As conveyors of water and sediment, rivers play an instrumental role in landscape evolution (Turner et al., 2015). River systems were traditionally considered as passive pipes of terrestrial organic carbon (OC), but are now viewed as active sites of OC processing, redistribution and storage (Aufdenkampe et al., 2011). Floodplains are an important part of this system and have the capacity to act as sources or sinks of carbon (Zehetner et al., 2009), but most importantly active hotspots of organic matter (OM) transformation (Hoffmann et al., 2009; Zocatelli et al., 2013). POC eroded from highly-organic peat soils, may be interrupted in its transport through the fluvial system, by temporary storage on floodplain landforms (Evans and Warburton, 2005; Evans et al., 2006). It is important to investigate the fate of fluvial peatland POC, in order to fully close the terrestrial peatland carbon budget, to account for subsequent mineralisation and explore the processes that lead to redistribution and storage. The River Ashop in the southern Pennines, UK, drains the slopes of both Bleaklow and Kinder Scout which are upland plateaux, which support an extensive cover of blanket peat (Evans and Lindsay, 2010). These peatlands have been severely eroded and are vulnerable to future erosion as they are marginal to the climatic space suitable for growth of peat bogs in the UK (Clark et al., 2010). The wider peatland catchment features cohesive, organic-rich floodplains, which are atypical in an upland landscape, and thus suitable for investigation in their role in the fate of eroded carbon. OM quality was an important focus of this research into the redistribution of terrestrial organic carbon. As such, OM quality was conceptualised, by identifying how different research disciplines identify with the term, and ultimately providing a classification scheme to assist individuals in their exploration of OM character. A novel approach using ITRAX core scanning data was used to establish carbon stocks of floodplains in the River Ashop catchment. Sedimentological characteristics were insufficient to distinguish between allochthonous and autochthonous organic matter storage. However, dating was used as a rapid and accurate tool to assess carbon source on the 'off-site' floodplain, and could perhaps be used in the wider environment where there are large discrepancies between the ages of source materials. Investigations into the OM quality, provided suitably convincing evidence that substantial overbank deposition of eroded 'old' peat had occurred. Despite this, viewing these sites simply as areas of carbon storage is misleading. In fact, these systems have potentially been turning over substantial quantities of carbon to the atmosphere. Contextual information from modern-day fluvial POC fluxes showed that both 'off-site' and 'on-site' floodplains only play a minor role in storing carbon. Geomorphological events, particularly the substantial sediment flux generated from peatland erosion were critical in the formation of these floodplains. In these peatland systems, erosion, deposition and turnover of carbon are intimately linked at the landscape scale, and floodplains are a dynamic component of this system.

This study investigates how the estimated thickening of the active layer will affectthe soil organic carbon in permafrost soils. The focus lies on estimating how muchof the upper permafrost soil organic carbon will be affected by the active layerdeepening due to global warming, on what timescale the deepening will take placeand if the estimated changes differ depending on the extent of permafrost in theregion. A model made in a Geographic Information System (GIS) combines datasetsfrom The Northern Circumpolar Soil Carbon Database, field data of soil organiccarbon content (SOCC) in different permafrost soil horizons in the Usa basin anddata of recent and future active layer depth from a spatially distributed permafrostdynamics model in the Pechora River Basin. The model shows that in 1980, 75% ofthe available 0–100 cm Gelisol soil organic carbon mass (SOCM) has affected byseasonal thawing. In 2050 the proportion is increased to 86% and by 2090 almostthe whole study area has an active layer deeper than 1 meter (98%). This indicatesan increase from approximately 0.64% to 0.84% of the total 1–100 cm SOCM in thenorthern permafrost region. The change is more gradual in the isolated and thesporadic permafrost zones and more abrupt in the continuous and discontinuous regions.

The development of novel bioremediation systems has widespread benefits for human health and natural ecosystems. Optimization of such systems is only possible with a thorough understanding of the processes that drive bioremediation. This thesis developed novel understanding of carbon sources and cycling relationships for microbial communities that are integral in controlling contaminant fate in two contaminated environments. In the first case (Chapter 2), biodegradation in the soil microbial community was determined to be the primary pathway for recalcitrant petroleum pollutant removal. Microbial uptake and metabolism of petroleum hydrocarbons was conclusively demonstrated via 14C analysis of their PLFA biomarkers. This microbial community was the most 14C depleted bacterial system detected in an environmental system to date. In addition, complete mineralization of petroleum carbon was demonstrated with 14C analysis of soil COz. The second paper (Chapter 3) identified unique Phospholipid Fatty Acid (PLFA) biomarkers and stable carbon isotopic fractionation patterns for heterotrophic and autotrophic bacterial communities of an acid mine drainage (AMD) system. The characteristic isotopic fractionations observed during biosynthesis of PLF A biomarkers in autotrophic versus heterotrophic metabolic pathways provided the basis for a model capable of elucidating the relative roles of these members of the microbial community in the environment. The major implications of the knowledge developed in this thesis, are two new methods to identify microbial carbon cycling pathways and processes in contaminated environments. These advances may lead to new methods for mitigating the effects of contamination in environmental systems through better understanding of the microbial processes at the contaminated sites. / Thesis / Master of Science (MSc)

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.

Thesis advisor: Tara Pisani Gareau / Salt marshes provide important ecosystem services, including carbon sequestration. Permanently inundated ponds are prominent features in the marsh landscape, encompassing up to 60% of the total marsh area, but they are rarely considered in biogeochemical assessments. I investigated two ponds in Plum Island Estuary, MA to measure and analyze their metabolism. The ponds varied in size and vegetation cover. Oxygen concentrations and pH values were recorded in 15-minute intervals during the entire study period. The ponds regularly become hypoxic or anoxic during night. This is a problem for the estimation of respiration rates which are based on nighttime measurements. To investigate this potential underestimation, several approaches to estimate respiration were used. First, additional measurements of surface water concentrations of dissolved inorganic carbon were made. A comparison of respiration estimates based on oxygen and DIC changes during tidal isolation revealed a reasonable agreement for the most time but not during periods of high productivity during the day or late at night. At this point, oxygen concentrations are so depleted that a change in concentration – the indicator of respiration – is barely detectable. However, DIC based respiration rates indicate that respiration is occurring under these hypoxic/anoxic conditions. This saturation changes during periods of tidal inundation, when a nighttime peak in oxygen concentrations indicates that the flood water is relatively enriched in oxygen compared to the pond water. On three days, it was tested whether under these conditions the oxygen-based respiration rate was higher than under hypoxic conditions (i.e., during tidal isolation). The rates were indeed higher than those under tidal isolation but still not in the range of DIC-based rates. Overall, metabolic rates differed between the two ponds in magnitude, which is likely caused by different vegetation cover, but may be influenced by size, sampling period, and duration as well. / Thesis (BS) — Boston College, 2018. / Submitted to: Boston College. College of Arts and Sciences. / Discipline: Departmental Honors. / Discipline: Earth and Environmental Sciences.

第23回名古屋大学年代測定総合研究センターシンポジウム平成22(2010)年度報告

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Cropland management practices have traditionally focused on maximising the production of food, feed and fibre. However, croplands also provide valuable regulating ecosystem services, including carbon (C) storage in soil and biomass. Consequently, management impacts the extents to which croplands act as sources or sinks of atmospheric carbon dioxide (CO2). And so, reliable information on cropland ecosystem C fluxes and yields are essential for policy-makers concerned with climate change mitigation and food security. Eddy-covariance (EC) flux towers can provide observations of net ecosystem exchanges (NEE) of CO2 within croplands, however the tower sites are temporally and spatially sparse. Process-based crop models simulate the key biophysical mechanisms within cropland ecosystems, including the management impacts, crop cultivar, soil and climate on crop C dynamics. The models are therefore a powerful tool for diagnosing and forecasting C fluxes and yield. However, crop model spatial upscaling is often limited by input data (including meteorological drivers and management), parameter uncertainty and model complexity. Earth observation (EO) sensors can provide regular estimates of crop condition over large extents. Therefore, EO data can be used within data assimilation (DA) schemes to parameterise and constrain models. Research presented in this thesis explores the key challenges associated with crop model upscaling. First, fine-scale (20-50 m) EO-derived data, from optical and radar sensors, is assimilated into the Soil-Plant-Atmosphere crop (SPAc) model. Assimilating all EO data enhanced the simulation of daily C exchanges at multiple European crop sites. However, the individually assimilation of radar EO data (as opposed to combined with optical data) resulted in larger improvements in the C fluxes simulation. Second, the impacts of reduced model complexity and driver resolution on crop photosynthesis estimates are investigated. The simplified Aggregated Canopy Model (ACM) – estimating daily photosynthesis using coarse-scale (daily) drivers – was calibrated using the detailed SPAc model, which simulates leaf to canopy processes at half-hourly time-steps. The calibrated ACM photosynthesis had a high agreement with SPAc and local EC estimates. Third, a model-data fusion framework was evaluated for multi-annual and regional-scale estimation of UK wheat yields. Aggregated model yield estimates were negatively biased when compared to official statistics. Coarse-scale (1 km) EO data was also used to constrain the model simulation of canopy development, which was successful in reducing the biases in the yield estimates. And fourth, EO spatial and temporal resolution requirements for crop growth monitoring at UK field-scales was investigated. Errors due to spatial resolution are quantified by sampling aggregated fine scale EO data on a per-field basis; whereas temporal resolution error analysis involved re-sampling model estimates to mimic the observational frequencies of current EO sensors and likely cloud cover. A minimum EO spatial resolution of around 165 m is required to resolve the field-scale detail. Monitoring crop growth using EO sensors with a 26-day temporal resolution results in a mean error of 5%; however, accounting for likely cloud cover increases this error to 63%.

The Amazon rain forest plays an important role in regional and global biogeochemical cycling, but the region may undergo an increase in the frequency and severity of drought conditions driven by global climate change, regional deforestation and fire. The effects of this drought on carbon cycling in the Amazon, particularly below-ground, are potentially large but remain poorly understood. This thesis examines the impacts of seasonal and longer-term drought upon ecosystem carbon allocation and cycling at an Amazon rain forest site with a particular focus upon below-ground processes. Measurements are made at three one-hectare forest plots with contrasting soil type and vegetation structure, to observe responses across a range of Amazon primary forest types. A fourth plot is subjected to partial rainfall exclusion to permit measurement of forest responses to a wider range of soil moisture levels than currently exists naturally. An analysis of the number of samples required to accurately quantify important ecosystem carbon stocks and fluxes is used to guide the sampling strategy at the field site. Quantifying root dynamics, in particular, presents methodological challenges. Thus, I critically review existing methods, and develop techniques to accurately measure root standing biomass and production. Subsequently, these techniques are used to record root responses, in terms of standing biomass, production, morphology, turnover and nutrient content, to variation in soil moisture across the four rain forest plots. There is substantial environmental variation in root characteristics. However, several responses remain consistent across plots: root production of biomass, length, and surface area, is lower where soil is dry, while root length and surface area per unit mass show the opposite pattern. The other major component of the below-ground carbon cycle is soil carbon dioxide efflux. I partition this efflux, on each plot, into contributions from organic ground surface litter, roots and soil organic matter, and investigate abiotic and biotic causes for observed differences within and between plots. On average, the percentage contribution of soil organic matter respiration to total soil carbon dioxide efflux declines during the dry season, while root respiration contribution displays the opposite trend. However, spatial patterns in soil respiration are not directly attributable to variation in either soil moisture or temperature. Instead, ground surface organic litter mass and root mass account for 44 % of observed spatial heterogeneity in soil carbon dioxide efflux. Finally, information on below-ground carbon cycling is combined with aboveround data, of canopy dynamics and stem wood production and mortality, to analyze the potential effects of drought upon carbon cycling in an Amazon forest ecosystem. Comparison of the rainfall exclusion plot with a similar, but unmodified, control plot reveals potentially important differences in tree carbon allocation, mortality, reproduction, soil respiration and root dynamics. The apparent net consequence of these changes is that, under drier conditions, the amount of CO2 moving out of the forest and into the atmosphere is diminished. This synthesis of above-ground and below-ground data advances understanding of carbon cycling in rain forests, and provides information which should allow more accurate modelling of the response of the Amazon region to future drought. Additional measurements at other sites, and of other ecosystem carbon fluxes, should further refine modelling predictions.

This work aimed to contribute to the understanding of tree - grass inter-cropping interactions so that the productivity and sustainability of extensive livestock husbandry can be increased. The work was carried out in the context of a small farm in Oaxaca, Mexico, where increases in productivity are limited by shortage of capital and where the tree component would be used as green manure. It is difficult to investigate the effectiveness of such a system by only using conventional field trials. I constructed a mathematical model to simulate how the main components of the system function under conditions that would not be evaluated in the field. Issues such as how many trees to plant and what tree species combine with grass cattle and environment, can be answered with the model. The particular features of the model are: 1) It describes an agro-ecosystem where trees perform several biological functions like nitrogen capture for use in the silvopastoral system, 2) It links grass and trees with the animal and 3) Nutrient availability depends mainly on soil organic matter decomposition and mineralisation rather than on external inputs. The present research consisted of 1) constructing the model prototype using data from the literature, 2) conducting field experiments to investigate the actual performance of the silvopastoral system, 3) perform laboratory research and greenhouse experiments complementarily to the field experiments and 4) elaborate on the carbon and nitrogen balance of the silvopastoral experiment, by combining research results and the mathematical model. The field experiment consisted of an array of 13 plots with one of the tree species Gliricidia sepium, Leucaena leucocephala, Delonix regia and Lysiloma auritum in a gradient of plant densities within a Brachiaria decumbens paddock. Results showed that the presence of trees in pastures is potentially useful for retaining nitrogen and carbon that would be lost in the grass mono-crop. Trees did not incorporate nitrogen through biological fixation, perhaps because the lack of adequate nodulation and they did not established their rooting systems to a depth beyond the grass roots (> 1.20m) so as to recover leached nutrients. However, trees produced mulch that was rich in nitrogen (3.8%) and whose decomposition rate ensures a slow release to prevent leaching. At the plant density used, the tree population caused no harm to grass as to production and nutritive value. Further increments in tree density in order to improve the potential for nitrogen capture should be evaluated in terms of the reduction of grass production. Several biological attributes of the species were determined, in some cases for the first time: biomass productivity, specific leaf area, nutritive value, phenolic content, root biomass, grass root longevity, root vertical distribution, etc. Such characterisation is useful for the understanding of the system inter-cropping and specially for the parameterisation of the silvopastoral model. Even though the mixtures proved able to survive for the span of the experiment, the sustainability of tree - grass inter-cropping as to the stabilisation of soil fertility requires longer monitoring. Other limiting factors such as phosphorus availability and the management of grazing systems have to be incorporated for an adequate evaluation of the silvopastoral system.