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- Genre: Doctoral Dissertation
Description
The oceans play an essential role in global biogeochemical cycles and in regulating climate. The biological carbon pump, the photosynthetic fixation of carbon dioxide by phytoplankton and subsequent sequestration of organic carbon into deep water, combined with the physical carbon pump, make the oceans the only long-term net sink for anthropogenic carbon dioxide. A full understanding of the workings of the biological carbon pump requires a knowledge of the role of different taxonomic groups of phytoplankton (protists and cyanobacteria) to organic carbon export. However, this has been difficult due to the degraded nature of particles sinking into particle traps, the main tools employed by oceanographers to collect sinking particulate matter in the ocean. In this study DNA-based molecular methods, including denaturing gradient gel electrophoresis, cloning and sequencing, and taxon-specific quantitative PCR, allowed for the first time for the identification of which protists and cyanobacteria contributed to the material collected by the traps in relation to their presence in the euphotic zone. I conducted this study at two time-series stations in the subtropical North Atlantic Ocean, one north of the Canary Islands, and one located south of Bermuda. The Bermuda study allowed me to investigate seasonal and interannual changes in the contribution of the plankton community to particle flux. I could also show that small unarmored taxa, including representatives of prasinophytes and cyanobacteria, constituted a significant fraction of sequences recovered from sediment trap material. Prasinophyte sequences alone could account for up to 13% of the clone library sequences of trap material during bloom periods. These observations contradict a long-standing paradigm in biological oceanography that only large taxa with mineral shells are capable of sinking while smaller, unarmored cells are recycled in the euphotic zone through the microbial loop. Climate change and a subsequent warming of the surface ocean may lead to a shift in the protist community toward smaller cell size in the future, but in light of these findings these changes may not necessarily lead to a reduction in the strength of the biological carbon pump.
ContributorsAmacher, Jessica (Author) / Neuer, Susanne (Thesis advisor) / Garcia-Pichel, Ferran (Committee member) / Lomas, Michael (Committee member) / Wojciechowski, Martin (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2011
Description
Microbial electrochemical cells (MXCs) are promising platforms for bioenergy production from renewable resources. In these systems, specialized anode-respiring bacteria (ARB) deliver electrons from oxidation of organic substrates to the anode of an MXC. While much progress has been made in understanding the microbiology, physiology, and electrochemistry of well-studied model ARB such as Geobacter and Shewanella, tremendous potential exists for MXCs as microbiological platforms for exploring novel ARB. This dissertation introduces approaches for selective enrichment and characterization of phototrophic, halophilic, and alkaliphilic ARB. An enrichment scheme based on manipulation of poised anode potential, light, and nutrient availability led to current generation that responded negatively to light. Analysis of phototrophically enriched communities suggested essential roles for green sulfur bacteria and halophilic ARB in electricity generation. Reconstruction of light-responsive current generation could be successfully achieved using cocultures of anode-respiring Geobacter and phototrophic Chlorobium isolated from the MXC enrichments. Experiments lacking exogenously supplied organic electron donors indicated that Geobacter could produce a measurable current from stored photosynthate in the dark. Community analysis of phototrophic enrichments also identified members of the novel genus Geoalkalibacter as potential ARB. Electrochemical characterization of two haloalkaliphilic, non-phototrophic Geoalkalibacter spp. showed that these bacteria were in fact capable of producing high current densities (4-8 A/m2) and using higher organic substrates under saline or alkaline conditions. The success of these selective enrichment approaches and community analyses in identifying and understanding novel ARB capabilities invites further use of MXCs as robust platforms for fundamental microbiological investigations.
ContributorsBadalamenti, Jonathan P (Author) / Krajmalnik-Brown, Rosa (Thesis advisor) / Garcia-Pichel, Ferran (Committee member) / Rittmann, Bruce E. (Committee member) / Torres, César I (Committee member) / Vermaas, Willem (Committee member) / Arizona State University (Publisher)
Created2013
Description
Human activity has increased loading of reactive nitrogen (N) in the environment, with important and often deleterious impacts on biodiversity, climate, and human health. Since the fate of N in the ecosystem is mainly controlled by microorganisms, understanding the factors that shape microbial communities becomes relevant and urgent. In arid land soils, these microbial communities and factors are not well understood. I aimed to study the role of N cycling microbes, such as the ammonia-oxidizing bacteria (AOB), the recently discovered ammonia-oxidizing archaea (AOA), and various fungal groups, in soils of arid lands. I also tested if niche differentiation among microbial populations is a driver of differential biogeochemical outcomes. I found that N cycling microbial communities in arid lands are structured by environmental factors to a stronger degree than what is generally observed in mesic systems. For example, in biological soil crusts, temperature selected for AOA in warmer deserts and for AOB in colder deserts. Land-use change also affects niche differentiation, with fungi being the major agents of N2O production in natural arid lands, whereas emissions could be attributed to bacteria in mesic urban lawns. By contrast, NO3- production in the native desert and managed soils was mainly controlled by autotrophic microbes (i.e., AOB and AOA) rather than by heterotrophic fungi. I could also determine that AOA surprisingly responded positively to inorganic N availability in both short (one month) and long-term (seven years) experimental manipulations in an arid land soil, while environmental N enrichment in other ecosystem types is known to favor AOB over AOA. This work improves our predictions of ecosystem response to anthropogenic N increase and shows that paradigms derived from mesic systems are not always applicable to arid lands. My dissertation also highlights the unique ecology of ammonia oxidizers and draws attention to the importance of N cycling in desert soils.
ContributorsMarusenko, Yevgeniy (Author) / Hall, Sharon J (Thesis advisor) / Garcia-Pichel, Ferran (Thesis advisor) / Mclain, Jean E (Committee member) / Schwartz, Egbert (Committee member) / Arizona State University (Publisher)
Created2013
Description
Sustainable urbanism offers a set of best practice planning and design prescriptions intended to reverse the negative environmental consequences of urban sprawl, which dominates new urban development in the United States. Master planned developments implementing sustainable urbanism are proliferating globally, garnering accolades within the planning community and skepticism among social scientists. Despite attention from supporters and critics alike, little is known about the actual environmental performance of sustainable urbanism. This dissertation addresses the reasons for this paucity of evidence and the capacity of sustainable urbanism to deliver the espoused environmental outcomes through alternative urban design and the conventional master planning framework for development through three manuscripts. The first manuscript considers the reasons why geography, which would appear to be a natural empirical home for research on sustainable urbanism, has yet to accumulate evidence that links design alternatives to environmental outcomes or to explain the social processes that mediate those outcomes. It argues that geography has failed to develop a coherent subfield based on nature-city interactions and suggests interdisciplinary bridging concepts to invigorate greater interaction between the urban and nature-society geographic subfields. The subsequent chapters deploy these bridging concepts to empirically examine case-studies in sustainable urbanism. The second manuscript utilizes fine scale spatial data to quantify differences in ecosystem services delivery across three urban designs in two phases of Civano, a sustainable urbanism planned development in Tucson, Arizona, and an adjacent, typical suburban development comparison community. The third manuscript considers the extent to which conventional master planning processes are fundamentally at odds with urban environmental sustainability through interviews with stakeholders involved in three planned developments: Civano (Tucson, Arizona), Mueller (Austin, Texas), and Prairie Crossing (Grayslake, Illinois). Findings from the three manuscripts reveal deep challenges in conceptualizing an empirical area of inquiry on sustainable urbanism, measuring the outcomes of urban design alternatives, and innovating planning practice within the constraints of existing institutions that facilitate conventional development. Despite these challenges, synthesizing the insights of geography and cognate fields holds promise in building an empirical body of knowledge that complements pioneering efforts of planners to innovate urban planning practice through the sustainable urbanism alternative.
ContributorsTurner, Victoria (Author) / Gober, Patricia (Thesis advisor) / Eakin, Hallie (Committee member) / Kinzig, Ann (Committee member) / Talen, Emily (Committee member) / Arizona State University (Publisher)
Created2013
Description
Irrigation agriculture has been heralded as the solution to feeding the world's growing population. To this end, irrigation agriculture is both extensifying and intensifying in arid regions across the world in an effort to create highly productive agricultural systems. Over one third of modern irrigated fields, however, show signs of serious soil degradation, including salinization and waterlogging, which threaten the productivity of these fields and the world's food supply. Surprisingly, little ecological data on agricultural soils have been collected to understand and address these problems. How, then, can expanding and intensifying modern irrigation systems remain agriculturally productive for the long-term? Archaeological case studies can provide critical insight into how irrigated agricultural systems may be sustainable for hundreds, if not thousands, of years. Irrigation systems in Mesopotamia, for example, have been cited consistently as a cautionary tale of the relationship between mismanaged irrigation systems and the collapse of civilizations, but little data expressly link how and why irrigation failed in the past. This dissertation presents much needed ecological data from two different regions of the world - the Phoenix Basin in southern Arizona and the Pampa de Chaparrí on the north coast of Peru - to explore how agricultural soils were affected by long-term irrigation in a variety of social and economic contexts, including the longevity and intensification of irrigation agriculture. Data from soils in prehispanic and historic agricultural fields indicate that despite long-lived and intensive irrigation farming, farmers in both regions created strategies to sustain large populations with irrigation agriculture for hundreds of years. In the Phoenix Basin, Hohokam and O'odham farmers relied on sedimentation from irrigation water to add necessary fine sediments and nutrients to otherwise poor desert soils. Similarly, on the Pampa, farmers relied on sedimentation in localized contexts, but also constructed fields with ridges and furrows to draw detrimental salts away from planting surfaces in the furrows on onto the ridges. These case studies are then compared to failing modern and ancient irrigated systems across the world to understand how the centralization of management may affect the long-term sustainability of irrigation agriculture.
ContributorsStrawhacker, Colleen (Author) / Spielmann, Katherine A. (Thesis advisor) / Hall, Sharon J (Committee member) / Nelson, Margaret C. (Committee member) / Sandor, Jonathan A (Committee member) / Arizona State University (Publisher)
Created2013
Improving cyanobacterial hydrogen production through bioprospecting of natural microbial communities
Description
Some cyanobacteria can generate hydrogen (H2) under certain physiological conditions and are considered potential agents for biohydrogen production. However, they also present low amounts of H2 production, a reaction reversal towards H2 consumption, and O2 sensitivity. Most attempts to improve H2 production have involved genetic or metabolic engineering approaches. I used a bio-prospecting approach instead to find novel strains that are naturally more apt for biohydrogen production. A set of 36, phylogenetically diverse strains isolated from terrestrial, freshwater and marine environments were probed for their potential to produce H2 from excess reductant. Two distinct patterns in H2 production were detected. Strains displaying Pattern 1, as previously known from Synechocystis sp. PCC 6803, produced H2 only temporarily, reverting to H2 consumption within a short time and after reaching only moderately high H2 concentrations. By contrast, Pattern 2 cyanobacteria, in the genera Lyngbya and Microcoleus, displayed high production rates, did not reverse the direction of the reaction and reached much higher steady-state H2 concentrations. L. aestuarii BL J, an isolate from marine intertidal mats, had the fastest production rates and reached the highest steady-state concentrations, 15-fold higher than that observed in Synechocystis sp. PCC 6803. Because all Pattern 2 strains originated in intertidal microbial mats that become anoxic in dark, it was hypothesized that their strong hydrogenogenic capacity may have evolved to aid in fermentation of the photosynthate. When forced to ferment, these cyanobacteria display similarly desirable characteristics of physiological H2 production. Again, L. aestuarii BL J had the fastest specific rates and attained the highest H2 concentrations during fermentation, which proceeded via a mixed-acid pathway to yield acetate, ethanol, lactate, H2, CO2 and pyruvate. The genome of L. aestuarii BL J was sequenced and bioinformatically compared to other cyanobacterial genomes to ascertain any potential genetic or structural basis for powerful H2 production. The association hcp exclusively in Pattern 2 strains suggests its possible role in increased H2 production. This study demonstrates the value of bioprospecting approaches to biotechnology, pointing to the strain L. aestuarii BL J as a source of useful genetic information or as a potential platform for biohydrogen production.
ContributorsKothari, Ankita (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Vermaas, Willem F J (Committee member) / Rittmann, Bruce (Committee member) / Torres, Cesar (Committee member) / Arizona State University (Publisher)
Created2013
Description
Future robotic and human missions to the Moon and Mars will need in situ capabilities to characterize the mineralogy of rocks and soils within a microtextural context. Such spatially-correlated information is considered crucial for correct petrogenetic interpretations and will be key observations for assessing the potential for past habitability on Mars. These data will also enable the selection of the highest value samples for further analysis and potential caching for return to Earth. The Multispectral Microscopic Imager (MMI), similar to a geologist's hand lens, advances the capabilities of current microimagers by providing multispectral, microscale reflectance images of geological samples, where each image pixel is comprised of a 21-band spectrum ranging from 463 to 1735 nm. To better understand the capabilities of the MMI in future surface missions to the Moon and Mars, geological samples comprising a range of Mars-relevant analog environments as well as 18 lunar rocks and four soils, from the Apollo collection were analyzed with the MMI. Results indicate that the MMI images resolve the fine-scale microtextural features of samples, and provide important information to help constrain mineral composition. Spectral end-member mapping revealed the distribution of Fe-bearing minerals (silicates and oxides), along with the presence of hydrated minerals. In the case of the lunar samples, the MMI observations also revealed the presence of opaques, glasses, and in some cases, the effects of space weathering in samples. MMI-based petrogenetic interpretations compare favorably with laboratory observations (including VNIR spectroscopy, XRD, and thin section petrography) and previously published analyses in the literature (for the lunar samples). The MMI was also deployed as part of the 2010 ILSO-ISRU field test on the slopes of Mauna Kea, Hawaii and inside the GeoLab as part of the 2011 Desert RATS field test at the Black Point Lava Flow in northern Arizona to better assess the performance of the MMI under realistic field conditions (including daylight illumination) and mission constraints to support human exploration. The MMI successfully imaged rocks and soils in outcrops and samples under field conditions and mission operation scenarios, revealing the value of the MMI to support future rover and astronaut exploration of planetary surfaces.
ContributorsNúñez Sánchez, Jorge Iván (Author) / Farmer, Jack D. (Thesis advisor) / Christensen, Philip R. (Committee member) / Garcia-Pichel, Ferran (Committee member) / Robinson, Mark S. (Committee member) / Sellar, R. Glenn (Committee member) / Williams, Lynda B. (Committee member) / Arizona State University (Publisher)
Created2012
Description
Biological soil crusts (BSCs) are critical components of arid and semiarid environments and provide the primary sources of bioavailable macronutrients and increase micronutrient availability to their surrounding ecosystems. BSCs are composed of a variety of microorganisms that perform a wide range of physiological processes requiring a multitude of bioessential micronutrients, such as iron, copper, and molybdenum. This work investigated the effects of BSC activity on soil solution concentrations of bioessential elements and examined the microbial production of organic chelators, called siderophores. I found that aluminum, vanadium, copper, zinc, and molybdenum were solubilized in the action of crusts, while nickel, zinc, arsenic, and zirconium were immobilized by crust activity. Potassium and manganese displayed behavior consistent with biological removal and mobilization, whereas phosphorus and iron solubility were dominated by abiotic processes. The addition of bioavailable nitrogen altered the effects of BSCs on soil element mobilization. In addition, I found that the biogeochemical activites of BSCs were limited by molybdenum, a fact that likely contributes to co-limitation by nitrogen. I confirmed the presence of siderophore producing microbes in BSCs. Siderophores are low-molecular weight organic compounds that are released by bacteria to increase element solubility and facilitate element uptake; siderophore production is likely the mechanism by which BSCs affect the patterns I observed in soil solution element concentrations. Siderophore producers were distributed across a range of bacterial groups and ecological niches within crusts, suggesting that siderophore production influences the availability of a variety of elements for use in many physiological processes. Four putative siderophore compounds were identified using electrospray ionization mass spectrometry; further attempts to characterize the compounds confirmed two true siderophores. Taken together, the results of my work provide information about micronutrient cycling within crusts that can be applied to BSC conservation and management. Fertilization with certain elements, particularly molybdenum, may prove to be a useful technique to promote BSC growth and development which would help prevent arid land degradation. Furthermore, understanding the effects of BSCs on soil element mobility could be used to develop useful biomarkers for the study of the existence and distribution of crust-like communities on ancient Earth, and perhaps other places, like Mars.
ContributorsNoonan, Kathryn Alexander (Author) / Hartnett, Hilairy (Thesis advisor) / Anbar, Ariel (Committee member) / Garcia-Pichel, Ferran (Committee member) / Shock, Everett (Committee member) / Sharp, Thomas (Committee member) / Arizona State University (Publisher)
Created2012
Description
The global transport and deposition of anthropogenic nitrogen (N) to downwind ecosystems are significant and continue to increase. Indeed, atmospheric deposition can be a significant source of N to many watersheds, including those in remote, unpopulated areas. Bacterial denitrification in lake sediments may ameliorate the effects of N loading by converting nitrate (NO3-) to N2 gas. Denitrification also produces nitrous oxide (N2O), a potent greenhouse gas. The ecological effects of atmospheric N inputs in terrestrial ecosystems and the pelagic zone of lakes have been well documented; however, similar research in lake sediments is lacking. This project investigates the effects N of deposition on denitrification and N2O production in lakes. Atmospheric N inputs might alter the availability of NO3- and other key resources to denitrifiers. Such altered resources could influence denitrification, N2O production, and the abundance of denitrifying bacteria in sediments. The research contrasts these responses in lakes at the ends of gradients of N deposition in Colorado and Norway. Rates of denitrification and N2O production were elevated in the sediments of lakes subject to anthropogenic N inputs. There was no evidence, however, that N deposition has altered sediment resources or the abundance of denitrifiers. Further investigation into the dynamics of nitric oxide, N2O, and N2 during denitrification found no difference between deposition regions. Regardless of atmospheric N inputs, sediments from lakes in both Norway and Colorado possess considerable capacity to remove NO3- by denitrification. Catchment-specific properties may influence the denitrifying community more strongly than the rate of atmospheric N loading. In this regard, sediments appear to be insulated from the effects of N deposition compared to the water column. Lastly, surface water N2O concentrations were greater in high-deposition lakes compared to low-deposition lakes. To understand the potential magnitude of deposition-induced N2O production, the greenhouse gas inventory methodology of Intergovernmental Panel on Climate Change was applied to available datasets. Estimated emissions from lakes are 7-371 Gg N y-1, suggesting that lakes could be an important source of N2O.
ContributorsMcCrackin, Michelle Lynn (Author) / Elser, James J (Thesis advisor) / Grimm, Nancy (Committee member) / Hall, Sharon J (Committee member) / Hartnett, Hilairy E (Committee member) / Souza, Valeria (Committee member) / Arizona State University (Publisher)
Created2010
Description
Some cyanobacteria, referred to as boring or euendolithic, are capable of excavating tunnels into calcareous substrates, both mineral and biogenic. The erosive activity of these cyanobacteria results in the destruction of coastal limestones and dead corals, the reworking of carbonate sands, and the cementation of microbialites. They thus link the biological and mineral parts of the global carbon cycle directly. They are also relevant for marine aquaculture as pests of mollusk populations. In spite of their importance, the mechanism by which these cyanobacteria bore remains unknown. In fact, boring by phototrophs is geochemically paradoxical, in that they should promote precipitation of carbonates, not dissolution. To approach this paradox experimentally, I developed an empirical model based on a newly isolated euendolith, which I characterized physiologically, ultrastructurally and phylogenetically (Mastigocoleus testarum BC008); it bores on pure calcite in the laboratory under controlled conditions. Mechanistic hypotheses suggesting the aid of accompanying heterotrophic bacteria, or the spatial/temporal separation of photosynthesis and boring could be readily rejected. Real-time Ca2+ mapping by laser scanning confocal microscopy of boring BC008 cells showed that boring resulted in undersaturation at the boring front and supersaturation in and around boreholes. This is consistent with a process of uptake of Ca2+ from the boring front, trans-cellular mobilization, and extrusion at the distal end of the filaments (borehole entrance). Ca2+ disequilibrium could be inhibited by ceasing illumination, preventing ATP generation, and, more specifically, by blocking P-type Ca2+ ATPase transporters. This demonstrates that BC008 bores by promoting calcite dissolution locally at the boring front through Ca2+ uptake, an unprecedented capacity among living organisms. Parallel studies using mixed microbial assemblages of euendoliths boring into Caribbean, Mediterranean, North and South Pacific marine carbonates, demonstrate that the mechanism operating in BC008 is widespread, but perhaps not universal.
ContributorsRamírez-Reinat, Edgardo L (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Chandler, Douglas (Committee member) / Farmer, Jack (Committee member) / Neuer, Susanne (Committee member) / Arizona State University (Publisher)
Created2010