Insights into Ammonia Adaptation and Methanogenic Precursor Oxidation by Genome-Centric Analysis

Abstract

Ammonia released from the degradation of protein and/or urea usually leads to suboptimal anaerobic digestion (AD) when N-rich organic waste is used. However, the insights behind the differential ammonia tolerance of anaerobic microbiomes remain an enigma. In this study, the cultivation in synthetic medium with different carbon sources (acetate, methanol, formate, and H 2 /CO 2 ) shaped a common initial inoculum into four unique ammonia-tolerant syntrophic populations. Specifically, various levels of ammonia tolerance were observed: consortia fed with methanol and H 2 /CO 2 could grow at ammonia levels up to 7.25 g NH + -N/L, whereas the other two groups (formate and acetate) only thrived at 5.25 and 4.25 g NH + -N/L, respectively. Metabolic reconstruction highlighted that this divergent microbiome might be achieved by complementary metabolisms to maximize biomethane recovery from carbon sources, thus indicating the importance of the syntrophic community in the AD of N-rich substrates. Besides, sodium/proton antiporter operon, osmoprotectant/K + regulator, and osmoprotectant synthesis operon may function as the main drivers of adaptation to the ammonia stress. Moreover, energy from the substrate-level phosphorylation and multiple energy-converting hydrogenases ( e.g. , Ech and Eha) could aid methanogens to balance the energy request for anabolic activities and contribute to thriving when exposed to high ammonia levels.

Integrating metagenomic binning with flux balance analysis to unravel syntrophies in anaerobic CO2 methanation

“…To investigate such a system, random sequencing allows de novo identification of uncultured microorganisms, reliable annotation and gene identification. Furthermore, newer and promising techniques, such as “third-generation sequencing”, have demonstrated to improve the assembly quality and completeness values of the recovered genomes, thus, enriching the knowledge about diverse microbiomes, including AD [ 16 – 18 ]. The generation of high-quality metagenome-assembled genomes (MAGs) is a key step in building genome scale metabolic models (GSMMs) for flux balance analysis (FBA).…”

Integrated Metagenomic and Metaproteomic Analyses Unravel Ammonia Toxicity to Active Methanogens and Syntrophs, Enzyme Synthesis, and Key Enzymes in Anaerobic Digestion

“…The influence of ammonia on anaerobic microbes has been reported to be one reason for the inhibition of AD performance, with fluorescence in situ hybridization, 16S rRNA genes amplicon sequencing, and metagenomic analysis being commonly used techniques for characterizing the changes in the entire microbiota under ammonia stress. ,, Methanogens have been reported to be the microorganisms most sensitive to ammonia toxicity of the microbiome during the process of anaerobic digestion. , In particular, the studies of Zhang et al have indicated that obligate acetotrophic methanogens (i.e., Methanosaeta ) were susceptible to ammonia toxicity as revealed by 16S rRNA gene analysis . In contrast, hydrogenotrophic methanogens have generally been reported to be more robust to ammonia than acetoclastic methanogens .…”

Simultaneous effect of cathode potentials and magnetite concentrations on methanogenesis of acetic acid under different ammonia conditions

“…Concurrent translocation of Na + /H + across the membrane leads to proton gradient generation that is required to synthesize adenosine triphosphate. Therefore, HMs can conserve energy in NH 3 stressed conditions [44]. This ability may explain the increase of HMs population in this study.…”