Biogeography of anaerobic ammonia-oxidizing (anammox) bacteria

Metagenomic evidence of a novel anammox community in a cold aquifer with high nitrogen pollution

The process of anaerobic ammonium oxidation by nitrite (anammox) is a globally essential part of N cycle. To date, 8 Candidatus genera and more than 22 species of anammox bacteria have been discovered in various anthropogenic and natural habitats, including nitrogen-polluted aquifers. In this work, anammox bacteria were detected for the first time in the groundwater ecosystem with high anthropogenic nitrogen pollution (up to 1760 mg NO3--N/L and 280 mg NH4+-N/L) and low year-round temperature (7-8 °C) in the zone of a uranium sludge repository. Further metagenomic analysis resulted in retrieval of metagenome-assembled genomes of 4 distinct anammox bacteria: a new genus named Ca. Frigussubterria, new species in Ca. Kuenenia, and two strains of a new species in Ca. Scalindua. Analysis of the genomes revealed essential genes involved in anammox metabolism. Both strains of Ca. Scalindua chemeplantae had a high copy number of genes encoding the cold shock proteins CspA/B, which can also function as an antifreeze protein (CspB). Ca. Kuenenia glazoviensis and Ca. Frigussubterria udmurtiae were abundant in less N-polluted site, while Ca. Scalindua chemeplantae inhabited both sites. Genes for urea utilization, reduction of insoluble Fe2O3 or MnO2, assimilatory sulfate reduction, reactive oxygen detoxification, nitrate reduction to ammonium, and putatively arsenate respiration were found. These findings enrich knowledge of the functional and phylogenetic diversity of anammox bacteria and improve understanding of the nitrogen cycle in polluted aquifers.

Nitrogen Removal Performance and Microbial Community Structure of IMTA Ponds (Apostistius japonicus-Penaeus japonicus-Ulva)

Denitrification and anaerobic ammonium oxidation (anammox) are key processes for nitrogen removal in aquaculture, reducing the accumulated nitrogen nutrients to nitrogen gas or nitrous oxide gas. Complete removal of nitrogen from aquaculture systems is an important measure to solve environmental pollution. In order to evaluate the nitrogen removal potential of marine aquaculture ponds, this study investigated the denitrification and anammox rates, the flux of nitrous oxide (N2O) at the water-air interface, the sediment microbial community structure, and the gene expression associated with the nitrogen removal process in integrated multi-trophic aquaculture (IMTA) ponds (Apostistius japonicus-Penaeus japonicus-Ulva) with different culture periods. The results showed that the denitrification and anammox rates in sediments increased with the increase of cultivation periods and depth, and there was no significant difference in nitrous oxide gas flux at the water-air interface between different cultivation periods (p > 0.05). At the genus and phylum levels, the abundance of microorganisms related to nitrogen removal reactions in sediments changed significantly with the increase of cultivation period and depth, and was most significantly affected by the concentration of particulate organic nitrogen (PON) in sediments. The expression of denitrification gene (narG, nirS, nosZ) in surface sediments was significantly higher than that in deep sediments (p < 0.05), and was negatively correlated with denitrification rate. All samples had a certain anammox capacity, but no known anammox bacteria were found in the microbial diversity detection, and the expression of gene (hzsB) related to the anammox process was extremely low, which may indicate the existence of an unknown anammox bacterium. The data of this study showed that the IMTA culture pond had a certain potential for nitrogen removal, and whether it could make a contribution to reducing the pollution of culture wastewater still needed additional practice and evaluation, and also provided a theoretical basis for the nitrogen removal research of coastal mariculture ponds.

Salinity Tolerance and Osmoadaptation Strategies in Four Genera of Anammox Bacteria: Brocadia, Jettenia, Kuenenia, and Scalindua

The salinity tolerance and osmoadaptation strategies in four phylogenetically distant anammox species, Brocadia, Jettenia, Kuenenia, and Scalindua, were investigated by using highly enriched cell cultures. The first-emerged "Ca. Scalindua sp." showed optimum growth at 1.5-3% salinity and was tolerant to ∼10% salinity (a slight halophile). The second-emerged "Ca. Kuenenia stuttgartiensis" was tolerant to ∼6% salinity with optimum growth at 0.25-1.5% (a halotolerant). These early-emerged "Ca. Scalindua sp." and ″Ca. K. stuttgartiensis" rapidly accumulated K+ ions and simultaneously synthesized glutamate as a counterion. Subsequently, part of the glutamate was replaced by trehalose. In contrast, the late-emerged "Ca. B. sinica" and "Ca. J. caeni" were unable to accumulate sufficient amounts of K+─glutamate and trehalose, resulting in a significant decrease in activity even at 1-2% salinity (nonhalophiles). In addition, the external addition of glutamate may increase anammox activity at high salinity. The species-dependent salinity tolerance and osmoadaptation strategies were consistent with the genetic potential required for the biosynthesis and transport of these osmolytes and the evolutionary history of anammox bacteria: Scalindua first emerged in marine environments and then Kuenenia and other two species gradually expanded their habitat to estuaries, freshwater, and terrestrial environments, while Brocadia and Jettenia likely lost their ability to accumulate K+─glutamate.

Microbial divergence and evolution. The case of anammox bacteria

Species differentiation and the appearance of novel diversity on Earth is a major issue to understand the past and future of microbial evolution. Herein, we propose the analysis of a singular evolutive example, the case of microorganisms carrying out the process of anammox (anaerobic ammonium oxidation). Anammox represents a singular physiology active on Earth from ancient times and, at present, this group is still represented by a relatively limited number of species carrying out a specific metabolism within the Phylum Planctomycetota. The key enzyme on the anammox pathway is hydrazine dehydrogenase (HDH) which has been used as a model in this study. HDH and rRNA (16S subunit) phylogenies are in agreement suggesting a monophyletic origin. The diversity of this singular phylogenetic group is represented by a few enriched bacterial consortia awaiting to be cultured as monospecific taxa. The apparent evolution of the HDH genes in these anammox bacteria is highly related to the diversification of the anammox clades and their genomes as pointed by phylogenomics, their GC content and codon usage profile. This study represents a clear case where bacterial evolution presents a paralleled genome, gene and species diversification through time from a common ancestor; a scenario that most times is masked by a web-like phylogeny and the huge complexity within the prokaryotes. Besides, this contribution suggests that microbial evolution of the anammox bacteria has followed an ordered, vertical diversification through Earth history and will present a potentially similar speciation fate in the future.

Collaborative metabolisms of urea and cyanate degradation in marine anammox bacterial culture

Anammox process greatly contributes to nitrogen loss occurring in oceanic oxygen minimum zones (OMZs), where the availability of NH4+ is scarce as compared with NO2-. Remineralization of organic nitrogen compounds including urea and cyanate (OCN-) into NH4+ has been believed as an NH4+ source of the anammox process in oxygen minimum zones. However, urea- or OCN-- dependent anammox has not been well examined due to the lack of marine anammox bacterial culture. In the present study, urea and OCN- degradation in a marine anammox bacterial consortium were investigated based on 15N-tracer experiments and metagenomic analysis. Although a marine anammox bacterium, Candidatus Scalindua sp., itself was incapable of urea and OCN- degradation, urea was anoxically decomposed to NH4+ by the coexisting ureolytic bacteria (Rhizobiaceae, Nitrosomonadaceae, and/or Thalassopiraceae bacteria), whereas OCN- was abiotically degraded to NH4+. The produced NH4+ was subsequently utilized in the anammox process. The activity of the urea degradation increased under microaerobic condition (ca. 32-42 μM dissolved O2, DO), and the contribution of the anammox process to the total nitrogen loss also increased up to 33.3% at 32 μM DO. Urea-dependent anammox activities were further examined in a fluid thioglycolate media with a vertical gradient of O2 concentration, and the active collaborative metabolism of the urea degradation and anammox was detected at the lower oxycline (21 μM DO).

A review of microbial nitrogen transformations and microbiome engineering for biological nitrogen removal under salinity stress

The osmotic stress caused by salinity exerts severe inhibition on the process of biological nitrogen removal (BNR), leading to the deterioration of biosystems and the discharge of nitrogen with saline wastewater. Feasible strategies to solve the bottleneck in saline wastewater treatment have attracted great attention, but relevant studies to improve nitrogen transformations and enhance the salt-tolerance of biosystems in terms of microbiome engineering have not been systematically reviewed and discussed. This work attempted to provide a more comprehensive explanation of both BNR and microbiome engineering approaches for saline wastewater treatment. The effect of salinity on conventional BNR pathways, nitrification-denitrification and anammox, was summarized at cellular and metabolic levels, including the nitrogen metabolic pathways, the functional microorganisms, and the inhibition threshold of salinity. Promising nitrogen transformations, such as heterotrophic nitrification-aerobic denitrification, ammonium assimilation and the coupling of conventional pathways, were introduced and compared based on advantages and challenges in detail. Strategies to improve the salt tolerance of biosystems were proposed and evaluated from the perspective of microbiome engineering. Finally, prospects of future investigation and applications on halophilic microbiomes in saline wastewater treatment were discussed.

Critical analysis on the transformation and upgrading strategy of Chinese municipal wastewater treatment plants: Towards sustainable water remediation and zero carbon emissions

In the light of circular economy aspects, processing of large-scale municipal wastewater treatment plants (WWTPs) needs reconsideration to limit the overuse of energy, implement of non-green technologies and emit abundant greenhouse gas. Along with the huge increase in the worldwide population and agro-industrial activities, global environmental organizations have issued several recent roles to boost scientific and industrial communities towards sustainable development. Over recent years, China has imposed national and regional standards to control and manage the discharged liquid and solid waste, as well as to achieve carbon peaking and carbon neutrality. The aim of this report is to analyze the current state of Chinese WWTPs routing and related issues such as climate change and air pollution. The used strategies in Chinese WWTPs and upgrading trends were critically discussed. Several points were addressed including the performance, environmental impact, and energy demand of bio-enhanced technologies, including hydrolytic acidification pretreatment, efficient (toxic) strain treatment, and anaerobic ammonia oxidation denitrification technology, as well as advanced treatment technologies composed of physical and chemical treatment technologies, biological treatment technology and combined treatment technology. Discussion and critical analysis based on the current data and national policies were provided and employed to develop the future development trend of municipal WWTPs in China from the construction of sustainable and "Zero carbon" WWTPs.

Dynamics of Benthic Nitrate Reduction Pathways and Associated Microbial Communities Responding to the Development of Seasonal Deoxygenation in a Coastal Mariculture Zone

Intensive mariculture activities result in eutrophication and enhance coastal deoxygenation. Deoxygenation profoundly influences nitrate reduction processes and further the fate of nitrogen (N) in coastal systems. Herein, 15N isotope labeling, real-time PCR, and high-throughput sequencing techniques were jointly used to investigate the participation and seasonal dynamics of sediment nitrate reduction pathways and the succession of functional microbial communities during the development of seasonal deoxygenation in a coastal aquaculture zone. Denitrification dominated benthic nitrate reduction (46.26-80.91%). Both denitrification and dissimilatory nitrate reduction to ammonium were significantly enhanced by summer deoxygenation (dissolved oxygen levels fell to 2.94 ± 0.28 mg L-1), while anammox remained unchanged. The abundance of the nitrous oxide reductase gene nosZ increased during deoxygenation. The community of the nosZ gene was sensitive to deoxygenation, with Azospirillum and Ruegeria accounting for the majority. Pelobacter was overwhelming in the nrfA gene (encoding dissimilatory nitrite reductase) community, which was less affected by deoxygenation. The variations of benthic nitrate reduction processes were driven by bottom water oxygen combined with temperature, chlorophyll a, and microbial gene abundances and community compositions. Our results implicated that seasonal oxygen-deficient zones could be substantial N sinks of coastal ecosystems and important for N balance. Effective management measures need to be developed to avoid further exacerbation of coastal deoxygenation and maintain the sustainable development of mariculture.

Mobilization pilot test of PCE sources in the transition zone to aquitards by combining mZVI and biostimulation with lactic acid

The potential toxic and carcinogenic effects of chlorinated solvents in groundwater on human health and aquatic ecosystems require very effective remediation strategies of contaminated groundwater to achieve the low legal cleanup targets required. The transition zones between aquifers and bottom aquitards occur mainly in prograding alluvial fan geological contexts. Hence, they are very frequent from a hydrogeological point of view. The transition zone consists of numerous thin layers of fine to coarse-grained clastic fragments (e.g., medium sands and gravels), which alternate with fine-grained materials (clays and silts). When the transition zones are affected by DNAPL spills, free-phase pools accumulate on the less conductive layers. Owing to the low overall conductivity of this zone, the pools are very recalcitrant. Little field research has been done on transition zone remediation techniques. Injection of iron microparticles has the disadvantage of the limited accessibility of this reagent to reach the entire source of contamination. Biostimulation of indigenous microorganisms in the medium has the disadvantage that few of the microorganisms are capable of complete biodegradation to total mineralization of the parent contaminant and metabolites. A field pilot test was conducted at a site where a transition zone existed in which DNAPL pools of PCE had accumulated. In particular, the interface with the bottom aquitard was where PCE concentrations were the highest. In this pilot test, a combined strategy using ZVI in microparticles and biostimulation with lactate in the form of lactic acid was conducted. Throughout the test it was found that the interdependence of the coupled biotic and abiotic processes generated synergies between these processes. This resulted in a greater degradation of the PCE and its transformation products. With the combination of the two techniques, the mobilization of the contaminant source of PCE was extremely effective.

Ecological interactions and the underlying mechanism of anammox and denitrification across the anammox enrichment with eutrophic lake sediments

BACKGROUND

Increasing attention has recently been devoted to the anaerobic ammonium oxidation (anammox) in eutrophic lakes due to its potential key functions in nitrogen (N) removal for eutrophication control. However, successful enrichment of anammox bacteria from lake sediments is still challenging, partly due to the ecological interactions between anammox and denitrifying bacteria across such enrichment with lake sediments remain unclear.

RESULTS

This study thus designed to fill such knowledge gaps using bioreactors to enrich anammox bacteria with eutrophic lake sediments for more than 365 days. We continuously monitored the influent and effluent water, measured the anammox and denitrification efficiencies, quantified the anammox and denitrifying bacteria, as well as the related N cycling genes. We found that the maximum removal efficiencies of NH₄⁺ and NO₂^- reached up to 85.92% and 95.34%, respectively. Accordingly, the diversity of anammox and denitrifying bacteria decreased significantly across the enrichment, and the relative dominant anammox (e.g., Candidatus Jettenia) and denitrifying bacteria (e.g., Thauera, Afipia) shifted considerably. The ecological cooperation between anammox and denitrifying bacteria tended to increase the microbial community stability, indicating a potential coupling between anammox and denitrifying bacteria. Moreover, the nirS-type denitrifiers showed stronger coupling with anammox bacteria than that of nirK-type denitrifiers during the enrichment. Functional potentials as depicted by metagenome sequencing confirmed the ecological interactions between anammox and denitrification. Metagenome-assembled genomes-based ecological model indicated that the most dominant denitrifiers could provide various materials such as amino acid, cofactors, and vitamin for anammox bacteria. Cross-feeding in anammox and denitrifying bacteria highlights the importance of microbial interactions for increasing the anammox N removal in eutrophic lakes.

CONCLUSIONS

This study greatly expands our understanding of cooperation mechanisms among anammox and denitrifying bacteria during the anammox enrichment with eutrophic lake sediments, which sheds new insights into N removal for controlling lake eutrophication. Video Abstract.

Effects of reducing, stabilizing, and antibiotic agents on "Candidatus Kuenenia stuttgartiensis"

Anaerobic ammon ium oxidizing (anammox) bacteria oxidize ammonium and reduce nitrite, producing N₂, and could play a major role in energy-optimized wastewater treatment. However, sensitivity to various environmental conditions and slow growth currently hinder their wide application. Here, we attempted to determine online the effect of environmental stresses on anammox bacteria by using an overnight batch activity test with whole cells, in which anammox activity was calculated by quantifying N₂ production via headspace-pressure monitoring. A planktonic mixed culture dominated by "Candidatus Kuenenia stuttgartiensis" strain CSTR1 was cultivated in a 30-L semi-continuous stirring tank reactor. In overnight resting-cell anammox activity tests, oxygen caused strong inhibition of anammox activity, which was reversed by sodium sulfite (30 µM). The tested antibiotics sulfamethoxazole, kanamycin, and ciprofloxacin elicited their effect on a dose-dependent manner; however, strain CSTR1 was highly resistant to sulfamethoxazole. Anammox activity was improved by activated carbon and Fe₂O₃. Protein expression analysis from resting cells after anammox activity stimulation revealed that NapC/NirT family cytochrome c (KsCSTR_12840), hydrazine synthase, hydrazine dehydrogenase, hydroxylamine oxidase, and nitrate:nitrite oxidoreductase were upregulated, while a putative hydroxylamine oxidoreductase HAO (KsCSTR_49490) was downregulated. These findings contribute to the growing knowledge on anammox bacteria physiology, eventually leading to the control of anammox bacteria growth and activity in real-world application. KEY POINTS: • Sulfite additions can reverse oxygen inhibition of the anammox process • Anammox activity was improved by activated carbon and ferric oxide • Sulfamethoxazole marginally affected anammox activity.

Long-term adaptation of two anammox granules with different ratios of Candidatus Brocadia and Candidatus Jettenia under increasing salinity and their application to treat saline wastewater

Nitrogen removal in saline wastewater is a challenge of the anaerobic ammonium oxidation (anammox) process, which is dominated by freshwater anammox bacteria (FAB). Candidatus Brocadia and Candidatus Jettenia, the most widely used FABs, have been separately applied and evaluated for their ability to treat saline wastewater. To understand the effect of salinity on nitrogen removal capability when they present together in an anammox granule, we compared two anammox granules: GRN1 was evenly dominated by Ca. Brocadia (42 %) and Ca. Jettenia (43 %), while GRN2 was dominated with mostly Ca. Brocadia (90 %) and a small amount of Ca. Jettenia (1 %). Each granule was inoculated into a continuous column reactor to treat artificial wastewater containing 150 mg NH₄⁺-N/L and 150 mg NO₂^--N/L under increasing saline conditions for 250 days. GRN1 showed superior and more stable nitrogen removal than GRN2 under saline conditions of up to 15 g NaCl/L. Under high-saline conditions, both the granules' sizes decreased (larger GRN1 than GRN2 in initial). The mass percent of Na salt increased (more in GRN2) and mineral contents decreased more in GRN1. High-throughput sequencing for microbial community analysis showed that Planctomycetes in GRN1 (85 %) and GRN2 (92 %) decreased to 14 % and 12 %, respectively. The ratio of Ca. Brocadia and Ca. Jettenia in GRN1 changed to 37 % and 63 %, respectively, whereas the ratio in GRN2 (99 % and 1 %, respectively) did not change. Both salt-adapted granules were applied to the two-stage partial nitritation and anammox (PN/A) process to treat high strength ammonium (400 mg/L) wastewater under high saline condition (15 g NaCl/L). The PN/A process containing GRN1 showed more stable nitrogen removal performance during approximately 100 days of operation. These results suggest that the anammox granules evenly dominated by two FABs, Ca. Brocadia and Ca. Jettenia, would be advantageous to treat high-strength NH₄⁺ wastewater under high-saline conditions.

Coupling of Anammox Activity and PAH Biodegradation: Current Insights and Future Directions

Anaerobic ammonium oxidation (anammox) has shown success in past years for the treatment of municipal and industrial wastewater containing inorganic nutrients (i.e., nitrogen). However, the increase in polycyclic aromatic hydrocarbon (PAH)-contaminated matrices calls for new strategies for efficient and environmentally sustainable remediation. Therefore, the present review examined the literature on the connection between the anammox process and PAHs using VOSviewer to shed light on the mechanisms involved during PAH biodegradation and the key factors affecting anammox bacteria. The scientific literature thoroughly discussed here shows that PAHs can be involved in nitrogen removal by acting as electron donors, and their presence does not adversely affect the anammox bacteria. Anammox activity can be improved by regulating the operating parameters (e.g., organic load, dissolved oxygen, carbon-to-nitrogen ratio) and external supplementation (i.e., calcium nitrate) that promote changes in the microbial community (e.g., Candidatus Jettenia), favoring PAH degradation. The onset of a synergistic dissimilatory nitrate reduction to ammonium and partial denitrification can be beneficial for PAH and nitrogen removal.

Transport-limited reactions in microbial systems

Predicting microbial metabolic rates and emergent biogeochemical fluxes remains challenging due to the many unknown population dynamical, physiological and reaction-kinetic parameters and uncertainties in species composition. Here, we show that the need for these parameters can be eliminated when population dynamics and reaction kinetics operate at much shorter time scales than physical mixing processes. Such scenarios are widespread in poorly mixed water columns and sediments. In this 'fast-reaction-transport' (FRT) limit, all that is required for predictions are chemical boundary conditions, the physical mixing processes and reaction stoichiometries, while no knowledge of species composition, physiology or population/reaction kinetic parameters is needed. Using time-series data spanning years 2001-2014 and depths 180-900 m across the permanently anoxic Cariaco Basin, we demonstrate that the FRT approach can accurately predict the dynamics of major electron donors and acceptors (Pearson r ≥ 0.9 in all cases). Hence, many microbial processes in this system are largely transport limited and thus predictable regardless of species composition, population dynamics and kinetics. Our approach enables predictions for many systems in which microbial community dynamics and kinetics are unknown. Our findings also reveal a mechanism for the frequently observed decoupling between function and taxonomy in microbial systems.

Anammox bacterial abundance and diversity in different temperatures of purple paddy soils by 13C-DNA stable-isotope probing combined with high-throughput sequencing

Introduction

Anaerobic ammonium oxidation (anammox) plays a vital role in the global nitrogen cycle by oxidizing ammonium to nitrogen under anaerobic environments. However, the existence, abundance, and diversity of anammox bacteria between different temperatures are less studied, particularly in purple paddy soils.

Methods

¹³C-DNA stable-isotope probe combined with Illumina MiSeq high-throughput sequencing was employed to explore soil abundance and diversity of anammox bacteria. In doing so, 40-60 cm depth soils from typical purple paddy soils in Chongqing, southwest China, were cultured under ¹²CO₂-labeled and ¹³CO₂-labeled at 35°C, 25°C, 15°C, and 5°C for 56 days.

Results and Discussion

Anammox bacteria were not labeled at all by ¹³CO₂ at 5°C. The highest abundance of anammox bacteria was found at 25°C (3.52 × 10⁶~3.66 × 10⁶ copies·g^-1 dry soil), followed by 35°C and 15°C (2.01 × 10⁶~2.37 × 10⁶ copies·g^-1 dry soil) and almost no increase at 5°C. The relative abundance of Candidatus Jettenia sp. was higher at 25°C and 15°C, while Candidatus Brocadia sp. was higher at 35°C and 5°C. Our results revealed differences in anammox bacteria at different temperatures in purple paddy soils, which could provide a better understanding of soil N cycling regulated by anammox bacteria.

Controlling anammox speciation and biofilm attachment strategy using N-biotransformation intermediates and organic carbon levels

Conventional nitrogen removal in wastewater treatment requires a high oxygen and energy input. Anaerobic ammonium oxidation (anammox), the single-step conversion of ammonium and nitrite to nitrogen gas, is a more energy and cost effective alternative applied extensively to sidestream wastewater treatment. It would also be a mainstream treatment option if species diversity and physiology were better understood. Anammox bacteria were enriched up to 80%, 90% and 50% relative abundance, from a single inoculum, under standard enrichment conditions with either stepwise-nitrite and ammonia concentration increases (R1), nitric oxide supplementation (R2), or complex organic carbon from mainstream wastewater (R3), respectively. Candidatus Brocadia caroliniensis predominated in all reactors, but a shift towards Ca. Brocadia sinica occurred at ammonium and nitrite concentrations > 270 mg NH₄-N L^-1 and 340 mg NO₂-N L^-1 respectively. With NO present, heterotrophic growth was inhibited, and Ca. Jettenia coexisted with Ca. B. caroliniensis before diminishing as nitrite increased to 160 mg NO₂-N L^-1. Organic carbon supplementation led to the emergence of heterotrophic communities that coevolved with Ca. B. caroliniensis. Ca. B. caroliniensis and Ca. Jettenia preferentially formed biofilms on surfaces, whereas Ca. Brocadia sinica formed granules in suspension. Our results indicate that multiple anammox bacteria species co-exist and occupy sub-niches in anammox reactors, and that the dominant population can be reversibly shifted by, for example, changing nitrogen load (i.e. high nitrite concentration favors Ca. Brocadia caroliniensis). Speciation has implications for wastewater process design, where the optimum cell immobilization strategy (i.e. carriers vs granules) depends on which species dominates.

Microbial dynamics reveal the adaptation strategies of ecological niche in distinct anammox consortia under mainstream conditions

The feasibility of anammox-based processes for nitrogen-contained wastewater treatment has been verified with different anammox bacteria, however, the ecological niche of anammox bacteria under mainstream conditions is still elusive. In this study, six sludge samples collected from different habitats were utilized to culture anammox bacteria under mainstream conditions, and two distinct anammox genera (Ca. Kuenenia and Ca. Brocadia) with a relative abundance of 6.31% (C1) and 3.09% (C3), respectively, were identified. Notably, the microbial dynamics revealed that anammox bacteria (AMX), ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), Chloroflexi bacteria (CFX), and heterotrophic denitrification bacteria (HDB) were the core members in anammox consortia. However, Ca. Kuenenia and Ca. Brocadia occupied different ecological niches in anammox consortia. The dissolved oxygen and microbial structures of the anammox-continuous stirred tank reactor systems were the main factors to affect their niche differentiation. Meanwhile, comammox might exist in the systems and occupy the ecological niche of AOB in nitrogen cycling. The network analysis suggested that Ignavibacterium could be the associated bacteria in Ca. Kuenenia-dominated consortia, while Ca. Nitrotoga was that in the Ca. Brocadia-dominated consortia. Our findings reveal a valuable reference for the observation of distinct anammox genera under mainstream conditions, which provides theoretical guidance for the engineering application of mainstream anammox-based processes.

An overview of deploying membrane bioreactors in saline wastewater treatment from perspectives of microbial and treatment performance

The discharged saline wastewater has severely influenced the aquatic environment as the treatment performance of many wastewater treatment techniques is limited. In addition, the sources of saline wastewater are also plentiful from agricultural and various industrial fields such as food processing, tannery, pharmaceutical, etc. Although high salinity levels negatively impact the performance of both physicochemical and biological processes, membrane bioreactor (MBR) processes are considered as a potential technology to treat saline wastewater under different salinity levels depending on the adaption of the microbial community. Therefore, this study aims to systematically review the application of MBR widely used in the saline wastewater treatment from the perspectives of microbial structure and treatment efficiencies. At last, the concept of carbon dioxide capture and storage will be proposed for the MBR-treating saline wastewater technologies and considered toward the circular economy with the target of zero emission.

The effects of salinity changes on anammox performance: The response rule and tolerance mechanism

Some wastewaters contain high concentrations of ammonia coexisting with large amounts of salt, which might negatively affect the anaerobic ammonium oxidation (anammox) process. In this study, the performance of the anammox process under different saline conditions was investigated using an upflow anaerobic sludge bed-anammox system. After long-term operating for 275 days, the results indicated that the nitrogen removal efficiency remained high under the 0-40 g NaCl/L, and low salinity (15 g NaCl/L) substantially promoted specific anammox activity. Affected by the saline environment, the appearance, color, and shape of sludge notably changed, and the amount of extracellular polymeric substances gradually increased with increasing salinity, which might be one of the reasons for the strong salt tolerance of the system. Chloroflexi and Planctomycetes were the dominant strains under long-term salinity, and Brocadiaceae_g_ unclassified exhibited halophilic characteristics. The redundancy analysis results showed that the concentration of influent NH₄ ⁺ -N and salinity were the main environmental factors affecting the microbial community of the system. PRACTITIONER POINTS: Provides data to support the maximum value for salinity wastewater treatment with anammox processes' tolerance of 40 g NaCl/L. EPS changes may be responsible for the response to salinity challenges and provide direction for high salinity wastewater treatment. Brocadiaceae_g_ unclassified exhibited a halophilic quality. And it can be focused on to improve treatment efficiency.

Glutamate Enhances Osmoadaptation of Anammox Bacteria under High Salinity: Genomic Analysis and Experimental Evidence

An osmoprotectant that alleviates the bacterial osmotic stress can improve the bioreactor treatment of saline wastewater. However, proposed candidates are expensive, and osmoprotectants of anammox bacteria and their ecophysiological roles are not fully understood. In this study, a comparative analysis of 34 high-quality public metagenome-assembled genomes from anammox bacteria revealed two distinct groups of osmoadaptation. Candidatus Scalindua and Kuenenia share a close phylogenomic relation and osmoadaptation gene profile and have pathways for glutamate transport and metabolisms for enhanced osmoadaptation. The batch assay results demonstrated that the reduced Ca. Kuenenia activity in saline conditions was substantially alleviated with the addition and subsequent synergistic effects of potassium and glutamate. The operational test of two reactors demonstrated that the reduced anammox performance under brine conditions rapidly recovered by 35.7-43.1% as a result of glutamate treatment. The Ca. Kuenenia 16S rRNA and hydrazine gene expressions were upregulated significantly (p < 0.05), and the abundance increased by approximately 19.9%, with a decrease in dominant heterotrophs. These data demonstrated the effectiveness of glutamate in alleviating the osmotic stress of Ca. Kuenenia. This study provides genomic insight into group-specific osmoadaptation of anammox bacteria and can facilitate the precision management of anammox reactors under high salinity.

Phylogenomic Evidence for the Origin of Obligate Anaerobic Anammox Bacteria Around the Great Oxidation Event

The anaerobic ammonium oxidation (anammox) bacteria can transform ammonium and nitrite to dinitrogen gas, and this obligate anaerobic process accounts for up to half of the global nitrogen loss in surface environments. Yet its origin and evolution, which may give important insights into the biogeochemistry of early Earth, remain enigmatic. Here, we performed a comprehensive phylogenomic and molecular clock analysis of anammox bacteria within the phylum Planctomycetes. After accommodating the uncertainties and factors influencing time estimates, which include implementing both a traditional cyanobacteria-based and a recently developed mitochondria-based molecular dating approach, we estimated a consistent origin of anammox bacteria at early Proterozoic and most likely around the so-called Great Oxidation Event (GOE; 2.32-2.5 Ga) which fundamentally changed global biogeochemical cycles. We further showed that during the origin of anammox bacteria, genes involved in oxidative stress adaptation, bioenergetics, and anammox granules formation were recruited, which might have contributed to their survival on an increasingly oxic Earth. Our findings suggest the rising levels of atmospheric oxygen, which made nitrite increasingly available, was a potential driving force for the emergence of anammox bacteria. This is one of the first studies that link the GOE to the evolution of obligate anaerobic bacteria.

Metagenomic evidence of a novel family of anammox bacteria in a subsea environment

Bacteria in the order 'Candidatus Brocadiales' within the phylum Planctomycetes (Planctomycetota) have the remarkable ability to perform anaerobic ammonium oxidation (anammox). Two families of anammox bacteria with different biogeographical distributions have been reported, marine Ca. Scalinduaceae and freshwater Ca. Brocadiaceae. Here we report evidence of three new species within a novel genus and family of anammox bacteria, which were discovered in biofilms of a subsea road tunnel under a fjord in Norway. In this particular ecosystem, the nitrogen cycle is likely fuelled by ammonia from organic matter degradation in the fjord sediments and the rock mass above the tunnel, resulting in the growth of biofilms where anammox bacteria can thrive under oxygen limitation. We resolved several metagenome-assembled genomes (MAGs) of anammox bacteria, including three Ca. Brocadiales MAGs that could not be classified at the family level. MAGs of this novel family had all the diagnostic genes for a full anaerobic ammonium oxidation pathway in which nitrite was probably reduced by a NirK-like reductase. A survey of published molecular data indicated that this new family of anammox bacteria occurs in many marine sediments, where its members presumably would contribute to nitrogen loss.

Microbial Biogeochemical Cycling of Nitrogen in Arid Ecosystems

Arid ecosystems cover ∼40% of the Earth's terrestrial surface and store a high proportion of the global nitrogen (N) pool. They are low-productivity, low-biomass, and polyextreme ecosystems, i.e., with (hyper)arid and (hyper)oligotrophic conditions and high surface UV irradiation and evapotranspiration. These polyextreme conditions severely limit the presence of macrofauna and -flora and, particularly, the growth and productivity of plant species. Therefore, it is generally recognized that much of the primary production (including N-input processes) and nutrient biogeochemical cycling (particularly N cycling) in these ecosystems are microbially mediated. Consequently, we present a comprehensive survey of the current state of knowledge of biotic and abiotic N-cycling processes of edaphic (i.e., open soil, biological soil crust, or plant-associated rhizosphere and rhizosheath) and hypo/endolithic refuge niches from drylands in general, including hot, cold, and polar desert ecosystems. We particularly focused on the microbially mediated biological nitrogen fixation, N mineralization, assimilatory and dissimilatory nitrate reduction, and nitrification N-input processes and the denitrification and anaerobic ammonium oxidation (anammox) N-loss processes. We note that the application of modern meta-omics and related methods has generated comprehensive data sets on the abundance, diversity, and ecology of the different N-cycling microbial guilds. However, it is worth mentioning that microbial N-cycling data from important deserts (e.g., Sahara) and quantitative rate data on N transformation processes from various desert niches are lacking or sparse. Filling this knowledge gap is particularly important, as climate change models often lack data on microbial activity and environmental microbial N-cycling communities can be key actors of climate change by producing or consuming nitrous oxide (N₂O), a potent greenhouse gas.

Metabolic Diversity and Aero-Tolerance in Anammox Bacteria from Geochemically Distinct Aquifers

Anaerobic ammonium oxidation (anammox) is important for converting bioavailable nitrogen into dinitrogen gas, particularly in carbon-poor environments. However, the diversity and prevalence of anammox bacteria in the terrestrial subsurface-a typically oligotrophic environment-are little understood. To determine the distribution and activity of anammox bacteria across a range of aquifer lithologies and physicochemistries, we analyzed 16S rRNA genes and quantified hydrazine synthase genes and transcripts sampled from 59 groundwater wells and metagenomes and metatranscriptomes from an oxic-to-dysoxic subset. Data indicate that anammox and anammox-associated bacteria (class "Candidatus Brocadiae") are prevalent in the aquifers studied, and that anammox community composition is strongly differentiated by dissolved oxygen (DO), but not ammonia/nitrite. While "Candidatus Brocadiae" diversity decreased with increasing DO, "Candidatus Brocadiae" 16S rRNA genes and hydrazine synthase (hzsB) genes and transcripts were detected across a wide range of bulk groundwater DO concentrations (0 to 10 mg/L). Anammox genes and transcripts correlated significantly with those involved in aerobic ammonia oxidation (amoA), potentially representing a major source of nitrite for anammox. Eight "Candidatus Brocadiae" genomes (63 to 95% complete), representing 2 uncharacterized families and 6 novel species, were reconstructed. Six genomes have genes characteristic of anammox, all for chemolithoautotrophy. Anammox and aerotolerance genes of up to four "Candidatus Brocadiae" genomes were transcriptionally active under oxic and dysoxic conditions, although activity was highest in dysoxic groundwater. The coexpression of nrfAH nitrite reductase genes by "Candidatus Brocadiae" suggests active regeneration of ammonia for anammox. Our findings indicate that anammox bacteria contribute to loss of fixed N across diverse anoxic-to-oxic aquifer conditions, which is likely supported by nitrite from aerobic ammonia oxidation. IMPORTANCE Anammox is increasingly shown to play a major role in the aquatic nitrogen cycle and can outcompete heterotrophic denitrification in environments low in organic carbon. Given that aquifers are characteristically oligotrophic, anammox may represent a major route for the removal of fixed nitrogen in these environments, including agricultural nitrogen, a common groundwater contaminant. Our research confirms that anammox bacteria and the anammox process are prevalent in aquifers and occur across diverse lithologies (e.g., sandy gravel, sand-silt, and volcanic) and groundwater physicochemistries (e.g., various oxygen, carbon, nitrate, and ammonium concentrations). Results reveal niche differentiation among anammox bacteria largely driven by groundwater oxygen contents and provide evidence that anammox is supported by proximity to oxic niches and handoffs from aerobic ammonia oxidizers. We further show that this process, while anaerobic, is active in groundwater characterized as oxic, likely due to the availability of anoxic niches.

Diversity and Distribution of Anaerobic Ammonium Oxidation Bacteria in Hot Springs of Conghua, China

Anaerobic ammonium oxidation (anammox) is an important process of the nitrogen cycle, and the anammox bacteria have been studied in a wide variety of environments. However, the distribution, diversity, and abundance of anammox bacteria in hot springs remain enigmatic. In this study, the anammox process was firstly investigated in hot springs of Conghua, China. Anammox-like bacterial sequences that closely affiliated to “Candidatus Brocadia,” “Candidatus Kuenenia,” “Candidatus Scalindua,” “Candidatus Anammoxoglobus,” and “Candidatus Jettenia” were detected. Several operational taxonomic units (OTUs) from this study shared low sequence identities to the 16S rRNA gene of the known anammox bacteria, suggesting that they might be representing putative novel anammox bacteria. A quantitative PCR analysis of anammox-specific 16S rRNA gene confirmed that the abundance of anammox bacteria ranged from 1.60 × 10⁴ to 1.20 × 10⁷ copies L^–1. Nitrate was a key environmental factor defining the geographical distribution of the anammox bacterial community in the hot spring ecosystem. Dissolved inorganic carbon had a significant influence on anammox bacterial biodiversity. Our findings for the first time revealed that the diverse anammox bacteria, including putative novel anammox bacterial candidates, were present in Conghua hot spring, which extended the existence of anammox bacteria to the hot springs in China and expands our knowledge of the biogeography of anammox bacteria. This work filled up the research lacuna of anammox bacteria in Chinese hot spring habitat and would guide for enrichment strategies of anammox bacteria of Conghua hot springs.

Maintenance power requirements of anammox bacteria "Candidatus Brocadia sinica" and "Candidatus Scalindua sp."

Little is known about the cell physiology of anammox bacteria growing at extremely low growth rates. Here, "Candidatus Brocadia sinica" and "Candidatus Scalindua sp." were grown in continuous anaerobic membrane bioreactors (MBRs) with complete biomass retention to determine maintenance energy (i.e., power) requirements at near-zero growth rates. After prolonged retentostat cultivations, the specific growth rates (μ) of "Ca. B. sinica" and "Ca. Scalindua sp." decreased to 0.000023 h^-1 (doubling time of 1255 days) and 0.000157 h^-1 (184 days), respectively. Under these near-zero growth conditions, substrate was continuously utilized to meet maintenance energy demands (m_e) of 6.7 ± 0.7 and 4.3 ± 0.7 kJ mole of biomass-C^-1 h^-1 for "Ca. B. sinica" and "Ca. Scalindua sp.", which accorded with the theoretically predicted values of all anaerobic microorganisms (9.7 and 4.4 kJ mole of biomass-C^-1 h^-1at 37 °C and 28 °C, respectively). These m_e values correspond to 13.4 × 10^-15 and 8.6 × 10^-15 watts cell^-1 for "Ca. B. sinica" and "Ca. Scalindua sp.", which were five orders of magnitude higher than the basal power limit for natural settings (1.9 × 10^-19 watts cells^-1). Furthermore, the minimum substrate concentrations required for growth (S_min) were calculated to be 3.69 ± 0.21 and 0.09 ± 0.05 μM NO₂^- for "Ca. B. sinica" and "Ca. Scalindua sp.", respectively. These results match the evidence that "Ca. Scalindua sp." with lower maintenance power requirement and S_min are better adapted to energy-limited natural environments than "Ca. B. sinica", suggesting the importance of these parameters on ecological niche differentiation in natural environments.

Classification of uncultivated anammox bacteria and Candidatus Uabimicrobium into new classes and provisional nomenclature as Candidatus Brocadiia classis nov. and Candidatus Uabimicrobiia classis nov. of the phylum Planctomycetes and novel family Candidatus Scalinduaceae fam. nov to accommodate the genus Candidatus Scalindua

The phylum Planctomycetes is metabolically unique group of bacteria divided in two classes Planctomycetia and Phycisphaerae. Anaerobic ammonia-oxidizing (anammox) bacteria are the uncultured representatives of the phylum Planctomycetes. Anammox bacterial genera are placed in the family Candidatus (Ca.) Brocadiaceae of the order Ca. Brocadiales, assigned to the class Planctomycetia. Phylogenetic analysis, showed that the anammox bacteria and Ca. Uabimicrobium form a divergent clade from the rest of the cultured representatives of the phylum Planctomycetes. The phylogenetic study, pairwise distance and Average Amino acid Identity (AAI) showed that anammox bacteria don't belong to the classes Planctomycetia and Phycisphaerae. Anammox bacteria and Ca. Uabimicrobium form a deep-branching third clade in the phylogenetic analysis indicating that it is the most ancient third class within the phylum Planctomycetes. Phenotypic characters also separate anammox bacteria from classes Planctomycetia and Phycisphaerae. Therefore, based on phenotypic, phylogenetic, pairwise distance, AAI and phylogenomic analysis we propose a novel class Ca. Brocadiia to accommodate the order Ca. Brocadiales of anammox bacteria except Ca. Anammoximicrobium. Genera Ca. Jettenia, Ca. Anammoxoglobus, Ca. Kuenenia and Ca. Brocadia show their phylogenetic affiliation to the family Ca. Brocadiaceae. However, Ca. Scalindua showed a distant relationship with the family Ca. Brocadiaceae. Therefore, we suggest the exclusion of the genus Ca. Scalindua from the family Ca. Brocadiaceae; and propose its inclusion under a novel family with a provisional name as Ca. Scalinduaceae fam. nov. Similarly, Ca. Uabimicrobium amporphum showed distinct phylogenetic affiliation, therefore we propose a novel class Ca. Uabimicrobiia classis nov. to accommodate the genus Ca. Uabimicrobium.

Submerged plants alleviated the impacts of increased ammonium pollution on anammox bacteria and nirS denitrifiers in the rhizosphere

Excess nitrogen input into water bodies can cause eutrophication and affect the community structure and abundance of the nitrogen-transforming microorganisms; thus, it is essential to remove nitrogen from eutrophic water bodies. Aquatic plants can facilitate the growth of rhizosphere microorganisms. This study investigated the impact of ammonium pollution on the anammox and denitrifying bacteria in the rhizosphere of a cultivated submerged macrophyte, Potamogeton crispus (P. crispus) by adding three different concentrations of slow-release urea (0, 400, 600 mg per kg sediment) to the sediment to simulate different levels of nitrogen pollution in the lake. Results showed that the ammonium concentrations in the interstitial water under three pollution treatments were significantly different, but the nitrate concentration remained stable. The abundance of anammox 16S rRNA and nitrite reductase (nirS) gene in rhizosphere sediments exhibited no significant differences under the three pollution conditions. The increase in the nitrogen pollution levels did not significantly affect the growth of anammox bacteria and nirS denitrifying bacteria (denitrifiers). The change trend of the abundance ratio of (anammox 16S rRNA)/nirS in different nitrogen treatment groups on the same sampling date was very close, indicating that this ratio was not affected by ammonium pollution levels when P. crispus existed. The redundancy analysis showed that there was a positive correlation between the abundance of anammox 16S rRNA and nirS gene and that the abundance of these bacteria was significantly affected by the mole ratio of NH₄⁺/NO₃^-. This study reveals that submerged plants weaken the environmental changes caused by ammonia pollution in the rhizosphere, thereby avoiding strong fluctuation of anammox bacteria and nirS denitrifiers.

Nano zero-valent iron improves anammox activity by promoting the activity of quorum sensing system

The addition of nano zero-valent iron (nZVI) has been proven to improve the efficiency of the anammox process, however, the mechnism is not clear. Here, the effect of nZVI on anammox microbial community was studied by metagenomic sequencing methods. It was found that 50 mg/L nZVI indeed promoted the removal of NH₄⁺ and NO₂^- of the anammox reactor and significantly improved the relative abundance of AnAOB (Ca. Brocadia) from 42.1% to 52.5%. What's more, 50 mg/L nZVI increased the abundance of c-di-GMP synthesized protein from 148 rpmr to 252 rpmr in the microbial community and decreased the abundance of c-di-GMP degradation protein from 238 rpmr to 204 rpmr, which indirectly led to the enrichment of c-di-GMP in the microbial community. The enrichment of c-di-GMP reduced the motility of microorganisms in the reactor and promoted the secretion of extracellular polymers by bacteria, which is beneficial to the formation of sludge particles in the anammox reactor. In conclusion, this research clarified the mechanism of nZVI promoting the anammox process and provided theoretical guidance for the engineering application of anammox.

The potential contributions to organic carbon utilization in a stable acetate-fed Anammox process under low nitrogen-loading rates

The unique ability of Anammox bacteria to metabolize short-chain fatty acids have been demonstrated. However, the potential contributions of active Anammox species to carbon utilization in a mixotrophic Anammox-denitrification process are less well understood. In this study, we combined genome-resolved metagenomics and DNA stable isotope probing (DNA-SIP) to characterize an Anammox process fed with acetate under COD/TN ratios of around 0.30-0.40 and low nitrogen-loading rates. A draft genome of "Candidatus Jettenia caeni" and a novel species that was phylogenetically close to "Candidatus Brocadia sinica" were recovered. Essential genes encoding the key enzymes for acetate metabolism and dissimilatory nitrate reduction to ammonium were identified in the two Anammox draft genomes. The DNA-SIP revealed that Ignavibacterium, "Candidatus Jettenia caeni," Thauera, Denitratisoma, and Calorithrix predominantly contributed to organic carbon utilization in the acetate-fed Anammox process. In particular, the "Candidatus Jettenia caeni" accounted for a higher proportion of ¹³C-DNA communities than "Candidatus Brocadia sinica." This result well confirmed the theory of maintenance energy between the interspecies competition of the two Anammox species under low nitrogen-loading rates. Our study revealed its potential important role of the Anammox genus "Candidatus Jettenia" in the treatment of wastewater containing low organic matter and ammonia.

Distribution and Community Composition of Anammox Bacteria in Shallow Groundwater of the Kathmandu Valley, Nepal

The abundance and diversity of anaerobic ammonium oxidation (anammox) bacteria were assessed in 152 groundwater samples in the Kathmandu Valley, Nepal. Anammox bacterial 16S rRNA genes were detected in 54% (37/68) of samples collected in the dry season at 1.6×10⁵–8.8×10⁶ copies L^–1, and in 60% (50/84) of samples collected in the wet season at 4.3×10⁴–1.2×10⁷ copies L^–1. The 16S rRNA genes of “Candidatus Brocadia”, “Candidatus Anammoxoglobus”, and five new deduced anammox bacterial phylotypes were detected in the shallow groundwater samples. Diverse anammox bacteria were broadly distributed in the shallow groundwater aquifer of the Kathmandu Valley.

Glycogen metabolism of the anammox bacterium "Candidatus Brocadia sinica"

Presence of glycogen granules in anaerobic ammonium-oxidizing (anammox) bacteria has been reported so far. However, very little is known about their glycogen metabolism and the exact roles. Here, we studied the glycogen metabolism in "Ca. Brocadia sinica" growing in continuous retentostat cultures with bicarbonate as a carbon source. The effect of the culture growth phase was investigated. During the growing phase, intracellular glycogen content increased up to 32.6 mg-glucose (g-biomass dry wt)-1 while the specific growth rate and ATP/ADP ratio decreased. The accumulated glycogen begun to decrease at the onset of entering the near-zero growth phase and was consumed rapidly when substrates were depleted. This clearly indicates that glycogen was synthesized and utilized as an energy storage. The proteomic analysis revealed that "Ca. B. sinica" synthesized glycogen via three known glycogen biosynthesis pathways and simultaneously degraded during the progress of active anammox, implying that glycogen is being continuously recycled. When cells were starved, a part of stored glycogen was converted to trehalose, a potential stress protectant. This suggests that glycogen serves at least as a primary carbon source of trehalose synthesis for survival. This study provides the first physiological evidence of glycogen metabolism in anammox bacteria and its significance in survival under natural substrate-limited habitat.

Microbial diversity reveals the partial denitrification-anammox process serves as a new pathway in the first mainstream anammox plant

A full-scale sewage treatment plant in Xi'an city is discovered as the first mainstream anaerobic ammonia oxidation (anammox) treatment process in China. Whether its biological mechanism is the nitritation-anammox or partial denitrification (PD)-anammox brought violent controversy between two groups. As a third party, here we uncovered the mystery of the moving-bed biofilm reactor (MBBR) as a PD-anammox process by analyzing the diversity and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) of microbes in anoxic pond. Anammox bacteria was found in the MBBR anoxic tank, which abundance is 8.9 times of that in the common anaerobic-anoxic-oxic process, confirming the existence of anammox process. The denitrifying bacteria (DNB) content in the anoxic tank is 5.9 times of the content of ammonia oxidizing bacteria (AOB), thus the DNB-anammox system is proved at the microbial composition level. The PICRUSt analysis found that ammonium nitrogen is mainly derived from the deamination of urea. The functional genes NAR and AMO of DNB and AOB are 910.84 and 5.80 rpms, respectively. The NAR gene content is 157.0 times of the AMO gene content and it is proved at the genetic level that the nitrite in the anoxic pool is mainly derived from denitrification. This study demonstrated the feasibility and advantages of the PD-anammox in the anammox process, which is different from the traditional nitritation-anammox demonstrated in Strass Wastewater Treatment Plant, Austria and Changi Water Reclamation Plant, Singapore and provided an alternative option for the mainstream application of anammox.

Deciphering nitrogen removal mechanism through marine anammox bacteria treating nitrogen-laden saline wastewater under various phosphate doses: Microbial community shift and phosphate crystal

The effect of phosphate on marine anammox bacteria (MAB)-dominated anammox process in nitrogen-laden saline wastewater was first investigated. The activity of MAB was enhanced by dosing low concentrations of phosphate (5-30 mg/L PO₄^3--P), and the time of complete ammonium removal was shortened by 0.5 h. When PO₄^3--P exceeded 160 mg/L, the calcium magnesium phosphate precipitation was formed in the reactor. The contact between substrates and biomass was hindered by the sediments, and the nitrogen removal performance of MAB was also worsened. At 400 mg/L PO₄^3--P, the ammonium removal rate and nitrite removal rate decreased to 0.45 and 0.43 kg/(m³⋅d), respectively. During the 158-day operation, MAB was still the dominant strain, but its relative abundance decreased by 15.4% at 400 mg/L PO₄^3--P. Besides, the presence of sediments stimulated the production of extracellular polymeric substances and the maximum yield reached 11.25 mg/g⋅wet weight at 200 mg/L PO₄^3--P.

Probing the dynamics of three freshwater Anammox genera at different salinity levels in a partial nitritation and Anammox sequencing batch reactor treating landfill leachate

Partial nitritation/Anammox was applied to treat NaCl-amended landfill leachate. The reactor established robust nitrogen removal of 85.7 ± 2.4% with incremental salinity from 0.61% to 3.10% and achieved 0.91-1.05 kg N/m³/d at salinity of 2.96%-3.10%. Microbial community analysis revealed Nitrosomonas, Nitrospira, and denitrifiers occupied 4.1%, <0.2% and 10.9%, respectively. Salinity variations impelled the dynamics of Anammox bacteria. Jettenia shifted to Brocadia and Kuenenia at salinity of 0.61%-0.81%. Kuenenia outcompeted Brocadia and occupied 51.5% and 50.9% at salinity of 1.48%-1.54% and 2.96%-3.10%, respectively. High nitrite affinity and fast growth rate were proposed as key factors fostering Brocadia overgrew Jettenia. Functionalities of sodium-motive-force facilitated energy generation and intracellular osmotic pressure equilibrium regulation crucially determined Kuenenia's dominance at elevated salinity. Co-occurrence network further manifested beneficial symbiotic relationships boosted Kuenenia's preponderance. Knowledge gleaned deepen understanding on survival niches of freshwater Anammox genera at saline environments and lead to immediate benefits to its applications treating relevant wastewaters.

The effect of the COD: N ratio on mainstream deammonification in an integrated fixed-film activated sludge sequencing batch reactor

For eight months, a sequencing batch reactor (SBR) with integrated fixed-film activated sludge (IFAS) was operated in ambient temperature to study engineering and practical aspects of application of deammonification for mainstream conditions. For biofilm formation, K3 Kaldnes carriers were used, where the anaerobic ammonium oxidation (anammox) process can occur in deep layers of biofilm, while partial nitritation occurs in oxygen-rich outer layers. After the initial running phase of the reactor (Phase 1) to provide time for microorganisms to adapt, the COD: N ratio increased to around 2.6 in Phase 2 through reducing the ammonium concentration and increasing COD in synthetic wastewater to get closer to mainstream conditions. The total reaction time in each half-day batch cycle was kept 625 min throughout various phases, but the duration of intermittent aeration was regulated at 4 ± 1 min. While final nitrogen removal efficiency (NRE) for Phase 1 was 43%, at the end of Phase 2, it decreased to 37%. However, a maximum NRE at 90% was achieved during Phase 2. The identification of the responsible microorganisms was made through Fluorescence in situ hybridization (FISH), while Mixed Liquor Suspended Solid (MLSS) and Mixed Liquor Volatile Suspended Solid (MLVSS) was used to estimate the physical presence of bacteria. Ammonium oxidizing bacteria (AOB) and anaerobic ammonia-oxidizing bacteria (AnAOB) were dominant bacteria, respectively. The adverse effects of a gradual increase of COD: N ratio from 0.17 to more than 2.0 caused a decline in NRE to around 15%.

Specific and effective detection of anammox bacteria using PCR primers targeting the 16S rRNA gene and functional genes

Anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the nitrogen cycle by coupling ammonium and nitrite to produce dinitrogen gas (N₂). Polymerase chain reaction (PCR) is a fast, simple, and sensitive method that is widely used to assess the diversity, abundance, and activity of the slow-growing bacteria. In this review, we summarize and evaluate the wide variety of PCR primers targeting the 16S rRNA gene and functional genes (hzo, nir, and hzs) of anammox bacteria for their effectiveness and efficiencies in detecting this group of bacteria in different sample types. Furthermore, the efficiencies of different universal high-throughput sequencing 16S rRNA gene primers in anammox bacteria investigations were also evaluated to provide a reference for primer selection. Based on our in silico evaluation results, none of the 16S rRNA gene primers could recover all of the known anammox bacteria, but multiple hzo and hzs gene primers could accomplish this task. However, uncertain copies (1-3 copies) of hzo genes were identified in the genomes, and the hydrazine oxidation reaction catalyzed by hydrazine oxidoreductases (HZOs) can also be catalyzed by other hydroxylamine oxidoreductases (HAOs) in anammox bacteria, which can potentially result in large deviations in hzo-based qPCR and RT-qPCR analyses and results. Therefore, the use of optimal primers targeting unique hzs genes are recommended, although the efficiencies of these newly designed primers need further verification in practical applications. This article provides comprehensive information for the effective and specific detection of anammox bacteria using specific primers targeting the 16S rRNA gene and functional genes and serves as a basis for future high-quality primer design.

Phase Transitions by an Abundant Protein in the Anammox Extracellular Matrix Mediate Cell-to-Cell Aggregation and Biofilm Formation

By employing biophysical and liquid-liquid phase separation concepts, this study revealed how a highly abundant extracellular protein enhances the key environmental and industrial bioprocess of anaerobic ammonium oxidation (anammox). Extracellular proteins of environmental biofilms are understudied and poorly annotated in public databases. Understanding the function of extracellular proteins is also increasingly important for improving bioprocesses and resource recovery. Here, protein functions were assessed based on theoretical predictions of intrinsically disordered domains, known to promote adhesion and liquid-liquid phase separation, and available surface layer protein properties. A model is thus proposed to explain how the protein promotes aggregation and biofilm formation by extracellular matrix remodeling and phase transitions. This work provides a strong foundation for functional investigations of extracellular proteins involved in biofilm development.

This study describes the first direct functional assignment of a highly abundant extracellular protein from a key environmental and biotechnological biofilm performing an anaerobic ammonium oxidation (anammox) process. Expression levels of Brosi_A1236, belonging to a class of proteins previously suggested to be cell surface associated, were in the top one percentile of all genes in the “Candidatus Brocadia sinica”-enriched biofilm. The Brosi_A1236 structure was computationally predicted to consist of immunoglobulin-like anti-parallel β-strands, and circular dichroism conducted on the isolated surface protein indicated that β-strands are the dominant higher-order structure. The isolated protein was stained positively by the β-sheet-specific stain thioflavin T, along with cell surface- and matrix-associated regions of the biofilm. The surface protein has a large unstructured content, including two highly disordered domains at its C terminus. The disordered domains bound to the substratum and thereby facilitated the adhesion of negatively charged latex microspheres, which were used as a proxy for cells. The disordered domains and isolated whole surface protein also underwent liquid-liquid phase separation to form liquid droplets in suspension. Liquid droplets of disordered protein wet the surfaces of microspheres and bacterial cells and facilitated their coalescence. Furthermore, the surface layer protein formed gels as well as ordered crystalline structures. These observations suggest that biophysical remodeling through phase transitions promotes aggregation and biofilm formation.

The interaction of dissolved organic nitrogen removal and microbial abundance in iron-filings based green environmental media for stormwater treatment

Nonpoint sources pollution from agricultural crop fields and urbanized regions oftentimes have elevated concentrations of dissolved organic nitrogen (DON) in stormwater runoff, which are difficult for microbial communities to decompose. The impact of elevated DON can be circumvented through the use of green sorption media, such as Biosorption Activated Media (BAM) and Iron-Filing Green Environmental Media (IFGEM), which, as integral parts of microbial ecology, can contribute to the decomposition of DON. To compare the fate, transport, and transformation of DON in green sorption media relative to natural soil (control), a series of fixed-bed columns, which contain natural soil, BAM, and two types of IFGEM, respectively, were constructed to compare nutrient removal efficiency under three distinct stormwater influent conditions containing nitrogen and phosphorus. The interactions among six microbial species, including ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, complete ammonia oxidation (comammox) bacteria, anaerobic ammonium oxidation (anammox) bacteria, dissimilatory nitrate reduction to ammonium bacteria, and iron-reducing bacteria, were further analyzed from microbial ecology perspectives to determine the DON impact on nutrient removal in BAM and IFGEM. Natural soil was only able to achieve adequate DON transformation at the influent condition of lower nutrient concentration. However, the two types of IFGEM showed satisfactory nutrient removals and achieved greater transformation of DON relative to BAM when treating stormwater in all three influent conditions.

Stability of microbial functionality in anammox sludge adaptation to various salt concentrations and different salt-adding steps

The stability of community functioning in anaerobic ammonia oxidation (anammox) sludge adaptation to various salinity changes are concerned but not fully explored. In this study, two anammox reactors were designed in response to different salt levels and salt-adding methods. The reactor PI, run with small stepwise salt increments (0.5%-1.0%), removed >90% of nitrite and ammonium in the influent over the range of 0%-4% salt. By contrast, the reactor SI, run with a sharp salt increment (>2.5%), exhibited a reduced performance (by up to 44%) over the same salt range with a new steady state. The observed resilience times after salt perturbations indicated that the PI reactor recovered substantially and rapidly at all imposed salt levels. Principal coordinates analysis of 16S rRNA gene amplicon sequences revealed that bacterial community structures of the anammox sludge altered conspicuously in response to the salinity changes. However, quantitative PCR analysis showed that the shift in copy number of studied nitrogen-converting genes encoding hydrazine synthase (hzsA), bacterial and archaeal ammonia monooxygenases (amoA), nitrite oxidoreductase (nxrB), nitrite reductase (nirK), and nitrous oxide reductase (nosZ) was not significant (p > 0.05) in anammox sludge across the salt levels of 0.5%-4%, which suggests the stability of microbial community functioning in the osmoadaptation processes. The freshwater anammox Ca. Kuenenia showed high osmoadaptation by potentially adopting both high-salt-in and low-salt-in strategies to dominate in both reactors. The quantitative transcript analysis showed that the active anammox bacteria represented by hzsA transcripts in the SI reactor were approximately two orders of magnitude lower than those in the PI reactor during the long-term exposure to 4% salinity, manifesting the influence by the salt-increasing methods. These results provided new insight into osmo-adaptation of the anammox microbiome and will be useful for managing salinity effects on nitrogen removal processes.

Diversity of sediment associated Planctomycetes and its related phyla with special reference to anammox bacterial community in a high Arctic fjord

The fjords of west Spitsbergen Svalbard, Arctic Norway, are undergoing a transformation as the impact of nutrient rich warmer Atlantic water is significantly altering the primary production and subsequently the carbon pool. Members of the phylum Planctomycetes are ubiquitous in marine systems and are important in the mineralization of organic matter. Hence, the phylogenetic diversity and distribution pattern of Planctomycetes in the surface sediments of a high Arctic fjord, the Kongsfjorden were studied. Further, considering the release of ammonium as a part of mineralization, the diversity of bacterial community involved in anaerobic ammonium oxidation (anammox) was also evaluated. The highly diverse Planctomycetes community, which consisted mainly of uncultivated and uncharacterized Planctomycetes, was observed in the study area with a total of 162 OTUs. The major genera observed were Blastopirellula (13.3%), Gimesia (13%), Rhodopirellula (10%), Planctomicrobium (2%) and Thermogutta (1.6%). Functional prediction revealed the dominance of carbohydrate metabolism genes and the presence of gene clusters for production of secondary metabolites and xenobiotic degradation. Anammox bacterial sequences were detected from all the samples with a total of 52 OTUs. Most of the OTUs belonged to the genus Candidatus Scalindua and three distinct clusters were observed in the phylogenetic tree, (a) Ca. Scalindua brodae (49%), (b) Ca. Scalindua wagneri (31%) and (c) Ca. Scalindua marina (12%) based on their phylogenic distance. Our findings suggest the existence of highly diverse Planctomycetes and anammox bacterial community with regional variants in the sediments of Kongsfjorden.

Comparative Genome-Centric Analysis of Freshwater and Marine ANAMMOX Cultures Suggests Functional Redundancy in Nitrogen Removal Processes

There is a lack of understanding of the interaction between anammox bacteria and the flanking microbial communities in both freshwater (non-saline) and marine (saline) ecosystems. Here, we present a comparative genome-based exploration of two different anammox bioreactors, through the analysis of 23 metagenome-assembled genomes (MAGs), 12 from freshwater anammox reactor (FWR), and 11 from marine anammox reactor (MWR). To understand the contribution of individual members to community functions, we applied the index of replication (iRep) to determine bacteria that are actively replicating. Using genomic content and iRep information, we provided a potential ecological role for the dominant members of the community based on the reactor operating conditions. In the non-saline system, anammox (Candidatus Brocadia sinica) and auxotrophic neighboring bacteria belonging to the phyla Ignavibacteriae and Chloroflexi might interact to reduce nitrate to nitrite for direct use by anammox bacteria. Whereas, in the saline reactor, anammox bacterium (Ca. Scalindua erythraensis) and flanking community belonging to phyla Planctomycetes (different than anammox bacteria)—which persistently growing in the system—may catabolize detritus and extracellular material and recycle nitrate to nitrite for direct use by anammox bacteria. Despite different microbial communities, there was functional redundancy in both ecosystems. These results signify the potential application of marine anammox bacteria for treating saline N-rich wastewaters.

Effects of Potamogeton crispus decline in the rhizosphere on the abundance of anammox bacteria and nirS denitrifying bacteria☆

Bacteria involved with ecosystem N cycling in the rhizosphere of submerged macrophytes are abundant and diverse. Any declines of submerged macrophytes can have a great influence on the abundance and diversity of denitrifying bacteria and anammox bacteria. Natural decline, tardy decline, and sudden decline methods were applied to cultivated Potamogeton crispus. The abundance of anammox bacteria and nirS denitrifying bacteria in rhizosphere sediment were detected using real-time fluorescent quantitative PCR of 16S rRNA, and phylogenetic trees were constructed to analyze the diversities of these two microbes. The results indicated that the concentration of NH₄⁺ in pore water gradually increased with increasing distances from the roots, whereas, the concentration of NO₃^- showed a reverse trend. The abundance of anammox bacteria and nirS denitrifying bacteria in sediment of declined P. crispus populations decreased significantly over time. The abundance of these two microbes in the sudden decline group were significantly higher (P > 0.05) than the other decline treatment groups. Furthermore, the abundances of these two microbes were positively correlated, with RDA analyses finding the mole ratio of NH₄⁺/NO₃^- being the most important positive factor affecting microbe abundance. Phylogenetic analysis indicated that the anammox bacteria Brocadia fuigida and Scalindua wagneri, and nirS denitrifying bacteria Herbaspirillum and Pseudomonas, were the dominant species in declined P. crispus sediment. We suggest the sudden decline of submerged macrophytes would increase the abundance of anammox bacteria and denitrifying bacteria in a relatively short time.

Dispersal limitation drives biogeographical patterns of anammox bacterial communities across the Yangtze River

Over the past few decades, anaerobic ammonium oxidation (anammox) has been extensively documented at different scales in natural ecosystems. Previous studies have stated that the community composition of anammox bacteria is shaped mainly by environmental factors, whereas spatial factors have been largely overlooked. This study investigated biogeographical patterns of anammox bacterial communities using 42 sediment samples along a 4300-km stretch of the Yangtze River, the longest river in Asia. A significant distance-decay relationship was observed for anammox bacterial community similarity, which was significantly influenced by mean dendritic distance rather than environmental factors. This implied that dispersal limitation plays an important role in shaping biogeographical pattern of anammox community. Furthermore, our results revealed that neutral processes played vital role in shaping community assembly of anammox bacteria, and their communities were seriously dispersal limited. These findings contrast with previous studies on community similarities between broad taxonomic groups, which are mainly determined by niche-based selection owing to greater niche distances within broad taxonomic groups than in anammox bacteria. Importantly, the slope of the distance-decay curve was much steeper than previously reported for whole bacteria, which indicating the species turnover rate of anammox bacterial community was significantly higher than that of the whole bacterial community. Anammox bacteria harbor strong adhesion ability and low dispersal potential, and ultimately exhibited a high species turnover rate. Together, in the context of biogeography, our results highlight the importance of dispersal limitation in shaping the biogeographical pattern of anammox bacterial community.

Ecological niche differentiation among anammox bacteria

Anaerobic ammonium oxidizing (anammox) bacteria can directly convert ammonium and nitrite to nitrogen gas anaerobically and were responsible for a substantial part of the fixed nitrogen loss and re-oxidation of nitrite to nitrate in freshwater and marine ecosystems. Although a wide variety of studies have been undertaken to investigate the abundance and biodiversity of anammox bacteria so far, ecological niche differentiation of anammox bacteria is still not fully understood. To assess their growth behavior and consequent population dynamics at a given environment, the Monod model is often used. Here, we summarize the Monod kinetic parameters such as the maximum specific growth rate (μ_max) and the half-saturation constant for nitrite (K_NO2-) and ammonium (K_NH4+) of five known candidatus genera of anammox bacteria. We also discuss potential pivotal environmental factors and metabolic flexibility that influence the community compositions of anammox bacteria. Particularly biodiversity of the genus "Scalindua" might have been largely underestimated. Several anammox bacteria have been successfully enriched from various source of biomass. We reevaluate their enrichment methods and culture medium compositions to gain a clue of niche differentiation of anammox bacteria. Furthermore, we formulate the current issues that must be addressed. Overall this review re-emphasizes the importance of enrichment cultures (preferably pure cultures), physiological characterization and direct microbial competition studies using enrichment cultures in laboratories.

Application of an enrichment culture of the marine anammox bacterium "Ca. Scalindua sp. AMX11" for nitrogen removal under moderate salinity and in the presence of organic carbon

Seawater can be directly used for toilet flushing in coastal areas to reduce our dependence on desalination and freshwater resources. The presence of high-salt content in the generated wastewater from seawater toilet flushing could limit the performance of conventional biological nitrogen removal processes. Anaerobic ammonium oxidation (anammox) process is regarded as one of the most energy-efficient process for nitrogen removal from N-rich waste streams. In this study, we demonstrated the application of a novel marine anammox bacterium (Candidatus Scalindua sp. AMX11) in a membrane bioreactor (MBR) to treat moderate-saline (∼1.2% salinity) and N-rich organic (2 mM acetate) solution, prepared using real seawater. The MBR showed stable performance with nitrogen removal rate of 0.3 kg-N m^-3 d^-1 at >90% N-removal efficiency. Furthermore, results of ¹⁵N stable isotope experiments revealed that anammox bacteria was mainly responsible for respiratory ammonification through NO₃^- reduction to NH₄⁺ via NO₂^-, and the by-products of respiratory ammonification were used as substrates by anammox bacteria. The dominant role of anammox bacteria in nitrogen removal under saline and organic conditions was further confirmed by genome-centric combined metagenomics and meta-transcriptomic approach. Taken together, these results highlight the potential application of marine anammox bacteria for treating saline wastewater generated from seawater toilet flushing practices.

Biogeographic pattern of the nirS gene-targeted anammox bacterial community and composition in the northern South China Sea and a coastal Mai Po mangrove wetland

Functional genes, namely hzo/hao, nirS, hzs, and ccs gene, are efficient with high specificity for detecting anammox bacteria. Sc-nirS and An-nirS primer sets were proposed for targeting Scalindua/non-Scalindua anammox bacterial groups; previously, they have not been assessed for biogeographic study on marine-terrestrial transitional systems, specifically marine and terrestrial ecosystems. Here, we report phylogenetic distribution pattern of anammox bacteria in both northern South China Sea (nSCS) and Mai Po wetland (a coastal mangrove) using nirS gene-based primers. A well-delineated biogeographic distribution pattern from ocean to continental shelf was evident by combining both gene-based analyses as previously depicted using 16S rRNA as the biomarker. Furthermore, factors affecting the abundance and composition of An-nirS genes in Mai Po wetland were identified as substrate (NO₃^-/NO₂^- concentration) and anoxic/oxic condition in association to depth. An-nirS gene abundance was from 2.6 × 10³ to 1.2-1.4 × 10⁴ copies/g dry sediment in nSCS; and it was around 5 × 10³ and 1-2 × 10⁴ copies/g dry sediment in surface and subsurface sediments of Mai Po wetland, respectively. In addition, nirS gene abundance and distribution pattern of denitrifiers and anammox bacteria in the wetland indicates a competition relationship between them. Mangrove vegetation affected the community composition of An-nirS gene considerably, and a more homogeneous distribution pattern was observed in the mangrove forest than intertidal mudflats. Sc/An-nirS gene-based biogeographic insights on anammox bacteria have shed lights on the compositional and potential functional dynamics and emphasized the importance of molecular tools on refining the current microbial ecological patterns.

Human activities aggravate nitrogen-deposition pollution to inland water over China

In the past three decades, China has built more than 87 000 dams with a storage capacity of ≈6560 km3 and the total surface area of inland water has increased by 6672 km2. Leaching of N from fertilized soils to rivers is the main source of N pollution in China, but the exposure of a growing inland water area to direct atmospheric N deposition and N leaching caused by N deposition on the terrestrial ecosystem, together with increased N deposition and decreased N flow, also tends to raise N concentrations in most inland waters. The contribution of this previously ignored source of  N deposition to freshwaters is estimated in this study, as well as mitigation strategies. The results show that the annual amounts of N depositions ranged from 4.9 to 16.6 kg · ha-1 · yr-1 in the 1990s to exceeding 20 kg · ha-1 · yr-1 in the 2010s over most of regions in China, so the total mass of ΔN (the net contribution of N deposition to the increase in N concentration) for lakes, rivers and reservoirs change from 122.26 Gg N · yr-1 in the 1990s to 237.75 Gg N · yr-1 in the 2010s. It is suggested that reducing the N deposition from various sources, shortening the water-retention time in dams and decreasing the degree of regulation for rivers are three main measures for preventing a continuous increase in the N-deposition pollution to inland water in China.

Increased replication of dissimilatory nitrate-reducing bacteria leads to decreased anammox bioreactor performance

BACKGROUND

Anaerobic ammonium oxidation (anammox) is a biological process employed to remove reactive nitrogen from wastewater. While a substantial body of literature describes the performance of anammox bioreactors under various operational conditions and perturbations, few studies have resolved the metabolic roles of their core microbial community members.

RESULTS

Here, we used metagenomics to study the microbial community of a laboratory-scale anammox bioreactor from inoculation, through a performance destabilization event, to robust steady-state performance. Metabolic analyses revealed that nutrient acquisition from the environment is selected for in the anammox community. Dissimilatory nitrate reduction to ammonium (DNRA) was the primary nitrogen removal pathway that competed with anammox. Increased replication of bacteria capable of DNRA led to the out-competition of anammox bacteria, and the loss of the bioreactor's nitrogen removal capacity. These bacteria were highly associated with the anammox bacterium and considered part of the core microbial community.

CONCLUSIONS

Our findings highlight the importance of metabolic interdependencies related to nitrogen- and carbon-cycling within anammox bioreactors and the potentially detrimental effects of bacteria that are otherwise considered core microbial community members.

Spatiotemporal distribution of nitrogen biogeochemical processes in the coastal regions of northern Beibu Gulf, south China sea

Nitrogen biogeochemistry occupies a central role in nitrogen cycles and exerts a significant influence on primary productivity and global carbon cycles. In order to better understand the nitrogen biogeochemistry in coastal regions, spatiotemporal nitrogen fixation, denitrification and anammox were investigated in the coastal regions of northern Beibu Gulf (NBG), South China Sea (SCS). Nitrogen fixation was mainly detected in the water column of outer bays, attributed to the low nitrate concentration and low N/P (N/P < 16). Comparisons of the nitrogen fixation rates between unicellular (<10 mm) and the filamentous diazotrophs (>10 mm) indicated that the contribution of unicellular diazotrophs was more important than filamentous diazotrophs. Besides, field investigation revealed that Richelia was the dominant species in filamentous diazotrophs. On the other hand, both denitrification and anammox were found in the surface sediment and denitrification dominated the nitrogen loss process. Denitrification was mainly related to the nitrate concentration in pore water and organic matter in the sediment, while anammox was mainly regulated by the concentration of nitrate and nitrite in pore water. Additionally, temperature, dissolved oxygen (DO) and salinity also had an impact on denitrification and anammox. The net areal yield of nitrogen biogeochemical processes was estimated to be -1079t/a, as an important pathway of nitrogen removal. This study adds to the knowledge of nitrogen biogeochemistry in the nutrient-replete coastal region and highlights its significance in such an environment.