No description available.

Abstract The process of nitrification is highly dependent on the microbial activities and transformation, which is carried out by autotrophic nitrifiers in general, however some heterotrophic nitrifiers also can carry out the process. The diversity of autotrophic and heterotrophic ammonia-oxidizing bacteria in aquaculture ponds in Kaohsiung county was investigated. Ten heterotrophic bacteria were isolated. The nitrification ability and 16S rDNA sequences were determined. Seven of the strains had higher nitrification ability, five of them are belong to the genus of Pseudomonas, and the other two belong to Alcaligenes and Serratia, respectively. Both 16S rDNA and amoA gene sequences results showed that all autotrophic ammonia-oxidizing strains in this study belong to Nitrosomonas genus. From the data of 16S rDNA sequences, the strains isolated from Linyuan Shiang were distinct to the other two sites. Besides, amoA gene represents a very powerful molecular tool for analyzing ammonia-oxidizing bacteria communities due to its specificity and fine-scale resolution of closely related populations.

No description available.

Aquarium biofilters are designed to promote the growth and activity of nitrifying microorganisms, which are primarily responsible for the removal of toxic nitrogen-cycle intermediates. Ammonia is a natural waste product excreted by fish that is lethal to aquatic life at relatively low concentrations. Ammonia-oxidizing archaea (AOA) outnumber ammonia-oxidizing bacteria (AOB) in biofilters of mature freshwater aquaria with low-ammonia conditions. However, no study has investigated the early establishment of AOA and AOB within biofilter communities, especially when aquarium ammonia concentrations are elevated. My thesis research investigated the relative abundance of AOA and AOB in freshwater aquarium biofilters through early aquarium establishment. AOA and AOB genes were detected in DNA extracts from the biofilters of 14 start-up freshwater aquaria with increasing fish biomass loads (Experiment 1), as well as from 12 biofilters of start-up aquaria treated with AOA and AOB supplements (Experiment 2). In start-up aquaria, early ammonia concentrations increased with fish biomass, and AOB amoA genes were strongly detected over AOA marker genes in all filters without initial AOA inoculation. Inoculation of AOA-dominated supplements into newly established biofilters improved early ammonia oxidation rates in comparison to filters supplemented with AOB or those lacking supplements. Inoculated AOA thrived in filter biofilm during and beyond stabilization of low-ammonia conditions in aquaria. Microbial activity experiments demonstrated that AOA were present and active in the biofilters eight months after inoculation, when aquaria were fully established. In addition, AOB and AOA populations were monitored in new aquaria in three unregulated home environments. Thaumarchaeal 16S rRNA genes were detected in all aquarium filters within one month of aquarium development. In one filter, AOA were the only ammonia-oxidizers detected in the biofilm during aquarium development, suggesting that AOA were the sole contributors to nitrification in this aquarium. The results from these experiments suggest that AOA may be key players in early aquarium nitrification once introduced into the aquarium environment. Further, this research provides insight into the ecology of AOB and AOA in engineered freshwater environments

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No description available.

Floodplain lakes are wetlands which receive flood waters from nearby rivers or other sources. Water samples were taken from floodplain lakes near the Illinois River, the Mississippi River, and the Cache River in Southern Illinois. Fluorescence in situ hybridization (FISH), spectrophotometry, and gene probes were used to investigate the effect of nutrient and chemical concentrations on the abundance of nitrifying bacteria; specifically ammonia-oxidizing Nitrosococcus and Nitrosomonadales and nitrite-oxidizing Nitrospira and Nitrobacter. Nitrosococcus was the dominant ammonia-oxidizing bacteria at each river system. Nitrospira and Nitrobacter had similar average abundances. Nitrosococcus abundances showed a significant positive correlation with nitrate (NO3-) (R2= 0.247, P=0.05, 95% confidence R2≥0.199) and a positive trend with nitrite (NO2-) (R2= 0.194, P=0.10, 90% confidence R2≥0.125). Nitrosomonadales abundance positively correlated with temperature (R2= 0.530, P=0.05, 95% confidence R2≥0.510). Nitrospira abundances positively correlated with ammonium (NH4+) (R2= 0.265, P=0.05, 95% confidence R2≥0.199), NO2- (R2= 0.372, P=0.05, 95% confidence R2≥0.199), and NO3- (R2= 0.482, P=0.05, 95% confidence R2≥0.199). None of the target bacterial abundances significantly correlated with pH or dissolved inorganic phosphate.

>Magister Scientiae - MSc / Molecular methods were used to investigate the microbial diversity and community structure of ammonia-oxidizing bacteria (AOB) associated with the roots of the Proteaceae plant family. The identification of ammonia oxidizing bacteria in this ecosystem is of particular interest since Proteaceae are adapted to acidic, low nutrient (e.g. nitrogen) soils. The ammonia monooxygenase operon was used as a molecular marker to identify ammonia-oxidizing bacteria associated with the proteoid roots of the three Proteaceae members and compared to non-plant associated soil. PCR amplification using primer sets targeting the ammonia monooxygenase gene (amoA subunits) were used to construct a clone library. Sequence diversity was determined by RFLP analysis of amoA to identify major groups of AOB of the ~-subclass of Proteobacteria in total community DNA, and DNA sequencing and phylogenetic analysis were also applied. DGGE analysis was performed to determine the community structure and distribution of ammonia-oxidizing bacteria in plant-associated and non-plant associated soils. The AOB genotypic diversity was similar in the plant-associated samples and non-plant associated soil. All AOB phylotypes belonged to Nitrosospira species and clustered with Nitrosospira cluster 3. The abundance of the amoA was quantified to be approximately 4.2 x 107 copies/g of dry soil, using a real-time PCR assay. These data suggest that the Nitrosospira species are the dominant phylotypes in that environment. This investigation provides new insights into the relationships between plants and ammonia-oxidizing bacteria in natural Fynbos ecosystems.

Ammonia-oxidizing bacteria (AOB) are chemolithotrophs that oxidize ammonia/ammonium to nitrite in a two-step process to obtain energy for survival. AOB are difficult to isolate from the environment and iso lated strains may not represent the diversity in soil. A genetic database and molecular tools were developed based on the ammonia monooxygenase (AMO) encoding genes that can be used to assess the diversity of AOB that exist in soil and aquatic environments without the isolation of pure cultures. The amo genes have excellent potential as molecular markers; since AMO is only found in the AOB and is essential for their metabolism, AOB must carry at least one functional copy of the amo operon. The operon is composed of at least three genes, amoC, amoA. and amoB (encoding for the subunits AmoC, AmoA, and AmoB). The amoC gene was first discovered and its sequence was obtained from Nitrosospira sp. NpA V. The amooperon is found in several copies within AOB genomes in the β-subdivision but as a single copy in y-subdivision genomes. In Southern analysis, cross-hybridization was only observed between amo genes within a subdivision. They-subdivision amo sequences have higher identity values to the genes encoding the related particulate methane monooxygenase than to the β-subdivision amo sequences. Since amoA encodes the subunit containing the active site, it was sequenced entirely for all the strains studied (16 amoA sequences total). The amoC and amoB genes were also sequenced for several strains. The amo genes allow for better discrimination between closely related strains than the 16S rRNA genes. In all cases, the amo operon consists of amoC, followed by a variable length intergenic region, and then by amoAB. The variability in length of the intergenic region is strain specific, and is therefore potentially useful for profiling AOB communities. The amo-gene database was the basis for the design of conserved oligonucleotide primers for the polymerase chain reaction (PCR). These primers were used to amplify amo sequences from a mixed template of DNA extracted directly from soil. Results indicate that the amo genes are excellent molecular markers for the assessment of AOB communities in the environment.

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第20009号 / 農博第2193号 / 新制||農||1045(附属図書館) / 学位論文||H28||N5018(農学部図書室) / 33105 / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 小川 順, 教授 阪井 康能, 教授 栗原 達夫 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM