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

<p>In this thesis I examine and evaluate the effects of a documented large-scale eutrophication on macroalgal vegetation on the Swedish coast. During the past century the load of nutrients has increased manifold in the Baltic Sea area, increasing primary production and organic sedimentation significantly. By re-investigating a unique reference material of macroalgal vegetation from the 1940-60s and by conducting new diving studies at the same sites, I showed that long-term trends in macroalgal community composition and species’ distributions are consistent with changes expected from an increased nutrient availability. In the Öregrund archipelago (northern Baltic Sea), I documented a declined depth distribution of the dominant canopy forming alga, <i>Fucus vesiculosus</i>, and an increased abundance of opportunistic ephemeral algae compared to 52-53 years ago. In the Gullmar Fjord area (Skagerrak), trends included increased abundances of functional groups with opportunistic algae, decreased abundances of large perennial algae and a general decline in the depth distribution of the vegetation compared to 36-57 years ago. Sediment removal experiments in the northern Baltic Sea confirmed the hypothesis that sedimentation influences macroalgal community composition. Species depending on short periods of reproduction were clearly favoured by sediment removal, especially <i>F. vesiculosus</i> that seemed limited in depth by the local sediment load. Species with long continuous periods of dispersal by spores and/or fragments (for example the ephemerals <i>Cladophora glomerata</i>, <i>Ceramium tenuicorne</i> and <i>Enteromorpha</i> spp.) were more tolerant to the natural sediment load. In general, sediment removal favoured macroalgal establishment and development, indicating that variation in the natural sediment load is an important constraint for sublittoral rocky-shore macroalgal community development. I conclude by suggesting that the documented long-term changes in macroalgal vegetation on the Swedish coast partly are explained by an increased organic sedimentation in these areas.</p>

<p>This thesis examines the role of dissolved inorganic nutrients in generating changes in phytoplankton community and pigment composition and if such changes can affect the production of the antioxidant astaxanthin in the ecosystem via pelagic copepods. The background of my studies is the possible relationship between eutrophication and a reproductive disturbance in Baltic populations of Atlantic salmon (M74), which is associated with astaxanthin and thiamine deficiencies and oxidative stress. In the southern Baltic Sea, changes in nutrient loads correlate with observed trends of flagellates replacing diatoms in the phytoplankton. Copepods are the main producers of astaxanthin and a major link between phytoplankton and higher trophic levels. In laboratory and field experiments in the Baltic Sea proper and the Norwegian Sea, I show that astaxanthin synthesis in copepods is fast and depends on pigment composition of the phytoplankton diet. Among single-species diets, a diatom and a green algal cyst yielded the highest astaxanthin levels in copepods, and another diatom species, a green alga and a cyanobacterium the lowest. In nutrient-generated phytoplankton blooms in mesocosms, copepods grazing on diverse communities dominated by weakly silicified diatoms produced more astaxanthin compared with copepods grazing on communities dominated by strongly silicified diatoms. This suggests that diatoms invested in defence mechanisms and escaped grazing at surplus Si. A nutrient-starved diatom culture subjected to intraspecific competition exhibited decreased pigment levels, increased thiamine levels and increased oxidative stress. </p><p>My results suggest that diatoms are beneficial for astaxanthin and thiamine production compared to other phytoplankton groups, but not under all circumstances. Copepod growth and development also responded to inorganic nutrient availability and affected total astaxanthin production per volume seawater, with highest production when the copepods grazed on diatoms. From an ecosystem perspective, increased N and P loads seem to promote high astaxanthin production, but not when diatoms disappear completely.</p>

Mysid shrimps (Mysidacea, Crustacea) are efficient zooplanktivores in both marine and freshwater systems as well as lipid rich prey for many species of fish.  Although some efforts have been made to study the role of mysids in the Baltic Sea, very few studies have been carried out in recent time and there are still knowledge gaps regarding various aspects of mysid ecology. This thesis aims to explore some of these gaps by covering a mixture of topics. Using multifrequency hydroacoustics we explored the possibility to separate mysids from fish echoes and successfully established a promising and effective method for obtaining mysid abundance/biomass estimates (paper I). An investigation of the current mysid community in a coastal area of the northern Baltic proper (paper II) demonstrated that the formerly dominant, pelagic mysid Mysis mixta had decreased substantially (~50%) in favor for phytoplanktivorous, juvenile Neomysis integer and Mysis relicta sp. By examining different aspects of mysid behavior, we studied the vertical size distribution of mysids in the field and found that size increased with depth/declining light, irrespective of temperature; indicating that their vertical size distribution primarily is a response to predation (paper II). In paper III, a combination of ecological and genetic markers was used to investigate intraspecific differences in migratory tendency. Both marker types indicated that some part of the Mysis salemaai population is sedentary on the bottom and that this strategy is a phenotypically plastic but persistent trait, analogous to the partial migrations seen in many birds and fishes. In paper IV a temperature and weight specific respiration model was developed for the littoral Praunus flexuosus. Routine respiration was moreover elevated by post-prandial effects (specific dynamic action) for longer times than previously suggested. Consequently, ignoring such effects could significantly bias respiration measurements. / At the time of doctoral defence the following papers were unpublished and had a status as follows: Paper  2: Accepted; Paper 3: Submitted; Paper  4: Accepted

There is a tendency in archaeology dealing with watercraft landing sites in a wider context to assume a direct relationship between sites in coastal and shore-bound areas and the practise of landing, without any deeper practical or theoretical exploration of the reality of any such relationship. This problem has its origins in the poor archaeological and conceptual definitions of watercraft landing sites obstructing any real understanding of the role of these sites in the maritime cultural landscape. Landing sites are taken for granted and they are undervalued as an archaeological source of explanation; notwithstanding, the concept of the landing site is readily used in archaeology in order to underpin archaeological interpretations on the maritime activities of past societies. In order to break away from the simplified understandings of past water-bound strategies based on the undefined concept of the landing site, this dissertation suggests a definition of watercraft landing sites in a wider social sense as water-bound contact zones; places of social interaction that can be archaeologically identified and investigated. This perspective integrates the understanding of the intentional character of human activity related to watercraft landing with the remaining archaeological traces. Archaeological definitions of landing sites that can be tested against the archaeological data are provided, and thereby, the dissertation contributes with the possibility to archaeologically evaluate and approach the social function of watercraft landing sites. This dissertation demonstrates that there can be an archaeology of landing sites.

In this thesis I examine and evaluate the effects of a documented large-scale eutrophication on macroalgal vegetation on the Swedish coast. During the past century the load of nutrients has increased manifold in the Baltic Sea area, increasing primary production and organic sedimentation significantly. By re-investigating a unique reference material of macroalgal vegetation from the 1940-60s and by conducting new diving studies at the same sites, I showed that long-term trends in macroalgal community composition and species’ distributions are consistent with changes expected from an increased nutrient availability. In the Öregrund archipelago (northern Baltic Sea), I documented a declined depth distribution of the dominant canopy forming alga, Fucus vesiculosus, and an increased abundance of opportunistic ephemeral algae compared to 52-53 years ago. In the Gullmar Fjord area (Skagerrak), trends included increased abundances of functional groups with opportunistic algae, decreased abundances of large perennial algae and a general decline in the depth distribution of the vegetation compared to 36-57 years ago. Sediment removal experiments in the northern Baltic Sea confirmed the hypothesis that sedimentation influences macroalgal community composition. Species depending on short periods of reproduction were clearly favoured by sediment removal, especially F. vesiculosus that seemed limited in depth by the local sediment load. Species with long continuous periods of dispersal by spores and/or fragments (for example the ephemerals Cladophora glomerata, Ceramium tenuicorne and Enteromorpha spp.) were more tolerant to the natural sediment load. In general, sediment removal favoured macroalgal establishment and development, indicating that variation in the natural sediment load is an important constraint for sublittoral rocky-shore macroalgal community development. I conclude by suggesting that the documented long-term changes in macroalgal vegetation on the Swedish coast partly are explained by an increased organic sedimentation in these areas.

Temporal and spatial variations of pelagic microorganisms in the northern Baltic Sea were studied, as well as factors influencing their abundance and growth rates. Three main questions were asked 1) How does increased productivity influence the structure of the microbial food web? 2) Does predation limitation vary between trophic levels? 3) What is the relative importance of resource and predation limitation at different trophic levels? A field study in the northern Baltic Sea showed that dominating protozoa, flagellates and ciliates, increased with increasing primary productivity from north to south. Furthermore, relatively small protozoan cells dominated in the low productive north, while larger cells became more dominant in the south. The relationship between plankton size structure and productivity was further studied in an experimental system. In agreement with present theories regarding nutrient status of pelagic food webs, increased productivity caused a lengthening of the food chain as well as a change in plankton size structure. While microplankton dominated in nutrient rich treatments pico- and nanoplankton dominated during nutrient poor treament. The flagellate community was dominated by a potentially mixotroph, Chrysochromulina sp., at low nutrient concentrations. To our knowledge this is the first experimental study showing that Chrysochromulina sp. in resemblance with other mixotrophs is favoured by nutrient poor conditions compared to strict autotrophs and heterotrophs. During a stratified summer period autotrophic microorganisms in the northern Baltic Sea did not respond to removal of potential predators, indicating that they were primarily limited by inorganic nutrients. An exception was small eucaryotic picoplankton that showed a large response to predator removal. Among the heterotrophic microorganisms direct effect of predation seemed to increase from ciliates, heterotrophic bacteria, small heterotrophic flagellates, medium flagellates to large flagellates. No quick indirect effect was observed, but after four days trophic cascades were detected. The relative importance of resource and predation limitation was studied among heterotrophic bacteria, flagellates and ciliates in the northern Baltic Sea. For all these groups, resource limitation seemed to prevail during the summer period. The results also indicated that the relative importance of predation increased with the productivity of the system. To our knowledge there are no earlier measurements on the relative importance of resource and predation limitation for micoorganisms in the pelagic environment.

The brackish Baltic Sea is a marginal environment for both marine and freshwater species. The rate of ecological differentiation is presumably high due to strong selection pressure from a gradient of decreasing salinity that has been present in its current state for only about 3 000 years. Even more recently, increased nutrient loading due to human activities has affected the growth rate of species, with potential effects on their competitive interactions and responses to other regulating factors. I have investigated the potential effects of low salinity and nutrient enrichment on the distributional ranges of two marine macroalgae with a wide distribution in the Baltic Sea, the red alga Ceramium tenuicorne (Kütz.) Wærn and the brown alga Fucus vesiculosus L. A field study in the northern Baltic Sea indicated a strong relationship between the community structure of macroalgae and abiotic factors even on a small, local scale. The abiotic factors are potentially modulated by eutrophication, which may have a strong effect on the depth distribution and abundance of macroalgae. On a regional scale, laboratory experiments suggested that nutrient enrichment is unlikely to affect the distribution of Ceramium and Fucus along the salinity gradient. Growth in Ceramium from the Baltic Proper was enhanced by nitrate and phosphate, but the response did not override growth constraints due to low salinity. Ceramium from the Gulf of Bothnia had an inherently lower growth rate that was not positively affected by nitrate and phosphate increase. In Fucus vesiculosus, reproductive performance was impaired by nitrate and phosphate levels corresponding to ambient levels in eutrophicated areas of the Baltic Sea, when measured by their effect on zygote attachment, germination, and rhizoid development. The wide distribution of Ceramium in the inner Baltic Sea is probably related to local adaptation, rather than a generalized tolerance of different salinity levels. Ecotypic differences were observed when comparing strains from the Baltic Proper (salinity 7 psu) and the Gulf of Bothnia (4 psu). A high rate of vegetative reproduction was evident, although sexual reproduction was occasionally observed in salinity 4. In Fucus vesiculosus, genetic and morphological analyses of sympatric and allopatric populations of the common, vesicular, morphotype and a dwarf morphotype, characteristic for the Gulf of Bothnia, showed that the dwarf morphotype represents a separate evolutionary lineage. Also, vegetative reproduction was observed in Fucus for the first time, as supported by genetic and experimental data. The results show that the biota of the inner Baltic Sea may have unique adaptive and genetic properties, and that it is highly relevant to consider subspecies diversity in Baltic Sea management.

Relevant information is essential for finding solutions in Integrated Water Management (IWM). Complex water systems and a need for increasing integration of sectors, actors and scales in IWM require new methods for developing and managing such information. This thesis investigates the role of information within the IWM process, as well as the main challenges for development of representative, accessibleand harmonized information. Results show how information needs and the information production process for IWM may be systematized, and indicate a large potential for information system development for IWM. However, in order to reach the full potential, today’s limited and heterogeneous water information needs to become more comprehensive, transparent, interoperable, dynamic, scalable and openly accessible. Large pressures on water systems are found in coastal catchment areas that are unmonitored across the local to the global scale, indicating a large importance of these areas for nutrient and pollutant loading. The globally accessible runoff data from catchment areas that are rich in pressures from population, agriculture and general economic activity further exhibit a rapidly declining trend during recent years. Major water system changes may therefore pass unnoticed if analyzed on the basis of openly accessible runoff global data. Furthermore, large discrepancies are found between land cover databases, which may result in major uncertainties in quantification of water and evapotranspiration flows. Identified information challenges may be relatively easily overcome by making better use of available information, while other challenges such as development of consistent baselines of core data and a possible re-prioritization of water-environmental monitoring programs may be both difficult and costly.

In order to understand how waves influence the exchange of momentum, latent heat and other parameters, between the ocean surface and the atmosphere, one can use models. A coupling between a wave model and an atmospheric regional climate model, for the Baltic Sea, will be performed at the Meteorology Institute in Uppsala University. The wave model is a state of the art, third generation wave model called WAM. The new version of the WAM model (cycle 4) needs to be validated. The aim of this thesis is to perform this validation and also to investigate what meteorological forcing one should use to achieve best results. Two different types of forcing are analyzed, ERA40 reanalysis and the RCA climate model. In order to do this, observations from six different buoys in the Baltic Sea will be compared with the model output from WAM. The parameters that will be compared in this study are significant wave height, direction and peak period. A consistent phenomenon for all the buoys is a slightly overestimation by the model of what the rate of this increases with increasing wave height. If one compares the model output when WAM are forced with the RCA climate model and when it is forced with ERA40 reanalysis, the differences between them are notable but not large. ERA40 is slightly better. Significant wave height is quite good and gives a reasonably result. Some buoys and periods are better and some are worse. There are some differences for the significant wave height between the east coast and the west coast of Sweden, when forcing the model with RCA. It is slightly better on the west coast. On the contrary, the results from ERA40 are very coherent. The quality of the hindcast for the direction and the peak period, in contrast to the significant wave height, is not that good. The results are not bad, but it only gives a rough picture of the sea state.