Data on rates of atmospheric deposition is limited in many montane ecosystems, where high spatial variability in meteorological, topographic, and vegetation factors contributes to elevated atmospheric inputs and to the creation of deposition hotspots. Addressing the ecological consequences of increasing deposition in these areas will require a better understanding of surface controls influencing atmospheric deposition rates at both large and small-scales. The overarching objective of this thesis research was to understand the influence of vegetation structure and canopy exposure on small-scale patterns of atmospheric sulfate, nitrate, and chloride deposition inputs to a conifer forest in the Santa Cruz Mountains, California. Throughfall ion fluxes (i.e., ions delivered in water that pass from the forest canopy to the forest floor), bulk deposition (i.e., primarily wet deposition), and rainfall data were collected during the rainy period from October 2012 to May 2013. Throughfall SO42-, Cl-, and NO3- fluxes were measured beneath eight clusters of Douglas fir (Pseudotsuga menziesii) trees (three trees per cluster) differing in tree size (i.e., diameter at breast height; DBH) and canopy exposure. In each cluster, a throughfall collector was placed 1-meter from the bole of an individual tree, for a total of 24 individual collectors. The position of each throughfall collector was recorded with a Trimble® GPS. In addition, tree height, tree diameter, and leaf area index, were measured for all trees. LiDAR data were obtained from GeoEarthScope’s Northern California Airborne LiDAR project and used to model the elevation (DEM), canopy surface height (DSM), tree height (CHM), slope, and curvature of the canopy surface across the entire study area. Over the rainy season, total throughfall flux of SO42--S, a conservative tracer of total deposition (wet + dry + fog), to Douglas fir clusters ranged from 1.44 - 3.84 kg S ha-1 wet season-1, while dry and fog deposition ranged from 0.13 -2.37 kg S ha-1 wet season-1. Total deposition to exposed mature tree clusters was 1.7-2.7 times higher than other clusters. Patterns of total Cl- fluxes (17.10 – 54.14 kg Cl- ha-1 wet season-1) resembled patterns of total SO42--S inputs. Overall, net throughfall fluxes (throughfall – bulk deposition) to Douglas fir trees clusters were more variable than total throughfall fluxes. Net SO42--S and Cl- fluxes to individual collectors increased with tree DBH and the convexity of the canopy surface. Compared to SO42--S and Cl- in throughfall, total NO3--N fluxes (0.17 - 4.03 kg N ha-1 wet season-1) were low and appeared to vary with small-scale changes in elevation. Geospatial technologies and remote sensing tools, such as LiDAR, are promising in the study of relationships between atmospheric deposition and topography (including vegetation), and in scaling-up estimates of atmospheric deposition to larger spatial scales. Understanding small-scale surface controls on atmospheric deposition has implications for different areas of research within geography, including modeling the spread of emerging infectious disease and assessing the effects of nitrogen cycling on native and invasive plant species composition.

Para identificar a influência de uma área de várzea do ribeirão do Feijão (São Carlos-SP) sobre a ciclagem de nitrogênio e sobre a qualidade da água superficial e subsuperficial, foram analisadas as características físicas e químicas da água e determinadas as taxas de nitrificação e desnitrificação dos sedimentos da várzea. A maior concentração dos compostos nitrogenados foi observada na água de interface subsuperficial da várzea, região mais ativa em termos de fluxos de água e materiais. As taxas de nitrificação variaram de 0,145 a 0,068 &#956mol N-NO3-.g-1.dia-1 e a rota metabólica predominante foi a autotrófica, na qual as bactérias utilizaram amônio como substrato. As taxas de desnitrificação tiveram um valor médio de 0,0081 nmol N2O.g-1.dia-1. Mediante um modelo de estimativa foi calculado que 70% da água que circula no Ribeirão do Feijão provém do lençol que flui sob terras secas e o restante das áreas de várzea da bacia. Foi observado que existe uma considerável redução das concentrações dos compostos nitrogenados, principalmente do amônio, desde as zonas ripárias mais distantes do curso do rio até o canal, passando pela área de várzea. O funcionamento da várzea como sistema de filtro e depuração das águas subsuperficiais que alimentam o rio foi evidenciada pelas características físicas e químicas da água do rio em relação ao uso do solo na bacia. / In order to identify the influence of a floodplain area of the Feijão stream (São Carlos-SP) on surface and subsurface water quality, the physical and chemical characteristics of the water were analyzed and the floodplain sediment\'s nitrification and denitrification rates were determined. The highest concentration of nitrogen compounds was observed at the floodplain\'s subsurface water interface it being the most active region with respect to water and solute flow. Nitrification rates varied between 0.145 and 0.068 &#956mol N-NO3-.g-1.day-1 and the autotrophic metabolic route dominated, in which bacteria use ammonia as a substrate. Denitrification rate average was 0.0081 nmol N2O.g-1.day-1. Through a model it was estimated that 70% of the water flowing in the Feijão stream came from the water table flowing under dry land, the remainder coming from the floodplain of the area. A significant reduction of nitrogen compound concentration, mainly ammonium, was observed between the more distant riparian zones and the river\'s channel going through the floodplain. The floodplain\'s action as a filtering system for the water reaching the river was brought out through the physical and chemical characteristics of the river water relative to land use in the catchment area.

O presente estudo objetiva avaliar os mecanismos de transferência de carbono entre os compartimentos atmosfera, vegetação, solo e igarapé em uma microbacia da Amazônia Ocidental. Dois igarapés drenandos, respectivamente, 2927 e 66,73 ha de floresta de terra firme, foram monitorados durante um ano. A área de estudo se encontra na zona de amortecimento de uma Unidade de Conservação de Uso Sustentável denominada Floresta Estadual do Amapá (FLOTA/AP), na região central do estado de mesmo nome. Foram coletadas as águas da chuva, da precipitação interna da floresta, do escoamento de água pelo tronco, do escoamento superficial pelo solo, da solução do solo, da água subterrânea e da água do igarapé. Os solos também foram investigados em relação a suas características físico-químicas. Para calcular a entrada e saída de C do sistema, foram determinadas as concentrações do carbono orgânico e inorgânico dissolvido (COD e CID, respectivamente) na água da chuva e do igarapé, em 16 eventos de chuva. As concentrações médias de COD na água da chuva foram de 1,6± 1,52 mg L-1, resultando em um aporte de 11,43 Kg C ha-1 ano-1. Na precipitação interna os valores médios observados foram de 9,1 ± 5,99 mg L-1, o que corresponde a um fluxo de 100,71 Kg C ha-1 ano-1. No escoamento do tronco, os valores médios observados foram de 17,4 ± 8,03 mg L-1 e no escoamento superficial do solo de 14,2 ± 6,4 mg L-1. Nos compartimentos amostrados abaixo do solo, solução do solo e água do lençol, as concentrações de COD foram relativamente mais baixas. A saída de COD pelo igarapé, os fluxos foram de 0,45 Kg C ha-1 ano-1. Em relação às concentrações de CID, o aporte pela água da chuva foi de 3,66 Kg C ha-1 ano-1, passando a 10,10 Kg C ha-1 ano-1 na precipitação interna e com uma saída pelo igarapé de 0,07 Kg C ha-1 ano-1. Os resultados mostram grande variabilidade espaço-temporal e retenção de C pelo sistema, seja na fase orgânica (COD) ou inorgânica (CID), demonstrando a importância destes processos para a compreensão do funcionamento destes ecossistemas. / This study aims to evaluate carbon transfer mechanisms between the atmosphere, vegetation, soil and stream in a microbasin of eastern Amazon. Two streams, draining respectively 2917 and 66.73 ha of \"terra firme\" forests were monitored during one year. The study area is located in a Conservation Unit named Amapá State Forest (FLOTA/AP), in the central region of the Amapá State. We sample rain water, throughfall, stemflow, soil surface flow, soil solution, groundwater and stream water. Physico-chemical characteristics of soils were also evaluated. To calculate inputs and outputs of C in this system, we determined the concentrations of dissolved organic and inorganic carbon (DOC and DIC, respectively) in rain and stream water during 16 rain events. Average concentrations of DOC in rain water were 1.6± 1.52 mg L-1, resulting in an input of 11.43 Kg C ha-1 year-1. Throughfall had average concentrations of 9.1 ± 5.99 mg L-1, which increased inputs to 100.71 Kg C ha-1 year-1. Stemflow had average concentrations of 17.4 ± 8.03 mg L-1 while those of soil surface flow were 14.2 ± 6.4 mg L-1. Bellow ground DOC concentrations were relatively lower. The export of DOC in stream water was 0.45 Kg C ha-1 year-1. In relation to DIC, the input from rain water was 3.66 Kg C ha-1 year-1, increasing to 10.10 Kg C ha-1 year-1 in throughfall and exiting the micro basin through the stream with a flux of 0.07 Kg C ha-1 year-1. The results show large spatiotemporal variations and C retention within the system, either in the organic (DOC) or inorganic (DIC) phases, showing the importance of these processes for the comprehension of the functioning of these ecosystems.

Coral reefs thrive in nutrient-deficient environments yet function among the most productive ecosystems on Earth as a consequence of the symbiosis between coral hosts and their symbiotic zooxanthellae. The symbiotic unit (holobiont) can utilize both inorganic and organic sources of nutrients for the accumulation of carbon and nitrogen required for metabolism, growth, and reproduction. An iterative model was created to describe the flux of carbon and nitrogen between a host and its algae. The model design is based on a previously published conceptual model of algal symbioses; functions and values of input parameters are based on published studies of the coral species Stylophora pistillata. The model is designed to simulate responses of the coral, zooxanthellae and the holobiont to different environmental variables, either one at a time or changing simultaneously. Simulations presented are for default values based on previously published data for S. pistillata adapted to high-light (shallow-euphotic) and low-light (deep-euphotic) environments, and for single-variable manipulations of rates of a) host feeding, b) photosynthesis, and c) dissolved inorganic nitrogen (DIN) uptake. Simulations examining feeding rates between 0% and 6.5% of host biomass indicate that biomass of both high-light and low-light adapted holobionts increase exponentially with increased feeding, with benefit to the high-light holobiont ~8 times greater than to the low-light holobiont. Increasing rates of photosynthesis illustrated that a low-light holobiont is carbon limited, is primarily dependent upon host feeding, and can benefit from a small increase in photosynthesis rate. Simulations examining rates of DIN input indicate that the high-light holobiont functions optimally when inorganic nitrogen input is very low. Increase in DIN up to 0.5% resulted in benefit to the holobiont, but more resulted in unrealistically excessive growth by the zooxanthellae until a function to maintain a fixed range for the host-zooxanthellae biomass ration function was included in the model. Simulations for the low-light holobiont did not indicate any benefit from DIN input. The model was originally designed using a spreadsheet-based program which frequently became overloaded when testing multiple variables. Modification of the model in software better designed for modeling is recommended for future work.

Microbial activity occurs year-round in Arctic soils, including during the winter when soils are frozen. From 2004 to 2008 I monitored soil microbial and nutrient dynamics in low Arctic wet and dry sedge meadows near Churchill, Manitoba. I documented a consistent annual pattern in which soil microbial biomass (MB) and soil nutrients peak in late winter, and decrease during the early stages of spring thaw, remaining in low abundance during the summer. Based on a series of experiments, resource shortages do not appear to be the cause of the microbial decline, as has been hypothesized. Observations and theoretical considerations regarding soil physical properties indicate that this decrease is driven by the influx of liquid water at thaw that brings about a rapid change in the chemical potential of water, leading to cell lysis. I have used 15N isotope tracing to show that inorganic nitrogen is taken up very quickly at thaw by the roots of the dominant plant, Carex aquatilis. This represents a critical window of opportunity for these plants, as nitrogen remains abundant only for a short time. The described annual pattern was pronounced in wet sedge sites, but some inter-annual variation is evident, for example a post-thaw soil nitrogen pulse in 2006, and low winter MB in 2008. In the dry sedge meadow, fluctuations in MB and nutrients were dampened relative to wet sites, and the annual pattern was variable, particularly after 2006. Over four years, peak winter values of soil MB and nutrient variables declined in both wet and dry sites, and this could be related to a drying trend. This work improves our understanding of the controls on decomposition and primary productivity in a system that is experiencing climate warming and increased precipitation. Changes to hydrology, carbon and nitrogen cycling, and primary productivity will have further effects on vegetation communities and higher trophic levels, including several species of migratory birds.

abstract: Humans have dramatically increased phosphorus (P) availability in terrestrial and aquatic ecosystems. As P is often a limiting nutrient of primary production, changes in its availability can have dramatic effects on ecosystem processes. I examined the effects of calcium carbonate (CaCO3) deposition, which can lower P concentrations via coprecipitation of phosphate, on P availability in two systems: streams in the Huachuca Mountains, Arizona, and a stream, Río Mesquites, in Cuatro Ciénegas, México. Calcium carbonate forms as travertine in the former and within the microbialites of the latter. Despite these differences, CaCO3 deposition led to lowered P availability in both systems. By analyzing a three-year dataset of water chemistry from the Huachuca Mountain streams, I determined that P concentrations were negatively related to CaCO3 deposition rates. I also discovered that CaCO3 was positively correlated with nitrogen concentrations, suggesting that the stoichiometric effect of CaCO3 deposition on nutrient availability is due not only to coprecipitation of phosphate, but also to P-related constraints on biotic nitrogen uptake. Building from these observations, bioassays of nutrient limitation of periphyton growth suggest that P limitation is more prevalent in streams with active CaCO3 deposition than those without. Furthermore, when I experimentally reduced rates of CaCO3 deposition within one of the streams by partial light-exclusion, areal P uptake lengths decreased, periphyton P content and growth increased, and periphyton nutrient limitation by P decreased. In Río Mesquites, CaCO3 deposition was also associated with P limitation of microbial growth. There, I investigated the consequences of reductions in CaCO3 deposition with several methods. Calcium removal led to increased concentrations of P in the microbial biomass while light reductions decreased microbial biomass and chemical inhibition had no effect. These results suggest that CaCO3 deposition in microbialites does limit biological uptake of P, that photoautotrophs play an important role in nutrient acquisition, and, combined with other experimental observations, that sulfate reduction may support CaCO3 deposition in the microbialite communities of Río Mesquites. Overall, my results suggest that the effects of CaCO3 deposition on P availability are general and this process should be considered when managing nutrient flows across aquatic ecosystems. / Dissertation/Thesis / Doctoral Dissertation Biology 2015

O presente estudo objetiva avaliar os mecanismos de transferência de carbono entre os compartimentos atmosfera, vegetação, solo e igarapé em uma microbacia da Amazônia Ocidental. Dois igarapés drenandos, respectivamente, 2927 e 66,73 ha de floresta de terra firme, foram monitorados durante um ano. A área de estudo se encontra na zona de amortecimento de uma Unidade de Conservação de Uso Sustentável denominada Floresta Estadual do Amapá (FLOTA/AP), na região central do estado de mesmo nome. Foram coletadas as águas da chuva, da precipitação interna da floresta, do escoamento de água pelo tronco, do escoamento superficial pelo solo, da solução do solo, da água subterrânea e da água do igarapé. Os solos também foram investigados em relação a suas características físico-químicas. Para calcular a entrada e saída de C do sistema, foram determinadas as concentrações do carbono orgânico e inorgânico dissolvido (COD e CID, respectivamente) na água da chuva e do igarapé, em 16 eventos de chuva. As concentrações médias de COD na água da chuva foram de 1,6± 1,52 mg L-1, resultando em um aporte de 11,43 Kg C ha-1 ano-1. Na precipitação interna os valores médios observados foram de 9,1 ± 5,99 mg L-1, o que corresponde a um fluxo de 100,71 Kg C ha-1 ano-1. No escoamento do tronco, os valores médios observados foram de 17,4 ± 8,03 mg L-1 e no escoamento superficial do solo de 14,2 ± 6,4 mg L-1. Nos compartimentos amostrados abaixo do solo, solução do solo e água do lençol, as concentrações de COD foram relativamente mais baixas. A saída de COD pelo igarapé, os fluxos foram de 0,45 Kg C ha-1 ano-1. Em relação às concentrações de CID, o aporte pela água da chuva foi de 3,66 Kg C ha-1 ano-1, passando a 10,10 Kg C ha-1 ano-1 na precipitação interna e com uma saída pelo igarapé de 0,07 Kg C ha-1 ano-1. Os resultados mostram grande variabilidade espaço-temporal e retenção de C pelo sistema, seja na fase orgânica (COD) ou inorgânica (CID), demonstrando a importância destes processos para a compreensão do funcionamento destes ecossistemas. / This study aims to evaluate carbon transfer mechanisms between the atmosphere, vegetation, soil and stream in a microbasin of eastern Amazon. Two streams, draining respectively 2917 and 66.73 ha of \"terra firme\" forests were monitored during one year. The study area is located in a Conservation Unit named Amapá State Forest (FLOTA/AP), in the central region of the Amapá State. We sample rain water, throughfall, stemflow, soil surface flow, soil solution, groundwater and stream water. Physico-chemical characteristics of soils were also evaluated. To calculate inputs and outputs of C in this system, we determined the concentrations of dissolved organic and inorganic carbon (DOC and DIC, respectively) in rain and stream water during 16 rain events. Average concentrations of DOC in rain water were 1.6± 1.52 mg L-1, resulting in an input of 11.43 Kg C ha-1 year-1. Throughfall had average concentrations of 9.1 ± 5.99 mg L-1, which increased inputs to 100.71 Kg C ha-1 year-1. Stemflow had average concentrations of 17.4 ± 8.03 mg L-1 while those of soil surface flow were 14.2 ± 6.4 mg L-1. Bellow ground DOC concentrations were relatively lower. The export of DOC in stream water was 0.45 Kg C ha-1 year-1. In relation to DIC, the input from rain water was 3.66 Kg C ha-1 year-1, increasing to 10.10 Kg C ha-1 year-1 in throughfall and exiting the micro basin through the stream with a flux of 0.07 Kg C ha-1 year-1. The results show large spatiotemporal variations and C retention within the system, either in the organic (DOC) or inorganic (DIC) phases, showing the importance of these processes for the comprehension of the functioning of these ecosystems.

Para identificar a influência de uma área de várzea do ribeirão do Feijão (São Carlos-SP) sobre a ciclagem de nitrogênio e sobre a qualidade da água superficial e subsuperficial, foram analisadas as características físicas e químicas da água e determinadas as taxas de nitrificação e desnitrificação dos sedimentos da várzea. A maior concentração dos compostos nitrogenados foi observada na água de interface subsuperficial da várzea, região mais ativa em termos de fluxos de água e materiais. As taxas de nitrificação variaram de 0,145 a 0,068 &#956mol N-NO3-.g-1.dia-1 e a rota metabólica predominante foi a autotrófica, na qual as bactérias utilizaram amônio como substrato. As taxas de desnitrificação tiveram um valor médio de 0,0081 nmol N2O.g-1.dia-1. Mediante um modelo de estimativa foi calculado que 70% da água que circula no Ribeirão do Feijão provém do lençol que flui sob terras secas e o restante das áreas de várzea da bacia. Foi observado que existe uma considerável redução das concentrações dos compostos nitrogenados, principalmente do amônio, desde as zonas ripárias mais distantes do curso do rio até o canal, passando pela área de várzea. O funcionamento da várzea como sistema de filtro e depuração das águas subsuperficiais que alimentam o rio foi evidenciada pelas características físicas e químicas da água do rio em relação ao uso do solo na bacia. / In order to identify the influence of a floodplain area of the Feijão stream (São Carlos-SP) on surface and subsurface water quality, the physical and chemical characteristics of the water were analyzed and the floodplain sediment\'s nitrification and denitrification rates were determined. The highest concentration of nitrogen compounds was observed at the floodplain\'s subsurface water interface it being the most active region with respect to water and solute flow. Nitrification rates varied between 0.145 and 0.068 &#956mol N-NO3-.g-1.day-1 and the autotrophic metabolic route dominated, in which bacteria use ammonia as a substrate. Denitrification rate average was 0.0081 nmol N2O.g-1.day-1. Through a model it was estimated that 70% of the water flowing in the Feijão stream came from the water table flowing under dry land, the remainder coming from the floodplain of the area. A significant reduction of nitrogen compound concentration, mainly ammonium, was observed between the more distant riparian zones and the river\'s channel going through the floodplain. The floodplain\'s action as a filtering system for the water reaching the river was brought out through the physical and chemical characteristics of the river water relative to land use in the catchment area.

For millions of years, the nutrient exchange symbiosis between corals and their endosymbiotic algae has formed the foundation of the ecological success of coral reefs. Yet, in recent decades anthropogenic climate change is increasingly destabilizing this symbiosis, and thus the reefs that rely on it. High-temperature anomalies have caused mass mortality of corals due to repeated coral bleaching, the expulsion or digestion of symbionts by the host during stress. Hence, in-depth knowledge of the cellular processes of bleaching is required to conceive strategies to maintain the ecological functioning of coral reefs. In this thesis, we investigated the role of symbiotic nutrient cycling in the bleaching response of corals. For this, we examined the mechanisms that underlie the functioning of the symbiosis in a stable state and how heat stress affects these metabolic interactions during coral bleaching. Our findings reveal that the functioning of the coral – algae symbiosis depends on the resource competition between host and symbionts. In a stable state, symbiotic competition for ammonium limits nitrogen availability for the algal symbiont, thereby ensuring symbiotic carbon translocation and recycling. During heat stress, however, increased metabolic energy demand shifts host metabolism from amino acid synthesis to degradation. The resulting net release of ammonium by the host, coupled with the stimulated activity of associated nitrogen-fixing microbes, substantially increases nitrogen availability for algal symbionts. Subsequently, stimulated algal growth causes selfish retention of carbon, thereby further reducing energy availability for the host. This positive feedback loop disturbs symbiotic nutrient recycling, eventually causing the collapse of carbon translocation by the symbiont. Hence, heat stress causes shifts in metabolic interactions, which directly and indirectly destabilizes the symbiosis, and ultimately undermines the ecological benefits of hosting algal symbionts for corals. In summary, this thesis shows that integrating symbiotic nutrient cycling into our conceptual understanding of coral bleaching is likely to improve our ability to predict coral bleaching in light of environmental conditions and may ultimately help to conceive new strategies to preserve coral reef functioning.

A continuously growing world population with a projected size of more than 9 billion inhabitants in the year 2040 requires huge efforts in food production while concurrently avoiding adverse side effects such as the use of pesticides or fertilizers. Among them phosphorous (P) is an important mineral fertilizer for which only few renewable sources exist and which is becoming increasingly scarce. Therefore, methods to reduce P fertilization or enhance fertilization efficiency are urgently needed. One idea is to look how plants in natural ecosystems cope with the problem of nutrient limitation. A strategy, found in almost all plant species is interaction with mycorrhizal fungi. Plants usually deliver carbohydrates (C) to the fungi and get nutrients, like phosphorous (P), in exchange. In natural ecosystems, plants usually interact with multiple fungi which perform differently in their P delivery. However, in agro-ecosystems not all these fungi are helpful. Fungi which are carbon demanding but deliver just few P, might even result in lower plant growth. Therefore a deep knowledge of the mechanisms driving the P and C dynamics is necessary. This can be gained by a computer simulation model which is possible to examine the influence of different nutrient exchange strategies in detail and make prediction how they perform. In this PhD thesis, a spatially explicit simulation model of arbuscular mycorrhizal fungi (AMF) was developed and specific laboratory experiments have been conducted and used for model calibration. This model has been used to evaluate the performance of different nutrient exchange strategies by the emerging maximum achievable fungal biomass, the C uptake rate from the plant and the P delivery rate to the plant. On this basis, three functional types could be identified: parasitic type, intermediate type, mutualistic type. In further steps these functional types have been used to investigate their performance to smooth temporal P pulses (i.e., by transforming them into a continuous P flux delivered to the plant) and to take up spatially heterogeneously distributed P. In both cases, the mutualistic type was found to perform worst and parasitic type best. Two key mechanisms for efficient resource use in spatiotemporally heterogeneous environments could be identified. By the ability of quick fungal biomass growth, AMF can efficiently explore space and store P inside the fungal mycelium. By the creation of spores that do not need C for 6 maintenance, AMF can use the saved C to grow new hypha for further spatial exploration. Through these two mechanisms AMF are able to adapt their mycelium to the spatial and temporal conditions of the P distribution and thus have the potential to largely enhance Puse efficiency. This finally might reduce the application of P fertilizers.