Landscape position and depth in the soil column influence the movement of microbial substrate throughout a catchment, from upslope areas to downslope areas, thereby impacting nutrient cycling rates and capabilities of the microbial communities in those areas. Wildfire also shapes the biogeochemistry of the landscape, creating a mosaic with variations in substrate type and concentration that also influence microbial communities and biogeochemical cycling. Nitrogen (N) in particular is altered by wildfire, as it is easily volatilized and the removal of organic matter (OM) reduces N inputs. We aimed to understand how landscape position and soil depth, first and foremost, influence microbial communities and their N-cycling, but also how this may differ from wildfires and their relative impacts on the soil microbial communities. Landscape position proved to influence few soil and microbial characteristics, while movement from soil surface to deep in the column and the incidence of wildfire caused many variations in soil physical and biogeochemical cycling properties. The interaction of landscape position and soil depth also showed little variation in any measurements, while wildfire and soil depth interactions showed drastic changes that indicate high order controls over the soil microbial community. It can be surmised that while landscape position is important for many soil properties, it is soil depth and wildfire that truly control the soil microbial communities and their N-cycling capabilities.

For decades the Baltic Sea has been subject to eutrophication due to heavy anthropogenic nutrient loads on the aquatic ecosystem. Quantitative projections of its effects require an understanding of its driving mechanisms, i.e., the hydrodynamics that are responsible for the physical transport and mixing and the biogeochemical nutrients pathways within the algal ecosystem and between the particulate and dissolved phases in the water and in the sediments. A simple basin-scale hydrodynamic framework is set for the Gulf of Finland to test different descriptions of the biogeochemical transformations and determine the most robust modelling strategy. A recently developed criterion to determine the occurrence of anoxic events, based on the amount of fresh carbon detritus in the sediments is implemented in comparison with the classical criterion based on the oxygen concentration in the bottom water. Time-averaging of the hydrodynamics over larger than daily intervals is proved to hinder the capture of rapid mixing events jeopardizing irremediably the water quality simulation. The new carbon based criterion for anoxia shows a better dynamic response and is less sensitive to the model’s internal parameters. An internal source in the sediments correlated to the amount of fresh detritus, to represent the release of iron-bound phosphorus is confirmed as a versatile modelling assumption.

The basin-fill aquifers of the American Southwest host elevated concentrations of arsenic in groundwater due to the local geology. Limited information is available on arsenic dynamics in semi-arid and arid regions of the world. This study describes arsenic biogeochemistry and mechanisms of arsenic solubilization for a soil profile collected from the surface to the depth of groundwater in the Cache Valley Basin, Northern Utah. The first objective was to delineate mechanisms of arsenic solubilization from sediments collected at the study site. Microcosms containing site groundwater and siteoxidized and site-reduced sediments, were monitored over time to observe changes in the solubilization and oxidation state of arsenic and changes in mineral phases of arsenic and iron. The observed solubilization of arsenic was decoupled from iron reduction in the site-oxidized sediments in the presence of native organic carbon, which disagreed with the widely accepted hypothesis that arsenic solubilization is derived from microbial driven reductive dissolution of iron oxides. Carbonate minerals were defined as the mineral phase associated with arsenic that contributed to the arsenic measured in solution. The second objective was to determine how altering redox and water conditions down a profile affects arsenic geochemistry and hence solubility. Redox stratification was delineated in two sediment cores based on chemical analyses and visual observation of redox-sensitive parameters. The vadose zone released a considerable amount of arsenic, while the next zone, the carbonate enrichment zone, released the highest concentration of arsenic. Soluble arsenic was exclusively As(V) in the redox transition zone, where As was primarily associated with iron oxides. Solubilization of arsenic was limited in the deeply reduced depletion zone due to the formation of sulfide minerals. Lateral resolution of oxidation state and elemental association of arsenic at the micron scale were delineated using synchrotron-based X-ray absorption spectroscopy under Objective 3. The presence of unaltered arsenic sulfides was revealed in the vadose zone, suggesting that arsenic was inputted continuously to the ground surface. From the water table to the deeply reduced depletion zone sediments, arsenic mineral association was dominated by manganese-bearing carbonate minerals and amorphous iron oxides, which are vulnerable to groundwater fluctuation and redox-cycling.

Thesis: Ph. D., Joint Program in Chemical Oceanography (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references. / This thesis examines the controls on organic, inorganic, and volatile species distributions in hydrothermal fluids venting at Von Damm and Piccard, two recently discovered vent fields at the ultra slow spreading Mid-Cayman Rise, Earth's deepest mid-ocean ridge. A wide variety of possible temperatures and substrates for fluid/rock reaction exist at ultraslow spreading ridges. The flux of chemicals delivered to the ocean by circulating vent fluids exerts a major control on mass transfer into and out of the oceanic crust and supports chemosynthetic ecosystems. In Chapter 2, abiotic organic synthesis is shown to occur via two distinct mechanisms in the serpentinizing Von Damm system. Longstanding questions concerning the spatial, temporal, and mechanistic nature of carbon transformations in deep-sea hot springs are addressed. In contrast with the current paradigm, CH4 is not actively forming during circulation of H2-rich vent fluids, but instead is derived from fluid inclusions in the host rocks. Chapters 3 and 4 present in-depth studies of the chemical and isotopic compositions of aqueous species in vent fluids at Von Damm and Piccard to elucidate the role of reaction temperature, pressure, substrate composition, and water/rock mass ratios during the chemical evolution of hydrothermal fluids at oceanic spreading centers. At Von Damm, sequential reaction of gabbroic and peridotite substrates at intermediate temperatures can explain generation of the observed fluids. Geochemical modeling shows that talc-quartz assemblage is expected to precipitate during fluid mixing with seawater at the seafloor. At Piccard, extremely high temperature subsurface water/rock reaction results in high temperature fluids that are richer in dissolved H2 than any previously observed fluids worldwide. At both locations, high-H2 conditions promote the abiotic reduction of [Epsilon]CO2 to formate species, which may fuel a subsurface biosphere. In Chapter 5, multiple sulfur isotopes were measured on metal sulfide deposits, So, and fluid H2S to constrain sulfur sources and the isotopic systematics of precipitation in a wide variety of seafloor hydrothermal vents. Areas studied include the eastern Manus Basin and Lau Basin back-arc spreading centers, the unsedimented basalt-hosted Southern East Pacific Rise, and the sediment-hosted Guaymas Basin mid-ocean ridge spreading centers. Limited isotope fractionation between fluid H2S and precipitating chalcopyrite implies that sulfur isotopes in a chimney lining may record past hydrothermal activity. / by Jill Marie McDermott. / Ph. D.

Thesis (Ph. D.)--Joint Program in Chemical Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2007. / Includes bibliographical references. / Zinc (Zn) stable isotopes can record information about important oceanographic processes. This thesis presents data on Zn isotopes in anthropogenic materials, hydrothermal fluids and minerals, cultured marine phytoplankton, natural plankton, and seawater. By measuring Zn isotopes in a diverse array of marine samples, we hope to understand how Zn isotopes are fractionated in the oceans and how Zn isotopes may be used as tracers of marine biogeochemical processes. Common forms of anthropogenic Zn had [delta]66Zn from +0.08 %o to +0.32 %o, a range similar to Zn ores and terrigenous materials. Larger variations were discovered in hydrothermal fluids and minerals, with hydrothermal fluids ranging in 666Zn from 0.02 %o to +0.93 %o, and chimney minerals ranging from -0.09 %o to +1.17 %o. Lower-temperature vent systems had higher [delta]666Zn values, suggesting that precipitation of isotopically light Zn sulfides drives much of the Zn isotope fractionation in hydrothermal systems. In cultured diatoms, a relationship was discovered between Zn transport by either high-affinity or low-affinity uptake pathways, and the magnitude of Zn isotope fractionation. We established isotope effects of [delta]66Zn = -0.2 %o for high-affinity uptake and [delta]66Zn = -0.8 %o for low-affinity uptake. This work is the first to describe the molecular basis for biological fractionation of transition metals. Biological fractionation of Zn isotopes under natural conditions was investigated by measuring Zn isotopes in plankton collected in the Peru Upwelling Region and around the world. / (cont.) Seawater dissolved Zn isotopes also reflect the chemical and biological cycling of Zn. The [delta]66Zn of deep seawater in the North Pacific and North Atlantic is about 0.5%0, and the dissolved [delta]66Zn gets lighter in the upper water column. This is unexpected based our observations of a biological preference for uptake of light Zn isotopes, and suggests that Zn transport to deep waters may occur by Zn adsorption to sinking particles rather than as primary biological Zn. The thesis, by presenting data on several important aspects of Zn isotope cycling in the oceans, lays the groundwork for further use of Zn isotopes as a marine biogeochemical tracer. / by Seth Greeley John. / Ph.D.

Thesis: Ph. D., Joint Program in Marine Geology and Geophysics (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2014. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Here I use a simple numerical model of reef profile evolution to show that the present-day morphology of carbonate islands has developed largely in response to late Pleistocene sea level oscillations in addition to variable vertical motion and reef accretion rates. In particular, large amplitude 'ice-house' sea-level variability resulted in long lagoonal depositional hiatuses, producing the morphology characteristic of modern-day barrier reefs. Reactivation of carbonate factories, transport of coarse reef material and rapid infilling of shallow water accommodation space since deglaciation makes these unique sites for reconstructing Holocene climate. Integration of new tropical cyclone reconstructions from both back-barrier reef (central Pacific) and carbonate bank (the Bahamas) settings with existing storm archives suggests a coordinated pattern of cyclone activity across storm basins since the late Holocene. Seesawing of intense tropical cyclone activity between the western Pacific (-0- 1000 yrs BP) and North Atlantic/Central Pacific (~1000 ~2500 yrs BP) appears closely tied with hydrographic patterns in the tropical Pacific and El Niflo-like variability. Decoupling of North Atlantic (inactive) and South Pacific (active) tropical cyclone patterns during the mid-Holocene suggests precession driven changes in storm season insolation may constrain ocean-atmosphere thermal gradients and therefore cyclone potential intensity on orbital timescales. / by Michael Toomey. / Ph. D.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2007. / Includes bibliographical references. / Basaltic ocean crust has the potential to host one of the largest endolithic communities on Earth. This portion of the biosphere, however, remains largely unexplored. In this study, we utilize molecular biological, microscopic, and geochemical tools to gain a better understanding of the geomicrobiology of the ocean crust. Specifically, we examine the phylogenetic diversity of microorganisms inhabiting basaltic lavas, the activities and abundances of these microorganisms, the spatial extent of the biosphere, and the potential effect that microbial activity has on the geochemistry of the ocean crust and overlying water column. Our study demonstrates that young, fresh volcanic lavas near mid-ocean ridges host an incredibly diverse and dense population of microorganisms dominated by Bacteria, quite distinct from the microbial communities found in surrounding deep seawater and hydrothermal vents. Furthermore, these communities may contribute to the elemental cycling of Fe, S, Mn, N, and C in this environment. The inability to definitively identify microorganisms in drill-cores of old (> 15 Ma) ocean crust, however, implies that these once prolific communities may become scarce as the crust ages and moves further away from the ridge axis. Finally, we provide evidence suggesting that these communities are fueled by oxidative alteration reactions occurring in the basaltic crust. / by Cara M. Santelli. / Ph.D.

<p>Freshwater wetlands are capable of processing large amounts of excess nutrients from agricultural fields. These systems also have the potential to produce substantial amounts of nitrous oxide (N2O) and methane (CH4), both potent greenhouse gasses. Agricultural land use alters delivery of nutrients and carbon to downstream wetlands. These changes can impact denitrification and methanogenesis, leading to increased or decreased rates of greenhouse gas production. While there have been studies on effects of carbon and nutrients on greenhouse gasses separately, few studies in the region have identified how the combination of nutrients and carbon come together to modulate greenhouse gasses. Identifying the variation of carbon and nutrient processing in wetlands systems with different hydrology and agricultural impacts could potentially change what we know about carbon and nutrient cycling and how they impact greenhouse gasses emitted from wetlands. This study showed that 1) watershed land cover and wetland size correlated to water chemistry including concentrations of nitrogen, phosphorus, sulfate, and dissolved organic carbon concentration and composition and that 2) wetlands with higher levels of labile carbon, lower concentrations of nitrogen and sulfate are linked to higher rates of methane in wetland water while higher levels of nitrate were linked to increased wetland nitrous oxide. </p>

<p>Northern peatlands (>45°N) mostly initiated during the Holocene and have been a large C sink to the atmosphere. Northern peatland formation prefers wet and cold condition where the productivity persistently exceeds decomposition and thereby C accumulates. As the northern high latitude region is likely to be warmer in the future, whether northern peatlands will continue being C sinks or switch to C sources is uncertain. To address this issue, I revise and apply a process-based model designed for describing peatland biogeochemical processes, Peatland Terrestrial Ecosystem Model (PTEM), to simulate the C dynamics at both site and regional level, from 15 ka BP-2300. For the site-level simulation, PTEM 1.0 is substantially revised into PTEM 2.0 in terms of peat accumulation process, plant functional types, productivity and decomposition, and soil thermal properties. A simulation from peat initiation to 2300 is conducted for three northern peatland sites. I found PTEM 2.0 can effectively capture the historical C accumulation progress, when compared with the observation. The future simulation indicates northern peatlands have reduced C sink capacity or switch to a C source under N insufficiency and water table deepening. </p> <p>Afterwards, a historical pan-Arctic simulation during 15ka BP-1990 is conducted. PTEM 2.0 is revised into PTEM 2.1 by adding spatially-explicit run-on and run off processes. The spatially-explicit peat initiation dataset is derived from neural network approach and a spatially-explicit peat expansion trend is established on top of it. My estimated pan-Arctic peatland C storage is 396-421 Pg C with the long-term C accumulation rate (CAR) of 22.9 g C∙m-2 yr-1. The simulated spatial distribution of peat C and the temporal pattern of CAR both agree with literature values. I analyzed northern peatlands’ response to historical climate change since 0.5 ka BP and found decreased CAR in the warmer non-permafrost and permafrost-thaw region, while the opposite was found in the colder permafrost region. The results indicate warmer southern peatlands will first switch to a C source under warming while more northern peatlands will become larger sinks. </p> <p>Based on the result of historical simulation, a future simulation is conducted for 1990-2300 with peatland expansion/shrinkage considered. PTEM 2.1 is revised into PTEM 2.2 such that the water table depth, run-on and run-off are estimated from a TOPMODEL approach. In the 21st century, northern peatlands are projected to be a C source of 1.2-13.3 Pg C under five out of six climate scenarios. During 2100-2300, northern peatlands under all scenarios are a C source under all climate scenarios. Northern peatlands switch to C sources due to deepening water table depth, insufficient N availability, and plant functional type shift. I found that northern peatlands remain as a C sink until a mean pan-Arctic peatlands annual temperature reaches -2.09 - -2.89°C. This study predicts a northern peatland sink to a source shift around 2050, earlier than previous estimates of after 2100, and emphasizes the vulnerability of northern peatlands to climate change. </p>

Tropical coral reefs are highly productive ecosystems thriving in oligotrophic waters, a phenomenon facilitated by efficient but delicate biogeochemical cycling within reef communities. Global climate change and local stressors are driving phase shifts from coral- to non-calcifier-dominated states in reefs worldwide, substantially altering reef biogeochemical functioning. While major benthic players such as coral and macroalgae have been investigated in detail regarding carbon and nutrient dynamics, the less conspicuous “reef cryptobiome” (sensu Carvalho et al., 2019) – comprising most of reef diversity – has only recently gained attention. Autonomous Reef Monitoring Structures (ARMS) have recently been developed to sample coral reef cryptobenthic communities in a non-destructive and standardised way, allowing exploration of these often overlooked biota. Here, 16 ARMS were deployed for seven months in four distinct habitats dominated by different benthic players (i.e., four units per habitat) in a nearshore Red Sea coral reef to investigate the cryptobiome associated with proxies of varying benthic states. Two of these habitats were coral-dominated, and one each dominated by turf algae or coral rubble. To assess the biogeochemical fluxes of pioneering cryptobenthic communities, ARMS were incubated in situ prior to retrieval using customised chambers. Subsequently, 16S rRNA gene amplicon and shotgun metagenomic sequencing of the ARMS sessile (i.e., encrusting) fractions were performed to link observed fluxes with prokaryotic taxonomic and functional profiles, particularly regarding nitrogen cycling. The results show that the pioneering cryptobiome represents a significant source of inorganic nutrients and that its associated microbial communities facilitate the mineralisation and assimilation of organic matter and provide crucial genetic functional pathways for nitrogen cycling. Functional similarities among habitats suggested functional redundancy despite variation in bacterial community composition. Hence, the reef cryptobiome can be considered an important biogeochemical player in coral reefs, actively shaping the abiotic conditions within niches of the reef framework and driving the recruitment and persistence of crytobenthic and other reef organisms. As communities associated with the algae-dominated reef habitat were most distinct compositionally and biogeochemically, and as non-calcifiers are becoming more dominant in many reefs, this has implications for intensifying phase shifts in coral reefs worldwide. Future ARMS studies will also benefit from adjustment of sample processing and molecular protocols, resulting in higher sample throughput and lower costs in times of increased application of ARMS.