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

PLoS Comput Biol. 2022 Feb 2;18(2):e1009828. doi: 10.1371/journal.pcbi.1009828. eCollection 2022 Feb.

Abstract

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, iGC535. 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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Ammonia / metabolism*
  • Nitrosomonas europaea / metabolism*
  • Oxidation-Reduction

Substances

  • Ammonia

Grants and funding

The study was supported by: • AZ Ciencia Básica-CONACyT No. 284140 • GC-E was funded by the Mexican Research Council CONACyT fellowship No. 1008117 • DT-C was funded by the Mexican Research Council CONACyT fellowship No. 932962 • AZ 2018 UC MEXUS Small Grant - Faculty • KZ 2018 UC MEXUS Small Grant - Faculty • KZ & CZ U.S. Department of Energy (DOE), Office of Science, Office of Biological & Environmental Research. Awards DE-SC0012658 and DE-SC0019388. • KZ & CZ U.S. National Science Foundation EFRI program (Grant number: 1332344) and CBET program (Grant number: 1804733) • KZ & CZ The University of California Office of the President via a grant from the Multicampus Research Programs and Initiatives (MRP-19–601384) and the Emergency Citrus Disease Research and Extension program (2018-70016-28198 and 2019-70016-29066) from the USDA National Institute of Food and Agriculture. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.