The increase in ecological restoration can be attributed to valuation of healthyecosystems and concerns for future climate changes. Freshwaters belong among theglobally most altered ecosystems and are restored to counteract human impacts.Many Swedish streams that were channelized to facilitate timber floating have beenrestored by returning boulders and reconnecting riparian with instream habitats.Evaluation of restoration lacks reliable indicators of organism performance, possiblydue to the complexity of ecosystem responses. Phytometers, i.e. standardized plantstransplanted to different environments, are important indicators of restorationsuccess. Phytometers integrate multiple environmental factors and measureecosystem functions directly. This thesis combines a literature review with threeexperiments and focuses on phytometer use for evaluating ecological restoration. Werecommend using different phytometer species, life-forms and life-stages and longexperiments (>1 year) to obtain high resolution and generality (I). In greenhouse andfield experiments we investigated the effect of restoring channelized rivers onphytometers and abiotic variables in the riparian zone. We hypothesized thatphytometer performance varies with stream size and climate. In the greenhouse, weanalysed differences in fertility between channelized and restored reaches by growingphytometers on soils from experimental sites (II). Phytometers grew better on soilsfrom restored sites in small streams, indicating a positive effect of restoration on soil.We detected this effect already 3-7 years after restoration, suggesting a fasterrecovery than predicted. In a short-term field experiment focusing on germinationand establishment of sunflowers, seedling survival, substrate availability, and soilnutrient content in large streams were enhanced by restoration (III). Overall,phytometers performed best at high altitudes and short growing seasons. The use ofMolinia caerulea and Filipendula ulmaria as phytometers in a long-term fieldexperiment (IV) revealed a better performance at restored sites. One reason was thatsummer flow-variability was higher, particularly in medium-sized streams. Sincephytometers allocated more biomass to belowground parts at restored compared tochannelized sites, it seems important to separate above- and belowground biomass inrestoration evaluation. Restoration outcomes vary with location in the catchment.Knowing such potentially different responses could guide restorationists in where tolocate restoration to be effective or successful. We suggest that small streams reactparticularly fast to restoration. Given that the proportion of small streams is high andthat restoration success in headwaters may favour downstream reaches, werecommend restoration to begin in tributaries to larger rivers. It is not always knownwhy phytometers react the way they do. Greenhouse experiments can disentangle thecauses of phytometer responses in the field by focusing on single environmentalfactors. We demonstrate that phytometers integrate ecosystem responses torestoration by reflecting how environmental factors affect plants under fieldconditions. Further studies are needed to better understand the underlyingmechanisms.

Coral reefs are experiencing increasing levels of stress due to climate change, overfishing, coastal development and nutrient runoff from agriculture to name a few. They are however, economically vital ecosystems in terms of both their income generating capacity and as a source of food for millions of people around the world. This predicament emphasises the need for effective ecosystem management to be able to balance the benefits of coral reefs with the inherent stressors associated with people utilising their resources. It is particularly important given the potential large scale impacts associated with climate change such as mass coral bleaching events. Similarly, much of the need for direct management of coral reefs exists in developing countries where the resources, information, and technology are limited or unavailable for such a task. This places them, in particular, at the high end of management uncertainty and impact vulnerability. Accordingly, there is a pronounced need to improve this capacity to understand coral reef ecosystem function and to use this to better predict the overall systems level outcome of management options. This thesis has sought to improve our understanding of key ecological elements of coral reef ecosystems and to build on this new knowledge to produce a widely applicable ecosystem model that will allow managers to better understand and predict the outcomes of their actions. Coral reef ecosystem behaviour is far from understood in its entirety and there are many facets that require detailed further investigations to be able to more confidently predict ecosystem response to any given disturbance. To enhance the current understanding of coral reef ecosystems prior to the model development, investigations were undertaken into the dynamics of nitrogen on a coral reef following bleaching induced coral mortality. The results showed that the rates of nitrogen fixation on surfaces made available due to a coral mortality event increased dramatically in the three months following coral mortality, potentially acting as a driving force for the ecosystem to pass through a phase shift to algal dominance. Application of these nitrogen dynamics to entire coral reef ecosystems required a methodology for scaling these sub coral colony processes to entire reefs. This scaling issue is particularly pertinent given the improved understanding of the overwhelming significance of micro-scale processes to community dynamics. The surface index (SI) concept, relating the two-dimensional projected area to the three-dimensional area of corals was refined and developed for variations of gross coral morphologies. This allowed for the scaling of nitrogen flux estimates to be made over entire reef systems, enabling the incorporation of these fluxes into an ecosystem scale model. One of the key factors associated with the potential for a coral reef to recover from a mass coral mortality event is the potential for new corals to successfully recruit. The process of coral recovery could potentially be enhanced if recruitment is viable in the immediate aftermath of a mortality event. Although investigations in this area were inconclusive, extensive herbivore action on turf assemblages up to eight months old indicated that recruitment may be inhibited through the high palatability of turf assemblages in this age bracket. Integrating these processes with the many other published dynamics of coral reefs allowed for the development of the dynamic systems model. By constraining the model structure to known relationships between the modelling parameters, the model can be calibrated to replicate the dynamics of any coral reef ecosystem. This allows the model to be applied to systems where limited data and/or resources are available, making it widely implementable in developing countries such as the small island states scattered around the tropics. The model is ideally suited to the adaptive management framework whereby managers can continually assess the potential future outcomes of management interventions. In addition, due to the spatially inexplicit and generic nature of the model, it can be easily adapted and integrated into large scale regional modelling frameworks or combined with other modelling packages such as socio-economic or fisheries models to provide enhanced management packages. The culmination of the targeted research and integration of existing knowledge has allowed for the development of an ecosystem model for coral reefs that can be easily adopted by coral reef managers throughout the world. It is however, by no means a definitive coral reef ecosystem model and there are many facets that can and should continue to be refined to enhance the reliability of the model.

Coral reefs are experiencing increasing levels of stress due to climate change, overfishing, coastal development and nutrient runoff from agriculture to name a few. They are however, economically vital ecosystems in terms of both their income generating capacity and as a source of food for millions of people around the world. This predicament emphasises the need for effective ecosystem management to be able to balance the benefits of coral reefs with the inherent stressors associated with people utilising their resources. It is particularly important given the potential large scale impacts associated with climate change such as mass coral bleaching events. Similarly, much of the need for direct management of coral reefs exists in developing countries where the resources, information, and technology are limited or unavailable for such a task. This places them, in particular, at the high end of management uncertainty and impact vulnerability. Accordingly, there is a pronounced need to improve this capacity to understand coral reef ecosystem function and to use this to better predict the overall systems level outcome of management options. This thesis has sought to improve our understanding of key ecological elements of coral reef ecosystems and to build on this new knowledge to produce a widely applicable ecosystem model that will allow managers to better understand and predict the outcomes of their actions. Coral reef ecosystem behaviour is far from understood in its entirety and there are many facets that require detailed further investigations to be able to more confidently predict ecosystem response to any given disturbance. To enhance the current understanding of coral reef ecosystems prior to the model development, investigations were undertaken into the dynamics of nitrogen on a coral reef following bleaching induced coral mortality. The results showed that the rates of nitrogen fixation on surfaces made available due to a coral mortality event increased dramatically in the three months following coral mortality, potentially acting as a driving force for the ecosystem to pass through a phase shift to algal dominance. Application of these nitrogen dynamics to entire coral reef ecosystems required a methodology for scaling these sub coral colony processes to entire reefs. This scaling issue is particularly pertinent given the improved understanding of the overwhelming significance of micro-scale processes to community dynamics. The surface index (SI) concept, relating the two-dimensional projected area to the three-dimensional area of corals was refined and developed for variations of gross coral morphologies. This allowed for the scaling of nitrogen flux estimates to be made over entire reef systems, enabling the incorporation of these fluxes into an ecosystem scale model. One of the key factors associated with the potential for a coral reef to recover from a mass coral mortality event is the potential for new corals to successfully recruit. The process of coral recovery could potentially be enhanced if recruitment is viable in the immediate aftermath of a mortality event. Although investigations in this area were inconclusive, extensive herbivore action on turf assemblages up to eight months old indicated that recruitment may be inhibited through the high palatability of turf assemblages in this age bracket. Integrating these processes with the many other published dynamics of coral reefs allowed for the development of the dynamic systems model. By constraining the model structure to known relationships between the modelling parameters, the model can be calibrated to replicate the dynamics of any coral reef ecosystem. This allows the model to be applied to systems where limited data and/or resources are available, making it widely implementable in developing countries such as the small island states scattered around the tropics. The model is ideally suited to the adaptive management framework whereby managers can continually assess the potential future outcomes of management interventions. In addition, due to the spatially inexplicit and generic nature of the model, it can be easily adapted and integrated into large scale regional modelling frameworks or combined with other modelling packages such as socio-economic or fisheries models to provide enhanced management packages. The culmination of the targeted research and integration of existing knowledge has allowed for the development of an ecosystem model for coral reefs that can be easily adopted by coral reef managers throughout the world. It is however, by no means a definitive coral reef ecosystem model and there are many facets that can and should continue to be refined to enhance the reliability of the model.

Coral reefs are experiencing increasing levels of stress due to climate change, overfishing, coastal development and nutrient runoff from agriculture to name a few. They are however, economically vital ecosystems in terms of both their income generating capacity and as a source of food for millions of people around the world. This predicament emphasises the need for effective ecosystem management to be able to balance the benefits of coral reefs with the inherent stressors associated with people utilising their resources. It is particularly important given the potential large scale impacts associated with climate change such as mass coral bleaching events. Similarly, much of the need for direct management of coral reefs exists in developing countries where the resources, information, and technology are limited or unavailable for such a task. This places them, in particular, at the high end of management uncertainty and impact vulnerability. Accordingly, there is a pronounced need to improve this capacity to understand coral reef ecosystem function and to use this to better predict the overall systems level outcome of management options. This thesis has sought to improve our understanding of key ecological elements of coral reef ecosystems and to build on this new knowledge to produce a widely applicable ecosystem model that will allow managers to better understand and predict the outcomes of their actions. Coral reef ecosystem behaviour is far from understood in its entirety and there are many facets that require detailed further investigations to be able to more confidently predict ecosystem response to any given disturbance. To enhance the current understanding of coral reef ecosystems prior to the model development, investigations were undertaken into the dynamics of nitrogen on a coral reef following bleaching induced coral mortality. The results showed that the rates of nitrogen fixation on surfaces made available due to a coral mortality event increased dramatically in the three months following coral mortality, potentially acting as a driving force for the ecosystem to pass through a phase shift to algal dominance. Application of these nitrogen dynamics to entire coral reef ecosystems required a methodology for scaling these sub coral colony processes to entire reefs. This scaling issue is particularly pertinent given the improved understanding of the overwhelming significance of micro-scale processes to community dynamics. The surface index (SI) concept, relating the two-dimensional projected area to the three-dimensional area of corals was refined and developed for variations of gross coral morphologies. This allowed for the scaling of nitrogen flux estimates to be made over entire reef systems, enabling the incorporation of these fluxes into an ecosystem scale model. One of the key factors associated with the potential for a coral reef to recover from a mass coral mortality event is the potential for new corals to successfully recruit. The process of coral recovery could potentially be enhanced if recruitment is viable in the immediate aftermath of a mortality event. Although investigations in this area were inconclusive, extensive herbivore action on turf assemblages up to eight months old indicated that recruitment may be inhibited through the high palatability of turf assemblages in this age bracket. Integrating these processes with the many other published dynamics of coral reefs allowed for the development of the dynamic systems model. By constraining the model structure to known relationships between the modelling parameters, the model can be calibrated to replicate the dynamics of any coral reef ecosystem. This allows the model to be applied to systems where limited data and/or resources are available, making it widely implementable in developing countries such as the small island states scattered around the tropics. The model is ideally suited to the adaptive management framework whereby managers can continually assess the potential future outcomes of management interventions. In addition, due to the spatially inexplicit and generic nature of the model, it can be easily adapted and integrated into large scale regional modelling frameworks or combined with other modelling packages such as socio-economic or fisheries models to provide enhanced management packages. The culmination of the targeted research and integration of existing knowledge has allowed for the development of an ecosystem model for coral reefs that can be easily adopted by coral reef managers throughout the world. It is however, by no means a definitive coral reef ecosystem model and there are many facets that can and should continue to be refined to enhance the reliability of the model.