Graduate Thesis Or Dissertation
 

Transcriptome Responses of the Nitrifying Bacteria Nitrosomonas europaea and Nitrobacter hamburgensis to Low Oxygen

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  • Nitrification is the process within the global Nitrogen Cycle where ammonia (NH3) is oxidized to nitrate (NO₃⁻) and can be carried out by two distinct groups of bacteria. The ammonia-oxidizing bacteria (AOB) first oxidize NH₃ to nitrite (NO₂⁻), and second, the nitrite-oxidizing bacteria (NOB) oxidize NO₂⁻ to NO₃⁻. In aerobic conditions, in either natural or engineered systems, nitrifying bacteria often compete for oxygen (O₂). In nitrification, low O₂ environments can cause the accumulation of NH₃, NO₂⁻ and the greenhouse gases NO and N₂O, compounds that can be detrimental to the environment. This work examined the effects of O₂ limitation on the AOB Nitrosomonas europaea and the NOB Nitrobacter hamburgensis, and determined their transcriptome responses under replete and limiting O₂. When grown in co-culture with replete O₂, both N. europaea and N. hamburgensis were capable of consuming ~99% of the available NH₃, or NO₂⁻, accordingly, and grew to 0.35 OD₆₀₀ in a steady state. Upon O₂ limitation in co-culture, N. europaea outcompeted N. hamburgensis for O₂. To consume 30 mM of the respective growth substrates, O₂ in the bioreactors was calculated at 9.25 µM O₂ for N. europaea and 54.8 µM O₂ for N. hamburgensis. In an O₂-limited co-culture bioreactor, N. europaea with higher O₂ affinity starved N. hamburgensis in 60 mM NH₄⁺ medium. In single bioreactor cultures, N. europaea showed ~35% of its genome differentially expressed between treatments. Genes related to lipid metabolism, intracellular trafficking and secretion, cell motility, signal transduction, transcription and ribosomal structure and translation were at higher mRNA transcript levels under low O₂. Genes related to secondary metabolites, inorganic ion transport, coenzyme metabolism, nucleotide synthesis, amino acid transport, carbohydrate transport, energy production, post translational modification, cell envelope biogenesis, defense mechanisms, cell division and DNA replication were all at lower levels. N. hamburgensis in single culture differentially expressed ~15% of its genome between treatments. The transcripts of genes for lipid, coenzyme, nucleotide and amino acid metabolism, energy production, intracellular trafficking, cell envelope biogenesis, defense mechanisms, cell division, DNA replication, transcription and ribosomal biogenesis were at higher levels under low O₂. Genes related to inorganic transport, carbohydrate metabolism, post-translational modification, cell motility, and signal transduction pathways were expressed at lower levels under low O₂. The transcriptome data shows that N. europaea and N. hamburgensis utilize different compensatory strategies for maintaining growth rates in limited O₂ environments.
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