Antibiotic use in agricultural ecosystems has the potential to increase resistance to antibiotics in soil microbial communities since 40-95% of an antibiotic dose administered to livestock is excreted intact or as metabolites. Exposure to antibiotics is also known to alter microbial community composition, biomass, and physiology, but the potential influences of antibiotic residues on the essential ecosystem processes that microbes regulate, e.g., carbon and nitrogen cycling are not well understood. I investigated the effects of antibiotic residues associated with dairy cattle operations on soil microbial communities and the ecosystem processes they regulate. I examined the effects of antibiotic exposure on the biogeochemical functioning of soil microbial communities by measuring the activity of extracellular enzymes associated with organic matter processing and nutrient mineralization in soils collected from dairy cattle operations across the United States. At each experimental station paired sites were identified by local managers that represented sites with high and low stocking rates of dairy cows who had been treated prophylactically with antibiotics to prevent mastitis. Responses varied among individual enzymes, but I found an overall significant decrease in total hydrolytic enzyme activity under high cattle stocking rates indicating a change in the functioning of the microbial community in soils exposed to antibiotic laden manure. Principle components analysis suggest that while some of the variation in enzyme activities are associated with the abundance of antibiotic resistance genes, soil organic matter (total organic, mineralizable, and particulate organic carbon) was the most significant variable accounting for differences in enzyme activities. This reflects an inherent challenge in studies of antibiotic exposure in agricultural landscapes: the difficulty of distinguishing direct effects of antibiotic residues from the organic matter and nutrient subsidy associated with manure applications. To address this concern I conducted a series of incubation experiments manipulating soils to isolate the influences of antibiotics, manure resource subsidies, and bovine microbiome inoculants into soils. Specifically, I examined soil respiration and antibiotic resistance gene counts using qPCR following treatment with cephapirin, pirilimycin and a positive and negative control. I found that pre-exposure to antibiotics and manure is important in modulating the response of microbial communities (soil respiration, and gene copy numbers of AmpC and TetO) to further antibiotic exposure. I conclude that antibiotics themselves have a direct effect on soil communities and their functioning that is additive to the effect of manure (i.e., as a resource subsidy). This effect is mediated by the history of previous exposure to antibiotics, i.e., cattle stocking density. These results suggest that antibiotic residues from dairy cattle operation may have significant effects on microbial communities and the biogeochemical cycling they regulate in agricultural ecosystems. / Master of Science / Antibiotic usage has become a widespread health concern. As development of new antibiotics slows down and bacteria resistant to all but last resort antibiotics become more common the scientific and health communities have begun researching antibiotic resistance. Most antibiotics used in the United States are not used on people but are instead used on farm animals to promote growth and increase production. These antibiotics are normally given to animals before they are even sick in order to stop any potential infections. As a result of this many of the antibiotics used go through the animal unused and are therefore released in waste product like urine and manure. That same manure is often spread onto fields as a fertilizer to allow crops to grow. This means that antibiotics are being applied to fields and pastures along with manure. These antibiotics are then killing soil microbial communities (bacteria and fungus that live within soil) while simultaneously creating a store of antibiotic resistance genes. Antibiotic resistance genes are what render bacteria immune to antibiotics themselves. In addition to the immunity the soil microbes may be less efficient at nutrient cycling, the process through which nutrients in the dirt are transformed to a form useable by plants, meaning more fertilizers and manure may be needed to reap the same amount of crop from the same area of land. This research found that antibiotics, when applied with manure, are leading to changes in soil microbial communities as well as a decrease in ecosy+stem functioning. This work is significant because it indicates that antibiotic resistance has implications beyond just public health, it could be affecting food growth and have real economic consequences.

<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.