Abstract The aims of this thesis included identifying ways to mitigate the economic losses of the commercial fishery in the Gulf of Bothnia resulting from fishery regulation enforced to protect wild Atlantic salmon stocks, the recent decline in survival of hatchery-reared salmon, and the dramatically increased seal-induced catch and gear damage. In addition, these solutions should facilitate safeguarding the recently-recovered wild salmon stocks and seal populations. Other goals included adding to and updating basic knowledge on the effects of increased seal populations, migrating salmon stocks, the coastal trap-net fishery, and their interactions. Seal-induced damage to the commercial fishery was found to be a significant problem throughout the Gulf of Bothnia. Catch and gear damage varied considerably among regions, fishing periods, target species and trap-net models. The regional patterns in seal-induced damage depended on the number of seals in the region and the type of gear, which is strongly associated with the netting materials. Strong and thick materials are more resistant to the attacks of hunting seals. Finer materials and larger mesh sizes that entangle fish are most prone to seal damage. Besides careful selection of the netting material it is also possible to markedly reduce damage by appropriate gear modifications. Three modified trap-net models showed promising results in terms of seal protection, with the pontoon trap being the most successful design. The total size of the spawning salmon population in the Gulf of Bothnia was c. 230 000 in the first two years of the 2000s. The proportions of wild salmon and hatchery-reared salmon, however, appeared to markedly change between years. The survival rate of cultured smolts seems to be considerably lower than that of wild smolts. Large variation in the returning migration patterns and run timing of salmon was found between sea age groups, stock components, and among and within regions. Run timing estimates revealed that the temporal regulation effectively safeguards the wild salmon, but, at the same time, a substantial proportion of the reared salmon escape the coastal fisheries in different regions. The likelihood of survival of wild salmon captured with trap-nets and then released was high, and the cumulative mortality even after several capture-and-release events was estimated to below. Trap-net capture and release did not lead to considerable changes in the normal migration behaviour of Atlantic salmon. This result suggests the potential for a selective harvesting strategy; a system where exploitable (e.g. hatchery-reared fish) and safeguarded (e.g. wild vulnerable stocks) fractions of a fish population complex could be separated in a mixed-stock fishery. However, before introducing a practical and successful selective trap-net fishery, several preconditions should be fulfilled.

<p>The global carbon cycle is subject to intense research, where sources and sinks for greenhouse gases, carbon dioxide in particular, are estimated for various systems and biomes. Lakes have previously been neglected in carbon balance estimations, but have recently been recognized to be significant net sources of CO2.</p><p>This thesis estimates emission of carbon dioxide (CO2) from boreal lakes and factors regulating the CO2 saturation from field measurements of CO2 concentration along with a number of chemical, biological and physical parameters. Concentration of dissolved organic carbon (DOC) was found to be the most important factor for CO2 saturation in lake water, whereas climatic parameters such as precipitation, temperature and global radiation were less influential. All lakes were supersaturated with and, thus, sources of CO2. Sediment incubation experiments indicated that in-lake mineralization processes during summer stratification mainly occurred in the pelagial. Approximately 10% of the CO2 emitted from the lake surface was produced in epilimnetic sediments. </p><p>The mineralization of DOC and emission of CO2 from freshwaters was calculated on a catchment basis for almost 80,000 lakes and 21 major catchments in Sweden, together with rates of sedimentation in lakes and export of organic carbon to the sea. The total export of terrestrial organic carbon to freshwaters could thereby be estimated and consequently also the importance of lakes for the withdrawal of organic carbon export from terrestrial sources to the sea. Lakes removed 30-80% of imported terrestrial organic carbon, and mineralization and CO2 emission were much more important than sedimentation of carbon. The carbon loss was closely related to water retention time, where catchments with short residence times (<1 year) had low carbon retentions, whereas in catchments with long residence times (>3 years) a majority of the imported TOC was removed in the lake systems. </p><p>The Gulf of Bothnia was also studied in this thesis and found to be a net heterotrophic system, emitting large amounts of CO2 to the atmosphere on an annual basis. The rate of CO2 emission was depending on the balance between primary production and bacterial respiration, and the system was oscillating between being a source and a sink of CO2.</p>

The global carbon cycle is subject to intense research, where sources and sinks for greenhouse gases, carbon dioxide in particular, are estimated for various systems and biomes. Lakes have previously been neglected in carbon balance estimations, but have recently been recognized to be significant net sources of CO2. This thesis estimates emission of carbon dioxide (CO2) from boreal lakes and factors regulating the CO2 saturation from field measurements of CO2 concentration along with a number of chemical, biological and physical parameters. Concentration of dissolved organic carbon (DOC) was found to be the most important factor for CO2 saturation in lake water, whereas climatic parameters such as precipitation, temperature and global radiation were less influential. All lakes were supersaturated with and, thus, sources of CO2. Sediment incubation experiments indicated that in-lake mineralization processes during summer stratification mainly occurred in the pelagial. Approximately 10% of the CO2 emitted from the lake surface was produced in epilimnetic sediments. The mineralization of DOC and emission of CO2 from freshwaters was calculated on a catchment basis for almost 80,000 lakes and 21 major catchments in Sweden, together with rates of sedimentation in lakes and export of organic carbon to the sea. The total export of terrestrial organic carbon to freshwaters could thereby be estimated and consequently also the importance of lakes for the withdrawal of organic carbon export from terrestrial sources to the sea. Lakes removed 30-80% of imported terrestrial organic carbon, and mineralization and CO2 emission were much more important than sedimentation of carbon. The carbon loss was closely related to water retention time, where catchments with short residence times (&lt;1 year) had low carbon retentions, whereas in catchments with long residence times (&gt;3 years) a majority of the imported TOC was removed in the lake systems. The Gulf of Bothnia was also studied in this thesis and found to be a net heterotrophic system, emitting large amounts of CO2 to the atmosphere on an annual basis. The rate of CO2 emission was depending on the balance between primary production and bacterial respiration, and the system was oscillating between being a source and a sink of CO2.

The Gulf of Bothnia consists of two sub-basins in the northern Baltic Sea: the Bothnian Sea (salinity 4-5‰) and Bothnian Bay (salinity 2-3‰). Changing nutrient concentrations and signs of eutrophication has recently been observed in the Gulf of Bothnia. Many rivers enter this sea area, and potentially river inflows constitute a source of nutrient pollution via waste-water emissions. The aim of this study was to elucidate effects of waste-water emissions in four rivers in northern Sweden, Luleå, Skellefteå, Umeå and Söderhamn. My approach was to compare nutrient concentrations at upstream and downstream sampling stations related to the position of waste-water treatment plants. Temporal data from 2006 to 2021 were used and statistically analyzed using non-parametric tests to establish spatial and temporal patterns for nutrient discharged to the coast. The results showed that there are statistically differences in dissolved inorganic phosphorus (DIP) in the form of phosphate (PO4), ammonia (NH4) and total nitrogen (TotN) between the upstream and downstream of Luleå and Umeå wastewater treatment plants. No statistically significant differences were observed in the upstream and downstream data for Söderhamn and Skellefteå. This suggest that better management and mitigation of nutrient loading from wastewater treatment plants that serve higher populations is paramount to achieve the zero-eutrophication goal in the Gulf of Bothnia.

The global carbon cycle is subject to intense research, where sources and sinks for greenhouse gases, carbon dioxide in particular, are estimated for various systems and biomes. Lakes have previously been neglected in carbon balance estimations, but have recently been recognized to be significant net sources of CO2. This thesis estimates emission of carbon dioxide (CO2) from boreal lakes and factors regulating the CO2 saturation from field measurements of CO2 concentration along with a number of chemical, biological and physical parameters. Concentration of dissolved organic carbon (DOC) was found to be the most important factor for CO2 saturation in lake water, whereas climatic parameters such as precipitation, temperature and global radiation were less influential. All lakes were supersaturated with and, thus, sources of CO2. Sediment incubation experiments indicated that in-lake mineralization processes during summer stratification mainly occurred in the pelagial. Approximately 10% of the CO2 emitted from the lake surface was produced in epilimnetic sediments. The mineralization of DOC and emission of CO2 from freshwaters was calculated on a catchment basis for almost 80,000 lakes and 21 major catchments in Sweden, together with rates of sedimentation in lakes and export of organic carbon to the sea. The total export of terrestrial organic carbon to freshwaters could thereby be estimated and consequently also the importance of lakes for the withdrawal of organic carbon export from terrestrial sources to the sea. Lakes removed 30-80% of imported terrestrial organic carbon, and mineralization and CO2 emission were much more important than sedimentation of carbon. The carbon loss was closely related to water retention time, where catchments with short residence times (&lt;1 year) had low carbon retentions, whereas in catchments with long residence times (&gt;3 years) a majority of the imported TOC was removed in the lake systems. The Gulf of Bothnia was also studied in this thesis and found to be a net heterotrophic system, emitting large amounts of CO2 to the atmosphere on an annual basis. The rate of CO2 emission was depending on the balance between primary production and bacterial respiration, and the system was oscillating between being a source and a sink of CO2.

<p>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 <i>Ceramium tenuicorne</i> (Kütz.) Wærn and the brown alga <i>Fucus vesiculosus</i> L. </p><p>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 <i>Ceramium</i> and <i>Fucus</i> along the salinity gradient. Growth in <i>Ceramium</i> from the Baltic Proper was enhanced by nitrate and phosphate, but the response did not override growth constraints due to low salinity. <i>Ceramium</i> from the Gulf of Bothnia had an inherently lower growth rate that was not positively affected by nitrate and phosphate increase. In <i>Fucus vesiculosus</i>, 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.</p><p>The wide distribution of <i>Ceramium</i> 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 <i>Fucus vesiculosus</i>, 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 <i>Fucus</i> for the first time, as supported by genetic and experimental data. </p><p>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.</p>

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.