Deciphering the evolution and metabolism of an anammox bacterium from a community genome

Physiological and transcriptomic response of enriched anammox culture upon elevated hydrazine exposure

Anammox has emerged as a cost-effective and eco-friendly biological treatment technology for high-strength wastewater, and hydrazine (N2H4) is a unique intermediate in the anammox metabolism. This study presents the first investigation into the genetic responses of anammox bacteria to elevated N2H4 concentrations, offering critical insights into their potential for sustainable environmental applications. In this scope, anammox cultures were exposed to high levels of N2H4 (up to 3 g/L) over a short-term period to evaluate their nitrogen treatment capacity and transcriptional responses. The results indicated that anammox activity continued at N2H4 concentrations of 1.88 g/L or less. However, acute N2H4 exposure significantly downregulated key genes, such as acetyl-CoA synthase beta and delta subunits, hydrazine synthase, hydrazine dehydrogenase, and hydroxylamine oxidoreductase, except for AAA family ATPase. Overall, high exogenous N2H4 concentrations severely constrained the metabolism and survival of anammox bacteria at a molecular level. Understanding the genetic responses of anammox bacteria to elevated N2H4 concentrations is crucial for optimizing their application in further anammox-based technologies. Future studies should focus on improving the resilience of anammox bacteria to high N2H4 concentrations, thereby broadening their applicability in engineered wastewater treatment and biotechnological processes while maintaining system stability and efficiency.

Analysis of the regulation mechanism for salt-tolerant anammox process: process performance and metabolic insights

In this study, the start-up and microbial domestication of a salt-tolerant functional anammox system was investigated by gradually increasing the salinity level in a stabilized anammox system in the laboratory. After 44 days of stable operation, the salt-tolerant system was successfully activated, at which time the salinity of the influent water was 3 g/L, and the maximum removal efficiency of ammonia nitrogen and nitrite nitrogen in the system reached 94.18% and 96.66%, respectively, and then the ammonia nitrogen and nitrite nitrogen removal efficiency were stabilized at 88.17% and 96.48% after the enrichment domestication for 89 days. The system was operated in the salinity of 10 g/L, with the concentration of each nitrogen compound measured at the same time. The ammonia nitrogen removal efficiency decreased to 59.93% at a salinity of 10 g/L, which had a significant impact on the system. High-throughput sequencing revealed that the system was enriched with a large number of Chloroflexi, the relative abundance of which increased from 19.46% to 52.33%, and the genus of AnAOB was transformed from Candidatus Brocadia to Candidatus Kuenenia, Candidatus Kuenenia, with a percentage of 4.78%. The system successfully achieved the simultaneous removal of ammonia nitrogen and nitrite nitrogen under salinity stress, which to a certain extent indicated that AnAOB could achieve the initiation and enrichment domestication under salinity conditions, and could provide a basis for the efficient and low-consumption treatment of high salinity nitrogen-containing wastewater.HighlightsAnammox reaction can be successfully initiated under low salinity conditionsSalinity of 10 g/L has a severe shock effect on the anammox systemAfter salinity enrichment and domestication, the abundance of norank_f__norank__o___SBR1031 and Candidatus Kuenenia in the anammox reaction reached 26.7% and 4.78%, respectively.

Genome-Resolved Metagenomic and Metatranscriptomics Reveal Feammox Metabolism of Anaerobic Ammonia Oxidation Bacteria in Microaerobic Granular Sludge

Anammox is an energy-efficient nitrogen removal process in which anammox bacteria (AnAOB) oxidize NH4+-N to N2 using NO2--N as the electron acceptor. Recent evidence suggests that AnAOB can perform extracellular electron transfer (EET), potentially coupling Fe(III) reduction with NH4+-N oxidation (Feammox). However, whether AnAOB directly participate in Feammox within complex wastewater treatment systems remains unclear. Here, we investigated the iron-mediated nitrogen metabolism pathways in a microaerobic granular sludge (MGS) reactor by integrating enzyme inhibition assays with analyses of gene dynamics and co-occurrence patterns of nitrogen- and iron-cycling genes. Results demonstrate that AnAOB contributed to Feammox activity. The iron reduction gene CT573071, coding a porin-cytochrome c protein complex associated with EET, co-occurred with hao, hzsABC, and hdh genes in Candidatus Kuenenia, suggesting its role in Feammox. Furthermore, four high-quality metagenome-assembled genomes (MAGs) affiliated with Kuenenia stuttgartiensis_A harbored CT573071, hao-like, hzsABC, and hdh genes, along with the hao-cluster, which catalyzes the oxidation of NH4+-N to hydroxylamine. This genomic evidence further supports their dual metabolic capacity. Metatranscriptomic analysis confirmed CT573071 upregulation and its coexpression with the hao, hzsABC, and hdh genes. These findings establish the potential role of K. stuttgartiensis_A in Feammox, providing novel insights into nitrogen removal in low-strength wastewater treatment systems.

Metabolic products comparison in autotrophic and heterotrophic nitrogen removal: Insights into membrane fouling

Metabolic products play a significant role in membrane fouling during biological wastewater treatment. However, the differences in metabolic product composition and membrane fouling potentials between autotrophic (anammox, AN) and heterotrophic (denitrification, DN) nitrogen removal systems are not well understood. This study cultivated autotrophic and heterotrophic nitrogen removal systems and analyzed the compositions of their metabolic products. The analysis methods included fluorescence excitation-emission matrix-parallel factor analysis (EEM-PARAFAC), Fourier transform infrared spectroscopy (FTIR), size exclusion chromatography coupled with organic carbon and nitrogen detection (SEC-OCD-OND), and Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Subsequently, the membrane fouling potential of these metabolic products was evaluated by dead-end membrane filtration experiments with microfiltration (MF) and ultrafiltration (UF) membranes. Significant differences in metabolic product composition existed between AN and DN nitrogen removal systems, which led to a distinct impact on membrane fouling. In the AN nitrogen removal system, membrane fouling was relatively mild despite the high abundance of polysaccharides (with C-O-C ring vibrations) and tannin-like substances in metabolic products. Its fouling was primarily caused by the rejection of humic substances. Conversely, in the DN nitrogen removal system, the high rejection of proteins and polysaccharides in SMP (52 % and 62 %) and EPS (18 % and 59 %) caused a pronounced flux decline, greatly increasing membrane fouling potential. These findings enhance understanding of membrane fouling mechanisms in autotrophic and heterotrophic nitrogen removal systems, providing actionable strategies to mitigate membrane fouling in biological nitrogen removal coupled with MBR process.

Quorum sensing-enhanced electron transfer in anammox consortia: A mechanism for improved resistance to variable-valence heavy metals

Quorum sensing (QS) is recognized for enhancing bacterial resistance against heavy metals by regulating the production of extracellular substances that hinder metal penetration into the intracellular environment. However, it remains unclear whether QS contributes to resistance by regulating electron transfer, thereby transforming metals from more toxic to less toxic forms. This study investigated the regulatory mechanism of acyl-homoserine lactone (AHL)-mediated QS on electron transfer under As(III) and Cr(VI) stress. Metagenomic binning results revealed that Candidatus Brocadia sinica serves as a major contributor to AHL production for regulating heavy metal resistance, while other symbiotic bacteria offer complementary resistance pathways. In these bacteria, the AHL synthesis gene htdS plays a pivotal role in QS regulation of electron transfer and heavy metal resistance. Experimental findings demonstrated that AHL increased the electron transport system activity by 19.8 %, and upregulated electron transfer gene expression by 1.1- to 6.9-fold. The enhanced electron transfer facilitated a 28.7 % increase in the transformation of As(III) to less toxic As(V) and monomethylarsonic acid, ultimately achieving efficient nitrogen removal under As(III) stress. This study expands our understanding of how QS strengthens bacterial resistance to heavy metals, offering novel strategies for enhancing nitrogen removal of anammox in heavy metal-contaminated environments.

Mg²⁺ and magnesium ammonium phosphate (MAP)-induced anammox granulation for comparable nitrogen removal: Implementation pathways and microbial mechanisms

Anaerobic ammonium oxidation (anammox) process is a highly effective and economic technology for nitrogen removal from wastewater. However, the slow growth of anammox bacteria and sludge flotation often hinder its field application. Ion adsorption and crystal precipitation can potentially promote the sludge granulation and hence address the above issues. This study investigated two approaches to support anammox granulation through Mg2+ adsorption and magnesium ammonium phosphate (MAP) precipitation. Mg2+ addition improved the specific anammox activity (SAA) by 4.09 to 4.75-fold compared to MAP-mediated ones, which could be explained by the upregulations of nitrogen and inorganic carbon metabolisms. The active extracellular polymeric substances generation at metabolites level may also favor the granulation in Mg2+-mediated anammox. However, sludge loss halted the continuous size increase of sludge. Differently, MAP promoted granulation by physically increasing the granular density, which allowed for a greater retention of sludge within the reactor. However, the co-growth of MAP precipitates with anammox may lead to mass transfer limitations, resulting in down-regulated gene expressions and metabolites in inorganic carbon metabolism, which negatively impacted the SAA. Overall, both strategies achieved comparable nitrogen removal capacities. Nevertheless, the co-growth of MAP and anammox was promising for effectively mitigating sludge flotation. Our study provided strategies and omics-based evidences for anammox granulation and activity variations, benefiting anammox practical applications.

DNA stable isotope probing and metagenomics reveal temperature responses of sulfur-driven autotrophic partial denitrification coupled with anammox (SPDA) system

The sulfur-driven autotrophic partial denitrification coupled with anammox (SPDA) process showed significant advantages in energy conservation and resource recovery in municipal wastewater treatment. However, its application in regions with seasonal temperature fluctuations and high latitudes is challenged by low temperatures. In this study, the feasibility of the SPDA process for treating low-strength municipal wastewater across a wide temperature range (30-10 °C) was systematically investigated. The results demonstrated that thiosulfate-driven autotrophic partial denitrification maintained an efficient nitrate removal rate of 7.82 mg NO3--N/gVSS/h and a nitrate to nitrite transformation rate of 62.7 % even at temperatures as low as 10 °C. Molecular ecological network and DNA-SIP revealed that dominant sulfur-oxidizing bacteria (SOB) shifted from norank_f_Hydrogenophilaceae and Thiobacillus at higher temperatures (30-20 °C) to Thiobacillus and Sulfurimonas as temperature decreased, thus ensuring the performance of autotrophic partial denitrification and consistent nitrite supply for anammox. Metagenomic analysis showed that the abundance of functional genes related to sulfur conversion increased almost universally, ensuring a stable electron supply for nitrate reduction through sulfur oxidation at low temperatures. The functional genes responsible for nitrate reduction changed from nar genes at higher temperatures to nap genes at lower temperatures, while a decrease in the abundance of hzs and hdh genes corresponding to reduced anammox performance. This study highlights the stable performance of the sulfur-driven autotrophic denitrification at low temperatures and the reliability of coupling with anammox, extending the applicability of SPDA to a broader geographical range.

Interspecific competition and adaptation of anammox bacteria at different salinities: Experimental validation of the Monod growth model with salinity inhibition

Ecological niche segregation of anaerobic ammonium oxidizing (anammox) bacteria under saline environments remains unresolved despite its ecological and practical importance. In this study, niche segregation by salinity for Ca. Brocadia sinica, Ca. Jettenia caeni, Ca. Kuenenia stuttgartiensis and Ca. Scalindua sp. was systematically studied. The inhibitory effect of salinity on specific anammox activity (SAA) was measured experimentally and model-fitted to obtain the salinity-dependent maximum specific growth rates (µmax). The resulting µmax were incorporated into a Monod growth model with nitrite as the limiting substrate to predict which anammox bacterial species would dominate at a given salinity. The model predictions revealed that there were threshold salinity ranges where specific growth rates were comparable and the determining factor for the dominant species was the availability of nitrite. Ca. B sinica, Ca. J. caeni, and Ca. K. stuttgartiensis could compete at 0 - 0.5% salinity, while Ca. K. stuttgartiensis and Ca. Scalindua sp. could coexist at around 2% salinity. The model prediction was validated by conducting interspecific competition experiments among the four anammox species in nitrite-limiting membrane bioreactors (MBRs) under different salinity concentrations. The interspecific competition experiments showed that Ca. K. stuttgartiensis with relatively high affinity for nitrite was dominant at a wide range of salinities from 0.25 to 1.75%. Outside this salinity range, Ca. B. sinica was dominant at salinity 0 %, and Ca. Scalindua sp. outcompeted exclusively the other species due to its high salinity tolerance at salinities above 2.0%. These experimental results are in good agreement with the model predictions, demonstrating the validity of the Monod model in accounting for salinity inhibition and reflecting the salinity-dependent distributions of anammox bacteria reported in a variety of engineered and natural saline environments.

Polyphenolic compounds mitigate the oxidative damage of anammox sludge under long-term light irradiation

Continuous high-intensity light exposure can inhibit anaerobic ammonium oxidation (anammox) bacteria activity, though the specific impacts on anammox reactor performance remain unclear. This study investigates the effects of long-term light stress on anammox sludge reactors and explores the use of tea polyphenols as an engineering interventions to mitigate photo oxidation damage. The results showed that the nitrogen removal efficiency (NRE) of the reactor rapidly deteriorated to 41.4 % under 10,000 lx light conditions. However, reactors supplemented with 1 mg·L-1 and 5 mg·L-1 tea polyphenols sustained NREs of 75.2 % and 82.5 %, respectively. The addition of tea polyphenols alleviated oxidative stress by scavenging reactive oxygen species such as ·OH and H2O2, and by enhancing the activities of antioxidant enzymes including total superoxide dismutase and glutathione peroxidase. Candidatus Kuenenia was negatively impacted by light, while unclassified_f__Brocadiaceae thrived under light stress. These findings provide insights for the development of stable nitrogen removal systems under light exposure.

Roles of acyl carrier proteins in ladderane fatty acid producing-organisms

Ladderanes are highly strained hydrocarbons consisting of two or more linearly concatenated cyclobutane rings. Strikingly, ladderane moieties are part of unique fatty acids and fatty alcohols that are exclusively found in the membrane lipids of anaerobic ammonium-oxidizing (anammox) bacteria. These bacteria express a distinctive gene cluster (cluster I) that has been suggested to be responsible for ladderane fatty acid (FA) biosynthesis in addition to a cluster likely involved in canonical FA biosynthesis (cluster III). In the anammox organism Kuenenia stuttgartiensis, cluster I encodes a unique acyl carrier protein (amxACP), whereas the ACP encoded by cluster III (KsACPII) was suggested to be involved in the production of canonical fatty acids. Here we present targeted isotope labeling studies using 13C-malonyl-ACPs to distinguish the roles of these ACPs. While in-vitro13C incorporation into ladderane FAs was not observed, we show that KsACPII indeed functions in palmitate biosynthesis in the anammox organism Kuenenia stuttgartiensis. We present an experimental framework for continuing studies into fatty acid biosynthesis in anammox- and similar organisms.

Fractionating proteins with nitrite-reducing activity in "Candidatus Kuenenia stuttgartiensis" strain CSTR1

The anammox bacteria "Candidatus Kuenenia stuttgartiensis" (Ca. Kuenenia) are able to gain energy by combining ammonium and nitrite to produce nitrogen gas, which is an ecologically and technically significant activity process. In this reaction, nitric oxide serves as a recognized intermediate in the reduction of nitrite, which is subsequently combined with ammonium to produce hydrazine. However, the enzyme that converts nitrite to nitric oxide remains elusive. In this study, we investigated the nitrite-reducing activity in "Ca. Kuenenia stuttgartiensis" strain CSTR1 to identify candidates for such an enzyme. An optimized in vitro assay was established to measure nitrite-reducing activities, with which we followed the activity in protein fractions obtained from various fractionation methods. Separation of the cell extract of strain CSTR1 with size exclusion chromatography yielded active fractions corresponding to a molecular size range of 150-200 kDa. Several proteins coeluted with the nitrite-reducing activity, including the hydroxylamine dehydrogenase HOX, an NADP-dependent isopropanol dehydrogenase (Adh), an electron-transfer 4Fe-4S subunit protein (Fcp), and a nitric oxide detoxifying flavorubredoxin (NorVW). However, further separation of the cell extract with anion exchange chromatography, resulted in much lower activity yields, and activities were distributed among several fractions. In addition, fractionation of cell extracts using ultracentrifugation and ultrafiltration linked the activity to HOX, but could not exclude the involvement of other proteins in the activity. Overall, our results suggest that the molecular mechanism for nitrite reduction in "Ca. Kuenenia" strains is more complex than that currently described in the literature. Nitrite reduction appears to be strongly associated with HOX but may additionally require the participation of other proteins.

A powerful but frequently overlooked role of thermodynamics in environmental microbiology: inspirations from anammox

Thermodynamics has long been applied in predicting undiscovered microorganisms or analyzing energy flows in microbial metabolism, as well as evaluating microbial impacts on global element distributions. However, further development and refinement in this interdisciplinary field are still needed. This work endeavors to develop a whole-cycle framework integrating thermodynamics with microbiological studies, focusing on representative nitrogen-transforming microorganisms. Three crucial concepts (reaction favorability, energy balance, and reaction directionality) are discussed in relation to nitrogen-transforming reactions. Specifically, reaction favorability, which sheds lights on understanding the diversity of nitrogen-transforming microorganisms, has also provided guidance for novel bioprocess development. Energy balance, enabling the quantitative comparison of microbial energy efficiency, unravels the competitiveness of nitrogen-transforming microorganisms under substrate-limiting conditions. Reaction directionality, revealing the niche-differentiating patterns of nitrogen-transforming microorganisms, provides a foundation for predicting biogeochemical reactions under various environmental conditions. This review highlights the need for a more comprehensive integration of thermodynamics in environmental microbiology, aiming to comprehensively understand microbial impacts on the global environment from micro to macro scales.

Bioenergetic trade-offs can reveal the path to superior microbial CO2 fixation pathways

A comprehensive optimization of known prokaryotic autotrophic carbon dioxide (CO2) fixation pathways is presented that evaluates all their possible variants under different environmental conditions. This was achieved through a computational methodology recently developed that considers the trade-offs between energy efficiency (yield) and growth rate, allowing us to evaluate candidate metabolic modifications in silico for microbial conversions. The results revealed the superior configurations in terms of both yield (efficiency) and rate (driving force). The pathways from anaerobic organisms appear to fix carbon at lower net ATP cost than those found in aerobic organisms, and the reverse TCA cycle pathway shows the lowest overall energy cost and maximum adaptability across a broad range of CO2 and electron donor (H2) concentrations. The reverse tricarboxylic acid cycle and Wood-Ljungdahl pathways appear highly efficient under a broad range of conditions, while the 3-hydroxypropionate 4-hydroxybutyrate cycle and the 3-hydroxypropionate bicycle appear capable of generating large thermodynamic driving forces at only moderate ATP yield losses.IMPORTANCEBiotechnology can lead to cost-effective processes for capturing carbon dioxide using the natural or genetically engineered metabolic capabilities of microorganisms. However, introducing desirable genetic modifications into microbial strains without compromising their fitness (growth yield and rate) during industrial-scale cultivation remains a challenge. The approach and results presented can guide optimal pathway configurations for enhanced prokaryotic carbon fixation through metabolic engineering. By aligning strain modifications with these theoretically revealed near-optimal pathway configurations, we can optimally engineer strains of good fitness under open culture industrial-scale conditions.

Cold seeps are potential hotspots of deep-sea nitrogen loss driven by microorganisms across 21 phyla

Nitrogen bioavailability, governed by fixation and loss processes, is crucial for oceanic productivity and global biogeochemical cycles. The key nitrogen loss organisms-denitrifiers and anaerobic ammonium-oxidizing (anammox) bacteria-remain poorly understood in deep-sea cold seeps. This study combined geochemical measurements, 15N stable isotope tracer analysis, metagenomics, metatranscriptomics, and three-dimensional protein structural simulations to explore cold-seeps nitrogen loss processes. Geochemical evidence from 359 sediment samples shows significantly higher nitrogen loss rates in cold seeps compared to typical deep-sea sediments, with nitrogen loss flux from surface sediments estimated at 4.96-7.63 Tg N yr-1 (1.65-2.54% of global marine sediment). Examination of 147 million non-redundant genes indicates a high prevalence of nitrogen loss genes, including nitrous-oxide reductase (NosZ; 6.88 genes per million reads, GPM), nitric oxide dismutase (Nod; 1.29 GPM), and hydrazine synthase (HzsA; 3.35 GPM) in surface sediments. Analysis of 3,164 metagenome-assembled genomes expands the nitrous-oxide reducers by three phyla, nitric oxide-dismutating organisms by one phylum and two orders, and anammox bacteria by ten phyla going beyond Planctomycetota. These microbes exhibit structural adaptations and complex gene cluster enabling survival in cold seeps. Cold seeps likely are previously underestimated nitrogen loss hotspots, potentially contributing notably to the global nitrogen cycle.

Insight into enhanced enrichment and nitrogen removal performance of Anammox bacteria with novel biochar/tourmaline polyurethane sponge modified biocarrier

A novel biochar/tourmaline polyurethane sponge modified biocarrier (BTP) could enhance Anammox bacteria (AnAOB) enrichment and nitrogen removal performance. With higher hydrophilicity and specific surface area, BTP significantly improved total inorganic nitrogen (TIN) removal efficiency to 80 ± 2 %, compared to unmodified biocarrier of 67 ± 3 % when influent TIN reached 633.9 ± 22.0 mg/L. BTP stimulated the upregulation of amino acid synthases genes abundance and improved protein secretion in extracellular polymer substances (EPS). Moreover, significant increases were found in heme concentration, specific anammox activity and hydrazine dehydrogenase of AnAOB with BTP compared to unmodified biocarrier. Extracellular electron transfer pathway of AnAOB was improved by BTP via upregulating cytochrome C and ferredoxin synthesis. Candidatus Brocadia was the main genus in Anammox biofilm, with relative abundance of 20.1 % and 27.6 % in the control and BTP, respectively, which explained the improvement of nitrogen removal performance.

Redox potential tuning by calcium ions in a novel c-type cytochrome from an anammox organism

The electrochemical potentials of redox-active proteins need to be tuned accurately to the correct values for proper biological function. Here, we describe a diheme cytochrome c with high heme redox potentials of about +350 mV, despite having a large overall negative charge, which typically reduces redox potentials. High-resolution crystal structures, spectroelectrochemical measurements, and high-end computational methods show how this is achieved: each heme iron has a calcium cation positioned next to it at a distance of only 6.9 Å, raising their redox potentials by several hundred millivolts through electrostatic interaction. We suggest that this has evolved to provide the protein with a high redox potential despite its large negative surface charge, which it likely requires for interactions with redox partners.

Effects of granule disintegration and re-granulation on the physiological characteristics and microbial diversity of anammox granules

The impact of artificial disintegration and re-granulation of anammox granules on the granule size, Extra-cellular Polymeric Substances (EPS) composition, microbial community characteristics, and the performance of the anammox process was investigated. Before the granule disintegration, the Dv50 and Granulation Index (GI) were 1280 μm and 54.62%, respectively. Following two cycles of disintegration and re-granulation process, these values shifted to 463 μm and 81.53%, respectively. This indicates that the disintegration and re-granulation process helped to form denser particles. The reduction in total EPS content and the increase in the PS/PN ratio of EPS well reflect these particle characteristics. Additionally, the disintegration and re-granulation process increased the dominance of Kuenenia Stuttgartiensis, which is well adapted to high salinity (2%) conditions, from 11.2% to 68.1%. By artificially disintegrating the granules and inducing re-granulation, it was possible to increase the dominance of specific anammox microorganisms with enhanced resilience of the anammox process.

Anammox-based technologies: A review of recent advances, mechanism, and bottlenecks

The removal of nitrogen via the ANAMMOX process is a promising green wastewater treatment technology, with numerous benefits. The incessant studies on the ANAMMOX process over the years due to its long start-up and high operational cost has positively influenced its technological advancement, even though at a rather slow pace. At the moment, relatively new ANAMMOX technologies are being developed with the goal of treating low carbon wastewater at low temperatures, tackling nitrite and nitrate accumulation and methane utilization from digestates while also recovering resources (phosphorus) in a sustainable manner. This review compares and contrasts the handful of ANAMMOX -based processes developed thus far with plausible solutions for addressing their respective bottlenecks hindering full-scale implementation. Ultimately, future prospects for advancing understanding of mechanisms and engineering application of ANAMMOX process are posited. As a whole, technological advances in process design and patents have greatly contributed to better understanding of the ANAMMOX process, which has greatly aided in the optimization and industrialization of the ANAMMOX process. This review is intended to provide researchers with an overview of the present state of research and technological development of the ANAMMOX process, thus serving as a guide for realizing energy autarkic future practical applications.

Thermodynamics Underpinning the Microbial Community-Level Nitrogen Energy Metabolism

Nitrogen compounds often serve as crucial electron donors and acceptors in microbial energy metabolism, playing a key role in biogeochemical cycles. The energetic favorability of nitrogen oxidation-reduction (redox) reactions, driven by the thermodynamic properties of these compounds, may have shaped the evolution of microbial energy metabolism, though the extent of their influence remains unclear. This study quantitatively evaluated the similarity between energetically superior nitrogen reactions, identified from 988 theoretically plausible reactions, and the nitrogen community-level network, reconstructed as a combination of enzymatic reactions representing intracellular to interspecies-level reaction interactions. Our analysis revealed significant link overlap rates between these networks. Notably, composite enzymatic reactions aligned more closely with energetically superior reactions than individual enzymatic reactions. These findings suggest that selective pressure from the energetic favorability of redox reactions can operate primarily at the species or community level, underscoring the critical role of thermodynamics in shaping microbial metabolic networks and ecosystem functioning.

MBGD: Microbial Genome Database for Comparative Analysis Featuring Enhanced Functionality to Characterize Gene and Genome Functions Through Large-scale Orthology Analysis

Microbial Genome Database for Comparative Analysis (MBGD) is a comprehensive ortholog database encompassing published complete microbial genomes. The ortholog tables in MBGD are constructed in a hierarchical manner. The top-level ortholog table is now constructed from 1,812 genus-level pan-genomes, 6,268 species-level pan-genomes, and 34,079 genomes in total. To support analyses of newly sequenced genomes, MBGD updates MyMBGD functionality, which offers two analysis modes: assignment mode and clustering mode. Assignment mode rapidly classifies genes in the query genomes into existing MBGD ortholog groups, while clustering mode performs de novo clustering of query genomes using the DomClust program. In assignment mode, users can evaluate the presence of genomic functions, as defined in the KEGG Module database, in each query genome using the Genomaple software and compare the results across multiple genomes. To enhance this analysis, we developed a method to subdivide MBGD ortholog groups as needed to improve cross-references to the KEGG Orthology groups. Another notable feature is the phylogenetic profile search interface, which enables users to specify a set of organisms in which orthologs are present or absent (i.e., a phylogenetic profile), and search for ortholog groups with similar phylogenetic profiles. To construct a phylogenetic profile, users can search organisms by specifying phenotype, environment, taxonomy, or a particular ortholog group. MBGD is available at https://mbgd.nibb.ac.jp/.

Insight into nitrogen removal through sulfate reducing anaerobic ammonia oxidation coupled with sulfur cycle: A comparative study on inorganic and organic conditions

Sulfate reducing anaerobic ammonium oxidation (S-Anammox) is a novel biological process that involves the oxidation of NH4+ coupled with the reduction of SO42-. This process has been observed under both inorganic and organic conditions; however, the nitrogen removal performance and the specific functional species in these two contexts remain poorly understood. Furthermore, the simultaneous occurrence of coupled sulfate reduction and sulfide oxidation adds complexity to the understanding of nitrogen and sulfur conversions. This study conducted a comparative analysis of the effects of inorganic and organic conditions on S-Anammox. The results demonstrated that the inorganic treatment exhibited a higher NH4+-N removal rate and activity (0.11 kgN/(m3 d) and 1.10 mgN/(gVSS h)) compared to the organic treatment (0.04 kgN/(m3 d) and 0.34 mgN/(gVSS h)). The sulfur cycle was particularly evident in the inorganic treatment, which showed a limited sulfate reduction rate of 0.02 kgS/(m3 d). More sulfate was removed in the organic treatment, resulting in an increase in the retention of sulfur (from 0.8% to 6.0%) in the sludge. qPCR analysis revealed that organic matter inhibited the abundances of key genes involved in ammonia oxidation (amoA and hao) and sulfide oxidation (soxB). Inorganic conditions are more favorable for S-Anammox. Sulfate reducing bacteria such as Desulfococcus multivovans and unidentified species, along with sulfide oxidizing bacteria including Comamonas flocculans, Candidatus Desulfobacillus denitrificans, and Thiobacillus denitrificans, were identified as contributors to the enhancement of the sulfur cycle under inorganic conditions.

The Structural Diversity of Encapsulin Protein Shells

Subcellular compartmentalization is a universal feature of all cells. Spatially distinct compartments, be they lipid- or protein-based, enable cells to optimize local reaction environments, store nutrients, and sequester toxic processes. Prokaryotes generally lack intracellular membrane systems and usually rely on protein-based compartments and organelles to regulate and optimize their metabolism. Encapsulins are one of the most diverse and widespread classes of prokaryotic protein compartments. They self-assemble into icosahedral protein shells and are able to specifically internalize dedicated cargo enzymes. This review discusses the structural diversity of encapsulin protein shells, focusing on shell assembly, symmetry, and dynamics. The properties and functions of pores found within encapsulin shells will also be discussed. In addition, fusion and insertion domains embedded within encapsulin shell protomers will be highlighted. Finally, future research directions for basic encapsulin biology, with a focus on the structural understand of encapsulins, are briefly outlined.

Enrichment and characterization of thermophilic anaerobic ammonium oxidizing bacteria from hot spring

Anaerobic ammonium oxidization (Anammox) process plays a crucial role in the global nitrogen cycle and sustainable biological nitrogen removal from wastewater. Although Anammox bacteria have been detected across mesophilic and thermophilic conditions, the direct cultivation of Anammox bacteria from thermal environments has remained elusive. This impedes limiting our understanding of their physiology and ecology in high-temperature habitats. Here, we successfully enriched Anammox bacteria from hot spring sediments at 45 °C, achieving an ammonium oxidation rate of 158.0 mg NH4+-N l-1d-1, with the genus 'Candidatus Brocadia' presenting 22.9 % of the total microbial community after about 500 days of operation. Metagenomic analysis recovered two high-quality genomes of novel Anammox bacteria, which we designed as 'Candidatus Brocadia thermophilus' and 'Candidatus Brocadia thermoanammoxidans'. Both of them encoded and actively expressed key metabolic genes involved in Anammox process and several genes associated with thermotolerance, demonstrating their remarkable ability to perform Anammox reaction in thermophilic environments. Notably, phylotypes related to 'Candidatus Brocadia thermoanammoxidans' have frequently been retrieved from geographically distinct natural habitats. These findings expand our understanding of thermophilic Anammox bacteria and underscore their potential in the nitrogen cycle of thermal natural and engineering ecosystems.

Oxygen-induced evolution of anammox granular sludge explains its unique responses during preservation

Anammox granular sludge (AnGS) preservation is indispensable for the application of anammox technology. Oxygen is a common and crucial factor for anammox, yet its long-term effects on AnGS during preservation remain incomplete clarification. This study investigated the effect of oxygen on AnGS in two simulated preservation systems with open and sealed conditions, and the mechanism was discussed. The results showed that the open system was in an oxidized state with an average dissolved oxygen (DO) concentration and oxidation-reduction potential (ORP) of (3.10 ± 1.36) mg·L-1 and (112.58 ± 46.78) mV, while a reduced state for the sealed system with no detected DO and a lower average ORP of (-153.96 ± 64.32) mV. Both systems showed declines in AnGS activity, while with different responses of AnGS demonstrated by the evolution in terms of granular morphology and structure, bacterial communities, bacteria survival, and bacteria antioxidation. In the open system, reactive oxygen species were generated and destroyed the unsaturated fatty acids in the cell membrane, further leading to the destructed cell structure and declined activity. However, in the sealed system, AnAOB tended to enter a dormant state after long-term preservation, contributing to better conditions in granular morphology and structure, higher AnAOB abundance, and higher live cell ratio. The findings of this study are expected to offer vital information and guidelines for the preservation technologies of AnGS.

Multidimensional Insights into Organics Stress on Anammox systems: From a "Molecule-Cell-Ecology" Perspective

Anaerobic ammonium oxidation (anammox) is efficient and cost-effective for treating high-strength ammonia wastewater, but the organics in wastewater will affect its stability. To address this challenge, it is crucial to gain a deep understanding of the inhibitory effects and mechanisms of organics stress on anammox bacteria. The review provided a comprehensive classification of organics and evaluated their specific effects on the anammox system according to their respective characteristics. Based on the micro to macro perspective, the "molecule-cell-ecology" inhibitory mechanism of organics on anammox bacteria was proposed. The molecular observation systematically summarized the binding process and action sites of organics with anammox bacteria. At the cellular observation, the mechanisms of organics effects on extracellular polymeric substances, membranes, and anammoxosome of anammox bacteria were also expounded. At the ecological observation, the dynamic changes in coexisting populations and their role in organics transformation were further discussed. Further revelations on response mechanisms and inhibition mitigation strategies were proposed to broaden the applicability of anammox systems for organic wastewater. This review offered a multidimensional understanding of the organics inhibitory mechanism of anammox bacteria and provided a theoretical foundation for anammox systems.

Genomic synergistic efficient carbon fixation and nitrogen removal induced by excessive inorganic carbon in the anammox-centered coupling system

Given the significance of HCO3- for autotrophic anammox bacteria (AnAOB), excessive HCO3- was always provided in anammox-related systems and engineering applications. However, its impact mechanism on anammox process at genome-level remains unknown. This study firstly established an anammox-centered coupling system that entails heterotrophic partial denitrification (PD) and hydrolytic acidification (A-PDHA) fed mainly with inorganic carbon (high HCO3- concentration and low C/N ratio). Metagenomic binning and metatranscriptomics analyses indicated that high HCO3- concentration enhanced expression of natural most efficient phosphoenolpyruvate (PEP) carboxylase within AnAOB, by up to 30.59 folds. This further induced AnAOB to achieve high-speed carbon-fixing reaction through cross-feeding of phosphate and PEP precursors with heterotrophs. Additionally, the enhanced activity of transporters and catalytic enzymes (up to 4949-fold) induced by low C/N ratio enabled heterotrophs to eliminate extracellular accumulated energy precursors mainly derived from carbon fixation products of AnAOB. This maintained high-speed carbon-fixing reaction within AnAOB and supplemented heterotrophs with organics. Moreover, assimilated energy precursors stimulated nitrogen metabolism enzymes, especially NO2- reductase (968.14 times), in heterotrophs. This established an energy-saving PD-A process mediated by interspecies NO shuttle. These variation resulted in efficient nitrogen removal (>95 %) and reduced external organic carbon demand (67 %) in A-PDHA system. This study unveils the great potential of an anammox-centered autotrophic-heterotrophic coupling system for achieving cost-effective nitrogen removal and enhancing carbon fixation under excessive HCO3- doses.

Activation of iron oxides through organic matter-induced dissolved oxygen penetration depth dynamics enhances iron-cycling driven ammonium oxidation in microaerobic granular sludge

The iron redox cycle can enhance anammox in treating low-strength ammonia wastewater. However, maintaining an effective iron redox cycle and suppressing nitrite-oxidizing bacteria in a one-stage partial nitritation and anammox (PN/A) process poses challenges during long-term aeration. We proposed a novel and simple strategy to achieve an efficient iron redox cycle in an iron-mediated anoxic-microaerobic (A/O) process by controlling organic matter (OM) at medium-strength levels (30-110 mg COD/L) in microaerobic granular sludge (MGS)-dominated reactor. The developed A/O process consistently achieved >90 % OM removal and >75 % nitrogen removal. Medium-strength OM varied the penetration depths of dissolved oxygen (DO) in MGS, regulating redox conditions and promoting redox reactions across MGS layers, thus activating accumulated inert iron oxides. Ammonia-oxidizing bacteria (Nitrosomonas), iron-reducing bacteria (e.g., Ignavibacterium, Geobacter), and anammox bacteria (Ca. Kuenenia) coexisted harmoniously in MGS. This coexistence ensured high anammox and Feammox rates along with a robust iron redox cycle, thereby mitigating the adverse impacts of fluctuating DO and OM on one-stage PN/A process stability. The identification of iron reduction-associated genes within Ca. Kuenenia, Ignavibacterium, and Geobacter suggests their potential roles in supporting Feammox coupled in one-stage PN/A process. This study introduces an iron-cycle-driven A/O process as an energy-efficient alternative for simultaneous carbon and nitrogen removal from low-strength wastewater.

Novel insights into Feammox coupled with the NDFO: A critical review

Ammonium oxidation coupled with Fe(III) reduction, known as Feammox, and nitrate-dependent ferrous oxidation (NDFO) are two processes that can be synergistically achieved through the Fe(III)/Fe(II) cycle. This integrated approach enables the simultaneous removal of ammonia nitrogen (NH4+-N) and nitrate nitrogen (NO3--N) from wastewater, representing a novel method for complete nitrogen removal. This study presents a systematic and exhaustive examination of the Feammox-NDFO coupled process. An initial thorough exploration of the underlying mechanisms behind the coupling process is conducted, highlighting how the Fe(III)/Fe(II) cycle enables the concurrent occurrence of these reactions. Further, the functional microorganisms associated with and playing a crucial role in the Feammox-NDFO process are summarized. Next, the key influencing factors that govern the efficiency of the Feammox-NDFO process are explored. These include parameters such as pH, temperature, carbon source, iron source, nitrogen source, and various electron shuttles that may mediate electron transfer. Understanding the impact of these factors is essential for optimizing the process. The most recent trends and endeavors on the Feammox-NDFO coupling technology in wastewater treatment applications are also examined. This includes examining both laboratory-scale studies and field trials, highlighting their successes and challenges. Finally, an outlook is presented regarding the future advancement of the Feammox-NDFO technology. Areas of improvement and novel strategies that could further enhance the efficiency of simultaneous nitrogen removal from the iron cycle are discussed. In summary, this study aspires to offer a thorough comprehension of the Feammox-NDFO coupled process, with a focus on its mechanisms, influencing factors, applications, and prospects. It is anticipated to yield invaluable insights for the advancement of process optimization, thus sparking fresh ideas and strategies aimed at accomplishing the thorough elimination of nitrogen from wastewater via the iron cycle.

Arginine enhances activity of anammox consortia and process stability with increased nitrogen loading

Cross-feeding based on amino acids metabolism is an important strategy by which anammox bacteria and the co-existing heterotrophs facilitate their own growth and survival. Arginine is one of the necessary amino acids required for bacterial protein biosynthesis but whether adding arginine could benefit growth of anammox bacteria remains unknown. In this study, arginine was supplemented at dose of 5 mg·L-1 to promote the nitrogen removal performance of anammox bioreactors under varied loading rates. The results showed that nitrogen removal efficiency increased by 10.2 % under higher loading rates. Arginine addition substantially simulated the secretion of extracellular proteins and polysaccharides within anammox consortia as a strategy against unfavorable conditions. Canditatus Kuenenia dominated the anammox consortia and their 16S rRNA abundance and anammox-related functional genes were significantly increased by up to 0.42 times and 5.81 times, respectively. The findings of this study provided a feasible strategy to improve the performance of anammox reactors with arginine supplementation.

Mechanisms of inhibition and recovery under multi-antibiotic stress in anammox: A critical review

With the escalating global concern for emerging pollutants, particularly antibiotics, microplastics, and nanomaterials, the potential disruption they pose to critical environmental processes like anaerobic ammonia oxidation (anammox) has become a pressing issue. The anammox process, which plays a crucial role in nitrogen removal from wastewater, is particularly sensitive to external pollutants. This paper endeavors to address this knowledge gap by providing a comprehensive overview of the inhibition mechanisms of multi-antibiotic on anaerobic ammonia-oxidizing bacteria, along with insights into their recovery processes. The paper dives deeply into the various ways antibiotics interact with anammox bacteria, focusing specifically on their interference with the bacteria's extracellular polymers (EPS) - crucial components that maintain the structural integrity and functionality of the cells. Additionally, it explores how anammox bacteria utilize quorum sensing (QS) mechanisms to regulate their community structure and respond to antibiotic stress. Moreover, the paper summarizes effective removal methods for these antibiotics from wastewater systems, which is crucial for mitigating their inhibitory effects on anammox bacteria. Finally, the paper offers valuable insights into how anammox communities can recuperate from multi-antibiotic stress. This includes strategies for reintroducing healthy bacteria, optimizing operational conditions, and using bioaugmentation techniques to enhance the resilience of anammox communities. In summary, this paper not only enriches our understanding of the complex interactions between antibiotics and anammox bacteria but also provides theoretical and practical guidance for the treatment of antibiotic pollution in sewage, ensuring the sustainability and effectiveness of wastewater treatment processes.

Aquatic macrophytes mitigate the conflict between nitrogen removal and nitrous oxide emissions during tailwater treatments

Tailwater from wastewater treatment plants (WWTP) usually reduces the nitrogen (N) removal efficiency while simultaneously elevates nitrous oxide (N2O) emissions due to the low carbon-nitrogen (C/N) ratio. Conflicts between N removal and N2O emissions require mitigation by selecting appropriate aquatic plants for tailwater treatment. In this study, a simulated tailwater mesocosm was established using three aquatic plants including Eichhornia crassipes, Myriophyllum aquaticum and Pistia stratiotes. Results of the 15N isotope mass balance analysis revealed the considerable contributions from plant uptake and benthic retention to overall N removal. It was demonstrated that the N assimilation efficiency of aquatic plants depended more on the root-shoot ratio rather than on growth rate. Furthermore, aquatic plants indirectly influence microbial N removal and N2O emissions by altering the water quality parameters. Additionally, aquatic plants could regulate the N transformation through affecting the structure of bacterial community, including microbial abundance, diversity and association networks. Overall, the study underlined the enormous capacities of E. crassipes and P. stratiotes for N uptake and N2O mitigation in tailwater treatment. Utilizing these two aquatic plants for phytoremediation may help mitigate the conflict between tailwater purification and N2O production.

Rapid start-up of mainstream partial denitrification /anammox and enhanced nitrogen removal through inoculation of precultured biofilm for treating low-strength municipal sewage

This study investigated the rapid start-up of mainstream partial denitrification coupled with anammox (PD/A) and nitrogen removal performance by inoculating precultured PD/A biofilm. The results showed mainstream PD/A in the anaerobic-anoxic-aerobic (A2O) process was rapidly established within 30 days. Nitrogen removal efficiency (NRE) improved by 23.8 % contrasted to the traditional A2O process. The mass balance showed that anammox contribution to total nitrogen (TN) removal were maintained at 37.9 %∼55.7 %, and reducing hydraulic retention time (HRT) strengthened simultaneously denitrification and anammox activity. The microbial community showed that the dominant bacteria such as denitrifying bacteria (DNBs) and glycogen accumulating organisms (GAOs) both in biofilm and flocculent sludge (floc), integrating with anammox bacteria (AnAOB) in biofilm might lead to enhanced nitrogen removal. Overall, this study offered a fast start-up strategy of mainstream PD/A with enhanced nitrogen removal, which are valuable for upgradation and renovation of existed municipal wastewater treatment plants (WWTPs).

Insights into chemoautotrophic traits of a prevalent bacterial phylum CSP1-3, herein Sysuimicrobiota

Candidate bacterial phylum CSP1-3 has not been cultivated and is poorly understood. Here, we analyzed 112 CSP1-3 metagenome-assembled genomes and showed they are likely facultative anaerobes, with 3 of 5 families encoding autotrophy through the reductive glycine pathway (RGP), Wood-Ljungdahl pathway (WLP) or Calvin-Benson-Bassham (CBB), with hydrogen or sulfide as electron donors. Chemoautotrophic enrichments from hot spring sediments and fluorescence in situ hybridization revealed enrichment of six CSP1-3 genera, and both transcribed genes and DNA-stable isotope probing were consistent with proposed chemoautotrophic metabolisms. Ancestral state reconstructions showed that the ancestors of phylum CSP1-3 may have been acetogens that were autotrophic via the RGP, whereas the WLP and CBB were acquired by horizontal gene transfer. Our results reveal that CSP1-3 is a widely distributed phylum with the potential to contribute to the cycling of carbon, sulfur and nitrogen. The name Sysuimicrobiota phy. nov. is proposed.

Efficient nitrite accumulation in partial sulfide autotrophic denitrification (PSAD) system: insights of S/N ratio, pH and temperature

To provide the necessary nitrite for the Anaerobic Ammonium Oxidation (ANAMMOX) process, the effect of nitrite accumulation in the partial sulfide autotrophic denitrification (PSAD) process was investigated using an SBR reactor. The results revealed that the effectiveness of nitrate removal was unsatisfactory when the S/N ratio (mol/mol) fell below 0.6. The optimal conditions for nitrate removal and nitrite accumulation were achieved within the S/N ratio range of 0.7-0.8, resulting in an average Nitrate Removal Efficiency (NRE) of 95.84%±4.89% and a Nitrite Accumulation Rate (NAR) of 75.31%±6.61%, respectively. It was observed that the nitrate reduction rate was three times faster than that of nitrite reduction during a typical cycle test. Furthermore, batch tests were conducted to assess the influence of pH and temperature conditions. In the pH tests, it became evident that the PSAD process performed more effectively in alkaline environment. The highest levels of nitrate removal and nitrite accumulation were achieved at an initial pH of 8.5, resulting in a NRE of 98.30%±1.93% and a NAR of 85.83%±0.47%, respectively. In the temperature tests, the most favourable outcomes for nitrate removal and nitrite accumulation were observed at 22±1 ℃, with a NRE of 100.00% and a NAR of 81.03%±1.64%, respectively. Moreover, a comparative analysis of 16S rRNA sequencing results between the raw sludge and the sulfide-enriched culture sludge sample showed that Proteobacteria (49.51%) remained the dominant phylum, with Thiobacillus (24.72%), Prosthecobacter (2.55%), Brevundimonas (2.31%) and Ignavibacterium (2.04%) emerging as the dominant genera, assuming the good nitrogen performance of the system.

One-stage anammox and thiocyanate-driven autotrophic denitrification for simultaneous removal of thiocyanate and nitrogen: Pathway and mechanism

The coupled process of anammox and reduced-sulfur driven autotrophic denitrification can simultaneously remove nitrogen and sulfur from wastewater, while minimizing energy consumption and sludge production. However, the research on the coupled process for removing naturally toxic thiocyanate (SCN-) is limited. This work successfully established and operated a one-stage coupled system by co-cultivating mature anammox and SCN--driven autotrophic denitrification sludge in a single reactor. In this one-stage coupled system, the average total nitrogen removal efficiency was 89.68±3.33 %, surpassing that of solo anammox (81.80±2.10 %) and SCN--driven autotrophic denitrification (85.20±1.54 %). Moreover, the average removal efficiency of SCN- reached 99.50±3.64 %, exceeding that of solo SCN--driven autotrophic denitrification (98.80±0.65 %). The results of the 15N stable isotope tracer labeling experiment revealed the respective reaction rates of anammox and denitrification as 106.38±10.37 μmol/L/h and 69.07±8.07 μmol/L/h. By analyzing metagenomic sequencing data, Thiobacillus_denitrificans was identified as the primary contributor to SCN- degradation in this coupled system. Furthermore, based on the comprehensive analysis of nitrogen and sulfur metabolic pathways, as well as the genes associated with SCN- degradation, it can be inferred that the cyanate (CNO) pathway was responsible for SCN- degradation. This work provided a deeper insight into coupling anammox with SCN--driven autotrophic denitrification in a one-stage coupled system, thereby contributing to the development of an effective approach for wastewater treatment involving both SCN- and nitrogen.

Potential Growth of Anammox Bacteria under Aerobic Conditions

Anammox bacteria are obligate anaerobic bacteria that exist widely in nature with sufficient amounts of dissolved oxygen. However, whether anammox bacteria can grow under aerobic conditions remains unclear. In this study, we found that the production of nitrate in the anammox system under aerobic conditions was significantly higher than that under anaerobic conditions without total nitrogen loss. Anammox bacteria can grow by oxidizing nitrite and dehydrogenating hydrazine to produce electrons for carbon fixation. The hydrazine dehydrogenase in anammox bacteria was inhibited under aerobic conditions, and the nitrite oxidoreductase transcription expression of anammox bacteria increased by 2.7 times compared to that under anaerobic conditions, which was the main way for anammox bacteria perform carbon fixation. DNA-stable isotope probing with 13C bicarbonate found the existence of anammox bacteria with 13C isotopes in aerobic cultivation, further proving that anammox bacteria can grow under aerobic condition. More than half of the pathways in glycolysis, the Wood-Ljungdahl pathway, and the tricarboxylic acid cycle were upregulated in anammox bacteria in aerobic condition. Large amounts of bacterioferritins are the important antioxidative enzymes in anammox bacteria in the aerobic environment, which contributes to their stronger oxygen adaptation than other anaerobes. This study expands our understanding of the growth mechanism of anammox bacteria as well as the oxygen adaptation strategies of obligate anaerobic bacteria.

Metatranscriptomics provides an in-depth perspective on the resistance and detoxification of anammox bacteria to dissolved oxygen in a pilot CANON process

In the completely autotrophic nitrogen removal over nitrite (CANON) process, the conflicting oxygen requirements of anammox and ammonium-oxidizing bacteria often lead to retardation in anammox activity. However, our study achieved stable nitrogen removal with a maximum capacity of 1096 g-N/m3/d in a 20 m3 CANON reactor under long-term intensive aeration. The anammox bacteria unusually distributed in the outer layer of the biofilm and demonstrated remarkable oxygen tolerance. Their activity only declined by 18.5 % under 2.0 mg/L of dissolved oxygen. When anammox bacteria encountered oxygen exposure, they adopted some strategies. Metatranscriptomics revealed that Candidatus Kuenenia, the dominant anammox species in our system, downregulated its gene expressions involved in carbon metabolism and oxidative phosphorylation. This may reduce electron leakage that combines with O2, thereby minimizing the generation of reactive oxygen species (ROS). By contrast, the secretion of extracellular proteins and conversion of O2·- were upregulated to eliminate ROS promptly. This behavior endowed Ca. Kuenenia with a unique oxygen detoxification pathway: O2·- were initially converted to H2O2 by superoxide dismutase SOD2 and superoxide reductase dfx (major role), followed by reduction to H2O via non-heme chloroperoxidase cpo (a newly recognized mechanism in the oxygen detoxification of anammox) and catalase katE. These results expanded the current knowledge of anammox alleviating oxidative stress.

Insights into the individual and combined effects of Cu(Ⅱ) and Ni(Ⅱ) on anammox: Nitrogen removal performance, enzyme activity and microbial community

Anaerobic ammonium oxidation (anammox) is an efficient and economical nitrogen removal process for treating ammonium-rich industrial wastewaters. However, Cu(Ⅱ) and Ni(Ⅱ) present in industrial wastewaters are toxic to anaerobic ammonium-oxidizing bacteria (AnAOB). Unfortunately, the effects of Cu(Ⅱ) and Ni(Ⅱ) on anammox have not been thoroughly investigated, especially when Cu(Ⅱ) and Ni(Ⅱ) coexist. This work comprehensively investigated the individual and combined effects of Cu(Ⅱ) and Ni(Ⅱ) on anammox and revealed the inhibitory mechanisms. With the influent NH4+-N and NO2--N concentration of 230 and 250 mg L-1, the inhibition thresholds on anammox are 2.00 mg L-1 Cu(Ⅱ), 1.00 mg L-1 Ni(Ⅱ) and 1.00 mg L-1 Cu(Ⅱ) + 1.00 mg L-1 Ni(Ⅱ), and higher Cu(Ⅱ) or Ni(Ⅱ) concentrations resulted in sharp deteriorations of nitrogen removal performance. The inhibition of Ni(Ⅱ) on anammox was mainly attributed to the adverse effect on NiR activity, while the inhibition mechanism of Cu(Ⅱ) seemed to be unrelated to the four functional enzymes, but associated with disruption of cellular and organellar membranes. The behavior of extracellular polymeric substances (EPS) contributed to the antagonistic effect between Cu(Ⅱ) and Ni(Ⅱ) on anammox. In addition, the niche of Candidatus Brocadia and Candidatus Jettenia shifted under the Cu(II) and Ni(II) stress, and Candidatus Jettenia displayed greater tolerance to Cu(II) and Ni(II) stress. In conclusion, this research clarified the combined effect and the inhibitory mechanism of multiple heavy metals on anammox, and provide the guidances for anammox process application in treating high-ammonium industrial wastewaters containing heavy metals.

Copper sulfide mineral performs non-enzymatic anaerobic ammonium oxidation through a hydrazine intermediate

Anaerobic ammonium oxidation (anammox)-the biological process that activates ammonium with nitrite-is responsible for a significant fraction of N2 production in marine environments. Despite decades of biochemical research, however, no synthetic models capable of anammox have been identified. Here we report that a copper sulfide mineral replicates the entire biological anammox pathway catalysed by three metalloenzymes. We identified a copper-nitrosonium {CuNO}10 complex, formed by nitrite reduction, as the oxidant for ammonium oxidation that leads to heterolytic N-N bond formation from nitrite and ammonium. Similar to the biological process, N2 production was mediated by the highly reactive intermediate hydrazine, one of the most potent reductants in nature. We also found another pathway involving N-N bond heterocoupling for the formation of hybrid N2O, a potent greenhouse gas with a unique isotope composition. Our study represents a rare example of non-enzymatic anammox reaction that interconnects six redox states in the abiotic nitrogen cycle.

Metagenomic unveils the promotion of mainstream PD-anammox process at lower nZVI concentration and inhibition at higher dosage

The partial-denitrification-anammox (PdNA) process exhibits great potential in enabling the simultaneous removal of NO3--N and NH4+-N. This study delved into the impact of exogenous nano zero-valent iron (nZVI) on the PdNA process. Adding 10 mg L-1 of nZVI increased nitrogen removal efficiency up to 83.12 % and maintained higher relative abundances of certain beneficial bacteria. The maximum relative abundance of Candidatus Brocadia (1.6 %), Candidatus Kuenenia (1.5 %), Ignavibacterium (1.3 %), and Azospira (1.2 %) was observed at 10 mg L-1 of nZVI. However, the greatest relative abundance of Thauera (1.3 %) was recorded under 50 mg L-1. Moreover, applying nZVI selectively enhanced the abundance of NO3--N reductase genes. So, keeping the nZVI concentration at 10 mg L-1 or below is advisable to ensure a stable PdNA process in mainstream conditions. Considering nitrogen removal efficiency, using nZVI in the PD-anammox process could be more cost-effective in enhancing its adoption in industrial and mainstream settings.

Mechanistic insight into microbial interaction and metabolic pattern of anammox consortia on surface-modified biofilm carrier with extracellular polymeric substances

The extremely slow growth rate of anaerobic ammonia oxidation (anammox) bacteria limits full-scale application of anammox process worldwide. In this study, extracellular polymeric substances (EPS)-coated polypropylene (PP) carriers were prepared for biofilm formation. The biomass adhesion rate of EPS-PP carrier was 12 times that of PP carrier, and EPS-PP achieved significant enrichment of E. coli BY63. The 120-day continuous flow experiment showed that the EPS-PP carrier accelerated the formation of anammox biofilm, and the nitrogen removal efficiency increased by 10.5 %. In addition, the abundance of Candidatus Kuenenia in EPS-PP biofilm was 27.1%. Simultaneously, amino acids with high synthesis cost and the metabolites of glycerophospholipids related to biofilm formation on EPS-PP biofilm were significantly up-regulated. Therefore, EPS-PP carriers facilitated the rapid formation of anammox biofilm and promoted the metabolic activity of functional bacteria, which further contributed to the environmental and economic sustainability of anammox process.

Effect of long-term dosage of hydrazine on mainstream anammox process: Biofilm characteristics and microbial community

The impact of the long-term trace hydrazine (N2H4) exogenous supplementation on activity of the anaerobic ammonium oxidation (anammox) biofilm was investigated in a moving bed biofilm reactor (MBBR) for mainstream wastewater treatment. The results of this study demonstrated that the addition of 2-5 mg/L N2H4 enhanced anammox biofilm activity, as evidenced by the augmented nitrogen removal rate (NRR), which increased from 113.4 g/(m3·d) to 126.7 g/(m3·d) with the introduction of 2 mg/L N2H4. However, a higher concentration of N2H4 (10 mg/L) suppressed anammox activity, leading to a reduced NRR of 91.5 g/(m3·d). Bioindicators revealed that the long-term addition of 2 mg/L N2H4 fostered the accumulation of anammox bacteria (AnAOB) biomass, elevating the volatile suspended solids (VSS) content by 12%. Moreover, the structural composition of extracellular polymeric substances (EPS) within the biofilm was altered, resulting in enhanced biofilm strength within the reactor. The protective mechanism of the biofilm was activated, and EPS secretion was stimulated by the continuous N2H4 supplementation. The introduction of an excess dosage of N2H4 led to alterations in the microbial communities, ultimately resulting in a decline in the performance of the reactor. These findings collectively illustrate that N2H4, as an intermediate product, can effectively enhance anammox activity within the MBBR for mainstream wastewater treatment. This study contributes to the understanding of the optimization strategies for anammox processes in wastewater treatment systems.

Study on the mechanism of enhanced anaerobic ammonia oxidation performance by extracellular electron acceptor biochar

ABSTRACTAnaerobic ammonia oxidation process has the advantages of energy and cost reduction, therefore, it has been considered as one of the main alternatives to conventional biological denitrification process in recent years. Biochar has been applied in the anammox process for nitrogen removal efficiency. But, due to its extracellular electron transfer capacity and abundance of redox-specific functional groups, which served as extracellular electron acceptor to anaerobically oxidize NH4+ is still controversy. In this study, the anaerobic ammonia oxidation was investigated when biochar was used as electron acceptor in the wastewater. According to the optimal process variables determined in the batch tests, when the influent NH4+-N concentration in the anaerobic ammonia oxidation reaction was 30-50 mg/L and the biochar dosing was at 10 g/L, it showed some promotion in the long-term experiments. The anaerobic ammonia oxidation process with biochar as the electron acceptor reached more than 60% NH4+-N removal efficiency in the system, and the ΔNO3--N/ΔNH4+-N ratio reached 0.19 which tended to the theoretical value. After 20 days, the voltage in the system keeps fluctuating about 4 mV, indicated that the functional bacteria using biochar as the electron acceptor gradually dominated the system. In addition, the abundance of norank_f__norank_o__SBR1031 in the Chloroflexi phylum has increased significantly at 29.92%, while the abundance of the major genus Candidatus_Kuenenia in AnAOB has decreased slightly at 11.47%.

Potential electron acceptors for ammonium oxidation in wastewater treatment system under anoxic condition: A review

Anaerobic ammonium oxidation has been considered as an environmental-friendly and energy-efficient biological nitrogen removal (BNR) technology. Recently, new reaction pathway for ammonium oxidation under anaerobic condition had been discovered. In addition to nitrite, iron trivalent, sulfate, manganese and electrons from electrode might be potential electron acceptors for ammonium oxidation, which can be coupled to traditional BNR process for wastewater treatment. In this paper, the pathway and mechanism for ammonium oxidation with various electron acceptors under anaerobic condition is studied comprehensively, and the research progress of potentially functional microbes is summarized. The potential application of various electron acceptors for ammonium oxidation in wastewater is addressed, and the N2O emission during nitrogen removal is also discussed, which was important greenhouse gas for global climate change. The problems remained unclear for ammonium oxidation by multi-electron acceptors and potential interactions are also discussed in this review.

Chemomixoautotrophy and stress adaptation of anammox bacteria: A review

Anaerobic ammonium oxidizing (anammox) bacteria, which were first discovered nearly three decades ago, are crucial for treating ammonium-containing wastewater. Studies have reported on the biochemical nitrogen conversion process and the physiological, phylogenic, and ecological features of anammox bacteria. For a long time, anammox bacteria were assumed to have a lithoautotrophic lifestyle. However, recent studies have suggested the functional versatility of anammox bacteria. Genome-based analysis and experiments with enrichment cultures have demonstrated the association of the metabolic activities of anammox bacteria with different stress conditions, revealing the importance of utilizing specific organic substances, including organoautotrophy, for growth and adaptation to stress conditions. Our understanding regarding the utilization and metabolism of organic substances and their associations with anammox reactions in anammox bacteria is growing but still incomplete. In this review, we summarize the effect of the utilization of organic substances by anammox bacteria under environmental stress conditions, emphasizing their potential organoautotrophic activity and metabolic flexibility. Although most anammox bacteria may utilize specific organic substances, Ca. Brocadia exhibited the highest level of mixoautotrophic activity. The environmental factors that substantially affect the organoautotrophic activities of anammox bacteria were also examined. This review provides a new perspective on the organoautotrophic capacity of anammox bacteria.

Response mechanism of a highly efficient partial nitritation-anammox (PN/A) process under antibiotic stress: Extracellular polymers, microbial community, and functional genes

The Partial nitritation-Anammox (PN/A) process can be restricted when treating high ammonia nitrogen wastewater containing antibiotics. This study aims to explore the response mechanism of the PN/A process under antibiotic stress. Results showed the PN/A process achieved a nitrogen removal rate higher than 1.01 ± 0.03 kg N/m3/d under long-term sulfamethazine stress. The increase of extracellular polymers from 22.52 to 43.96 mg/g VSS was conducive to resisting antibiotic inhibitory. The increase of Denitratisoma and SM1A02 abundance as well as functional genes nirS and nirK indicated denitrifiers should play an important role in the stability of the PN/A system under sulfamethazine stress. In addition, antibiotic-resistant genes (ARGs) sul1 and intI1 significantly increased by 8.78 and 5.12 times of the initial values to maintain the resistance of PN/A process to sulfamethazine stress. This study uncovers the response mechanism of the PN/A process under antibiotic stress, offering a scientific basis and guidance for further application in the future.

Influence of vegetation and substrate type on removal of emerging organic contaminants and microbial dynamics in horizontal subsurface constructed wetlands

Constructed wetlands (CWs) offer an efficient alternative technology for removing emerging organic contaminants (EOCs) from wastewater. Optimizing CW performance requires understanding the impact of CW configuration on EOC removal and microbial community dynamics. This study investigated EOC removal and microbial communities in horizontal subsurface flow (HSSF) CWs over a 26-month operational period. Comparison between tuff-filled and gravel-filled CWs highlighted the superior EOC removal in tuff-filled CWs during extended operation, likely caused by the larger surface area of the tuff substrate fostering microbial growth, sorption, and biodegradation. Removal of partially positively charged EOCs, like atenolol (29-98 %) and fexofenadine (21-87 %), remained constant in the different CWs, and was mainly attributed to sorption. In contrast, removal rates for polar non-sorbing compounds, including diclofenac (3-64 %), acyclovir (9-85 %), and artificial sweeteners acesulfame (5-60 %) and saccharin (1-48 %), seemed to increase over time due to enhanced biodegradation. The presence of vegetation and different planting methods (single vs. mixed plantation) had a limited impact, underscoring the dominance of substrate type in the CW performance. Microbial community analysis identified two stages: a startup phase (1-7 months) and a maturation phase (19-26 months). During this transition, highly diverse communities dominated by specific species in the early stages gave way to more evenly distributed and relatively stable communities. Proteobacteria and Bacteroidetes remained dominant throughout. Alphaproteobacteria, Acidobacteria, Planctomycetes, Salinimicrobium, and Sphingomonas were enriched during the maturation phase, potentially serving as bioindicators for EOC removal. In conclusion, this study emphasizes the pivotal role of substrate type and maturation in the removal of EOCs in HSSF CW, considering the complex interplay with EOC physicochemical properties. Insights into microbial community dynamics underscore the importance of taxonomic and functional diversity in assessing CW effectiveness. This knowledge aids in optimizing HSSF CWs for sustainable wastewater treatment, EOC removal, and ecological risk assessment, ultimately contributing to environmental protection.

Revealing the comprehensive impact of organic compounds on the partial nitrification-anammox system during incineration leachate treatment: metabolic hierarchy and adaptation

Organics, as widespread pollutants in high-strength ammonia wastewater, typically exert adverse effects on the performance of partial nitrification-anammox (PNA) systems. However, the in-depth knowledge on how microbial consortia respond to these disturbances remains limited. In this study, we unveiled the evolution of complex organic matter flow and its impact on the metabolic hierarchy and adaptation of microbial consortia, employing multi-omics approaches, i.e., 16S amplicon sequencing, metagenomics, and metabolomics. In a two-stage PNA system sequentially treating synthetic wastewater and incineration leachate over 230 days, partial nitrification stayed stable (nitrite accumulation > 97%) while anammox efficiency dropped (nitrogen removal decreased from 86% to 78%). The phenomenon was revealed to be correlated with the evolution of dissolved organic matter (DOM) and xenobiotic organic compounds (XOCs). In the PN stage, ammonia-oxidizing bacteria (AOB) exhibited excellent adaptability through active metabolic regulation after treating leachate. Numerous heterotrophs proliferated to utilize DOM and XOCs, triggering a "boom" state evident in the glycerophospholipid metabolism. However, in the anammox stage, the competition between carbon fixation and central carbon metabolism within autotrophs and heterotrophs became evident. Increased biosynthesis costs inhibited the central metabolism (specific anammox activity decreased by 66%) and the Wood-Ljungdahl pathway of anammox bacteria (AnAOB) in the presence of recalcitrant organics. Additionally, the degradation of organics was limited, exhibiting a "bust" state. This study revealed the metabolic adaption and susceptibility of AOB and AnAOB in response to organics from the leachate, demonstrating the applicability of the two-stage configuration for treating high-strength wastewater containing abundant and diverse organics.

New insights into functional divergence and adaptive evolution of uncultured bacteria in anammox community by complete genome-centric analysis

Anaerobic ammonium-oxidation (anammox) bacteria play a crucial role in global nitrogen cycling and wastewater nitrogen removal, but they share symbiotic relationships with various other microorganisms. Functional divergence and adaptive evolution of uncultured bacteria in anammox community remain underexplored. Although shotgun metagenomics based on short reads has been widely used in anammox research, metagenome-assembled genomes (MAGs) are often discontinuous and highly contaminated, which limits in-depth analyses of anammox communities. Here, for the first time, we performed Pacific Biosciences high-fidelity (HiFi) long-read sequencing on the anammox granule sludge sample from a lab-scale bioreactor, and obtained 30 accurate and complete metagenome-assembled genomes (cMAGs). These cMAGs were obtained by selecting high-quality circular contigs from initial assemblies of long reads generated by HiFi sequencing, eliminating the need for Illumina short reads, binning, and reassembly. One new anammox species affiliated with Candidatus Jettenia and three species affiliated with novel families were found in this anammox community. cMAG-centric analysis revealed functional divergence in general and nitrogen metabolism among the anammox community members, and they might adopt a cross-feeding strategy in organic matter, cofactors, and vitamins. Furthermore, we identified 63 mobile genetic elements (MGEs) and 50 putative horizontal gene transfer (HGT) events within these cMAGs. The results suggest that HGT events and MGEs related to phage and integration or excision, particularly transposons containing tnpA in anammox bacteria, might play important roles in the adaptive evolution of this anammox community. The cMAGs generated in the present study could be used to establish of a comprehensive database for anammox bacteria and associated microorganisms. These findings highlight the advantages of HiFi sequencing for the studies of complex mixed cultures and advance the understanding of anammox communities.

Effects of C/N ratio on N2O emissions and nitrogen functional genes during vegetable waste composting

Nitrous oxide (N2O) generation during composting not only leads to losses of nitrogen (N) but also reduces the agronomic values and environmental benefits of composting. This study aimed to investigate the effect of the C/N ratio on N2O emissions and its underlying mechanisms at the genetic level during the composting of vegetable waste. The experiment was set up with three treatments, including low C/N treatment (LT, C/N = 18), middle C/N treatment (MT, C/N = 30), and high C/N treatment (HT, C/N = 50). The results showed that N2O emission was mainly concentrated in the cooling and maturation periods, and the cumulative N2O emissions decreased as the C/N ratio increased. Specifically, the cumulative N2O emission was 57,401 mg in LT, significantly higher than 2155 mg in MT and 1353 mg in HT. Lowering the C/N ratio led to increasing TN, NH4+-N, and NO3--N contents throughout the composting process. All detected nitrification-related gene abundances in LT continued to increase during composting, significantly surpassing those in MT during the cooling period. By contrast, in HT, there was a slight increase in the abundance of detected nitrification-related genes but a significant decrease in the abundance of narG, napA, and norB genes in the thermophilic and cooling periods. The structural equation model revealed that hao and nosZ genes were vital in N2O emissions. In conclusion, increasing the C/N ratio effectively contributed to N2O reduction during vegetable waste composting.