Heterotrophic nitrification and related functional gene expression characteristics of Alcaligenes faecalis SDU20 with the potential use in swine wastewater treatment

Integrative chemical and omics analysis of the ammonia nitrogen removal characteristics and mechanism of a novel oligotrophic heterotrophic nitrification-aerobic denitrification bacterium

A novel oligotrophic heterotrophic nitrification-aerobic denitrification bacterium designated as Pseudomonas sp. N31942, was isolated from a eutrophic lake. Strain N31942 exhibits high ammonia nitrogen removal ability in oligotrophic environment as ammonia nitrogen can be efficiently (86.97 %) removed within 10 h with no accumulation of nitrite. In the nitrification process, strain N31942 can convert ammonia into nitrate in the absence of hydroxylamine oxidase and nitrite oxidoreductase. As for the denitrification process, nitrate or nitrite were reduced to ammonia and further converted into glutamate by dissimilatory nitrate reduction pathway. Transcriptomic analysis detected 2080 differentially expressed genes. Among them, the expression of the related genes in dissimilatory nitrate reduction process was all up-regulated at low ammonia concentrations, which indicates that the strain has excellent nitrogen removal efficiency for further nitrogen removal. Integrative omics analyses revealed that strain N31942 may have two possible pathways for the NH₄⁺-N removal as direct GDH/GS-GOGAT pathway (NH₄⁺-N → Glutamate) and indirect GDH/GS-GOGAT pathway (NH₄⁺-N → NH₂OH → NO₂^--N → NO₃^--N → NO₂^--N → NH₄⁺-N → Glutamate). Moreover, strain N31942 also has excellent nitrogen removal ability for real sewage and 77.21 % total nitrogen could be removed within 48 h. The results presented here provide new insights into ammonia nitrogen removal characteristics and mechanism of heterotrophic nitrification-aerobic denitrification bacterium under oligotrophic conditions.

A mechanistic review on aerobic denitrification for nitrogen removal in water treatment

The traditional biological nitrogen removal technology consists of two steps: nitrification by autotrophs in aerobic circumstances and denitrification by heterotrophs in anaerobic situations; however, this technology requires a huge area and stringent environmental conditions. Researchers reached the conclusion that the denitrification process could also be carried out in aerobic circumstances with the discovery of aerobic denitrification. The aerobic denitrification process is carried out by aerobic denitrifying bacteria (ADB), most of which are heterotrophic bacteria that can metabolize various forms of nitrogen compounds under aerobic conditions and directly convert ammonia nitrogen to N₂ for discharge from the system. Despite the fact that there is no universal agreement on the mechanism of aerobic denitrification, this article reviewed four current explanations for the denitrification mechanism of ADB, including the microenvironment theory, theory of enzyme, electron transport bottlenecks theory, and omics study, and summarized the parameters affecting the denitrification efficiency of ADB in terms of carbon source, temperature, dissolved oxygen (DO), and pH. It also discussed the current status of the application of aerobic denitrification in practical processes. Following the review, the difficulties of present aerobic denitrification technology are outlined and future research options are highlighted. This review may help to improve the design of current wastewater treatment facilities by utilizing ADB for effective nitrogen removal and provide the engineers with relevant references.

Isolation and application of a thermotolerant nitrifying bacterium Gordonia paraffinivorans N52 in sewage sludge composting for reducing nitrogen loss

A thermotolerant strain with heterotrophic nitrification capability obtained from sludge composting was identified as Gordonia paraffinivorans N52. Strain N52 utilized 51.8% of ammonium nitrogen (NH₄⁺-N) at 60℃, and the nitrogen balance results indicated that 25.5% of the consumed NH₄⁺-N was changed into nitrification intermediates, 53.0% to intracellular nitrogen, and only 5.2% was lost. The successful detection of enzymes related to nitrification and PCR amplification of functional genes further demonstrated nitrification ability of the isolated strain. Moreover, orthogonal test indicated that conditions for the optimal nitrification performance were C/N 15, 50℃, 150 rpm and pH 8. Compared with the control group, the addition of Gordonia paraffinivorans N52 to sewage sludge composting reduced 27.6% of ammonia emissions, accelerated the conversion from NH₄⁺-N to nitrate nitrogen and decreased the total nitrogen loss. These results suggested that inoculation of Gordonia paraffinivorans N52 effectively controlled ammonia emissions and reduced nitrogen loss in composting.

Nitrous oxide emission mitigation from biological wastewater treatment - A review

Nitrous oxide (N₂O) emitted from wastewater treatment processes has emerged as a focal point for academic and practical research amidst pressing environmental issues. This review presents an updated view on the biological pathways for N₂O production and consumption in addition to the critical process factors affecting N₂O emission. The current research trends including the strain and reactor aspects were then outlined with discussions. Last but not least, the research needs were proposed. The holistic life cycle assessment needs to be performed to evaluate the technical and economic feasibility of the proposed mitigation strategies or recovery options. This review also provides the background information for the proposed future research prospects on N₂O mitigation and recovery technologies. As pointed out, dilution effects of the produced N₂O gas product would hinder its use as renewable energy; instead, its use as an effective oxidizing agent is proposed as a promising recovery option.

Metagenomic Insights Into the Changes of Antibiotic Resistance and Pathogenicity Factor Pools Upon Thermophilic Composting of Human Excreta

In times of climate change, practicing a form of sustainable, climate-resilient and productive agriculture is of primordial importance. Compost could be one form of sustainable fertilizer, which is increasing humus, water holding capacity, and nutrient contents of soils. It could thereby strengthen agriculture toward the adverse effects of climate change, especially when additionally combined with biochar. To get access to sufficient amounts of suitable materials for composting, resources, which are currently treated as waste, such as human excreta, could be a promising option. However, the safety of the produced compost regarding human pathogens, pharmaceuticals (like antibiotics) and related resistance genes must be considered. In this context, we have investigated the effect of 140- and 154-days of thermophilic composting on the hygienization of human excreta and saw dust from dry toilets together with straw and green cuttings with and without addition of biochar. Compost samples were taken at the beginning and end of the composting process and metagenomic analysis was conducted to assess the fate of antibiotic resistance genes (ARGs) and pathogenicity factors of the microbial community over composting. Potential ARGs conferring resistance to major classes of antibiotics, such as beta-lactam antibiotics, vancomycin, the MLS_B group, aminoglycosides, tetracyclines and quinolones were detected in all samples. However, relative abundance of ARGs decreased from the beginning to the end of composting. This trend was also found for genes encoding type III, type IV, and type VI secretion systems, that are involved in pathogenicity, protein effector transport into eukaryotic cells and horizontal gene transfer between bacteria, respectively. The results suggest that the occurrence of potentially pathogenic microorganisms harboring ARGs declines during thermophilic composting. Nevertheless, ARG levels did not decline below the detection limit of quantitative PCR (qPCR). Thresholds for the usage of compost regarding acceptable resistance gene levels are yet to be evaluated and defined.

Genetic Foundations of Direct Ammonia Oxidation (Dirammox) to N2 and MocR-like Transcriptional Regulator DnfR in Alcaligenes faecalis JQ135

Ammonia oxidation is an important process of both the natural nitrogen cycle and nitrogen removal from engineered ecosystems. Recently, a new ammonia oxidation pathway termed Dirammox (direct ammonia oxidation, NH₃→NH₂OH→N₂) has been identified in Alcaligenes ammonioxydans. However, whether Dirammox is present in other microbes and its genetic regulation remains unknown. In this study, it was found that the metabolically versatile bacterium Alcaligenes faecalis strain JQ135 could efficiently convert ammonia into N₂ via NH₂OH under aerobic conditions. Genetic deletion and complementation results suggest that dnfABC is responsible for the ammonia oxidation to N₂ in this strain. Strain JQ135 also employs aerobic denitrification, mainly producing N₂O and trace amounts of N₂ with nitrite as sole nitrogen source. Deletion of genes nirK and nosZ that are essential for denitrification did not impair the capability of JQ135 to oxidize ammonia to N₂ (i.e., Dirammox is independent of denitrification). Furthermore, it was also demonstrated that pod (which encodes pyruvic oxime dioxygenase) was not involved in Dirammox and AFA_16745 (which was previously annotated as ammonia monooxygenase and is widespread in heterotrophic bacteria) was not an ammonia monooxygenase. The MocR-family transcriptional regulator DnfR was characterized as an activator of the dnfABC operon with the binding motif 5'-TGGTCTGT-3' in the promotor region. Bioinformatic survey showed that homologs to dnf genes are widely distributed in heterotrophic bacteria. In conclusion, this work demonstrates that besides A. ammonioxydans, Dirammox also occurs in other bacteria, and is regulated by the MocR-family transcriptional regulator DnfR. Importance Microbial ammonia oxidation is a key and rate-limiting step of the nitrogen cycle. Three previous known ammonia oxidation pathways (i.e., nitrification, anaerobic ammonia oxidation (Anammox), and complete ammonia oxidation (Comammox)) are mediated by autotrophic microbes. However, the genetic foundations of ammonia oxidation by heterotrophic microorganisms have not been investigated in depth. Recently, a previously unknown pathway, termed direct ammonia oxidation to N₂ (Dirammox), has been identified in the heterotrophic bacterium Alcaligenes ammonioxydans HO-1. This paper shows that in the metabolically versatile bacterium Alcaligenes faecalis JQ135, the Dirammox pathway is mediated by dnf genes, which are independent of the denitrification pathway. Bioinformatic survey suggests that homologs to dnf genes are widely distributed in bacteria. These findings enhance the understanding of the molecular mechanisms of heterotrophic ammonia oxidation to N₂.