Systems Microbiology and Engineering of Aerobic-Anaerobic Ammonium Oxidation

Abstract

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>

Thermal and alkaline pre‐treatments of inoculum halt methanogenesis and enable cheese whey valorization by batch acidogenic fermentation

“…44 This set of primers is known to cover both bacteria and archaea with high specificity, except for Planctomycetes. 45…”

Thermal and alkaline pre-treatments of inoculum halt methanogenesis and enables cheese whey valorization by batch acidogenic fermentation

“…The targeted hypervariable regions V3-V4 of the 16S rRNA gene were amplified by PCR with the pair of barcoded primers 341F (CCTAYGGGRBGCASCAG) and 806R (GGACTACNNGGGTATCTAAT) (Yu et al, 2005). This set of primers is known to cover both bacteria and archaea with high specificity, except for Planctomycetes (Weissbrodt et al, 2020).…”

“…(GGACTACNNGGGTATCTAAT) (Yu et al, 2005). This set of primers is known to cover both bacteria and archaea with high specificity, except for Planctomycetes (Weissbrodt et al, 2020).…”

Efficient management of the nitritation-anammox microbiome through intermittent aeration: absence of the NOB guild and expansion and diversity of the NOx reducing guild suggests a highly reticulated nitrogen cycle

“…The PNA process relies on the provision of controlled (limited) supply of oxygen and the spatial or temporal variation in redox conditions [6,7]. Yet, the PNA process remains tested by microbial community management, especially the suppression of the aerobic NO 2 − oxidation guild (aerobic nitrite oxidizing prokaryotes or NOBs) [7,8]. Indeed, all metagenetic and metagenomic analyses of PNA communities to date indicate the persistent presence of NOBs; and their excessive presence would deteriorate or collapse the PNA process [8,9].…”

“…Yet, the PNA process remains tested by microbial community management, especially the suppression of the aerobic NO 2 − oxidation guild (aerobic nitrite oxidizing prokaryotes or NOBs) [7,8]. Indeed, all metagenetic and metagenomic analyses of PNA communities to date indicate the persistent presence of NOBs; and their excessive presence would deteriorate or collapse the PNA process [8,9]. Selection for AOB against NOBs has variously relied on growth inhibition by free ammonia or nitrous acid [10] or oxygen limitation driven by the low O 2 affinity of the NOB [9,[11][12][13].…”