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>i</i>)
quantitative biotechnological measurement of stoichiometry and kinetics of
nitrogen turnovers; (<i>ii</i>)
genome-centric metagenomic fingerprinting of the microbiome; (<i>ii</i>) ecophysiological examination of the
main metabolizing lineages; (<i>iii</i>)
multi-omics elucidation of expressed metabolic functionalities across the
microbial network; and (<i>iv</i>)
translation of microbial and functional ecology principles into physical
designs.<br>
Environmental Systems Lab & Sustainable Material Cycle Lab Department of Environmental Systems Engineering College of Science and Engineering Ritsumeikan University