Northern lakes and ponds are abundant and emit large amounts of the potent climate forcer methane to the atmosphere at rates prone to change with amplified Arctic warming. In spite of being important, fluxes from surface waters are not well understood. Long-term measurements are lacking and the dominant and irregular transport mode ebullition (bubbling) is rarely quantified, which complicate the inclusion of lakes and ponds in the global methane budget. This thesis focuses on variations in emissions on both local and regional scales. A synthesis of methane fluxes from almost all studied sites constrains uncertainties and demonstrates that northern lakes and ponds are a dominant source at high latitudes. Per unit area variations in flux magnitudes among different types of water bodies are mainly linked to water depth and type of sediment. When extrapolated, total area is key and thus post-glacial lakes dominate emissions over water bodies formed by peat degradation or thermokarst processes. Further, consistent multiyear measurements in three post-glacial lakes in Stordalen, northern Sweden, reveal that seasonal ebullition, primarily driven by fermentation of acetate, can be predicted by easily measured parameters such as temperature and heat energy input over the ice-free season. Assuming that most water bodies respond similarly to warming, this thesis also suggests that northern lakes and ponds will release substantially more methane before the end of the century, primarily as a result of longer ice-free seasons. Improved uncertainty reductions of both current and future estimates rely on increased knowledge of landscape-level processes related to changes in aquatic systems and organic loading with permafrost thaw, as well as more high-quality measurements, seldom seen in contemporary data. Sampling distributed over entire ice-free seasons and across different depth zones is crucial for accurately quantifying methane emissions from northern lakes and ponds. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.</p>

Landscapes are comprised of multiple ecosystems shaped by disturbances varying in severity and source. Moderate disturbance from weather, pathogens, insects, and age-related senescence, in contrast to severe disturbances that fell trees, may increase standing woody debris and alter the contribution of coarse woody debris (CWD) to total ecosystem respiration (RE). However, woody debris dynamics are rarely examined following moderate disturbances that substantially increase standing dead wood stocks. We used an experimental manipulation of moderate disturbance in an upper Great Lakes forest to: 1) examine decadal changes in CWD stocks through a moderate disturbance; 2) quantify in situ CWD respiration during different stages of decay for downed and standing woody debris and; 3) estimate the annual contribution of CWD respiration to the ecosystem C balance through comparison with RE and net ecosystem production (NEP). We found that the standing dead wood mass of 24.5 Mg C ha-1 was an order of magnitude greater than downed woody debris stocks and a large source of ecosystem C flux six years following disturbance. Instantaneous in situ respiration rates from standing and downed woody debris in the earliest stages of decay were not significantly different from one another. Independently derived estimates of ecosystem CWD respiration of 1.1to 2.1 Mg C ha-1 yr-1 six years following disturbance were comparable in magnitude to NEP and 12.5 % to 23.8 % of RE, representing a substantial increase relative to pre-disturbance levels. Ecosystem respiration and NEP were stable following moderate disturbance even though ecosystem CWD respiration increased substantially, suggesting a reduction in the respiratory C contribution from other sources. We conclude that CWD is an essential component of the ecosystem C balance following a moderate forest disturbance.

Shrub expansion in herbaceous ecosystems is emerging as an important ecological response to global change, especially in mesic systems where increases in canopy biomass are greatest. Two consequences of woody encroachment are increases in belowground resources, such as carbon and nitrogen, and reductions in above-ground resources such as light, which affect diversity, community trajectory, and ecosystem function. My objective was to determine how expansion of the nitrogen-fixing shrub Morella cerifera affected the resource environment across a chronosequence of shrub expansion on a Virginia barrier island. I quantified changes in carbon (C) and nitrogen (N) cycling, canopy structure and understory light associated with M. cerifera expansion. Litterfall in shrub thickets exceeded litterfall for other woody communities in the same region, and due to high N concentration, resulted in a return of as much as 169 kg N ha-1 yr-1 to the soil, 70% of which was from symbiotic N fixation. Litter and soil C and N pools were 3-10 times higher in shrub thickets than in adjacent grasslands. Understory light in shrub thickets decreased to as low as 0.5% of above-canopy light. Sunflecks in shrub thickets were shorter, smaller and less intense than sunflecks in forest understories. However, relative to other shrub species such as Elaeagnus umbellata, M. cerifera was less efficient at intercepting light. Although M. cerifera had the highest leaf area index (LAI) of five shrub species studied, M. cerifera was relatively inefficient at light attenuation due to low levels of branching, steep leaf angles and a relatively shallow canopy. The shift from grassland to shrub thicket on barrier islands, and in other mesic systems, results in a significant change in canopy structure that alters understory resource availability and greatly alters ecosystem function and trajectory.

abstract: Dissolved organic matter (DOM) is an important part of aquatic foodwebs because it contains carbon, nitrogen, and other elements required by heterotrophic organisms. It has many sources that determine its molecular composition, nutrient content, and biological lability and in turn, influence whether it is retained and processed in the stream reach or exported downstream. I examined the composition of DOM from vascular wetland plants, filamentous algae, and riparian tree leaf litter in Sonoran Desert streams and its decomposition by stream microbes. I used a combination of field observations, in-situ experiments, and a manipulative laboratory incubation to test (1) how dominant primary producers influence DOM chemical composition and ecosystem metabolism at the reach scale and (2) how DOM composition and nitrogen (N) content control microbial decomposition and stream uptake of DOM. I found that differences in streamwater DOM composition between two distinct reaches of Sycamore Creek did not affect in-situ stream respiration and gross primary production rates. Stream sediment microbial respiration rates did not differ significantly when incubated in the laboratory with DOM from wetland plants, algae, and leaf litter, thus all sources were similarly labile. However, whole-stream uptake of DOM increased from leaf to algal to wetland plant leachate. Desert streams have the potential to process DOM from leaf, wetland, and algal sources, though algal and wetland DOM, due to their more labile composition, can be more readily retained and mineralized. / Dissertation/Thesis / Masters Thesis Biology 2018

Rising atmospheric CO2 concentrations have motivated efforts to better quantify reservoirs and fluxes of Earth’s carbon. Of these fluxes from the atmosphere, one that has received relatively little attention is the atmospheric carbon sink associated with carbonate mineral dissolution. Osterhoudt (2014) and Salley (2016) explored new normalization techniques to improve and standardize a process for measuring this flux over large river basins. The present research extends this work to the 490,600 km2 Ohio River drainage basin and 11 subbasins. The study estimated the DIC flux leaving these basins between October 1, 2013, and September 30, 2014, based on secondary hydrogeochemical, geologic, and climatic data. The total annual DIC flux for the Ohio River basin was estimated to be 7.54 x 1012 g carbon (C). The time-volume normalized value of DIC flux for the Ohio basin was 3.36 x 108 g C/km3 day, where the km3 refers to the amount of water available during the year. This was within 71.4% agreement with the Barren River data (Salley, 2016) and within 63.9% agreement with the Green River data (Osterhoudt, 2014). In general, normalized DIC flux values of sub-basins containing at least modest amounts (more than 8%) of exposed carbonates (Tennessee, Cumberland, Green, Kentucky, Licking, Monongahela, and Allegheny) were in strong agreement with the normalized DIC flux of the Ohio River basin, whereas inclusion of basins with little or no near surface carbonates (Wabash, Great Miami, Scioto and Kanawha) yielded poor agreement. Regression analysis yielded strong agreement between DIC flux and the normalization parameters for the carbonate-bearing sub-basins (R2 = 0.97, p =

Over the past few decades, there has been increased research focus on carbon cycling within aquatic systems, especially with the changing global climate. Inland waters play a major role in the global carbon cycle, but the fundamental features remain poorly understood, particularly the large lakes of the world. Our experimental approach assessing the carbon budget of Lake Superior, the largest freshwater lake by area, provides spatial and temporal variability that has been previously overlooked but may be critical to our understanding on the biogeochemical processes controlling the lake. Multiple stations were chosen across the lake, both nearshore and offshore, to evaluate the variability in physical mixing regimes and biogeochemical processing. Short and long-term carbon consumption measurements were coupled to assess the heterotrophic activity relative to the lability of dissolved organic carbon. Partial pressure of carbon dioxide (pCO2) was directly measured to determine the metabolic nature of the lake and the amount of carbon dioxide (CO2) that fluxes across the air-water interface. The pCO2 results were further coupled with an isotopic approach measuring oxygen-18 (δ18O) to evaluate how the metabolism of Lake Superior has changed over a decadal scale. A range of environmental factors, including temperature, photodegradation and source/quality of organic carbon, influenced short and long-term carbon consumption. In-situ pCO2 observations supported a temporal switch in metabolism from the lake being a source of CO2 in the spring to being a sink in the summer driven by biological components of the system. When the pCO2 results were coupled with the isotopic measurements over the past decade (1999-2011), Lake Superior was dominated by respiration during isothermal conditions and production during stratification. In the past decade, Lake Superior has experienced increased surface water temperatures, shifting the metabolic state to a shorter net heterotrophic period in the spring and a longer net autotrophic period in the summer. This research highlights fundamental aspects of Lake Superior’s metabolism that have been previously understudied, as well as providing key information about processes controlling its carbon budget, and giving a better understanding of how climate change will continue to impact Lake Superior.

This thesis focuses on the interactions among microbiota in clearwater lakes. Field sampling and field experiments were performed to evaluate interactions among microbiota and the importance of benthic versus pelagic microbiota in terms of biomass and production. In addition, carbon cycling in an oligotrophic clearwater lake was calculated. Biomass and production of microbiota was clearly focused to the benthic habitat. During natural nutrient concentrations growth of heterotrophic bacteria (benthic and pelagic) was coupled to production of microphytobenthos in Lake Eckarfjärden, indicating interactions between autotrophic and heterotrophic microbiota in, as well as between, habitats. At increased nutrient concentrations, growth of heterotrophic bacteria was not correlated to microphytobenthos production. This was explained by less release of dissolved organic carbon (DOC) from microphytobenthos when they got access to more nutrients. Further investigations showed different scenarios in oligotrophic clearwater lakes following increased nutrient concentrations. The interactions between microbiota may be altered following increased nutrient concentrations and the microbial mat either positively or negatively affect the pelagic microbiota. The most striking result was that the expected shift towards dominance of pelagic primary production does not necessarily occur. Major flows of carbon were identified between different habitats in the oligotrophic clearwater Lake Eckarfjärden, and the net result was that the benthic habitat provided carbon to the pelagial. High DOC concentrations in the lake together with low pelagic production are factors that would indicate net heterotrophy. Accordingly, the pelagial of Lake Eckarfjärden was net heterotrophic but when the benthic and littoral habitats were included in the calculations, the lake turned out to be net autotrophic. In conclusion, the benthic microbiota contributed significantly to the total production in the investigated lakes and had a major role in the lake metabolism. Thus, this thesis emphasises the importance of benthic microbiota in shallow clearwater lakes.

Inland waters have long been neglected in the global carbon cycle. They represent only 2,8% of the land area, but it has come clear that inland waters play a key role in the transformation of terrestrial fixed carbon to the atmosphere. Human activities do have an impact on the carbon cycling and it is important to understand how these changes affects natural biogeochemical and climatological processes. The purpose of this report was to investigate how forestry impacts the emission of carbon dioxide from boreal lakes and to evaluate which role lakes play in the global carbon cycle. The study was accomplished as a literature study and the search words that have been used are carbon cycling, carbon dioxide, forestry, boreal lakes, dissolved organic carbon and pCO2. The results show that in many studies does forestry increase the export of dissolved organic carbon from terrestrial environments to boreal lakes. This increase subsidies the net heterotrophy in boreal lakes, making them net sources of carbon dioxide to the atmosphere. The processes behind increased concentrations and emissions are however complex and factors like local topography, hydrology and climate are thought to have impacts on how much carbon dioxide that is produced at a given level of dissolved organic carbon. Forestry seems to have an increasing effect on the carbon dioxide emissions, but the key drivers behind this process are expressed differently between regions and the reasons underlying these differences remain to be explored in order to make precise global carbon models.

In aquatic ecosystems, dissolved organic matter (DOM) is an important source of detrital energy on which microorganisms rely. However, its dynamics are not well understood in an ecological context. By isolating watershed sources, the work reported in this thesis has attempted to characterize the seasonal patterns of DOM in the hyporheic zone of a temperate stream and to find the likely sources that contribute to this pool of organic carbon. Hyporheic DOM characteristics described by UV spectroscopy indicated temporal rather than spatial dependence. Excitation-emission matrices (EEMs) showed that hyporheic DOM was mainly comprised of fulvic- and humic-like fluorescence with small amounts of protein-like fluorescence. Increases in dissolved organic carbon (DOC) concentrations from birch litter isolates were greater than those from cedar litter in early autumn, but less in late autumn. Although streambed biofilm was not significant in increasing DOC concentrations, it was also a source of protein-like fluorescence.

In aquatic ecosystems, dissolved organic matter (DOM) is an important source of detrital energy on which microorganisms rely. However, its dynamics are not well understood in an ecological context. By isolating watershed sources, the work reported in this thesis has attempted to characterize the seasonal patterns of DOM in the hyporheic zone of a temperate stream and to find the likely sources that contribute to this pool of organic carbon. Hyporheic DOM characteristics described by UV spectroscopy indicated temporal rather than spatial dependence. Excitation-emission matrices (EEMs) showed that hyporheic DOM was mainly comprised of fulvic- and humic-like fluorescence with small amounts of protein-like fluorescence. Increases in dissolved organic carbon (DOC) concentrations from birch litter isolates were greater than those from cedar litter in early autumn, but less in late autumn. Although streambed biofilm was not significant in increasing DOC concentrations, it was also a source of protein-like fluorescence.