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DOE OSTI2022

Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds

The ammonia-oxidizing bacterium Nitrosomonas europaea has been widely recognized as an important player in the nitrogen cycle as well as one of the most abundant members in microbial communities for the treatment of industrial or sewage wastewater. Its natural metabolic versatility and extraordinary ability to degrade environmental pollutants (e.g., aromatic hydrocarbons such as benzene and toluene) enable it to thrive under various harsh environmental conditions. Constraint-based metabolic models constructed from genome sequences enable quantitative insight into the central and specialized metabolism within a target organism. These genome-scale models have been utilized to understand, optimize, and design new strategies for improved bioprocesses. Reduced modeling approaches have been used to elucidate Nitrosomonas europaea metabolism at a pathway level. However, genome-scale knowledge about the simultaneous oxidation of ammonia and pollutant metabolism of N . europaea remains limited. Here, we describe the reconstruction, manual curation, and validation of the genome-scale metabolic model for N . europaea , i GC535. This reconstruction is the most accurate metabolic model for a nitrifying organism to date, reaching an average prediction accuracy of over 90% under several growth conditions. The manually curated model can predict phenotypes under chemolithotrophic and chemolithoorganotrophic conditions while oxidating methane and wastewater pollutants. Calculated flux distributions under different trophic conditions show that several key pathways are affected by the type of carbon source available, including central carbon metabolism and energy production.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Impacts of anthropogenic gadolinium on the activity of the ammonia oxidizing bacterium Nitrosomonas europaea

Widespread use of gadolinium-based contrast agents in medical imaging has resulted in increased Gd inputs to municipal wastewater treatment plants. Others have reported that typical wastewater treatment does not attenuate Gd, resulting in discharges to natural waters. However, whether elevated Gd impacts the performance of biological treatment has not been investigated. We examined whether gadolinium chloride or Gd chelated with diethylenetriaminepentaacetic acid (DTPA) affected the activity of the model nitrifying bacterium Nitrosomonas europaea. At nominal GdCl 3 additions ranging from 1 to 500 µM, no impact was observed compared to the control. Most (>98%) of the added Gd precipitated, and extracellular GdPO 4 nanoparticles were observed. When chelated with DTPA, Gd remained soluble, but no statistically significant impact on ammonia oxidation was observed until the highest concentrations tested. At 300 and 500 µM Gd-DTPA, a temporary reduction of nitrite production relative to the control (effect size 1.3 mg l -1 and 1.5 mg l -1 , respectively, at 24 h) was seen. By itself, DTPA was highly inhibitory. Modeling suggested that DTPA likely chelated other metals, but adjusting the concentrations of the most abundant metals in the medium, calcium and magnesium, indicated that lowering their free ion activities was probably not the cause of inhibition. Complexation of other essential metals was more likely. Furthermore, our studies indicate that while the low bioavailability of Gd may limit its ecosystem impacts, the role of synthetic ligands used with Gd and other rare earth elements should e considered as the production, use and disposal of these elements increases.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Simultaneous occupancy of Cu C and Cu D in the ammonia monooxygenase active site

Ammonia monooxygenase (AMO), a copper-dependent membrane enzyme, catalyzes the first and rate-limiting step of nitrification: the oxidation of ammonia to hydroxylamine. Despite its central role in the global nitrogen cycle and its biotechnological relevance, structural characterization of AMO has lagged behind that of its homolog, particulate methane monooxygenase (pMMO), due to the slow growth rates of ammonia-oxidizing bacteria and the instability of AMO upon purification. Recent cryoEM studies of Nitrosomonas europaea AMO and Methylococcus capsulatus (Bath) pMMO in native membranes revealed new structural features, including two adjacent copper-binding sites in the transmembrane region, Cu C and Cu D , believed to constitute the active site. Although multiple structures were determined under various conditions, simultaneous occupancy of Cu C and Cu D was never observed, leaving their potential functional interplay unresolved. Here we report the 2.6 Å resolution cryoEM structure of AMO from Nitrosospira briensis C-128 in isolated native membranes. This structure reveals the first instance of simultaneous copper occupancy of the Cu C and Cu D sites, along with occupancy of the periplasmic Cu B site. Electron paramagnetic resonance (EPR) spectroscopic data indicate that the Cu B site is primarily occupied by Cu(II), while Cu C and Cu D are primarily occupied by diamagnetic ions, presumably Cu(I). Notably, a lipid molecule is bound between the Cu C and Cu D sites, separating them by ∼8.0 Å. The results underscore the importance of studying these enzymes in their native environments across species to resolve conserved and divergent molecular features.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Effects of Lithium-ion Battery Recycling Wastes on Ammonia-Oxidizing Bacteria

Increased demand for lithium-ion batteries (LIB) necessitates development of effective recycling methods for critical battery materials. Oak Ridge National Laboratory (ORNL) is exploring membrane solvent extraction (MSX) for the hydrometallurgical recycling of LIB materials. In this study, waste from MSX was investigated for its impact on the ammonia-oxidizing organism, Nitrosomonas europaea—a model organism for nitrogen removal during wastewater treatment. It was found that Raffinate 4 from ORNL was inhibitory to the growth and nitrite production of N. europaea, likely due to its nickel content. Further investigation is currently underway.

99 GENERAL AND MISCELLANEOUS↗