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.

Penguin colonies from permanently cold environments have a strong impact on their surrounding ecosystem because their excrements provide ample nutrients to the soils and sediments. The high phosphate content of the penguin guano directly affects primary productivity. However, phosphate solubility is dependent on the presence of iron and other metals, which can form stable PO4-rich minerals. Phosphate can also be sorbed onto minerals, including iron oxides. The present study investigated the biogeochemistry of phosphorus in a 42 cm-deep soil profile on Gardiner Island in Antarctica in order to assess the effect of penguin excrements on P partitioning in the solid and aqueous phases. The results indicate that the porewaters were slightly acidic (pH 5-6) and contained extremely high levels of dissolved organic carbon (DOC; 120 mM), PO4 (120 mM), SO4 (27 mM), NO3 (18 mM), Cl (320 mM), F (2 mM), Sr (0.10 mM), Ca (18 mM) and Mg (150 mM) at the top of the soil profile. Dissolved iron concentrations were generally low (< 0.04 mM) and increased at a depth of 15-20 cm and at the bottom of the profile. Chemical extraction revealed the presence of two zones of reactive phosphorus (P-ascorbate extractable fraction) in the soil profile, i.e., at the surface and between 16 and 20 cm. Enriched reactive and crystalline iron fractions were also present at a depth of 16-20 cm, but fluctuated throughout the profile. The Fe(II)/Fe(III) molar ratio of the soil was greater than 1 at the surface of the profile and declined with depth. X-ray diffraction analysis showed that the soil likely contained berlinite, strengite and vivianite, along with silicates and quartz. Saturation index calculations also indicated that Ca and Mg-rich phosphate minerals were likely present in the soil. Based on the above results, the presence of penguin colonies on Gardiner Island strongly impacted the geochemical and mineralogical composition of the soil, as observed in other studies on bird guano impacted (ornithogenic) soils. In addition, the presence of both Fe(II) and Fe(III) points to the fact that the soil undergos redox changes, likely as a result of seasonal water table fluctuations. Microcosm experiments with selected samples from the soil profile and an iron-reducing bacterium indeed showed that iron and phosphorus were released into solution as a result of microbial iron reduction. However, abiotic systems also showed a release of phosphorus indicating that non Fe-rich phosphate minerals are soluble under the conditions prevailing in the growth medium.

It is government policy that the UK’s intermediate level radioactive wastes (ILW) will be disposed of in a deep geological disposal facility (GDF), where cementitious materials will be ubiquitous. After ILW disposal, groundwater ingress through the engineered facility is expected, forming a hyperalkaline plume from the cementitious materials into the surrounding host rock. This will form a persistent, high pH, “chemically disturbed zone” over timescales of 105 - 106 years, that will evolve from pH >13 to pH 10 over time. In the deep subsurface, microbial processes, particularly metal reduction may immobilise redox active radioactive contaminants in the waste, yet these reactions remain poorly characterised under these extreme conditions. In this project, microbiologically-mediated Fe(III) reduction was explored under alkaline conditions in sediment from a lime workings site in Buxton, UK, as an analogue for an ILW impacted subsurface environment. In addition, the impact of these processes on radionuclide (U, Tc and Np) behaviour was considered. Microcosms were set up using sediments taken from the site, adjusted to pH 10, augmented with electron donor (organic acids with yeast extract) and Fe(III), U(VI), Tc(VII) or Np(V) as electron acceptors. Biogeochemical processes were monitored using geochemistry, microbial ecology and X-ray absorption spectroscopy (XAS) techniques. A cascade of microbial reduction processes occurred at pH 10 – 10.5 in all microbially active systems. In Fe(III) enriched systems, the dominant post-reduction mineral phase was magnetite and the rate and extent of Fe(III) reduction was increased in the presence of extracellular (AQDS, Aldrich humic acid) and endogenous (riboflavin) electron shuttles. In U(VI) supplemented sediment systems, partial U(VI) reduction occurred to a non-uraninite phase, which was susceptible to reoxidation by air (O2) and nitrate. By contrast, in Fe(III)-augmented microcosms, more complete U removal to solids was noted, with uraninite identified as the end product, which was also reoxidised by air (O2) and nitrate. In these experiments there was, however, evidence to suggest that uranium was associated with the reoxidised Fe(III) mineral. In Tc supplemented microcosm experiments, complete Tc(VII) reduction occurred in systems with and without added Fe(III). In the microcosms with no added Fe(III) however, only partial Tc removal from solution occurred, despite evidence for complete reduction, suggesting that soluble or colloidal Tc(IV) may be present. Moderate Tc reoxidation occurred with air (O2) in both systems with and without added Fe(III) however no Tc remobilisation occurred during reoxidation with added nitrate. XAS on Fe(III) enriched sediments that had been microbially reduced and then re-oxidised by air, indicated that Tc may be associated with the reoxidised Fe mineral phase in these experiments. In the Np experiments, significant Np(V) sorption to sediments with and without added Fe(III) occurred initially, followed by Np(V) bioreduction to Np(IV). In all experiments, microbial (16S rRNA gene) profiling suggested a role for novel Gram-positive bacteria in Fe(III) and radionuclide reduction. These results highlight the significance of microorganisms on radionuclide biogeochemistry at high pH and have implications for the safe disposal of intermediate level nuclear wastes.

Coastal oceans play an important role in the carbon cycle and are hotspots of ocean primary production and ocean acidification. These coastal regions are strongly influenced by rives, especially in the Arctic. Despite the importance of the riverine delivery of carbon and nutrients, their effect on the Arctic Ocean is still poorly understood due to hostile conditions and the consequently low number of observations. This thesis aims at improving our understanding of the influence of Arctic riverine delivery of carbon and nutrients by using ocean biogeochemical models.The first part of the thesis evaluated the model skills of the ocean biogeochemical model NEMO-PISCES in the Arctic Ocean. By analyzing model results at different horizontal resolutions, the importance of lateral influx from the adjacent oceans for anthropogenic carbon cycle in the Arctic Ocean wasdemonstrated. These results were then used to adjust a previously published data-based estimate of anthropogenic carbon storage in the Arctic Ocean and the corresponding ocean acidification.In the second part, a pan-Arctic observation-based dataset of riverine carbon and nutrient fluxes was created. This dataset was then used to force the ocean biogeochemical model and the river fluxes were quantified. River fluxes have been shown to sustain up to 24% of Arctic Ocean primary production, to reduce the air-sea CO2 uptake by 20%, and to reduce surface ocean acidification seasonally. Eventually, idealized simulations were made to quantify the sensitivity of the Arctic Ocean biogeochemistry to future changes in riverine delivery of carbon and nutrients. Sensitivities are of small magnitude on a pan-Arctic scale, importance in the coastal areas, and the dominant factor close to river mouths. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

The coastal ocean is a marginal region of the global ocean, but is home to metabolically intense ecosystems which increase the structural complexity of the benthos. These ecosystems have the ability to alter the carbon chemistry of surrounding waters through their metabolism, mainly through processes which directly release or consume carbon dioxide. In this way, coastal habitats can engineer their environment by acting as sources or sinks of carbon dioxide and altering their environmental chemistry from the regional norm. In most coastal water masses, it is difficult to resolve the ecosystem effect on coastal carbon biogeochemistry due to the mixing of multiple offshore end members, complex geography or the influence of variable freshwater inputs. The Red Sea provides a simple environment for the study of ecosystem processes at a coastal scale as it contains only one offshore end-member and negligible freshwater inputs due to the arid climate of adjacent land. This work explores the ability of three Red Sea benthic coastal habitats (coral reefs, seagrass meadows and mangrove forests) to create characteristic ecosystem end-members, which deviate from the biogeochemistry of offshore source waters. This is done by both calculating non-conservative deviations in carbonate stocks collected over each ecosystem, and by quantifying net carbonate fluxes (in seagrass meadows and mangrove forests only) using 24 hour incubations. Results illustrate that carbonate stocks over ecosystems conform to broad ecosystem trends, which are different to the offshore end-member, and are influenced by inherited properties from surrounding ecosystems. Carbonate fluxes also show ecosystem dependent trends and further illustrate the importance of sediment processes in influencing CaCO3 fluxes in blue carbon benthic habitats, which warrants further attention. These findings show the respective advantages of studying both carbonate stocks and fluxes of coastal benthic ecosystems in order to understand the spatial, temporal and net effects of their metabolism on the coastal ocean.

abstract: Cyanobacteria and algae living inside carbonate rocks (endoliths) have long been considered major contributors to bioerosion. Some bore into carbonates actively (euendoliths); others simply inhabit pre-existing pore spaces (cryptoendoliths). While naturalistic descriptions based on morphological identification have traditionally driven the field, modern microbial ecology has shown that this approach is insufficient to assess microbial diversity or make functional inferences. I examined endolithic microbiomes using 16S rRNA genes and lipid-soluble photosynthetic pigments as biomarkers, with the goal of reassessing endolith diversity by contrasting traditional and molecular approaches. This led to the unexpected finding that in all 41 littoral carbonate microbiomes investigated around Isla de Mona (Puerto Rico) and Menorca (Spain) populations of anoxygenic phototrophic bacteria (APBs) in the phyla Chloroflexi and Proteobacteria, were abundant, even sometimes dominant over cyanobacteria. This was not only novel, but it suggested that APBs may have been previously misidentified as morphologically similar cyanobacteria, and opened questions about their potential role as euendoliths. To test the euendolithic role of photosynthetic microbes, I set a time-course experiment exposing virgin non-porous carbonate substrate in situ, under the hypothesis that only euendoliths would be able to initially colonize it. This revealed that endolithic microbiomes, similar in biomass to those of mature natural communities, developed within nine months of exposure. And yet, APB populations were still marginal after this period, suggesting that they are secondary colonizers and not euendolithic. However, elucidating colonization dynamics to a sufficiently accurate level of molecular identification among cyanobacteria required the development of a curated cyanobacterial 16S rRNA gene reference database and web tool, Cydrasil. I could then detect that the pioneer euendoliths were in a novel cyanobacterial clade (named UBC), immediately followed by cyanobacteria assignable to known euendoliths. However, as bioerosion proceeded, a diverse set of likely cryptoendolithic cyanobacteria colonized the resulting pore spaces, displacing euendoliths. Endolithic colonization dynamics are thus swift but complex, and involve functionally diverse agents, only some of which are euendoliths. My work contributes a phylogenetically sound, functionally more defined understanding of the carbonate endolithic microbiome, and more specifically, Cydrasil provides a user-friendly framework to routinely move beyond morphology-based cyanobacterial systematics. / Dissertation/Thesis / APPENDIX A / APPENDIX B / APPENDIX C / Doctoral Dissertation Microbiology 2020

abstract: Mantle derived basalts along the entirety of the Earth’s Mid-Ocean Ridge (MOR) spreading centers are continuously altered by seawater, allowing the hydrosphere to subsume energy and exchange mass with the deep, slowly cooling Earth. Compositional heterogeneities inherent to these basalts—the result of innumerable geophysical and geochemical processes in the mantel and crust—generate spatial variation in the equilibrium states toward which these water-rock environments cascade. This alteration results in a unique distribution of precipitate assemblages, hydrothermal fluid chemistries, and energetic landscapes among ecosystems rooted within and above the seafloor. The equilibrium states for the full range of basalt compositional heterogeneity present today are calculated over all appropriate temperatures and extents of reaction with seawater, along with the non-equilibrium mixtures generated when hydrothermal fluids mix back into seawater. These mixes support ancient and diverse ecosystems fed not by the energy of the sun, but by the geochemical energy of the Earth. Facilitated by novel, high throughout code, this effort has yielded a high-resolution compositional database that is mapped back onto all ridge systems. By resolving the chemical and energetic consequences of basalt-seawater interaction to sub-ridge scales, alteration features that are globally homogeneous can be distinguished from those that are locally unique, guiding future field observations with testable geochemical and biochemical predictions. / Dissertation/Thesis / Doctoral Dissertation Geological Sciences 2020

Environmental change in the Arctic proceeds at an unprecedented rate. The Pliocene epoch (5-2.65 million years ago) represents an analog for future climate conditions, with pCO2 and continental configurations similar to present. Yet conditions in the Pliocene Arctic are poorly characterized because of sparse sampling. The records that do exist indicate periods of extreme warmth, as well as the first expansion of large ice-sheets in the Northern Hemisphere, took place from the end of the Pliocene into the early Pleistocene. Understanding these deposits and their implications for our future requires developing a sense of climatic evolution across the Plio-Pleistocene transition and especially during the intensification of Northern Hemisphere Glaciation (iNHG) ~2.7 million years ago. Here we reconstruct environmental change in the Arctic using a suite of organic geochemical proxies in a sedimentary archive recovered from Lake El'gygytgyn, Arctic Northeast Russia. We use the distribution of branched glycerol dialkyl glycerol tetraethers (brGDGTs) and the hydrogen isotopic composition (δD) of plant leaf-waxes (n-alkanes) to reconstruct relative temperature change across the interval spanning 2.8 to 2.4 million years ago. Our work demonstrates that, following the first major glaciation of the Northern Hemisphere, it took multiple glacial cycles for the Arctic to become synchronized with the climatic changes recorded in the deep ocean. This work has implications for understanding the role of sea-level, sea-ice, vegetation and carbon-cycle feedbacks in a changing Arctic.

Soils contain nearly three times the amount of carbon (C) than the atmosphere, with C turnover times ranging from centuries to millennia. Although wetland soils represent a relatively small portion of the terrestrial landscape, they account for an estimated 20-30% of the global C reservoir. Seasonally flooded soils are likely the most vulnerable wetlands to climate change, as changing temperature and precipitation patterns are expected to alter the timing and duration of flooding. Seasonal variations in soil moisture are recognized as a critical control on soil C stocks and CO2emissions. However, the relative influence of associated changes in soil oxygen availability, root dynamics and the stability of mineral-organic associations are largely unknown. The overarching goal of this study was to examine the relative influence of redox state, root density and mineralogy on C cycling within seasonally flooded soil. To accomplish this goal, we combined seasonal monitoring of soil moisture, redox potential, and carbon dioxide emissions with a characterization of organic matter composition, mineralogy and root biomass along upland to lowland transects. We found that water saturation was the limiting factor for CO2emissions from seasonal flooded lowland soils, whereas soil temperature primarily regulated emissions from upland soils. Seasonal water saturation also resulted in topsoil C accumulation in lowlands compared to uplands, despite experiencing prolonged aerobic periods. Moreover, the C that accumulated in lowland topsoils was more chemically reduced compared to upland soils. However, the C chemistry in the subsoil showed the opposite trend of being more reduced in uplands compared to lowland subsoils. In sum, our results suggest that anaerobically protected soil C in seasonal flooded soils is particularly vulnerable to changing moisture regimes in response to climate change. To what extent this expected C loss is compensated by upland plant encroachment, or the neoformation of mineral-organic associations, warrants future research.

The existing observations and model simulations indicate that mesoscale eddies and the Eastern Boundary Current (EBC) have a significant role in the complex circulation of the Red Sea. However, a full understanding of the processes that contribute to the physics and biological responses of the central Red Sea (CRS) has been limited due to the lack of sustained in-situ observations. In this dissertation study, in-situ observations extending over a thirty-three month period from spring 2013 through winter 2015 include an intensive ship-based and glider monitoring program to understand the key dynamic features of the CRS circulation. Nine glider missions and five ship-based surveys provide concrete resolution of both spatial and temporal variability in the CRS. The quasicontinuous glider observations resolve the influence of distinct water masses with a different origin that is present in the study area. Our results show that mesoscale eddies and the an intrusion of Gulf of Aden water governs the physical and biochemical characteristics of the CRS during the winter to summer transition period in 2013. During this period, an anticyclonic eddy appears to redirect the northward flow along the eastern boundary. Ship-based observations in fall 2013 indicate that the EBC can periodically transport patches of less salty and warmer water containing higher chlorophyll concentrations from south into the CRS. During spring 2014, ship observations show the presence of a cyclonic/anticyclonic eddy pair. The cyclonic eddy contribute an upward nutrient flux, resulting in an increase integrated chlorophyll concentration within the eddy. Higher chlorophyll and CDOM concentrations and lower N:P ratios characterized the inflow of lower salinity Gulf of Aden water from the south. To understand better how the mesoscale eddy activity, stratification, and the EBC modulate the nutrient availability and planktonic food web architecture in Red Sea two addition hydrographic surveys with plankton sampling were conducted in fall 2014 and spring 2015. The seasonal availability of Gulf of Aden water, stratification and eddies exerted a demonstrable effect on the plankton community by modulating the availability and utilization of allochthonous vs. autochthonous macronutrients by phytoplankton. Strong stratification, higher temperatures and depletion of nutrients by phytoplankton, subjected the plankton community to an overall nitrogen and phosphorus deficit in fall. To evaluate the role of the winter mixing, mesoscale eddies, and EBC within CRS during the winter to spring period, a sustained glider study (~91 days) was initiated from December 2014 to March 2015. Glider observations show the seasonal contrasts and transitions from strong summer stratification to winter mixing, with a corresponding transition from a well defined deep chlorophyll maximum to phytoplankton population intrusions of lower salinity water from the Gulf of Aden contributed to both the physical and biochemical variability within the region. Both GASW and GAIW can be entrained and diverted across the basin by larger eddies. Eddies play a role in the mixing between warmer, fresher water from the Gulf of Aden, and cooler, saltier water from the northern Red Sea.