All natural aquatic systems harbour a vast variety of microorganisms. In the aquatic microbial food web, the larger microorganisms (i.e. protozoa) feed on the smaller microorganisms (i.e. bacteria and phytoplankton). An increase in nutrient availability results in changes of the microbial food web structure, like altered community composition and blooms of toxic phytoplankton. In this thesis work I hypothesised that nutrient-rich aquatic environments, with strong protozoan predation, favour the occurrence of predation-resistant bacteria like F. tularensis, and that the microbial food web may provide a reservoir for the bacterium between outbreaks. By using a size-structured ecosystem food web model it was shown that the protozoan predation pressure on bacteria, defined as protozoan predation per bacterial biomass, increases with increasing nutrient availability in aquatic systems (estimated chlorophyll a 0.2 to 112 μg L-1). This dynamics was caused by increasing growth-rate of a relatively constant number of bacterial cells, maintaining the growth of an increasing number of protozoan cells. The results were supported by meta-analysis of field studies. Thus my results suggest that protozoa control the bacterial community by predation in nutrient-rich environments. In a field study in a natural productivity gradient (chlorophyll a 1.4 to 31 μg L-1) it was shown that intense selection pressure from protozoan predators, favours predation-resistant forms of bacteria. Thus, the abundance of predation-resistant bacteria increases with increasing nutrient availability in lakes. Furthermore, I could demonstrate that the bacterium Francisella tularensis, the causative agent of tularemia, was present in eutrophic aquatic systems in an emerging tularemia area. Isolated strains of the bacterium were found to be resistant to protozoan predation. In a microcosm study, using natural lake water, high nutrient availability in combination with high abundance of a small colourless flagellate predator favoured the occurrence of F. tularensis holarctica. In laboratory experiments F. tularensis strains were able to form biofilm at temperatures between 30-37°C, but not below 30°C. In conclusion, I have shown that the protozoan predation pressure on bacteria increases with increasing nutrient availability in aquatic systems. Predation-resistant forms of bacteria, such as F. tularensis are favoured in nutrient-rich environments. The complexity of the microbial food web and nutrient-richness of the water, influence the transmission of the pathogenic F. tularensis holarctica. However, over long periods of time, the bacterium survives in lake water but may lose its virulence. The temperature-regulated biofilm formation by F. tularensis may play a role in colonization of vectors or for colonization of hosts, rather than for survival in aquatic environments.

Anlagda våtmarker i avrinningsområden från jordbruksmarker mottar ofta vatten med höga halter av partikelbunden fosfor. Den viktigaste processen för avskiljning av inkommande partikelbunden fosfor är sedimentation. Resuspension är en process som motverkar netto-sedimentationen av partiklar och kan således minska våtmarkers förmåga att hålla kvar fosfor. Syftet med den här studien var att undersöka om A. aquaticus påverkar resuspensionen av partiklar, och om större tätheter av A. aquaticus orsakar större turbiditet i vattenmassan. Två försök genomfördes i plastakvarier med sediment insamlat från våtmarker anlagda på lerjord. Varje försöksuppställning bestod av en behandling och en kontroll utan några djur. I det första försöket innehöll behandlingen A. aquaticus motsvarande en täthet på 2083 individer m-2 och i det andra försöket en täthet på 500 individer m-2. Turbiditeten mättes med en turbidimeter en gång per dag under sju dygn. Aktiviteten hos A. aquaticus orsakade en signifikant högre turbiditet i vattenmassan i behandlingen än i kontrollen. Turbiditeten var i genomsnitt 161 NTU i akvarier med 2083 individer m-2 och 37 NTU i akvarier med 500 individer m-2. Slutsatsen som drogs är att förekomst av A. aquaticus skulle kunna öka resuspensionen av partiklar i våtmarker. Detta kan i sin tur ha en påverkan på våtmarkers förmåga att hålla kvar fosfor som är bundet till lerpartiklar. / Constructed wetlands in agricultural catchments with clay soils often receive water with high concentrations of particle-bound phosphorus. Sedimentation of particle-bound phosphorus is the main retention process. Resuspension is a process that counteracts net sedimentation of the particles and can therefore reduce phosphorus retention in wetlands. The aim of this study was to investigate if A. aquaticus through bioturbation affects the resuspension of particles, and if a larger density of A. aquaticus causes a larger turbidity in the water column. The experimental design included plastic aquariums with sediment collected from wetlands constructed on clay soils. There were two experiments, each with a treatment and a control with no animals. In the first experiment, the treatment contained A. aquaticus at a density of 2083 individuals m-2. In the second experiment the treatment contained A. aquaticus at a density of 500 individuals m-2. Turbidity was measured with a turbidimeter once a day over the course of seven days. The bioturbation activity of the A. aquaticus caused a significantly larger turbidity in the water column in the treatment than in the control. The turbidity was on average 161 NTU in the presence of 2083 individuals m-2 and 37 NTU in the presence of 500 individuals m-2. The conclusion was that the presence of A. aquaticus can increase resuspension of particles in wetlands. This could have a negative impact on the ability of wetlands to retain phosphorus that is bound to particles.

Fosfor (P) är ofta det begränsande ämnet i akvatiska system och kan i höga mängder bidra till övergödning i sjöar och hav. För att minska tillförseln av partikelbunden fosfor som läcker från jordbruksmark kan våtmarker anläggas i avrinningsområdet. För en effektiv avskiljning är det viktigt att partiklar sedimenterar i våtmarken och stannar i sedimentet. Studier har visat att vissa karpfiskar och märlkräftor genom bioturbation kan orsaka resuspension av partiklar, samt att effekten ökar med ökad täthet. Syftet med denna studie var att undersöka om även makroevertebraten Asellus aquaticus (sötvattensgråsugga) kan orsaka resuspension av partiklar. Två hypoteser undersöktes: (i) A. aquaticus orsakar resuspension av sedimenterade partiklar; (ii) ökad täthet av A. aquaticus ger ökad resuspension. Två försök genomfördes och varje försöksuppställning bestod av 15 akvarier, varav finpartikulärt sediment och bäckvatten tillsattes till tio stycken medan fem innehöll endast bäckvatten. I hälften av akvarierna med sediment tillsattes A. aquaticus i olika täthet för försöken. Försöken pågick i sju dygn med dagliga mätningar av vattnets grumlighet. Resultat från försöken bekräftade båda hypoteserna. Genomsnittlig grumlighet efter sju dygn var 161 NTU (143 mg L-1 TSS) vid en täthet på 2083 A. aquaticus m-2 och 37 NTU (26 mg L-1 TSS) vid 500 A. aquaticus m-2. Studiens resultat indikerar att A. aquaticus kan ha en negativ påverkan på retentionen av partikelbunden fosfor i våtmarker. / Phosphorus (P) is often the limiting nutrient in aquatic systems and can in excessive quantities cause eutrophication in lakes and seas. To reduce the input of particle-bound phosphorus leaking from agricultural land, wetlands can be constructed as traps for particles. It is important that particles settle in the wetland and remain in the sediment. Studies have shown that bioturbation by e.g. common carp and amphipods can cause resuspension of settled particles, and that the effect increases with an increasing density of organisms. The purpose of this study was to examine if the macroinvertebrate Asellus aquaticus can also cause resuspension of particles. Two hypotheses were tested: (i) bioturbation by A. aquaticus will cause resuspension of particles; (ii) an increased density of A. aquaticus increases the resuspension of particles. This was tested in two experiments, each of which included 15 aquaria. In ten of these, sediment and stream water were added. To five of the aquaria with sediment, A. aquaticus were added in different densities for the two experiments. Water turbidity was measured daily for seven days. The results confirmed both hypotheses. Average turbidity after seven days was 161 NTU (143 mg L-1 TSS) at a density of 2083 m-2 and 37 NTU (26 mg L-1 TSS) at 500 m-2. The results indicate that the presence of A. aquaticus may have a negative impact on the retention of particle-bound phosphorus in wetlands.

Inland waters process large amounts of organic carbon, contributing to CO2 and CH4 emissions, as well as storing organic carbon (OC) over geological timescales. Recently, it has been shown that the magnitude of these processes is of global significance. It is therefore important to understand what regulates OC cycling in inland waters and how is that affected by climate change. This thesis investigates the constraints on microbial processing of sediment OC, as a key factor of the carbon cycling in boreal lakes. Sediment bacterial metabolism was primarily controlled by temperature but also regulated by OC quality/origin. Temperature sensitivity of sediment OC mineralization was similar in contrasting lakes and over long-term. Allochthonous OC had a strong constraining effect on sediment bacterial metabolism and biomass, with increasingly allochthonous sediments supporting decreasing bacterial metabolism and biomass. The bacterial biomass followed the same pattern as bacterial activity and was largely regulated by similar factors. The rapid turnover of bacterial biomass as well as the positive correlation between sediment mineralization and bacterial biomass suggest a limited effect of bacterial grazing. Regardless of the OC source, the sediment microbial community was more similar within season than within lakes. A comparison of data from numerous soils as well as sediments on the temperature response of OC mineralization showed higher temperature sensitivity of the sediment mineralization. Furthermore, the low rates of areal OC mineralization in sediments compared to soils suggest that lakes sediments are hotspots of OC sequestration. Increased sediment mineralization due to increase in temperature in epilimnetic sediments can significantly reduce OC burial in boreal lakes. An increase of temperature, as predicted for Northern latitudes, under different climate warming scenarios by the end of the twenty-first century, resulted in 4–27% decrease in lake sediment OC burial for the entire boreal zone.

Forests surrounding streams affect aquatic communities in numerous ways, contributing to energy fluxes between terrestrial and lotic ecosystems. The five papers in this thesis focus on woody debris, terrestrial invertebrates and light, three factors influenced by riparian zone structure, potentially affecting streams and brown trout (Salmo trutta). The individual strength of these stressors and their interactions with each other are not well studied, and their qualitative effects may differ both spatially and temporally as well as with the size-structure of specific fish populations. Using a combination of laboratory and field experiments, I examined the effects of woody debris, terrestrial invertebrates and light on prey availability and on the growth rates, diets and behavior of different size-classes of trout. My field experiments showed that addition of high densities of large wood affected trout growth in a positive way. This positive effect of large wood on trout growth may be related to prey abundance, as indicated by the high standing crop of aquatic macroinvertebrates on the wood. The positive effects on trout may also be related to decreased energy expenditures in wood habitats, as trout increased the ratio between numbers of prey captured and time spent active and that swimming activity and level of aggression decreased as wood densities were increased in a laboratory experiment. Terrestrial invertebrates are generally assumed to be a high quality prey resource for fish and my field experiments showed that reduction of terrestrial invertebrate inputs had a negative effect on trout growth. The availability of terrestrial prey in the stream was also coupled to trout diet and linked to growth, as fish with high growth rates had high proportions of terrestrial prey in their diets. Light, measured as PAR, did not have an effect on chlorophyll biomass, nor was there an effect on aquatic macroinvertebrates or trout. Hence, even if light levels were sufficient for increased photosynthesis, other factors such as low nutrient content may have limited the effects. Many of my results were dependent on fish-size. I observed, for example, that large trout had higher capture rates on surface-drifting terrestrial prey than small trout when prey densities were intermediate or high, but at low prey densities, the consumption of terrestrial prey by large and small trout were similar. Moreover, although large wood and terrestrial invertebrates affected growth of both small and large trout, the effects were generally more consistent for large trout. Although changes in riparian forests typically induce an array of interacting effects that certainly call for further research, the overall conclusion from this thesis is that many of the factors I have studied have profound effects on stream biota and trout. The positive effects from large wood also propose that adding trees to streams may partly compensate for negative effects associated with riparian deforestation.

This research aims to investigate the effects that dredging may have on benthic fauna. The dredging took place in the stream Ireån on northern Gotland during the early summer 2010. My area of research was taking place in a scenic area downstream in Ireån close to the Baltic Sea. I chose this area due to the dredging that started just upstream of this area and continued further upstream. Thus it is not the direct impact of the dredging that is the focus for this paper but the side-effect the dredging may have on the area downstream. In this research I used the M42-method and BQI- index in order to evaluate the results. The effects on the dredging were weaker than expected, with only minor changes occurring within the benthic fauna (BQI-value before dredging: 3.35, BQI-value after dredging: 3.51).

It is increasingly recognized that individuals of the same species differ from each other and influence and respond to their environment in unique ways. This thesis deals with size variation among individuals that not only are of the same species but also of similar age. Such variation may develop even when individuals are born in the same environment, i.e. within a cohort. I have studied the sources and consequences of variation within and among cohorts from egg through early ontogeny using young-of-the-year (YOY) perch (Perca fluviatilis) as study organism. In agreement with predictions based on model results only taking exploitative interactions among individuals into account, I found that the broader the initial size distributions were, the more did the degree of size variation among individuals decrease over time. Still, with initially small size variation among individuals, in several experiments also size divergence was observed. Furthermore, size variation among individuals increased more under high compared to at low densities. Increased size variation over time may be explained by size-dependent diet shifts allowing for initially larger individuals to make an early diet shift when the first resource becomes limiting. However, as size divergence also was observed in situations with only shared resources available, it can be concluded that diet shifts are not a prerequisite for size divergence in young animal cohorts. Hence, I also suggest that mechanisms not related to competition for limiting resources, such as genetic variation, stochasticity and behavioural traits must be taken into account, especially when initial size differences are small. The importance of considering size variation among individuals within cohorts was demonstrated in a study of winter mortality in YOY perch cohorts. A large individual size in autumn was shown to increase overwinter survival within cohorts. However, late summer growth rather than average body size reached in autumn explained variation in overwinter survival between cohorts. Higher accumulation to lipid reserves and accordingly lower mortality over winter was observed in years with high growth rates late in the season. In another study I showed that apparent patterns of density-dependent growth can emerge among larval fish, but rather than a result of density-dependent resource limitation this was due to variation in size-selective predation pressure. Individuals in the right end of the size distributions grew in to a high predation pressure from cannibalistic perch when cannibal density was high, coinciding with high larval perch densities. Finally, as substantial size variation among individuals can develop within cohorts, also intra-cohort cannibalism can occur. Using a physiologically structured population model it was shown that the development of size bimodality within cohorts as a result of intra-cohort cannibalism is critically dependent on long hatching periods, high victim densities and density-dependent feedbacks on shared resources. / Det faktum att individer som tillhör samma art skiljer sig från varandra och påverkar och påverkas av sin omgivande miljö på ett unikt sätt tillskrivs allt större betydelse inom ekologin. Den här avhandlingen handlar framför allt om storleksvariation mellan individer som förutom att tillhöra samma art dessutom tillhör samma årsklass. Sådan storleksvariation kan till och med utvecklas mellan individer som föds och växer upp i samma miljö (inom en kohort). Jag har studerat orsaker bakom och konsekvenser av variation inom och mellan kohorter. Som studieorganism har jag använt mig av årsyngel av abborre (Perca fluviatilis). I överensstämmelse med förutsägelser baserade på en modell som enbart tar hänsyn till konkurrens om en gemensam resurs visade det sig såväl i ett dammexperiment som i en naturlig sjö att ju bredare den initiala storleksfördelningen var desto mer minskade graden av variation i kroppsstorlek mellan individer över tid. Å andra sidan, när den initiala variationen var relativt liten observerades i flera oberoende experiment även storleksdivergens över tid mellan individer. Variationen i storlek ökade särskilt i miljöer med höga tätheter av konsumenter (abborrar). För att förstå de bakomliggande mekanismerna av sådana täthetseffekter måste man ta hänsyn till den återkoppling som sker mellan antalet konsumenter och mängden resurser. Ökad storleksvariation över tid skulle kunna förklaras med storleksberoende dietskiften som tillåter individer med en initial storleksfördel att genomgå ett tidigt dietskifte samtidigt som tillgången av den första resursen begränsar övriga individers tillväxt. Eftersom storleksdivergens även observerades i situationer där enbart en delad resurs var tillgänglig kan man dock dra slutsatsen att dietskiften inte är en förutsättning för storleksdivergens inom kohorter. Jag föreslår därför också att mekanismer som inte är relaterade till konkurrens om en begränsad resurs, såsom inneboende variation mellan individer och variation i beteendemönster bör beaktas för att förklara uppkomsten av storleksvariation, speciellt i de fall då den initiala variationen är liten. De resultat som presenteras visar på betydelsen av att ta hänsyn till storleksvariation mellan individer. Storlek efter den första tillväxtsäsongen var viktig för att förklara vilka individer inom en kohort av årsyngel som överlever sin första vinter. För att förklara variation i vinteröverlevnad mellan kohorter (mellan år och sjöar) var däremot hög tillväxt sent på säsongen (oberoende av medelstorlek på hösten) avgörande. Högre ackumulering av fettreserver och lägre mortalitet inom kohorter av årsyngel under vintern observerades under år med hög tillväxt under den senare delen av tillväxtsäsongen. I en annan studie visade jag att mönster som tyder på täthetsberoende tillväxt kan uppkomma hos fiskyngel men att detta fenomen snarare än täthetsberoende resursbegränsning förklaras av variation i storleksberoende predationstryck. De större individerna inom kohorterna växte in i ett högt predationstryck från kannibalistiska abborrar när tätheten av kannibaler var hög, något som samkorrelerade med höga tätheter av yngel. Slutligen, då en hög grad av storleksvariation mellan individer kan utvecklas inom kohorter är även kannibalism mellan individer inom en kohort möjligt. Genom att använda mig av en så kallad fysiologiskt strukturerad populationsmodell kunde jag visa att divergerande tillväxtkurvor mellan kannibaler och deras byten (vilket resulterar i storleksbimodalitet) som ett resultat av kannibalism inom kohorter är beroende av den tid det tar för ynglen att kläcka ut, antalet bytesfiskar per kannibal samt den återkoppling som finns mellan konsumenterna och deras gemensamma resurs (djurplankton).

Unproductive lakes are one of few natural landscape compartments with net release of carbon to the atmosphere. Lakes also generally decrease the net terrestrial carbon uptake, since most of the CO2 production in unproductive lakes are derived from organic carbon produced on land (e.g. in forests). High latitude lakes are predicted to be particularly affected by the global climate change. The carbon cycling in these lakes and their role in the landscape are therefore important to study. In this thesis, carbon turnover processes were studied in two lakes above the arctic circle (Lake Diktar-Erik and Lake Merasjärvi) in year 2004 and 2005. Both lakes were net heterotrophic, with large variations in CO2 concentrations both on shorter (30min) and longer (24h) time-scales. The pelagic habitat supported a major part of the net production of CO2, with larger dynamics in the CO2 production than the sediments. The CO2 variations of the surface water were related to respiration of allochthonous organic carbon, and were affected by the concentration and quality of the DOC, as well as the whole lake water temperatures, and vertical water movements. The emission of CO2 from Lake Merasjärvi was measured with the eddy covariance tech­nique. The results showed that the gas transfer rate during moderate winds were higher than expected, causing the two most commonly used models to underestimate the long term fluxes of CO2 from the lake. Taken together, the results of the thesis show that the studied lakes contributed to bring terrestrial organic carbon back into the atmosphere, driven by a substantial internal CO2 production based on mineralization of allochthonous organic carbon. Major results are that the eddy covariance technique indicated that commonly used models tend to underestimate the net release rate of CO2 from lakes to the atmosphere, and that the lake CO2 dynamics can be the results of interactions between biogeochemical and physical processes in the lake water.

According to the Water Framework Directive of the European Union, macrophytes should be used as indicators in the ecological and environmental monitoring of lakes. In the member state Sweden the Environmental Protection Agency has elaborated assessment criteria for determining lake status based on macrophytes. The main focus of this thesis is to evaluate the efficiency of the assessment criteria for macrophytes. In addition the concordance between the ecological status classes of the four quality factors included was analysed. The assessment criteria for macrophytes are based on the total phosphorus preference of the respective species. The focus is thus mainly on the nutrient level of the investigated lakes and the environmental problem monitored is eutrophication. Macrophytes are one of the five biological quality factors used for lakes. The others are phytoplankton, diatoms, benthic fauna and fish. The two latter were included in this thesis. In addition to the biological factors the chemical factor, nutrients in lakes, i.e. the total phosphorus, was included. The macrophyte composition was investigated in two eutrophic Uppland lakes: Lake Trehörningen and Lake Edasjön. Since the assessment criteria were launched in 2007 there have been problems reported regarding the outcome of the methods. The results are sometimes inconclusive for eutrophicated lakes and especially for lakes with naturally high levels of nutrients. In this study the macrophyte species composition was compared with the nutrient level of different lakes. Some species were found in equal shares in oligotrophic lakes as in eutrophic, e.g. Nymphaea candida and Nuphar lutea. Hence they were considered less suitable as elements in the method evaluated. A couple of species were present in predominantly oligotrophic (e.g. Lobelia dortmanna) or eutrophic (e.g. Hydrocharis morsus-ranae) lakes, respectively. They were regarded as better indicators since they ”preferred” lakes either poor or rich in nutrients. It is important to point out that all the other biological quality factors used, except for macrophytes, are multimetric. I conclude that more parameters are needed for evaluation of macrophytes in lakes. Tentatively, the degree of coverage of the plants and algae, the presence and degree of coverage of invasive nonnative species, lake lowerings and the consequent composition and abundance change, all should be tested as additional parameters.  A high level of concordance was verified for the status classifications of the four quality factors in lakes of oligotrophy as well as in lakes of eutrophy, i.e. no particular  pattern based on trophy level was found. The macrophyte inventories of the two Uppland lakes both resulted in a moderate ecological status for macrophytes.

Den här studien undersöker hur vegetationen förändras mellan 1979 och 2010 i området som idag är Hornborgasjöns naturreservat. Sjösänkningar i området ledde till att ett igenväxt träskområde ersatte en viktig vattenreservoar och närsaltfälla. Restaureringsarbetet under 80-talet var banbrytande och antagligen ett av vår tids mest omfattande naturvårdsarbete. Studien svarar också på om restaureringen uppnådde sitt mål och om resultatet blev som man tänkt sig. I arbetet skapades en aktuell vegetationskarta för 2010, denna jämfördes med en i arbetet digitaliserad vegetationskarta från 1979. Kartbilder skapades och justerades i ArcGIS och vegetationsytornas area framtogs för att möjliggöra en vegetationsanalys mellan kartorna. Vegetationsförändringarna i området visade sig vara omfattande mellan 1979 och 2010, där tydlig igenväxtningsmark med stora monokulturer ersattes med öppnare marker där vegetationstyperna var spridda över hela området i mindre ytor. Mångfalden i området ökade liksom vattenytan. Vattenytans stora utbredning efter restaureringen blev den stora överraskningen tillsammans med att sävvegetationen helt försvann. Undervattensvegetationens stora spridning räddade dock restaureringens syfte att gynna fågellivet trots sävruggarnas frånvaro. En ny viktig naturtyp framkom i vegetationskartan 2010, öppet vatten med död vegetation, där stora delar av vegetationstypen består av den för många hotade arter vitala biotopen död sumplövskog. / This study investigates vegetation changes in the nature reserve of Lake Hornborga between 1979 and 2010. Lowering of the surface of the lake had changed an important water reserve and nutritive salt trap into an overgrown fen and during the 80's a total pioneering restoration, perhaps the most important work of nature conservation of our time, was made. This study claims to answer if the restoration was successful and if its goals were reached. A current vegetation map for 2010 was created and adjusted in ArcGIS and this map was compared with a vegetation map of 1979. Vegetation areas were calculated to facilitate analyses between the maps. Large-scale vegetation changes have occurred between 1979 and 2010. Overgrown fenland with monoculture vegetation has been replaced by a more open landscape with a diversified growth and an open surface of water. The large extension of open surface and the disappearance of rush vegetation are two great surprises of the restoration. Thanks to a large-scale spread of underwater vegetation the aim of furthering birdlife could be reached despite the loss of rush vegetation. A new type of vegetation area has also been created, where  open water submerges dead vegetation, one of which is a biotope of dead marsh broadleaf trees, vital to many threatened species. / Vid kontakt med Lantmäteriet har muntlig bekräftelse getts gällande tillstånd av publicering av deras upphovsrätts skyddade material, där alla högskolearbeten ges sådant tillstånd vid alla Sveriges lärosäten. I mitt arbete gäller detta figur 1.