Thesis (D.P.H.)--University of Michigan.

Dissertation (D.P.H.)--University of Michigan.

In der vorliegenden Arbeit wurden Untersuchungen zur mikrobiellen Aktivität von Pseudomonas putida DSM12735 durchgeführt. Als Messgröße diente die mikrobielle Wärmeleistung, basierend auf dem Stoffumsatz durch die Mikroorganismen. Ziel war es, die Vor- und Nachteile der verwendeten Kalorimeter herauszuarbeiten. Dafür wurden klassische Batch-Wachstumskurven aufgenommen. Ein weiteres Ziel bestand darin, eine Methode zur schnellen kalorimetrischen Detektion der mikrobiellen Aktivität insbesondere für die stationäre Phase zu entwickeln. In dieser Phase findet kein signifikanter Stoffumsatz statt. Durch das gezielte Auslösen einer zweiten Wachstumsphase und damit einem Stoffumsatz wird die mikrobielle Aktivität kalorimetrisch wieder messbar. Eingesetzt wurden folgende Kalorimeter: der Thermal Activity Monitor 2277 (TAM) mit den Kalorimetern Micro Reaction System 2250-4 ml und 2250-20 ml (kurz: TAM-4ml, TAM-20ml), das IC-Chip-Kalorimeter FCC22 (Institut für Physikalische Chemie, TU Freiberg) und das Kalorimeter Micro-DSC II (MDSC).

The aim of this work is study of utilization of PHA producing bacteria in bioremediation technologies. For this study were used bacteria Pseudomonas putida KT2440 and two isolates from soil contaminated by petroleum - Pseudomonas gessardii (D2) a Pseudomonas fulva (D3). The experimental part describes especially study of feather biodegradation using selected microbial strains. All the tested bacterial strains were capable of feather degradation and utilization as the sole carbon source. During biodegradation experiment, we monitored weight loss of feather, protease and keratinase activity, concentration of bacterial biomass and PHA content as well as pH. The highest biodegradation ability and keratinase activity was observed in Pseudomonas putida. None of tested bacteria accumulated detectable amount of PHA during growth on waste feather, nevertheless, bacterial biomass grown during feather degradation can be used as an inoculum for PHA production on waste frying oil and octanoic acid. Using this experimental setup, high PHA content (54% of cell dry weight) was achiaved in Pseudomonas putida. Another part of the thesis deals with biodegradation of petroleum oil. The highest capability of growth on this carbon source were determined in Pseudomonas fulva.

Call number: LD2668 .T4 1960 K55

Pea aphids, Acyrthosiphon pisum, have the potential to increase reproduction as a defence against pathogens, though how frequently this occurs or how infection with live pathogens influences this response is not well understood. Here we determine the minimum infective dose of an environmentally common bacterium and possible aphid pathogen, Pseudomonas syringae, to determine the likelihood of pathogenic effects to pea aphids. Additionally, we used P. syringae infection to investigate how live pathogens may alter reproductive rates. We found that oral bacterial exposure decreased subsequent survival of aphids in a dose-dependent manner and we estimate that ingestion of less than 10 bacterial cells is sufficient to increase aphid mortality. Pathogen dose was positively related to aphid reproduction. Aphids exposed to low bacterial doses showed decreased, although statistically indistinguishable, fecundity compared to controls. Aphids exposed to high doses reproduced significantly more than low dose treatments and also more, but not significantly so, than controls. These results are consistent with previous studies suggesting that pea aphids may use fecundity compensation as a response to pathogens. Consequently, even low levels of exposure to a common plant-associated bacterium may therefore have significant effects on pea aphid survival and reproduction.

published_or_final_version / Botany / Doctoral / Doctor of Philosophy

published_or_final_version / Ecology and Biodiversity / Doctoral / Doctor of Philosophy

Pseudomonas is a diverse genus of Gram-negative bacteria that includes pathogens of plants, insects, and humans as well as environmental strains with no known pathogenicity. Pseudomonas fluorescens itself encompasses a heterologous group of bacteria that are prevalent in soil and on foliar and root surfaces of plants. Some strains of P. fluorescens suppress plant diseases and the genomic sequences of many biological control strains are now available. I used a combination of bioinformatic and phylogenetic analyses along with mutagenesis and biological assays to identify and compare the TonB-dependent outer-membrane proteins (TBDPs) of ten plant-associated strains of P. fluorescens and related species. TBDPs are common in Gram-negative bacteria, functioning in the uptake of ferric-siderophore complexes and other substrates into the cell. I identified 14 to 45 TBDRs in each strain of P. fluorescens or P. chlororaphis. Collectively, the ten strains have 317 TBDPs, which were grouped into 84 types based upon sequence similarity and phylogeny. As many as 13 TBDPs are unique to a single strain and some show evidence of horizontal gene transfer. Putative functions in the uptake of diverse groups of microbial siderophores, sulfur-esters, and other substrates were assigned to 28 of these TBDP types based on similarity to characterized orthologs from other Pseudomonas species. Redundancy of TBDP function was evident in certain strains of P. fluorescens, especially Pf-5, which has three TBDPs for ferrichrome/ferrioxamine uptake, two for ferric-citrate uptake and three for heme uptake. Five TBDP types are present in all ten strains, and putative functions in heme, ferrichrome, cobalamin, and copper/zinc uptake were assigned to four of the conserved TBDPs. The fluorescent pseudomonads are characterized by the production of pyoverdine siderophores, which are responsible for the diffusible UV fluorescence of these bacteria. Each of the ten plant-associated strains of P. fluorescens or P. chlororaphis has three to six TBDPs with putative roles in ferric-pyoverdine uptake (Fpv). To confirm the roles of the six Fpv outer membrane proteins in P. fluorescens Pf-5, I introduced deletions into each of the six fpv genes in this strain and evaluated the mutants and the parental strain for heterologous pyoverdine uptake. I identified at least one ferric-pyoverdine that was taken up by each of the six Fpv outer-membrane proteins of Pf-5. By comparing the ferric-pyoverdine uptake assay results to a phylogenetic analysis of the Fpv outer-membrane proteins, I observed that phylogenetically-related Fpv outer-membrane proteins take up structurally-related pyoverdines. I then expanded the phylogenetic analysis to include nine other strains within the P. fluorescens group, and identified five additional types of Fpv outer-membrane proteins. Using the characterized Fpv outer-membrane proteins of Pf-5 as a reference, pyoverdine substrates were predicted for many of the Fpv outer-membrane proteins in the nine other strains. Redundancy of Fpv function was evident in Pf-5, as some pyoverdines were recognized by more than one Fpv. It is apparent that heterologous pyoverdine recognition is a conserved feature, giving these ten strains flexibility in acquiring iron from the environment. Overall, the TBDPs of the P. fluorescens group are a functionally diverse set of structurally-related proteins present in high numbers in many strains. While putative functions have been assigned to a subset of the proteins, the functions of most TBDPs remain unknown, providing targets for further investigations into nutrient uptake by P. fluorescens spp.. The work presented here provides a template for future studies using a combination of bioinformatic, phylogenetic, and molecular genetic approaches to predict and analyze the function of these TBDPs. / Graduation date: 2012

In this work, a model microbial agent for bioremediation was improved using fermentation and formulation methods. The outcomes of the fermentation work include the development of a new culture medium which increased the cell productivity greater than one order of magnitude. A robust functionality to degrade the herbicide atrazine was expressed. The new medium was scaled-up to a 2L bioreactor. Liquid bacterial culture was not inherently stable and lost viability at both 4°C and 25°C storage. When liquid bacterial culture was formulated by encapsulation in a biopolymer gel and applied to zeolite the transfer of cells from bacterial culture to formulated carrier was highly efficient. No loss of viability was measured from the immobilization process, and the functionality of the agent was retained. The formulated agent expressed an extended shelf life of at least 10 weeks when stored in ambient (25°C) temperature. When the formulation granules were inoculated into sterile soil, viability of the granules was stable and also retained the maximum level of functionality for the full test period of 10 weeks. The soil surrounding the formulation granules was also enumerated. The number of cells in the soil increased after a single inoculation of the formulation and the maximum level of functionality was conveyed from the formulation to the surrounding soil. The formulated inoculant constitutes an improvement for a bioremediation strain to stabilize the agent, produce an extended shelf life at ambient temperatures, and maintain the functionality of a microbe to utilize atrazine. In this thesis we have used a biopolymer formulation in which an inoculum is simply mixed into a gel and applied directly to the surface of the zeolite with no special equipment, drying, temperatures, or secondary re-growth steps required. It is a simple model system consisting of a carrier, and a artificial biofilm. As a technique to produce stable functional inoculants for bioremediation, the work presented here demonstrates an approach that is simple, practical, effective, and robust.