Habitat heterogeneity is a driving factor for speciation and ecosystem functioning and is well studied in macro-ecology. Yet our understanding of microbial adaptations, and governing processes is incomplete. The here presented thesis aims at giving us a better understanding of patterns in micro-heterogeneity, and microbial adaptations to such heterogeneity with particular focus on surface-dominated, aquatic habitats. The most prominent microbial adaptation to surface associated mode of life is biofilm formation. Biofilms rely heavily on type IV pili. These pili systems are well studied in Bacteria, but largely unknown in Archaea. Therefore, the first part of this thesis focuses on resolving genetic and structural feature of the type IV like aap-pilus of the thermo-acidophilic Sulfolobus acidocaldarius. We found the aap-pilus to be indispensible for biofilm formation, and to be unparalleled in variability of its quaternary structure and cross regulation with other filaments. The second part of this thesis investigates particle colonization in the water column, focusing on diatoms as a model system, allowing an in situ assessment of different stages of particle colonization, and potential particle-specificity of the associated bacterial community. Opposing reports from marine systems, we did not observe diatom-specificity in the associated bacterial community. Instead we found bacterial community subsets, one likely originating from sediment resuspension, and the other being controlled by biofilm-forming populations (e.g. Flexibacter), able to attach to newly formed particle surfaces and subsequently facilitate secondary colonization by other bacteria. Finally, the habitat heterogeneity in top-layers of lake sediments were investigated in experimental microcosms. Cell-specific oxygen consumption rates were determined, to assess microbial activity across different scales. Individual activity rates differed strongly across all investigated scales, likely due to spatially heterogeneous distribution of nutrients with differing quality. Vice versa, the influence of microbial activity on micro-habitat-heterogeneity was investigated. We correlated sediment redox-state with bacterial community composition and populations. Our results indicate that habitat heterogeneity is generally beneficial for microorganism, and greater heterogeneity results in greater bacterial diversity. However, this heterogeneity-diversity relationship is limited and microorganisms actively stabilize their immediate redox environment to a preferred, community-specific, stable state, if cell abundances exceed a minimum threshold.

Doctor of Philosophy / Department of Biology / Brett K. Sandercock / Habitat heterogeneity is a key driver of biodiversity in many ecosystems. In native ecosystems, habitat heterogeneity can arise from multiple drivers including nutrients, topoedaphic conditions, and ecological disturbance. Historically, the prairies of North America existed as a heterogeneous mosaic of habitat conditions created by the interaction of fire and grazing by native ungulates. The focus of many grazing systems has been to minimize disturbance caused by grazing by promoting uniform distributions of grazing animals across management units. Patch-burn grazing is an alternative rangeland management practice that has been proposed to restore historical patch dynamics and biodiversity to rangelands by simulating historical disturbance processes. In my dissertation research, I tested the hypothesis that patch- burn grazing restores habitat heterogeneity to rangelands, and that the resulting habitat heterogeneity can promote biodiversity of native wildlife. I focus on responses of small mammals and coyotes to patch-burn grazing to gain a better understanding of wildlife responses to rangeland management, and because grassland mammals are an ecologically important group. My 3.5-year field study of habitat and small mammal responses to rangeland management showed that: 1) patch-burn grazing created greater heterogeneity in vegetative structure and composition of plant functional groups than in positive and negative controls; 2) habitat heterogeneity created by the interaction of fire and grazing increased small mammal richness and diversity compared to a negative control managed for uniform grazing distributions; 3) the interaction of fire and grazing structured small mammal communities in tallgrass prairie; and 4) population dynamic responses of small mammals to fire and grazing disturbance were species- specific. My 3-year study of coyote survival and resource selection revealed that: 1) rangeland management influences resource selection by coyotes in seasons when they depend on small mammal prey, but not during other seasons; and 2) anthropogenic sources of mortality are important for coyotes at a protected area, even in the absence of harvest. My field results show that restoring the drivers of historical patch dynamics to managed rangelands and publicly held grasslands that are not currently grazed could have profound effects on biodiversity conservation in North America, while continuing to provide ecosystem services to society.

Doctor of Philosophy / Department of Biology / Brett K. Sandercock / Habitat heterogeneity is a key driver of biodiversity in many ecosystems. In native ecosystems, habitat heterogeneity can arise from multiple drivers including nutrients, topoedaphic conditions, and ecological disturbance. Historically, the prairies of North America existed as a heterogeneous mosaic of habitat conditions created by the interaction of fire and grazing by native ungulates. The focus of many grazing systems has been to minimize disturbance caused by grazing by promoting uniform distributions of grazing animals across management units. Patch-burn grazing is an alternative rangeland management practice that has been proposed to restore historical patch dynamics and biodiversity to rangelands by simulating historical disturbance processes. In my dissertation research, I tested the hypothesis that patch- burn grazing restores habitat heterogeneity to rangelands, and that the resulting habitat heterogeneity can promote biodiversity of native wildlife. I focus on responses of small mammals and coyotes to patch-burn grazing to gain a better understanding of wildlife responses to rangeland management, and because grassland mammals are an ecologically important group. My 3.5-year field study of habitat and small mammal responses to rangeland management showed that: 1) patch-burn grazing created greater heterogeneity in vegetative structure and composition of plant functional groups than in positive and negative controls; 2) habitat heterogeneity created by the interaction of fire and grazing increased small mammal richness and diversity compared to a negative control managed for uniform grazing distributions; 3) the interaction of fire and grazing structured small mammal communities in tallgrass prairie; and 4) population dynamic responses of small mammals to fire and grazing disturbance were species- specific. My 3-year study of coyote survival and resource selection revealed that: 1) rangeland management influences resource selection by coyotes in seasons when they depend on small mammal prey, but not during other seasons; and 2) anthropogenic sources of mortality are important for coyotes at a protected area, even in the absence of harvest. My field results show that restoring the drivers of historical patch dynamics to managed rangelands and publicly held grasslands that are not currently grazed could have profound effects on biodiversity conservation in North America, while continuing to provide ecosystem services to society.

<p>The introduction of the North American beaver (Castor canadensis) to Tierra del Fuego is a widely known example of a successful biological invasion. Beavers have impacted enormously the biodiversity of the island of Tierra del Fuego, and they are now spreading northward on the continent, prompting the governments of Argentina and Chile to seek methods to control their spread. Beavers first established in forests, where they were initially introduced, but by the 1990s they began to establish in the adjacent steppe. In this dissertation, I study the biology of invasive beavers across the two major habitat types in Patagonia and attempt to develop modeling tools that might be useful to manage their spread.</p><p>In chapter one I studied the history of the beaver introduction in Patagonia and provide evidence that the beaver introduction occurred as a single release event of 20 beavers from northern Manitoba, Canada. This not only clarifies the origin of the invasion, but also suggests that the beaver population of Patagonia descends from a smaller number of individuals than previously assumed.</p><p>In chapter two I studied the demography of invasive North American beavers in the two contrasting habitat types of the island of Tierra del Fuego, forest and steppe. Habitat differences can affect vital rates which may in turn impact the speed of the invasion, but this has been rarely addressed when managing the spread of invaders. I use repeated observations, mark-resight methods, telemetry and camera traps to estimate colony size and vital rates of beavers in the two habitats. Colony size and the number of offspring (“kits”) produced per colony per year were higher in the steppe, contrary to the belief that forest is better habitat. Here I suggest this may be the result of the longer time since invasion in the forests of Tierra del Fuego and that the forest subpopulation is showing density dependent regulation. Beaver survival was high in all age classes and was higher than survival rates recorded in North America. My work shows that beaver plasticity and predator release have likely facilitated the invasion in Patagonia. </p><p>In chapter three, I investigated the more recent invasion of beavers in an area of the Patagonian steppe. I utilized repeated high resolution satellite images to identify beaver ponds, and used them to study changes in beaver abundance and habitat use over time. The number of beaver ponds increased 85 % between 2005 and 2014. During this period, beavers changed their habitat selection pattern, presumably as a response to increased density. Beavers established on small watercourses in canyons first, but as more canyons became occupied over time, beavers moved to less preferred watercourses in plains and U-shaped valleys. Potential new beaver colonies established close to existing beaver ponds, suggesting proximity to a beaver pond is an important determinant of beaver colonization. Identifying habitat preferred by beavers in the steppe could help to increase early detection of the invader at the invasion front. This work highlights the importance of the use of high resolution remote sensing technologies to better understand and monitor biological invasions. </p><p>Finally, in chapter four, I built a spatially explicit individual-based model parameterized with data I collected in the field and use it to make management recommendations. Specifically I assessed the efficacy of a potential management strategy in which a “fire-break” (a zone beyond the current population front in which beavers are removed) perpendicular to the population front is instituted to attempt to prevent further northward spread of the beaver in continental Patagonia. I found that even a 100 km wide firebreak is insufficient to contain the spread of beavers, long dispersal events being the major cause of this failure. Further, I found that increasing the fraction of beavers culled within the firebreak does not decrease either the arrival time or the number of beavers that cross the firebreak. Counterintuitively, my model indicates that moderate levels of culling within the firebreak (rather than high) may be a more effective method to manage the invasion, likely as a result of inversely density dependent dispersal.</p> / Dissertation

Small standing water bodies that support colonization and help the survival of many species are nowadays often under threat. Since relationships between species and environments are often complex and not fully understood in these systems, this literature review has been written and a mesocosm experiment has been carried out in order to identify main mechanisms driving community assembly in habitats differing in complexity. I investigated the influence of artificial vegetation and clay on the community composition over a period of time. I found that a turbid environment (with clay) was not suitable for predators. This corresponds to our finding that in these environments, prey groups should be better developed, although the environment is different for each species.

No description available.

Boreal mixedwood forest stands are comprised of a mixture of small canopy patches of varying dominance by conifer (mostly white spruce (Picea glauca (Moench) Voss)) and broadleaf (mostly trembling aspen (Populus tremuloides Michx.) trees. The purpose of this work was to extend our understanding of the patterns and causes of variation in understory vascular plant communities in unmanaged, mature boreal mixedwood forests. First, I assessed variation in understory community composition in relation to canopy patch type (conifer, mixed conifer-broadleaf, broadleaf, gaps) within mixedwood stands. The mosaic of canopy patches leads to different micro-habitat conditions for understory species, allowing for communities that include both early and late successional species and contributing to greater understory diversity. This study suggests that the mosaic of small canopy patches within mixed forest stands resembles a microcosm of the boreal mixedwood landscape, across which understory community composition varies with canopy composition at the stand scale. Second, I investigated the hierarchical organization of understory diversity in relation to the heterogeneous mosaic of canopy patch types through additive partitioning of diversity. The largest proportion of species richness was due to turnover among patches within patch type while individual patches had higher evenness. The mosaic of canopy patch types within mixedwood forests likely plays a crucial role in maintaining the hierarchical levels at which understory diversity is maximized. Third, I examined interactions among understory plant species by investigating the effect of shrub removal on biomass, composition and diversity of herbs using a 3-yr removal study in a natural understory community. There is asymmetric competition for light between erect shrub and herb species but herb response to erect shrub removal was species-specific. Plant interactions play an important role in structuring boreal understory communities. Finally, I explored the relative influence of space, environmental variables, and their joint effects, on understory composition and richness. The environmental variation caused by small canopy patches and biotic processes, such as species interactions, converge at the fine scale to create a spatially patchy structure in understory communities in boreal mixedwood forests. Modifications in the natural mixture of small canopy patches could disrupt the spatial and environmental structures that shape understory composition and diversity patterns. / Forest Biology & Management

Boreal mixedwood forest stands are comprised of a mixture of small canopy patches of varying dominance by conifer (mostly white spruce (Picea glauca (Moench) Voss)) and broadleaf (mostly trembling aspen (Populus tremuloides Michx.) trees. The purpose of this work was to extend our understanding of the patterns and causes of variation in understory vascular plant communities in unmanaged, mature boreal mixedwood forests. First, I assessed variation in understory community composition in relation to canopy patch type (conifer, mixed conifer-broadleaf, broadleaf, gaps) within mixedwood stands. The mosaic of canopy patches leads to different micro-habitat conditions for understory species, allowing for communities that include both early and late successional species and contributing to greater understory diversity. This study suggests that the mosaic of small canopy patches within mixed forest stands resembles a microcosm of the boreal mixedwood landscape, across which understory community composition varies with canopy composition at the stand scale. Second, I investigated the hierarchical organization of understory diversity in relation to the heterogeneous mosaic of canopy patch types through additive partitioning of diversity. The largest proportion of species richness was due to turnover among patches within patch type while individual patches had higher evenness. The mosaic of canopy patch types within mixedwood forests likely plays a crucial role in maintaining the hierarchical levels at which understory diversity is maximized. Third, I examined interactions among understory plant species by investigating the effect of shrub removal on biomass, composition and diversity of herbs using a 3-yr removal study in a natural understory community. There is asymmetric competition for light between erect shrub and herb species but herb response to erect shrub removal was species-specific. Plant interactions play an important role in structuring boreal understory communities. Finally, I explored the relative influence of space, environmental variables, and their joint effects, on understory composition and richness. The environmental variation caused by small canopy patches and biotic processes, such as species interactions, converge at the fine scale to create a spatially patchy structure in understory communities in boreal mixedwood forests. Modifications in the natural mixture of small canopy patches could disrupt the spatial and environmental structures that shape understory composition and diversity patterns. / Forest Biology & Management

Marine epibenthic communities are influenced by both pre- and post-recruitment processes. For instance, the larval supply and cues that influence settlement (pre-recruitment), as well as the growth and mortality of individuals (post-recruitment), may differ across reef type and depth. Determining the relative influence of these processes is important to understanding how epibenthic communities can develop in a region. Using both a recruitment experiment that controlled grazing by urchins and in situ photographic surveys of epibenthic communities, this study examined the recruitment and composition of epibenthos on natural limestone and artificial reefs in the eastern Gulf of Mexico (eGOM). In the experiment, tiles that were open to urchin grazing had lower percent cover of algae (-12%) and higher cover of crustose coralline algae (CCA) (13%) than those that excluded urchins. Patterns in tile cover were likely the result of CCA either resisting grazing mortality or recolonizing exposed areas after algae were removed. Prevalence of estuarine species on inshore tiles was indicative of variation in recruitment across depth. Urchin density was positively correlated with the structural complexity of the habitats, which was higher on artificial reefs than natural ones, a factor that potentially had important effects on several observed patterns. Results from photographic surveys indicated that natural reef communities had higher algal cover and lower cover of invertebrates (e.g., corals and hydroids) than artificial reefs. These findings were consistent with previous work conducted in both temperate and tropical ecosystems, and suggested that grazing from urchins plays an important role in shaping epibenthic community structure in the subtropical eGOM.

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.