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<p>Investigating the presence of microbial communities in the Earth's deep terrestrial subsurface and the metabolic processes taking place in these environments provides insight into the some of the ultimate limits for life on Earth, as well as the potential for microbial life to exist within the subsurface of other planetary bodies. This Master's thesis project utilized phospholipid fatty acid (PLFA) analysis, in combination with carbon isotope analyses (δ¹³C and Δ¹⁴C), to explore the presence and activity of microbial communities living within deep terrestrial subsurface fracture water systems and low permeability, deep sedimentary rocks. Deep fracture water systems, ranging from 0.9 to 3.2 km below land surface, were sampled for microbial communities via deep mine boreholes in the Witwatersrand Basin of South Africa. PLFA concentrations revealed low biomass microbial communities, ranging from 2x10¹ to 5x10⁴ cells per mL and the PLFA profiles contained indicators for environmental stressors, including high temperatures and nutrient deprivation. δ¹³C and Δ¹⁴C analyses of PLFAs and potential carbon sources (dissolved inorganic carbon (DIC), dissolved organic carbon (DOC) and methane) identified microbial utilization of methane in some systems and utilization of DIC in others. Evidence for microbial oxidation of methane and chemoautotrophy in these systems is consistent with a self-sustaining deep terrestrial subsurface biosphere that is capable of surviving independent of the photosphere. Viable microbial communities were also identified within deep (334 to 694 m depth) sedimentary rock cores sampled from the Michigan Basin, Canada. PLFA analyses revealed microbial cell densities ranging from 1-3 x 10⁵ cells/mL and identified PLFA indicators for environmental stressors. These results demonstrate the ubiquity of microbial life in the deep terrestrial subsurface and provide insight into microbial carbon sources and cycling in deep microbial systems which may persist in isolation over geologic timescales.</p> / Master of Science (MSc)

Continental margin sediments play an important role in marine biogeochemical cycles, partly due to high primary production rates and efficient export of organic matter to sediments in margin environments. This thesis presents studies of solute exchange in fine-grained sediments representative of slope and rise environments, and carbon and nitrogen cycling in sandy sediments dominant in continental shelves worldwide. Results of these studies advance understanding of the role of benthic processes on marine ecosystems. In fine-grained sediments, solute exchange by diffusion, biological mixing and bioirrigation can be quantified using in situ flux chambers with inert tracer additions. Mechanistic models of chamber tracer transport across the seabed indicate that in organic-rich sediments, bioirrigation and mixing dominate over a wide range of bottom water oxygen levels, reflecting the patchiness and versatility of benthic macrofaunal communities. Positive correlations between benthic oxygen and tracer fluxes appear site-specific. Reliable chamber volume estimates derived from mechanistic models reveal that empirical fits to chamber tracer datasets may overestimate chamber volume and benthic solute fluxes. The biogeochemistry of sandy, highly permeable sediments that dominate continental shelves is largely unknown because of the difficulty in sampling and studying them under natural conditions. Novel sediment reactors were developed and used to mimic in situ porewater advection and natural sedimentary conditions. Compositional changes of natural seawater, with and without the addition of

The tropical forests on the island of Borneo are among of the richest in the world in terms of tree diversity, and their capacity to store a large reservoir of carbon. The Southeast Asian forests are fundamentally different from Neotropical and African forests, with their single-family dominance by dipterocarp trees, and with inherently greater stature and biomass. The carbon productivity and allocation in Asian tropical forests is still poorly quantified, and their responses to environmental drivers are still poorly understood. Almost all recent advances in tropical forest carbon cycling research have occurred in the Neotropics, with very few studies in Asia. The principal aim of this thesis is to quantify the carbon budget of a lowland dipterocarp forest in the Lambir Hills National Park, Miri, Sarawak, Malaysian Borneo. I examined and explored the productivity and carbon cycling processes and their responses to environmental factors across two major and contrasting soil types, in particular the clay and sandy loam soils. I recorded and analysed the Net Primary Productivity (NPP) and respiration for the above- and below-ground components, and observed the responses to seasonal variation and environmental drivers. Total soil respiration was relatively high and contributed a great deal to ecosystem respiration. Variation in soil respiration rates appeared closely related to soil moisture content. I found a strong diurnal cycle in soil respiration. On the basis of the first soil carbon dioxide (CO2) efflux partitioning study undertaken in a tropical forest, the diurnal cycle in total soil respiration appeared to be entirely driven by the diurnal cycle in litter respiration, and in turn litter is strongly controlled by moisture. There was little seasonal variation in allocation of net primary productivity (NPP), but there was evidence showing potential inter-annual variability for several components of NPP. Further, the allocation of NPP showed a strong seasonal shift between the forest plots on clay and sandy loam soils. Combining all the data measured and obtained in this D.Phil. thesis, the overall carbon budget assessed in this lowland dipterocarp forest showed a high level of agreement with other studies in Asia using micrometeorological techniques and the situation appears to be comparable to tropical forests in Amazonia. The key difference is that the aboveground NPP is higher and is the largest component contributing to the overall carbon budget, with relatively higher carbon use efficiency (CUE). The lowland dipterocarp forest in Lambir shows higher allocation in the above-ground NPP, and there were also differences in NPP and its allocation between sandy and clay-rich plots.

In dieser Studie wird ein neues Modul “CLM-Palm” für mehrjährige Nutzpflanzen zur Modellierung einer funktionellen Gruppe (plant functional type) für Ölpalmen im Rahmen des Community Land Models (CLM4.5) entwickelt, um die Auswirkungen der Transformation eines tropischen Waldes in eine Ölpalmenplantage auf die Kohlenstoff-, Wasser- und Energieflüsse zwischen Land und Atmosphäre zu quantifizieren. Um die Morphologie der Ölpalme möglichst detailgetreu darzustellen (das heißt, dass ungefähr 40 Phytomere einen mehrschichtigen Kronenraum formen), wird in dem Modul CLM-Palm eine phänologische und  physiologische Parametrisierung auf Skalen unterhalb des Kronraums eingeführt, so dass jedem Phytomer sein eigenes prognostisches Blattwachstum und seine Erntekapazität zugeordnet wird, während Stamm und Wurzeln gemeinsam genutzt werden. Das Modul CLM-Palm wurde ausschließlich für Ölpalmen getestet, ist aber auch für andere Palmarten (z. B. Kokospalmen) interessant.  Im ersten Kapitel dieser Arbeit werden Hintergrund und Motivation dieser Arbeit vorgestellt. In Kapitel 2 wird die Entwicklung des Haupt- bzw. Kernmodells beschrieben,  inklusive Phänologie und Allokationsfunktionen zur Simulation des Wachstums und des Ertrags der Palme PFT, wodurch die Basis zur Modellierung  der biophysikalischen und biogeochemicalischen Kreisläufe innerhalb dieser Monokultur bereitgestellt wird. Die neuen Parameter für die Phänologie und die Allokation wurden sorgfältig mit Feldmessungen des Blattflächenindexes (LAI), des Ertrags und der Nettoprimärproduktion (NPP) verschiedener Ölpalmenplantagen auf Sumatra (Indonesien) kalibriert und validiert. Die Validierung zeigte die Eignung von CLM-Palm zur adäquaten Vorhersage des mittleren Blattwachstums und Ertrags für verschiedene Standorte und repräsentiert in ausreichendem Maß die signifikante Variabilität bezüglich des Stickstoffs und Alters von Standort zu Standort.  In Kapitel 3 wird die weitere Modellentwicklung und die Implementierung eines Norman-Mehrschichtmodells für den Strahlungstransport vorgestellt, das an den  mehrschichtigen Kronenraum der Ölpalme angepasst ist. Dieses Norman-Mehrschichtmodell des Strahlungstransports zeigte im Vergleich zu dem in CLM4.5 implementierten Standardmodell (basierend auf großen Blättern) bei der Simulation der Licht-Photosynthese-Kurve leichte Verbesserungen und hat  lediglich marginale Vorteile gegenüber dem ebenfalls in CLM4.5 implementierten alternativen statistischen Mehrschichtmodell.  Dennoch liefert das Norman-Modell eine detailliertere und realistischere Repräsentation des Belaubungszustands wie etwa dem dynamischen LAI, der Blattwinkelverteilung in verschiedenen Höhen, und ein ausgewogeneres Profil der absorbierten photosynthetisch aktiven Strahlung (PAR). Die Validierung mit Hilfe der Eddy-Kovarianz Flussdaten zeigte die Stärke von CLM-Palm bei der Simulation der Kohlenstoffflüsse, offenbarte aber auch Abweichungen in der simulierten Evapotranspiration (ET), dem sensiblen und dem latenten Wärmefluss (H und LE). Eine Reihe von hydrologischen Messungen im Kronenraum wird in Kapitel 4 beschrieben. Dies beinhaltet eine Adaption des in CLM4.5 eingebauten Standardmodells für Niederschlag, Interzeption und Speicherfunktionen für die speziellen Merkmale eines Ölpalmen-Kronenraums. Die überarbeitete Hydrologie des Kronenraums behob die Probleme bei der Simulation der Wasserflüsse (ET und Transpiration im Kronenraum) und verbesserte die Energieaufteilung zwischen H und LE. Kapitel 5 dokumentiert die Implementierung eines neuen dynamischen Modells für Stickstoff (nitrogen, N) in CLM-Palm zur Verbesserung der Simulation der C- und N-Dynamik, insbesondere mit Bezug auf den N-Düngeeffekte in landwirtschaftlich genutzten Systemen. Das dynamische N-Modell durchbricht die Limitierung des Standardmodells in CLM4.5, mit fixierter C-N-Stöchiometrie und erlaubt die Variation des C:N-Verhältnisses in lebendem Gewebe in Abhängigkeit der N-Verfügbarkeit und dem N-Bedarf der Pflanze.  Eine Reihe von Tests bezüglich der Düngung zeigte beispielhaft die Vorteile des dynamischen N-Modells, wie zum Beispiel die Verbesserung des Netto-Ökosystemaustauschs (net ecosystem exchange, NEE), ein realistischeres C:N-Verhältnis im Blatt, eine verbesserte Repräsentation der Effizienz des Stickstoffeinsatzes (nitrogen-use efficiency, NUE), sowie der Effekte von Düngung auf Wachstum und Ertrag. Abschließend wird in Kapitel 6 eine Anwendungsstudie gezeigt, in der die zentralen Modellentwicklungen aus den vorangegangenen Kapiteln verwendet werden. Eine junge und eine  erntereife Ölpalmenplantage sowie ein Primärregenwald wurden simuliert und verglichen. Sie wiesen klare Unterschiede in den C-Flüssen und in den biophysikalischen Merkmalen (z.B. ET und Oberflächentemperatur) auf. Ölpalmenplantagen können durch Wachstumsentwicklung (im Alter von etwa 4 Jahren)  ebenso hohe und darüber hinausgehende C-Assimilation und Wassernutzungsraten erreichen wie Regenwälder, haben jedoch im Allgemeinen eine höhere Oberflächentemperatur als eine bewaldete Fläche – dies gilt auch für erntereife Plantagen. Eine Simulation des Übergangs, die zwei Rotationsperioden mit Neubepflanzungen alle 25 Jahre umspannt, zeigte dass der Anbau von Ölpalmen auf längeren Zeitskalen lediglich in etwa die Hälfte des ursprünglichen C-Speichers der bewaldeten Fläche vor dem Kahlschlag  rückspeichern kann. Das im Boden gespeicherte C nimmt in einer bewirtschafteten Plantage aufgrund des begrenzten Streurücklaufs langsam und graduell ab. Insgesamt reduziert die Umwandlung eines Regenwaldes in eine Ölpalmenplantage die langfristigen C-Speicher und die Kapazität der Fläche zur C-Sequestrierung und trägt potentiell zur Erwärmung der Landoberfläche bei – trotz des schnellen Wachstums und der hohen C-Assimilationsrate einer stark gedüngten Plantage. Zur Einschätzung der regionalen und globalen Effekte der Ausbreitung der Kultivierung von Ölpalmen auf die Austauschprozesse zwischen Land und Atmosphäre und auf das Klima ist es notwendig eine Upscaling-Studie durchzuführen.

Anthropogenic activities perturb the global carbon and nitrogen cycle with large implications for the earth’s climate. Land use activities deliver excess carbon and nitrogen to aquatic ecosystems. In the boreal biome, this is mainly due to forestry and atmospheric deposition. Yet, impacts of these anthropogenically mediated inputs of carbon and nitrogen on the processing and emissions of greenhouse gases from recipient streams and lakes are largely unknown. Understanding the ecosystem-scale response of aquatic greenhouse gas cycling to land use activities is critical to better predict anthropogenic effects on the global climate system and design more efficient climate change mitigation measures. This thesis assesses the effects of forest clearcutting and nitrate enrichment on greenhouse gas emissions from boreal inland waters. It also advances methods to quantify sources and sinks of these emissions. Short-term clearcut and nitrate enrichment effects were assessed using two whole-ecosystem experiments, carried out over four years in nine headwater catchments in boreal Sweden. In these experiments, I measured or modeled air-water fluxes of carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O), combining concentration, ebullition and gas-transfer velocity measurements in groundwater, streams and lakes. By using Swedish national monitoring data, I also assessed broad-scale effects of forest clearcutting by relating CO2 concentrations in 439 forest lakes to the areal proportion of catchment forest clearcuts. To improve quantifications of CO2 sources and sinks in lakes, I analyzed time series of oxygen concentrations and water temperature in five lakes on conditions under which whole-lake metabolism estimates can be inferred from oxygen dynamics given the perturbing influence of atmospheric exchange, mixing and internal waves. The experiments revealed that aquatic greenhouse gas emissions did not respond to nitrate addition or forest clearcutting. Importantly, riparian zones likely buffered clearcut-induced increases in groundwater CO2 and CH4 concentrations. Experimental results were confirmed by monitoring data showing no relationship between CO2 patterns across Swedish lakes and clearcut gradients. Yet, conclusions on internal vs. external CO2 controls largely depended on whether spatially or temporally resolved data was used. Partitioning CO2 sources and sinks in lakes using time series of oxygen was greatly challenged by physical transport and mixing processes. Conclusively, ongoing land use activities in the boreal zone are unlikely to have major effect on headwater greenhouse gas emissions. Yet, system- and scale specific effects cannot be excluded. To reveal these effects, there is a large need of improved methods and design of monitoring programs that account for the large spatial and temporal variability in greenhouse gas dynamics and its controls by abiotic and biotic factors.

Living (biotic) and non-living (abiotic) factors drive the function of ecosystems across a variety of scales from the root-soil interface to the watershed. Biotic and abiotic global change pressures such as increasing temperature and invasive species are shifting how ecosystems function. Thus, exploring and understanding how these factors shape function across the landscape is an important research area. For example, climate change both directly and indirectly affects soil microbial functions – such as carbon mineralization and nitrogen transformations – through increasing activity under warming and altering inputs to the soil through species composition changes. Mountains provide a useful tool for studying relationships among biotic and abiotic factors because climate and species diversity shift along gradients. Here, I measured carbon and nitrogen soil processes as well as microbial extracellular enzyme activity along an elevational gradient to explore how changes in climate, edaphic properties, and biotic composition affects ecosystem function. As expected, climate and species composition varied in predictable ways along the gradient – actual evapotranspiration declined, and conifer dominance increased. Soil functions also shifted along the gradient. Potential carbon mineralization increased with elevation and with conifer dominance. Potential nitrogen mineralization rates increased with elevation and with conifer dominance. Surprisingly, there were few predictors for potential soil nitrification, which increased only with soil functional diversity. While temperature and moisture availability drive ecosystem function at broad scales and biotic factors typically drive function at the regional scale, we saw that function of soils at the mountain watershed scale was best explained by a combination of both abiotic and biotic factors.

Coastal wetlands store immense amounts of carbon (C) in vegetation and sediments, but this store of C is under threat from climate change. Accelerated sea level rise (SLR), which leads to saltwater intrusion, and more frequent periods of droughts will both impact biogeochemical cycling in wetlands. Coastal peat marshes are especially susceptible to saltwater intrusion and changes in water depth, but little is known about how exposure to salinity affects organic matter accumulation and peat stability. I investigated freshwater and brackish marsh responses to elevated salinity, greater inundation, drought, and increased nutrient loading. Elevated salinity pulses in a brackish marsh increased CO2 release from the marsh but only during dry-down. Elevated salinity increased root mortality at both a freshwater and brackish marsh. Under continuously elevated salinity in mesocosms, net ecosystem productivity (NEP) was unaffected by elevated salinity in a freshwater marsh exposed to brackish conditions (0 à 8 ppt), but NEP significantly increased with P enrichment. Elevated salinity led to a higher turnover of live to dead roots, resulting in a ~2-cm loss in soil elevation within 1 year of exposure to elevated salinity. When exposing a brackish marsh to more saline conditions (10 à 20 ppt), NEP, aboveground biomass production, and root growth all significantly decreased with elevated salinity, shifting the marsh from a net C sink to a net C source to the atmosphere. Elevated salinity (10 à 20 ppt) did not increase soil elevation loss, which was already occurring under brackish conditions, but when coupled with a drought event, elevation loss doubled. My findings suggest these hypotheses for the drivers and mechanisms of peat collapse. When freshwater marshes are first exposed to elevated salinity, soil structure and integrity are negatively affected through loss of live roots within the soil profile, leaving the peat vulnerable to collapse even though aboveground productivity and NEP may be unaffected. Subsequent dry-down events where water falls below the soil surface further accelerate peat collapse. Although saltwater intrusion into freshwater wetlands may initially stimulate primary productivity through a P subsidy, the impact of elevated salinity on root and soil structure has a greater deleterious effect and may ultimately be the factors that lead to the collapse of these marshes.

Ongoing climate change has emerged as a major scientific challenge in the current century. Grassland ecosystems are considered net carbon (C) sinks to mitigate climate change. However, they are in turn, influenced by climate change and management practices, providing feedback to climate change via soil microbial community and biogeochemical fluxes. In this thesis, I examined the impact of warming, altered precipitation, and defoliation on soil microbial composition and function, C and N dynamics, and fluxes in soil respiration (CO2), nitrous oxide (N2O) and methane (CH4), together with other belowground ecosystem functions, within two ecosites in a northern native temperate grassland in central Alberta, Canada, over a two-year period. Fungi-to-bacteria ratio was not affected by climatic parameters or defoliation, indicating a high degree of resistance in the below ground community to the treatments imposed. However, C substrate utilization was influenced by warming and defoliation, as was soil microbial biomass. In contrast, soil respiration (or C loss) was not. Soil respiration acclimatized rather quickly to warming, and N2O and CH4 effluxes showed minor responses to warming at both ecosites, regardless of defoliation. These results suggest warming is unlikely to lead to positive climate change feedback due to soil-based responses, regardless of ongoing land use. However, altered precipitation ( 50%) demonstrated greater impacts on C and N fluxes relative to warming and defoliation. Increased precipitation stimulated soil C loss to the atmosphere, potentially generating positive feedback for climatic warming in this northern temperate grassland. / Soil Science