In nature, microbial consortia are often resilient and adaptable to environmental challenges and perturbations due to their highly coordinated community-level functions and behaviors, enabled by division of labor and intracellular communication. These features make microbial consortia a powerful chassis for synthetic biology and biotechnology innovations. A critical challenge for designing synthetic consortia is to accurately predict the population dynamics of microbial ecosystems, due to the large number of variables involved and the complexity of the underlying biochemical and ecological networks. This is largely due to our limited understanding of how microbial interactions are shaped by environmental nutrients, and how these interspecies interactions scale to affect community function and stability. Despite numerous computational modeling approaches and high-throughput experimental methods devised to address this knowledge gap, challenges remain in integrating high-throughput experimental techniques such as -omics measurements with dynamic models to both provide a mechanistic understanding on communities at the scale of molecular effectors, and offer reliable predictions at an ecological level. In this thesis work, I combine experimental and computational approaches to study synthetic ecosystem assembly and dynamics, and propose a computational framework to integrate experimental data for predicting and manipulating microbial consortia. The first chapter of this dissertation is an introduction on the background and motivations of this work, in particular on the challenges of predicting community responses. The second chapter details the development of an experimentally-informed modeling approach to study metabolic interactions and interdependency of a synthetic model system of root-associated microbes, which was then used to guide further design of subcommunities with certain community features. The third chapter describes a computer-aided design (CAD) network partitioning tool that distributes community function in an engineered consortium of microbes, with the goal of overcoming the limitations of performing complicated tasks by a single population. The final chapter lays out future directions to combine -omics data, different modeling approaches, and high-throughput experimental techniques such as droplet microfluidics for the study and design of microbial communities, and how we envision these tools to be connected to generate microbial communities of increasing complexity. / 2026-01-11T00:00:00Z

<div> <div> <div> <p>Parental care has evolved promote fitness gains. Burying beetles engage in extensive pre- hatching and post-hatching parental care providing several avenues to transmit bacteria to their offspring. One aspect of pre-hatching parental care consists of preserving a small vertebrate carcass via oral and anal secretions, allowing the carcass to be used as a reproductive resource. Post-hatching parental care consists in large part of parental regurgitations of the preserved carcass. We sought to determine if pre-hatching parental care resulted in bacterial transmission from adults to carcasses via anal secretions. We then sought to determine if lab-rearing conditions affected the digestive tract bacterial communities of F1 and F2 generation adults. We finally sought to determine if carcasses and post-hatching parental care in the form of parental regurgitations resulted into bacterial transmission to larvae. Using High-Throughput Illumina MiSeq, we were able to characterize bacterial communities of adult and larval digestive tracts, anal secretions, and unprepared and prepared carcasses. Our results show that bacterial communities of adults are dissimilar from anal secretions and prepared carcasses. We then show that lab-rearing conditions do not significantly alter digestive tract bacterial communities of F1 and F2 generation adults relative to wild caught adults. We proceed to show that larvae receiving parental regurgitations have digestive tract bacterial communities similar to their parents whereas larvae that do not receive parental regurgitations have dissimilar digestive tract bacterial communities from their parents. We further show that bacterial communities of prepared carcasses are dissimilar from all larvae. Our evidence suggests that anal secretions to preserve carcasses for the reproductive bout and have no influence on bacterial transmission to neither carcasses nor larvae. Our evidence also suggests that parental regurgitations influence bacterial transmission to offspring. </p> </div> </div> </div>

No description available.

Chemolithotrophic oxidation of ammonia to nitrate via nitrite (autotrophic nitrification) is a key link in the cycling of nitrogen in the biosphere.  It is facilitated by diverse communities of microorganisms including the autotrophic ammonia oxidising bacteria (AOB).  A good understanding of niche differentiation among members of such communities will aid in the prediction of how a community structure and function may respond to environmental change. The work presented here aims to extend the available ecophysiological data on soil AOB with an emphasis on comparative observations between organisms under the same conditions.  Under a set of standardised conditions, several potentially ecologically relevant traits were quantified and comparisons were made between organisms in the context of their phylogenetic relationships.  <i>Nitrosomonas europaea </i>ATCC 19718, <i>Nitrosomonas europaea </i>ATCC 25978, <i>Nitrosospira </i>‘Apple Valley’, <i>Nitrosospira briensis </i>C-128, <i>Nitrosospira multiformis </i>ATCC 25196, <i>Nitrosospira tenuis </i>NV-12, and <i>Nitrosospira </i>40KI in pure culture were examined. Specific growth rates in batch culture, maximum velocities, Michaelis constants and specific oxidation velocities of ammonia oxidation, AMO transcript decay half-life and transcriptional and metabolic response to re-supply of ammonia following energy starvation were quantified.  Significant phenotypic diversity was observed and hypotheses were tested with respect to trade-offs in niche adaptation and the influence of phylogeny.  It is hoped these new data will aid in the formation and testing of further ecological and evolutionary hypotheses and will contribute to the long term goal of developing predictive models for biogeochemical cycling.

Human intestinal microbiomes exhibit a large degree of interindividual compositional variation. Animal models, such as the zebrafish, facilitate the design of controlled and highly replicated studies that allow us to understand the normal variation in vertebrate intestinal composition and to study the rules guiding normal assembly of these complex communities. The smaller intestinal size and high fecundity of the zebrafish allow us to fully sample the intestinal contents of many animals, while the optical transparency allows direct in vivo observation of fluorescently labeled bacterial species within the intestine. The studies in this dissertation utilize these advantages to investigate the composition, colonization dynamics and functional requirements for colonization in the vertebrate intestine. We first describe the taxonomic composition and diversity of the zebrafish intestinal microbiota from wild-caught and domesticated zebrafish. In the process, we identify a set of core bacterial genera that are consistently present in zebrafish intestines. We then use species from two of these genera in subsequent studies to gain a detailed understanding of the colonization dynamics and genetic requirements of the two species. We initially describe the application of light sheet microscopy to imaging the zebrafish intestine and associated colonizing bacteria. We find that a single species, Aeromonas veronii, does not occupy the entire intestinal space and that competition within the same species appears to prevent further colonization. These results are extended to a zebrafish isolated Vibrio species as well as A. veronii by tagging bacteria with transposon insertions and tracking the changes in colonizing population sizes. These insertion libraries also identify genes in each bacterial species that are important in the process of colonization, highlighting the key role for motility and chemotaxis in this process. The descriptions and methods discussed in this dissertation advance the use of this important model organism towards the understanding of vertebrate host-microbial interactions. This dissertation includes previously published co-authored material as well as unpublished co-authored material. / 10000-01-01

The North American Great Lakes are a vital source on a global scale, as they hold ~18 % of the potable water resources on our planet. Cyanobacteria of the genus Microcystis are commonly found in fresh water environments around the world, and since the mid-1990s also in Lake Erie. The reasons for the success for these potentially toxic cyanobacteria in Lake Erie are not completely understood. In this study we have applied modern molecular tools to analyze field samples to provide an insight into the genotypic composition and diversity of the Microcystis community in the past and present day Lake Erie. We have also analyzed a three-year data set to identify specific environmental factors that contribute to the abundance of Microcystis genotypes and microcystin production. In addition, in a laboratory-based study we examined the effect of nutrients on transcriptional activity of the microcystin synthetase gene mcyD. The results of this study suggest that, although toxic Microcystis form < 10 % of the total cyanobacterial population in Lake Erie, the toxin-producing Microcystis community in Lake Erie is diverse, and that these populations are stabile on a time scale of decades. Sediments acting as a reservoir of Microcystis are likely contributing to the persistence of the population. Although Microcystis is the dominant microcystin producer in the lake, other microcystin-producing cyanobacteria were also found in spatially isolated regions of the lake. While microcystin concentration in Lake Erie is correlated positively with total phosphorus (P<0.001) and surface reactive phosphorus (P<0.001), and negatively with the molar ratio total nitrogen to total phosphorus (P<0.001); toxic Microcystis abundance correlates negatively with NO3 concentration (P=0.04) and positively with surface water temperatures (ranging from 20.8 °C to 27.4 °C) (P=0.03). These observations, along with findings from culture based experiments, suggest decoupling of the factors governing proliferation of toxic cells and toxin production. Culture based experiments also suggested that the chemical form of phosphorus may be an important factor in regulating microcystin biosynthesis in Microcystis based on monitoring relative transcriptional activity of the mcyD gene. The transcriptional activity of mcyD was higher (P=0.118) in cells grown in BG11-medium containing 2.3 μM organic phosphorus (glycerol 2-phosphate disodium salt hydrate) than in cells grown in BG11-medium containing 2.3 μM inorganic phosphorus (K2HPO4).

Thesis (M. Sc.)--University of Canterbury, 2009. / Typescript (photocopy). Includes bibliographical references (p. 169-189). Also available via the World Wide Web.

Thesis (Ph. D.)--University of Hong Kong, 2010. / Includes bibliographical references (leaves 276-317). Also available in print.

Deserts comprise the largest terrestrial biome, making up approximately one third of the Earth’s land mass. They are defined in terms of moisture deficit using the Aridity Index with values <1. A further delineation based on mean annual temperatures into hot (>18°C), cold (<18°C) and polar (<0°C) deserts is employed. In the absence of significant macrobiota, microorganisms are key to desert ecosystems. They are located in near-surface soils, and include a widespread hypolithic mode of colonization, where microbial biomass develops on the ventral surfaces of quartz and other translucent stones. A literature review was conducted to appreciate the status of existing knowledge on these systems. Amongst unresolved questions that arose were the following, which form the basis of this inquiry: What are the taxonomic and functional differences between hypolithic and near-soil communities? Do hypolithic communities assemble differently in deserts of different xeric and thermal stresses? Can the keystone cyanobacterial taxa be cultivated under laboratory conditions to allow manipulative studies? The Mojave Desert in the USA was used as a model to test the extent to which hypolithic and near-surface soil communities vary in both taxonomic and putative functional composition. A common phylogenetic marker (16S rRNA gene ITS region) was used to conclude that soil and hypolithic communities are significantly different, although both were dominated by cyanobacteria. The ubiquitous hypolithic cyanobacterial taxon Chroococcidiopsis was encountered, although communities appeared to be dominated functionally by the diazotrophic genus Nostoc. The data strongly suggest that carbon and nitrogen fixation pathways in desert soils are mediated by the same taxa, although heterotrophic pathways may differ and support distinct assemblages of heterotrophic bacteria. An opportunistic sampling of three sites along a latitudinal gradient in China allowed some inference about adaptations in hypoliths. Communities recovered from the cold Tibetan Desert, Taklamakan Basin Desert, and exposed hillsides in tropical Hong Kong, did not display significant differences at the level of community assembly. This suggests that hypolithic taxa undergo strong selection for xeric and extreme thermal stresses. A cultivation strategy for the keystone taxon Chroococcidiopsis has been lacking and is an obvious impediment to manipulative physiological studies. Here various methods for laboratory cultivation were attempted. This bacterium proved extremely fastidious and displayed slow growth rates. After extensive trials a novel cultivation method was developed. This involved using plastic petri dishes containing liquid growth medium, into which glass coverslips were introduced along with cell suspensions. The surface energy of glass served as a nucleation site for Chroococcidiopsis biofilms (which do not develop on plastic surfaces) and this method was evaluated in growth studies as a means of quantifying growth. This research includes key advances to demonstrate that hypoliths and soil, whilst supporting different communities, likely perform similar functional roles in the desert soil. Selection due to the severe environmental stresses results in similar communities across large latitudinal and environmental gradients. The development of a cultivation strategy paves the way for manipulative physiological studies on these important organisms. / published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

Thesis (M.S.)--Oregon State University, 2009. / Printout. Includes bibliographical references (leaves 47-52). Also available on the World Wide Web.