Lakes are increasingly being recognized as an important component of the global carbon cycle, yet anthropogenic activities that alter their community structure may change the way they transport and process carbon. This research focuses on the relationship between carbon cycling and community structure of primary producers in small, shallow lakes, which are the most abundant lake type in the world, and furthermore subject to intense terrestrial-aquatic coupling due to their high perimeter:area ratio. Shifts between macrophyte and phytoplankton dominance are widespread and common in shallow lakes, with potentially large consequences to regional carbon cycling. I thus compared a lake with clear-water conditions and a submerged macrophyte community to a turbid, phytoplankton-dominated lake, describing differences in the availability, processing, and export of organic and inorganic carbon. I furthermore examined the effects of increasing terrestrial carbon inputs on internal carbon cycling processes. Pelagic diel (24-hour) oxygen curves and independent fluorometric approaches of individual primary producers together indicated that the presence of a submerged macrophyte community facilitated higher annual rates of gross primary production than could be supported in a phytoplankton-dominated lake at similar nutrient concentrations. A simple model constructed from the empirical data suggested that this difference between regime types could be common in moderately eutrophic lakes with mean depths under three to four meters, where benthic primary production is a potentially major contributor to the whole-lake primary production. It thus appears likely that a regime shift from macrophyte to phytoplankton dominance in shallow lakes would typically decrease the quantity of autochthonous organic carbon available to lake food webs. Sediment core analyses indicated that a regime shift from macrophyte to phytoplankton dominance was associated with a four-fold increase in carbon burial rates, signalling a major change in lake carbon cycling dynamics. Carbon mass balances suggested that increasing carbon burial rates were not due to an increase in primary production or allochthonous loading, but instead were due to a higher carbon burial efficiency (carbon burial / carbon deposition). This, in turn, was associated with diminished benthic mineralization rates and an increase in calcite precipitation, together resulting in lower surface carbon dioxide emissions. Finally, a period of unusually high precipitation led to rising water levels, resulting in a feedback loop linking increasing concentrations of dissolved organic carbon (DOC) to severely anoxic conditions in the phytoplankton-dominated system. High water levels and DOC concentrations diminished benthic primary production (via shading) and boosted pelagic respiration rates, diminishing the hypolimnetic oxygen supply. The resulting anoxia created redox conditions which led to a major release of nutrients, DOC, and iron from the sediments. This further transformed the lake metabolism, providing a prolonged summertime anoxia below a water depth of 1 m, and leading to the near-complete loss of fish and macroinvertebrates. Pelagic pH levels also decreased significantly, increasing surface carbon dioxide emissions by an order of magnitude compared to previous years. Altogether, this thesis adds an important body of knowledge to our understanding of the significance of the benthic zone to carbon cycling in shallow lakes. The contribution of the benthic zone towards whole-lake primary production was quantified, and was identified as an important but vulnerable site for primary production. Benthic mineralization rates were furthermore found to influence carbon burial and surface emission rates, and benthic primary productivity played an important role in determining hypolimnetic oxygen availability, thus controlling the internal sediment loading of nutrients and carbon. This thesis also uniquely demonstrates that the ecological community structure (i.e. stable regime) of a eutrophic, shallow lake can significantly influence carbon availability and processing. By changing carbon cycling pathways, regime shifts in shallow lakes may significantly alter the role of these ecosystems with respect to the global carbon cycle. / Seen werden zunehmend als wichtige Komponente im globalen Kohlenstoffkreislauf anerkannt. Natürliche Veränderungen und anthropogene Aktivitäten beeinflussen die Struktur der Artengemeinschaft von Seen, was Auswirkungen auf den Transport und Umsatz von Kohlenstoff hat. Diese Arbeit konzentriert sich auf die Beziehung zwischen Kohlenstoffkreislauf und der Gemeinschaftsstruktur der Primärproduzenten in kleinen Flachseen. Diese sind der weltweit häufigste Seentyp und weisen durch ihren im Vergleich zur Fläche großen Umfang eine intensive aquatisch-terrestrische Kopplung auf. In Flachseen treten oft Regimewechsel zwischen Makrophyten- und Phytoplankton-Dominanz auf. Diese können potenziell große Konsequenzen für den regionalen Kohlenstoffkreislauf haben. In dieser Dissertation vergleiche ich einen Klarwassersee mit submersen Makrophyten und einen trüben, Phytoplankton-dominierten See hinsichtlich Verfügbarkeit, Umsatz und Export von organischem und anorganischem Kohlenstoff. Des Weiteren habe ich den Effekt der erhöhten Zufuhr von terrestrischem Kohlenstoff auf den internen Kohlenstoffumsatz untersucht. Sowohl die Tagesgänge der pelagischen Sauerstoff-Konzentrationen als auch Fluoreszenz-basierte Messungen der Primärproduktion bewiesen, dass die Präsenz von submersen Makrophyten eine höhere jährliche Brutto-Primärproduktion im Vergleich zu einem Phytoplankton-dominierten See mit ähnlichen Nährstoffkonzentrationen ermöglicht. Ein einfaches, auf den empirischen Daten basierendes Model zeigt, dass diese Unterschiede in der Brutto-Primärproduktion typisch sind für moderat eutrophe Seen mit einer mittleren Tiefe von unter 3 bis vier Metern. In diesen Seen leistet die benthische Primärproduktion den Hauptbeitrag zur Primärproduktion des ganzen Sees. Daraus wird ersichtlich, dass Regimewechsel von Makrophyten- zur Phytoplankton-Dominanz in Flachseen die Verfügbarkeit von autochthonem organischem Kohlenstoff für das Nahrungsnetz reduzieren. Paläolimnologische Analysen in Sedimentkernen beider Seen wiesen darauf hin, dass der Verlust der Makrophyten mit einer vierfachen Zunahme der Kohlenstoff-Speicherraten einhergeht, und somit zu einer großen Veränderung der Dynamik des Kohlenstoffkreislaufs im See führt. Unsere Kohlenstoff-Massenbilanzen zeigen, dass die Erhöhung der Kohlenstoff-Speicherung im Sediment nicht durch die Erhöhung der Primärproduktion oder durch externe Quellen, sondern durch erhöhte der Effizienz der Speicherung begründet war. Dies geht mit einer reduzierten benthischen Mineralisierungsrate und einer erhöhten Calcitfällung einher und führt zu reduzierten Kohlendioxid-Emissionen. Eine Periode ungewöhnlich hoher Niederschläge mit erhöhten Wasserständen führte im Phytoplankton-dominierten See zu zu einem starken Anstieg der Konzentrationen an gelöstem organischem Kohlenstoff (DOC) und zu anoxischen Bedingungen. Es wurde postuliert, dass zwischen diesen Prozessen eine positive Rückkopplung besteht. Die hohen Wasserstände und DOC-Konzentrationen reduzierten die Lichtversorgung und damit die Primärproduktion im Benthal und erhöhten die pelagischen Respirationsraten. Dadurch verringerte sich die Sauerstoffverfügbarkeit im Hypolimnion. Die dadurch erzeugten Redox-Verhältnisse führten zu einer Freisetzung großer Mengen an Nährstoffen, DOC und Eisen aus dem Sediment. Die während des gesamten Sommers andauernden anoxischen Verhältnisse in Wassertiefen unter 1 m führten zu einem fast vollständigen Verlust von Fischen und Makroinvertebraten. Zusätzlich wurde der pH-Wert im Pelagial signifikant erniedrigt und die Kohlenstoffdioxid-Emissionen im Vergleich zu früheren Jahren verzehnfacht. Insgesamt trägt diese Dissertation wesentliche Aspekte zum besseren Verständnis der Bedeutung des Benthals für den Kohlenstoffkreislauf in Flachseen bei. Der Anteil der benthischen Zone an der Primärproduktion in kleinen Flachseen wurde in Relation zur Gesamtproduktion des Systems quantifiziert. Letztlich zeigt diese Arbeit, dass die Gemeinschaftsstruktur der Primärproduzenten eines eutrophen Flachsees die Verfügbarkeit und den Umsatz von Kohlenstoff signifikant beeinflusst. Regimewechsel in Flachseen können durch Änderungen im internen Kohlenstoffkreislauf deren Rolle im globalen Kohlenstoffkreislauf verändern.

Lake browning in the northern hemisphere is endangering crucial ecosystem services. Darker water decreases fish and primary production as well as touristic and recreational values. It furthermore requires intensive treatment to receive safe drinking water. Brownification is connected to iron and coloured dissolved organic carbon (DOC). In Sweden, spruce plantations leak DOC, possibly depending in their DOC rate on tree age. Whereas wetlands are known to purify water and might contribute to the degradation of DOC. This thesis aims to investigate how different land use types and other parameters affect water colour. Ditches flowing through old spruce forests, young spruce forests, and peat wetlands in the Lake Bolmen catchment, southwestern Sweden, were sampled at in- and outlet. Highly significantly positive relationships between DOC, iron and absorbance were found. The relationship was strongest between DOC and absorbance (R² = 0.88; p < 0.001) and weakest between DOC and iron (R² = 0.54; p < 0.001). High variability led to no significant differences in the release of DOC and iron between the three land use types. However, older forests tended to increase DOC and iron loading compared to younger forests. This study suggests that not only spruce forests in general are affecting the brownification, but that several different factors like age and underlying soil type might play a critical role.

Organic carbon concentrations are increasing in freshwaters in the northern hemisphere. A significant brownification is observed in Lake Mälaren in south-east Sweden since 1965. This process has an impact on drinking water production, ecological functions and might also increase the loss of greenhouse gases to the atmosphere. Drivers behind the brownification have been attributed to the reduced sulphur deposition, warmer and wetter climate and changing land use. This study aims at examining how growing degree days, water discharge and volume of pine and spruce in Mälaren catchment have contributed to the increased water colour since 1965. Based on that analysis, some predictions are made to what can be expected in the future. Data over climate variables have been collected from SMHI and water colour from SLU and Norrvatten. All variables were found to be correlated to water colour, with the strongest correlations found between water colour and pine and spruce volume. Growing degree days increased 30 days since 1968-1972 and water discharge revealed an overall decline for the period 1981-2018. Climate scenarios predict warmer temperatures and higher yearly precipitation for this region. Overall change in discharge is uncertain since a higher evaporation is also expected. An increase would likely lead to an increase in water colour. This could especially affect the eastern basins where increase in water colour currently is slowed down by higher water retention times. The findings in this study indicate that water colour in Mälaren will increase in the future, mainly due to warmer temperatures and increased volume of pine and spruce.

Climate change and human land use leads to browning of waters with decreased visual conditions. This impacts the fish community via changes in foraging ability and food chain efficiency. There are indications that brownification leads to decreased body size of the Eurasian perch (Perca fluviatilis) and that roach (Rutilus rutilus) are favoured over perch in brown lakes since roach is less dependent on its eyesight when foraging. The aim with this project is to examine how browning impacts the fish community in lakes in the south of Sweden and if browning reduces the size of perch in relation to their age. Data on water colour and length-at-age for 1+ and 5+ perch as well as the number of perch and roach captured was collected from 20 lakes. The data was examined using linear regression and paired samples T-test in SPSS. The results show that browning does reduce the body size of perch. Perch is smaller in relation to their age in brown lakes. There was however no evidence indicating that roach is favoured over perch in brown lakes, but there was a difference between the number of 1+ and 5+ perch caught in relation to roach. The perch: roach ration decreased for older fish (from 1+ to 5+) indicating that there is a difference in survival rate. Survival rate of perch was however not dependent on water colour or TOC. This shows that climate change and increased browning could result in changes of the fish community and size structure of fish.

Allochthonous organic carbon is increasing and leading to browning of freshwaters in the northern hemisphere. It is already known that an increase in allochthonous dissolved organic carbon (DOC) affects benthic primary production and respiration negatively via light limitation, however, little is known about the impact on benthic bacteria. This report aims at examining how DOC and other environmental variables affect the production and growth of benthic bacteria. This was done by analyzing data from 18 lakes in northern Sweden with different DOC concentrations. This analysis was divided into two datasets: one including data at the whole lake scale and the other including data over depth within the lakes. The result showed that DOC, average depth, and the light extinction coefficient all had a negative impact on bacterial production on a whole lake scale. The light extinction coefficient was also affecting the whole lake bacterial growth efficiency (BGE) negatively. Over depth within the lakes a higher light input increased the bacterial production. In the same dataset, light was also affecting the BGE positively, while temperature had a negative effect. The results can thus be linked to the increase in allochthonous carbon and brownification. Because allochthonous DOC have a negative effect on benthic primary production, there will be less autochthonous DOC available for benthic bacteria. Allochthonous DOC is considered less degradable than autochthonous DOC. The increase in allochthonous DOC therefore has a negative impact on benthic bacterial production, likely connected to a decrease in production of autochthonous DOC by benthic algae.

Climate change is causing water temperature to rise, and many lakes in the boreal zone will experience browning of waters (brownification) due to increased input of dissolved organic carbon (DOC). In fish, warming may cause resource limitation and decrease both fish size and population abundance. Many fish species display ontogenetic niche shifts during their lifetime, shifting to larger prey as they grow. Brownification may change the timing for, the benefits from or prevent individuals from displaying ontogenetic niche shifts by decreasing large prey abundance in the benthic zone or making fast-moving prey harder to see. This can cause resource limitations, suppressing growth and population growth. This study investigated the effects of increasing DOC and water temperature on ontogenetic diet shifts, size structure, and population abundance in nine-spine stickleback (Pungitius pungitius) in an experimental pond system with a warming treatment and a gradient of DOC concentration. Warming had a negative effect on population number, biomass, maximum fish size, stomach fullness, and consumption of large prey. Contrary to expected outcomes, increasing DOC input resulted in higher population, biomass, and larger maximum sized fish as DOC increased. DOC did not negatively affect ontogenetic diet shifts. In the relatively shallow enclosures, the highest DOC concentration may not have reached the threshold where the shading effect of DOC overturns the benefits of extra nutrients associated with DOC. Hence, in shallow lake ecosystems, climate change induced DOC increase may support fish production, while warming may have strong negative effects on fish population abundance and size.

The theoretical framework of ecosystem services and that of resilience thinking are combined in an empiricalcase study of a social-ecological system. In the River Helge å catchment in southern Sweden, a slow increase in dissolved organiccarbon (DOC) results in brownification of the water with consequences on ecosystem services in the lower part of the catchmentof concern by local resource managers. An assessment of ecosystem service delivery was conducted to (1) identify plausibledrivers of brownification in the study site and assess future ecosystem service delivery for stakeholders in downstream areas.An analysis of the perspective of beneficiaries, using qualitative methods, was pursued to (2) evaluate the impacts ofbrownification on downstream stakeholders.

Increased DOC and Fe concentrations from terrestrial landscapes has led to the browning of boreal surface waters. The negative societal and ecological impacts of brownification are increased cost of water purification, increased presences of algae and cyanobacteria, loss of ecosystem services and reduced recreational value. Impacts of climate change, changes in land use and reduced sulfur deposition have been identified as drivers of brownification. While it has been recognized that DOC and Fe from terrestrial landscapes is increasing, little has been done to understand the impact of different land use practices on brownification. This research aims at evaluating the DOC and Fe runoff from spruce plantations, clear-cuts and wetland landscapes and determining the export of DOC from these landscapes into humic lakes. To do that, streams running through these three different land use types were sampled for water colour, pH, temperature, conductivity, DOC and Fe both at upstream and downstream of each land use type. Further, water discharge was calculated with the help of flow speed measurements and stream profiling (width, depth and channel shape). DOC (but not Fe) concentrations changed significantly depending on land use type. Wetlands lead to reduced DOC concentrations, whereas especially spruce plantations lead to increased stream water DOC concentrations.

During recent decades the brownification through leaching of organic carbon into Northern hemisphere water bodies has become apparent. This is considered a problem because of the implications it has on ecosystems and freshwater sources used for drinking water. It could be beneficial if wetlands can be used for reducing brownification but also detrimental if wetlands instead increase it as construction of wetlands is common practice for treating agricultural runoff in Sweden.  This study compares inlet and outlet absorbance in five wetlands in Kalmar County in Sweden and finds that one removes colour, two increases colour and two does not change the colour of the water at all. The study also compares absorbance values with variables concerning flow and temperature and concludes that a higher absorbance at inlet increases removal similar to how nutrient removal in wetlands work. Inlet absorbance is also dependent on flow with higher flow resulting in higher absorbance. Periods of no flow did not contribute to any changes in absorbance, but this could be because of a limited sample pool. Future recommendations for research include a more extensive look into periods of no flow and affecting variables to ensure wetlands do not contribute to brownification.

Dissolved organic matter (DOM) in surface waters affect many important ecological functions. For instance, transporting metals, nutrients, carbon, affecting pH and water colour. In large parts of the Northen hemisphere, surface waters have become browner as a consequense of increasing DOM concentrations and, to some extent, iron. Therfore, altering ecological functions in waters. As such, knowing the causes and extent of the increase is of great importance. This paper used monthly data from the national Swedish monitoring program to investigate trends in DOM-concentrations in the Rickleå river, Västerbotten, Sweden. Results showed a large increase in concentrations of DOM from 1970-2019. However, the increase was most pronounced between 1970-1990, showing no trend after 2003 and indications of a decrease from 2009. DOM-quality changed as well to larger and more colored molecules during 1987-2002 and less coloured, smaller molecules after 2003. Changes in water flow could be an explanation for short-term fluctuations in DOM-concentration, but did not correlate well to increasing trends. However, a large lake at the river inlet as well as hydroelectric dams along the watershead complicates the interpretation between flow and DOM correlation. Climate change did not seem to be an important driver of long term increases in DOM. Further investigations should be carried out to test this hypothesis as well to investigate the cause for the increase.