The increasing regulatory demands to achieve greater nutrient removal from wastewater treatment plant effluents, while minimizing infrastructure investments and operating costs, has resulted in the development of several innovative biological nitrogen removal (BNR) processes. Partial nitrification based processes such as the single reactor system for high ammonium removal over nitrite (SHARON 1 ) and its variants are attractive for treating high-strength nitrogen waste streams such as anaerobic digestion reject water or centrate, owing to their reduced consumption of energy (for aeration) and organic carbon (for denitrification). Indeed, separate treatment of centrate via partial nitrification is one of the options for limiting nitrogen discharges to Jamaica Bay in New York City 2 and is part of PlaNYC, a sustainability plan for New York City targeted for 2030.The energy and carbon savings of partial nitrification processes for nitrogen removal are by virtue of restricting ammonia oxidation to nitrite rather than to nitrate. On the other hand, nitrite is a known trigger for nitrous oxide (N 2 O) and nitric oxide (NO) production via nitrification 3,4 and denitrification 5,6 pathways. Full-scale measurements also point to nitrite as a factor in N 2 O production.7,8 Low (but not zero) dissolved oxygen concentrations were initially implicated as a significant factor for N 2 O and NO emissions from nitrification.9-11 However, the production of N 2 O by nitrifying bacteria under aerobic conditions has also been shown. 3,4,12,13 Recent reports suggest that N 2 O and NO emissions by ammonia oxidizing bacteria are related to imbalances in their metabolism and gene-expression patterns. 14,15 Given that the greenhouse impact of N 2 O is about three hundred times that of carbon dioxide 16 and both N 2 O and NO contribute to ozone layer depletion, 17 it needs to be determined whether N-removal processes based on transient nitrite accumulation are systematically greater contributors of N 2 O and NO than full nitrification based processes. The mechanisms of such differential N 2 O production from partial and full-nitrification systems at the microbial level also need to be understood. Therefore, the overarching goal of this study was to compare the microbial ecology, gene expression, biokinetics, and N 2 O emissions from a lab-scale bioreactor operated sequentially in full-nitrification and partial-nitrification modes. It was hypothesized that operation in partial nitrification mode would result in higher N 2 O and NO emissions than operation in full nitrification mode. It was additionally hypothesized that the high emissions of the gases would parallel the sustained elevated expression of the genes coding for their production. ABSTRACT: The goal of this study was to compare the microbial ecology, gene expression, biokinetics, and N 2 O emissions from a lab-scale bioreactor operated sequentially in full-nitrification and partial-nitrification modes. Based on sequencing of 16S rRNA and ammonia monooxygenase subunit A (amoA) g...