Molecular biology and biochemistry of ammonia oxidation by Nitrosomonas europaea

Implementation of in situ aerobic cometabolism for groundwater treatment: State of the knowledge and important factors for field operation

In situ aerobic cometabolism of groundwater contaminants has been demonstrated to be a valuable bioremediation technology to treat many legacy and emerging contaminants in dilute plumes. Several well-designed and documented field studies have shown that this technology can concurrently treat multiple contaminants and reach very low cleanup goals. Fundamentally different from metabolism-based biodegradation of contaminants, microorganisms that cometabolically degrade contaminants do not obtain sufficient carbon and energy from the degradation process to support their growth and require an exogenous growth supporting primary substrate. Successful applications of aerobic cometabolic treatment therefore require special considerations beyond conventional in situ bioremediation, such as competitive inhibition between growth-supporting primary substrate(s) and contaminant non-growth substrates, toxic effects resulting from contaminant degradation, and differences in microbial population dynamics exhibited by biostimulated indigenous consortia versus bioaugmentation cultures. This article first provides a general review of microbiological factors that are likely to affect the rate of aerobic cometabolic biodegradation. We subsequently review fourteen well documented field-scale aerobic cometabolic bioremediation studies and summarize the underlying microbiological factors that may affect the performance observed in these field studies. The combination of microbiological and engineering principles gained from field testing leads to insights and recommendations on planning, design, and operation of an in situ aerobic cometabolic treatment system. With a vision of more aerobic cometabolic treatments being considered to tackle large, dilute plumes, we present several novel topics and future research directions that can potentially enhance technology development and foster success in implementing this technology for environmental restoration.

The potential of enhanced phytoremediation to clean up multi-contaminated soil - insights from metatranscriptomics

This study aimed to (i) investigate the potential for enhanced phytoremediation to remove contaminants from soil historically co-contaminated with petroleum hydrocarbons (PHs) and heavy metals (HMs) and (ii) analyze the expression of crucial bacterial genes and whole metatranscriptomics profiles for better understanding of soil processes during applied treatment. Phytoremediation was performed using Zea mays and supported by the Pseudomonas qingdaonensis ZCR6 strain and a natural biofertilizer: meat and bone meal (MBM). In previous investigations, mechanisms supporting plant growth and PH degradation were described in the ZCR6 strain. Here, ZCR6 survived in the soil throughout the experiment, but the efficacy of PH removal from all soils fertilized with MBM reached 32 % regardless of the bacterial inoculation. All experimental groups contained 2 % (w/w) MBM. The toxic effect of this amendment on plants was detected 30 days after germination, irrespective of ZCR6 inoculation. Among the 17 genes tested using the qPCR method, only expression of the acdS gene, encoding 1-aminocyclopropane-1-carboxylic acid deaminase, and the CYP153 gene, encoding cytochrome P450-type alkane hydroxylase, was detected in soils. Metatranscriptomic analysis of soils indicated increased expression of methane particulated ammonia monooxygenase subunit A (pmoA-amoA) by Nitrosomonadales bacteria in all soils enriched with MBM compared to the non-fertilized control. We suggest that the addition of 2 % (w/w) MBM caused the toxic effect on plants via the rapid release of ammonia, and this led to high pmoA-amoA expression. In parallel, due to its wide substrate specificity, enhanced bacterial hydrocarbon removal in MBM-treated soils was observed. The metatranscriptomic results indicate that MBM application should be considered to improve bioremediation of soils polluted with PHs rather than phytoremediation. However, lower concentrations of MBM could be considered for phytoremediation enhancement. From a broader perspective, these results indicated the superior capability of metatranscriptomics to investigate the microbial mechanisms driving various bioremediation techniques.

Favipiravir biotransformation by a side-stream partial nitritation sludge: Transformation mechanisms, pathways and toxicity evaluation

Information on biotransformation of antivirals in the side-stream partial nitritation (PN) process was limited. In this study, a side-stream PN sludge was adopted to investigate favipiravir biotransformation under controlled ammonium and pH levels. Results showed that free nitrous acid (FNA) was an important factor that inhibited ammonia oxidation and the cometabolic biodegradation of favipiravir induced by ammonia oxidizing bacteria (AOB). The removal efficiency of favipiravir reached 12.6% and 35.0% within 6 days at the average FNA concentrations of 0.07 and 0.02 mg-N L-1, respectively. AOB-induced cometabolism was the sole contributing mechanism to favipiravir removal, excluding AOB-induced metabolism and heterotrophic bacteria-induced biodegradation. The growth of Escherichia coli was inhibited by favipiravir, while the AOB-induced cometabolism facilitated the alleviation of the antimicrobial activities with the formed transformation products. The biotransformation pathways were proposed based on the roughly identified structures of transformation products, which mainly involved hydroxylation, nitration, dehydrogenation and covalent bond breaking under enzymatic conditions. The findings would provide insights on enriching AOB abundance and enhancing AOB-induced cometabolism under FNA stress when targeting higher removal of antivirals during the side-stream wastewater treatment processes.

Direct Methane Oxidation by Copper- and Iron-Dependent Methane Monooxygenases

Methane is a potent greenhouse gas that contributes significantly to climate change and is primarily regulated in Nature by methanotrophic bacteria, which consume methane gas as their source of energy and carbon, first by oxidizing it to methanol. The direct oxidation of methane to methanol is a chemically difficult transformation, accomplished in methanotrophs by complex methane monooxygenase (MMO) enzyme systems. These enzymes use iron or copper metallocofactors and have been the subject of detailed investigation. While the structure, function, and active site architecture of the copper-dependent particulate methane monooxygenase (pMMO) have been investigated extensively, its putative quaternary interactions, regulation, requisite cofactors, and mechanism remain enigmatic. The iron-dependent soluble methane monooxygenase (sMMO) has been characterized biochemically, structurally, spectroscopically, and, for the most part, mechanistically. Here, we review the history of MMO research, focusing on recent developments and providing an outlook for future directions of the field. Engineered biological catalysis systems and bioinspired synthetic catalysts may continue to emerge along with a deeper understanding of the molecular mechanisms of biological methane oxidation. Harnessing the power of these enzymes will necessitate combined efforts in biochemistry, structural biology, inorganic chemistry, microbiology, computational biology, and engineering.

Ammonia and aquatic ecosystems - A review of global sources, biogeochemical cycling, and effects on fish

The purpose of this review is to better understand the full life cycle and influence of ammonia from an aquatic biology perspective. While ammonia has toxic properties in water and air, it also plays a central role in the biogeochemical nitrogen (N) cycle and regulates mechanisms of normal and abnormal fish physiology. Additionally, as the second most synthesized chemical on Earth, ammonia contributes economic value to many sectors, particularly fertilizers, energy storage, explosives, refrigerants, and plastics. But, with so many uses, industrial N2-fixation effectively doubles natural reactive N concentrations in the environment. The consequence is global, with excess fixed nitrogen driving degradation of soils, water, and air; intensifying eutrophication, biodiversity loss, and climate change; and creating health risks for humans, wildlife, and fisheries. Thus, the need for ammonia research in aquatic systems is growing. In response, we prepared this review to better understand the complexities and connectedness of environmental ammonia. Even the term "ammonia" has multiple meanings. So, we have clarified the nomenclature, identified units of measurement, and summarized methods to measure ammonia in water. We then discuss ammonia in the context of the N-cycle, review its role in fish physiology and mechanisms of toxicity, and integrate the effects of human N-fixation, which continuously expands ammonia's sources and uses. Ammonia is being developed as a carbon-free energy carrier with potential to increase reactive nitrogen in the environment. With this in mind, we review the global impacts of excess reactive nitrogen and consider the current monitoring and regulatory frameworks for ammonia. The presented synthesis illustrates the complex and interactive dynamics of ammonia as a plant nutrient, energy molecule, feedstock, waste product, contaminant, N-cycle participant, regulator of animal physiology, toxicant, and agent of environmental change. Few molecules are as influential as ammonia in the management and resilience of Earth's resources.

Juglone, a plant-derived 1,4-naphthoquinone, binds to hydroxylamine oxidoreductase and inhibits the electron transfer to cytochrome c554

IMPORTANCE

Nitrification, the microbial conversion of ammonia to nitrate via nitrite, plays a pivotal role in the global nitrogen cycle. However, the excessive use of ammonium-based fertilizers in agriculture has disrupted this cycle, leading to groundwater pollution and greenhouse gas emissions. In this study, we have demonstrated the inhibitory effects of plant-derived juglone and related 1,4-naphthoquinones on the nitrification process in Nitrosomonas europaea. Notably, the inhibition mechanism is elucidated in which 1,4-naphthoquinones interact with hydroxylamine oxidoreductase, disrupting the electron transfer to cytochrome c554, a physiological electron acceptor. These findings support the notion that phytochemicals can impede nitrification by interfering with the essential electron transfer process in ammonia oxidation. The findings presented in this article offer valuable insights for the development of strategies aimed at the management of nitrification, reduction of fertilizer utilization, and mitigation of greenhouse gas emissions.

Ammonia-oxidizing archaea and bacteria differentially contribute to ammonia oxidation in soil under precipitation gradients and land legacy

Background

Global change has accelerated the nitrogen cycle. Soil nitrogen stock degradation by microbes leads to the release of various gases, including nitrous oxide (N2O), a potent greenhouse gas. Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) participate in the soil nitrogen cycle, producing N2O. There are outstanding questions regarding the impact of environmental processes such as precipitation and land use legacy on AOA and AOB structurally, compositionally, and functionally. To answer these questions, we analyzed field soil cores and soil monoliths under varying precipitation profiles and land legacies.

Results

We resolved 28 AOA and AOB metagenome assembled genomes (MAGs) and found that they were significantly higher in drier environments and differentially abundant in different land use legacies. We further dissected AOA and AOB functional potentials to understand their contribution to nitrogen transformation capabilities. We identified the involvement of stress response genes, differential metabolic functional potentials, and subtle population dynamics under different environmental parameters for AOA and AOB. We observed that AOA MAGs lacked a canonical membrane-bound electron transport chain and F-type ATPase but possessed A/A-type ATPase, while AOB MAGs had a complete complex III module and F-type ATPase, suggesting differential survival strategies of AOA and AOB.

Conclusions

The outcomes from this study will enable us to comprehend how drought-like environments and land use legacies could impact AOA- and AOB-driven nitrogen transformations in soil.

Phylogenetic diversity, distribution, and gene structure of the pyruvic oxime dioxygenase involved in heterotrophic nitrification

Some heterotrophic microorganisms carry out nitrification to produce nitrite and nitrate from pyruvic oxime. Pyruvic oxime dioxygenase (POD) is an enzyme that catalyzes the degradation of pyruvic oxime to pyruvate and nitrite from the heterotrophic nitrifying bacterium Alcaligenes faecalis. Sequence similarity searches revealed the presence of genes encoding proteins homologous to A. faecalis POD in bacteria of the phyla Proteobacteria and Actinobacteria and in fungi of the phylum Ascomycota, and their gene products were confirmed to have POD activity in recombinant experiments. Phylogenetic analysis further classified these POD homologs into three groups. Group 1 POD is mainly found in heterotrophic nitrifying Betaproteobacteria and fungi, and is assumed to be involved in heterotrophic nitrification. It is not clear whether group 2 POD, found mainly in species of the Gammaproteobacteria and Actinobacteria, and group 3 POD, found simultaneously with group 1 POD, are involved in heterotrophic nitrification. The genes of bacterial group 1 POD comprised a single transcription unit with the genes related to the metabolism of aromatic compounds, and many of the genes group 2 POD consisted of a single transcription unit with the gene encoding the protein homologous to 4-hydroxy-tetrahydrodipicolinate synthase (DapA). LysR- or Cro/CI-type regulatory genes were present adjacent to or in the vicinity of these POD gene clusters. POD may be involved not only in nitrification, but also in certain metabolic processes whose functions are currently unknown, in coordination with members of gene clusters.

Immobilization of Bacillus Thuringiensis and applicability in removal of sulfamethazine from soil

Microbial degradation is considered an essential and promising treatment for sulfadimidine contamination of soil. To address the low colonization rates and inefficiencies of typical antibiotic-degrading bacteria, sulfamethazine (SM2)-degrading strain H38 is converted into immobilized bacteria in this study. Results show that the removal rate of SM2 by immobilized strain H38 reaches 98% at 36 h, whereas the removal rate of SM2 by free bacteria reaches 75.2% at 60 h. In addition, the immobilized bacteria H38 exhibits tolerance to a wide range of pH (5-9) and temperature (20 °C-40 °C). As the amount of inoculation increases and the initial concentration of SM2 decreases, the removal rate of SM2 by the immobilized strain H38 increases gradually. Laboratory soil remediation tests show that the immobilized strain H38 can remove 90.0% of SM2 from the soil on the 12th day, which exceeds the removal by free bacteria by 23.9% in the same period. Additionally, the results show that the immobilized strain H38 enhances the overall activity of microorganisms in SM2-contaminated soil. Compared with the SM2 only (control group containing no bacteria) and free bacterial treatment groups, the gene expression levels of ammonia-oxidizing archaea, ammonia-oxidizing bacteria, cbbLG, and cbbM increased significantly in the treatment group with immobilized strain H38. This study shows that immobilized strain H38 can reduce the effect of SM2 on soil ecology to a greater extent than free bacteria, while providing safe and effective remediation.

Nitrification and beyond: metabolic versatility of ammonia oxidising archaea

Ammonia oxidising archaea are among the most abundant living organisms on Earth and key microbial players in the global nitrogen cycle. They carry out oxidation of ammonia to nitrite, and their activity is relevant for both food security and climate change. Since their discovery nearly 20 years ago, major insights have been gained into their nitrogen and carbon metabolism, growth preferences and their mechanisms of adaptation to the environment, as well as their diversity, abundance and activity in the environment. Despite significant strides forward through the cultivation of novel organisms and omics-based approaches, there are still many knowledge gaps on their metabolism and the mechanisms which enable them to adapt to the environment. Ammonia oxidising microorganisms are typically considered metabolically streamlined and highly specialised. Here we review the physiology of ammonia oxidising archaea, with focus on aspects of metabolic versatility and regulation, and discuss these traits in the context of nitrifier ecology.

Enhancement of Ammonium Oxidation at Microoxic Bioanodes

Bioelectrochemical systems (BESs) are considered to be energy-efficient to convert ammonium, which is present in wastewater. The application of BESs as a technology to treat wastewater on an industrial scale is hindered by the slow removal rate and lack of understanding of the underlying ammonium conversion pathways. This study shows ammonium oxidation rates up to 228 ± 0.4 g-N m-3 d-1 under microoxic conditions (dissolved oxygen at 0.02-0.2 mg-O2/L), which is a significant improvement compared to anoxic conditions (120 ± 21 g-N m-3 d-1). We found that this enhancement was related to the formation of hydroxylamine (NH2OH), which is rate limiting in ammonium oxidation by ammonia-oxidizing microorganisms. NH2OH was intermediate in both the absence and presence of oxygen. The dominant end-product of ammonium oxidation was dinitrogen gas, with about 75% conversion efficiency in the presence of a microoxic level of dissolved oxygen and 100% conversion efficiency in the absence of oxygen. This work elucidates the dominant pathways under microoxic and anoxic conditions which is a step toward the application of BESs for ammonium removal in wastewater treatment.

Investigating chemical and microbial functional indicators of nutrient retention capacity in greenhouse stormwater retention ponds in southwestern Ontario, Canada

The tributaries flowing through Leamington, Ontario are unique in the Canadian Lake Erie watershed due to the broad spatial extent of greenhouse operations, which more than doubled in size and density from 2011 to 2022. These greenhouse operations are considered to be potential nutrient point sources with respect to observed nutrient concentrations in tributaries adjacent to greenhouse stormwater retention ponds (GSWPs). Identifying causal factors of nutrient release, whether this be chemical or biological, within these ponds may be critical for mitigating their impact on the watershed and ultimately the receiving waters of Lake Erie. Specifically, phosphorus and nitrogen accumulation in freshwater ponds can contribute to environmental damage proximal to adjacent streams, serving as a potential catalyst for algal blooms and eutrophication. This study compared correlations between the water column N:P stoichiometry, sediment nutrient retention capacity, and drivers of microbial metabolism within GSWP sediments. Correlations between water column TN:TP ratios and sediment nutrient retention capacity were observed, suggesting an interplay between N and P in terms of nutrient limitation. Further, clear shifts were observed in the bacterial metabolic pathways analyzed through metatranscriptomics. Specifically, genes related to nitrogen fixation, nitrification and denitrification, and other metabolic processes involving sulfur and methane showed differential expression depending on the condition of the respective pond (i.e., naturalized wetland vs. dredged, eutrophic pond). Collectively, this research serves to highlight the interconnected role of chemical-biological processes particularly as they relate to significant ecosystem processes such as nutrient loading and retention dynamics in impaired freshwater systems.

Ecological restoration performance enhanced by nano zero valent iron treatment in constructed wetlands under perfluorooctanoic acid stress

Perfluorooctanoic acid (PFOA) of widespread use can enter constructed wetlands (CWs) via migration, and inevitably causes negative impacts on removal efficiencies of conventional pollutants due to its ecotoxicity. However, little attention has been paid to strengthen performance of CWs under PFOA stress. In this study, influences of nano zero valent iron (nZVI), which has been demonstrated to improve nutrients removal, were explored after exemplifying threats of PFOA to operation performance in CWs. The results revealed that 1 mg/L PFOA suppressed the nitrification capacity and phosphorus removal, and nZVI distinctly improved the removal efficiency of ammonia and total phosphorus in CWs compared to PFOA exposure group without nZVI, with the maximum increases of 3.65 % and 16.76 %. Furthermore, nZVI significantly stimulated dehydrogenase (390.64 % and 884.54 %) and urease (118.15 % and 246.92 %) activities during 0-30 d and 30-60 d in comparison to PFOA group. On the other hand, nitrifying enzymes were also promoted, in which ammonia monooxygenase increased by 30.90 % during 0-30 d, and nitrite oxidoreductase was raised by 117.91 % and 232.10 % in two stages. Besides, the content of extracellular polymeric substances (EPS) under nZVI treatment was 72.98 % higher than PFOA group. Analyses of Illumina Miseq sequencing further certified that nZVI effectively improved the community richness and caused the enrichment of microorganisms related to nitrogen and phosphorus removal and EPS secreting. These results could provide valuable information for ecological restoration and decontamination performance enhancement of CWs exposed to PFOA.

Achieving PN through the selective recovery of AOB activity in inactivated nitrifying bacteria: Combined aerobic starvation and FA

A novel strategy combining aerobic starvation and free ammonia (FA) was proposed to achieve partial nitrification (PN). The impact of the combined strategy on nitrifying bacteria was explored in a 200-day experiment. The effluent concentration of ammonia was below the detection limits (0.1 mg/L), and the effluent concentration of nitrite and nitrate was 68.12 mg/L and 3.46 mg/L without adding carbon source to the artificial wastewater. The nitrite accumulation rate (NAR) was maintained at 90.15% even when the dissolved oxygen (DO) concentration was 1.50 mg/L. Further analysis showed that PN was achieved by selectively restoring the activity of ammonia-oxidizing bacteria (AOB) in nitrifying bacteria that had lost their activity after starvation. The specific ammonia oxidation rate (SAOR) was 46.25 mg N/g MLVSS/h, and the specific nitrate product rate (SNPR) was only 0.73 mg N/g MLVSS/h in the stable operation stage. The increase in AOB abundance (from 2.79% to 7.13%) and the decrease in nitrite-oxidizing bacteria (NOB) abundance (from 8.75% to 1.44%) explained this phenomenon. Finally, the analyses on the secretion of extracellular polymer substance (EPS), strategies to resist harsh environments, and physical properties of sludge explored the potential mechanism and provided references for applying the combined strategy.

Key enzymes involved in anammox-based processes for wastewater treatment: An applied overview

The anaerobic ammonium oxidation (anammox) process has attracted significant attention as an economic, robustness, and sustainable method for the treatment of nitrogen (N)-rich wastewater. Anammox bacteria (AnAOB) coexist with other microorganisms, and particularly with ammonia-oxidizing bacteria (AOB) and/or heterotrophic bacteria (HB), in symbiosis in favor of the substrate requirement (ammonium and nitrite) of the AnAOB being supplied by these other organisms. The dynamics of these microbial communities have a significant effect on the N-removal performance, but the corresponding metabolic pathways are still not fully understood. These processes involve many common metabolites that may act as key factors to control the symbiotic interactions between these organisms, to maximize N-removal efficiency from wastewater. Therefore, this work overviews the current state of knowledge about the metabolism of these microorganisms including key enzymes and intermediate metabolites and summarizes already reported experiences based on the employment of certain metabolites for the improvement of N-removal using anammox-based processes. PRACTITIONER POINTS: Approaches knowledge about the biochemistry and metabolic pathways involved in anammox-based processes. Some molecular tools can be used to determine enzymatic activity, serving as an optimization in nitrogen removal processes. Enzymatic evaluation allied to the physical-chemical and biomolecular analysis of the nitrogen removal processes expands the application in different effluents.

Influence of organic ammonium derivatives on the equilibria between NH4+, NO2- and NO3- ions in the Nistru River water

The toxic effects of ammonium derivatives in the river water depend dramatically on their natural or synthetic origins and on their chemical structures. It has been proved that 1-naphtylamine (1-NA) and diphenylamine (DPA) breaking impact on the ammonium oxidation and especially on nitrite ions oxidation processes in natural waters is associated with its toxicity. The NH₄⁺ oxidation process slows down for about five days and ten days in river water samples with 0.5 mg/L DPA and corresponding 0.5 mg/L 1-NA. The NO₂⁻ oxidation delay in model samples of river water with 0.025 and 0.05 mg/L 1-NA, is four days and 35 days in the one with 0.5 mg/L 1-NA. For the sample with 0.05 mg/L DPA the delay of the NO₂⁻ oxidation is approximately of six days and 25 days for sample with 0.5 mg/L, DPA. The laboratory simulations have revealed: (1) absorption–desorption, the micro biotic reaction to the instantaneous increase of the concentration of ammonium ion in the river water (so-called shock/stress effect) and (2) the NH₄⁺ increase stimulated by a certain (0.05 mg/L) concentration of 1-NA.The diethylamine (DEA) decomposition leads to increasing with approximately 3.8 mg/L NH₄⁺ in river water samples of 20.0 mg/L DEA.

Abundance and Niche Differentiation of Comammox in the Sludges of Wastewater Treatment Plants That Use the Anaerobic-Anoxic-Aerobic Process

Complete ammonia oxidizers (comammox), which directly oxidize ammonia to nitrate, were recently identified and found to be ubiquitous in artificial systems. Research on the abundance and niche differentiation of comammox in the sludges of wastewater treatment plants (WWTPs) would be useful for improving the nitrogen removal efficiency of WWTPs. Here, we investigated the relative abundance and diversity of comammox in fifteen sludges of five WWTPs that use the anaerobic−anoxic−aerobic process in Jinan, China, via quantitative polymerase chain reaction and high-throughput sequencing of the 16S rRNA gene and ammonia monooxygenase gene. In the activated sludges in the WWTPs, comammox clade A.1 was widely distributed and mostly comprised Candidatus Nitrospira nitrosa-like comammox (>98% of all comammox). The proportion of this clade was negatively correlated (p < 0.01) with the dissolved oxygen (DO) level (1.7−8 mg/L), and slight pH changes (7.20−7.70) affected the structure of the comammox populations. Nitrospira lineage I frequently coexisted with Nitrosomonas, which generally had a significant positive correlation (p < 0.05) with the DO level. Our study provided an insight into the structure of comammox and other nitrifier populations in WWTPs that use the anaerobic−anoxic−aerobic process, broadening the knowledge about the effects of DO on comammox and other nitrifiers.

Electrocatalytic, Homogeneous Ammonia Oxidation in Water to Nitrate and Nitrite with a Copper Complex

Electrocatalytic ammonia oxidation at room temperature and pressure allows energy-economical and environmentally friendly production of nitrites and nitrates. Few molecular catalysts, however, have been developed for this six- or eight-electron oxidation process. We now report [Cu(bipyalk)]⁺, a homogeneous electrocatalyst that realizes the title reaction in water at 94% Faradaic efficiency. The catalyst exhibits high selectivity against water oxidation in aqueous media, as [Cu(bipyalk)]⁺ is not competent for water oxidation.

Changes in microbial community diversity, composition, and functions upon nitrate and Cr(VI) contaminated groundwater

With the increasing occurrences of nitrate and Cr(VI) pollution globally, microbially driven pollutant reduction and its interaction effects were of growing interest. Despite the increasing number of experimental reports on the simultaneous reduction of nitrate and Cr(VI), a broad picture of the keystone species and metabolic differences in this process remained elusive. This study explored the changing of microorganisms with the introduction of Cr(VI)/NO₃^- through analyzing 242 samples from the NCBI database. The correlation between microbial abundance and environmental factors showed that, the types of energy substances and pollutants species in the environment had an impact on the diversity of microorganisms and community structure. The genus of Zoogloea, Candidatus Accumulibacter, and Candidatus Kapabacteria sp. 59-99 had the ability of denitrification, while genus of Alcaligenes, Kerstersia, Petrimonas, and Leucobacter showed effectively Cr(VI) resistance and reducing ability. Azoarcus, Pseudomonas, and Thauera were recognized as important candidates in the simultaneous reduction of nitrate and Cr(VI). Metagenomic predictions of these microorganisms using PICRUSt2 further highlighted the enrichment of Cr(VI)and nitrate reduction-related genes (such as chrA and norC). Special attention should therefore be paid to these bacteria in subsequent studies to evaluate their performance and mechanisms involved in simultaneous denitrification and chromium removal. The microbial co-occurrence network analysis conducted on this basis emphasized a strong association between community collaboration and pollution removal. Collectively, either site surveys or laboratory experiments, subsequent studies should focus on these microbial populations and the interspecific collaborations as they strongly influence the occurrence of simultaneous nitrate and Cr(VI) reduction.

Biochemistry shapes growth kinetics of nitrifiers and defines their activity under specific environmental conditions

Is it possible to find trends between the parameters that define microbial growth to help us explain the vast microbial diversity? Through an extensive database of kinetic parameters of nitrifiers, we analyzed if the dominance of specific populations of nitrifiers could be predicted and explained. We concluded that, in general, higher growth yield (Y_XS) and ammonia affinity (a⁰_NH3) and lower growth rate (µ_max) are observed for ammonia‐oxidizing archaea (AOA) than bacteria (AOB), which would explain their considered dominance in oligotrophic environments. However, comammox (CMX), with the maximum energy harvest per mole of ammonia, and some AOB, have higher a⁰_NH3 and lower µ_max than some AOA. Although we were able to correlate the presence of specific terminal oxidases with observed oxygen affinities (a⁰_O2) for nitrite‐oxidizing bacteria (NOB), that correlation was not observed for AOB. Moreover, the presumed dominance of AOB over NOB in O₂‐limiting environments is discussed. Additionally, lower statistical variance of a⁰_O2 values than for ammonia and nitrite affinities was observed, suggesting nitrogen limitation as a stronger selective pressure. Overall, specific growth strategies within nitrifying groups were not identified through the reported kinetic parameters, which might suggest that mostly, fundamental differences in biochemistry are responsible for underlying kinetic parameters.

Improved Nitrogen Use Efficiency and Greenhouse Gas Emissions in Agricultural Soils as Producers of Biological Nitrification Inhibitors

Based on an analysis of the current situation of nitrogen fertiliser application, it is suggested that improving the nitrogen utilisation efficiency of crops is an important means of promoting the sustainable development of agriculture and realises the zero increase in chemical fertiliser application. Nitrate loss and nitrous oxide (N₂O) emissions caused by nitrification and denitrification are the main reasons for the low utilisation rate of nitrogen fertilisers. N₂O is a greenhouse gas that has caused a sharp increase in global temperature. Biological nitrification inhibition refers to releasing natural compounds that inhibit nitrification from plant roots. The natural compounds released are called biological nitrification inhibitors (BNIs), which specifically inhibit the activity of microorganisms in soil nitrification. Biological nitrification inhibitors can significantly improve rice (Oryza sativa), corn (Zea mays) and other crops by 5-10%, which can increase the nitrogen utilisation rate of corn by 3.1%, and reduce greenhouse gas N₂O emissions. Compared with plants that do not produce BNI, the amount of N₂O released can be reduced by up to 90%. The BNI released by Brachialactone (Brachiaria humidicola) accounted for 60-90% of the total inhibition of nitrification. In summary, biological nitrification inhibitors that inhibit nitrification, improve nitrogen utilisation and crop yield, and reduce greenhouse gas emissions play an important role. This paper reviews the plants known to release BNIs, reviews the plants known to inhibit soil nitrification but with unknown BNIs and further discusses the important role of bio nitrification inhibition in agricultural systems.

Metagenomics of Antarctic Marine Sediment Reveals Potential for Diverse Chemolithoautotrophy

The microbial biogeochemical processes occurring in marine sediment in Antarctica remain underexplored due to limited access. Further, these polar habitats are unique, as they are being exposed to significant changes in their climate. To explore how microbes drive biogeochemistry in these sediments, we performed a shotgun metagenomic survey of marine surficial sediment (0 to 3 cm of the seafloor) collected from 13 locations in western Antarctica and assembled 16 high-quality metagenome assembled genomes for focused interrogation of the lifestyles of some abundant lineages. We observe an abundance of genes from pathways for the utilization of reduced carbon, sulfur, and nitrogen sources. Although organotrophy is pervasive, nitrification and sulfide oxidation are the dominant lithotrophic pathways and likely fuel carbon fixation via the reverse tricarboxylic acid and Calvin cycles. Oxygen-dependent terminal oxidases are common, and genes for reduction of oxidized nitrogen are sporadically present in our samples. Our results suggest that the underlying benthic communities are well primed for the utilization of settling organic matter, which is consistent with findings from highly productive surface water. Despite the genetic potential for nitrate reduction, the net catabolic pathway in our samples remains aerobic respiration, likely coupled to the oxidation of sulfur and nitrogen imported from the highly productive Antarctic water column above. IMPORTANCE The impacts of climate change in polar regions, like Antarctica, have the potential to alter numerous ecosystems and biogeochemical cycles. Increasing temperature and freshwater runoff from melting ice can have profound impacts on the cycling of organic and inorganic nutrients between the pelagic and benthic ecosystems. Within the benthos, sediment microbial communities play a critical role in carbon mineralization and the cycles of essential nutrients like nitrogen and sulfur. Metagenomic data collected from sediment samples from the continental shelf of western Antarctica help to examine this unique system and document the metagenomic potential for lithotrophic metabolisms and the cycles of both nitrogen and sulfur, which support not only benthic microbes but also life in the pelagic zone.

Envisioning role of ammonia oxidizing bacteria in bioenergy production and its challenges: a review

Ammonia oxidizing bacteria (AOB) play a key role in the biological oxidation of ammonia to nitrite and mark their significance in the biogeochemical nitrogen cycle. There has been significant development in harnessing the ammonia oxidizing potential of AOB in the past few decades. However, very little is known about the potential applications of AOB in the bioenergy sector. As alternate sources of energy represent a thrust area for environmental sustainability, the role of AOB in bioenergy production becomes a significant area of exploration. This review highlights the role of AOB in bioenergy production and emphasizes the understanding of the genetic make-up and key cellular biochemical reactions occurring in AOB, thereby leading to the exploration of its various functional aspects. Recent outcomes in novel ammonia/nitrite oxidation steps occurring in a model AOB - Nitrosomonas europaea propel us to explore several areas of environmental implementation. Here we present the significant role of AOB in microbial fuel cells (MFC) where Nitrosomonas sp. play both anodic and cathodic functions in the generation of bioelectricity. This review also presents the potential role of AOB in curbing fuel demand by producing alternative liquid fuel such as methanol and biodiesel. Herein, the multiple roles of AOB in bioenergy production namely: bioelectricity generation, bio-methanol, and biodiesel production have been presented.

Effects of biological nitrification inhibitors on nitrogen use efficiency and greenhouse gas emissions in agricultural soils: A review

To maintain and increase crop yields, large amounts of nitrogen fertilizers have been applied to farmland. However, the nitrogen use efficiency (NUE) of chemical fertilizer remains very low, which may lead to serious environmental problems, including nitrate pollution, air quality degradation and greenhouse gas (GHG) emissions. Nitrification inhibitors can alleviate nitrogen loss by inhibiting nitrification; thus, biological nitrification inhibition by plants has gradually attracted increasing attention due to its low cost and environmental friendliness. Research progress on BNI is reviewed in this article, including the source, mechanisms, influencing factors and application of BNIs. In addition, the impact of BNI on agriculture and GHG emissions is summarized from the perspective of agricultural production and environmental protection, and the key future research prospects of BNIs are also noted.

Competition of Ammonia-Oxidizing Archaea and Bacteria from Freshwater Environments

In the environment, nutrients are rarely available in constant supply. Therefore, microorganisms require strategies to compete for limiting nutrients. In freshwater systems, ammonia-oxidizing archaea (AOA) and bacteria (AOB) compete with heterotrophic bacteria, photosynthetic microorganisms, and each other for ammonium, which AOA and AOB utilize as their sole source of energy and nitrogen. We investigated the competition between highly enriched cultures of an AOA (AOA-AC1) and an AOB (AOB-G5-7) for ammonium. Based on the amoA gene, the newly enriched archaeal ammonia oxidizer in AOA-AC1 was closely related to Nitrosotenuis spp. and the bacterial ammonia oxidizer in AOB-G5-7, Nitrosomonas sp. Is79, belonged to the Nitrosomonas oligotropha group (Nitrosomonas cluster 6a). Growth experiments in batch cultures showed that AOB-G5-7 had higher growth rates than AOA-AC1 at higher ammonium concentrations. During chemostat competition experiments under ammonium-limiting conditions, AOA-AC1 dominated the cultures, while AOB-G5-7 decreased in abundance. In batch cultures, the outcome of the competition between AOA and AOB was determined by the initial ammonium concentrations. AOA-AC1 was the dominant ammonia oxidizer at an initial ammonium concentration of 50 μM and AOB-G5-7 at 500 μM. These findings indicate that, during direct competition, AOA-AC1 was able to use ammonium that was unavailable to AOB-G5-7, while AOB-G5-7 dominated at higher ammonium concentrations. The results are in strong accordance with environmental survey data suggesting that AOA are mainly responsible for ammonia oxidation under more oligotrophic conditions, whereas AOB dominate under eutrophic conditions. Importance Nitrification is an important process in the global nitrogen cycle. The first step - ammonia oxidation to nitrite - can be carried out by Ammonia-oxidizing Archaea (AOA) and Ammonia-oxidizing Bacteria (AOB). In many natural environments, these ammonia oxidizers coexist. Therefore, it is important to understand the population dynamics in response to increasing ammonium concentrations. Here, we study the competition between AOA and AOB enriched from freshwater systems. The results demonstrate that AOA are more abundant in systems with low ammonium availabilities and AOB when the ammonium availability increases. These results will help to predict potential shifts in community composition of ammonia oxidizers in the environment due to changes in ammonium availability.

The ammonia oxidizing bacterium Nitrosomonas eutropha blocks T helper 2 cell polarization via the anti-inflammatory cytokine IL-10

The prevalence of atopic diseases has been steadily increasing since the mid twentieth century, a rise that has been linked to modern hygienic lifestyles that limit exposure to microbes and immune system maturation. Overactive type 2 CD4+ helper T (Th2) cells are known to be closely associated with atopy and represent a key target for treatment. In this study, we present an initial characterization of ammonia oxidizing bacteria (AOB) Nitrosomonas eutropha D23, an environmental microbe that is not associated with human pathology, and show AOB effectively suppress the polarization of Th2 cells and production of Th2-associated cytokines (IL-5, IL-13, and IL-4) by human peripheral blood mononuclear cells (PBMC). We show that AOB inhibit Th2 cell polarization not through Th1-mediated suppression, but rather through mechanisms involving the anti-inflammatory cytokine IL-10 and the potential inhibition of dendritic cells, as evidenced by a reduction in Major Histocompatibility Complex Class II (MHC II) and CD86 expression following AOB treatment. This is the first report of immunomodulatory properties of AOB, and provides initial support for the development of AOB as a potential therapeutic for atopic diseases.

Anaerobic Ammonium Removal Pathway Driven by the Fe(II)/Fe(III) Cycle through Intermittent Aeration

Feammox, that is, Fe(III) reduction coupled to anaerobic ammonium oxidation, has been reported to play an important role in the nitrogen cycle in natural environments. However, the application of Feammox in wastewater treatment is limited because continuous Fe(III) supplementation is required for achieving continuous nitrogen removal, which is not feasible in practice. In this study, air was aerated intermittently into the Feammox system containing iron and high-content ammonium for oxidizing Fe(II) generated from Feammox to Fe(III), then, the produced Fe(III) participated in the next round of Feammox, leading to continuous nitrogen removal through the Fe(II)/Fe(III) cycle. The results showed that after each 10 min of aeration (150 mL/min), every 6-7 days, dissolved oxygen (DO) increased from 0 to about 0.4 mg/L, accompanied by a decrease in Fe(II) and an increase in Fe(III). One day after the aeration, DO was undetectable, and then, Fe(II) content increased and Fe(III) content decreased. On day 90, NH₄⁺-N content in the aerated reactor was only 10.2 mg/L, while it remained at around 288.3 mg/L in the aeration-free group. X-ray diffraction showed that the generated Fe(III) through air aeration was Fe(OH)₃. Microbial analysis showed that anammox and nitrification/denitrification could be excluded in the system. This NH₄⁺ removal process, driven by the Fe(II)/Fe(III) cycle with O₂ as the terminal electron acceptor, might be used as an in situ remediation method for treating high-content NH₄⁺.

Nitrogen Fertilization. A Review of the Risks Associated with the Inefficiency of Its Use and Policy Responses

Nitrogen (N) is a key input to food production. Nearly half of N fertilizer input is not used by crops and is lost into the environment via emission of gases or by polluting water bodies. It is essential to achieve production levels, which enable global food security, without compromising environmental security. The N pollution level expected by 2050 is projected to be 150% higher than in 2010, with the agricultural sector accounting for 60% of this increase. In this paper, we review the status of the pollution from N fertilizers worldwide and make recommendations to address the situation. The analysis reviews the relationship between N fertilizer use, N use efficiency, no-point pollution, the role of farmer management practices, and policy approaches to address diffuse pollution caused by N fertilization. Several studies show a lack of information as one of the main hurdles to achieve changes in habits. The objective of this study is to highlight the gravity of the current global non-point pollution as well as the need for a communication effort to make farmers aware of the relationship between their activity and N pollution and, therefore, the importance of their fertilizer management practices.

The effects of engineered nanoparticles on nitrification during biological wastewater treatment

Technological advancements in the past few decades have made it possible to manufacture nanomaterials at a large scale, and engineered nanoparticles (ENPs) are increasingly found in consumer products, such as cosmetics, sports products, and LED displays. A large amount of these ENPs end up in wastewater and potentially impact the performance of wastewater treatment plants (WWTPs). One important function of the WWTP is nitrification, which is carried out by the actions of two groups of bacteria, ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB). Since most ENPs are found to have or are designed to have antimicrobial activities, it is a legitimate concern that ENPs entering WWTPs may have negative impacts on nitrification. In this paper, the effects of ENPs on nitrification are discussed, focusing mainly on autotrophic nitrification by AOBs and NOBs. This review also covers ENP effects on anaerobic ammonium oxidation (anammox). Generally, nitrifiers in pure and mixed cultures can be inhibited by a variety of ENPs, but stress response mechanisms may attenuate toxicity. Long-term studies demonstrated that a wide range of NPs could cause severe deterioration of AOBs and/or NOBs when the influent concentration exceeded an inhibition threshold. Proposed mechanisms include the generation of reactive oxygen species, dissolved metals, physical disruption of cell membranes, bacterial engulfment, and intracellular accumulation of ENPs. Future research needs are also discussed.

Biological nitrification inhibition in the rhizosphere: determining interactions and impact on microbially mediated processes and potential applications

Nitrification is the microbial conversion of reduced forms of nitrogen (N) to nitrate (NO3-), and in fertilized soils it can lead to substantial N losses via NO3- leaching or nitrous oxide (N2O) production. To limit such problems, synthetic nitrification inhibitors have been applied but their performance differs between soils. In recent years, there has been an increasing interest in the occurrence of biological nitrification inhibition (BNI), a natural phenomenon according to which certain plants can inhibit nitrification through the release of active compounds in root exudates. Here, we synthesize the current state of research but also unravel knowledge gaps in the field. The nitrification process is discussed considering recent discoveries in genomics, biochemistry and ecology of nitrifiers. Secondly, we focus on the 'where' and 'how' of BNI. The N transformations and their interconnections as they occur in, and are affected by, the rhizosphere, are also discussed. The NH4+ and NO3- retention pathways alternative to BNI are reviewed as well. We also provide hypotheses on how plant compounds with putative BNI ability can reach their targets inside the cell and inhibit ammonia oxidation. Finally, we discuss a set of techniques that can be successfully applied to solve unresearched questions in BNI studies.

Biochemistry of aerobic biological methane oxidation

Methanotrophic bacteria represent a potential route to methane utilization and mitigation of methane emissions. In the first step of their metabolic pathway, aerobic methanotrophs use methane monooxygenases (MMOs) to activate methane, oxidizing it to methanol. There are two types of MMOs: a particulate, membrane-bound enzyme (pMMO) and a soluble, cytoplasmic enzyme (sMMO). The two MMOs are completely unrelated, with different architectures, metal cofactors, and mechanisms. The more prevalent of the two, pMMO, is copper-dependent, but the identity of its copper active site remains unclear. By contrast, sMMO uses a diiron active site, the catalytic cycle of which is well understood. Here we review the current state of knowledge for both MMOs, with an emphasis on recent developments and emerging hypotheses. In addition, we discuss obstacles to developing expression systems, which are needed to address outstanding questions and to facilitate future protein engineering efforts.

Role of Ammonia Oxidation in Organic Micropollutant Transformation during Wastewater Treatment: Insights from Molecular, Cellular, and Community Level Observations

Organic micropollutants (OMPs) are a threat to aquatic environments, and wastewater treatment plants may act as a source or a barrier of OMPs entering the environment. Understanding the fate of OMPs in wastewater treatment processes is needed to establish efficient OMP removal strategies. Enhanced OMP biotransformation has been documented during biological nitrogen removal and has been attributed to the cometabolic activity of ammonia-oxidizing bacteria (AOB) and, specifically, to the ammonia monooxygenase (AMO) enzyme. Yet, the exact mechanisms of OMP biotransformation are often unknown. This critical review aims to fundamentally and quantitatively evaluate the role of ammonia oxidation in OMP biotransformation during wastewater treatment processes. OMPs can be transformed by AOB via direct and indirect enzymatic reactions: AMO directly transforms OMPs primarily via hydroxylation, while biologically produced reactive nitrogen species (hydroxylamine (NH₂OH), nitrite (NO₂^-), and nitric oxide (NO)) can chemically transform OMPs through nitration, hydroxylation, and deamination and can contribute significantly to the observed OMP transformations. OMPs containing alkyl, aliphatic hydroxyl, ether, and sulfide functional groups as well as substituted aromatic rings and aromatic primary amines can be biotransformed by AMO, while OMPs containing alkyl groups, phenols, secondary amines, and aromatic primary amines can undergo abiotic transformations mediated by reactive nitrogen species. Higher OMP biotransformation efficiencies and rates are obtained in AOB-dominant microbial communities, especially in autotrophic reactors performing nitrification or nitritation, than in non-AOB-dominant microbial communities. The biotransformations of OMPs in wastewater treatment systems can often be linked to ammonium (NH₄⁺) removal following two central lines of evidence: (i) Similar transformation products (i.e., hydroxylated, nitrated, and desaminated TPs) are detected in wastewater treatment systems as in AOB pure cultures. (ii) Consistency in OMP biotransformation (r_bio, μmol/g VSS/d) to NH₄⁺ removal (r_NH4+, mol/g VSS/d) rate ratios (r_bio/r_NH4+) is observed for individual OMPs across different systems with similar r_NH4+ and AOB abundances. In this review, we conclude that AOB are the main drivers of OMP biotransformation during wastewater treatment processes. The importance of biologically driven abiotic OMP transformation is quantitatively assessed, and functional groups susceptible to transformations by AMO and reactive nitrogen species are systematically classified. This critical review will improve the prediction of OMP transformation and facilitate the design of efficient OMP removal strategies during wastewater treatment.

Changes in the fluorescence intensity, degradability, and aromaticity of organic carbon in ammonium and phenanthrene-polluted aquatic ecosystems

Mixed cultures were established by a sediment to investigate the changes in organic carbon (C) in a combined ammonium and phenanthrene biotransformation process in aquatic ecosystems. The microorganisms in the sediment demonstrated significant ammonium-N and phenanthrene biotransformation capacity with removal efficiencies of 99.96% and 99.99%, respectively. The changes in the organic C characteristics were evaluated by the fluorescence intensity, degradability (humification index (HIX) and UV absorbance at 254 nm (A₂₅₄)), aromaticity (specific UV absorbance at 254 nm (SUVA₂₅₄) and fluorescence index (FI)). Compared with C2 (the second control), the lower values of fluorescence intensity (after the 15^th d), HIX (after the 8^th d), A₂₅₄ (after the 11^th d), and SUVA₂₅₄ (after the 8^th d) and the higher FI value (after the 8^th d) in ammonium and phenanthrene-fed mixed cultures (N_PHE) suggest that aromatic structures and some condensed molecules were easier to break down in N_PHE. Similar results were obtained from Fourier transformation infrared spectroscopy (FTIR) and nuclear magnetic resonance (¹H NMR) spectra. Changes in organic C characteristics may be due to two key organisms Massilia and Azohydromonas. The biodiversity also suggested that the selective pressure of ammonium and phenanthrene is the decisive factor for changes in organic C characteristics. This study will shed light on theoretical insights into the interaction of N and aromatic compounds in aquatic ecosystems.

Mixed cultures were established by a sediment to investigate the changes in organic carbon (C) in a combined ammonium and phenanthrene biotransformation process in aquatic ecosystems.

Heme P460: A (Cross) Link to Nitric Oxide

Ammonia-oxidizing bacteria (AOB) convert ammonia (NH₃) to nitrite (NO₂^-) as their primary metabolism and thus provide a blueprint for the use of NH₃ as a chemical fuel. The first energy-producing step involves the homotrimeric enzyme hydroxylamine oxidoreductase (HAO), which was originally reported to oxidize hydroxylamine (NH₂OH) to NO₂^-. HAO uses the heme P460 cofactor as the site of catalysis. This heme is supported by seven other c hemes in each monomer that mediate electron transfer. Heme P460 cofactors are c-heme-based cofactors that have atypical protein cross-links between the peptide backbone and the porphyrin macrocycle. This cofactor has been observed in both the HAO and cytochrome (cyt) P460 protein families. However, there are differences; specifically, HAO uses a single tyrosine residue to form two covalent attachments to the macrocycle whereas cyt P460 uses a lysine residue to form one. In Nitrosomonas europaea, which expresses both HAO and cyt P460, these enzymes achieve the oxidation of NH₂OH and were both originally reported to produce NO₂^-. Each can inspire means to effect controlled release of chemical energy.Spectroscopically studying the P460 cofactors of HAO is complicated by the 21 non-P460 heme cofactors, which obscure the active site. However, monoheme cyt P460 is more approachable biochemically and spectroscopically. Thus, we have used cyt P460 to study biological NH₂OH oxidation. Under aerobic conditions substoichiometric production of NO₂^- was observed along with production of nitrous oxide (N₂O). Under anaerobic conditions, however, N₂O was the exclusive product of NH₂OH oxidation. We have advanced our understanding of the mechanism of this enzyme and have showed that a key intermediate is a ferric nitrosyl that can dissociate the bound nitric oxide (NO) molecule and react with O₂, thus producing NO₂^- abiotically. Because N₂O was the true product of one P460 cofactor-containing enzyme, this prompted us to reinvestigate whether NO₂^- is enzymatically generated from HAO catalysis. Like cyt P460, we showed that HAO does not produce NO₂^- enzymatically, but unlike cyt P460, its final product is NO, establishing it as an intermediate of nitrification. More broadly, NO can be recognized as a molecule common to the primary metabolisms of all organisms involved in nitrogen "defixation".Delving deeper into cyt P460 yielded insights broadly applicable to controlled biochemical redox processes. Studies of an inactive cyt P460 from Nitrosomonas sp. AL212 showed that this enzyme was unable to oxidize NH₂OH because it lacked a glutamate residue in its secondary coordination sphere that was present in the active N. europaea cyt P460 variant. Restoring the Glu residue imbued activity, revealing that a second-sphere base is Nature's key to controlled oxidation of NH₂OH. A key lesson of bioinorganic chemistry is reinforced: the polypeptide matrix is an essential part of dictating function. Our work also exposed some key functional contributions of noncanonical heme-protein cross-links. The heme-Lys cross-link of cyt P460 enforces the relative position of the cofactor and second-sphere residues. Moreover, the cross-link prevents the dissociation of the axial histidine residue, which stops catalysis, emphasizing the importance of this unique post-translational modification.

Experimental sulphide inhibition calibration method in nitrification processes: A case-study

Sulphide is one of the inhibitors in the nitrification process in WWTP in regions with sulphate rich soils. As little information is currently available on sulphide nitrification inhibition, the aim of this study was to develop a method based on a modification of the Successive Additions Method to calibrate the effect of sulphide on the activity of ammonia-oxidising bacteria (AOB) and nitrite-oxidising bacteria (NOB). The developed method was then applied to activated sludge samples from two WWTPs with different influent sulphide concentrations. In both cases, sulphide had a greater inhibitory effect on NOB than AOB activity. The sulphide inhibition was found to be lower in the activated sludge fed with sulphide-rich wastewater. The AOB and NOB activity measured at different sulphide concentrations could be accurately modelled with the Hill inhibition equation.

Unclassified Anammox bacterium responds to robust nitrogen removal in a sequencing batch reactor fed with landfill leachate

Treatment of landfill leachate was conducted in a lab-scale sequencing batch reactor (SBR). The SBR was started through inoculating activated sludge with controlling dissolved oxygen of 0.5-1.0 mg/L. Anammox reaction took place within around three months. The SBR established robust nitrogen removal with incremental NLRs of 0.25-2.17 kg N/m³/d. At the final phase, it achieved elevated nitrogen removals of 1.68-1.91 kg N/m³/d. 16S rRNA gene amplicon sequencing analysis revealed Nitrosomonas, unclassified Anammox bacterium, and diverse denitrifying populations coexisted and accounted for 4.02%, 20.05% and 34.69%, respectively. Phylogenic analysis and average nucleotide identity comparison jointly suggested the unclassified Anammox bacterium potentially pertained to a novel Anammox lineage. The functional profiles' prediction suggested sulfate reduction, arsenate reduction and eliminations of antibiotics and drugs likely occurred in the SBR. The finding from this study suggests contribution of unclassified Anammox bacteria in influencing nitrogen budget in natural and engineering systems is currently being underestimated.

The key role of Geobacter in regulating emissions and biogeochemical cycling of soil-derived greenhouse gases

In the past two decades, more and more attentions have been paid to soil-derived greenhouse gases (GHGs) including carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O) because there are signs that they have rising negative impacts on the sustainability of the earth surface system. Farmlands, particularly paddy soils, have been regarded as the most important emitter of GHGs (nearly 17%) due to a large influx of fertilization and the abundance in animals, plants and microorganisms. Geobacter, as an electroactive microorganism widely occurred in soil, has been well studied on electron transport mechanisms and the direct interspecies electron transfer. These studies on Geobacter illustrate that it has the ability to be involved in the pathways of soil GHG emissions through redox reactions under anaerobic conditions. In this review, production mechanisms of soil-derived GHGs and the amount of these GHGs produced had been first summarized. The cycling process of CH₄ and N₂O was described from the view of microorganisms and discussed the co-culture relationships between Geobacter and other microorganisms. Furthermore, the role of Geobacter in the production of soil-derived GHGs is defined by biogeochemical cycling. The complete view on the effect of Geobacter on the emission of soil-derived GHGs has been shed light on, and appeals further investigation.

Identification of Bacterial and Fungal Communities in the Roots of Orchids and Surrounding Soil in Heavy Metal Contaminated Area of Mining Heaps

Orchids represent a unique group of plants that are well adapted to extreme conditions. In our study, we aimed to determine if different soil contamination and pH significantly change fungal and bacterial composition. We identified bacterial and fungal communities from the roots and the surrounding soil of the family Orchidaceae growing on different mining sites in Slovakia. These communities were detected from the samples of Cephalanthera longifolia and Epipactis pontica from Fe deposit Sirk, E. atrorubens from Ni-Co deposit Dobšiná and Pb-Zn deposit Jasenie and Platanthera bifolia by 16S rRNA gene and ITS next-generation sequencing method. A total of 171 species of fungi and 30 species of bacteria were detected from five samples of orchids. In summary, slight differences in pH of the initial soils do not significantly affect the presence of fungi and bacteria and thus the presence of the studied orchids in these localities. Similarly, the toxic elements in the studied localities, do not affect the occurrence of fungi, bacteria, and orchids. Moreover, Cortinarius saturatus, as a dominant fungus, and Candidatus Udaeobacter as a dominant bacterium were present in all soil samples and some root samples. Finally, many of these fungal and bacterial communities have the potential to be used in the bioremediation of the mining areas.

Effect of Nitrification Inhibitors on N2O Emissions after Cattle Slurry Application

Cattle slurry injection (INJ) has shown to be an efficient measure to reduce ammonia (NH3) losses from soils but it might also significantly increase nitrous oxide (N2O) emissions, which can dominate the total greenhouse gas (GHG) release in silage maize production (Zea mays L.). Nitrification inhibitors (NIs) are known for their potential to mitigate N2O. Therefore, we tested the effect of NIs added to cattle slurry before INJ on N2O fluxes from a Haplic Luvisol under silage maize in southwest Germany. We determined N2O fluxes at least weekly, with the closed chamber method over two full years. NIs differ in their chemical and physical behavior and we therefore tested a range of commercially available NIs: 3,4-dimethylpyrazole phosphate, 3,4-dimethylpyrazol succinic acid, a mixture of both, nitrapyrin, dicyandiamide, and 1,2,4 triazol and 3-methylpyrazol. Although not significant, INJ treatments with NI showed lower mean annual N2O emissions than the INJ treatment without NI in the 1st year. The emission reduction by NI of 46% in the 2nd year was statistically significant. In both years, we did not find any difference in N2O release, crop yield, or nitrogen removal between the different NI treatments. In the 1st year, which was extraordinary dry and warm, emission factors (EFs) for all INJ treatments were 4 to 8-fold higher than default EF from the IPCC. Even in the 2nd year, only three NI treatments reached EFs within the range provided by the IPCC. Direct N2O accounted for between 81 and 91% of the total GHG emission. Area- and yield-related GHG emission of the broadcast application with subsequent incorporation was in both years in the statistical class with lowest emission. In contrast, INJ with NIs showed similar GHG emissions in only one year, and consequently, incorporation was found to be the optimum management practice for livestock farmers in our study region.

Chemiosmotic misunderstandings

Recent publications have questioned the appropriateness of the chemiosmotic theory, a key tenet of modern bioenergetics originally described by Mitchell and since widely improved upon and applied. In one of them, application of Gauss' law to a model charge distribution in mitochondria was argued to refute the possibility of ATP generation through H⁺ movement in the absence of a counterion, whereas a different author advocated, for other reasons, the impossibility of chemiosmosis and proposed that a novel energy-generation scheme (referred to as "murburn") relying on superoxide-catalyzed (or superoxide-promoted) ADP phosphorylation would operate instead. In this letter, those proposals are critically examined and found to be inconsistent with established experimental data and new theoretical calculations.

A study on the treatment efficiency of internal circulation biological aerated filters for refinery wastewater and the transformation of main organic pollutants

In this study, an internal circulation biological aerated filter (ICBAF) reactor was applied to pretreat refinery wastewater containing large amounts of organic pollutants. According to the composition change of inlet-and-outlet water, the main organic pollutants, including micromolecular organic-acids, aldehydes, ketones, phenols, and so forth, degraded well in ICBAF unit. The concentration of organic acids, alcohols, and esters changed from 648 to 90 mg/L, 130 to 90 mg/L, and 158 to 228 mg/L, respectively. The average removal efficiencies of chemical oxygen demand (COD) and biological oxygen demand (BOD₅) reached 54.62% and 83.64%, respectively. It was clear that the concentration of effluent organic acids in the ICBAF unit decreased significantly. The degradation process of organic acids, alcohols, and esters (among others) and the degradation pathway of organic acids were also discussed. Straight chain organic acids and naphthenic acids were degraded by α-oxidation, β-oxidation, α- and β-combined oxidation, or aromatization. The study demonstrates the potential of the ICBAF as an alternative for the high-efficiency pretreatment of refinery wastewater.

Community structure - Ecosystem function relationships in the Congo Basin methane cycle depend on the physiological scale of function

Belowground ecosystem processes can be highly variable and difficult to predict using microbial community data. Here, we argue that this stems from at least three issues: (a) complex covariance structure of samples (with environmental conditions or spatial proximity) can make distinguishing biotic drivers a challenge; (b) communities can control ecosystem processes through multiple mechanisms, making the identification of these controls a challenge; and (c) ecosystem function assessments can be broad in physiological scale, encapsulating multiple processes with unique microbially mediated controls. We test these assertions using methane (CH₄ )-cycling processes in soil samples collected along a wetland-to-upland habitat gradient in the Congo Basin. We perform our measurements of function under controlled laboratory conditions and statistically control for environmental covariates to aid in identifying biotic drivers. We divide measurements of microbial communities into four attributes (abundance, activity, composition, and diversity) that represent different forms of community control. Lastly, our process measurements differ in physiological scale, including broader processes (gross methanogenesis and methanotrophy) that involve more mediating groups, to finer processes (hydrogenotrophic methanogenesis and high-affinity CH₄ oxidation) with fewer mediating groups. We observed that finer scale processes can be more readily predicted from microbial community structure than broader scale processes. In addition, the nature of those relationships differed, with broad processes limited by abundance while fine-scale processes were associated with diversity and composition. These findings demonstrate the importance of carefully defining the physiological scale of ecosystem function and performing community measurements that represent the range of possible controls on ecosystem processes.

Nitrogen combined with biochar changed the feedback mechanism between soil nitrification and Cd availability in an acidic soil

Inorganic nitrogen (N) inputs increase soil nitrification, acidification and trace metal toxicity e.g. cadmium (Cd). Biochar (B) has been widely used for metal immobilization. However, little is known about how the combination of N fertilizers with biochar (N-B) changes soil Cd availability through altering nitrification process. Here, (NH₄)₂SO₄ or CO(NH₂)₂ was applied in combination with biochar to an acidic, artificially enriched Cd contaminated soil. Not as we expected, available Cd did not increase following (NH₄)₂SO₄ or CO(NH₂)₂ addition. Nitrification and acidification of Cd contaminated soils were greatly inhibited, accompanied by elimination of ammonia-oxidizing bacteria (AOB). Exchangeable H⁺ of Cd contaminated soils was significantly lower than that of uncontaminated soils, thus inhibiting Cd itself from mobilization. N-B addition nearly halved soil available Cd and significantly increased nitrification by promoting AOB recovery. However, the restored nitrification did not cause soil acidification, due to the high buffering and slow liming effects of biochar. Available Cd continuously decreased with decreasing soil acidity and exchangeable Al. This study firstly demonstrated a feedback between soil nitrification and Cd after N application, and how biochar modified the feedback. Biochar, therefore, provides a feasible strategy for eliminating potential Cd toxicity on both soil biological and chemical processes.

Microbial communities and biogenic Mn-oxides in an on-site biofiltration system for cold Fe-(II)- and Mn(II)-rich groundwater treatment

This study investigated relationships between microbial communities, groundwater chemistry, and geochemical and mineralogical characteristics in field-aged biofilter media from a two-stage, pilot-scale, flow-through biofiltration unit designed to remove Fe(II) and Mn(II) from cold groundwater (8 to 15 °C). High-throughput 16S rRNA gene amplicon sequencing of influent groundwater and biofilter samples (solids, effluents, and backwash water) revealed significant differences in the groundwater, Fe filter, and Mn filter communities. These community differences reflect conditions in each filter that select for populations that biologically oxidize Fe(II) and Mn(II) in the two filters, respectively. Genera identified in both filters included relatives of known Fe(II)-oxidizing bacteria (FeOB), Mn(II)-oxidizing bacteria (MnOB), and ammonia-oxidizing bacteria (AOB). Relatives of AOB and nitrite-oxidizing bacteria were abundant in sequencing reads from both filters. Relatives of FeOB in class Betaproteobacteria dominated the Fe filter. Taxa related to Mn-oxidizing organisms were minor members of the Mn-filter communities; intriguingly, while Alphaproteobacteria dominated (40 ± 10% of sequencing reads) the Mn filter community, these Alphaproteobacteria did not classify as known MnOB. Isolates from Fe and Mn filter backwash enrichment studies provide insight on the identity of MnOB in this system. Novel putative MnOB isolates included Azospirillum sp. CDMB, Solimonas soli CDMK, and Paenibacillus sp. CDME. The isolate Hydrogenophaga strain CDMN can oxidize Mn(II) at 8 °C; this known FeOB is likely capable of Mn(II) oxidation in this system. Synchrotron-based X-ray near-edge spectroscopy (XANES) coupled with electron paramagnetic resonance (EPR) revealed the dominant Mn-oxide that formed was biogenic birnessite. Co-existence of amorphous and crystallized Mn-oxide surface morphologies on the Mn-filter media suggest occurrence of both biological and autocatalytic Mn(II) oxidation in the biofilter. This study provides evidence that biofiltration is a viable approach to remove iron, manganese, and ammonia in cold groundwater systems, and that mineralogical and microbiological approaches can be used to monitor biofiltration system efficacy and function.

Small Sample Stress: Probing Oxygen-Deprived Ammonia-Oxidizing Bacteria with Raman Spectroscopy In Vivo

The stress response of ammonia-oxidizing bacteria (AOB) to oxygen deprivation limits AOB growth and leads to different nitrification pathways that cause the release of greenhouse gases. Measuring the stress response of AOB has proven to be a challenge due to the low growth rates of stressed AOB, making the sample volumes required to monitor the internal stress response of AOB prohibitive to repeated analysis. In a proof-of-concept study, confocal Raman microscopy with excitation resonant to the heme c moiety of cytochrome c was used to compare the cytochrome c content and activity of stressed and unstressed Nitrosomonas europaea (Nm 50), Nitrosomonas eutropha (Nm 57), Nitrosospira briensis (Nsp 10), and Nitrosospira sp. (Nsp 02) in vivo. Each analysis required no more than 1000 individual cells per sampling; thus, the monitoring of cultures with low cell concentrations was possible. The identified spectral marker delivered reproducible results within the signal-to-noise ratio of the underlying Raman spectra. Cytochrome c content was found to be elevated in oxygen-deprived and previously oxygen-deprived samples. In addition, cells with predominantly ferrous cytochrome c content were found in deprived Nitrosomonas eutropha and Nitrosospira samples, which may be indicative of ongoing electron storage at the time of measurement.

Transcriptomic Response of Nitrosomonas europaea Transitioned from Ammonia- to Oxygen-Limited Steady-State Growth

Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, Nitrosomonas europaea, growing under oxygen-limited conditions.

Ammonia-oxidizing microorganisms perform the first step of nitrification, the oxidation of ammonia to nitrite. The bacterium Nitrosomonas europaea is the best-characterized ammonia oxidizer to date. Exposure to hypoxic conditions has a profound effect on the physiology of N. europaea, e.g., by inducing nitrifier denitrification, resulting in increased nitric and nitrous oxide production. This metabolic shift is of major significance in agricultural soils, as it contributes to fertilizer loss and global climate change. Previous studies investigating the effect of oxygen limitation on N. europaea have focused on the transcriptional regulation of genes involved in nitrification and nitrifier denitrification. Here, we combine steady-state cultivation with whole-genome transcriptomics to investigate the overall effect of oxygen limitation on N. europaea. Under oxygen-limited conditions, growth yield was reduced and ammonia-to-nitrite conversion was not stoichiometric, suggesting the production of nitrogenous gases. However, the transcription of the principal nitric oxide reductase (cNOR) did not change significantly during oxygen-limited growth, while the transcription of the nitrite reductase-encoding gene (nirK) was significantly lower. In contrast, both heme-copper-containing cytochrome c oxidases encoded by N. europaea were upregulated during oxygen-limited growth. Particularly striking was the significant increase in transcription of the B-type heme-copper oxidase, proposed to function as a nitric oxide reductase (sNOR) in ammonia-oxidizing bacteria. In the context of previous physiological studies, as well as the evolutionary placement of N. europaea’s sNOR with regard to other heme-copper oxidases, these results suggest sNOR may function as a high-affinity terminal oxidase in N. europaea and other ammonia-oxidizing bacteria.

IMPORTANCE Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, Nitrosomonas europaea, growing under oxygen-limited conditions.

A Rapid Assay to Assess Nitrification Inhibition Using a Panel of Bacterial Strains and Partial Least Squares Modeling

As a proof of concept, a rapid assay consisting of a cell-based biosensor (CBB) panel of pure bacterial strains, a fluorescent dye, and partial least squares (PLS) modeling was developed to assess the nitrification inhibition potential of industrial wastewater (WW) samples. The current standard method used to assess the nitrification inhibition potential is the specific nitrification rate (SNR) batch test, which requires approximately 4 h to complete under the watch of an experienced operator. In this study, we exposed the CBB panel of seven bacterial strains (nitrifying and non-nitrifying) to 28 different industrial WW samples and then probed both the membrane integrity and cellular activity using a commercially available "live/dead" fluorescent dye. The CBB panel response acts as a surrogate measurement for the performance of nitrification. Of the seven strains, four (Nitrospira, Escherichia coli, Bacillus subtilis, Bacillus cereus) were identified via the modeling technique to be the most significant contributors for predicting the nitrification inhibition potential. The key outcome from this work is that the CBB panel fluorescence data (collected in approximately 10 min) can accurately predict the outcome of an SNR batch test (that takes 4 h) when performed with the same WW samples and has a strong potential to approximate the chemical composition of these WW samples using PLS modeling. Overall, this is a powerful technique that can be used for point-of-use detection of nitrification inhibition.