Matching Items (174)
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
This work focuses on a generalized assessment of source zone natural attenuation (SZNA) at chlorinated aliphatic hydrocarbon (CAH) impacted sites. Given the numbers of sites and technical challenges for cleanup there is a need for a SZNA method at CAH impacted sites. The method anticipates that decision makers will be interested in the following questions: 1-Is SZNA occurring and what processes contribute? 2-What are the current SZNA rates? 3-What are the longer-term implications? The approach is macroscopic and uses multiple lines-of-evidence. An in-depth application of the generalized non-site specific method over multiple site events, with sampling refinement approaches applied for improving SZNA estimates, at three CAH impacted sites is presented with a focus on discharge rates for four events over approximately three years (Site 1:2.9, 8.4, 4.9, 2.8kg/yr as PCE, Site 2:1.6, 2.2, 1.7, 1.1kg/y as PCE, Site 3:570, 590, 250, 240kg/y as TCE). When applying the generalized CAH-SZNA method, it is likely that different practitioners will not sample a site similarly, especially regarding sampling density on a groundwater transect. Calculation of SZNA rates is affected by contaminant spatial variability with reference to transect sampling intervals and density with variations in either resulting in different mass discharge estimates. The effects on discharge estimates from varied sampling densities and spacings were examined to develop heuristic sampling guidelines with practical site sampling densities; the guidelines aim to reduce the variability in discharge estimates due to different sampling approaches and to improve confidence in SZNA rates allowing decision-makers to place the rates in perspective and determine a course of action based on remedial goals. Finally bench scale testing was used to address longer term questions; specifically the nature and extent of source architecture. A rapid in-situ disturbance method was developed using a bench-scale apparatus. The approach allows for rapid identification of the presence of DNAPL using several common pilot scale technologies (ISCO, air-sparging, water-injection) and can identify relevant source architectural features (ganglia, pools, dissolved source). Understanding of source architecture and identification of DNAPL containing regions greatly enhances site conceptualization models, improving estimated time frames for SZNA, and possibly improving design of remedial systems.
ContributorsEkre, Ryan (Author) / Johnson, Paul Carr (Thesis advisor) / Rittmann, Bruce (Committee member) / Krajmalnik-Brown, Rosa (Committee member) / Arizona State University (Publisher)
Created2013
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
Surface plasmon resonance (SPR) has emerged as a popular technique for elucidating subtle signals from biological events in a label-free, high throughput environment. The efficacy of conventional SPR sensors, whose signals are mass-sensitive, diminishes rapidly with the size of the observed target molecules. The following work advances the current SPR sensor paradigm for the purpose of small molecule detection. The detection limits of two orthogonal components of SPR measurement are targeted: speed and sensitivity. In the context of this report, speed refers to the dynamic range of measured kinetic rate constants, while sensitivity refers to the target molecule mass limitation of conventional SPR measurement. A simple device for high-speed microfluidic delivery of liquid samples to a sensor surface is presented to address the temporal limitations of conventional SPR measurement. The time scale of buffer/sample switching is on the order of milliseconds, thereby minimizing the opportunity for sample plug dispersion. The high rates of mass transport to and from the central microfluidic sensing region allow for SPR-based kinetic analysis of binding events with dissociation rate constants (kd) up to 130 s-1. The required sample volume is only 1 μL, allowing for minimal sample consumption during high-speed kinetic binding measurement. Charge-based detection of small molecules is demonstrated by plasmonic-based electrochemical impedance microscopy (P-EIM). The dependence of surface plasmon resonance (SPR) on surface charge density is used to detect small molecules (60-120 Da) printed on a dextran-modified sensor surface. The SPR response to an applied ac potential is a function of the surface charge density. This optical signal is comprised of a dc and an ac component, and is measured with high spatial resolution. The amplitude and phase of local surface impedance is provided by the ac component. The phase signal of the small molecules is a function of their charge status, which is manipulated by the pH of a solution. This technique is used to detect and distinguish small molecules based on their charge status, thereby circumventing the mass limitation (~100 Da) of conventional SPR measurement.
ContributorsMacGriff, Christopher Assiff (Author) / Tao, Nongjian (Thesis advisor) / Wang, Shaopeng (Committee member) / LaBaer, Joshua (Committee member) / Chae, Junseok (Committee member) / Arizona State University (Publisher)
Created2013
Description
Biofuel from microbial biomass is a viable alternative to current energy production practices that could mitigate greenhouse gas levels and reduce dependency on fossil fuels. Sustainable production of microbial biomass requires efficient utilization of nutrients like phosphorus (P). P is a limited resource which is vital for global food security. This paper seeks to understand the fate of P through biofuel production and proposes a proof-of-concept process to recover P from microbial biomass. The photosynthetic cyanobacterium Synechocystis sp. PCC 6803 is found to contain 1.4% P by dry weight. After the crude lipids are extracted for biofuel processing, 92% of the intercellular P is found within the residual biomass. Most intercellular P is associated with nucleic acids which remain within the cell after lipids are extracted. Phospholipids comprise a small percentage of cellular P. A wet chemical advanced oxidation process of adding 30% hydrogen peroxide followed by 10 min of microwave heating converts 92% of the total cellular P from organic-P and polyphosphate into orthophosphate. P was then isolated and concentrated from the complex digested matrix by use of resins. An anion exchange resin impregnated with iron nanoparticles demonstrates high affinity for P by sorbing 98% of the influent P through 20 bed volumes, but only was able to release 23% of it when regenerated. A strong base anion exchange resin sorbed 87% of the influent P through 20 bed volumes then released 50% of it upon regeneration. The overall P recovery process was able to recover 48% of the starting intercellular P into a pure and concentrated nutrient solution available for reuse. Further optimization of elution could improve P recovery, but this provides a proof-of-concept for converting residual biomass after lipid extraction to a beneficial P source.
ContributorsGifford, James McKay (Author) / Westerhoff, Paul (Thesis advisor) / Rittmann, Bruce (Committee member) / Vannela, Ravindhar (Committee member) / Arizona State University (Publisher)
Created2012
Description
Biological soil crusts (BSCs), topsoil microbial assemblages typical of arid land ecosystems, provide essential ecosystem services such as soil fertilization and stabilization against erosion. Cyanobacteria and lichens, sometimes mosses, drive BSC as primary producers, but metabolic activity is restricted to periods of hydration associated with precipitation. Climate models for the SW United States predict changes in precipitation frequency as a major outcome of global warming, even if models differ on the sign and magnitude of the change. BSC organisms are clearly well adapted to withstand desiccation and prolonged drought, but it is unknown if and how an alteration of the precipitation frequency may impact community composition, diversity, and ecosystem functions. To test this, we set up a BSC microcosm experiment with variable precipitation frequency treatments using a local, cyanobacteria-dominated, early-succession BSC maintained under controlled conditions in a greenhouse. Precipitation pulse size was kept constant but 11 different drought intervals were imposed, ranging between 416 to 3 days, during a period of 416 days. At the end of the experiments, bacterial community composition was analyzed by pyrosequencing of the 16s rRNA genes in the community, and a battery of functional assays were used to evaluate carbon and nitrogen cycling potentials. While changes in community composition were neither marked nor consistent at the Phylum level, there was a significant trend of decreased diversity with increasing precipitation frequency, and we detected particular bacterial phylotypes that responded to the frequency of precipitation in a consistent manner (either positively or negatively). A significant trend of increased respiration with increasingly long drought period was detected, but BSC could recover quickly from this effect. Gross photosynthesis, nitrification and denitrification remained essentially impervious to treatment. These results are consistent with the notion that BSC community structure adjustments sufficed to provide significant functional resilience, and allow us to predict that future alterations in precipitation frequency are unlikely to result in severe impacts to BSC biology or ecological relevance.
ContributorsMyers, Natalie Kristine (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Hall, Sharon (Committee member) / Turner, Benjamin (Committee member) / Krajmalnik-Brown, Rosa (Committee member) / Arizona State University (Publisher)
Created2013
Description
This dissertation investigates the condition of skeletal muscle insulin resistance using bioinformatics and computational biology approaches. Drawing from several studies and numerous data sources, I have attempted to uncover molecular mechanisms at multiple levels. From the detailed atomistic simulations of a single protein, to datamining approaches applied at the systems biology level, I provide new targets to explore for the research community. Furthermore I present a new online web resource that unifies various bioinformatics databases to enable discovery of relevant features in 3D protein structures.
ContributorsMielke, Clinton (Author) / Mandarino, Lawrence (Committee member) / LaBaer, Joshua (Committee member) / Magee, D. Mitchell (Committee member) / Dinu, Valentin (Committee member) / Willis, Wayne (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
As engineered nanomaterials (NMs) become used in industry and commerce their loading to sewage will increase. However, the fate of widely used NMs in wastewater treatment plants (WWTPs) remains poorly understood. In this research, sequencing batch reactors (SBRs) were operated with hydraulic (HRT) and sludge (SRT) retention times representative of full-scale biological WWTPs for several weeks. NM loadings at the higher range of expected environmental concentrations were selected. To achieve the pseudo-equilibrium state concentration of NMs in biomass, SBR experiments needed to operate for more than three times the SRT value, approximately 18 days. Under the conditions tested, NMs had negligible effects on ability of the wastewater bacteria to biodegrade organic material, as measured by chemical oxygen demand (COD). NM mass balance closure was achieved by measuring NMs in liquid effluent and waste biosolids. All NMs were well removed at the typical biomass concentration (1~2 gSS/L). However, carboxy-terminated polymer coated silver nanoparticles (fn-Ag) were removed less effectively (88% removal) than hydroxylated fullerenes (fullerols; >90% removal), nano TiO2 (>95% removal) or aqueous fullerenes (nC60; >95% removal). Although most NMs did not settle out of the feed solution without bacteria present, approximately 65% of the titanium dioxide was removed even in the absence of biomass simply due to self-aggregation and settling. Experiments conducted over 4 months with daily loadings of nC60 showed that nC60 removal from solution depends on the biomass concentration. Under conditions representative of most suspended growth biological WWTPs (e.g., activated sludge), most of the NMs will accumulate in biosolids rather than in liquid effluent discharged to surface waters. Significant fractions of fn-Ag were associated with colloidal material which suggests that efficient particle separation processes (sedimentation or filtration) could further improve removal of NM from effluent. As most NMs appear to accumulate in biosolids, future research should examine the fate of NMs during disposal of WWTP biosolids, which may occur through composting or anaerobic digestion and/or land application, incineration, or landfill disposal.
ContributorsWang, Yifei (Author) / Westerhoff, Paul (Thesis advisor) / Krajmalnik-Brown, Rosa (Committee member) / Rittmann, Bruce (Committee member) / Hristovski, Kiril (Committee member) / Arizona State University (Publisher)
Created2012