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MBio Mar 2020The recent discovery of complete ammonia oxidizers (comammox) contradicts the paradigm that chemolithoautotrophic nitrification is always catalyzed by two different...
The recent discovery of complete ammonia oxidizers (comammox) contradicts the paradigm that chemolithoautotrophic nitrification is always catalyzed by two different microorganisms. However, our knowledge of the survival strategies of comammox in complex ecosystems, such as full-scale wastewater treatment plants (WWTPs), remains limited. Analyses of genomes and transcriptomes of four comammox organisms from two full-scale WWTPs revealed that comammox were active and showed a surprisingly high metabolic versatility. A gene cluster for the utilization of urea and a gene encoding cyanase suggest that comammox may use diverse organic nitrogen compounds in addition to free ammonia as the substrates. The comammox organisms also encoded the genomic potential for multiple alternative energy metabolisms, including respiration with hydrogen, formate, and sulfite as electron donors. Pathways for the biosynthesis and degradation of polyphosphate, glycogen, and polyhydroxyalkanoates as intracellular storage compounds likely help comammox survive unfavorable conditions and facilitate switches between lifestyles in fluctuating environments. One of the comammox strains acquired from the anaerobic tank encoded and transcribed genes involved in homoacetate fermentation or in the utilization of exogenous acetate, both pathways being unexpected in a nitrifying bacterium. Surprisingly, this strain also encoded a respiratory nitrate reductase which has not yet been found in any other genome and might confer a selective advantage to this strain over other strains in anoxic conditions. The discovery of comammox in the genus changes our perception of nitrification. However, genomes of comammox organisms have not been acquired from full-scale WWTPs, and very little is known about their survival strategies and potential metabolisms in complex wastewater treatment systems. Here, four comammox metagenome-assembled genomes and metatranscriptomic data sets were retrieved from two full-scale WWTPs. Their impressive and-among nitrifiers-unsurpassed ecophysiological versatility could make comammox an interesting target for optimizing nitrification in current and future bioreactor configurations.
Topics: Ammonia; Bacteria; Genome, Bacterial; Metagenome; Multigene Family; Nitrification; Oxidation-Reduction; Phylogeny; Transcriptome; Wastewater; Water Purification
PubMed: 32184251
DOI: 10.1128/mBio.03175-19 -
Environment International Oct 2020Emissions of hydrogen sulfide and methane are two of the major concerns in sewers, causing corrosion, odour and health problems. This study proposed a new free ammonia...
Emissions of hydrogen sulfide and methane are two of the major concerns in sewers, causing corrosion, odour and health problems. This study proposed a new free ammonia (FA)-based approach for controlling the biological production of sulfide and methane in sewers. This is based on the discovery that the FA contained in urine wastewater is strongly biocidal to anaerobic sewer biofilms. Long-term operation of two laboratory sewer reactors, with one being dosed with urine wastewater and the other being dosed with raw sewage as a control, revealed the effectiveness of the proposed FA approach. The results showed that dosing of real urine wastewater at FA concentration of 154 mg NH-N/L with exposure for 24 h immediately reduced over 80% sulfide and methane in the experimental sewer reactor, while the time for recovering 50% sulfide and methane production were 6 days and 28 days, respectively. It also showed that intermittent dosing with an interval time of 5-15 days reduced around 60% sulfide on average. As suggested by community analysis, the remaining sulfide might be produced by a sulfate-reducing bacterial genus Desulfobulbus. Collectively, urine is a part of municipal sewage, and thus separation and re-dosing of the urine wastewater into the sewer for sulfide and methane control should enable the minimization of operational costs and environmental impacts, compared with the previous dosing of chemicals.
Topics: Ammonia; Methane; Sewage; Sulfates; Sulfides
PubMed: 32673907
DOI: 10.1016/j.envint.2020.105928 -
International Journal of Molecular... Sep 2023Liquid hydrogen carriers will soon play a significant role in transporting energy. The key factors that are considered when assessing the applicability of ammonia... (Review)
Review
Liquid hydrogen carriers will soon play a significant role in transporting energy. The key factors that are considered when assessing the applicability of ammonia cracking in large-scale projects are as follows: high energy density, easy storage and distribution, the simplicity of the overall process, and a low or zero-carbon footprint. Thermal systems used for recovering H from ammonia require a reaction unit and catalyst that operates at a high temperature (550-800 °C) for the complete conversion of ammonia, which has a negative effect on the economics of the process. A non-thermal plasma (NTP) solution is the answer to this problem. Ammonia becomes a reliable hydrogen carrier and, in combination with NTP, offers the high conversion of the dehydrogenation process at a relatively low temperature so that zero-carbon pure hydrogen can be transported over long distances. This paper provides a critical overview of ammonia decomposition systems that focus on non-thermal methods, especially under plasma conditions. The review shows that the process has various positive aspects and is an innovative process that has only been reported to a limited extent.
Topics: Ammonia; Biological Transport; Carbon; Cold Temperature; Hydrogen; Plasma Gases
PubMed: 37762700
DOI: 10.3390/ijms241814397 -
Biosensors & Bioelectronics May 2024Invasive methods such as blood collection and biopsy are commonly used for testing liver and kidney function, which are painful, time-consuming, require trained... (Review)
Review
Invasive methods such as blood collection and biopsy are commonly used for testing liver and kidney function, which are painful, time-consuming, require trained personnel, and may not be easily accessible to people for their routine checkup. Early diagnosis of liver and kidney diseases can prevent severe symptoms and ensure better management of these patients. Emerging approaches such as breath and sweat analysis have shown potential as non-invasive methods for disease diagnosis. Among the many markers, ammonia is often used as a biomarker for the monitoring of liver and kidney functions. In this review we provide an insight into the production and expulsion of ammonia gas in the human body, the different diseases that could potentially use ammonia as biomarker and analytical devices such as chemiresistive gas sensors for non-invasive monitoring of this gas. The review also provides an understanding into the different materials, doping agents and substrates used to develop such multifunctional sensors. Finally, the current challenges and the possible future trends have been discussed.
Topics: Humans; Ammonia; Biosensing Techniques; Point-of-Care Testing; Biomarkers
PubMed: 38364327
DOI: 10.1016/j.bios.2024.116100 -
Mathematical Biosciences and... Jul 2022This work proposes a mathematical model on partial nitritation/anammox (PN/A) granular bioreactors, with a particular interest in the start-up phase. The formation and...
This work proposes a mathematical model on partial nitritation/anammox (PN/A) granular bioreactors, with a particular interest in the start-up phase. The formation and growth of granular biofilms is modelled by a spherical free boundary problem with radial symmetry and vanishing initial value. Hyperbolic PDEs describe the advective transport and growth of sessile species inhabiting the granules. Parabolic PDEs describe the diffusive transport and conversion of soluble substrates, and the invasion process mediated by planktonic species. Attachment and detachment phenomena are modelled as continuous and deterministic fluxes at the biofilm-bulk liquid interface. The dynamics of planktonic species and substrates within the bulk liquid are modelled through ODEs. A simulation study is performed to describe the start-up process of PN/A granular systems and the development of anammox granules. The aim is to investigate the role that the invasion process of anaerobic ammonia-oxidizing (anammox) bacteria plays in the formation of anammox granules and explore how it affects the microbial species distribution of anaerobic ammonia-oxidizing, aerobic ammonia-oxidizing, nitrite-oxidizing and heterotrophic bacteria. Moreover, the model is used to study the role of two key parameters in the start-up process: the anammox inoculum size and the inoculum addition time. Numerical results confirm that the model can be used to simulate the start-up process of PN/A granular systems and to predict the evolution of anammox granular biofilms, including the ecology and the microbial composition. In conclusion, after being calibrated, the proposed model could provide quantitatively reliable results and support the start-up procedures of full-scale PN/A granular reactors.
Topics: Ammonia; Anaerobic Ammonia Oxidation; Bioreactors; Nitrites; Nitrogen
PubMed: 36031999
DOI: 10.3934/mbe.2022486 -
MSystems Feb 2022Microbes commonly exist in diverse and complex communities where species interact, and their genomic repertoires evolve over time. Our understanding of species...
Microbes commonly exist in diverse and complex communities where species interact, and their genomic repertoires evolve over time. Our understanding of species interaction and evolution has increased during the last decades, but most studies of evolutionary dynamics are based on single species in isolation or in experimental systems composed of few interacting species. Here, we use the microbial ecosystem found in groundwater-fed sand filter as a model to avoid this limitation. In these open systems, diverse microbial communities experience relatively stable conditions, and the coupling between chemical and biological processes is generally well defined. Metagenomic analysis of 12 sand filters communities revealed systematic co-occurrence of at least five comammox species, likely promoted by low ammonium concentrations. These species showed intrapopulation sequence diversity, although possible clonal expansion was detected in a few abundant local comammox populations. species showed low homologous recombination and strong purifying selection, the latter process being especially strong in genes essential in energy metabolism. Positive selection was detected for genes related to resistance to foreign DNA and phages. We found that, compared to other habitats, groundwater-fed sand filters impose strong purifying selection and low recombination on comammox populations. These results suggest that evolutionary processes are more affected by habitat type than by species identity. Together, this study improves our understanding of species interaction and evolution in complex microbial communities and sheds light on the environmental dependency of evolutionary processes. Microbial species interact with each other and their environment (ecological processes) and undergo changes in their genomic repertoire over time (evolutionary processes). How these two classes of processes interact is largely unknown, especially for complex communities, as most studies of microbial evolutionary dynamics consider single species in isolation or a few interacting species in simplified experimental systems. In this study, these limitations are circumvented by examining the microbial communities found in stable and well-described groundwater-fed sand filters. Combining metagenomics and strain-level analyses, we identified the microbial interactions and evolutionary processes affecting comammox , a recently discovered bacterial type capable of performing the whole nitrification process. We found that abundant and co-occurrent populations in groundwater-fed sand filters are characterized by low recombination and strong purifying selection. In addition, by comparing these observations with those obtained from species inhabiting other environments, we revealed that evolutionary processes are more affected by habitat type than by species identity.
Topics: Ammonia; Nitrites; Oxidation-Reduction; Bacteria; Microbiota
PubMed: 35014874
DOI: 10.1128/msystems.01139-21 -
The ISME Journal Nov 2022The nitrogen cycle plays a major role in aquatic nitrogen transformations, including in the terrestrial subsurface. However, the variety of transformations remains...
The nitrogen cycle plays a major role in aquatic nitrogen transformations, including in the terrestrial subsurface. However, the variety of transformations remains understudied. To determine how nitrogen cycling microorganisms respond to different aquifer chemistries, we sampled groundwater with varying nutrient and oxygen contents. Genes and transcripts involved in major nitrogen-cycling pathways were quantified from 55 and 26 sites, respectively, and metagenomes and metatranscriptomes were analyzed from a subset of oxic and dysoxic sites (0.3-1.1 mg/L bulk dissolved oxygen). Nitrogen-cycling mechanisms (e.g. ammonia oxidation, denitrification, dissimilatory nitrate reduction to ammonium) were prevalent and highly redundant, regardless of site-specific physicochemistry or nitrate availability, and present in 40% of reconstructed genomes, suggesting that nitrogen cycling is a core function of aquifer communities. Transcriptional activity for nitrification, denitrification, nitrite-dependent anaerobic methane oxidation and anaerobic ammonia oxidation (anammox) occurred simultaneously in oxic and dysoxic groundwater, indicating the availability of oxic-anoxic interfaces. Concurrent activity by these microorganisms indicates potential synergisms through metabolite exchange across these interfaces (e.g. nitrite and oxygen). Fragmented denitrification pathway encoding and transcription was widespread among groundwater bacteria, although a considerable proportion of associated transcriptional activity was driven by complete denitrifiers, especially under dysoxic conditions. Despite large differences in transcription, the capacity for the final steps of denitrification was largely invariant to aquifer conditions, and most genes and transcripts encoding NO reductases were the atypical Sec-dependant type, suggesting energy-efficiency prioritization. Results provide insights into the capacity for cooperative relationships in groundwater communities, and the richness and complexity of metabolic mechanisms leading to the loss of fixed nitrogen.
Topics: Ammonia; Ammonium Compounds; Denitrification; Methane; Nitrates; Nitrites; Nitrogen; Nitrogen Cycle; Oxidation-Reduction; Oxidoreductases; Oxygen
PubMed: 35941171
DOI: 10.1038/s41396-022-01300-0 -
The ISME Journal Feb 2022Ammonia oxidizers are key players in the global nitrogen cycle, yet little is known about their ecological performances and adaptation strategies for growth in saline...
Ammonia oxidizers are key players in the global nitrogen cycle, yet little is known about their ecological performances and adaptation strategies for growth in saline terrestrial ecosystems. This study combined C-DNA stable-isotope probing (SIP) microcosms with amplicon and shotgun sequencing to reveal the composition and genomic adaptations of active ammonia oxidizers in a saline-sodic (solonetz) soil with high salinity and pH (20.9 cmol exchangeable Na kg soil and pH 9.64). Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) exhibited strong nitrification activities, although AOB performed most of the ammonia oxidation observed in the solonetz soil and in the farmland soil converted from solonetz soil. Members of the Nitrosococcus, which are more often associated with aquatic habitats, were identified as the dominant ammonia oxidizers in the solonetz soil with the first direct labeling evidence, while members of the Nitrosospira were the dominant ammonia oxidizers in the farmland soil, which had much lower salinity and pH. Metagenomic analysis of "Candidatus Nitrosococcus sp. Sol14", a new species within the Nitrosococcus lineage, revealed multiple genomic adaptations predicted to facilitate osmotic and pH homeostasis in this extreme habitat, including direct Na extrusion/H import and the ability to increase intracellular osmotic pressure by accumulating compatible solutes. Comparative genomic analysis revealed that variation in salt-tolerance mechanisms was the primary driver for the niche differentiation of ammonia oxidizers in saline-sodic soils. These results demonstrate how ammonia oxidizers can adapt to saline-sodic soil with excessive Na content and provide new insights on the nitrogen cycle in extreme terrestrial ecosystems.
Topics: Ammonia; Archaea; Ecosystem; Nitrification; Oxidation-Reduction; Phylogeny; Salt Tolerance; Soil; Soil Microbiology
PubMed: 34389794
DOI: 10.1038/s41396-021-01079-6 -
Ecotoxicology and Environmental Safety Sep 2022Ammonia is one of the most important toxic metabolites in the intestine of animals. It can cause intestinal damage and associated intestinal diseases through different...
Ammonia is one of the most important toxic metabolites in the intestine of animals. It can cause intestinal damage and associated intestinal diseases through different endogenous or exogenous stimuli. However, the definition of harmful ammonia concentration and the molecular mechanism of ammonia - induced intestinal epithelial injury remain unclear. In this study, we found that the viability of porcine IPEC-J2 intestinal epithelial cells significantly decreased with the increase of NHCl dose (20-80 mM). Ammonia (40 mM NHCl) increased the expression level of ammonia transporter RHCG and disrupted the intestinal barrier function of IPEC-J2 cells by reducing the expression levels of the tight junction molecules ZO-1 and Claudin-1. Ammonia caused elevated levels of ROS and apoptosis in IPEC-J2 cells. This was manifested by decreased activity of antioxidant enzymes SOD and GPx, decreased mitochondrial membrane potential, and increased cytoplasmic Ca concentration. In addition, the expression levels of apoptosis-related molecules Caspase-9, Caspase-3, Fas, Caspase-8, p53 and Bax were increased, the expression level of anti-apoptotic molecule Bcl-2 was decreased. Moreover, the antioxidant NAC (N-acetyl-L-cysteamine) effectively alleviated ammonia-induced cytotoxicity, reduced ROS level, Ca concentration, and the apoptosis of IPEC-J2 cells. The results suggest that ammonia-induced excess ROS triggered apoptosis through mitochondrial pathway, death receptor pathway and DNA damage. This study can provide reference and theoretical basis for the definition of harmful ammonia concentration in pig intestine and the effect and mechanism of ammonia on pig intestinal health.
Topics: Ammonia; Animals; Antioxidants; Apoptosis; Cell Line; Epithelial Cells; Intestines; Reactive Oxygen Species; Swine
PubMed: 36037632
DOI: 10.1016/j.ecoenv.2022.114006 -
International Journal of Environmental... Dec 2020There is a huge potential for nutrient recovery from organic waste materials for soil fertility restoration as well as negative environmental emission mitigation....
There is a huge potential for nutrient recovery from organic waste materials for soil fertility restoration as well as negative environmental emission mitigation. Previous research has found vermicomposting the optimal choice for converting organic waste into beneficial organic fertilizer while reducing reactive N loss. However, a great deal of the processes of greenhouse gases (GHG) and ammonia volatilization during vermicomposting are not well-documented. A field vermicomposting experiment was conducted by deploying earthworms () with three types of agricultural by-products-namely, cow manure (VCM), pig manure (VPM), and biochar (VBC)-and crop (maize) residues compared with traditional composting (COM) without earthworms in the Sichuan Basin, China. Results showed that vermicomposting caused a decrease in electrical conductivity (EC) and total organic carbon (TOC) while increasing total nitrogen (TN). The greatest TN increase was found with VCM. The cumulative NH volatilization in COM, VCM, VPM, and VBC during experimental duration was 9.00, 8.02, 15.16, and 8.91 kg N ha, respectively. The cumulative CO emissions in COM, VCM, VPM, and VBC were 2369, 2814, 3435, and 2984 (g·C·m), while for CH, they were 0.36, 0.28, 4.07, and 0.19 (g·C·m) and, for NO, they were 0.12, 0.06, 0.76, and 0.04 (g·N m), respectively. Lower emissions of NO, CH, and NH were observed in VBC. We concluded that earthworms, as ecological engineers, enhanced reactive nutrients and reduced ammonia volatilization during vermicomposting in our test system. Overall, vermicomposting is proposed as an eco-friendly, sustainable technique that helps to reduce environmental impacts and associated health risks.
Topics: Ammonia; Animals; Cattle; Charcoal; China; Composting; Greenhouse Gases; Manure; Nitrogen; Oligochaeta; Soil; Swine; Volatilization
PubMed: 33383747
DOI: 10.3390/ijerph18010178