definition of goals and purposes lead to a more fractured stage for the actors and the debate. While the Oostvaardersplassen is successful as an area for experimentation, learning, and as a nature reserve in the midst of the Netherlands, these concluding issues are an important consideration in making the Oostvaardersplassen’s debate less volatile.

Os estudos apresentados nesta tese tiveram como objetivo compreender aspectos da organização de assembleias de algas bênticas em riachos. Foi avaliado especificamente o efeito da heterogeneidade de habitat na escala de rugosidade de substratos e sua interação com distúrbios hidrológicos e organismos pastejadores (grazers). Utilizou-se uma abordagem experimental in situ com substratos lisos e rugosos (com fendas) constituindo os tratamentos. Os experimentos foram conduzidos no Rio do Marco, um riacho de quarta ordem na região dos Campos de Cima da Serra, em São José dos Ausentes, Rio Grande do Sul. Após uma introdução geral acerca do assunto são apresentados os capítulos com os estudos. O Capítulo 1 avaliou os efeitos da rugosidade de substratos sobre a riqueza de espécies, densidade, composição e padrões de distribuição de assembleias de algas bênticas. Assembleias em substratos rugosos foram mais ricas que assembleias em substratos lisos, porém esse resultado diferiu entre grupos com diferentes formas de vida, assim como as diferenças na composição de espécies, indicando que somente alguns grupos foram beneficiados pela ocorrência de refúgios em substratos rugosos. Observou-se também que diferenças na composição da assembleia entre substratos lisos e rugosos resultaram de aninhamento e substituição de espécies. No Capítulo 2 foi testada a hipótese de que substratos rugosos abrigam assembleias mais persistentes que substratos lisos. Os resultados encontrados confirmaram esta hipótese e foram atribuídos ao efeito da rugosidade per se após a exclusão de alguns fatores de confundimento, como estabilidade física dos substratos e diferenças na riqueza de espécies. Concluiu-se que o mecanismo mais plausível para explicar a maior persistência em substratos rugosos é a maior disponibilidade de refúgios em relação a substratos lisos. O objetivo do Capítulo 3 foi avaliar o efeito da rugosidade de substratos sobre assembleias de algas frente a um distúrbio hidrológico experimental, testando especificamente se a resistência e a resiliência de algas é maior em substratos rugosos que em substratos lisos e se a resposta de diferentes formas de vida é distinta. Os resultados indicaram que a rugosidade de substratos não apresenta efeitos pronunciados sobre a resistência e a resiliência de algas bênticas. Porém, grupos de algas com distintas formas de vida diferiram quanto à resistência e resiliência, de forma que o padrão observado está relacionado a atributos biológicos que conferem habilidades para suportar distúrbios. Os resultados deste estudo em conjunto com os resultados obtidos no Capítulo 2 e resultados obtidos por outros autores permitiram que fosse proposto que a importância da heterogeneidade de habitas e de refúgios é mediada pela intensidade de distúrbios. No Capítulo 4 foram avaliados os efeitos independentes e as interações de rugosidade de substratos, peixes pastejadores e tipos de mesohabitats (corredeiras e remansos) sobre a biomassa algal, matéria orgânica e peso seco total. O efeito de peixes pastejadores não foi mediado pelos mesohabitats, sendo que a exclusão de peixes causou aumento nas três variáveis resposta, independente do tipo de mesohabitat. Por outro lado, houve uma interação entre mesohabitats e substratos para determinar o acúmulo de peso seco total, sendo que substratos rugosos acumularam maior quantidade de material em remansos que em corredeiras, enquanto substratos lisos acumularam quantidades similares entre os dois tipos de mesohabitats. Já a biomassa algal e matéria orgânica apresentaram maior acúmulo nos substratos rugosos em relação aos lisos, independente do mesohabitat. Os resultados encontrados indicam que a perda de organismos pastejadores pode afetar o acúmulo de biomassa algal e material orgânico, importantes recursos alimentares em riachos. Finalmente, na última seção são apresentadas as considerações finais. / The studies presented in this thesis aimed at understanding some aspects of the organization of benthic algal assemblages in streams. Specifically, the studies evaluated the effect of habitat heterogeneity on the scale of substrate roughness and its interaction with hydrological disturbances and grazing organisms. An experimental in situ approach was used, in which the treatments were constituted by smooth and rough (with crevices) substrates. The experiments were conducted in the Marco River, a fourth-order stream at the region of Campos de Cima da Serra, São José dos Ausentes, Rio Grande do Sul, Brazil. After a general introduction on the subjects of this thesis, the chapters with the studies are presented. The Chapter 1 describes a study to evaluate the effects of substrate roughness on species richness, density, composition and distribution patterns of benthic algal assemblages. Algal assemblages on rough substrates were richer than on smooth substrates, but this result differed among algal life forms. Similarly, results on species composition also differed among life forms, indicating that only some groups were benefited by the occurrence of refuges on rough substrates. It was also observed that differences in the composition of assemblages between rough and smooth substrates resulted from nestedness and turnover. The Chapter 2 describes a study in which was tested the hypothesis that rough substrates harbor more persistent assemblages than smooth substrates. The results confirmed this hypothesis and were attributed to the effect of roughness per se after the exclusion of some confounding factors, such as the physical stability of substrates and differences in species richness. It was concluded that the most plausible mechanism that could explain the higher persistence in rough substrates is the greater availability of refuges in relation to smooth substrates. The main aim of the study described in Chapter 3 was to evaluate the effect of substrate roughness on algal assemblages in the face of an experimental hydrological disturbance. Specifically, it was tested if the resistance and resilience of algae is higher on rough than on smooth substrates and if algal life forms differ in their response to disturbance. The results indicated that substrate roughness had no pronounced effects on benthic algal resistance and resilience. However, algal life forms differ in their resistance and resilience, and the observed pattern was mostly related to biological traits that confer abilities to support disturbances. The results of this study, in addition to the results obtained in Chapters 1 and 2, allowed us to suggest that the importance of habitat heterogeneity and refuges is mediated by the intensity of disturbances. The Chapter 4 describes a study that evaluated the independent and interacting effects of substrate roughness, grazing fish and mesohabitats (pools and riffles) on algal biomass, organic matter and total dry mass accrual. The effect of grazers was not mediated by mesohabitats, and their exclusion caused an increase in the three response variables, regardless of mesohabitat. On the other hand, mesohabitats and substrates interacted to determine the accrual of total dry mass, since rough substrates accumulated greater amounts of dry mass in pools than in riffles, while smooth substrates accumulated similar amounts in both mesohabitats. Algal biomass and organic matter showed greater accrual on rough than on smooth substrates, independently of mesohabitat. These results indicate that the loss of grazers may affect the accrual of algal biomass and organic matter, which are important food resources in streams. Finally, in the last section are presented the concluding remarks.

Os estudos apresentados nesta tese tiveram como objetivo compreender aspectos da organização de assembleias de algas bênticas em riachos. Foi avaliado especificamente o efeito da heterogeneidade de habitat na escala de rugosidade de substratos e sua interação com distúrbios hidrológicos e organismos pastejadores (grazers). Utilizou-se uma abordagem experimental in situ com substratos lisos e rugosos (com fendas) constituindo os tratamentos. Os experimentos foram conduzidos no Rio do Marco, um riacho de quarta ordem na região dos Campos de Cima da Serra, em São José dos Ausentes, Rio Grande do Sul. Após uma introdução geral acerca do assunto são apresentados os capítulos com os estudos. O Capítulo 1 avaliou os efeitos da rugosidade de substratos sobre a riqueza de espécies, densidade, composição e padrões de distribuição de assembleias de algas bênticas. Assembleias em substratos rugosos foram mais ricas que assembleias em substratos lisos, porém esse resultado diferiu entre grupos com diferentes formas de vida, assim como as diferenças na composição de espécies, indicando que somente alguns grupos foram beneficiados pela ocorrência de refúgios em substratos rugosos. Observou-se também que diferenças na composição da assembleia entre substratos lisos e rugosos resultaram de aninhamento e substituição de espécies. No Capítulo 2 foi testada a hipótese de que substratos rugosos abrigam assembleias mais persistentes que substratos lisos. Os resultados encontrados confirmaram esta hipótese e foram atribuídos ao efeito da rugosidade per se após a exclusão de alguns fatores de confundimento, como estabilidade física dos substratos e diferenças na riqueza de espécies. Concluiu-se que o mecanismo mais plausível para explicar a maior persistência em substratos rugosos é a maior disponibilidade de refúgios em relação a substratos lisos. O objetivo do Capítulo 3 foi avaliar o efeito da rugosidade de substratos sobre assembleias de algas frente a um distúrbio hidrológico experimental, testando especificamente se a resistência e a resiliência de algas é maior em substratos rugosos que em substratos lisos e se a resposta de diferentes formas de vida é distinta. Os resultados indicaram que a rugosidade de substratos não apresenta efeitos pronunciados sobre a resistência e a resiliência de algas bênticas. Porém, grupos de algas com distintas formas de vida diferiram quanto à resistência e resiliência, de forma que o padrão observado está relacionado a atributos biológicos que conferem habilidades para suportar distúrbios. Os resultados deste estudo em conjunto com os resultados obtidos no Capítulo 2 e resultados obtidos por outros autores permitiram que fosse proposto que a importância da heterogeneidade de habitas e de refúgios é mediada pela intensidade de distúrbios. No Capítulo 4 foram avaliados os efeitos independentes e as interações de rugosidade de substratos, peixes pastejadores e tipos de mesohabitats (corredeiras e remansos) sobre a biomassa algal, matéria orgânica e peso seco total. O efeito de peixes pastejadores não foi mediado pelos mesohabitats, sendo que a exclusão de peixes causou aumento nas três variáveis resposta, independente do tipo de mesohabitat. Por outro lado, houve uma interação entre mesohabitats e substratos para determinar o acúmulo de peso seco total, sendo que substratos rugosos acumularam maior quantidade de material em remansos que em corredeiras, enquanto substratos lisos acumularam quantidades similares entre os dois tipos de mesohabitats. Já a biomassa algal e matéria orgânica apresentaram maior acúmulo nos substratos rugosos em relação aos lisos, independente do mesohabitat. Os resultados encontrados indicam que a perda de organismos pastejadores pode afetar o acúmulo de biomassa algal e material orgânico, importantes recursos alimentares em riachos. Finalmente, na última seção são apresentadas as considerações finais. / The studies presented in this thesis aimed at understanding some aspects of the organization of benthic algal assemblages in streams. Specifically, the studies evaluated the effect of habitat heterogeneity on the scale of substrate roughness and its interaction with hydrological disturbances and grazing organisms. An experimental in situ approach was used, in which the treatments were constituted by smooth and rough (with crevices) substrates. The experiments were conducted in the Marco River, a fourth-order stream at the region of Campos de Cima da Serra, São José dos Ausentes, Rio Grande do Sul, Brazil. After a general introduction on the subjects of this thesis, the chapters with the studies are presented. The Chapter 1 describes a study to evaluate the effects of substrate roughness on species richness, density, composition and distribution patterns of benthic algal assemblages. Algal assemblages on rough substrates were richer than on smooth substrates, but this result differed among algal life forms. Similarly, results on species composition also differed among life forms, indicating that only some groups were benefited by the occurrence of refuges on rough substrates. It was also observed that differences in the composition of assemblages between rough and smooth substrates resulted from nestedness and turnover. The Chapter 2 describes a study in which was tested the hypothesis that rough substrates harbor more persistent assemblages than smooth substrates. The results confirmed this hypothesis and were attributed to the effect of roughness per se after the exclusion of some confounding factors, such as the physical stability of substrates and differences in species richness. It was concluded that the most plausible mechanism that could explain the higher persistence in rough substrates is the greater availability of refuges in relation to smooth substrates. The main aim of the study described in Chapter 3 was to evaluate the effect of substrate roughness on algal assemblages in the face of an experimental hydrological disturbance. Specifically, it was tested if the resistance and resilience of algae is higher on rough than on smooth substrates and if algal life forms differ in their response to disturbance. The results indicated that substrate roughness had no pronounced effects on benthic algal resistance and resilience. However, algal life forms differ in their resistance and resilience, and the observed pattern was mostly related to biological traits that confer abilities to support disturbances. The results of this study, in addition to the results obtained in Chapters 1 and 2, allowed us to suggest that the importance of habitat heterogeneity and refuges is mediated by the intensity of disturbances. The Chapter 4 describes a study that evaluated the independent and interacting effects of substrate roughness, grazing fish and mesohabitats (pools and riffles) on algal biomass, organic matter and total dry mass accrual. The effect of grazers was not mediated by mesohabitats, and their exclusion caused an increase in the three response variables, regardless of mesohabitat. On the other hand, mesohabitats and substrates interacted to determine the accrual of total dry mass, since rough substrates accumulated greater amounts of dry mass in pools than in riffles, while smooth substrates accumulated similar amounts in both mesohabitats. Algal biomass and organic matter showed greater accrual on rough than on smooth substrates, independently of mesohabitat. These results indicate that the loss of grazers may affect the accrual of algal biomass and organic matter, which are important food resources in streams. Finally, in the last section are presented the concluding remarks.

Os estudos apresentados nesta tese tiveram como objetivo compreender aspectos da organização de assembleias de algas bênticas em riachos. Foi avaliado especificamente o efeito da heterogeneidade de habitat na escala de rugosidade de substratos e sua interação com distúrbios hidrológicos e organismos pastejadores (grazers). Utilizou-se uma abordagem experimental in situ com substratos lisos e rugosos (com fendas) constituindo os tratamentos. Os experimentos foram conduzidos no Rio do Marco, um riacho de quarta ordem na região dos Campos de Cima da Serra, em São José dos Ausentes, Rio Grande do Sul. Após uma introdução geral acerca do assunto são apresentados os capítulos com os estudos. O Capítulo 1 avaliou os efeitos da rugosidade de substratos sobre a riqueza de espécies, densidade, composição e padrões de distribuição de assembleias de algas bênticas. Assembleias em substratos rugosos foram mais ricas que assembleias em substratos lisos, porém esse resultado diferiu entre grupos com diferentes formas de vida, assim como as diferenças na composição de espécies, indicando que somente alguns grupos foram beneficiados pela ocorrência de refúgios em substratos rugosos. Observou-se também que diferenças na composição da assembleia entre substratos lisos e rugosos resultaram de aninhamento e substituição de espécies. No Capítulo 2 foi testada a hipótese de que substratos rugosos abrigam assembleias mais persistentes que substratos lisos. Os resultados encontrados confirmaram esta hipótese e foram atribuídos ao efeito da rugosidade per se após a exclusão de alguns fatores de confundimento, como estabilidade física dos substratos e diferenças na riqueza de espécies. Concluiu-se que o mecanismo mais plausível para explicar a maior persistência em substratos rugosos é a maior disponibilidade de refúgios em relação a substratos lisos. O objetivo do Capítulo 3 foi avaliar o efeito da rugosidade de substratos sobre assembleias de algas frente a um distúrbio hidrológico experimental, testando especificamente se a resistência e a resiliência de algas é maior em substratos rugosos que em substratos lisos e se a resposta de diferentes formas de vida é distinta. Os resultados indicaram que a rugosidade de substratos não apresenta efeitos pronunciados sobre a resistência e a resiliência de algas bênticas. Porém, grupos de algas com distintas formas de vida diferiram quanto à resistência e resiliência, de forma que o padrão observado está relacionado a atributos biológicos que conferem habilidades para suportar distúrbios. Os resultados deste estudo em conjunto com os resultados obtidos no Capítulo 2 e resultados obtidos por outros autores permitiram que fosse proposto que a importância da heterogeneidade de habitas e de refúgios é mediada pela intensidade de distúrbios. No Capítulo 4 foram avaliados os efeitos independentes e as interações de rugosidade de substratos, peixes pastejadores e tipos de mesohabitats (corredeiras e remansos) sobre a biomassa algal, matéria orgânica e peso seco total. O efeito de peixes pastejadores não foi mediado pelos mesohabitats, sendo que a exclusão de peixes causou aumento nas três variáveis resposta, independente do tipo de mesohabitat. Por outro lado, houve uma interação entre mesohabitats e substratos para determinar o acúmulo de peso seco total, sendo que substratos rugosos acumularam maior quantidade de material em remansos que em corredeiras, enquanto substratos lisos acumularam quantidades similares entre os dois tipos de mesohabitats. Já a biomassa algal e matéria orgânica apresentaram maior acúmulo nos substratos rugosos em relação aos lisos, independente do mesohabitat. Os resultados encontrados indicam que a perda de organismos pastejadores pode afetar o acúmulo de biomassa algal e material orgânico, importantes recursos alimentares em riachos. Finalmente, na última seção são apresentadas as considerações finais. / The studies presented in this thesis aimed at understanding some aspects of the organization of benthic algal assemblages in streams. Specifically, the studies evaluated the effect of habitat heterogeneity on the scale of substrate roughness and its interaction with hydrological disturbances and grazing organisms. An experimental in situ approach was used, in which the treatments were constituted by smooth and rough (with crevices) substrates. The experiments were conducted in the Marco River, a fourth-order stream at the region of Campos de Cima da Serra, São José dos Ausentes, Rio Grande do Sul, Brazil. After a general introduction on the subjects of this thesis, the chapters with the studies are presented. The Chapter 1 describes a study to evaluate the effects of substrate roughness on species richness, density, composition and distribution patterns of benthic algal assemblages. Algal assemblages on rough substrates were richer than on smooth substrates, but this result differed among algal life forms. Similarly, results on species composition also differed among life forms, indicating that only some groups were benefited by the occurrence of refuges on rough substrates. It was also observed that differences in the composition of assemblages between rough and smooth substrates resulted from nestedness and turnover. The Chapter 2 describes a study in which was tested the hypothesis that rough substrates harbor more persistent assemblages than smooth substrates. The results confirmed this hypothesis and were attributed to the effect of roughness per se after the exclusion of some confounding factors, such as the physical stability of substrates and differences in species richness. It was concluded that the most plausible mechanism that could explain the higher persistence in rough substrates is the greater availability of refuges in relation to smooth substrates. The main aim of the study described in Chapter 3 was to evaluate the effect of substrate roughness on algal assemblages in the face of an experimental hydrological disturbance. Specifically, it was tested if the resistance and resilience of algae is higher on rough than on smooth substrates and if algal life forms differ in their response to disturbance. The results indicated that substrate roughness had no pronounced effects on benthic algal resistance and resilience. However, algal life forms differ in their resistance and resilience, and the observed pattern was mostly related to biological traits that confer abilities to support disturbances. The results of this study, in addition to the results obtained in Chapters 1 and 2, allowed us to suggest that the importance of habitat heterogeneity and refuges is mediated by the intensity of disturbances. The Chapter 4 describes a study that evaluated the independent and interacting effects of substrate roughness, grazing fish and mesohabitats (pools and riffles) on algal biomass, organic matter and total dry mass accrual. The effect of grazers was not mediated by mesohabitats, and their exclusion caused an increase in the three response variables, regardless of mesohabitat. On the other hand, mesohabitats and substrates interacted to determine the accrual of total dry mass, since rough substrates accumulated greater amounts of dry mass in pools than in riffles, while smooth substrates accumulated similar amounts in both mesohabitats. Algal biomass and organic matter showed greater accrual on rough than on smooth substrates, independently of mesohabitat. These results indicate that the loss of grazers may affect the accrual of algal biomass and organic matter, which are important food resources in streams. Finally, in the last section are presented the concluding remarks.

In the field of marine microbial ecology, many questions remain unanswered with regards to the physiological trade-offs made by phytoplankton to maximize growth (e.g., nutrient acquisition) and minimize loss (e.g., predation defenses). These tradeoffs, which occur at the cellular level, have wide reaching impacts on food web dynamics and global biogeochemical cycles. In the first chapter, we explored the use of a non-canonical amino acid (NCAA) technique, bioorthogonal non-canonical amino-acid tagging (BONCAT), in phytoplankton model systems. This technique has potential to work well in natural systems by enabling isolation of only newly synthesized proteins during an incubation period with the NCAA, reducing the complexity of natural proteomics and easing the elucidation of patterns. However, in testing BONCAT across several groups of cultured phytoplankton, we discovered that the NCAA molecule induced a stress response in the globally ubiquitous marine picocyanobacteria, Synechococcus sp. Therefore, in addition to confirming the uptake of modified amino acids by phytoplankton, chapter one investigated the implications of this stress response and limitations when using this technique to study marine microbial communities. In chapter two, we addressed our initial question by exploring tradeoffs at the protein level in a simplified culture system. This approach revealed insights into metabolic tradeoffs in response to predation pressure and nutrient stress. These insights into how phytoplankton negotiate these physiological tradeoffs at the protein level could ultimately allow for targeted proteomic studies in natural systems.

Les microorganismes agissent comme un puits et une source de N et Pdisponibles car ils sont responsables des cycles biogéochimiques de N et P. La bouclemicrobienne, basée sur la prédation des bactéries par les microprédateurs tels que lesnématodes bactérivores, est considérée comme un facteur majeur de la minéralisation de Net de P dans les écosystèmes terrestres. Cependant, peu de données sont disponibles surl'impact de la prédation par les nématodes sur la nutrition minérale des plantes ligneusesectomycorhizées. Différentes expérimentations ont été conduites pour quantifier le rôle dela prédation des bactéries par les nématodes sur l'architecture et la croissance racinaire, lanutrition minérale (N et P) d'une espèce ligneuse, Pinus pinaster, associée ou non avec lebasidiomycète ectomycorhizien Hebeloma cylindrosporum. Les plantes ont été cultivéesdans un système expérimental simplifié et stérile, et inoculées ou non avec Bacillus subtiliset des nématodes bactérivores (de la famille des Rhabditidae ou des Cephalobidae) isolés àpartir d'ectomycorhizes et de sol provenant d'une plantation de Pin maritime. L'effet de laprédation sur la croissance des plantes et le devenir du 15N bactérien vers les partiesaériennes dépend très fortement de la disponibilité en P du milieu. De plus, la prédationdes bactéries est indispensable pour permettre à la plante d'utiliser le P du phytate, unesource de P organique très peu disponible pour la plante mais très facilement utilisable parB. subtilis car cette bactérie est capable de libérer de la phytase dans le milieu. Cesrésultats ouvrent de nouvelles perspectives pour améliorer l'utilisation du phytate pour lanutrition phosphatée des plantes. / Soil microorganisms act as a sink and a source of available N and P bymediating key processes in the biogeochemical N and P cycling. The microbial loop, basedupon the grazing of bacteria by predators such as bacterial-feeding nematodes, is thoughtto play a major role in the mineralization of nutrients such as nitrogen (N) and phosphorus(P) in terrestrial ecosystems. However, little is known about the impact of grazing bynematodes on mineral nutrition of ectomycorrhizal woody plants. Different studies wereundertaken to quantify the role of nematode grazing on bacteria on the root growth andarchitecture, mineral nutrition (N and P) of a woody species, Pinus pinaster, whether ornot associated with the ectomycorrhizal basidiomycete Hebeloma cylindrosporum. Plantswere grown in a sterile simplified experimental system, whether inoculated or not withBacillus subtilis and bacterial-feeding nematodes (belonging to Rhabditidae orCephalobidae families) that were isolated from ectomycorrhizae and from soil of a P.pinaster plantation. The effect of nematode grazing on plant growth and the fate ofbacterial 15N towards plant shoots was strongly dependent upon medium P availability. Inaddition, nematode grazing was required to enable the plant to access P from phytate, awell-known poorly available P source to plants but that was used by bacterial populationsof B. subtilis due to its ability to release phytase in the medium. These results open analternative route to increase the use of phytate for plant P nutrition.

The origins of population dynamics depend on interplay between abiotic and biotic factors; the relative importance of each changing across space and time. Predation is a central feature of ecological communities that removes individuals (consumption) and alters prey traits (non-consumptive). Resource quality mitigates non-consumptive predator effects by stimulating growth and reproduction. Disturbance resets predator-prey interactions by removing both. I integrate experiments, time-series analysis, and performance trials to examine the relative importance of these on the population dynamics of a snail species by studying a variety of their traits. A review of ninety-three published articles revealed that snail abundance was much less in the Everglades and similar ecosystems compared to all other freshwater ecosystems considered. Separating consumptive from non-consumptive (cues) predator effects at different phosphorous levels with an experiment determined that phosphorous stimulated, but predator cues inhibited snail growth (34% vs. 23%), activity (38% vs. 53%), and reproductive effort (99% vs. 90%) compared to controls. Cues induced taller shells and smaller openings and moved to refugia where they reduced periphyton by 8%. Consumptive predator effects were minor in comparison. In a reciprocal transplant cage experiment along a predator cue and phosphorous gradient created by a canal, snails grew 10% faster and produced 37% more eggs far from the canal (fewer cues) when fed phosphorous-enriched periphyton from near the canal. Time-series analysis at four sites and predator performance trials reveal that phosphorous-enriched regions support larger snail populations, seasonal drying removes snails at all sites, crayfish negatively affect populations in enriched regions, and molluscivorous fish consume snails in the wet season. Combining these studies reveals interplay between resources, predators, and seasonality that limit snail populations in the Everglades and lead to their low abundance compared to other freshwater ecosystems. Resource quality is emerging as the critical factor because improving resources profoundly improved growth and reproduction; seasonal drying and predation become important at times and places. This work contributes to the general understanding in ecology of the relative importance of different factors that structure populations and provides evidence that bolsters monitoring efforts to assess the Comprehensive Everglades Restoration Plan that show phosphorous enrichment is a major driver of ecosystem change.