Evidence for Assimilatory Nitrate Reduction as a Previously Overlooked Pathway of Reactive Nitrogen Transformation in Estuarine Suspended Particulate Matter

Different effects of seasonal impoundment and land use change on microbiome in a tributary sediment of the three gorgers reservoir

Anthropogenic activities significantly impact river ecosystem nutrient fluxes and microbial metabolism. Here, we examined the seasonal and spatial variation of sediments physicochemical parameters and the associated microbiome in the Pengxi river, a representative tributary of Three Gorges Reservoir, in response to seasonal impoundment and land use change by human activities. Results revealed that seasonal impoundment and land use change enhanced total organic carbon (TOC), total nitrogen (TN) and ammonium nitrogen (NH4+-N) concentration in the sediment, but have different effects on sediment microbiome. Sediment microbiota showed higher similarity during the seasonal high-water level (HWL) in consecutive two years. The abundant phyla Acidobacteria, Gemmatimonadetes, Cyanobacteria, Actinobacteria and Planctomycetes significantly increased as water level increased. Along the changes in bacterial taxa, we also observed changes in predicted carbon fixation functions and nitrogen-related functions, including the significantly higher levels of Calvin cycle, 4HB/3HP cycle, 3HP cycle and assimilatory nitrate reduction, while significantly lower level of denitrification. Though land use change significantly increased TOC, TN and NH4+-N concentration, its effects on spatial variation of bacterial community composition and predicted functions was not significant. The finding indicates that TGR hydrologic changes and land use change have different influences on the carbon and nitrogen fluxes and their associated microbiome in TGR sediments. A focus of future research will be on assessing on carbon and nitrogen flux balance and the associated carbon and nitrogen microbial cycling in TGR sediment.

Impact of hydrogen sulfide on anammox and nitrate/nitrite-dependent anaerobic methane oxidation coupled technologies

The coupling between anammox and nitrate/nitrite-dependent anaerobic methane oxidation (n-DAMO) has been considered a sustainable technology for nitrogen removal from sidestream wastewater and can be implemented in both membrane biofilm reactor (MBfR) and granular bioreactor. However, the potential influence of the accompanying hydrogen sulfide (H2S) in the anaerobic digestion (AD)-related methane-containing mixture on anammox/n-DAMO remains unknown. To fill this gap, this work first constructed a model incorporating the C/N/S-related bioprocesses and evaluated/calibrated/validated the model using experimental data. The model was then used to explore the impact of H2S on the MBfR and granular bioreactor designed to perform anammox/n-DAMO at practical levels (i.e., 0∼5% (v/v) and 0∼40 g/S m3, respectively). The simulation results indicated that H2S in inflow gas did not significantly affect the total nitrogen (TN) removal of the MBfR under all operational conditions studied in this work, thus lifting the concern about applying AD-produced biogas to power up anammox/n-DAMO in the MBfR. However, the presence of H2S in the influent would either compromise the treatment performance of the granular bioreactor at a relatively high influent NH4+-N/NO2--N ratio (e.g., >1.0) or lead to increased energy demand associated with TN removal at a relatively low influent NH4+-N/NO2--N ratio (e.g., <0.7). Such a negative effect of the influent H2S could not be attenuated by regulating the hydraulic residence time and should therefore be avoided when applying the granular bioreactor to perform anammox/n-DAMO in practice.

Current status and emerging frontiers in enzyme engineering: An industrial perspective

Protein engineering mechanisms can be an efficient approach to enhance the biochemical properties of various biocatalysts. Immobilization of biocatalysts and the introduction of new-to-nature chemical reactivities are also possible through the same mechanism. Discovering new protocols that enhance the catalytic active protein that possesses novelty in terms of being stable, active, and, stereoselectivity with functions could be identified as essential areas in terms of concurrent bioorganic chemistry (synergistic relationship between organic chemistry and biochemistry in the context of enzyme engineering). However, with our current level of knowledge about protein folding and its correlation with protein conformation and activities, it is almost impossible to design proteins with specific biological and physical properties. Hence, contemporary protein engineering typically involves reprogramming existing enzymes by mutagenesis to generate new phenotypes with desired properties. These processes ensure that limitations of naturally occurring enzymes are not encountered. For example, researchers have engineered cellulases and hemicellulases to withstand harsh conditions encountered during biomass pretreatment, such as high temperatures and acidic environments. By enhancing the activity and robustness of these enzymes, biofuel production becomes more economically viable and environmentally sustainable. Recent trends in enzyme engineering have enabled the development of tailored biocatalysts for pharmaceutical applications. For instance, researchers have engineered enzymes such as cytochrome P450s and amine oxidases to catalyze challenging reactions involved in drug synthesis. In addition to conventional methods, there has been an increasing application of machine learning techniques to identify patterns in data. These patterns are then used to predict protein structures, enhance enzyme solubility, stability, and function, forecast substrate specificity, and assist in rational protein design. In this review, we discussed recent trends in enzyme engineering to optimize the biochemical properties of various biocatalysts. Using examples relevant to biotechnology in engineering enzymes, we try to expatiate the significance of enzyme engineering with how these methods could be applied to optimize the biochemical properties of a naturally occurring enzyme.

Overlooked in-situ sulfur disproportionation fuels dissimilatory nitrate reduction to ammonium in sulfur-based system: Novel insight of nitrogen recovery

Sulfur-based denitrification is a promising technology in treatments of nitrate-contaminated wastewaters. However, due to weak bioavailability and electron-donating capability of elemental sulfur, its sulfur-to-nitrate ratio has long been low, limiting the support for dissimilatory nitrate reduction to ammonium (DNRA) process. Using a long-term sulfur-packed reactor, we demonstrate here for the first time that DNRA in sulfur-based system is not negligible, but rather contributes a remarkable 40.5 %-61.1 % of the total nitrate biotransformation for ammonium production. Through combination of kinetic experiments, electron flow analysis, 16S rRNA amplicon, and microbial network succession, we unveil a cryptic in-situ sulfur disproportionation (SDP) process which significantly facilitates DNRA via enhancing mass transfer and multiplying 86.7-210.9 % of bioavailable electrons. Metagenome assembly and single-copy gene phylogenetic analysis elucidate the abundant genomes, including uc_VadinHA17, PHOS-HE36, JALNZU01, Thiobacillus, and Rubrivivax, harboring complete genes for ammonification. Notably, a unique group of self-SDP-coupled DNRA microorganism was identified. This study unravels a previously concealed fate of DNRA, which highlights the tremendous potential for ammonium recovery and greenhouse gas mitigation. Discovery of a new coupling between nitrogen and sulfur cycles underscores great revision needs of sulfur-driven denitrification technology.

An indispensable role of overlying water in nitrogen removal in shallow lakes

The nitrogen (N) removal characteristics in water columns and sediments of shallow lakes, influenced by various factors, may exhibit spatial variations in lakes with algal-macrophyte dominance. The N removal rates in water columns and sediments of Lake Taihu were investigated. Our findings indicated that the total N removal rates in Lake Taihu followed the order of algae-dominance > macrophyte-dominance > pelagic lake (without the presence of algae and macrophytes). Correlation analysis revealed that the key environmental factors affecting denitrification and anammox in sediments of algae/macrophyte-type lakes were nitrate nitrogen (NO3--N), nitrite nitrogen (NO2--N), ammonia nitrogen (NH4+-N), and chlorophyll a (Chl-a). The linear regression demonstrated that a significant correlation between the denitrification and the anammox in sediments, with a correlation coefficient of 0.81 (p < 0.01). The contributions to N removal from the water columns and sediments in Lake Taihu were 53 % and 47 %, respectively. Denitrification predominantly drove N removal from sediments, whereas anammox dominated the N removal in water columns. Thus, N removal from the water columns is nonnegligible in shallow eutrophic lakes. This study enhances our understanding of N biogeochemical cycling dynamics in sediment-water and algae/macrophyte ecosystems across various shallow eutrophic lake regions.

Fungal community diversity and their contribution to nitrogen cycling in in-situ aerated landfills: Insights from field and laboratory studies

The application of in-situ aeration technology in landfills has been reported to promote fungal growth, but the community diversity and function of fungi in the aerated landfill system remain unknown. This study firstly investigated an in-situ aerated remediation landfill site to characterize the fungal community diversity in refuse. And to further reveal the fungal involvement in the nitrogen cycling system, laboratory-scale simulated aerated landfill reactors were then constructed. The results in the aerated landfill site showed a significant correlation between fungal community structure and ammonia nitrogen content in the refuse. Dominant fungi in the fungal community included commonly found environmental fungi such as Fusarium, Aspergillus, Gibberella, as well as unique fungi in the aerated system like Chaetomium. In the laboratory-scale aerated landfill simulation experiments, the fungal system was constructed using bacterial inhibitor, and nitrogen balance analysis confirmed the significant role of fungal nitrification in the nitrogen cycling process. When ammonia nitrogen was not readily available, fungi converted organic nitrogen to nitrate, serving as the main nitrification mechanism in the system, with a contribution rate ranging from 62.71 % to 100 % of total nitrification. However, when ammonia nitrogen was present in the system, autotrophic nitrification became the main mechanism, and the contribution of fungal nitrification to total nitrification was only 15.96 %. Additionally, fungi were capable of directly utilizing nitrite for nitrate production with a rate of 4.65 mg L-1 d-1. This research article contributes to the understanding of the importance of fungi in the aerated landfill systems, filling a gap in knowledge.

Nitrogen metabolism pathways and functional microorganisms in typical karst wetlands

Aha Lake artificial reservoir wetland, Niangniang Mountain karst mountain wetland, and Caohai plateau lake wetland are typical karst wetlands in Guizhou Province with unique topography and geomorphic features. They were selected as research objects in this study to explore microorganisms and functional genes in nitrogen metabolism adopting macro-genome sequencing technology. It was found that Proteobacteria, Actinobacteria, and Acidobacteria were the dominant phyla in nitrogen metabolism in these three wetlands, similar to previous studies. However, at the genus level, there was a significant difference, with the dominant bacteria being Bradyrhizobium, Methylocystis, and Anaeromyxobacter. Six nitrogen metabolism pathways, including nitrogen fixation, nitrification, denitrification, dissimilatory nitrate reduction, assimilatory nitrate reduction, and complete nitrification, comammox, were revealed, but anaerobic ammonia oxidation genes were not detected. Nitrogen metabolism microorganisms and pathways were more affected by SOM, pH, NO3-, and EC in karst wetlands. This study further discussed microorganisms and functions of nitrogen metabolism in karst wetlands, which was of great significance to nitrogen cycles of karst wetland ecosystems.

Start-up of solid-phase denitrification process for treatment of nitrate-rich water in recirculating mariculture system: Carbon source selection and nitrate removal mechanism

Efficient nitrate removal from recirculating mariculture system (RMS) water is of significance since high concentration of nitrate would cause chronic health effects on aquatic organisms and eutrophication. Solid-phase denitrification (SPD) is a safer and more sustainable approach than conventional heterotrophic denitrification by dosing liquid carbon sources. Thus, its application for treating nitrate-rich RMS water was investigated in this study. Poly 3-hydroxybutyrate-co-3-hydroxyvalerate (PHBV) was identified with the best nitrate removal among four kinds of carbon sources. PHBV-filled reactors started with mariculture, municipal and mixing sludges (at the ratio of 1:1) and fed with 200 mg L-1 nitrate-rich RMS water all achieved over 81% nitrate removals with a HRT of 4 days. The dissolved organic carbon concentrations of the reactors were in the range of 3-9 mg L-1. Arcobacter, Halomonas, and Psedomonas were dominant genera responsible for nitrate removal in different reactors. Metagenomic analyses indicate that both denitrification and assimilatory nitrate reduction (ANR) are the main contributors to nitrate removals. Metagenomic results illustrated nirB/D cooperated with nasA may perform ANR pathway, which transformed nitrate to ammonia for biosynthesis. These results indicate that SPD could be a safer alternative for treating nitrate-rich RMS water, and provide new insights into nitrogen metabolism pathways in SPD process.

Shifts in the high-resolution spatial distribution of dissolved N2O and the underlying microbial communities and processes in the Pearl River Estuary

Estuaries are significant sources of the ozone-depleting greenhouse gas N2O. However, owing to large spatial heterogeneity and discrete measurements, N2O emissions from estuaries are considerably uncertain. Microbial processes are disputed in terms of the dominant N2O production under severe human disturbance. Herein, combining real-time and high-resolution measurements with bioinformatics analysis, we accurately mapped the consecutive two-dimensional N2O distribution in the Pearl River Estuary (PRE), China, and revealed its underlying microbial mechanisms. Both the horizontal and vertical distributions of N2O concentrations varied greatly at fine scales. Supersaturated N2O concentrations (9.1 to 132.2 nmol/L) in the surface water decreased along the estuarine salinity gradient, with several emission hotspots scattering upstream. The vertical N2O distribution showed marked differences from complete mixing upstream to incomplete mixing downstream, with constant or changeable concentrations with increasing depth. Furthermore, spatially varied denitrifying and nitrifying microorganisms controlled the N2O production and distribution in the PRE, with denitrification playing the dominant role. The nirK-type and nirS-type denitrifying bacteria were the primary producers of N2O in the water and sediment columns, respectively. In addition, substrate concentration (NO3- and DOC) regulated N2O production by affecting key microbial processes, while physical influences (water-mass mixing and salt wedges) reshaped N2O distribution. With these information, a conceptual model of estuarine N2O production and distribution was constructed to generalize the possible biochemical processes under environmental constraints, which could provide insights into the N2O biogeochemical cycle and emission mitigation from a mechanistic perspective.

Nitrite-resistance mechanisms on wastewater treatment in denitrifying phosphorus removal process revealed by machine learning, co-occurrence, and metagenomics analysis

Nitrite is a key intermediate in nitrogen metabolism that determines microbial transformations of N and P, greenhouse gas (N₂O) emissions, and system nutrient removal efficiency. However, nitrite also exerts toxic effects on microorganisms. A lack of understanding of high nitrite-resistance mechanisms at community- and genome-scale resolutions hinders the optimization for robustness of wastewater treatment systems. Here, we established nitrite-dependent denitrifying and phosphorus removal (DPR) systems under a gradient concentration of nitrite (0, 5, 10, 15, 20, and 25 mg N/L), relying on 16S rRNA gene amplicon and metagenomics to explore high nitrite-resistance mechanism. The results demonstrated that specific taxa were adopted to change the metabolic relationship of the community through phenotypic evolution to resist toxic nitrite contributing to the enhancement of denitrification and inhibition of nitrification and phosphorus removal. The key specific species, Thauera enhanced denitrification, whereas Candidatus Nitrotoga decreased in abundance to maintain partial nitrification. The extinction of Candidatus Nitrotoga induced a simpler restructuring-community, forcing high nitrite-stimulating microbiome to establish a more focused denitrification rather than nitrification or P metabolism in response to nitrite toxicity. Our work provides insights for understanding microbiome adaptation to toxic nitrite and giving theoretical support for operation strategy of nitrite-based wastewater treatment technology.

Characterization and metabolic pathway of Pseudomonas fluorescens 2P24 for highly efficient ammonium and nitrate removal

The ammonium and nitrate removal performance and metabolic pathways of a biocontrol strain, Pseudomonas fluorescens 2P24, were investigated. Strain 2P24 could completely remove 100 mg/L ammonium and nitrate, with removal rates of 8.27 mg/L/h and 4.29 mg/L/h, respectively. During these processes, most of the ammonium and nitrate were converted to biological nitrogen via assimilation, and only small amounts of nitrous oxide escaped. The inhibitor allylthiourea had no impact on ammonium transformation, and diethyl dithiocarbamate and sodium tungstate did not inhibit nitrate removal. Intracellular nitrate and ammonium were detectable during the nitrate and ammonium transformation process, respectively. Moreover, the nitrogen metabolism functional genes (glnK, nasA, narG, nirBD, nxrAB, nirS, nirK, and norB) were identified in the strain. All results highlighted that P. fluorescens 2P24 is capable of assimilatory and dissimilatory nitrate reduction, ammonium assimilation and oxidation, and denitrification.

Water quality improvement and consequent N2O emission reduction in hypoxic freshwater utilizing green oxygen-carrying biochar

Declines in dissolved oxygen (DO) levels in aquatic systems worldwide negatively influence biodiversity, nutrient biogeochemistry, drinking water quality, and greenhouse gas emission. As a response, oxygen-carrying dual-modified sediment-based biochar (O-DM-SBC) as a green and sustainable emerging material was utilized for simultaneous hypoxia restoration, water quality improvement, and greenhouse gas reduction. Column incubation experiments were carried out using the water and sediment samples from a tributary of the Yangtze River. The application of O-DM-SBC effectively increased the DO concentration from ~1.99 mg/L to ~6.44 mg/L and decreased the concentrations of TN and NH₄⁺-N by 61.1 % and 78.3 %, respectively, during the 30-day incubation period. Moreover, the N₂O emission was apparently inhibited by O-DM-SBC with a 50.2 % decrease in daily flux under the functional coupling of biochar (SBC) and oxygen nanobubbles (ONBs). Path analysis supported that the treatments (SBC, modification, and ONBs) had joint effects on N₂O emission by changing the concentration and composition of dissolved inorganic nitrogen (e.g., NH₄⁺-N, NO₂^--N and NO₃^--N). The nitrogen-transforming bacteria were found to be significantly promoted by O-DM-SBC at the end of the incubation, while the archaeal community seemed to be more active in the SBC groups without ONB, confirming their different mechanisms. The PICRUSt2 prediction results revealed that most nitrogen metabolism genes including nitrification (i.e., amoABC), denitrification (i.e., nirK and nosZ), and assimilatory nitrate reduction (i.e., nirB and gdhA) were largely enriched in O-DM-SBC, indicating the active nitrogen-cycling network was established, thus achieving simultaneous nitrogen pollution control and N₂O emission reduction. Our findings not only confirm the beneficial effect of O-DM-SBC amendment on nitrogen pollution control and N₂O emission mitigation in hypoxic freshwater, but also contribute to a more comprehensive understanding of the effect of oxygen-carrying biochar on nitrogen cycling microbial communities.

In Situ/Operando Methods for Understanding Electrocatalytic Nitrate Reduction Reaction

With the development of industrial and agricultural, a large amount of nitrate is produced, which not only disrupts the natural nitrogen cycle, but also endangers public health. Among the commonly used nitrate treatment techniques, the electrochemical nitrate reduction reaction (eNRR) has attracted extensive attention due to its mild conditions, pollution-free nature, and other advantages. An in-depth understanding of the eNRR mechanism is the prerequisite for designing highly efficient electrocatalysts. However, some traditional characterization tools cannot comprehensively and deeply study the reaction process. It is necessary to develop in situ and operando techniques to reveal the reaction mechanism at the time-resolved and atomic level. This review discusses the eNRR mechanism and summarizes the possible in situ techniques used in eNRR. A detailed introduction of various in situ techniques and their help in understanding the reaction mechanism is provided. Finally, the current challenges and future opportunities in this research area are discussed and highlighted.

Spatial assessment of triazole organic compounds in surface water from the coastal estuaries to the East China sea

Triazole is widely used in the synthesis of pharmaceuticals, pesticides, and fungicides. However, triazole organic compounds are often a source of toxicity in the water environment due to the presence of chlorobenzene. This study reported on the occurrence and distribution of 15 TrOCs in the surface waters of estuaries and the East China sea, and identified the influences of TrOCs originating from the estuarine environment on the ocean. The results showed that the total concentrations of ∑TrOCs in the surface water of estuaries along the coasts of Jiangsu (JS), Zhejiang (ZJ), and Shanghai (SH), China ranged from 0.020 to 104 ng L^-1 (7.49 ± 18.2 ng L^-1), whereas they ranged from 0.235 to 1.25 ng L^-1 (mean 0.711 ± 0.235 ng L^-1) in the East China sea. Difenoconazole and tebuconazole were the dominant TrOCs in the estuaries, whereas fenbuconazole and hexaconazole dominated in the ocean. TrOCs in surface water of estuaries showed a continuous spatial distribution and presented regional characteristics mainly related to agricultural activities. In contrast, TrOCs in the East China Sea showed a low spatial variation and dispersion, which may be related to complex disturbance by currents and dilution. The low levels of estuarine TrOCs measured in SH estuaries (<0.5 ng L^-1) indicates that the Yangtze River may only pose a low-level TrOC contamination risk to the East China Sea. Moreover, estuary transport in the estuaries of ZJ may have influenced the occurrence of TrOCs in the offshore East China Sea area, although they may have also undergone a filter process in the estuary turbid zone; whereas it had little influence on the open sea. This study can act as a critical reference for the presence of TrOCs in surface water both estuaries and the ocean.