Matching Items (4)
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- All Subjects: Cyanobacteria
- Creators: Chandler, Douglas
Description
Sexually transmitted diseases like gonorrhea and chlamydia, standardly treated with antibiotics, produce over 1.2 million cases annually in the emergency department (Jenkins et al., 2013). To determine a need for antibiotics, hospital labs utilize bacterial cultures to isolate and identify possible pathogens. Unfortunately, this technique can take up to 72 hours, leading to several physicians presumptively treating patients based solely on history and physical presentation. With vague standards for diagnosis and a high percentage of asymptomatic carriers, several patients undergo two scenarios; over- or under-treatment. These two scenarios can lead to consequences like unnecessary exposure to antibiotics and development of secondary conditions (for example: pelvic inflammatory disease, infertility, etc.). This presents a need for a laboratory technique that can provide reliable results in an efficient matter. The viability of DNA-based chip targeted for C. trachomatis, N. gonorrhoeae, and other pathogens of interest were evaluated. The DNA-based chip presented several advantages as it can be easily integrated as a routine test given the process is already well-known, is customizable and able to target multiple pathogens within a single test and has the potential to return results within a few hours as opposed to days. As such, implementation of a DNA-based chip as a diagnostic tool is a timely and potentially impactful investigation.
ContributorsCharoenmins, Patherica (Author) / Penton, Christopher (Thesis director) / Moore, Marianne (Committee member) / College of Integrative Sciences and Arts (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Euendolithic cyanobacteria have the remarkable ability to actively excavate and grow within certain minerals. Their activity leads to increased erosion of marine and terrestrial carbonates, negatively affecting coral reef and bivalve ecology. Despite their environmental relevance, the boring mechanism has remained elusive and paradoxical, in that cyanobacteria alkalinize their surroundings, typically leading to carbonate precipitation, not dissolution. Thus, euendoliths must rely on unique adaptations to bore. Recent work using the filamentous model euendolith Mastigocoleus testarum strain BC008 indicated that excavation relied on transcellular calcium transport mediated by P-type ATPases, but the phenomenon remained unclear. Here I present evidence that excavation in M. testarum involves an unprecedented set of adaptations. Long-range calcium transport is achieved through the coordinated pumping of multiple cells, orchestrated by the localization of calcium ATPases in a repeating annular pattern, positioned at a single cell pole, adjacent to each cell septum along the filament. Additionally, specialized chlorotic cells that I named calcicytes, differentiate and accumulate calcium at concentrations more than 500 fold those of canonical cells, likely allowing for fast calcium flow at non-toxic concentrations through undifferentiated cells. I also show, using 13C stable isotope tracers and NanoSIMS imaging, that endolithic M. testarum derives most of its carbon from the mineral carbonates it dissolves, the first autotroph ever shown to fix mineral carbon, confirming the existence of a direct link between oxidized solid carbon pools and reduced organic pools in the biosphere. Finally, using genomic and transcriptomic approaches, I analyze gene expression searching for additional adaptations related to the endolithic lifestyle. A large and diverse set of genes (24% of 6917 genes) were significantly differentially regulated while boring, including several master regulators and genes expectedly needed under this condition (such as transport, nutrient scavenging, oxidative stress, and calcium-binding protein genes). However, I also discovered the up-regulation of several puzzling gene sets involved in alternative carbon fixation pathways, anaerobic metabolism, and some related to photosynthesis and respiration. This transcriptomic data provides us with several new, readily testable hypotheses regarding adaptations to the endolithic lifestyle. In all, my data clearly show that boring organisms show extraordinarily interesting adaptations.
ContributorsGuida, Brandon Scott (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Chandler, Douglas (Committee member) / Bingham, Scott (Committee member) / Roberson, Robert (Committee member) / Arizona State University (Publisher)
Created2016
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
Desert organisms lead harsh lives owing to the extreme, often unpredictable environmental conditions they endure. Climate change will likely make their existence even harsher. Predicting the ecological consequences of future climate scenarios thus requires understanding how the biota will be affected by climatic shifts. Biological soil crusts (biocrusts) are an important ecosystem component in arid lands, one that covers large portions of the landscape, improving soil stability and fertility. Because cyanobacteria are biocrust’s preeminent primary producers, eking out an existence during short pulses of precipitation, they represent a relevant global change object of study. I assessed how climate scenarios predicted for the Southwestern United States (US) will affect biocrusts using long-term, rainfall-modifying experimental set-ups that imposed either more intense drought, a seasonally delayed monsoon season, or a shift to smaller but more frequent precipitation events. I expected drought to be detrimental, but not a delay in the monsoon season. Surprisingly, both treatments showed similar effects on cyanobacterial community composition and population size after four years. While successionally incipient biocrusts were unaffected, mature biocrusts lost biomass and diversity with treatment, especially among nitrogen-fixing cyanobacteria. In separate experiments, I assessed the effect of rainfall with modified event size and frequency after a decade of treatment. Small, frequent rainfall events surprisingly enhanced the diversity and biomass of bacteria and cyanobacteria, with clear winners and losers: nitrogen-fixing Scytonema sp. benefited, while Microcoleus vaginatus lost its dominance. As an additional finding, I could also show that water addition is not always beneficial to biocrusts, calling into question the notion that these are strictly water-limited systems.
Finally, results interpretation was severely hampered by a lack of appropriate systematic treatment for an important group of biocrust cyanobacteria, the “Microcoleus steenstrupii complex”. I characterized the complex using a polyphasic approach, leading to the formal description of a new family (Porphyrosiphonaceae) of desiccation resistant cyanobacteria that includes 11 genera, of which 5 had to be newly described. Under the new framework, the distribution and abundance of biocrust cyanobacteria with respect to environmental conditions can now be understood. This body of work contributes significantly to explain current distributional patterns of biocrust cyanobacteria and to predict their fate in the face of climate change.
Finally, results interpretation was severely hampered by a lack of appropriate systematic treatment for an important group of biocrust cyanobacteria, the “Microcoleus steenstrupii complex”. I characterized the complex using a polyphasic approach, leading to the formal description of a new family (Porphyrosiphonaceae) of desiccation resistant cyanobacteria that includes 11 genera, of which 5 had to be newly described. Under the new framework, the distribution and abundance of biocrust cyanobacteria with respect to environmental conditions can now be understood. This body of work contributes significantly to explain current distributional patterns of biocrust cyanobacteria and to predict their fate in the face of climate change.
ContributorsMoreira Camara Fernandes, Vanessa (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Rudgers, Jennifer (Committee member) / Sala, Osvaldo (Committee member) / Penton, Christopher (Committee member) / Arizona State University (Publisher)
Created2020