Ammonia-oxidizing bacteria dominate ammonia oxidation in a full-scale wastewater treatment plant revealed by DNA-based stable isotope probing

Multi-omics illuminates the functional significance of previously unknown species in a full-scale landfill leachate treatment plant

Landfill leachate treatment plants (LLTPs) harbor a vast reservoir of uncultured microbes, yet limited studies have systematically unraveled their functional potentials within LLTPs. Combining 36 metagenomic and 18 metatranscriptomic datasets from a full-scale LLTP, we unveiled a double-edged sword role of unknown species in leachate biotreatment and environmental implication. We identified 655 species-level genome bins (SGBs) spanning 47 bacterial and 3 archaeal phyla, with 75.9 % unassigned to any known species. Over 90 % of up-regulated functional genes in biotreatment units, compared to the leachate influent, were carried by unknown species and actively participated in carbon, nitrogen, and sulfur cycles. Approximately 79 % of the 37,366 carbohydrate active enzymes (CAZymes), with ∼90 % novelty and high expression, were encoded by unknown species, exhibiting great potential in biodegrading carbohydrate compounds linked to human meat-rich diets. Unknown species offered a valuable genetic resource of thousands of versatile, abundant, and actively expressed metabolic gene clusters (MGCs) and biosynthetic gene clusters (BGCs) for enhancing leachate treatment. However, unknown species may contribute to the emission of hazardous N2O/H2S and represented significant reservoirs for antibiotic-resistant pathogens that posed environmental safety risks. This study highlighted the significance of considering both positive and adverse effects of LLTP microbes to optimize LLTP performance.

Synergy between Nitrogen Removal and Fermentation Bacteria Ensured Efficient Nitrogen Removal of a Mainstream Anammox System at Low Temperatures

Simultaneous partial nitrification, anammox, denitrification, and fermentation (SNADF) is a novel process achieving simultaneous advanced sludge reduction and nitrogen removal. The influence of low temperatures on the SNADF reactor was explored to facilitate the application of mainstream anammox. When temperature decreased from 32 to 16 °C, efficient nitrogen removal was achieved, with a nitrogen removal efficiency of 81.9-94.9%. Microbial community structure analysis indicated that the abundance of Candidatus Brocadia (dominant anaerobic ammonia oxidizing bacteria (AnAOB) in the system) increased from 0.03% to 0.18%. The abundances of Nitrospira and Nitrosomonas increased from 1.6% and 0.16% to 2.5% and 1.63%, respectively, resulting in an increase in the ammonia-oxidizing bacteria (AOB) to nitrite-oxidizing bacteria (NOB) abundance ratio from 0.1 to 0.64. This ensured sufficient nitrite for AnAOB, promoting nitrogen removal. In addition, Candidatus Competibacter, which plays a role in partial denitrification, was the dominant denitrification bacteria (DNB) and provided more nitrite for AnAOB, facilitating AnAOB enrichment. Based on the findings from microbial correlation network analysis, Nitrosomonas (AOB), Thauera, and Haliangium (DNB), and A4b and Saprospiraceae (fermentation bacteria), were center nodes in the networks and therefore essential for the stability of the SNADF system. Moreover, fermentation bacteria, DNB, and AOB had close connections in substrate cooperation and resistance to adverse environments; therefore, they also played important roles in maintaining stable nitrogen removal at low temperatures. This study provided new suggestions for mainstream anammox application.

Multidrug-resistant plasmid RP4 inhibits the nitrogen removal capacity of ammonia-oxidizing archaea, ammonia-oxidizing bacteria, and comammox in activated sludge

In wastewater treatment plants (WWTPs), ammonia oxidation is primarily carried out by three types of ammonia oxidation microorganisms (AOMs): ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and comammox (CMX). Antibiotic resistance genes (ARGs), which pose an important public health concern, have been identified at every stage of wastewater treatment. However, few studies have focused on the impact of ARGs on ammonia removal performance. Therefore, our study sought to investigate the effect of the representative multidrug-resistant plasmid RP4 on the functional microorganisms involved in ammonia oxidation. Using an inhibitor-based method, we first evaluated the contributions of AOA, AOB, and CMX to ammonia oxidation in activated sludge, which were determined to be 13.7%, 41.1%, and 39.1%, respectively. The inhibitory effects of C2H2, C8H14, and 3,4-dimethylpyrazole phosphate (DMPP) were then validated by qPCR. After adding donor strains to the sludge, fluorescence in situ hybridization (FISH) imaging analysis demonstrated the co-localization of RP4 plasmids and all three AOMs, thus confirming the horizontal gene transfer (HGT) of the RP4 plasmid among these microorganisms. Significant inhibitory effects of the RP4 plasmid on the ammonia nitrogen consumption of AOA, AOB, and CMX were also observed, with inhibition rates of 39.7%, 36.2%, and 49.7%, respectively. Moreover, amoA expression in AOB and CMX was variably inhibited by the RP4 plasmid, whereas AOA amoA expression was not inhibited. These results demonstrate the adverse environmental effects of the RP4 plasmid and provide indirect evidence supporting plasmid-mediated conjugation transfer from bacteria to archaea.

Ubiquitous occurrence and functional dominance of comammox Nitrospira in full-scale wastewater treatment plants

The recent discovery of complete ammonia oxidation (comammox) bacteria has fundamentally upended the traditional two-step nitrification conception, but their functional importance in wastewater treatment plants (WWTPs) is still poorly understood. This study investigated distributions of comammox Nitrospira, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in activated sludge samples collected from 25 full-scale WWTPs. Using quantitative PCR (qPCR) and 16S rRNA gene amplicon sequencing, our results revealed that comammox Nitrospira ubiquitously occurred in all of 25 WWTPs and even outnumbered AOB and AOA with an average abundance of 1∼183 orders of magnitude higher in 19 WWTPs. Moreover, DNA-based stable isotope probing (DNA-SIP) assays validated that comammox Nitrospira actively participated in ammonia oxidation in the three microcosms seeding with activated sludge from three typical WWTPs, in which the ratios of comammox amoA to AOB amoA were at the range of 1∼10, 10∼100 and >100, respectively. Phylogenetic analysis in heavy fractions further indicated that Nitrospira nitrosa (N. nitrosa) was the dominant and active species. We quantified the contribution of ammonia oxidizers based on the currently available kinetic parameters of the representative species and found that comammox made major contributions to ammonia oxidation than other nitrifiers (5 ∼ 106 times that of AOB). The findings not only demonstrate the ubiquitous occurrence of comammox, but also highlight their functional dominance in ammonia oxidation in WWTPs.

Effects of dam building on the occurrence and activity of comammox bacteria in river sediments and their contribution to nitrification

The recent discovery of complete ammonia oxidizers (comammox) has fundamentally changed our understanding of nitrification. However, studies on the occurrence and activity of comammox bacteria and their contribution to nitrification remain unclear. Here, we investigated the abundance, activity, and diversity of comammox bacteria and their contribution to nitrification in sediments from dammed rivers in winter and summer. Our results indicated that comammox clade A was ubiquitous in all sediment samples and the community structure in comammox varied between the upper and lower reaches, but not on the time scale (winter and summer). Comammox activity in the dammed river sediments in summer was prominently higher than in winter (summer: 1.08 ± 0.52; winter: 0.197 ± 0.148 mg N kg-1 day-1). Furthermore, the activity of comammox bacteria in summer appeared higher in the vicinity of the dammed river and in the Sanjiang estuary, which is located downstream of the dammed river. The activity of ammonia-oxidizing bacteria (AOB) (0.77 ± 0.478 mg N kg-1 day-1) was higher compared to comammox (0.639 ± 0.588 mg N kg-1 day-1) and ammonia-oxidizing archaea (AOA) (0.026 ± 0.022 mg N kg-1 day-1) in both winter and summer. In terms of contribution to the nitrification process, AOB (winter: 67.13 ± 12.21 %; summer: 50.57 ± 16.14 %) outperformed comammox (winter: 28.59 ± 12.51 %; summer: 48.38 ± 16.62 %) and AOA (winter: <7.39 %; summer: <2.09 %). These findings indicated that the nitrification process in dammed river sediments was mainly dominated by AOB. Additionally, comammox activity was significantly affected by temperature and NH4+, suggesting that these variables were key determinants of the niche partitioning of comammox. Collectively, our findings provide novel perspectives into the widespread distribution and contribution of comammox to nitrification in dammed river ecosystems, thus broadening our understanding of the nitrification processes.

Superior nitrogen removal and efficient sludge reduction via partial nitrification-anammox driven by addition of sludge fermentation products for real sewage treatment

Efficient retention and enrichment of anammox bacteria (AnAOB) are essential for the application of municipal wastewater anammox. Herein, an innovative process for highly enriching AnAOB within suspended carrier was developed in a single-stage anaerobic/oxic/anoxic reactor with 5.5 % carrier filling ratio for real sewage. Addition of sludge fermentation products promoted stable maintenance of partial nitrification (nitrite accumulation rate > 90.0 %) and achieved efficient external sludge reduction (27.6-37.9 %). Continuous nitrite supply and carrier addition promoted AnAOB enrichment (2.4 × 1011 gene copies/g dry sludge). Candidatus Brocadia was the predominant bacteria in carriers (18.6 %). The average effluents of total inorganic nitrogen (TIN) and NH4+-N were 1.9 and 0.8 mg/L with removal rates of 97.0 % and 98.7 %. In the anoxic stage, TIN removal rate reached 71.5 %, and the proportion of anammox to nitrogen removal accounted for 82.7 %. This study broadens the application of mainstream sewage anammox and the resource utilization of waste activated sludge.

Novel database and cut-off value for bacterial amoA gene revealed a spatial variability pattern of the ammonia-oxidizing bacteria community from river to sea

Ammonia-oxidizing bacteria (AOB) catalyze the first step of nitrification, oxidizing ammonia to nitrite, and are characterized by amoA gene encoding ammonia monooxygenase. To analyze the AOB community effectively, an integral taxonomy database containing 14,058 amoA sequences and the optimal cut-off value at 95 % for OTU clustering were determined. This method was evaluated to be efficient by the analysis of environmental samples from the river, estuary, and sea. Using this method, a significant spatial variance of the AOB community was found. The diversity of AOB was highest in the estuary and lowest in the ocean. Nitrosomonas were the predominant AOB in the sediments of the freshwater river and estuary. Nearly all the AOB-amoA sequences belonged to uncultured bacterium in the sediments of deep sea. In general, an integral AOB taxonomic database and a suitable cut-off value were constructed for the comprehensive exploration of the diversity of AOB from river to sea.

Activity enhancement and the anammox mechanism under low temperature via PVA-SA and nano Fe2O3-PVA-SA entrapped beads

Anaerobic ammonia-oxidizing bacteria (AAOB) have a long growth time and low activity at low temperatures. In suspended systems, sludge is easily lost, which limits the mainstream application of anaerobic ammonia oxidation (anammox).Entrapment provides effective ideas for solving these problems. In this study, polyvinyl‑sodium alginate (PVA-SA) and nano Fe₂O₃-PVA-SA entrapment beads were prepared to discuss the effectiveness of entrapment enhanced anammox sludge at low temperatures. The differences in the entrapped beads and granules were compared to analyze the strengthening mechanism. The results show that the nitrogen removal performance of granules, PVA-SA and nano Fe₂O₃-PVA-SA entrapped beads, first decreased and then increased during the cooling and low-temperature operation. Nano Fe₂O₃-PVA-SA entrapped beads showed the smallest decline and the highest degree of recovery. Reaction metering ratio (△NO₂^--N/△NH₄⁺-N and △NO₃^--N/△NH₄⁺-N) showed that entrapment could realize Nitrite oxidizing bacteria (NOB) inhibition and improve the activity of denitrifying bacteria (DNB) to promote the removal of total nitrogen by providing a strict anaerobic environment. The results demonstrate that entrapment is beneficial for maintaining the content of heme c, specifically, nano Fe₂O₃ can stimulate its production, and is beneficial for alleviating the reduction of hydrazine dehydrogenase (HDH) enzyme activity. The extracellular polymeric substances (EPS) content and analysis showed that entrapment does not change the composition of EPS, and can maintain the EPS content. Nano Fe₂O₃ can stimulate AAOB to secrete more EPS to maintain sludge stability. From a molecular perspective, entrapment can maintain the expression of functional genes, promote the enrichment of AAOB, thus improving the nitrogen removal performance from the dual perspectives of "quality" and "quantity".

Comammox bacteria predominate among ammonia-oxidizing microorganisms in municipal but not in refinery wastewater treatment plants

Comammox bacteria have proved to be one dominant and significant ammonia-oxidizing microorganisms (AOMs) in municipal wastewater treatment plants (WWTPs), however, it still remains unknown about their abundance and diversity in industrial WWTPs. In this study, activated sludge samples from 8 municipal WWTPs and 6 industrial WWTPs treating refinery wastewater were taken and analyzed using qPCR and amoA gene sequencing. Intriguingly, quantitative real-time PCR (qPCR) results suggested that comammox bacteria had a higher numerical abundance compared with ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in municipal WWTPs but did not in refinery WWTPs. Moreover, comammox amoA sequences obtained from high-throughput sequencing were retrieved from all the 8 municipal samples but only 1 industrial sample. Further phylogenetic analysis revealed that N. nitrosa cluster accounted for as high as 79.56% of the total comammox affiliated sequences, which was the most numerically abundant comammox species in municipal WWTPs. This study provided new insights into the abundance and diversity of comammox bacteria in the biological nitrification process in municipal and refinery wastewater treatment systems.

Advanced nitrogen removal from real municipal wastewater by multiple coupling nitritation, denitritation and endogenous denitritation with anammox in a single suspended sludge bioreactor

Achieving advanced nitrogen removal based on anammox for treating mainstream municipal wastewater in a single suspended sludge bioreactor is a challenging research topic. In this study, multiple coupling nitritation, denitritation and endogenous denitritation with anammox (PNA-(E)PDA) was simultaneously achieved in a 10 L step-feed bioreactor, which enhanced stable nitrogen removal. After 223 days of operation, the total nitrogen concentrations of the influent and effluent were 70.7 ± 6.1 and 4.3 ± 1.8 mg/L, respectively, when treating municipal wastewater even at C/N ratio of 2.24 with only 5 h of aerobic time (DO: 0.5-0.8 mg/L). After the evolution of nitritation/anammox to PNA-(E)PDA, the contribution of anammox to nitrogen removal increased to 78.6% and the anammox activity increased from 4.3 ± 0.2 to 15.2 ± 0.7 mg NH₄⁺-N/gVSS/d. qPCR results showed that the abundance of anammox bacteria increased from 4.1 × 10⁹ to 4.5 × 10¹⁰ copies/ (g VSS). High-throughput sequencing further revealed that the relative abundance of Candidatus Brocadia, the dominant anammox genus, increased from 0.09 to 0.46%. Based on the strong competitiveness of anammox on nitrite, this novel PNA-(E)PDA process provides a potential strategy for enriching anammox bacteria in municipal wastewater treatment plants.

Ammonia-oxidizing archaea and complete ammonia-oxidizing Nitrospira in water treatment systems

Nitrification, the oxidation of ammonia to nitrate via nitrite, is important for many engineered water treatment systems. The sequential steps of this respiratory process are carried out by distinct microbial guilds, including ammonia-oxidizing bacteria (AOB) and archaea (AOA), nitrite-oxidizing bacteria (NOB), and newly discovered members of the genus Nitrospira that conduct complete ammonia oxidation (comammox). Even though all of these nitrifiers have been identified within water treatment systems, their relative contributions to nitrogen cycling are poorly understood. Although AOA contribute to nitrification in many wastewater treatment plants, they are generally outnumbered by AOB. In contrast, AOA and comammox Nitrospira typically dominate relatively low ammonia environments such as drinking water treatment, tertiary wastewater treatment systems, and aquaculture/aquarium filtration. Studies that focus on the abundance of ammonia oxidizers may misconstrue the actual role that distinct nitrifying guilds play in a system. Understanding which ammonia oxidizers are active is useful for further optimization of engineered systems that rely on nitrifiers for ammonia removal. This review highlights known distributions of AOA and comammox Nitrospira in engineered water treatment systems and suggests future research directions that will help assess their contributions to nitrification and identify factors that influence their distributions and activity.

The dissimilarity of antibiotic and quorum sensing inhibitor on activated sludge nitrification system: Microbial communities and antibiotic resistance genes

Effects of antibiotics (azithromycin, AZM, 1-40 mg/L) and quorum sensing inhibitor (QSI, 2(5H)-furanone, 1-40 mg/L) combined pollution with environmental concentration of copper on bacterial/archaeal community and antibiotic resistance genes (ARGs) in activated sludge system were explored. QSI inhibited nitrification more obviously than AZM. AZM and QSI were synergistic inhibitions on bacterial diversity, and AZM inhibited bacterial compositions more than QSI. While, QSI had more impacts on archaeal diversity/compositions. Less interactions among bacteria and archaea communities with Aquimonas as keystone genus. Functional differences in bacteria/archaea communities were little, and AZM had more effects on metabolism. AZM mainly affected nitrifying bacteria (Candidatus Nitrospira nitrificans and Nitrosomonas). Specific denitrifying bacteria were enriched by AZM (Brevundimonas, 1.76-31.69%) and QSI (Comamonas, 0.61-9.61%), respectively. AZM enriched ARGs more easily than QSI and they were antagonistic to proliferation of ARGs. Bacteria were main hosts of ARGs (macrolide-lincosamide-streptogramin B, other/efflux, etc.) and archaea (Methanosphaerula, Methanolobus) carried multiple ARGs.

The nitrification recovery capacity is the key to enhancing nitrogen removal in the AOA system at low temperatures

Anaerobic/aerobic/anoxic (AOA) is suitable for advanced nitrogen removal of low C/N wastewater as an energy-saving process. Investigations of the temperature impact on the AOA process are critical to its application in cold regions or seasons. In this study, the nitrogen removal performance in AOA at low and room temperatures was investigated. The nitrification capacity of the AOA process was recovered at low temperature and the endogenous denitrification performance was enhanced by converting the partial aerobic zone into anoxic. At 15 °C, treating real municipal sewage with a low C/N ratio (3.36), TIN and NH₄⁺-N removal efficiencies of 84.3 ± 6.6% and 97.4 ± 3.3% respectively, were achieved. The oxygen uptake rate test, quantitative PCR, and high-throughput sequencing results indicated that the activity and abundance of ammonia-oxidizing bacteria (AOB) increased at low temperature, which was the key for nitrification capacity recovery. Overall, the recoverability of nitrification capacity in the AOA system made advanced nitrogen removal possible at low temperatures.

Robustness of the partial nitrification-anammox system exposing to triclosan wastewater: Stress relieved by extracellular polymeric substances and resistance genes

The partial nitrification-anammox (PN/A) process is a promising method for the treatment of municipal wastewater. It is necessary to clarify the responses of PN/A system to antimicrobial agent triclosan (TCS) widely existed in the influent of wastewater treatment plants. In this study, it was found that PN/A system was robust to cope with 0.5 mg/L TCS. Specifically, the control reactor reached 80% total nitrogen removal efficiency (TNRE) on day 107, while the reactor feeding with 0.5 mg/L TCS reached the same TNRE on day 84. The results of the activity test, high-throughput sequencing and DNA-based stable isotope probing showed that 0.5 mg/L TCS did not impede the performance of ammonia oxidizing archaea, ammonia oxidizing bacteria (Nitrosomonas) and anammox bacteria (Candidatus Brocadia and Ca. Kuenenia), but significant inhibited the nitrite oxidizing bacteria (Nitrospira and Ca. Nitrotoga) and denitrifying bacteria. The influent TCS led to the increase of EPS content and enrichment of four resistance genes (RGs) (intI1, sul1, mexB, and tnpA), which might be two principal mechanisms by which PN/A can resist TCS. In addition, functional bacteria carrying multiple RGs also contributed to the maintenance of PN/A system function. These findings improved the understandings of antimicrobial effects on the PN/A system.

Cometabolic biodegradation of antibiotics by ammonia oxidizing microorganisms during wastewater treatment processes

Studies on antibiotic removal during wastewater treatment processes are crucial since their release into the environment could bring potential threats to human health and ecosystem. Cometabolic biodegradation of antibiotics by ammonia oxidizing microorganisms (AOMs) has received special attentions due to the enhanced removal of antibiotics during nitrification processes. However, the interactions between antibiotics and AOMs are less well-elucidated. In this review, the recent research proceedings on cometabolic biodegradation of antibiotics by AOMs were summarized. Ammonia oxidizing bacteria (AOB), ammonia oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) played significant roles in both nitrification and cometabolic biodegradation of antibiotics. Antibiotics at varying concentrations might pose inhibiting or stimulating effect on AOMs, influencing the microbial activity, community abundance and ammonia monooxygenase subunit A gene expression level. AOMs-induced cometabolic biodegradation products were analyzed as well as the corresponding pathways for each type of antibiotics. The effects of ammonium availability, initial antibiotic concentration, sludge retention time and temperature were assessed on the cometabolic biodegradation efficiencies of antibiotics. This work might provide further insights into the fate and removal of antibiotics during nitrification processes.

Realization of partial nitrification and in-situ anammox in continuous-flow anaerobic/aerobic/anoxic process with side-stream sludge fermentation for real sewage

A continuous-flow anaerobic/aerobic/anoxic reactor with complete suspended activated sludge using sludge alkaline fermentation products as carbon source was utilized to strengthen nitrogen removal performance for low C/N ratio (<4) wastewater. Long-time performance indicated that the nitrite accumulation rate reached 60.40%, which strengthened the contribution of anammox. The average total inorganic nitrogen removal efficiency improved 19.40%. The abundance of ammonia oxidizing bacteria has not changed, but the abundance of nitrite oxidizing bacteria reduced from 5.79% to 0.69%. Quantitative PCR results demonstrated that the abundance of anammox bacteria has raised by 80.5 times. These results indicated that side-stream sludge alkaline fermentation promoted the mainstream partial nitrification, consequently accelerating the in-situ enrichment of anammox bacteria. No external carbon source dosing and short oxic hydraulic retention time (5.3 h) save energy and reduce consumption significantly in this system.

Impacts of combined pollution under gradient increasing and gradient decreasing exposure modes on activated sludge: Microbial communities and antibiotic resistance genes

The responses of microbial communities and antibiotic resistance genes (ARGs) to azithromycin and copper combined pollution under gradient increasing (from 0.5 to 10 mg/L) and decreasing exposure (from 10 to 0.5 mg/L) modes were investigated. Nitrification was inhibited more obviously under gradient increasing exposure mode. Responses of archaeal community and function structure were more obvious than bacteria under both exposure modes. The dominant bacterial and archaeal compositions (Hyphomicrobium, Euryarchaeota, etc.) were affected by two exposure modes, except some rare archaea (Methanoregula and Methanosarcina). There were more positive correlations between bacteria and archaea, and Nitrospira was keystone genus. Ammonia-oxidizing archaea (0.37-3.06%) and complete ammonia oxidizers (Nitrospira_ENR4) were enriched, and Nitrososphaera_viennensis was closely related to denitrifying genes (napA/B, nosZ, etc.). 50 ARG subtypes were detected and specific ARG subtypes (aac, ImrA, etc.) proliferated in two exposure modes. Bacteria and archaea were common hosts for 24 ARGs and contributed to their shifts.

Insight into the mechanism of nitritation establishment through external fermented sludge addition

In this study, a novel strategy for nitritation establishment through external fermented sludge addition is proposed. The nitrifying activities under various fermentation times were assessed; batch tests results revealed that the decay rate of nitrite oxidizing bacteria (0.53 ± 0.08 d^-1) was much higher than that of ammonia oxidizing bacteria (0.15 ± 0.04 d^-1), during alkaline fermentation with high endogenous free ammonia concentrations (0.57-138.79 mg·L^-1). The long-term effects of fermented sludge addition were constantly monitored in an anaerobic/oxic/anoxic sequencing batch reactor. During 60 days of operation, the nitrite accumulation rate reached above 90% and could be maintained stably. Total inorganic nitrogen removal achieved 94.7%, with an average external sludge reduction rate of 61.3%, after incorporation of the sludge addition. Illumina MiSeq sequencing demonstrated that nitrite oxidizing bacteria were successfully eliminated and the relative abundance of ammonia oxidizing bacteria remained at 0.39%, resulting in nitrite accumulation.

Nitrification mainly driven by ammonia-oxidizing bacteria and nitrite-oxidizing bacteria in an anammox-inoculated wastewater treatment system

Anaerobic ammonium oxidation (anammox) process has been acknowledged as an environmentally friendly and time-saving technique capable of achieving efficient nitrogen removal. However, the community of nitrification process in anammox-inoculated wastewater treatment plants (WWTPs) has not been elucidated. In this study, ammonia oxidation (AO) and nitrite oxidation (NO) rates were analyzed with the incubation of activated sludge from Xinfeng WWTPs (Taiwan, China), and the community composition of nitrification communities were investigated by high-throughput sequencing. Results showed that both AO and NO had strong activity in the activated sludge. The average rates of AO and NO in sample A were 6.51 µmol L⁻¹ h⁻¹ and 6.52 µmol L⁻¹ h⁻¹, respectively, while the rates in sample B were 14.48 µmol L⁻¹ h⁻¹ and 14.59 µmol L⁻¹ h⁻¹, respectively. The abundance of the nitrite-oxidizing bacteria (NOB) Nitrospira was 0.89–4.95 × 10¹¹ copies/g in both samples A and B, the abundance of ammonia-oxidizing bacteria (AOB) was 1.01–9.74 × 10⁹ copies/g. In contrast, the abundance of ammonia-oxidizing archaea (AOA) was much lower than AOB, only with 1.28–1.53 × 10⁵ copies/g in samples A and B. The AOA community was dominated by Nitrosotenuis, Nitrosocosmicus, and Nitrososphaera, while the AOB community mainly consisted of Nitrosomonas and Nitrosococcus. The dominant species of Nitrospira were Candidatus Nitrospira defluvii, Candidatus Nitrospira Ecomare2 and Nitrospira inopinata. In summary, the strong nitrification activity was mainly catalyzed by AOB and Nitrospira, maintaining high efficiency in nitrogen removal in the anammox-inoculated WWTPs by providing the substrates required for denitrification and anammox processes.

Efficiency of hybrid systems enhanced with different sludge ratios in improving resistance to short-term low temperatures

Complete autotrophic nitrogen removal over nitrite (CANON) is used in wastewater treatment. However, the performance of the CANON system significantly decreases at low temperatures; thus, a new strategy to improve the resistance of the CANON system is required. To investigate the impact of sludge ratio control (high-granule, equivalent, and high-floc systems) on the resistance of CANON to low temperatures, and their recovery after restoring to normal temperature, the nitrogen removal performance of hybrid systems with different ratios was evaluated. The equivalent system had the lowest nitrite accumulation rate and highest nitrogen removal rate. Anaerobic ammonia oxidation was the rate-limiting step of each system, and hzs was the rate-limiting gene. The higher anaerobic ammonium oxidizing bacteria (AAOB) abundance and hzs expression levels resulted in an equivalent system with better resistance and recovery to short-term low temperatures at the gene level.

Temperature Influenced the Comammox Community Composition in Drinking Water and Wastewater Treatment Plants

Nitrification is a pivotal step applied in water engineered systems for nitrogen removal. Temperature variation due to seasonal changes is a great challenge for maintaining nitrogen removal efficiency in water engineered ecosystems by affecting nitrifier activities. Research on the abundance, activity, and metabolic characteristics of nitrifiers can provide information for selecting suitable design parameters to ensure efficient nitrogen removal in different seasons. To date, the temperature-related niche separation of comammox, a newly discovered nitrifier with potential high-growth yield, has been rarely investigated. This study addressed the distribution of comammox and canonical nitrifying guilds in drinking water treatment plants (DWTPs) and wastewater treatment plants (WWTPs) in different seasons. qPCR-based surveys showed that comammox ubiquitously distributed and greatly outnumbered other ammonia-oxidizing prokaryotes in both DWTPs and WWTPs, except in Aug samples from DWTPs, suggesting the potential competitive advantage of AOA in summer. The nitrificans-like comammox and nitrosa-like comammox comprised the majority of the comammox community in DWTPs and WWTPs, respectively, and COD and NH₄⁺ concentrations significantly contributed to the distinct comammox phylotype distribution between DWTPs and WWTPs. The temperature-related distribution pattern of the comammox community was observed at each site. Moreover, the network complex of comammox communities was highest in Dec at all the sites, possibly contributing to the survival of comammox community in low temperature conditions.

Light Irradiation Enables Rapid Start-Up of Nitritation through Suppressing nxrB Gene Expression and Stimulating Ammonia-Oxidizing Bacteria

Nitritation facilitates the application of anaerobic ammonium oxidation (Anammox)-based processes for cost-efficient nitrogen removal from wastewater. This study proposed light irradiation as a novel strategy to rapidly start up nitritation by stimulating both the activities and growth of ammonia-oxidizing bacteria (AOB) while suppressing that of nitrite-oxidizing bacteria (NOB). Batch assays and kinetic model jointly suggested that AOB activity presented an initial increase followed by a decline while NOB decreased continuously throughout the light energy densities applied. Under optimal light energy densities (0.03-0.08 kJ/mg VSS), the highest nitrite accumulation ratio of 70.0% was achieved in sequencing batch reactors with both mainstream online and sidestream offline light treatments when treating real or synthetic municipal wastewater. Light irradiation induced different responses of AOB and NOB, leading to microbial structure optimization. Specifically, the expression of nxrB was downregulated, while the expression of amoA was upregulated under appropriate light irradiation. Moreover, although Nitrosomonas as typical AOB disappeared, the family Nitrosomonadaceae was doubled with enrichment of Ellin6067 and another four Nitrosomonadaceae genera that were only identified in light-treated reactors, thus ensuring AOB predominance and stable nitritation. These findings offer a new approach to rapidly establishing nitritation using light irradiation in municipal wastewater, especially for nitritation/microalgae system.

Distribution patterns of microbial community and functional characteristics in full-scale wastewater treatment plants: Focusing on the influent types

The impacts of the influent type in wastewater treatment plants (WWTPs) on the distribution patterns of the microbial community and functional characteristics were investigated. The obtained results indicated that the influent types exhibited evident influences on the microbial distribution patterns. The diversity and richness of functional microbes in HI-WWTP (with a ratio of >30% industrial wastewater in influents) were evidently decreased compared with those in HM- (with 70-90% municipal wastewater in influents) and M-WWTPs (with >90% municipal wastewater in influents). The core functional bacteria included denitrifiers, anaerobic fermentation bacteria (AFB), organic degrading bacteria (ODB), phosphorus accumulating organisms (PAO) and nitrite oxidizing bacteria (NOB), but they exhibited distinct abundances in WWTPs receiving different categories of wastewater. The denitrifiers in HI-WWTPs was 15.6-32.5% higher than that in other WWTPs, while PAOs had higher abundances in M - and HI-WWTPs (28.9% and 39.3%, respectively) compared with HM-WWTPs. Clear co-occurrence relationships were found among the main functional microbes with similar metabolic characteristics. Moreover, information on functional genes related to carbon, nitrogen and phosphorus metabolism, which is closely associated with pollutant removal efficiency, was obtained. M-WWTPs had higher abundances of genetic expressions for organic matters degradation (i.e. amino acid (10.42%) and carbohydrate (9.86%) metabolisms). Nar, Nir and Nor showed lowest abundances in HM-WWTPs, causing the low nitrogen removal (63.04-65.79%). However, influent type had little effect on genetic expression related with phosphorus removal. This work provided new insights into the interrelationship among bacterial co-occurrence, microbial activity and pollutant removal in WWTPs with different influent types.

Effects of chronic exposure of antibiotics on microbial community structure and functions in hyporheic zone sediments

Microbial communities in hyporheic zones (HZ) provide vital biogeochemical functions such as contaminant degradation for river ecosystems. Antibiotics are contaminants that have been increasingly detected in HZ sediments. In this study, sediments from different HZ locations in a contaminated river, Maozhou river, China were sampled and analyzed using qPCR and high-throughput sequencing to investigate the effect of antibiotic contamination on microbial community structures and functions in HZ sediments. Results indicated that types and concentrations of antibiotics in HZ sediments were heterogeneously distributed that were largely consistent with the distribution of antibiotic sources. Sediments near animal farm and hospital contained higher antibiotic concentrations compared with those from mainstream. The distribution of ARGs was well correlated with antibiotics. Bacterial indicator genera indicating differences between mainstream area and other sampling areas were positively correlated with antibiotics, suggesting the influences of antibiotics on reshaping microbial community structures. PICRUSt revealed positive relationships between antibiotics and predicted functional genes involved in defense, signal transduction, and recombination and repair. This imply the defensive response of microbial communities on antibiotic attack. These results indicated that antibiotic contamination in the watershed posed a potential risk on HZ microbial community structures and functions, which may further threaten river ecosystem functions.

Bacterial community compositions and nitrogen metabolism function in a cattle farm wastewater treatment plant revealed by Illumina high-throughput sequencing

Bacteria play an important role in pollutant transformation in activated sludge-based wastewater treatment plants (WWTPs). Exploring the microbial community structure and diversity is essential to improving the performance of wastewater treatment processes. This study employed Illumina MiSeq high-throughput sequencing to investigate the microbial community composition and diversity in a cattle farm wastewater treatment plant (Cf-WWTP). The results showed that the dominant phyla in the whole process were Proteobacteria, Bacteroidetes, and Firmicutes. The principal coordinate analysis (PCoA) indicated that the different stages had a significant impact on the microbial community structure; Bacteroidetes was the dominant phylum in the anearobic stage and Proteobacteria was the dominant phylum in the anoxic-oxic stage. Redundancy analysis (RDA) revealed that total phosphorus (TP) was the most significant factor that regulated the microbial community composition, followed by chemical oxygen demand (COD), total nitrogen (TN), and pH. Proteobacteria, Patescibacteria, and Chloroflexi were simultaneously negatively correlated with TN, COD, and TP. Nitrogen metabolic pathway and transformation mechanism was elucidated by a complete denitrification function predicted with phylogenetic investigation of communities with reconstruction of unobserved states (PICRUSt), as well as detection of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). These results provide new insights into our understanding of microbial community and metabolic functions of Cf-WWTP.

Sludge ratio affects the start-up performance and functional bacteria distribution of a hybrid CANON system

To investigate the effect of sludge ratio on the hybrid CANON system, autotrophic nitrogen removal sludge was inoculated with different granule/floc ratios to initiate the CANON system, and maintained the sludge ratio during the operation process. The start-up performances were compared, and the distribution characteristics of functional bacteria were investigated. The results show that the Equivalent system (granules:flocs = 1:1-1:1.5) successfully started-up on day 19, and the nitrogen removal rate (NRR) reached 0.299 kgN m^-3·d^-1 on day 63. At the same time, it was less affected by the load shock than High-granules and High-flocs systems. Therefore, the Equivalent system had the strongest start-up performance. The activities of the functional bacteria conformed to spatial heterogeneity, unlike the abundance. With the increased floc proportion, the difference in the activity and abundance of anaerobic ammonium-oxidizing bacteria (AAOB) between the granules and flocs increased, while there was a decrease in the difference in aerobic ammonium-oxidizing bacteria (AOB). However, the abundance of Nitrosomonas in the granules was higher than in the flocs when the proportion of flocs was higher than 50%. This study provides new ideas and insights for the fast start-up of the CANON system and can conform to the varying needs of engineering applications.

A novel denitrifying phosphorus removal and partial nitrification, anammox (DPR-PNA) process for advanced nutrients removal from high-strength wastewater

This study developed a novel DPR-PNA (denitrifying phosphorus removal, partial nitrification and anammox) process for sustaining high-strength wastewater treatment in a modified continuous flow reactor without external carbon source. After 259-days operation, a synchronous highly-efficient total inorganic nitrogen, PO₄^3--P and COD_cr removal efficiencies of 88.5%, 89.5% and 90.1% were obtained, respectively even influent nitrogen loading rate up to 3.2 kg m^-3 d^-1. Batch tests revealed that denitrifying phosphorus accumulating organisms (DPAOs) using NO₃^--N as electron acceptors significantly enriched (74% in total PAOs), which emerged remarkable positive impacts on deep-level nutrient removal as the key limiting factor. Furthermore, the NO₂^--N inhibitory threshold value (∼20.0 mg L^-1) for DPAOs was identified, which demonstrated as an inhibitory component in excessive recycling NO_x^--N. From the molecular biology perspective, Dechloromonas-DPAOs group (18.59%) dominated the excellent dephosphatation performance, while Nitrosomonas-AOB (ammonia oxidizing bacteria) group (16.26%) and Candidatus_Brocadia-AnAOB (anammox bacteria) group (15.12%) were responsible for the desirable nitrogen loss process. Overall, the present work highlighted the novel DPR-PNA process for nutrients removal is a promising alternation for wastewater of high nitrogen but low carbon.

BALOs Improved Gut Microbiota Health in Postlarval Shrimp (Litopenaeus vannamei) After Being Subjected to Salinity Reduction Treatment

White shrimp, Litopenaeus vannamei, is a widely farmed species. In China, shrimp postlarvae (PL) are frequently subjected to salinity reduction treatment to meet end growers' needs. However, although this treatment effectively reduces vibrio counts, its impact on gut microbiota health is still unknown. In this study, we applied a euryhaline strain of BALOs, BDN-1F2 (BD), and Bacillus subtilis (SD) to the rearing of second-generation shrimp PL after salinity reduction treatment so as to determine if they could impact PL gut microbiota by using high-throughput sequencing analysis. Results show that PL gut microbiota, both compositionally and functionally, have been badly wrecked after salinity reduction treatment with the generally recognized as opportunistic pathogens Gammaproteobacteria being the only dominant class at day 1 of test, viz., 99.43, 85.61, and 83.28% in BD, SD, and control (CD) groups, respectively. At day 7, Gammaproteobacteria was still the only dominant class in the SD and CD groups with relative abundance of 99.77 and 99.87% correspondingly, whereas in the BD group, its value dropped to 8.44%. Regarding biodiversity parameter the Shannon index, over the 7-day test period, while the SD group was unchanged (0.98-0.93), the CD group dropped to 0.94 from 2.94, and the BD group was raised to 7.14 from 0.93. Functionally, compared to control, the SD group displayed similar strength of various predicted community functions, but the BD group had hugely enhanced its various capabilities (p < 0.05). These results demonstrated that the addition of BDN-1F2 had exceedingly improved PL gut microbiota health by raising its biodiversities and strengthening its functionalities. On reviewing data derived from this as well as relevant studies, a Shannon index cutoff value was tentatively suggested so as to differentiate microbiota-healthy PL7-15 from the unhealthy ones. Furthermore, a conceptual mechanism of BALOs in the rectification/improvement of the microbial community health has also been proposed.

Responses of AOA and AOB activity and DNA/cDNA community structure to allylthiourea exposure in the water level fluctuation zone soil

Ammonia oxidation is mainly performed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Allylthiourea (ATU) has been found to specifically inhibit ammonia oxidation. However, the effect of ATU on AOA and AOB transcription has been infrequently studied. In the present study, we examined the responses of AOA and AOB activity and DNA/cDNA community structure to ATU exposure. The ammonia oxidation activity in the 100-mg/L ATU group was 4.3% of that in the control group after 7 days. When exposed to ATU, the gene abundance of AOA was favored compared with that of AOB, and there were no statistically significant differences in the abundance of AOB amoA in DNA and cDNA between the two groups. Compared with the control group, the gene abundance of AOA significantly increased by 5.23 times, while the transcription of AOA significantly decreased by 0.70 times. Moreover, the transcriptional ratio of AOA in the ATU group was only 0.05 times as high as that in the control group. ATU selectively affected AOB and completely inhibited Nitrosomonas europaea and Bacterium amoA.22.HaldeII.kultur at the genetic level. Under ATU exposure, all AOA clusters were transcribed, but three AOB clusters were not transcribed. Our results indicated that the ammonia oxidation potential of the soil of water level fluctuation areas, based on ATU inhibition, was associated mainly with AOA amoA gene abundance and AOB community shifts in DNA and cDNA.

Effect of different operational modes on the performance of granular sludge in continuous-flow systems and the successions of microbial communities

Continuous flow reactors with time intermittent operational (TIO) mode and spatial intermittent operational (SIO) mode were operated to evaluate the effects of operational modes on the removal performances, the characteristics of granules and the dynamics of microbial communities in simultaneous nitrification, denitrification and phosphorus removal (SNDPR) granular system. The results showed that the removal efficiency of TP, TN were 81.3%, 86.7% under TIO mode, and 70.6%, 77.4% under SIO mode, respectively. Meanwhile, the PN and value of PN/PS in SIO were higher than those in TIO. Besides, results of high-throughput pyrosequencing illustrated that the combination of filamentous archaea (Methanothrix) and filamentous bacteria (Thiothrix) had resulted in the increase of EPS and SVI under SIO mode. Finally, functional bacterial and archaeal species, involving HMA, AMA, AOA, DPAOs etc., were identified to reveal the effects of operational modes on the mechanism of nutrients removal in granular SNDPR continuous-flow system.

Startup and stable operation of advanced continuous flow reactor and the changes of microbial communities in aerobic granular sludge

In this study, the granular sludge was operated under low aeration condition in sequencing batch reactor (SBR) and advanced continuous flow reactor (ACFR), respectively. Through increasing the sludge retention time (SRT) from 22 days to 33 days, the ACFR was successful startup in 30 days and achieved long term stable operation. Under SBR operation condition, the aerobic granular sludge (AGS) showed good nitrogen (60%), phosphorus (96%) and COD removal performance. During stable operation of continuous-flow, the nitrogen removal efficiency was increasing to 70%, however, the phosphorus removal efficiency could only be restored to 65%. Meanwhile, the sludge discharge volume from ACFR was about half of that in SBR. Results of high-throughput pyrosequencing illustrated that methanogenic archaea (MA), ammonia oxidizing archaea (AOA), denitrifying bacteria (DNB), denitrifying polyphosphate-accumulating organisms (DPAOs) played an important role in the removal of nutrients in ACFR. This study could have positive effect on the practical application of AGS continuous flow process for simultaneous biological nutrient removal (SBNR).

Differential responses of encoding-amoA nitrifiers and nir denitrifiers in activated sludge to anatase and rutile TiO2 nanoparticles: What is active functional guild in rate limiting step of nitrogen cycle?

The long-terms effects of different crystal-composition TiO₂ nanoparticles (NPs) on nitrogen-cycle-related functional guilds in activated sludge remain unclear, especially under natural light irradiation. Accordingly, activated sludge was exposed to anatase TiO₂-NPs (TiO₂-A) and rutile TiO₂-NPs (TiO₂-R) for up to 45 days. With markedly (p < 0.05) reducing nitrification-/denitrification-enzymatic-activities and abundances of ammonia-oxidizing-microorganisms (AOMs) and nitrite-reducing-bacteria (NRB), TiO₂-NPs triggered bacteria and archaea UPGMA clustering and a deep modification of N-cycling functional diversity guided by crystal structure. in situ¹³C-DNA-SIP confirmed ammonia-oxidizing-bacteria (AOB) (Nitrosomonas and Nitrosospira) in original sludge as main active AOMs with 75.4 times more abundance than ammonia-oxidizing-archaea (AOA), while AOA within Nitrosopumilus and Nitrososphaera genera were the main active AOMs and tended to aggregate inside sludge after 10-mg/L TiO₂-NPs exposure. Encoding-nirK NRB were more sensitive, while encoding-nirS Zoogloea with a total share of 4.97% to 14.93%, etc. were the main active NRB. AOB was more sensitive to TiO₂-A, while TiO₂-R showed the stronger toxicity to AOA and NRB resulting from differences in water environmental behaviors and crystal characteristics of two TiO₂-NPs. This work expands understanding of the ecological risks of titanium-dioxide-crystal-NPs in aquatic environment and may help devise better methods to alleviate environmental stress caused by NPs at wastewater treatment plants.

Nitrite accumulation in comammox-dominated nitrification-denitrification reactors: Effects of DO concentration and hydroxylamine addition

In this study, nitrite accumulation was investigated under different DO conditions and different hydroxylamine addition methods during the domestic wastewater treatment. Two sequencing batch reactors in parallel were operated under cyclic aerobic and anoxic conditions with the DO concentration of 2.0 and 4.0 mg/L in aerobic phase. The nitrite accumulation rate during high DO conditions increased to 44.8 and 66.7% in 20 days. During hydroxylamine addition, the NAR increased over 90% under the continuous and intermittent hydroxylamine addition. Continuous hydroxylamine addition could result in a more efficient and rapid nitrite accumulation. The findings suggested that comammox could be the main reason for the failure of partial nitrification in a low DO environment (< 0.5 mg/L). The nitrogen variation during typical cycles showed that the continuous hydroxylamine addition suppressed the activity of NOB and the ammonia oxidation rate. Further, the qPCR results indicated that the abundance of comammox amoA (ranged from 6.25 × 10⁷ to 4.16 × 10⁸ copies/g VSS) was higher than those of AOB amoA and Nitrobacter in sludge samples. The findings from the current study may enrich our understanding of partial nitrification and its control strategy.

Nitrogen removal pathway and dynamics of microbial community with the increase of salinity in simultaneous nitrification and denitrification process

In this study, simultaneous nitrification and denitrification (SND) process was successfully established in a hybrid sequencing batch biofilm reactor (HSBBR). High removal efficiency of NH₄⁺-N (98.0±2.4% to 99.8±0.4%) and COD (86.6±4.0% to 91.6±1.8%) was observed in the salinity range of 0.0 to 2.4%. SND via nitrite, replacing SND via nitrate, became the main nitrogen removal pathway at 1.6% and 2.4% salinity. Suspended sludge and biofilm shared similar microbial composition. Dominant genera were substituted by salt-adaptable microbes as salinity increasing. Abundance of autotrophic ammonia-oxidizing bacteria (Nitrosomonas) increased with elevated salinity, while autotrophic nitrite-oxidizing bacteria (Nitrospira) exhibited extreme sensitivity to salinity. The presence of Gemmata demonstrated that heterotrophic nitrification co-existed with autotrophic nitrification in the SND process. Aerobic denitrifiers (Denitratisoma and Thauera) were also identified. Thiothrix, Sedimenticola, Sulfuritalea, Arcobacter (sulfide-based autotrophic denitrifier) and Hydrogenophaga (hydrogen-based autotrophic denitrifier) were detected in both S-sludge and biofilm. The occurrence of ANAMMOX bacteria Pirellula and Planctomyces indicated that ANAMMOX process was another pathway for nitrogen removal. Nitrogen removal in the HSBBR was accomplished via diverse pathways, including traditional autotrophic nitrification/heterotrophic denitrification, heterotrophic nitrification, aerobic and autotrophic denitrification, and ANAMMOX.

Effect of aeration modes on simultaneous nitrogen and phosphorus removal and microbial community in a continuous flow reactor with granules

In this study, a continuous flow reactor with simultaneous nitrification, denitrification and phosphorus removal (SNDPR) granular sludge was operated in the continuous aeration (CA) and intermittent aeration (IA) modes to examine the effect of aeration on the performance of continuous-flow system. Then the experimental results showed that the IA₁ mode (4 h aeration and 1 h non-aeration) could improve the simultaneous nitrogen and phosphorus removal and the settleability of granules in continuous flow system. Results of high-throughput pyrosequencing illustrated that the methanogens, AOA, ANAMMOX, DNB, denitrifying polyphosphate-accumulating organisms (DPAOs) were the important participant of simultaneous biological nutrients removal (SBNR), meanwhile, the IA₁ mode could effectively inhibit the growth of filamentous microorganisms (Thiothrix and Acinetobacter). Finally, a conceptual model of the SNDPR granular microbial ecosystem under IA₁ mode was proposed as a base for analyzing the mechanism of simultaneous nutrient removal in continuous flow system.

Abundance and community composition of comammox bacteria in different ecosystems by a universal primer set

Complete ammonia oxidizing bacteria (CAOB) have been recognized as a new member of ammonia-oxidizing microorganisms (AOMs) due to its single-step nitrification capability. However, the abundance and diversity of CAOB in environmental ecosystems were still far from known owing to the lack of specific molecular marker. Herein, a universal primer set specifically targeting both clades of CAOB amoA gene with high specificity and coverage was successfully designed. Intriguingly, real-time quantitative PCR tests revealed that CAOB were ubiquitous and unexpectedly abundant in agricultural soils, river sediments, intertidal zones, drinking water and wastewater treatment systems. Phylogenetic analysis indicated that clade A existed in all the five types of ecosystems, while clade B were only detected in soil and sediment samples. Four sub-clusters were further classified within clade A, in which N. nitrosa cluster dominated CAOB amoA in activated sludge samples while the new recognized soil cluster was the primary constitute in soils. Moreover, the niche specialization between different CAOB species and the environmental conditions were supposed to be the primary driven force to shape the diversity and community of CAOB. This study provided a strong evidence in support of the ubiquities and high abundances of CAOB in various environmental ecosystems and highlighted the significance of including CAOB as the new member of AOMs to re-evaluate the biogeochemical nitrogen cycle.

A single Thaumarchaeon drives nitrification in deep oligotrophic Lake Constance

Ammonia released during organic matter mineralization is converted during nitrification to nitrate. We followed spatiotemporal dynamics of the nitrifying microbial community in deep oligotrophic Lake Constance. Depth-dependent decrease of total ammonium (0.01-0.84 μM) indicated the hypolimnion as the major place of nitrification with ¹⁵ N-isotope dilution measurements indicating a threefold daily turnover of hypolimnetic total ammonium. This was mirrored by a strong increase of ammonia-oxidizing Thaumarchaeota towards the hypolimnion (13%-21% of bacterioplankton) throughout spring to autumn as revealed by amplicon sequencing and quantitative polymerase chain reaction. Ammonia-oxidizing bacteria were typically two orders of magnitude less abundant and completely ammonia-oxidizing (comammox) bacteria were not detected. Both, 16S rRNA gene and amoA (encoding ammonia monooxygenase subunit B) analyses identified only one major species-level operational taxonomic unit (OTU) of Thaumarchaeota (99% of all ammonia oxidizers in the hypolimnion), which was affiliated to Nitrosopumilus spp. The relative abundance distribution of the single Thaumarchaeon strongly correlated to an equally abundant Chloroflexi clade CL500-11 OTU and a Nitrospira OTU that was one order of magnitude less abundant. The latter dominated among recognized nitrite oxidizers. This extremely low diversity of nitrifiers shows how vulnerable the ecosystem process of nitrification may be in Lake Constance as Central Europe's third largest lake.

The dominance of non-halophilic archaea in autotrophic ammonia oxidation of activated sludge under salt stress: A DNA-based stable isotope probing study

Dynamics of nitrification activity, ammonia-oxidizing archaea (AOA) and bacteria (AOB) abundance and active ammonia oxidizers of activated sludge were explored under different salinities. Results showed that specific ammonium oxidation rates were significantly negative with increasing salinity. The responses of AOA and AOB populations to salt stress were distinct. AOA abundance decreased at moderate salinities (2.5, 5 and 7 g L^-1) and increased at high salinities (10, 15, 20 and 30 g L^-1), while AOB abundance showed opposite tendency. DNA-based stable isotope probing assays indicated AOA exclusively dominated active ammonia oxidation of test samples under different salinities. The active AOA communities retrieved were all non-halophilic and regulated by salinities. Candidatus Nitrosocosmicus exaquare and Ca. Nitrosocosmicus franklandus were the predominantly active AOA in both salt-free and salt-containing microcosms, while ¹³C-labeled Nitrososphaera viennensis and Ca. Nitrososphaera gargensis were only retrieved from the microcosms amended with 0 and 30 g L^-1 salinity, respectively.

Impacts of long-term exposure to tetracycline and sulfamethoxazole on the sludge granules in an anoxic-aerobic wastewater treatment system

Occurrence and effects of antibiotics and antibiotic resistance in various wastewater treatment systems have been widely investigated. However, few reports address the impacts of antibiotic exposure on wastewater treatment system operating characteristics, especially the characteristics of sludge granules under long-term operation. In this study, two laboratory scale anoxic-aerobic systems were established to investigate the combined effects of tetracycline and sulfamethoxazole. The results indicated that under long-term exposure to 5 mg·L^-1 tetracycline and 1 mg·L^-1 sulfamethoxazole, removals of chemical oxygen demand and total nitrogen were inhibited, the tendency of sludge bulking was increased, more filamentous bacteria were observed and more extracellular polymeric substance was secreted. This tendency was stronger than that from exposure to tetracycline alone. Molecular biological analysis indicated that the microbial community changed significantly especially with Thiothrix (instead of Sphaerotilus under tetracycline alone) becoming the dominant population under combined antibiotics. The results are relevant for operation of WTS receiving wastewater with high antibiotic concentrations.

Responses of Active Ammonia Oxidizers and Nitrification Activity in Eutrophic Lake Sediments to Nitrogen and Temperature

Ammonium concentrations and temperature drive the activities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), but their effects on these microbes in eutrophic freshwater sediments are unclear. In this study, surface sediments collected from areas of Taihu Lake (China) with different degrees of eutrophication were incubated under three levels of nitrogen input and temperature, and the autotrophic growth of ammonia oxidizers was assessed using ¹³C-labeled DNA-based stable-isotope probing (SIP), while communities were characterized using MiSeq sequencing and phylogenetic analysis of 16S rRNA genes. Nitrification rates in sediment microcosms were positively correlated with nitrogen inputs, but there was no marked association with temperature. Incubation of SIP microcosms indicated that AOA and AOB amoA genes were labeled by ¹³C at 20°C and 30°C in the slightly eutrophic sediment, and AOB amoA genes were labeled to a much greater extent than AOA amoA genes in the moderately eutrophic sediment after 56 days. Phylogenetic analysis of ¹³C-labeled 16S rRNA genes revealed that the active AOA were mainly affiliated with the Nitrosopumilus cluster, with the Nitrososphaera cluster dominating in the slightly eutrophic sediment at 30°C with low ammonium input (1 mM). Active AOB communities were more sensitive to nitrogen input and temperature than were AOA communities, and they were exclusively dominated by the Nitrosomonas cluster, which tended to be associated with Nitrosomonadaceae-like lineages. Nitrosomonas sp. strain Is79A3 tended to dominate the moderately eutrophic sediment at 10°C with greater ammonium input (2.86 mM). The relative abundance responses of the major active communities to nitrogen input and temperature gradients varied, indicating niche differentiation and differences in the physiological metabolism of ammonia oxidizers that are yet to be described.IMPORTANCE Both archaea and bacteria contribute to ammonia oxidation, which plays a central role in the global cycling of nitrogen and is important for reducing eutrophication in freshwater environments. The abundance and activities of ammonia-oxidizing archaea and bacteria in eutrophic limnic sediments vary with different ammonium concentrations or with seasonal shifts, and how the two factors affect nitrification activity, microbial roles, and active groups in different eutrophic sediments is unclear. The significance of our research is in identifying the archaeal and bacterial responses to anthropogenic activity and climate change, which will greatly enhance our understanding of the physiological metabolic differences of ammonia oxidizers.

Nitrification Rates Are Affected by Biogenic Nitrate and Volatile Organic Compounds in Agricultural Soils

The processes regulating nitrification in soils are not entirely understood. Here we provide evidence that nitrification rates in soil may be affected by complexed nitrate molecules and microbial volatile organic compounds (mVOCs) produced during nitrification. Experiments were carried out to elucidate the overall nature of mVOCs and biogenic nitrates produced by nitrifiers, and their effects on nitrification and redox metabolism. Soils were incubated at three levels of biogenic nitrate. Soils containing biogenic nitrate were compared with soils containing inorganic fertilizer nitrate (KNO₃) in terms of redox metabolism potential. Repeated NH₄–N addition increased nitrification rates (mM NO₃^1- produced g^-1 soil d^-1) from 0.49 to 0.65. Soils with higher nitrification rates stimulated (p < 0.01) abundances of 16S rRNA genes by about eight times, amoA genes of nitrifying bacteria by about 25 times, and amoA genes of nitrifying archaea by about 15 times. Soils with biogenic nitrate and KNO₃ were incubated under anoxic conditions to undergo anaerobic respiration. The maximum rates of different redox metabolisms (mM electron acceptors reduced g^-1 soil d^-1) in soil containing biogenic nitrate followed as: NO₃^1- reduction 4.01 ± 0.22, Fe³⁺ reduction 5.37 ± 0.12, SO₄^2- reduction 9.56 ± 0.16, and CH₄ production (μg g^-1 soil) 0.46 ± 0.05. Biogenic nitrate inhibited denitrificaton 1.4 times more strongly compared to mineral KNO₃. Raman spectra indicated that aliphatic hydrocarbons increased in soil during nitrification, and these compounds probably bind to NO₃ to form biogenic nitrate. The mVOCs produced by nitrifiers enhanced (p < 0.05) nitrification rates and abundances of nitrifying bacteria. Experiments suggest that biogenic nitrate and mVOCs affect nitrification and redox metabolism in soil.

Transcriptional activity and diversity of comammox bacteria as a previously overlooked ammonia oxidizing prokaryote in full-scale wastewater treatment plants

The discovery of complete ammonia oxidizing bacteria (CAOB) has fundamentally overturned the traditional recognition of nitrification. However, little was known about the transcriptional activity and diversity of the newly recognized ammonia oxidizing prokaryote in engineered ecosystems. To fill this gap, transcriptional investigations of CAOB amoA genes were carried out comparatively with the canonical ammonia oxidizing bacteria (AOB) and archaea (AOA) in eight full-scale wastewater treatment plants (WWTPs). Remarkably, qPCR results revealed the transcriptional levels of CAOB amoA gene were unexpectedly high in most of samples with the highest 24-fold that of AOB amoA, suggesting CAOB were actively participating in ammonia oxidation while they were previously overlooked. This result also well explained the confusing high abundances of genus Nitrospira which were frequently detected in WWTPs. Furthermore, phylogenetic analysis based on high throughput sequencing indicated the CAOB amoA gene sequences formed three well-supported clusters and Nitrospira nitrosa cluster accounted for 97% of all the retrieved sequences, which was supposed to be the dominant taxon of CAOB in the ammonia-intensive environment due to niche partitioning. This study highlighted the significance of including the newly discovered ammonia oxidizing bacterial member when assessing the nitrification process and ecological function in the future.

Newly designed primer pair revealed dominant and diverse comammox amoA gene in full-scale wastewater treatment plants

The discovery of complete ammonia oxidizing bacteria (CAOB) capable of performing the two-step nitrification process on their own has fundamentally upended our traditional perception. However, their environmental distribution and ecological significance in driving ammonia oxidation are still urgently awaited to be assessed. In this study, the diversity and abundance of CAOB amoA gene in wastewater treatment plants (WWTPs) were presented taking advantage of a newly designed primer pair specifically targeting CAOB amoA gene. Phylogenetic results demonstrated the novel amoA gene formed a clearly distinct cluster from the canonical amoA and pmoA genes. Among the five well-supported sub-clusters, Nitrospira nitrosa cluster accounted for 94.34% of all the currently retrieved sequences from WWTPs. More importantly, qPCR results demonstrated a remarkably high abundance of CAOB amoA gene, which were up to 182.7-fold more abundant than AOB amoA gene. This study provided new dimension and fundamental basis for future researches towards biogeochemical nitrogen cycle.

The more important role of archaea than bacteria in nitrification of wastewater treatment plants in cold season despite their numerical relationships

Nitrification failure of wastewater treatment plants (WWTPs) in cold season calls into investigations of the functional ammonia-oxidizing microorganisms (AOMs). In this study, we report the abundance of ammonia-oxidizing archaea (AOA), bacteria (AOB) and complete ammonia-oxidizing (comammox) Nitrospira in 23 municipal WWTPs in cold season, and explore the correlations between AOMs abundance and their relative contribution to nitrification. The copy numbers of AOA and AOB amoA gene ranged from 2.42 × 10⁷ to 2.47 × 10⁹ and 5.54 × 10⁶ to 3.31 × 10⁹ copies/g sludge, respectively. The abundance of amoA gene of Candidatus Nitrospira inopinata, an important strain of comammox Nitrospira, was stable with averaged abundance of 8.47 × 10⁶ copies/g sludge. DNA-based stable isotope probing (DNA-SIP) assays were conducted with three typical WWTPs in which the abundance of AOA was lower than, similar to and higher than that of AOB, respectively. The results showed that considerable ¹³C-assimilation by AOA was detected during active nitrification in all WWTPs, whereas just a much lesser extent of ¹³C-incorporation by AOB and comammox Nitrospira was found in one WWTP. High-throughput sequencing with ¹³C-labeled DNA also showed the higher reads abundance of AOA than AOB and comammox Nitrospira. Nitrososphaera viennensis was the dominant active AOA, while Nitrosomonas oligotropha and Nitrosomonas europaea were identified as active AOB. The results obtained suggest that AOA, rather than AOB and comammox Nitrospira, dominate ammonia oxidation in WWTPs in cold season despite the numerical relationships of AOMs.

Functional genera, potential pathogens and predicted antibiotic resistance genes in 16 full-scale wastewater treatment plants treating different types of wastewater

This study aimed to investigate the bacterial communities and antibiotic resistance genes (ARGs) in 16 wastewater treatment plants (WWTPs) treating municipal, industrial and mixed wastewater. Wastewater types showed obvious effects on bacterial communities and functions. Nitrosomonas, Nitrospira, Hyphomicrobium and Accumulibacter were the main functional genera. Mycobacterium was the dominant potential pathogens. A total of 69 ARGs were obtained, and the dominant ARGs subtypes were similar in different WWTPs. Efflux pumps were the most common resistance mechanisms. Copper and zinc resistance genes were the main metal resistance genes (MRGs). Wastewater types affected the distributions of ARGs and MRGs, and they were more similar in industrial and mixed wastewater. The co-occurrence of ARGs existed within or across ARG types, and they were also positively linked to MRGs, some functional and pathogenic genera or environmental factors. This study furthers the understanding of interactions between bacterial communities, ARGs and MRGs in different WWTPs.

Resistant ammonia-oxidizing archaea endure, but adapting ammonia-oxidizing bacteria thrive in boreal lake sediments receiving nutrient-rich effluents

Climate change along with anthropogenic activities changes biogeochemical conditions in lake ecosystems, modifying the sediment microbial communities. Wastewater effluents introduce nutrients and organic material but also novel microbes to lake ecosystems, simulating forthcoming increases in catchment loadings. In this work, we first used 16s rRNA gene sequencing to study how the overall sediment microbial community responds to wastewater in six boreal lakes. To examine forthcoming changes in the lake biogeochemistry, we focused on the ammonia‐oxidizing archaea (AOA) and bacteria (AOB), and examined their functional and compositional community response to wastewater. Although we found the least diverse and least resistant prokaryotic communities from the most wastewater‐influenced sediments, the community changed fast toward the natural composition with the diminishing influence of wastewater. Each lake hosted a unique resistant AOA community, while AOB communities were adapting, responding to environmental conditions as well as receiving new members from WWTPs. In general, AOB dominated in numbers in wastewater‐influenced sediments, while the ratio between AOA and AOB increased when moving toward pristine conditions. Our results suggest that although future climate‐change‐driven increases in nutrient loading and microbial migration might significantly disrupt lake sediment microbiomes, they can promote nitrification through adapting and abundant AOB communities.

A Genomic Outlook on Bioremediation: The Case of Arsenic Removal

Microorganisms play a major role in biogeochemical cycles. As such they are attractive candidates for developing new or improving existing biotechnological applications, in order to deal with the accumulation and pollution of organic and inorganic compounds. Their ability to participate in bioremediation processes mainly depends on their capacity to metabolize toxic elements and catalyze reactions resulting in, for example, precipitation, biotransformation, dissolution, or sequestration. The contribution of genomics may be of prime importance to a thorough understanding of these metabolisms and the interactions of microorganisms with pollutants at the level of both single species and microbial communities. Such approaches should pave the way for the utilization of microorganisms to design new, efficient and environmentally sound remediation strategies, as exemplified by the case of arsenic contamination, which has been declared as a major risk for human health in various parts of the world.