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All cells spatially organize their interiors, and this arrangement is necessary for cell viability. Until recently, it was believed that only eukaryotic cells spatially segregate their components. However, it is becoming increasingly clear that bacteria also assemble their proteins into complex patterns. In eukaryotic cells, spatial organization arises from membrane bound organelles as well as motor transport proteins which can move cargos within the cell. To date, there are no known motor transport proteins in bacteria and most microbes lack membrane bound organelles, so it remains a mystery how bacterial spatial organization emerges. In hind-sight it is not surprising that bacteria also exhibit complex spatial organization considering much of what we have learned about the basic processes that take place in all cells, such as transcription and translation was first discovered in prokaryotic cells. Perhaps the fundamental principles that govern spatial organization in prokaryotic cells may be applicable in eukaryotic cells as well. In addition, bacteria are attractive model organism for spatial organization studies because they are genetically tractable, grow quickly and much biochemical and structural data is known about them. A powerful tool for observing spatial organization in cells is the fluorescence microscope. By specifically tagging a protein of interest with a fluorescent probe, it is possible to examine how proteins organize and dynamically assemble inside cells. A significant disadvantage of this technology is its spatial resolution (approximately 250 nm laterally and 500 nm axially). This limitation on resolution causes closely spaced proteins to look blurred making it difficult to observe the fine structure within the complexes. This resolution limit is especially problematic within small cells such as bacteria. With the recent invention of new optical microscopies, we now can surpass the existing limits of fluorescence imaging. In some cases, we can now see individual proteins inside of large complexes or observe structures with ten times the resolution of conventional imaging. These techniques are known as super-resolution microscopes. In this dissertation, I use super-resolution microscopes to understand how a model microbe, Escherichia coli, assembles complex protein structures. I focus on two spatially organized systems, the chemotaxis network and the cell division machinery. These assembly mechanisms could be general mechanisms for protein assembly in all organisms. I also characterize new fluorescent probes for use in multiple super-resolution imaging modalities and discuss the practicalities of using different super-resolution microscopes. The chemotaxis network in E. coli is the best understood signal transduction network in biology. Chemotaxis receptors cluster into complexes of thousands of proteins located at the cell poles and are used to move bacteria towards favorable stimuli in the environment. In these dense clusters, the receptors can bind each other and communicate to filter out noise and amplify weak signals. It is surprising that chemotaxis receptors are spatially segregated and the mechanism for polar localization of these complexes remains unclear. Using data from PALM images, we develop a model to understand how bacteria organize their receptors into large clusters. The model, stochastic cluster nucleation, is surprising in that is generates micron-scale periodic patterns without the need for accessory proteins to provide scaffolding or active transport. This model may be a general mechanism that cells utilize to organize small and large complexes of proteins. During cell division, E. coli must elongate, replicate its DNA and position its components properly prior to binary fission. Prior to septum formation, a ubiquitous protein called FtsZ, assembles into a ring at mid-cell (Z-ring) which constricts during cell division and recruits the remaining proteins necessary for cytokinesis. Though many details have been revealed about FtsZ, the detailed in vivo structure of the Z-ring is not well understood, and many questions remain about how ring constriction occurs. Using multiple super-resolution imaging modalities, in combination with conventional time-lapse fluorescence imaging, we show that the Z-ring does not form a long uniform filament around the circumference of the bacterium. We detail how this structure changes during division and how removal of proteins that help to position FtsZ affects the Z-ring as it proceeds through cytokinesis. Ultimately we present a simple model for Z-ring constriction during division.
My research uses a multi-prong approach to understand the ecological and evolutionary processes that drive and maintain diversity. Specifically, I examine how competition and spatial structure drive evolutionary change. Part 1. A population under selection to improve one trait may evolve a sub-optimal state for a second trait due to tradeoffs and other evolutionary constraints. How the duration of evolution under conditions favoring the first trait affects the capacity of a population to adapt when conditions change to favor the second trait is an open question. We investigated this question using isolates from a lineage spanning 60,000 generations of the Long-Term Evolution Experiment (LTEE) with Escherichia coli. In the LTEE, cells have access to a shared pool of resources, and the bacteria have evolved increased competitive ability and a concomitant reduction in numerical yield. Here, we shifted the focus of selection to numerical yield by propagating LTEE-derived populations in media-in-oil emulsions, in which cells grew in isolated patches with private resources. We found that the length of time evolving under shared resources (i.e., duration in the LTEE) did not affect the ability to re-evolve toward higher numerical yield. The evolution of numerical yield in emulsified populations commonly occurred through mutations in the phosphoenolpyruvate phosphotransferase system. These mutants exhibit slower uptake of glucose, which makes them poorer competitors for public resources. However, these mutants also produce smaller cells that release less carbon as overflow metabolites, which makes them more numerically productive when resources are private. Our results demonstrate that mutations that were not part of adaptation under one selective regime may enable access to ancestral phenotypes when selection changes to favor evolutionary reversion. Part 2. Chemical warfare in the microbial world is ubiquitous. One kind of chemical weapon microbes employ is a proteinaceous toxin called a bacteriocin. The best-studied bacteriocins are the colicins, produced by and active against Escherichia coli. Many colicin systems encode suicidal lysis genes, such that the producing cell releases the toxin through cell lysis. Released colicin kills sensitive competing cells allowing immune clones of the producer to capitalize on the liberated resources. However, a major group of colicin systems lack this lysis gene, and it has been unclear how such toxins were released from the producing cell. I explore a newly discovered union between such a colicin system and a prophage (bacterial virus that has been incorporated into the bacterium’s genome), where release of the colicin occurs via phage-encoded cell lysis. This union should be detrimental to susceptible cells, which would be hit twice: once by the colicin, once by the phage. Mathematical modeling shows that the success of this dual killing system depends on the prophage’s ability to produce infectious virions in a well-mixed environment. If the prophage is cryptic (encoding lysis, but not producing infectious phage), then this dual system is susceptible to invasion by “cheaters” that only possess the colicin system (and its immunity) but do not lyse. I use agent-based simulations to model this scenario in a spatially structured environment. Under spatial conditions, the social dilemma and is resolved when the population exhibits fluctuating rock-paper-scissors dynamics (where rock chases scissor, scissor chases paper, and paper chases rock), providing insights into what ecological conditions were necessary in order to maintain this union.
Although we can't usually see them, microbes are essential for every part of human life-indeed all life on Earth. The emerging field of metagenomics offers a new way of exploring the microbial world that will transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas. Metagenomics allows researchers to look at the genomes of all of the microbes in an environment at once, providing a "meta" view of the whole microbial community and the complex interactions within it. It's a quantum leap beyond traditional research techniques that rely on studying-one at a time-the few microbes that can be grown in the laboratory. At the request of the National Science Foundation, five Institutes of the National Institutes of Health, and the Department of Energy, the National Research Council organized a committee to address the current state of metagenomics and identify obstacles current researchers are facing in order to determine how to best support the field and encourage its success. The New Science of Metagenomics recommends the establishment of a "Global Metagenomics Initiative" comprising a small number of large-scale metagenomics projects as well as many medium- and small-scale projects to advance the technology and develop the standard practices needed to advance the field. The report also addresses database needs, methodological challenges, and the importance of interdisciplinary collaboration in supporting this new field.
Microbiology covers the scope and sequence requirements for a single-semester microbiology course for non-majors. The book presents the core concepts of microbiology with a focus on applications for careers in allied health. The pedagogical features of the text make the material interesting and accessible while maintaining the career-application focus and scientific rigor inherent in the subject matter. Microbiology’s art program enhances students’ understanding of concepts through clear and effective illustrations, diagrams, and photographs. This is an adaptation of Microbiology by OpenStax. You can access the textbook as pdf for free at openstax.org. Minor editorial changes were made to ensure a better ebook reading experience. Textbook content produced by OpenStax is licensed under a Creative Commons Attribution 4.0 International License.
This volume highlights recent advances that have contributed to our understanding of spatial patterns and scale issues in microbial ecology. The book brings together research conducted at a range of spatial scales (from μm to km) and in a variety of different types of environments. These topics are addressed in a quantitative manner, and a primer on statistical methods is included. In soil ecosystems, both bacteria and fungi are discussed.
The Principles of Biology sequence (BI 211, 212 and 213) introduces biology as a scientific discipline for students planning to major in biology and other science disciplines. Laboratories and classroom activities introduce techniques used to study biological processes and provide opportunities for students to develop their ability to conduct research.
Eukaryotic Microbes presents chapters hand-selected by the editor of the Encyclopedia of Microbiology, updated whenever possible by their original authors to include key developments made since their initial publication. The book provides an overview of the main groups of eukaryotic microbes and presents classic and cutting-edge research on content relating to fungi and protists, including chapters on yeasts, algal blooms, lichens, and intestinal protozoa. This concise and affordable book is an essential reference for students and researchers in microbiology, mycology, immunology, environmental sciences, and biotechnology. Written by recognized authorities in the field Includes all major groups of eukaryotic microbes, including protists, fungi, and microalgae Covers material pertinent to a wide range of students, researchers, and technicians in the field