The most abundant clone found in ribosomal RNA clone libraries obtained from the world's oceans belongs to the SAR11 phylogenetic group of environmental marine bacteria. Imaging and counting SAR11 bacterial cells in situ has been an important research objective for the past decade. This objective has been especially challenging due to the extremely small size, and hypothetically, the low abundance of ribosomes contained by the cells. To facilitate the imaging of small dim oligotrophic bacterial cells, digital imaging technology featuring very small pixel size, high quantum yield scientific grade CCD chips was integrated with the use of multiple oligonucleotide probes on cells mounted on a non-fluorescing solid substrate. Research into the composition of bacterioplankton populations in natural marine systems follows a two-fold path. Increasing the culturability of microbes found in the natural environment is one research path. Identifying and enumerating the relative fractions of microorganisms in situ by culture-independent methods is another. The accumulation and systematic comparison of ribosomal RNA clones from the marine environment has resulted in a philosophical shift in marine microbiology away from dependence upon cultured strains and toward investigations of in situ molecular signals. The design and use of oligonucleotide DNA probes targeting rRNA targets has matured along with the growth in size and complexity of the public sequence databases. Hybridizing a fluorescently labeled oligonucleotide probe to an rRNA target inside an intact cell provides both phylogenetic and morphological information (a technique called Fluorescence in situ Hybridization (FISH)). To facilitate the imaging of small, dim oligotrophic bacterial cells, digital imaging technology featuring very small pixel size, high quantum yield, scientific grade CCD chips is integrated with the use of multiple oligonucleotide probes on cells mounted on a non-fluorescing solid substrate. This research develops the protocols necessary to acquire and analyze digital images of marine bacterial cells. Experiments were conducted with Bermuda Atlantic Time Series (BATS) environmental samples obtained during cruise BV21 (1998) and B138 (2000). The behavior of the SAR11⁴*Cy3 probe set when hybridized to bacterial cells from these samples was investigated to determine the optimal hybridization reaction conditions. The challenges of bacterial cell counting after cell transfer from PCTE membrane to treated microslides were addressed. Experiments with aged Oregon Coast seawater were performed to investigate the protocol used to transfer cells from membrane to microslides, and examined the distribution of cells and the statistics of counting cells using traditional epifluorescence microscopy and image analysis techniques. / Graduation date: 2002

Tetracycline is a front line antibiotic for the treatment of chlamydial infections in both humans and animals, and the emergence of tetracycline resistant (tet[superscript R]) Chlamydia is of significant clinical importance. Recently, several tet[superscript R] chlamydial strains have been isolated from swine (Sus scrofa) raised in production facilities in Nebraska. Here, the intracellular development of two C. suis tet[superscript R] strains, R19 and R27, is characterized through the use of tissue culture and immunofluorescence. The strains grow in tetracycline up to 4 ��g/ml, while a tetracycline sensitive (tet[superscript S]) C. suis swine strain (S45) and a C. trachomatis strain of the human serovar L2 (LGV-434) grow in tetracycline up to 0.1 ��g/ml. Although inclusions form in the presence of tetracycline, many contain large aberrant RBs that do not differentiate into infectious EBs. The percentage of inclusions containing typical developmental forms decreases with increasing tetracycline concentrations, and at 3 ��g/ml of tetracycline, 100% of inclusions contain aberrant RBs. However, upon removal of the tetracycline, the aberrant RBs revert to typical RBs and a productive developmental cycle resumes. In addition, inclusions were found that contained both C. suis R19 and C. trachomatis L2 after sequential infection, demonstrating that two biologically distinct chlamydial strains could both develop within a single inclusion. / Graduation date: 2002

Thesis (Ph. D.)--Oregon State University, 2007. / Printout. Includes bibliographical references. Also available on the World Wide Web.

Microorganisms and their interactions in soil play a critical role in nutrient transformations and cycling, and in sustaining soil productivity. Arbuscular mycorrhizal fungi (AMF) are a keystone group of fungi influencing nutrient cycling. In turn, the activity and composition of microorganisms in soil are influenced by management practices such as the choice of crop species and fertilization. Long-term effects of cropping, manuring and mineral fertilization on the soil-plant system were defined in three selected agro-ecosystems of Canada. A greenhouse experiment was also conducted to define the involvement of AMF in organic residue decomposition and nitrogen (N) mineralization.<p> In the greenhouse experiment, pasteurized soil was inoculated or not with a strain of <i>Glomus claroideum, G. clarum</i> or <i>G. intraradices</i>. 15N-labelled organic residue in a nylon mesh was buried in the soil. The fate of residue-N was determined after 24 weeks. Arbuscular mycorrhizal fungal species enhanced mineralization of organic residue to different degrees. The highest recovery of mineralized N by plants (25%) occurred when inoculated with <i>G. clarum</i>. The AMF enhanced N-mineralization differentially leading to differential plant growth stimulation, differences in the C-to-N ratio of the decomposing organic residue, and in soil microbial community structure.<p> In a field trial conducted on a Brown Chernozemic soil at the Semiarid Prairies Agricultural Research Centre in Swift Current, SK, eight years of phosphorus (P) (0, 20 and 40 kg P2O5 ha-1) application to alfalfa monoculture and alfalfa-Russian wildrye (RWR) dual culture modified the soil microbial community structure. Low levels of phosphorus (0 and 20 kg P2O5 ha-1) fertilization in alfalfa-RWR dual culture increased the abundance of fungivorous nematodes and grazing of AMF hyphae thus increasing the carbon drain from plants and ultimately reducing plant biomass.<p> In a sub-humid region of Saskatchewan on a a Black Chernozem soil, mineral N (0, 20 or 40 kg N ha-1) was applied for 10 years to pea grown continuously or in rotation with wheat. Lower yields in continuous-pea were associated with reduced abundance of beneficial Gram positive bacteria and AMF, and an increase in uptake of plant available Fe to toxic levels. These differences in soil properties were related to root rot which increased with years in continuous-pea. The soil environment in the continuous-pea rotation further led to lower organic carbon inputs, and to reduced soil microbial biomass and soil enzyme activity indicating a negative impact on nutrient cycling.<p> In the south coastal region of Agassiz, British Columbia, dairy manure slurry (DMS) and ammonium nitrate (AN) had been applied on a Regosol at the same annual rate of mineral N (50 or 100 kg mineral N ha-1) for nine years to perennial tall fescue, followed by one year of stand renovation through reseeding without fertilization. The multi-year application of DMS improved soil organic C, soil organic N, light fraction of organic matter, microbial biomass and enzyme activity as compared to mineral fertilization but the DMS-related increase in soil yield potential was lost in the process of stand rejuvenation. Dairy manure slurry application based on the crop N requirement also increased soil phosphate indicating increased environmental hazard. In conclusion, long-term use of DMS in multi-cut tall fescue can increase soil quality parameters but can also increase the risk of eutrophication of water bodies.<p> Overall, data showed that higher levels of soil nutrients can select for certain bacteria while AMF and other bacteria are more abundant under low soil fertility. On the other hand, different soil microbial groups were associated with different soil enzyme activities. From this study, I succeded in proving my hypothesis that practice of fertilization and choice of crop influence soil microbial community structure which further affect soil functioning.

Microorganisms and their interactions in soil play a critical role in nutrient transformations and cycling, and in sustaining soil productivity. Arbuscular mycorrhizal fungi (AMF) are a keystone group of fungi influencing nutrient cycling. In turn, the activity and composition of microorganisms in soil are influenced by management practices such as the choice of crop species and fertilization. Long-term effects of cropping, manuring and mineral fertilization on the soil-plant system were defined in three selected agro-ecosystems of Canada. A greenhouse experiment was also conducted to define the involvement of AMF in organic residue decomposition and nitrogen (N) mineralization.<p> In the greenhouse experiment, pasteurized soil was inoculated or not with a strain of <i>Glomus claroideum, G. clarum</i> or <i>G. intraradices</i>. 15N-labelled organic residue in a nylon mesh was buried in the soil. The fate of residue-N was determined after 24 weeks. Arbuscular mycorrhizal fungal species enhanced mineralization of organic residue to different degrees. The highest recovery of mineralized N by plants (25%) occurred when inoculated with <i>G. clarum</i>. The AMF enhanced N-mineralization differentially leading to differential plant growth stimulation, differences in the C-to-N ratio of the decomposing organic residue, and in soil microbial community structure.<p> In a field trial conducted on a Brown Chernozemic soil at the Semiarid Prairies Agricultural Research Centre in Swift Current, SK, eight years of phosphorus (P) (0, 20 and 40 kg P2O5 ha-1) application to alfalfa monoculture and alfalfa-Russian wildrye (RWR) dual culture modified the soil microbial community structure. Low levels of phosphorus (0 and 20 kg P2O5 ha-1) fertilization in alfalfa-RWR dual culture increased the abundance of fungivorous nematodes and grazing of AMF hyphae thus increasing the carbon drain from plants and ultimately reducing plant biomass.<p> In a sub-humid region of Saskatchewan on a a Black Chernozem soil, mineral N (0, 20 or 40 kg N ha-1) was applied for 10 years to pea grown continuously or in rotation with wheat. Lower yields in continuous-pea were associated with reduced abundance of beneficial Gram positive bacteria and AMF, and an increase in uptake of plant available Fe to toxic levels. These differences in soil properties were related to root rot which increased with years in continuous-pea. The soil environment in the continuous-pea rotation further led to lower organic carbon inputs, and to reduced soil microbial biomass and soil enzyme activity indicating a negative impact on nutrient cycling.<p> In the south coastal region of Agassiz, British Columbia, dairy manure slurry (DMS) and ammonium nitrate (AN) had been applied on a Regosol at the same annual rate of mineral N (50 or 100 kg mineral N ha-1) for nine years to perennial tall fescue, followed by one year of stand renovation through reseeding without fertilization. The multi-year application of DMS improved soil organic C, soil organic N, light fraction of organic matter, microbial biomass and enzyme activity as compared to mineral fertilization but the DMS-related increase in soil yield potential was lost in the process of stand rejuvenation. Dairy manure slurry application based on the crop N requirement also increased soil phosphate indicating increased environmental hazard. In conclusion, long-term use of DMS in multi-cut tall fescue can increase soil quality parameters but can also increase the risk of eutrophication of water bodies.<p> Overall, data showed that higher levels of soil nutrients can select for certain bacteria while AMF and other bacteria are more abundant under low soil fertility. On the other hand, different soil microbial groups were associated with different soil enzyme activities. From this study, I succeded in proving my hypothesis that practice of fertilization and choice of crop influence soil microbial community structure which further affect soil functioning.

In this study we attempt to use phytoremediation techniques to treat the contaminated soil of cadmium. The experiment is divided into two stages. In the first stage, we selected three different species of plants which could tolerate heavy-metals: vetiver (Vetiveria zizanioides), Pteris ensiformis cv. 'Victoriae' according to the past records, and Alternanthera philoxeroides (Mart.) Griseb, which were sampled from the metal contaminated site in Hunei, Kaohsiung county. These three species were planted in three pots with 10, 20 and 30 mg Cd kg-1 in soil respectively. After 9 weeks of the growth, the vetiver was found accumulating the highest Cd and grew better than the other two species. Therefore, we selected the species of vetiver in the second stage of experiment. First, the species of vetiver was planted in the pots with concentrations of 30 and 50 mg Cd kg-1 in soil respectively. Then the pots were put in the greenhouse for incubation. After the test was run for 210 days, we found that the species of vetiver was helpful in the increasing the number of species and amounts of each species of microbe ( total bacteria, fungi and actinomycete ), as well as dehydrogenase activity. Meanwhile, it was effective to decrease the bioavailability of cadmium. In addition, the infection rate of mycorrhizal fungi was increased , which showed that the species of vetiver could resist the cadmium stress in soils and stimulate the soil fertility. Finally, we use molecular biotechniques of PCR-DGGE to observe the microbial diversity in the contaminated soil. We found that the pots with 30 mg Cd kg-1 in soil had more number of bands than the pots with different Cd concentrations in soil, while the pots without vegetation was found more fruitful than vegetated pots. These experimental results indicated that the pots planted with the species of vetiver under this situation would help some special microorganisms to grow, and thus that the microbial diversity was reduced. The results also showed that the pots planted with vetiver with initial cadmium concentrations of 30 and 50 mg Cd kg-1 respectively, in soil exhibited the degradation rate of about 30 percent for both. It was not satisfied to this result in this study. However, the phytoextraction rates of cadmium were measured equal to 7.8 and 8.9 percent, respectively. According to these results, we suggested that the plant, which could hyperaccumulate heavy metals, might be used to increase the removable ability of cadmium in the future.

In this study, the phytoremediation techniques are used to treat the soil contaminated by pentachlorophenol(PCP).First, four plants species were selected,including Allium tuberosum, Vigna radiata (L.) Wilczek, Pennisetum alopecuroides, and Medicago sativa to compare their treatment efficiencies for PCP in soil.The experimental results showed that the species of Allium tuberosum presented the highest degradation rate 76% after 35-day test run with the initial concentration of 20mg/kg in soil. In the second stage,the species of Allium tuberosum was thus selected to run the tests of feasibility of using phytoremediayion to treat the soils contaminated byPCP.During the e xperiment,the pot tests inside a greenhouse were run for 330 days.The result indicated that the species of Allium tuberosum contributed to the increase of microorganism and dehydrogenase activity in the soil. Bisides,we also found that adding with nutrients could help Allium tuberosum to depress the PCP stress.The test with vegetation of Allium tuberosum and addition of nutrients showed that the PCP degradation rate was measured equal to 98.4% with the concentration of PCP degraded from 42mgkg-1 to 0.68mgkg-1 after 330days. Finally, molecule biotechnology of PCR-DGGE was applied to the test of observing the microbiota in the soils.According to the test results,we found that the diversity of microorganisms could be raised through planting the species of Allium tuberosum. The microbiota in the soils with PCP pollutant have more varieties than the microbiota in soils without vegetation, which was infered that the addition of PCP might stimulate the vitality of microbes in the soils. Moreover, comparing the microbiota on rhizosphere of the plant species and in the bulk soils, it was found that the actitivies of root exudates might be able to increase the varieties of rhizospheric microorganisms.

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Thesis (M.S.)--Ohio State University, 2008. / Title from first page of PDF file. Includes bibliographical references (p. 65-71).

Thesis--Auburn University, 2009. / Abstract. Vita. Includes bibliographic references (p.64-77).