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- All Subjects: Microbiology
- Creators: Neuer, Susanne
- Status: Published
Description
Safe, readily available, and reliable sources of water are an essential component of any municipality’s infrastructure. Phoenix, Arizona, a southwestern city, has among the highest per capita water use in the United States, making it essential to carefully manage its reservoirs. Generally, municipal water bodies are monitored through field sampling. However, this approach is limited spatially and temporally in addition to being costly. In this study, the application of remotely sensed reflectance data from Landsat 7’s Enhanced Thematic Mapper Plus (ETM+) and Landsat 8’s Operational Land Imager (OLI) along with data generated through field-sampling is used to gain a better understanding of the seasonal development of algal communities and levels of suspended particulates in the three main terminal reservoirs supplying water to the Phoenix metro area: Bartlett Lake, Lake Pleasant, and Saguaro Lake. Algal abundances, particularly the abundance of filamentous cyanobacteria, increased with warmer temperatures in all three reservoirs and reached the highest comparative abundance in Bartlett Lake. Prymnesiophytes (the class of algae to which the toxin-producing golden algae belong) tended to peak between June and August, with one notable peak occurring in Saguaro Lake in August 2017 during which time a fish-kill was observed. In the cooler months algal abundance was comparatively lower in all three lakes, with a more even distribution of abundance across algae classes. In-situ data from March 2017 to March 2018 were compared with algal communities sampled approximately ten years ago in each reservoir to understand any possible long-term changes. The findings show that the algal communities in the reservoirs are relatively stable, particularly those of the filamentous cyanobacteria, chlorophytes, and prymnesiophytes with some notable exceptions, such as the abundance of diatoms, which increased in Bartlett Lake and Lake Pleasant. When in-situ data were compared with Landsat-derived reflectance data, two-band combinations were found to be the best-estimators of chlorophyll-a concentration (as a proxy for algal biomass) and total suspended sediment concentration. The ratio of the reflectance value of the red band and the blue band produced reasonable estimates for the in-situ parameters in Bartlett Lake. The ratio of the reflectance value of the green band and the blue band produced reasonable estimates for the in-situ parameters in Saguaro Lake. However, even the best performing two-band algorithm did not produce any significant correlation between reflectance and in-situ data in Lake Pleasant. Overall, remotely-sensed observations can significantly improve our understanding of the water quality as measured by algae abundance and particulate loading in Arizona Reservoirs, especially when applied over long timescales.
ContributorsRussell, Jazmine Barkley (Author) / Neuer, Susanne (Thesis advisor) / Fox, Peter (Committee member) / Myint, Soe (Committee member) / Arizona State University (Publisher)
Created2018
Description
Is it possible to treat the mouth as a natural environment, and determine new methods to keep the microbiome in check? The need for biodiversity in health may suggest that every species carries out a specific function that is required to maintain equilibrium and homeostasis within the oral cavity. Furthermore, the relationship between the microbiome and its host is mutually beneficial because the host is providing microbes with an environment in which they can flourish and, in turn, keep their host healthy. Reviewing examples of larger scale environmental shifts could provide a window by which scientists can make hypotheses. Certain medications and healthcare treatments have been proven to cause xerostomia. This disorder is characterized by a dry mouth, and known to be associated with a change in the composition, and reduction, of saliva. Two case studies performed by Bardow et al, and Leal et al, tested and studied the relationships of certain medications and confirmed their side effects on the salivary glands [2,3]. Their results confirmed a relationship between specific medicines, and the correlating complaints of xerostomia. In addition, Vissink et al conducted case studies that helped to further identify how radiotherapy causes hyposalivation of the salivary glands [4]. Specifically patients that have been diagnosed with oral cancer, and are treated by radiotherapy, have been diagnosed with xerostomia. As stated prior, studies have shown that patients having an ecologically balanced and diverse microbiome tend to have healthier mouths. The oral cavity is like any biome, consisting of commensalism within itself and mutualism with its host. Due to the decreased salivary output, caused by xerostomia, increased parasitic bacteria build up within the oral cavity thus causing dental disease. Every human body contains a personalized microbiome that is essential to maintaining health but capable of eliciting disease. The Human Oral Microbiomics Database (HOMD) is a set of reference 16S rRNA gene sequences. These are then used to define individual human oral taxa. By conducting metagenomic experiments at the molecular and cellular level, scientists can identify and label micro species that inhabit the mouth during parasitic outbreaks or a shifting of the microbiome. Because the HOMD is incomplete, so is our ability to cure, or prevent, oral disease. The purpose of the thesis is to research what is known about xerostomia and its effects on the complex microbiome of the oral cavity. It is important that researchers determine whether this particular perspective is worth considering. In addition, the goal is to create novel experiments for treatment and prevention of dental diseases.
ContributorsHalcomb, Michael Jordan (Author) / Chen, Qiang (Thesis director) / Steele, Kelly (Committee member) / Barrett, The Honors College (Contributor) / College of Letters and Sciences (Contributor)
Created2015-05
Description
Marine pico-cyanobacteria of the genera Synechococcus and Prochlorococcus carry out nearly two thirds of the primary production in oligotrophic oceans. These cyanobacteria are also considered an important constituent of the biological carbon pump, the photosynthetic fixation of CO2 to dissolved and particulate organic carbon and subsequent export to the ocean’s interior. But single cells of these cyanobacteria are too small to sink, so their carbon export has to be mediated by aggregate formation and/or consumption by zooplankton that produce sinking fecal pellets. In this dissertation, I investigated for the first time the aggregation of these cyanobacteria by studying the marine Synechococcus sp. strain WH8102 as a model organism. I first found in culture experiments that Synechococcus cells aggregated and that such aggregation of cells was related to the production of transparent exopolymeric particles (TEP), known to provide the main matrix of aggregates of eukaryotic phytoplankton. I also found that despite the lowered growth rates, cells in the nitrogen or phosphorus limited cultures had a higher cell-normalized TEP production and formed a greater total volume of aggregates with higher settling velocities compared to cells in the nutrient replete cultures. I further studied the Synechococcus aggregation in roller tanks that allow the simulation of aggregates settling in the water column, and investigated the effects of the clays kaolinite and bentonite that are commonly found in the ocean. In the roller tanks, Synechococcus cells formed aggregates with diameters of up to 1.4 mm and sinking velocities of up to 440 m/d, comparable to those of larger eukaryotic phytoplankton such as diatoms. In addition, the clay minerals increased the number but reduced the size of aggregates, and their ballasting effects increased the sinking velocity and the carbon export potential of the aggregates. Lastly, I investigated the effects of heterotrophic bacteria on the Synechococcus aggregation, and found that heterotrophic bacteria generally resulted in the formation of fewer, but larger and faster sinking aggregates, and eventually led to an enhanced aggregation of cells and particles. My study contributes to the understanding of the role of marine pico-cyanobacteria in the ecology and biogeochemistry of oligotrophic oceans.
ContributorsDeng, Wei (Author) / Neuer, Susanne (Thesis advisor) / Anbar, Ariel (Committee member) / Passow, Uta (Committee member) / Vermaas, Willem (Committee member) / Arizona State University (Publisher)
Created2016
Description
This thesis research focuses on phylogenetic and functional studies of microbial communities in deep-sea water, an untapped reservoir of high metabolic and genetic diversity of microorganisms. The presence of photosynthetic cyanobacteria and diatoms is an interesting and unexpected discovery during a 16S ribosomal rRNA-based community structure analyses for microbial communities in the deep-sea water of the Pacific Ocean. Both RT-PCR and qRT-PCR approaches were employed to detect expression of the genes involved in photosynthesis of photoautotrophic organisms. Positive results were obtained and further proved the functional activity of these detected photosynthetic microbes in the deep-sea. Metagenomic and metatranscriptomic data was obtained, integrated, and analyzed from deep-sea microbial communities, including both prokaryotes and eukaryotes, from four different deep-sea sites ranging from the mesopelagic to the pelagic ocean. The RNA/DNA ratio was employed as an index to show the strength of metabolic activity of deep-sea microbes. These taxonomic and functional analyses of deep-sea microbial communities revealed a `defensive' life style of microbial communities living in the deep-sea water. Pseudoalteromonas sp.WG07 was subjected to transcriptomic analysis by application of RNA-Seq technology through the transcriptomic annotation using the genomes of closely related surface-water strain Pseudoalteromonas haloplanktis TAC125 and sediment strain Pseudoalteromonas sp. SM9913. The transcriptome survey and related functional analysis of WG07 revealed unique features different from TAC125 and SM9913 and provided clues as to how it adapted to its environmental niche. Also, a comparative transcriptomic analysis of WG07 revealed transcriptome changes between its exponential and stationary growing phases.
ContributorsWu, Jieying (Author) / Meldrum, Deirdre R. (Thesis advisor) / Zhang, Weiwen (Committee member) / Abbaszadegan, Morteza (Committee member) / Neuer, Susanne (Committee member) / Arizona State University (Publisher)
Created2013
Description
Phytoplankton comprise the base of the marine food web, and, along with heterotrophic protists, they are key players in the biological pump that transports carbon from the surface to the deep ocean. In the world's subtropical oligotrophic gyres, plankton communities exhibit strong seasonality. Winter storms vent deep water into the euphotic zone, triggering a surge in primary productivity in the form of a spring phytoplankton bloom. Although the hydrographic trends of this "boom and bust" cycle have been well studied for decades, community composition and its seasonal and annual variability remains an integral subject of research. It is hypothesized here that proportions of different phytoplankton and protistan taxa vary dramatically between seasons and years, and that picoplankton represent an important component of this community and contributor to carbon in the surface ocean. Monthly samples from the Bermuda Atlantic Time-series Study (BATS) site were analyzed by epifluorescence microscopy, which permits classification by morphology, size, and trophic type. Epifluorescence counts were supplemented with flow cytometric quantification of Synechococcus, Prochlorococcus, and autotrophic pico- and nanoeukaryotes. Results from this study indicate Synechococcus and Prochlorococcus, prymnesiophytes, and hetero- and mixotrophic nano- and dinoflagellates were the major players in the BATS region plankton community. Ciliates, cryptophytes, diatoms, unidentified phototrophs, and other taxa represented rarer groups. Both flow cytometry and epifluorescence microscopy revealed Synechococcus to be most prevalent during the spring bloom. Prymnesiophytes likewise displayed distinct seasonality, with the highest concentrations again being noted during the bloom. Heterotrophic nano- and dinoflagellates, however, were most common in fall and winter. Mixotrophic dinoflagellates, while less abundant than their heterotrophic counterparts, displayed similar seasonality. A key finding of this study was the interannual variability revealed between the two years. While most taxa were more abundant in the first year, prymnesiophytes experienced much greater abundance in the second year bloom. Analyses of integrated carbon revealed further stark contrasts between the two years, both in terms of total carbon and the contributions of different groups. Total integrated carbon varied widely in the first study year but displayed less fluctuation after June 2009, and values were noticeably reduced in the second year.
ContributorsHansen, Amy (Author) / Neuer, Susanne (Thesis advisor) / Krajmalnik-Brown, Rosa (Committee member) / Sommerfeld, Milton (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
Description
The efficiency of the ocean’s biological carbon pump is mediated by fast-sinking particles that quickly settle out of the euphotic zone. These particles are conventionally associated with micro- (> 20 µm) sized diatoms and coccolithophorids, thought to efficiently transport carbon to depth owing to their dense mineral structures, while pico- (< 2 µm) and nanophytoplankton (2-20 µm) are considered to contribute negligibly due to their small size and low sinking speed. Despite burgeoning evidence of their export, the mechanisms behind it remain poorly understood. The objective of this dissertation is to acquire a mechanistic understanding of the contribution of pico- and nanophytoplankton to particle fluxes. I tested the hypotheses that pico- and nanophytoplankton may be exported via the following pathways: 1) physical aggregation due to the production of sticky Transparent Exopolymeric Particles (TEP), mediated by interactions with heterotrophic bacteria, 2) attachment to lithogenic minerals, and 3) repackaging by zooplankton. I found that despite the traditional view of being too small to sink, pico- and nanophytoplankton form aggregates rich in TEP, allowing cells to scavenge lithogenic minerals and thus increase their effective size and density. I discovered that interactions with heterotrophic bacteria were significant in mediating the process of aggregation by influencing the production and/or the composition of the phytoplankton-derived TEP. Bacteria differentially influenced aggregation and TEP production; some species enhanced aggregation without affecting TEP production, and vice-versa. Finally, by determining the microbial composition of sinking particles in an open-ocean site, I found pico- and nanophytoplankton significantly associated with particles sourced from crustaceous zooplankton, suggesting that their export is largely mediated by mesozooplankton.
Overall, I show that the hypothesized mechanisms of pico- and nanophytoplankton export are not mutually exclusive, but instead occur subsequently. Given the right conditions for their aggregation in the natural environment, such as interactions with aggregation-enhancing heterotrophic bacteria and/or the presence of lithogenic minerals, their cells and aggregates can escape remineralization within the euphotic zone, and thus be susceptible to grazing by mesozooplankton export within fecal pellets. The results of this dissertation provide a mechanistic framework for the contribution of pico- and nanophytoplankton to ocean particle fluxes.
ContributorsCruz, Bianca Nahir (Author) / Neuer, Susanne (Thesis advisor) / Lomas, Michael W (Committee member) / Passow, Uta (Committee member) / Cadillo-Quiroz, Hinsby (Committee member) / Arizona State University (Publisher)
Created2021
Description
The oceanic biological carbon pump is a key component of the global carbon cycle in which dissolved carbon dioxide is taken up by phytoplankton during photosynthesis, a fraction of which then sinks to depth and contributes to oceanic carbon storage. The small-celled phytoplankton (<5 µm) that dominate the phytoplankton community in oligotrophic oceans have traditionally been viewed as contributing little to export production due to their small size. However, recent studies have shown that the picocyanobacterium Synechococcus produces transparent exopolymer particles (TEP), the sticky matrix of marine aggregates, and forms abundant microaggregates (5-60 µm), which is enhanced under nutrient limited growth conditions. Whether other small phytoplankton species exude TEP and form microaggregates, and if these are enhanced under growth-limiting conditions remains to be investigated. This study aims to analyze how nutrient limitation affects TEP production and microaggregate formation of species that are found to be associated with sinking particles in the Sargasso Sea. The pico-cyanobacterium Prochlorococcus marinus (0.8 µm), the nano-diatom Minutocellus polymorphus (2 µm), and the pico-prasinophyte Ostreococcus lucimarinus (0.6 µm) were grown in axenic batch culture experiments under nutrient replete and limited conditions. It was hypothesized that phytoplankton subject to nutrient limitation will aggregate more than those under replete conditions due to an increased exudation of TEP and that Minutocellus would produce the most TEP and microaggregates while Prochlorococcus would produce the least TEP and microaggregates of the three phytoplankton groups. As hypothesized, nutrient limitation increased TEP concentration in all three species, however they were only significant in nitrogen-limited treatments of Prochlorococcus as well as nitrogen- and phosphorus-limited treatments of Minutocellus. Formation of microaggregates was significantly enhanced in Minutocellus and Ostreococcus cultures in distinct microaggregate size ranges. Minutocellus produced the most TEP per cell and aggregated at higher volume concentrations compared to Prochlorococcus and Ostreococcus. Surprisingly, Ostreococcus produced more TEP than Prochlorococcus and Minutocellus per unit cell volume. These findings show for the first time how nutrient limited conditions enhance TEP production and microaggregation of Prochlorococcus, Minutocellus, and Ostreococcus, providing a mechanism for their incorporation into larger, sinking particles and contribution to export production in oligotrophic oceans.
ContributorsShurtleff, Catrina (Author) / Neuer, Susanne (Thesis advisor) / Lomas, Michael W. (Committee member) / Garcia-Pichel, Ferran (Committee member) / Arizona State University (Publisher)
Created2022
Description
Sinking particles are important conduits of organic carbon from the euphotic zone to the deep ocean and microhabitats for diverse microbial communities, but little is known about what determines their origin and community composition. Events in the northwestern Sargasso Sea, such as winter convective mixing, summer stratification, and mesoscale (10–100 km) eddies, characteristic features of this region, affect the vertical and temporal composition and abundance of pelagic and particle-attached microorganisms. To assess the connections of the microbial communities between the euphotic zone and sinking particles, I carried out indicator and differential abundance analyses of prokaryotes and photoautotrophs based on the V4-V5 amplicons of the 16S rDNA from samples collected in the Sargasso Sea during the spring and summer of 2012. I found that gammaproteobacteria such as Pseudoalteromonas sp. and Vibrio sp., common particle-associated bacteria often linked with zooplankton, dominated the sequence libraries of the sinking particles. The analysis also revealed that members of Flavobacteria, particularly the fish pathogen Tenacibaculum sp., as well as Chloropicon sp. and Chloroparvula sp., among the smallest known green algae, were indicators taxa of sinking particles. The cryptophyte Teleaulax and the diatom Chaetoceros were overrepresented in the particle communities during both seasons. Interestingly, I also found that the large centric diatom, Rhizosolenia sp., generally rare in the oligotrophic Sargasso Sea, dominated photoautotrophic communities of sinking particles collected in the center of an anticyclonic eddy with unusual upwelling due to eddy-wind interactions. I hypothesize that the steady contribution by picophytoplankton to particle flux is punctuated by pulses of production and flux of larger-sized phytoplankton in response to episodic eddy upwelling events and can lead to higher export of particulate organic matter during the summer.
ContributorsFontánez Ortiz, Marc Alec (Author) / Neuer, Susanne (Thesis advisor) / Zhu, Qiyun (Committee member) / Trembath-Reichert, Elizabeth (Committee member) / Arizona State University (Publisher)
Created2022
Description
The biological carbon pump in the ocean is initiated by the photosynthetic fixation of atmospheric carbon dioxide into particulate or dissolved organic carbon by phytoplankton. A fraction of this organic matter sinks to depth mainly in the form of microaggregates (5-60 μm) and visible macroaggregates. These aggregates are composed of cells, minerals, and other sources of organic carbon. Exopolymeric substances (EPS) are exudated by heterotrophic bacteria and phytoplankton and may form transparent exopolymeric particles (TEP) that act as a glue-like matrix for marine aggregates. Heterotrophic bacteria have been found to influence the aggregation of phytoplankton and in some cases result in an increase in TEP production, but it is unclear if marine heterotrophic bacteria can produce TEP and how they contribute to aggregation. Pseudoalteromonas carrageenovora, Vibrio thalassae, and Marinobacter adhaerens HP15 are heterotrophic marine bacteria that were found associated with sinking particles in an oligotrophic gyre station in the subtropical North Atlantic. These bacteria were grown in axenic cultures to determine growth, TEP production, and aggregation. They were also inoculated into roller tanks used to simulate open ocean conditions to determine their ability to form macroaggregates. Treatments with added kaolinite clay simulated aeolic dust input from the Sahara. M. adhaerens HP15 had the highest TEP concentration but the lowest cell-normalized TEP production at all growth stages compared to the other bacteria. Additionally, M. adhaerens HP15 also had the lowest microaggregate formation. The cell-normalized TEP production and microaggregate formation was not significantly different between P. carrageenovora and V. thalassae. All bacteria formed visible macroaggregates in roller tanks with clay addition and exhibited high sinking velocities (150-1200 m d-1) that are comparable to those of aggregates formed by large mineral ballasted phytoplankton. Microaggregates in the clay treatments declined during incubation, indicating that they aggregated to form the macroaggregates. The findings from this study show for the first time that heterotrophic bacteria can contribute to aggregation and the export of organic carbon to depth in the ocean.
ContributorsLivar, Britni (Author) / Neuer, Susanne (Thesis advisor) / Hartnett, Hilairy (Committee member) / Cadillo-Quiroz, Hinsby (Committee member) / Arizona State University (Publisher)
Created2022