Systems Microbiology and Engineering of Aerobic-Anaerobic Ammonium Oxidation

Aerobic and anaerobic oxidations of ammonium are core biological processes driving the nitrogen cycle in natural and engineered microbial ecosystems. These conversions are tailored in mixed-culture biotechnology to propel partial nitritation and anammox (PN/A) for a complete chemolithoautotrophic removal of nitrogen from wastewater at low resource and energey expenditures. Good practices of microbiome science and engineering are needed to design microbial PN/A systems and translate them to a spectrum of wastewater environments. Inter-disciplinary investigations of systems microbiology and engineering are paramount to harness the microbial compositions and metabolic performance of complex microbiomes. We propose “process ecogenomics” as an integration ground to combine community systems microbiology and microbial systems engineering by establishing a synergy between the life and physical sciences. It drives a high-resolution analysis, engineering and management of microbial communities and their metabolic performance in mixed-culture systems. While addressing the key underpinnings of the science and engineering of aerobic-anaerobic ammonium oxidations, we advocate the need to formulate targeted research questions in order to elucidate and manage microbial ecosystems in wastewater environments. We propose a systems-level roadmap to investigate and functional engineer technical microbiomes like PN/A, via: (i) quantitative biotechnological measurement of stoichiometry and kinetics of nitrogen turnovers; (ii) genome-centric metagenomic fingerprinting of the microbiome; (ii) ecophysiological examination of the main metabolizing lineages; (iii) multi-omics elucidation of expressed metabolic functionalities across the microbial network; and (iv) translation of microbial and functional ecology principles into physical designs.