No description available.

Batch cultures of Candidatus Pelagibacter ubique were grown under iron-, organosulfur-, and nitrogen-limiting conditions to understand how this ubiquitous marine bacterium responds to and interacts with environments where growth is limited by the availability of these nutrients. Global gene expression was monitored using microarrays and quantitative mass spectrometry to observe both transcriptional and post-transcriptional responses to nutrient limitation. Iron- and nitrogen-limited cultures were characterized by increased transcription and translation of transporters involved in acquisition of the limiting nutrient, whereas organosulfur-limited cultures were not. Methionine synthesis genes downstream of S-adenosyl methionine riboswitches were up-regulated in mRNA and protein during organosulfur-replete stationary phase. Comparative genomics also revealed Ca. Pelagibacter to be the only genus among the free-living Alphaproteobacteria to lack a P[subscript II]-mediated nitrogen regulatory pathway – a pathway which may be complemented in Ca. P. ubique by putative riboswitches and a citric acid cycle able to bypass the glutamate precursor 2-oxoglutarate. Overall, the results of this study provide insight into the regulatory and metabolic processes of this ecologically significant organism, and enable better interpretation of metatranscriptomic and meta-proteomic surveys by identifying sfuC and amtB as likely biomarkers for iron and nitrogen limitation, respectively, in natural Ca. P. ubique populations. / Graduation date: 2012 / Access restricted to the OSU Community at author's request from Dec. 13, 2011 - Dec. 13, 2013

No description available.

Thesis (Ph. D.)--University of Washington, 2004. / Vita. Includes bibliographical references (leaves 106-121).

Thesis (Ph. D.)--University of Wisconsin--Madison, 1998. / Typescript. Vita. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references.

No description available.

Thesis (Ph. D.)--University of Washington, 2001. / Vita. Includes bibliographical references (leaves 76-85).

Biofilm communities were cultivated in rotating annular bioreactors using water from the South Saskatchewan River. The impacts of seasonal variations, nutrients, pollutants and dissolved oxygen on the activity and composition of the biofilms were assessed by using a combination of microcosm assays and molecular biology techniques. / The seasonal pattern in nitrification, denitrification and hexadecane mineralization, and in the occurrence of nirK in the South Saskatchewan River biofilms was: fall greater than winter, which was equivalent to spring. Hexadecane mineralization was higher in fall 1999 than in fall 2001, denitrification was similar in these two years, and no seasonal pattern of nitrification was observed. / The addition of combined nutrients (C, N, and P) resulted in significant increases in the measured bacterial activities and in the predominance of alkB, nirS and nirK in all seasons and years. The addition of individual nutrients did not stimulate hexadecane mineralization, denitrification, and the PCR amplification of nirS and nirK. In fall 1999, CNP and, to a lesser extent P, stimulated nitrification, whereas in fall 2001, no pattern was observed. The results showed that nutrients, especially P, were limiting for bacterial activities, and that the biofilm activities and composition varied with nutrient availability and time of year. / At the concentration assessed (1 ppb), hexadecane partially inhibited denitrification to similar extents in both years, had a negative impact on nitrification and hexadecane mineralization in fall 1999, and a positive impact on these two latter activities in fall 2001. Nickel (0.5 mg liter-1 ) negatively affected denitrification but had no effect on hexadecane mineralization. The alkB and nirS genes were less predominant and absent, respectively, in biofilms grown in the presence of nickel. DGGE analyses indicated that nickel reduced the biofilm bacterial diversity. / The results presented herein provide much needed information on the microbial ecology of river biofilms, and on the impact and interactive effects of pollutant and nutrient inputs on these biofilms. These results and the techniques used in this project can be applied to monitor environmental effects of anthropogenic activities on aquatic biofilms, and can contribute to establish or revise environmental regulations.

Two strains of Alcaligenes denitrificans, designated BRI 3010 and BRI 6011, were isolated from polychlorinated biphenyl (PCB) contaminated soil using 2,5-dichlorobenzoic acid (2,5-DCBA) and 2,4-DCBA, respectively, as sole carbon and energy sources. Both strains degraded 2-chlorobenzoic acid (2-CBA), 2,3-DCBA, and 2,5-DCBA. BRI 6011 alone degraded 2,4-DCBA. Metabolism of the chlorinated substrates resulted in the stoichiometric release of chloride, and degradation proceeded by intradiol cleavage of the aromatic ring. Growth of both strains on dichlorobenzoic acids induced pyrocatechase activities having catechol (catechol 1,2-dioxygenase) and chlorocatechols (chlorocatechol 1,2-dioxygenase) as substrates. Growth on 2-CBA and benzoic acid induced a pyrocatechase activity (catechol 1,2-dioxygenase) directed against catechol only. / The chlorocatechol 1,2-dioxygenase from BRI 6011 was purified, characterized, and compared with the chlorocatechol 1,2-dioxygenase from Pseudomonas sp. B13 and P. putida, organisms limited with respect to their CBA degradative versatility. These enzymes appear to be very similar based on biochemical and genetic data and possess sufficient broad substrate specificity to accommodate a wide range of chlorinated catechols, hence the increased versatility for chlorobenzoic acid degradation of A. denitrificans cannot be attributed to a more specialized chlorocatechol 1,2-dioxygenase. / Uptake of benzoic acid by BRI 3010 and BRI 6011 was inducible, exhibited saturation kinetics and the substrate was accumulated intracellularly against a concentration gradient by a factor of 8 and 10, respectively, indicative of active transport. Uptake of 2,4-DCBA by BRI 6011 was constitutive and saturation kinetics were not observed, suggesting passive diffusion of 2,4-DCBA and other CBAs into the cell down a concentration gradient. / Based on oxygen uptake experiments with whole cells, benzoic acid dioxygenase and chlorobenzoic acid dioxygenase activity was induced by benzoic acid and ortho-substituted chlorobenzoic acids, respectively. Since 2,4-DCBA diffuses across the membrane and the expected catecholic intermediates of 2,4-DCBA metabolism are metabolizable by BRI 3010, this suggests that the major difference between BRI 3010 and BRI 6011 might be the inability of the chlorobenzoic acid dioxygenase in BRI 3010 to recognize 2,4-DCBA as a substrate.

Thesis (M.S. - Hydrology and Water Resources)--University of Arizona. / Includes bibliographical references (leaves 241-246).