Browsing by Subject "Biogeochemistry"

Human welfare depends heavily on ecosystem services like water purification and nutrient cycling. Many of these ecosystem services, in turn, rely on reactions performed by microbes and yet remarkably little is known about how anthropogenic impacts are affecting the structure and function of microbial communities. To help address this knowledge gap, this dissertation uses field surveys and laboratory experiments to examine how watershed urbanization affects microbial communities in receiving streams. We focus on a specific functional group and its associated function - the denitrifying bacteria and denitrification. Denitrifying bacteria use reactive nitrogen and organic carbon as substrates to perform denitrification. Denitrification is one of the few ways to permanently remove reactive nitrogen from ecosystems. Since excess reactive nitrogen in water contributes to serious water quality and human health problems like toxic algal blooms and bowel cancer, denitrification in streams can be considered a valuable ecosystem service. Watershed urbanization, however, may alter the structure of denitrifying bacteria communities in ways that constrain their capacity to remove reactive nitrogen from streams.

Watershed urbanization leads to drastic changes in receiving streams, with urban streams receiving a high frequency of scouring flows, together with increased nutrient (nitrogen and carbon), contaminant (e.g., heavy metals), and thermal pollution. These changes are known to cause significant losses of sensitive insect and fish species from urban streams. Microbes like denitrifying bacteria may be similarly affected. In the first part of this dissertation, we describe results from four repeated surveys of eight central North Carolina streams affected to varying degrees by watershed urbanization. For each stream and sampling date, we characterized both overall and denitrifying bacterial communities and measured denitrification potentials. Differences in overall and denitrifying bacteria community composition were strongly associated with the urbanization gradient. Denitrification potentials, which varied widely, were not significantly associated with substrate supply. By incorporating information on the community composition of denitrifying bacteria together with substrate supply in a linear mixed-effects model, we explained 45% of the variation in denitrification potential (p < 0.001). Results suggest that 1) watershed urbanization can lead to significant changes in the composition of bacterial communities in streams and 2) such changes may have important functional consequences.

The second part of this dissertation examines how urbanization-driven changes to the structure of denitrifying bacteria communities might affect the way they respond to stress or disturbance. Some communities can resist changes to functionality in response to disturbance, potentially as a result of previous exposure and subsequent adaptation (legacy hypothesis) or high diversity (insurance hypothesis). We compare the resistance of two structurally distinct denitrifying bacteria communities to experimental disturbances in laboratory microcosms. Communities originated from either a polluted, warm urban streams or a relatively pristine, cool forest stream. In this case, the two communities had comparable compositions, but forest communities were more diverse than their urban counterparts. Urban communities experienced significant reductions in denitrification rates in response to the most severe increased pollution and temperature treatments, while forest communities were unaffected by those same treatments. These findings support the insurance, but not the legacy hypothesis and suggest that the functioning of urban streams may be more susceptible to further environmental degradation than forest streams not heavily impacted by human activities.

In the third part of this dissertation, we discuss results from a one-time survey of denitrifying bacteria communities and denitrification potentials in 49 central North Carolina streams affected to varying degrees by watershed urbanization. We use multivariate statistics and structural equation modeling to address two key questions: 1) How do different urban impacts affect the structure of denitrifying bacteria communities and 2) How do abiotic (e.g., temperature) versus biotic (denitrifying bacteria community structure) factors affect denitrification potentials in urban streams? Denitrifying bacteria community structure was strongly affected by the urban impacts measured. Community composition responded to increased temperatures, substrate supply, and contamination, while diversity responded negatively to increased temperatures and hydrologic disturbance. Moreover, increased temperatures and substrate supply had significant positive effects, while urbanization-driven changes to denitrifying bacteria community structure had significant negative effects on denitrification potential. The structural equation model captured 63% of the variation in denitrification potential among sites and highlighted the important role that microbial community structure can play in regulating ecosystem functioning. These findings provide a novel explanation for recent observations of decreasing denitrification efficiency with increasing urbanization. Ultimately, we hope findings from this dissertation will help inform more effective stream management and restoration plans and motivate ecologists to consider including microbial community structure in ecosystem models of microbe-mediated processes.

Rivers interact with their valleys from headwaters to mouth, but nowhere as dynamically as in their floodplains. Rivers deliver water, sediments, and solutes onto the floodplain land surface, and the land in turn supplies solutes, leaves, and woody debris to the channel. These reciprocal exchanges maintain both aquatic and terrestrial biodiversity and productivity. In this dissertation I examine river-floodplain exchanges on the well-studied Nyack Floodplain, a dynamic, gravel-bedded floodplain along the Middle Fork Flathead River in the mountains of northwest Montana. I quantify exchanges at multiple timescales, from moments to centuries, to better understand how connectivity between aquatic and terrestrial habitats shapes their ecology.

I first address connectivity in the context of a long-standing question in ecosystem ecology: What determines the rate of ecosystem development during primary succession? Rivers have an immediate effect on floodplains when scouring floods remove vegetation and nutrients such as nitrogen (N) and leave only barren soils, but they might also affect the ensuing primary succession through the gradual delivery of N and other materials to floodplain soils. I quantify N inputs to successional floodplain forest soils of the Nyack Floodplain and find that sediment deposition by river flood water is the dominant source of N to soils, with lesser contributions from dissolved N in the river, biological N fixation, and atmospheric deposition. I also synthesize published rates of soil N accumulation in floodplain and non-floodplain primary-successional systems around the world, and I find that western floodplains often accumulate soil N faster than non-floodplain primary successional systems. My results collectively point to the importance of riverine N inputs in accelerating ecosystem development during floodplain primary succession.

I next investigate the role of river-floodplain exchanges in shaping the spatial distribution of a suite of soil properties. Even after flood waters have receded, dissolved N, carbon (C), and moisture could be delivered from the river to floodplain soils via belowground water flow. Alternatively, C inputs and N withdrawals by floodplain vegetation might be a dominant influence on soil properties. To test these hypotheses, I excavated and sampled soil pits from the soil surface to the water table (50-270 cm) under forests, meadows, and gravel bars of the Nyack Floodplain. Near-surface soils had C and N pools and N flux rates that varied predictably with vegetation cover, but soil properties below ~50 cm reflected influence by neither vegetation cover nor aquifer delivery. Instead, soil properties at these depths appear to relate to soil texture, which in turn is structured by the river's erosional and depositional activities. This finding suggests the revised hypothesis that soil properties in gravel-bedded alluvial floodplains may depend more on the decadal-scale geomorphic influences of floods than on short-term vertical interactions with floodplain vegetation or aquifer water.

Lastly, I explore the potential sources of organic C to the diverse and active community of aquatic organisms in the floodplain aquifer, where the lack of light prohibits in-situ organic C production by photosynthesis. I quantify floodplain carbon pools and the fluxes of organic carbon connecting the aquifer, river, and overlying forest. Spring flood waters infiltrating the soil are responsible for the largest dissolved carbon flux into the aquifer, while very large floods are essential for the other major C input, the burial of woody carbon in the aquifer. These findings emphasize the importance of a dynamic river hydrograph - in particular, annual floods and extreme annual floods - in delivering organic C to the aquifer community.

Overall, this dissertation draws our attention not just to the current exchanges of C, N, water, and sediment but to the episodic nature of those exchanges. To fully understand floodplain ecosystems, we have to consider not just present-day interactions but also the legacies of past floods and their roles in delivering solutes, eroding forests, depositing sediments, and physically shaping the floodplain environment.

Mercury (Hg) is a globally circulating heavy metal released through both natural and anthropogenic sources. The largest anthropogenic source of mercury to the global atmosphere is artisanal and small-scale gold mining (ASGM). During the ASGM process, miners add elemental mercury to large quantities of sediment or soil in order to create gold-mercury amalgams that separate alluvial gold from the remaining geological host material. Miners then heat the amalgam using a blowtorch or similar device to separate the mercury and gold, exposing themselves to mercury vapor and releasing mercury to the environment. Following amalgam heating, mercury can deposit into aquatic ecosystems. There, anaerobic microorganisms can convert mercury to methylmercury (MeHg), a potent neurotoxin that rapidly accumulates in aquatic food webs. A high concentration of MeHg in fish poses serious human health risks, especially to pregnant women and children.

In Peru’s Region of Madre de Dios (MDD), mercury use for ASGM is widespread due to increasing global demand for gold. This region in the tropical Amazon is one of the world’s most biodiverse ecosystems and home to more than 150,000 Indigenous and non-Indigenous people, 40% of whom live below the poverty level. Recently, people living in the region have become more aware of negative impacts of Hg pollution through popular press. However, there is lack of controlled scientific studies to examine the environmental impacts of Hg from ASGM and subsequent exposures to surrounding communities.

This dissertation addresses four questions in order to better understand how mercury from ASGM impacts environmental health in Madre de Dios: (1) How is mercury distributed along the Madre de Dios River in areas of active ASGM activity, and what is the risk for mercury exposure to downstream communities? (2) How does land use change associated with ASGM activity affect soil-mediated mercury transport in the Colorado River, Madre de Dios, Peru? (3) Can sulfurized carbon be manufactured in a feasible way for developing countries and used to capture mercury during ASGM amalgam burning? (4) What is the mercury methylation potential of easy-to-manufacture spent, sulfurized carbon sorbents?

Despite significant information on the direct health impacts of mercury to ASGM miners, the impact of mercury contamination on downstream communities has not been well characterized, particularly in Madre de Dios. In this area, ASGM has increased significantly since 2000 and has led to substantial political and social controversy. The second chapter of this dissertation examines the spatial distribution and transport of mercury through the Madre de Dios River with distance from ASGM activity. It also characterizes risks for dietary mercury exposure to local residents who depend on fish from the river. River sediment, suspended solids from the water column, and fish samples were collected in 2013 at 62 sites near 17 communities over a 560 km stretch of the Madre de Dios River and its major tributaries. In areas downstream of know ASGM activity, mercury concentrations in sediment, suspended solids and fish within the Madre de Dios River were elevated relative to locations upstream of mining. Fish tissue mercury concentrations were observed at levels representing a public health threat, with greater than one-third of carnivorous fish exceeding the international health standard of 0.5 mg/kg. This research demonstrates that communities located hundreds of kilometers downstream of ASGM activity, including children and indigenous populations who may not be involved in mining, are at risk of dietary mercury exposure that exceed acceptable body burdens.

This research involved extensive field sampling in an active mining region and indicated suspended particulate transport may be an important source of mercury from mining areas to downstream communities. Chapter three of this research focused on understanding how land use changes can influence soil and sediment transport from mining regions. Within the MDD, a large portion of mining in concentrated within the Colorado River watershed. In the Colorado River watershed, mining and deforestation have increased dramatically since the 1980s, largely concentrated in the Puquiri subwatershed. Field sampling in Feb 2015 identified a strong correlation between Hg and suspended solids concentrations, with especially high suspended solids concentrations downstream of ASGM activity. This supported the hypothesis that Mercury transport in this region is facilitated by soil mobilization and runoff. In order to understand how ASGM activity in the Puquiri affects sediment mobilization from the watershed over time, we employed a watershed-scale soil mobilization model using satellite imagery from 1986 to 2014. The model estimated that soil mobilization in the Colorado River watershed increased by 2.5 times during the time period, and increased by six times in the Puquiri subwatershed, leading to between 10 and 60 kg of mercury mobilized in 2014. If deforestation continues at its current exponential rate through 2030, soil and heavy metal mobilization may increase by five times. This research shows that deforestation associated with ASGM in the Colorado River watershed can exacerbate soil mobilization and mercury contamination. While the impacts of mercury and deforestation are often considered separately, here we studied how deforestation associated with ASGM in the Madre de Dios region can significantly increase soil mobilization and mercury transport to downstream communities.

With a substantial portion of mercury releases coming from a non-industrialized process in developing countries, low-cost and low-tech mercury capture is becoming increasingly necessary. While impregnated activated carbon sorbents are well studied for mercury-capture in developed countries and large industrialized settings, there exist few suitable low-cost alternatives for mercury capture from artisanal and small-scale gold mining (ASGM) in developing countries. Chapter four sought to develop an easy-to-manufacture carbon sorbent using elemental sulfur and activated carbon or hardwood-based biochar for potential use during ASGM gold-amalgam heating. Consumer-grade sulfur powder was melted on granular activated carbon or hardwood biochar in a process feasible for a cook stove setting. Activated carbon and biochar were successfully sulfurized to more than 5% sulfur by weight using powdered, elemental sulfur. The sorbent products were tested for elemental mercury sorption from an air gas stream at room temperature. The sulfurized activated carbon achieved higher elemental mercury adsorption capacity in air stream (500 μg Hg m-3, 2 L min-2) relative to unsulfurized activated carbon and sulfurized biochar. Sorption isotherms were used to examine the sorption mechanism, and indicated that likely a pseudo first order reaction was occurring. This research provides a possible option for mercury control by modifying established mercury capture technologies to be easy to manufacture, locally available, and less hazardous to produce.

In Chapter 5 of this research, the sulfurized sorbents were examined further to understand methylation potential in sediment slurries. Anaerobic sediment slurries were constructed to examine methylmercury (MeHg) production of spent sorbents. Five sorbent types with approximately 10 mg/kg Hg each were added to slurries at 5 % by mass. Dissolved mercury was used as a control to simulate atmospheric deposition or highly reactive mercury. After a 5 d incubation at room temperature, MeHg production was ten times greater with low-technology sulfurized sorbents as compared to activated carbon or biochar alone. Sulfurized sorbents leached significantly more mercury than their non-sulfurized counterparts during desorption experiments and led to greater dissolved mercury concentrations. This research shows that low-cost mercury-contaminated sorbents can have unintended consequences with increased MeHg production and potential for more harm to local communities than atmospheric release.

Mercury releases from ASGM are expected to grow, leading to higher concentrations of mercury in the atmosphere that may affect ecosystems throughout the globe. Understanding the importance of mercury from ASGM to toxicity and accumulation requires in depth research on mercury transformations and MeHg production associated with ASGM. This research examines mercury distribution and transport from ASGM active regions. It identifies that deforestation, erosion, and particulate transport play important roles in overall mercury transport, leading to hazardous mercury concentrations downstream of ASGM activity. Effective point-of-use mercury capture technologies would dramatically decrease the mass of mercury released to the environment. The final chapters of this research serve as a proof of concept for using sulfurized activated carbon for mercury capture in developing countries.

Our research team has built strong relationships with several governmental and non-governmental organizations in Peru who will aid in distributing information. This research will provide invaluable environmental health information to residents, inform political intervention, and reveal a new potential avenue for low-cost mercury control.

Climate change is driving vegetation community shifts in coastal regions of the world, where low topographic relief makes ecosystems particularly vulnerable to sea level rise, salinization, storm surge, and other effects of global climate change. Salinization has clear effects on vegetation, as few plant species can survive in brackish water, and these shifts in vegetation lead to declines in biomass carbon stocks, as well as significant changes in habitat structure and biodiversity. The rate and extent of these impacts on other wetland ecosystem properties and function is far less certain. This dissertation investigates the ecosystem consequences of saltwater intrusion in coastal wetlands, from shifting vegetation at the landscape scale, to soil biogeochemistry and wetland carbon cycling.Coastal plant communities globally are highly vulnerable to future sea-level rise and storm damage, but the extent to which these habitats are affected by the various environmental perturbations associated with chronic salinization remains unclear. In 2016, a series of vegetation plots across the Albemarle-Pamlico Peninsula that had been surveyed 7-13 years earlier were revisited in order to measure changes in tree basal area and community composition over time. I found reduced tree basal area in plots at lower elevations and with higher current soil salt content, while these factors explained only a small fraction of the measured changes in tree community composition. While tree basal area increased in the majority of plots, I measured declines in basal area in multiple sites with high soil salt content or low elevation. This decadal comparison provides convincing evidence that increases in soil salinity and saturation can explain recent changes in tree biomass, and potential shifts in community composition in low-elevation sites along the North Carolina coast. In Chapter 3, I quantified land and land cover change in the Alligator River National Wildlife Refuge (ARNWR), North Carolina’s largest coastal wildlife preserve, from 1985 to 2019 using classification algorithms applied to a long-term record of satellite imagery. Despite ARNWR’s protected status, and in the absence of any active forest management, 32 % (31,600 hectares) of the refuge area has changed land cover classification during the study period. A total of 1151 hectares of land was lost to the sea and ~19,300 hectares of coastal forest habitat were converted to shrubland or marsh habitat. As much as 11 % of all forested cover in the refuge transitioned to ghost forest, a unique land cover class that is characterized by standing dead trees and fallen tree trunks. This is the first attempt to map and quantity coastal ghost forests using remote sensing. These unprecedented rates of deforestation and land cover change due to climate change may become the status quo for coastal regions worldwide, with implications for wetland function, wildlife habitat and global carbon cycling. Salinization of freshwater wetlands is a symptom of climate change induced sea level rise. The ecosystem consequences of increasing salinity are poorly constrained and highly variable within prior observational and experimental studies. Chapter 4 presents the results of the first attempt to conduct a salinization experiment in a coastal forested wetland. Over four years, marine salts were applied to experimental plots several times annually with the goal of raising soil salinity to brackish levels while soil porewater in control plots remained fresh. Each year I measured aboveground and belowground vegetation biomass along with soil carbon stocks and fluxes. Despite adding more than 1.5 kg of salt per m2 to our experimental plots over four years, the ecosystem responses to salt treatments were subtle and varied over the multi-year experiment. In the final year of the experiment, soil respiration was suppressed, and bulk and aromatic soil carbon became less soluble as a result of salt treatments. The more stable carbon pools—soil organic carbon and vegetation associated carbon—remained unaffected by the salt treatment. This experiment demonstrates substantial ecosystem resistance to low dose salinity manipulations. The inconsistent soil carbon responses to experimental salinization I observed in the field led me to question how differences in soil pH and base saturation might alter the impacts of salinity of soil microbial activity. To test this, I performed a salt addition experiment on two series of wetland soils with independently manipulated salt concentrations and solution pH to tease apart the effect of these seawater components on soil carbon cycling (Chapter 5). Microbial respiration and dissolved organic carbon solubility were depressed by marine salts in both soils, while pH manipulation alone had no effect. Salinity treatments had a far greater effect on soil pH than did our intentional pH manipulation and there was a strong interaction between salt treatments and soil type that affected the magnitude of soil carbon responses. Site soils varied significantly in pH and base saturation, suggesting that the interaction between salinity and edaphic factors is mediating soil carbon processes. The degree of salinization and the effective pH shift following seawater exposure may vary widely based on initial soil conditions and may explain much of the variation in reports of salt effects on soil carbon dynamics. I suggest that these edaphic factors may help explain the heretofore inconsistent reports of carbon cycle responses to experimental salinization reported in the literature to date.

As the human population continues to increase, the effects of land use change on streams and their watersheds will be one of the central problems facing humanity, as we strive to find ways to preserve important ecosystem services, such as drinking water, irrigation, and wastewater processing. This dissertation explores the effects of land use change on watershed nitrate concentrations, and on several biogeochemical ecosystem functions in streams, including nitrate uptake, ecosystem metabolism, and heterotrophic carbon processing.

In a literature synthesis, I was able to conclude that nitrate concentrations in streams in forested watersheds tend to be correlated with soil solution and shallow groundwater nitrate concentrations in those watersheds. Watershed disturbances, such as ice storms or clear-cutting, did not alter this relationship. However both urban and agricultural land use change increased the nitrate concentrations in streams, soil solution, and groundwater, and altered the correlation between them, increasing the slope and intercept of the regression line. I conclude that although the correlation between these concentrations allows for predictions to be made, further research is needed to better understand the importance of dilution, removal, and transformation along the flowpaths from uplands to streams.

From a multi-site comparison of forested, urban, and urban restored streams, I demonstrated that ecosystem functions like nitrate uptake and ecosystem metabolism do not change in a linear unidirectional way with increasing urbanization. I also showed that Natural Channel Design stream restoration as practiced at my study sites had no net effect on ecosystem function, except those effects that came from clearing the riparian vegetation for restoration construction. This study suggested further consideration is needed of the ecosystem effects of stream restoration as it was practiced at these sites. It also suggested that more study was needed of the effects of urbanization on ecosystem metabolism and heterotrophic processes in streams.

In a 16-month study of ecosystem metabolism at four sites along an urbanization gradient, I demonstrated that ecosystem metabolism in urban streams may be controlled by multiple separate effects of urbanization, including eutrophication, light, temperature, hydrology, and geomorphology. One site, with high nutrients, high light, and stable substrate for periphyton growth but flashy hydrology, demonstrated a boom-bust cycle of gross primary production. At another site, high benthic organic matter standing stocks combined with low velocities and high depths to create hypoxic conditions when temperature increased. I propose a new conceptual framework representing different trajectories of these effects based on the balance of increases in scour, thermal energy and light, eutrophication, and carbon loading.

Finally, in a study of 50 watersheds across a landscape urbanization gradient, I show that urbanization is correlated with a decrease in particulate carbon stocks. I suggest that an increase in dissolved organic matter quality may serve to compensate for the loss of particulate carbon as fuel for heterotrophic microbial activity. Although I saw no differences among watershed landuses in microbial activity per gram of sediment, there was a strong increase in the efficiency of microbial activity per unit organic sediment with increasing watershed urbanization. Ultimately, I hope that this research contributes to our understanding of stream ecosystem functions and the way land use change can alter these functions, with the possibility of better environmental management of urban streams in the future.

Marine productivity is limited by nitrogen in a large portion of the global ocean. Marine nitrogen fixation, catalyzed by a select group of microorganisms called diazotrophs, converts nitrogen gas (N2) into bioavailable nitrogen that can support the growth of marine phytoplankton. By supplying new nitrogen to marine ecosystems, marine N2 fixation affects marine primary production, the uptake of carbon dioxide and ultimately the global climate. However, the environmental controls on N2 fixation and the physiologies of diverse diazotrophs remain elusive, in great part due to the limited number of observations. As part of this dissertation, I applied a variety of approaches including statistical modeling, high-resolution field measurements, and gene sequencing to characterize the biogeography of marine diazotrophy.

The first approach was to model marine N2 fixation and diazotrophs using machine learning methods. To that end, I conducted meta-analyses to update the global datasets of N2 fixation and diazotrophs. The number of observations in these updated datasets are ~80% and over 100% larger than previous datasets, respectively. Simple correlation analyses between N2 fixation rates and different environmental factors failed to identify a single factor explaining marine N2 fixation at a global scale. In contrast, individual diazotrophic phylotypes showed distinct relations to environmental properties. Machine learning methods including random forest (RF) and support vector regression (SVR) simulated the observed N2 fixation and diazotrophs fairly well by accounting for nonlinearities among multiple environmental factors. The estimated global N2 fixation fluxes from the two statistical models were within the range of other studies. However, the machine learning estimates and other simulations in some cases showed substantial disagreement in both the magnitude and distribution of N2 fixation and diazotrophs, especially in high latitudes and the eastern equatorial Pacific, where observations are scarce. The large uncertainties in simulated N2 fixation and diazotrophs emphasized the need for a better understanding of the factors regulating N2 fixation and the physiology of diazotrophs.

Achieving this goal can be labor-intensive and difficult with current techniques, which are based on discrete sampling and long incubation time. To overcome some of the drawbacks of traditional methods, our laboratory developed a method for high-frequency underway N2 fixation measurements. This method provides better coverage of the spatial and temporal heterogeneity in N2 fixation. I deployed this method over large swaths of the western North Atlantic Ocean in the summers of 2015, 2016, and 2017, covering over 10,000 km cruise tracks. This extensive survey identified new hotspots of N2 fixation in the coastal waters of the mid-Atlantic Bight. By coupling high-resolution N2 fixation observations with underway estimates of net community production (NCP) derived from O2/Ar measurements, I revealed the heterogeneous contribution of N2 fixation to NCP and to the carbon cycle, with a surprisingly large contribution in coastal waters.

In addition to the spatial distribution of N2 fixation, I also characterized types of diazotrophs responsible for N2 fixation and how they responded to varying environmental conditions. By measuring diazotrophic diversity, abundance and activity at high-resolution using newly developed underway sampling and sensing techniques, I captured a shift between diazotrophs from Trichodesmium to UCYN-A from oligotrophic warm (25-29°C) subtropical Sargasso Sea to the relatively nutrient-enriched cold (13-24°C) eastern American coastal waters. Meanwhile, N2 fixation rates were significantly enhanced when phosphorus and Fe availabilities, and chlorophyll-a concentration increased across the Gulf Stream into the subpolar and coastal waters. Phosphorus limitation was confirmed with changes in the expression of phosphorus uptake genes in Trichodesmium and UCYN-A. While temperature was the major factor controlling the diazotrophic community, phosphorous was dominantly driving the changes of N2 fixation rates in the western North Atlantic.

Overall, this dissertation significantly improves our understanding of the distribution of N2 fixation and diazotrophs and their environmental controls in the western North Atlantic and in the global ocean.

Invasive species are rapidly expanding in riparian wetlands while concurrently anthropogenic causes are increasing nitrogen (N) into these ecosystems. Microstegium vimineum (Microstegium) is a particularly abundant invasive grass in the Southeast United States. To evaluate impacts of Microstegium on both plant diversity and N cycling in a riparian floodplain, paired plots of Microstegium hand-weeded and unweeded were established for three years. Plots without Microstegium increased from 4 to 15 species m-2 and 90% of the newly establishing species were native. The Microstegium community accumulated approximately half the annual N in biomass of the diverse community, 5.04 versus 9.36 g-N m-2 year-1, respectively (p=0.05). Decomposition and release of N from Microstegium detritus was much less than in the diverse community, 1.19 versus 5.24 g-N m-2 year-1. Rates of soil N mineralization estimated by in-situ incubations were relatively similar in all plots. While Microstegium invasion appears to greatly diminish within-ecosystem circulation of N through the under-story plants, it might increase ecosystem N losses through enhanced denitrification (due to lower redox potentials under Microstegium plots). Microstegium removal ceased in the fourth growing season and formerly weeded plots increased to 59% (± 11% SE) Microstegium cover and species richness decreased to <8 species m-2.

To learn how Microstegium responds to increased N, we conducted a greenhouse competition experiment between Microstegium and four native plants across an N gradient. There was a unique competition outcome in each species combination, yet Microstegium was most dominant in the high levels of N.

Last, we disturbed a floodplain similar to wetland restoration disturbance and tracked available N. We also established a native community of plants with and without Microstegium in three levels of N. Disturbance to the floodplain dramatically increased inorganic N, especially in the form of NO₃ which was five times higher in the disturbed floodplain than the undisturbed floodplain. N levels remained elevated for over a year. Microstegium was N responsive, but did not show negative effects to the planted vegetation until the second year. Ironically, restoration activities are increasing available N, and favoring invasive species which in turn detracts from restoration success.

An increasingly large fraction of Earth’s surface has been reshaped and contaminated by humans, leading experts to suggest we’ve entered into a new geologic epoch – the Anthropocene. Nowhere are these changes more obvious than in mining-impacted landscapes. Mining reshapes landscapes, liberates trace elements, and alters the fate, transport, and transformation of trace elements. In this dissertation, I examine the extent to which mining both alters landscape features and mobilizes trace elements, and how these paired changes together determine the bioavailability of toxic trace elements. Specifically, in this dissertation, I focus on the mobilization and transformation of selenium (Se) and mercury (Hg) from mountaintop mining (MTM) in West Virginia; the biogeochemical interactions between Se and Hg in ecosystems and organisms; and the fate of Hg derived from artisanal and small-scale gold mining (ASGM) in Senegal and Peru.

In chapter 2, I examine the fate of Hg and Se from MTM of coal. Coal is naturally enriched in trace elements, including Hg and Se. Alkaline mine drainage from MTM – the dominant form of surface coal mining in Appalachia, USA – releases large quantities of Se into streams draining mined catchments, resulting in elevated bioaccumulation of Se in aquatic and riparian organisms. Yet, the release of Hg into these streams from MTM has not yet been studied. I measured total Hg, methyl Hg (MeHg), and Se in stream water, sediment, biofilm, cranefly larvae, and riparian spiders in alkaline streams (pH range: 6.9-8.4) across a mining gradient (0-98% watershed mined) in central Appalachia. Hg concentrations ranged from below detection limit (BDL)-6.9 ng/L in unfiltered water, BDL-0.05 μg/g in bulk sediment, 0.016-0.098 μg/g in biofilm, 0.038-0.11 μg/g in cranefly larvae, and 0.046-0.25 μg/g in riparian spiders. In contrast to Se, I found that Hg concentrations in all environmental compartments were not related to the proportion of the watershed mined, suggesting that Hg is not being released from, nor bioaccumulating within, MTM-VF watersheds. I also did not find clear evidence for a reduction in Hg methylation or bioaccumulation under elevated Se concentrations: water, sediment, biofilm, and riparian spiders exhibited no relationship between Hg and Se; only cranefly larvae exhibited a negative relationship (p=0.0002, r2=0.42). I suggest that the type of surface mining matrix rock, with resultant alkaline or acid mine drainage, is important for the speciation, mobility, and bioaccumulation of trace elements within watersheds affected by mining activities.

In chapter 3, I examine evidence for an interaction between Hg and Se. Hg is a pervasive environmental pollutant and contaminant of concern for both people and wildlife that has been a focus of environmental remediation efforts for decades. A growing body of literature has motivated calls for revising Hg consumption advisories to co-consider Se levels in seafood and implies that remediating aquatic ecosystems with ecosystem-scale Se additions could be a robust solution to Hg contamination. Provided that elevated Se concentrations are also known toxicological threats to aquatic animals, I performed a literature search to evaluate the strength of evidence supporting three assertions underpinning the ameliorating benefits of Se: (1) dietary Se reduces MeHg toxicity in consumers; (2) environmental Se reduces Hg bioaccumulation and biomagnification in aquatic food webs; and (3) Se inhibits Hg bioavailability to, and/or MeHg production by, microbial communities. Limited or ambiguous support for each criterion indicates that many scientific uncertainties and gaps remain regarding Se mediation of Hg behavior and toxicity in abiotic and biotic compartments. Significantly more information is needed to provide a strong scientific basis for modifying current fish consumption advisories on the basis of Se:Hg ratios or for applying Se amendments to remediate Hg-contaminated ecosystems.

In chapter 4, I examine evidence for Hg and Se interaction at the base of the food web. Hg, a potent neurotoxin, can biomagnify through food webs once converted into MeHg. Some studies have found that Se exposure may reduce MeHg bioaccumulation and toxicity, though this pattern is not universal. Se itself can also be toxic at elevated levels. We experimentally manipulated the relative concentrations of dietary MeHg and Se (as selenomethionine [SeMet]) for an aquatic grazer (the mayfly, Neocloeon triangulifer) and its food source (diatoms). Under low MeHg treatment (0.2 ng/L), diatoms exhibited a quadratic pattern, with decreasing diatom MeHg concentration up to 2.0 g Se/L and increasing MeHg accumulation at higher SeMet concentrations. Under high MeHg treatment (2 ng/L), SeMet concentrations had no effect on diatom MeHg concentrations. Mayfly MeHg concentrations and biomagnification factors (concentration of MeHg in mayflies: concentration of MeHg in diatoms) declined with SeMet addition only in the high MeHg treatment. Mayfly biomagnification factors decreased from 5.3 to 3.3 in the high MeHg treatment, while the biomagnification factor was constant with an average of 4.9 in the low MeHg treatment. The benefit of reduced MeHg biomagnification was offset by non-lethal effects and high mortality associated with ‘protective’ levels of SeMet exposure. Mayfly larvae escape behavior (i.e., startle response) was greatly reduced at early exposure days. Larvae took nearly twice as long for all to metamorphose to adults at high Se concentrations. The minimum number of days to emergence did not differ by SeMet exposure, with an average of 13 days. We measured an LC50SeMet for mayflies of 3.9 μg Se/L, with complete mortality at concentrations ≥6.0 μg Se/L. High reproductive mortality occurred at elevated SeMet exposures, with only 0-18% emergence at ≥4.12 g Se/L. Collectively our results suggest that while there is some evidence that Se can reduce MeHg accumulation at the base of the food web at specific exposure levels of SeMet and MeHg, Se is also toxic to mayflies and could lead to negative effects that extend across ecosystem boundaries.

In chapter 5, I examine the fate of total and MeHg from ASGM in Senegal. The largest source of global Hg anthropogenic inputs to the environment is derived from ASGM activities in developing countries. While our understanding of global Hg emissions from ASGM is growing, there is limited empirical documentation about the levels of total Hg (THg) and MeHg contamination near ASGM sites. I measured THg and MeHg concentrations in soil (n=119) sediment (n=22), and water (n=25) from four ASGM villages and one non-ASGM reference village in Senegal, West Africa with active ASGM. Nearly all samples had THg and MeHg concentrations that exceeded the reference village concentrations and USEPA regulatory standards. The highest median THg concentrations were found in huts where Hg-gold amalgams were burned (7.5 μg/g), while the highest median MeHg concentrations and percent Hg as MeHg were found in river sediments (4.2 ng/g, 0.41%). Median river water concentrations of THg and MeHg were also elevated compared to values at the reference site (22 ng THg/L, 0.037 ng MeHg/L in ASGM sites). This study provides direct evidence that Hg from ASGM is entering both the terrestrial and aquatic ecosystems where it is converted to the neurotoxic and bioavailable form of MeHg in soils, sediment, and water.

In chapter 6, I examine pathways of Hg deposition and storage from ASGM in the Peruvian Amazon. Hg emissions from ASGM now exceed coal combustion as the largest global source of Hg to the atmosphere and are being released into some of the most biodiverse ecosystems on Earth. Hg, following microbial conversion to MeHg, is a potent neurotoxin with deleterious impacts on people and wildlife. However, while we know ASGM is an important source of Hg to the atmosphere, we know very little about the fate of this source of Hg. Here, I examine Hg deposition and storage in the Peruvian Amazon by analyzing THg and MeHg in atmospheric, precipitation, leaf, and soil samples from remote and mining-impacted areas. I found that intact forests in the Peruvian Amazon near ASGM receive extremely high inputs of Hg in throughfall (71 µg m-2 yr-1) and litterfall (66 μg m-2 yr-1) and have accumulated significant quantities of soil Hg (9100 μg Hg m-2 within the top five cm). My findings show for the first time that intact forests near ASGM are intercepting high levels of Hg deposition, and that songbirds inhabiting these forests have elevated levels of mercury. Our findings raise important questions about how mercury pollution may constrain modern and future conservation efforts in these ecosystems.

In chapter 7, I examine the combined effects of landscape change and Hg loading from ASGM in the Peruvian Amazon. ASGM is the largest global source of anthropogenic Hg emissions. However, little is known about how effectively Hg released from ASGM is converted into the bioavailable form of MeHg in ASGM-altered landscapes. Through examination of ASGM-impacted river basins in Peru, I show that lake area in heavily mined watersheds has increased by 670% between 1985 and 2018, and that lakes in this area convert Hg into MeHg at net rates 5-7 times greater than rivers. These results suggest that synergistic increases in lake area and Hg loading associated with ASGM are significantly increasing exposure risk for people and wildlife. Similarly dramatic increases in lake area in other ASGM hotspots suggest that ‘hydroscape’ (hydrological landscape) alteration is an important and previously unrecognized component of Hg risk from ASGM.

In chapter 8, I develop several of the emergent themes that connect the distinct elements of this dissertation research. Here I develop a conceptual framework for merging perspectives from geochemistry, landscape ecology, and toxicology to understand the movement, fate and impact of toxic trace elements in the natural world. In the Anthropocene, we typically study the increasing mobilization of toxic trace elements and the changing land cover of our planet as separate issues. Yet the way we alter our landscapes plays a critical role in the likelihood that any particular place will retain, sequester, and alter the transport and bioavailability of trace elements to people and wildlife. The goal of this chapter is to provide examples that demonstrate that the risk of contaminant exposure is not merely a function of loading, but arises through interactions among loading, landscape capture, and biological transformation, all of which are simultaneously altered by human activities. I posit that successful prevention and mitigation of trace element toxicity requires a merging of these diverse perspectives and traditions.

The main conclusion of this dissertation is that global H2 production within young ocean crust (<10 Mya) is higher than currently recognized, in part because current estimates of H2 production accompanying the serpentinization of peridotite may be too low (Chapter 2) and in part because a number of abiogenic H2-producing processes have heretofore gone unquantified (Chapter 3). The importance of free H2 to a range of geochemical processes makes the quantitative understanding of H2 production advanced in this dissertation pertinent to an array of open research questions across the geosciences (e.g. the origin and evolution of life and the oxidation of the Earth’s atmosphere and oceans).

The first component of this dissertation (Chapter 2) examines H2 produced within young ocean crust [e.g. near the mid-ocean ridge (MOR)] by serpentinization. In the presence of water, olivine-rich rocks (peridotites) undergo serpentinization (hydration) at temperatures of up to ~500°C but only produce H2 at temperatures up to ~350°C. A simple analytical model is presented that mechanistically ties the process to seafloor spreading and explicitly accounts for the importance of temperature in H2 formation. The model suggests that H2 production increases with the rate of seafloor spreading and the net thickness of serpentinized peridotite (S-P) in a column of lithosphere. The model is applied globally to the MOR using conservative estimates for the net thickness of lithospheric S-P, our least certain model input. Despite the large uncertainties surrounding the amount of serpentinized peridotite within oceanic crust, conservative model parameters suggest a magnitude of H2 production (~1012 moles H2/y) that is larger than the most widely cited previous estimates (~1011 although previous estimates range from 1010-1012 moles H2/y). Certain model relationships are also consistent with what has been established through field studies, for example that the highest H2 fluxes (moles H2/km2 seafloor) are produced near slower-spreading ridges (<20 mm/y). Other modeled relationships are new and represent testable predictions. Principal among these is that about half of the H2 produced globally is produced off-axis beneath faster-spreading seafloor (>20 mm/y), a region where only one measurement of H2 has been made thus far and is ripe for future investigation.

In the second part of this dissertation (Chapter 3), I construct the first budget for free H2 in young ocean crust that quantifies and compares all currently recognized H2 sources and H2 sinks. First global estimates of budget components are proposed in instances where previous estimate(s) could not be located provided that the literature on that specific budget component was not too sparse to do so. Results suggest that the nine known H2 sources, listed in order of quantitative importance, are: Crystallization (6x1012 moles H2/y or 61% of total H2 production), serpentinization (2x1012 moles H2/y or 21%), magmatic degassing (7x1011 moles H2/y or 7%), lava-seawater interaction (5x1011 moles H2/y or 5%), low-temperature alteration of basalt (5x1011 moles H2/y or 5%), high-temperature alteration of basalt (3x1010 moles H2/y or <1%), catalysis (3x108 moles H2/y or <<1%), radiolysis (2x108 moles H2/y or <<1%), and pyrite formation (3x106 moles H2/y or <<1%). Next we consider two well-known H2 sinks, H2 lost to the ocean and H2 occluded within rock minerals, and our analysis suggests that both are of similar size (both are 6x1011 moles H2/y). Budgeting results suggest a large difference between H2 sources (total production = 1x1013 moles H2/y) and H2 sinks (total losses = 1x1011 moles H2/y). Assuming this large difference represents H2 consumed by microbes (total consumption = 9x1011 moles H2/y), we explore rates of primary production by the chemosynthetic, sub-seafloor biosphere. Although the numbers presented require further examination and future modifications, the analysis suggests that the sub-seafloor H2 budget is similar to the sub-seafloor CH4 budget in the sense that globally significant quantities of both of these reduced gases are produced beneath the seafloor but never escape the seafloor due to microbial consumption.

The third and final component of this dissertation (Chapter 4) explores the self-organization of barchan sand dune fields. In nature, barchan dunes typically exist as members of larger dune fields that display striking, enigmatic structures that cannot be readily explained by examining the dynamics at the scale of single dunes, or by appealing to patterns in external forcing. To explore the possibility that observed structures emerge spontaneously as a collective result of many dunes interacting with each other, we built a numerical model that treats barchans as discrete entities that interact with one another according to simplified rules derived from theoretical and numerical work, and from field observations: Dunes exchange sand through the fluxes that leak from the downwind side of each dune and are captured on their upstream sides; when dunes become sufficiently large, small dunes are born on their downwind sides (“calving”); and when dunes collide directly enough, they merge. Results show that these relatively simple interactions provide potential explanations for a range of field-scale phenomena including isolated patches of dunes and heterogeneous arrangements of similarly sized dunes in denser fields. The results also suggest that (1) dune field characteristics depend on the sand flux fed into the upwind boundary, although (2) moving downwind, the system approaches a common attracting state in which the memory of the upwind conditions vanishes. This work supports the hypothesis that calving exerts a first order control on field-scale phenomena; it prevents individual dunes from growing without bound, as single-dune analyses suggest, and allows the formation of roughly realistic, persistent dune field patterns.

The Arctic Ocean and Western Antarctic Peninsula (WAP) are the fastest warming regions on the planet and are undergoing rapid climate and ecosystem changes. Until we can fully resolve the coupling between biological and physical processes we cannot predict how warming will influence carbon cycling and ecosystem function and structure in these sensitive and climactically important regions. My dissertation centers on the use of high-resolution measurements of surface dissolved gases, primarily O2 and Ar, as tracers or physical and biological functioning that we measure underway using an optode and Equilibrator Inlet Mass Spectrometry (EIMS). Total O2 measurements are common throughout the historical and autonomous record but are influenced by biological (net metabolic balance) and physical (temperature, salinity, pressure changes, ice melt/freeze, mixing, bubbles and diffusive gas exchange) processes. We use Ar, an inert gas with similar solubility properties to O2, to devolve distinct records of biological (O2/Ar) and physical (Ar) oxygen. These high-resolution measurements that expose intersystem coupling and submesoscale variability were central to studies in the Arctic Ocean, WAP and open Southern Ocean that make up this dissertation.

Key findings of this work include the documentation of under ice and ice-edge blooms and basin scale net sea ice freeze/melt processes in the Arctic Ocean. In the WAP O2 and pCO2 are both biologically driven and net community production (NCP) variability is controlled by Fe and light availability tied to glacial and sea ice meltwater input. Further, we present a feasibility study that shows the ability to use modeled Ar to derive NCP from total O2 records. This approach has the potential to unlock critical carbon flux estimates from historical and autonomous O2 measurements in the global oceans.

Headwater streams serve multiple important biogeochemical, hydrologic, and ecological functions, including: transporting solutes from the terrestrial landscape to downstream fluvial ecosystems; providing a surface for gas evasion to the atmosphere; integrating terrestrial, riparian and aquatic ecosystems, amalgamating surface and groundwater; accumulating and storing sediment; and transforming and retaining solutes. The numerous mechanisms mediating these physical and biological processes remain poorly understood despite their prominent influence on catchment outlet biogeochemical dynamics.

In light of this research need, this study sought to determine the influence of hydrologic, ecological, and biogeochemical processes on solute (specifically carbon and nitrogen) concentrations and fluxes in a paired set of headwater stream networks.

This research was conducted at the Tenderfoot Creek Experimental Forest in Montana. An empirical, field-based approach that combined observational monitoring using a network of high temporal resolution sensors and experimental solute additions was used to quantify carbon and nitrogen uptake, metabolism, and export across the snowmelt and baseflow recession periods.

Based on analysis of this data set, we determined that headwater streams show strong demand for carbon and nitrogen across a range of concentrations from ambient to saturating concentrations; that the variation in uptake kinetics seasonally and between sites is driven by substrate availability; that this retention capacity is linked to the magnitude of metabolic demand; and that through the metabolism of the biological community carbon and nitrogen cycles are coupled. We then demonstrate that these biological processes can have variable roles in mediating carbon and nitrogen export at the catchment scale, but during some periods of the year they can be as influential as physically driven fluxes in mediating watershed export.

This study integrates disparate ecological and hydrologic perspectives to address how energy and macronutrients move through headwater stream networks. We believe the findings presented here begin to reconcile the seemingly incompatible paradigms of streams as highly retentive biogeochemical reactors and streams as “passive pipes” that reflect and integrate the terrestrial landscape.

To satisfy a growing population, much of Earth’s surface has been designed to suit humanity’s needs. Although these ecosystem designs have improved human welfare, they have also produced significant negative environmental impacts, which applied ecology as a field has attempted to address and solve. Many of the failures in applied ecology to achieve this goal of reducing neg- ative environmental impacts are design failures, not failures in the science. Here, we review (a) how humans have designed much of Earth’s surface, (b) the history of design ideas in ecology and the philosophical and practical critiques of these ideas, (c) design as a conceptual process, (d) how changing approaches and goals in subfields of applied ecology reflect changes and failures in design, and (e) why it is important not only for ecologists to en- courage design fields to incorporate ecology into their practice but also for design to be more thoroughly incorporated into ours.

One of the most heavily altered and designed ecosystems in the world is the mountaintop mines of Central Appalachia. Mountaintop mining is the most common form of coal mining in the Central Appalachian ecoregion. Previous estimates suggest that active, reclaimed, or abandoned mountaintop mines cover ∼7% of Central Appalachia. While this is double the areal extent of development in the ecoregion (estimated to occupy <3% of the land area), the impacts are far more extensive than areal estimates alone can convey as the impacts of mines extend 10s to 100s of meters below the current land surface. Here, we provide the first estimates for the total volumetric and topographic disturbance associated with mining in an 11 500 km2 region of southern West Virginia. We find that the cutting of ridges and filling of valleys has lowered the median slope of mined landscapes in the region by nearly 10 degrees while increasing their average elevation by 3 m as a result of expansive valley filling. We estimate that in southern West Virginia, more than 6.4km3 of bedrock has been broken apart and deposited into 1544 headwater valley fills. We used NPDES monitoring datatsets available for 91 of these valley fills to explore whether fill characteristics could explain variation in the pH or selenium concentrations reported for streams draining these fills. We found that the volume of overburden in individual valley fills correlates with stream pH and selenium concentration, and suggest that a three-dimensional assessment of mountaintop mining impacts is necessary to predict both the severity and the longevity of the resulting environmental impacts.

Chemical weathering of bedrock is the ultimate source of solutes for all ecosystems, a geologic sink of C, and controls the rate at which mountains dissolve into the sea. Human activities bring large volumes of bedrock to the surface and enhance global weathering rates. Here, we show watersheds impacted by mountaintop mining for coal have among the highest rates of chemical weathering ever reported. Mined watersheds deliver nearly 9,000 kg ha-1 y-1 of dissolved ions downstream. This translates into a chemical weathering rate ~ 330 mm ky-1, which is 55-times higher than background total (chemical and physical) weathering. These exceptionally high dissolution rates result from the production of sulfuric acid by pyrite oxidation. As this strong acid rapidly weathers surrounding carbonate materials, it not only releases large amounts of dissolved solutes, it also liberates 10-50 g of rock-derived C m-2 yr-1. This shifts mined watersheds from net geologic carbon sinks to net geologic carbon sources, further adding to the carbon costs from burning coal and deforesting these landscapes.

The impact from mining will likely last decades for some aspects of recovery and centuries to millennia for others. To examine the paired forest, hydrologic, and biogeochemical changes from mining we used a combination of remote sensing and watershed monitoring. We show that forest recovery on mines is at least twice as slow as typical forest recovery from clearcutting, and that mined areas have persistent low canopy height gaps. These vegetative changes are coupled with decreases in runoff ratios as mines age and water moves through flatter, vegetated landscapes. However, the vegetation change is uncoupled from biogeochemical processes, with strong alkaline mine drainage signals persisting for decades, even as vegetation recovers.

Microorganisms mediate many biogeochemical processes critical to the functioning of ecosystems, which places them as an intermediate between environmental change and the resulting ecosystem response. Yet, we have an incomplete understanding of these relationships, how to predict them, and when they are influential. Understanding these dynamics will inform ecological principles developed for macroorganisms and aid expectations for microbial responses to new gradients. To address this research goal, I used two studies of environmental gradients and a literature synthesis.

With the gradient studies, I assessed microbial community composition in stream biofilms across a gradient of alkaline mine drainage. I used multivariate approaches to examine changes in the non-eukaryote microbial community composition of taxa (chapter 2) and functional genes (chapter 3). I found that stream biofilms at sites receiving alkaline mine drainage had distinct community composition and also differed in the composition of functional gene groups compared with unmined reference sites. Compositional shifts were not dominated by groups that could benefit from mining associated increases of terminal electron acceptors; two-thirds of responsive taxa and functional gene groups were negatively associated with mining. The majority of subsidies and stressors (nitrate, sulfate, conductivity) had no consistent relationships with taxa or gene abundances. However, methane metabolism genes were less abundant at mined sites and there was a strong, positive correlation between selenate reductase gene abundance and mining-associated selenium. These results highlighted the potential for indirect factors to also play an important role in explaining compositional shifts.

In the fourth chapter, I synthesized studies that use environmental perturbations to explore microbial community structure and microbial process connections. I examined nine journals (2009–13) and found that many qualifying papers (112 of 148) documented structure and process responses, but few (38 of 112 papers) reported statistically testing for a link. Of these tested links, 75% were significant. No particular approach for characterizing structure or processes was more likely to produce significant links. Process responses were detected earlier on average than responses in structure. Together, the findings suggested that few publications report statistically testing structure-process links; but when tested, links often occurred yet shared few commonalities in linked processes or structures and the techniques used for measuring them.

Although the research community has made progress, much work remains to ensure that the vast and growing wealth of microbial informatics data is translated into useful ecological information. In part, this challenge can be approached through using hypotheses to guide analyses, but also by being open to opportunities for hypothesis generation. The results from my dissertation work advise that it is important to carefully interpret shifts in community composition in relation to abiotic characteristics and recommend considering ecological, thermodynamic, and kinetic principles to understand the properties governing community responses to environmental perturbation.

Although microbes may strongly influence wetland phosphorus (P) cycling, specific microbial communities and P metabolic processes have not been characterized in wetlands, and microbial P cycling is poorly understood across global ecosystems, especially in soils. The goal of this work is to test the effects of stress and growth factors on microbial communities in wetlands, and on microbial P metabolism and P cycling at ecosystem scales in wetland soils and beyond. I conducted field and laboratory research experiments in wetland soils, which by definition lie along gradients between terrestrial and aquatic ecosystems, and I explicitly compared results in wetlands to adjacent ecosystems to improve inference and impact.

To test relationships between microbial communities, soil stress and resource supply, I compared the distribution and abundance of uncultured bacterial communities to environmental factors across a range of wetland soils including a well-characterized P enrichment gradient, and restoration sequences on organic soils across freshwater wetland types. The strongest predictor of bacterial community composition and diversity was soil pH, which also corresponded with the abundance of some bacterial taxa. Land use and restoration were also strong predictors of bacterial communities, diversity, and the relative abundance of some taxonomic groups. Results from wetland soils in this study were similar to both terrestrial and aquatic ecosystems in the relationship of pH to microbial communities. However, patterns of biogeography I observed in wetlands differed from aquatic systems in their poor relationships to nutrient availability, and from terrestrial ecosystems in the response of microbial diversity to ecosystem restoration.

Accumulation of inorganic polyphosphate (PolyP) is a critical factor in the survival of multiple environmental stresses by bacteria and fungi. This physiological mechanism is best characterized in pure cultures, wastewater, sediments, and I used 31P-NMR experiments to test whether similar processes influence microbial P cycling in wetland soils. I surveyed PolyP accumulation in soils from different wetland types, and observed PolyP dynamics with flooding and seasonal change in field soils and laboratory microcosms. I found PolyP accumulation only in isolated pocosin peatlands, similar to patterns in the published literature. I observed rapid degradation of PolyP with flooding and anerobic conditions in soils and microcosms, and I characterized the biological and intracellular origin of PolyP with soil cell lysis treatments and bacterial cultures. While degradation of PolyP with flooding and anaerobic conditions appeared consistent with processes in aquatic sediments, some seasonal patterns were inconsistent, and experimental shifts in aerobic and anaerobic conditions did not result in PolyP accumulation in soil slurry microcosms. Similar to patterns in wetlands, I found prior observations of PolyP accumulation in published 31P-NMR studies of terrestrial habitats were limited to acid organic soils, where PolyP accumulation is thought to be fungal in origin. Fungal accumulation of PolyP may be useful as an alternative model for PolyP accumulation in wetlands, although I did not test for fungal activity or PolyP metabolism.

To evaluate relationships between microbial P metabolism and growth, I compared concentrations of P in soil microbial biomass with the soil metabolic quotient (qCO2) by compiling a large-scale dataset of the carbon (C), nitrogen (N) and P contents of soils and microbial biomass, along with C mineralization rates across global wetland and terrestrial ecosystems (358 observations). The ratios of these elements (stoichiometry) in biomass may reflect nutrient limitation (ecological stoichiometry), or be related to growth rates (Biological Stoichiometry). My results suggest that the growth of microbial biomass pools may be limited by N availability, while microbial metabolism was highly correlated to P availability, which suggests P limitation of microbial metabolism. This pattern may reflect cellular processes described by Biological Stoichiometry, although microbial stoichiometry was only indirectly related to respiration or metabolic rates. I found differences in the N:P ratios of soil microbial biomass among ecosystems and habitats, although high variation within habitats may be related to available inorganic P, season, metabolic states, or P and C rich energy storage compounds. Variation in microbial respiration and metabolic rates with soil pH suggests important influences of microbial communities and their responses to stress on metabolism and P cycling.

My dissertation research represents early contributions to the understanding of microbial communities and specific processes of microbial P metabolism in wetlands, including PolyP accumulation and Biological Stoichiometry, which underpin microbial cycling of P and C. Together, my research findings broadly indicate differences in microbial P metabolism among habitats in wetlands and other ecosystems, which suggests the prevailing paradigm of uniform P cycling by microbes will be inadequate to characterize the role of microbes in wetland P cycling and retention. While I observed some concomitant shifts in microbial communities, PolyP accumulation, and microbial stoichiometry with soil pH, land use, and habitat factors, relationships between specific microbial groups and their P metabolism is beyond the scope of this work, but represents an exciting frontier for future research studies.

One of the major challenges in understanding aquatic ecosystems is teasing apart the interrelated influences of multiple stressors on ecosystem function to determine their relative importance. Urban areas are expanding across the globe at unprecedented rates, and as low-lying areas within landscapes, streams and ponds are particularly hard hit by the multiple stressors associated with the urban stream syndrome. This dissertation investigates the effects of stressors as fundamental drivers of urban freshwater ecosystem function in lentic and lotic systems.

Stormwater ponds and retention basins are ubiquitous lentic features throughout urban landscapes that potentially serve as important control points for nitrogen (N) removal from surface water bodies via denitrification. However, there are possible tradeoffs to this water quality benefit if high N and contaminant concentrations in stormwater pond sediments decrease the complete reduction of nitrous oxide (N₂O), a potent greenhouse gas, to dinitrogen (N₂) during denitrification. Here, I evaluated whether urban stormwater pond sediments from 64 ponds across eight major US cities had elevated potential emissions of N₂O (Chapter 2). I found surprisingly little correlation between surrounding land cover urbanization intensity and pond sediment chemistry. I measured highly variable potential rates of denitrification, but generally low proportions of N₂O relative to total denitrification, allaying the concerns that motivated the study. However, the lack of a relationship between land cover and sediment chemistry within urban ponds calls into question our commonly held assumptions about the relationships between development intensity and the loading, routing, and retention of nutrient and contaminants within urban landscapes.

The typically elevated loading of chemical constituents into urban freshwater lotic ecosystems is due to the efficient routing of water over surfaces heavily modified by human activities (i.e. stormwater and wastewater infrastructure). In this study, I investigated the dominant controls on ion routing and loading within 24 urban watersheds that fell within a narrow range of development intensity but spanned the widest possible range in spatial configuration and connectivity metrics in the Triangle region of the North Carolina Piedmont (Chapter 3). By pairing analysis of land cover attributes with temporal trends in baseflow chemistry and high-frequency data of specific conductance and discharge, I found that increases in watershed road and pipe density lead to increasingly chemically distinct stormflows and baseflows. This enhanced bimodality of both flow and chemistry results in more variable chemical regimes in watersheds where linear urban infrastructure (roads and pipes) connects impervious surfaces directly to streams.

In addition to altered chemical loading, headwater streams draining urbanized catchments are subject to frequent and intense flooding. Here, I investigated how altered hydrologic regimes in urban landscapes affect headwater stream form and function (Chapter 4). I found a surprisingly wide range in dissolved oxygen regimes, ranging from frequent hypoxia to near constant saturation, both of which resulted in net heterotrophic streams with low rates of productivity. This work, paired with work presented in Chapter 3, advances understanding of carbon cycling within streams by documenting a shift in ecosystem dynamics in urban streams towards bimodality between the fast dynamics of advective transport from pavements and hillslopes during storms, and the slow dynamics of redox active zones in eutrophic and organically enriched stream pools at base flow.

Stream ecosystems draining highly urbanized areas are often some of the most extreme cases of altered physical and chemical stressor regimes and provide a testbed for examining the influence of these drivers on ecosystem function. The findings presented improve our understanding of how nutrients and contaminants move through landscapes, undergo biogeochemical transformations, and their ultimate effect on aquatic ecosystem processes.

Methane is an important greenhouse gas, and an ideal target for greenhouse gas emissions reductions. Unlike carbon dioxide, methane has a relatively short atmospheric lifetime, so reductions in methane emissions could have large and immediate impacts on anthropogenic radiative forcing. A more detailed understanding of the global methane budget could help guide effective emissions reductions efforts.

Humans have greatly altered the methane budget. Anthropogenic methane sources are approximately equal in flux to natural sources, and the current atmospheric methane concentration is ~2.5 times pre-industrial levels. The advent of hydraulic fracturing and resulting increase in unconventional natural gas extraction have introduced new uncertainties in the methane budget. At the same time, the next few decades could be a crucial period for controlling greenhouse gas emissions to avoid irreversible and catastrophic changes in global climate. Natural gas could provide lower-carbon fossil energy, but the climate benefits of this fuel source are highly dependent on the associated methane emissions. In this context of increasing uncertainty and growing necessity, quantifying the impact of natural gas extraction and use on the methane budget is an essential step in making informed decisions about energy.

In the work presented here, I track methane in the environment to address several areas of uncertainty in our present understanding of the methane budget. I apply the tools of methane analysis in a variety of environments, from rural groundwater supplies to an urban atmosphere, and at a range of scales, from individual point sources to regional flux. I first show that carbon isotopes of methane and co-occurrence of ethane are useful techniques for differentiating a range of methane sources. In so doing, I also show that leaks from natural gas infrastructure are a major source of methane in my study area, Boston, MA. I then build on this work by applying the same methane carbon isotope and ethane signatures to partition methane flux for the Boston metro region. I find that 88% of the methane enhancement in the atmosphere above Boston is due to pipeline natural gas.

In the final portion of this thesis and the two appendices, I move from the distribution side of the natural gas production chain to extraction, specifically addressing the potential impacts from hydraulic fracturing in my home state of North Carolina. I combine the methane source identification techniques of the previous sections with additional geochemical analyses to document the pre-drilling water quality in the Deep River Triassic Basin, an area which could be drilled for natural gas in the future. This data set is unique in that North Carolina has no pre-existing commercial oil and gas extraction, unlike other states where unconventional gas extraction is currently taking place. This research is, to my knowledge, the first to examine the hydrogeology of the Deep River Basin, in addition to providing an important background data set that could be used to track changes in water quality accompanying hydraulic fracturing in the region in the future.

Marine microbes play key roles in driving patterns of important biogeochemical processes including primary production across the global ocean. Despite the importance of such interactions between the marine microbial community and ocean biogeochemistry, oceanographers have yet to attain a deep understanding of the ecological mechanisms underlying these connections. Due to the vast scale of ocean ecosystems, however, large-scale yet high-resolution surveys are necessary to uncover specific relationships between biology and elemental cycling for more detailed study.

With this need in mind, this dissertation takes advantage of recent advances in both underway techniques to measure in situ biogeochemical rates—most notably the dissolved O2/Ar method for measuring net community production (NCP)—as well as molecular sequencing methods to directly investigate relationships between marine microbial community structure, productivity, nitrogen (N2) fixation, and nutrient availability across large ocean regions. At the same time, this work also improves our understanding of the O2/Ar technique by evaluating its performance and key assumptions in a dynamic upwelling environment and by presenting recommendations to improve the accuracy of productivity estimates generated using this approach.

Presenting data and measurements from the most comprehensive survey of marine microbial community structure and patterns of productivity and N2 fixation in the western North Atlantic to date, this manuscript highlights intriguing connections between regional peaks in productivity and N2 fixation, the mixotrophic algae Chrysophyceae and Aureococcus anophagefferens, and Braarudosphaera bigelowii, a eukaryotic host organism for N2-fixing bacteria. In addition, we report a strong negative relationship between eukaryotic marine microbial diversity and productivity across the region. We further highlight the importance of considering diel cycles of productivity/respiration, other non-steady-state conditions, and vertical fluxes of O2/Ar when calculating and interpreting NCP rates obtained from surface O2/Ar measurements. Ultimately, these findings contribute to our ability to evaluate community production using surface ocean dissolved gas measurements and provide important insights into patterns of marine microbial activity and community structure into the western North Atlantic.

Oceanic net community production (NCP), defined as photosynthesis in excess of respiration, lowers the CO2 concentration at the ocean surface and in the process regulates atmospheric CO2 levels on seasonal to glacial-interglacial time scales. The magnitude of oceanic NCP, and the regulating factors are however poorly constrained. This dissertation aims to derive estimates of the large-scale distribution of NCP and to explore the mechanisms driving this variability, at regional scales (Western Antarctic Peninsula; Chapter 2), basin scales (Southern Ocean, Chapter 3), and global scale (world oceans, Chapter 4).

In Chapter 2, we use remotely sensed properties and in-situ observations of O2/Ar-NCP from 2008 to 2014 to explore the interannual variability in NCP at the Western Antarctic Peninsula. We find that annual NCP in the shelf and coastal regions is up to eight times higher than in offshore regions, with hotspots observed around canyons. The interannual variability in annual NCP observed in the region is likely controlled by the iron supply from subsurface or horizontal advection.

In Chapter 3, we use remotely sensed properties to investigate the impact of mixed-layer dynamics on NCP in the Southern Ocean. We find that, as expected, NCP is largely controlled by light availability on seasonal time scales. On intra-seasonal time scales, a deepening of mixed layer increases NCP which we attribute to increased nutrient availability. On interannual time scales, NCP correlates with a host of parameters (i.e., stratification, wind kinetic energy, and mixed layer depth), but not to mixed layer depth (MLD). Although we do not observe a secular trend in NCP for the entire Southern Ocean, NCP increases (decreases) in the Atlantic (Pacific) sector over the 1997-2014 period. Overall, our results show that the driving mechanisms behind the NCP distribution vary as a function of the temporal and spatial scales under study.

In Chapter 4, we derive two global satellite NCP algorithms using O2/Ar measurements and the machine-learning methods of genetic programming and support vector machine. Our new algorithms are comparable to other algorithms in their prediction accuracy and magnitude of global biological carbon fluxes at the ocean surface, but predict a more spatially uniform NCP distribution for the world’s oceans.

In Chapter 5, we develop a mechanistic model of the carbon export potential from the mixed layer as a function of light availability. We show that the model is remarkably consistent with in-situ observations of O2/Ar-derived NCP and export production estimates from 234Th and sediment traps. Our model suggests that carbon export production in the Southern Ocean is likely co-limited by light and nutrient availability.

We end with a discussion of future projects in the concluding chapter 6.

Patterns of primary productivity are primarily dictated by seasonal factors like light availability and temperature. In small rivers, primary productivity often peaks opposite that of terrestrial ecosystems, where overhanging canopies shade the river channel impeding light reaching the water surface. The degree to which river primary productivity is affected by the surrounding terrestrial environment depends on the river size. As rivers widen, river primary productivity increases, with more light reaching the stream channel. While light availability may set up the “window of metabolic opportunity” for river primary producers, factors like flow disturbance and grazing pressure from invertebrates can constrain the overall magnitude of gross primary productivity, or GPP. My dissertation seeks to evaluate what processes control the pattern and magnitude of primary productivity in rivers. I evaluate this driving question by analyzing the efficiency by which river ecosystems convert light energy into autotrophic biomass across 64 rivers (Chapter 2), through a series of in-depth experiments and careful monitoring of algae in a small forested river (Chapter 3), and in evaluating whether ice cover determines patterns of primary productivity along a river continuum (Chapter 4). Finally, I provide a framework for evaluating how climate change may be impacting the patterns of primary productivity in rivers (Chapter 5). In Chapter 2, we found that rivers are extremely efficient at converting light energy to biomass (i.e. have a high ecosystem light use efficiency, LUE). The range of LUEs reported in our study encompasses the entire range for any ecosystem LUE measured in forests, crops, lakes, and previous river studies. While river ecosystems have the potential to have high LUE on their “best days,” variability of flow constrains LUE throughout the year. In Chapter 3, we found that algae in the oligotrophic and steep headwaters of Hubbard Brook Experimental Forest were both more abundant than past studies and preferentially grew within substrates that simulate the physical structure of bryophytes. Throughout four separate nutrient diffusing substrate deployments, we found that nutrients rarely limited algal biomass. This chapter explores the previously unsuspected role of bryophytes in providing refugia for algae in this high-gradient and nutrient-poor stream. In Chapter 4, we combined three metrics of ice cover (satellite-, field camera-, and temperature-based) with a proxy for primary productivity across a river continuum. We found that satellite and field camera-based ice cover records reveal two important aspects of ice dynamics in a 3rd to 6th Strahler order river. First, river ice in narrow channels is dynamic, with more complete ice cover days and mid-winter breakups happening on the narrowest section of the reach. Second, ice cover is habitat-specific, with riffle sequences along the river never reaching complete ice cover. In comparing ice dynamics to a proxy of GPP, diel dissolved oxygen amplitude, we found that ice on rivers not only affects the overall pattern of primary productivity, but also affects our ability to measure primary productivity by affecting river gas exchange. Finally, in Chapter 5, I provide examples of relevant drivers of change for river ecosystem GPP in a warming climate. More studies that attempt to disentangle how climate change is affecting light availability, nutrients, temperature, ice cover, etc., or how climate change is shifting the “windows of metabolic opportunity” for rivers, will be imperative in the Anthropocene.

Rivers transform more than half of the organic inputs they receive from terrestrial systems through metabolic processes. In addition to providing the energetic base to sustain stream food webs, these transformations are linked to multiple elemental cycles and result in the release of greenhouse gasses to the atmosphere, oxygen depletion, and the mobilization of trace metals. Despite this central importance we lack a sufficient understanding of what drives processes within these ecosystems to make broad scale predictions about metabolic rates and biogeochemical cycles. This dissertation addresses how local controls interact with hydrologic and geomorphic constraints to determine the nature and magnitude of stream carbon and energy cycling. Through field observations and ecosystem process models, this study characterizes the spatial and seasonal biogeochemical dynamics of a single study system, New Hope Creek, a low gradient 3rd order river in the North Carolina Piedmont. I present a mechanistic explanation of stream ecosystem functioning from three different perspectives and use the insights gained to confront existing conceptual models and methods in river science. In chapter two, I examined the frequency and dynamics of river hypoxia, or depleted dissolved oxygen, in the North Carolina Piedmont by synthesizing state monitoring records since the 1960s and by collecting high resolution measurements of oxygen along a 20 km section of New Hope Creek. In chapter three, I monitored dissolved oxygen concentrations and modeled the metabolic regimes across six river segments over the course of three years. I compared the rates and seasonality of annual metabolism across space and time and examined the impact of climatic, hydrologic, and geomorphic drivers. Using the scales of this variation for context, I compared the metabolic regime in New Hope Creek today to a historical study of annual metabolism collected fifty years ago in the same site. In chapter four, I measured dissolved greenhouse gas concentrations from the autumn to the following spring at the six study locations from chapter three. I calculated the rate of exchange of CO2, CH4, N2O and O2 with the atmosphere, estimated the fraction of this flux that was attributable to instream metabolic processes, and determined the best predictors for each concentration and flux rate. The results from this research have implications for both conceptual models and methodological approaches. First, I found that hypoxia is widespread throughout New Hope Creek. It can arise through oxygen supply limitation due to seasonal low flows and warm water, even in the absence of high organic matter and nutrient loading. Hypoxia is most frequent at night and in pools, and is systematically underrepresented by state-wide monitoring records which rely on point samples and avoid both night and pools. Second, warmer water temperatures shift stream ecosystems toward more net heterotrophy. The effects of rising temperatures on stream ecosystem respiration are contingent upon organic matter inputs and storage, each of which are strongly constrained by flow regime and local geomorphology. Hydrologic settings in which storms are more frequent or more severe will drive high variability in the transport and fate of organic matter processing in streams. Third, the geomorphology and hydrology of New Hope Creek create conditions under which stream metabolic cycling is the dominant control on greenhouse gas concentrations and flux rates. These findings challenge preconceived notions about how rivers work and encourage us to reconsider conceptual models. Rivers are lotic ecosystems, which are defined by their advective flow, with the implication that they are well aerated and rarely hypoxic. Methods in stream ecology are not suited to study the conditions that arise during lentic, or non-flowing, time periods and as a result, the geomorphologies that create these conditions are avoided and understudied. However, these results suggest that they are control points of biogeochemical activity and that they may be more susceptible to change in response to anthropogenic drivers. Collectively, this study calls into question the binary distinction between lotic and lentic ecosystem dynamics with which we tend to categorize and study freshwater ecosystems. To understand the full range of variability of inland waters we must broaden our conceptual frameworks and adapt our methods of study to encompass ecosystems that span this divide.