Biotransformation of Two Pharmaceuticals by the Ammonia-Oxidizing Archaeon Nitrososphaera gargensis

Deciphering unique enzymatic pathways in sulfonamide biotransformation by direct ammonia oxidizer Alcaligenes ammonioxydans HO-1

Heterotrophic nitrification, similar to autotrophic nitrification, involves key enzymes and reactive nitrogen intermediates during ammonia oxidation, which may influence antibiotic transformation. However, the interference between antibiotic transformation products from ammonia oxidation and secondary metabolites in heterotrophic nitrifiers makes antibiotic transformation pathways more complicated. In this work, we observe that the heterotrophic nitrifier Alcaligenes ammonioxydans HO-1 can effectively convert sulfonamide antibiotics. Product analysis reveals the impacts of carbon and nitrogen concentrations as well as their ratio on the biotransformation of sulfamethazine (SMZ). The dnfABC gene cluster is identified as essential for mediating SMZ conversion. In vitro enzymatic activity reconstruction further confirms that DnfA exhibits N-oxygenase activity and can catalyze the conversion of various aryl-amines into aryl-nitro compounds. The results of this work not only expand our understanding of the functions of heterotrophic nitrifiers, but also provide a theoretical basis for developing efficient biotechnologies for treating antibiotics.

Impact of adaptation time on lincomycin removal in riverbank filtration: A long-term sand column study

Riverbank filtration (RBF) is an effective pretreatment technology for drinking water, removing organic micropollutants (OMPs) mainly through biodegradation. Despite documented improvements in OMP removal with extended adaptation time, the mechanisms remain poorly understood. This study assessed the removal of 128 OMPs over 82 d in a simulated RBF system, identified those with improved removal, and analyzed their properties. Additionally, microbial community shifts after 400 d of lincomycin exposure were studied to understand the underlying mechanisms. We found that the removal efficiencies of 24 OMPs, including lincomycin and fluconazole, improved by 3-77 % over 82 d while being positively correlated with the presence of tertiary amides and secondary sulfonamides. Lincomycin removal efficiency rose from 20 % to 95 % over 68 days and stayed high. We identified eight potential degradation products of lincomycin, occurring primarily via hydroxylation, N-demethylation, and amide hydrolysis. Additionally, lincomycin notably increased the abundances of specific antibiotic-resistant bacteria (e.g., Thiobacillus, 8.3-fold) and ammonia-oxidizing archaea (e.g., Nitrososphaera, 46.8-fold). The β-lactam resistance gene in Thiobacillus and the amoA gene in Nitrososphaera may enhance lincomycin's removal by promoting its hydrolysis and hydroxylation. Overall, this study provides insights into OMP biodegradation mechanisms and the impact of ng/L levels of lincomycin on microbial communities.

Key role of NH4+-N in the removal of oxacillin during managed aquifer recharge: Reconsidering the recharge limitation

Frequent occurrence of trace antibiotics in reclaimed water is concerning, which inevitably causes aquifer contamination in the case of managed aquifer recharge (MAR). Global governments have formulated strict reclaimed water standards to ensure the safety of water reuse. Recent studies have found that improved antibiotics removal is intimately associated with high ammonia-oxidizing activity. However, the role of NH4+-N in the removal of residual antibiotics of reclaimed water during MAR remains unknown. NH4+-N removal and the effects of ammonia oxidation on antibiotics biodegradation in the aquifer are the most significant facts for solving the above collision. In this work, the effects of NH4+-N (0, 1 and 5 mg/L) in a model refractory antibiotic (oxacillin (OXA), 100 μg/L) attenuation were deciphered by employing three individual simulated MAR columns, which so called N0, N1 and N5. The results showed that 5 mg/L NH4+-N in influent upregulated the abundance of amo genes by 28.9 %-68.0 % in N5. And the enriched functional genes encoding key degradation enzymes enhanced the OXA removal by 18.7 % and alleviated the oxidative stress caused by antibiotics. Subsequently, antibiotic resistance genes (ARGs), mobile gene elements (MGEs) and human bacterial pathogens (HBPs) abundance were all significantly decreased. Moreover, the intimate association between ammonia-oxidizing microorganisms (AOM) and candidate OXA degraders based on microbial network analysis further supported the significance of AOM on OXA biodegradation. This study provides comprehensive evidence that appropriate amounts of NH4+-N are beneficial in antibiotics and antibiotic resistance risk reduction, providing compelling insights for refine NH4+-N recharge limitation.

Sulfamethoxazole exposure shifts partial denitrification to complete denitrification: Reactor performance and microbial community

This study elucidated the influence on a partial denitrification (PD) system under 0-1 mg/L sulfamethoxazole (SMX) stress in a sequencing batch reactor. The results showed that the nitrite accumulation rate (NAR) significantly (P ≤ 0.01) decreased from 68.68 ± 9.00% to 49.05 ± 11.68%, while the total nitrogen removal efficiency significantly (P ≤ 0.001) increased from 23.19 ± 4.42% to 31.36 ± 2.73% in presence of SMX. The results indicated that SMX exposure switched the PD process to complete denitrification through the deterioration of the nitrite accumulation and the promotion of further nitrite reduction. The SMX removal loading rate increased from 0.21 ± 0.04 to 5.03 ± 0.77 mg-SMX/(g-MLVSS·d) with the extended reactor operation under SMX stress. Low SMX concentration exposure increased extracellular polymeric substances (EPS) content from 107.69 ± 20.78 mg/g-MLVSS (0.05 mg-SMX/L) to 123.64 ± 9.66 mg/g-MLVSS (0.5 mg-SMX/L), while EPS secretion was inhibited under high SMX concentration exposure (i.e., 1 mg-SMX/L). Moreover, SMX exposure promoted the synthesis of aromatic protein-like compounds and changed the functional groups as revealed by EEM and FTIR analysis. Additionally, SMX exposure significantly shifted the microbial community structures at both phylum and genus levels. Particularly, the abundance of Thauera, i.e., functional bacteria related to PD, considerably decreased from 41.69% to 11.62% after SMX exposure, whereas the abundances of Denitratisoma and SM1A02 significantly rose under different SMX concentrations. These outcomes hinted that the addition of SMX resulted in the shifting of partial denitrification to complete denitrification.

Cooperation among nitrifying microorganisms promotes the irreversible biotransformation of sulfamonomethoxine

Ammonia-oxidizing microorganisms, including AOA (ammonia-oxidizing archaea), AOB (ammonia-oxidizing bacteria), and Comammox (complete ammonia oxidization) Nitrospira, have been reported to possess the capability for the biotransformation of sulfonamide antibiotics. However, given that nitrifying microorganisms coexist and operate as communities in the nitrification process, it is surprising that there is a scarcity of studies investigating how their interactions would affect the biotransformation of sulfonamide antibiotics. This study aims to investigate the sulfamonomethoxine (SMM) removal efficiency and mechanisms among pure cultures of phylogenetically distinct nitrifiers and their combinations. Our findings revealed that AOA demonstrated the highest SMM removal efficiency and rate among the pure cultures, followed by Comammox Nitrospira, NOB, and AOB. However, the biotransformation of SMM by AOA N. gargensis is reversible, and the removal efficiency significantly decreased from 63.84 % at 167 h to 26.41 % at 807 h. On the contrary, the co-culture of AOA and NOB demonstrated enhanced and irreversible SMM removal efficiency compared to AOA alone. Furthermore, the presence of NOB altered the SMM biotransformation of AOA by metabolizing TP202 differently, possibly resulting from reduced nitrite accumulation. This study offers novel insights into the potential application of nitrifying communities for the removal of sulfonamide antibiotics (SAs) in engineered ecosystems.

Quantitative structure-biotransformation relationships of organic micropollutants in aerobic and anaerobic wastewater treatments

Biotransformation is one of the dominant processes to remove organic micropollutants (OMPs) in wastewater treatment. However, studies on the role of molecular structure in determining the biotransformation rates of OMPs are limited. We evaluated the biotransformation of 14 OMPs belonging to different chemical classes under aerobic and anaerobic conditions, and then explored the quantitative structure-biotransformation relationships (QSBRs) of the OMPs based on biotransformation rates using valid molecular structure descriptors (electrical and physicochemical parameters). Pseudo-first-order kinetic modeling was used to fit the biotransformation rate, and only 2 of the 14 OMPs showed that the biotransformation rate constant (kbio) values were higher under anaerobic conditions than aerobic conditions, indicating that aerobic conditions were more favorable for biotransformation of most OMPs. QSBRs infer that the electrophilicity index (ω) is a reliable predictor for OMPs biotransformation under aerobic conditions. ω corresponds to the interaction between OMPs and microbial enzyme active sites, this process is the rate-limiting step of biotransformation. However, under anaerobic conditions the QSBR based on ω was not significant, indicating that specific functional groups may be more critical than electrophilicity. In conclusion, QSBRs can serve as alternative tools for the prediction of the biotransformation of OMPs and provide further insights into the factors that influence biotransformation.

Nitrification and beyond: metabolic versatility of ammonia oxidising archaea

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

A new strategy for the enrichment of ammonia-oxidizing archaea in wastewater treatment systems: The positive role of quorum-sensing signaling molecules

Ammonia-oxidizing archaea (AOA) play an important role in natural nitrogen cycle, but are difficult to be enriched in wastewater treatment systems. In this experiment, under ambient temperature and high dissolved oxygen, different types of acyl-homoserine lactones (C₆-HSL, C₈-HSL, C₁₀-HSL, C₁₄-HSL and 3-oxo-C₁₄-HSL) were added to five wastewater nitrification systems to achieve AOA enrichment. Results showed that AOA couldn't be detected in the blank group without the addition of signaling molecules, while the AOA could be detected in all the reactors with the addition. The enrichment effect of AOA was not obvious with added 100 or 200 nmol/L signaling molecules, while the enrichment effect was both obvious with added C₈-HSL of 400 nmol/L and C₁₀-HSL of 800 nmol/L. And relative abundance of AOA increased from undetected in the control group to 1.10 % and 0.96 %, respectively. The exogenous signaling molecules may provide new view for AOA enrichment in wastewater treatment systems.

Predicting and improving the microbial removal of organic micropollutants during wastewater treatment: A review

Organic micropollutants (OMPs) consist of widely used chemicals such as pharmaceuticals and pesticides that can persist in surface and groundwaters at low concentrations (ng/L to μg/L) for a long time. The presence of OMPs in water can disrupt aquatic ecosystems and threaten the quality of drinking water sources. Wastewater treatment plants (WWTPs) rely on microorganisms to remove major nutrients from water, but their effectiveness at removing OMPs varies. Low removal efficiency might be the result of low concentrations, inherent stable chemical structures of OMPs, or suboptimal conditions in WWTPs. In this review, we discuss these factors, with special emphasis on the ongoing adaptation of microorganisms to degrade OMPs. Finally, recommendations are drawn to improve the prediction of OMP removal in WWTPs and to optimize the design of new microbial treatment strategies. OMP removal seems to be concentration-, compound-, and process-dependent, which poses a great complexity to develop accurate prediction models and effective microbial processes targeting all OMPs.

Benzimidazole fungicide biotransformation by comammox Nitrospira bacteria: Transformation pathways and associated proteomic responses

Benzimidazole fungicides are frequently detected in aquatic environments and pose a serious health risk. Here, we investigated the metabolic capacity of the recently discovered complete ammonia-oxidizing (comammox) Nitrospira inopinata and kreftii to transform a representative set of benzimidazole fungicides (i.e., benzimidazole, albendazole, carbendazim, fuberidazole, and thiabendazole). Ammonia-oxidizing bacteria and archaea, as well as the canonical nitrite-oxidizing Nitrospira exhibited no or minor biotransformation activity towards all the five benzimidazole fungicides. In contrast, the investigated comammox bacteria actively transformed all the five benzimidazole fungicides, except for thiabendazole. The identified transformation products indicated hydroxylation, S-oxidation, and glycosylation as the major biotransformation pathways of benzimidazole fungicides. We speculated that these reactions were catalyzed by comammox-specific ammonia monooxygenase, cytochrome P450 monooxygenases, and glycosylases, respectively. Interestingly, the exposure to albendazole enhanced the expression of the antibiotic resistance gene acrB of Nitrospira inopinata, suggesting that some benzimidazole fungicides could act as environmental stressors that trigger cellular defense mechanisms. Altogether, this study demonstrated the distinct substrate specificity of comammox bacteria towards benzimidazole fungicides and implies their significant roles in the biotransformation of these fungicides in nitrifying environments.

Microbial communities and processes in biofilters for post-treatment of ozonated wastewater treatment plant effluent

Ozonation is an established solution for organic micropollutant (OMP) abatement in tertiary wastewater treatment. Biofiltration is the most common process for the biological post-treatment step, which is generally required to remove undesired oxidation products from the reaction of ozone with water matrix compounds. This study comparatively investigates the effect of filter media on the removal of organic contaminants and on biofilm properties for biologically activated carbon (BAC) and anthracite biofilters. Biofilms were analysed in two pilot-scale filters that have been operated for >50,000 bed volumes as post-treatment for ozonated wastewater treatment plant effluent. In parallel, the removal performance of bulk organics and OMP, including differentiation of adsorption and biotransformation through sodium azide inhibition, were carried out in bench-scale filter columns filled with material from the pilot filters. The use of BAC instead of anthracite resulted in an improved removal of organic bulk parameters, dissolved oxygen, and OMP. The OMP removal observed in the BAC filter but not in the anthracite filter was based on adsorption for most of the investigated compounds. For valsartan, however, biotransformation was found to be the dominant pathway, indicating that conditions for biotransformation of certain OMP are better on BAC than on anthracite. Adenosine triphosphate analyses in the media-attached biofilms of the pilot filters showed that biomass concentrations in the BAC filter were significantly higher than in the anthracite filter. The microbial communities (16S rRNA gene sequencing) appeared to be similar with respect to the types of organisms occurring on both filter materials. Alpha diversity also exhibited little variation between filter media. Beta diversity analysis, however, revealed that filter media and bed depth substantially influenced the biofilm composition. In practice, the impact of filter media on biofilm properties and biotransformation processes should be considered for the design of biofilters.

Removal of sulfamethoxazole and antibiotic resistance genes in paddy soil by earthworms (Pheretima guillelmi): Intestinal detoxification and stimulation of indigenous soil bacteria

Vermiremediation, which use earthworms to remove contaminants from soil, has been proven to be an alternative, low-cost technology. However, the effects of earthworm activity, especially the degraders in earthworm intestines, on the fate of sulfamethoxazole (SMX), and the effects of intestinal bacteria on degrading bacteria in soil are unclear. In this study, the effects of earthworms on the fate of SMX and related antibiotic resistance genes (ARGs) were investigated. Special attention was paid to the impact of earthworms on SMX degradation efficiency, degradation products, related ARGs, and degraders in both soil and earthworm intestines; the effect of intestinal bacteria on soil bacteria associated with SMX was also studied. Earthworms significantly accelerated SMX degradation by both intestinal detoxification and the stimulation of indigenous soil bacteria. Compared with the treatment without earthworms, the treatment with earthworms reduced SMX residues by 25.1 %, 49.2 %, 35.7 %, 34.2 %, and 35.7 % on the 10th, 20th, 30th, 60th, and 90th days, respectively. Compared with those in soil (treated with earthworms), the SMX residues in wormcasts were further reduced by 12.2-29.0 % from the 2nd to the 20th day, producing some unique anaerobic degradation products that were distinct from those in the soil. In earthworm intestines, SMX degradation was enhanced by bacteria of the genera Microvirga, Sphingomonas, Methylobacterium, Bacillus, and Tumebacillus. All of these bacteria (except Bacillus spp.) entered and colonised the soil with wormcasts, further promoting SMX degradation. Additionally, earthworms removed a significant number of ARGs by increasing the fraction of potential SMX degraders and inhibiting the potential hosts of ARGs and int1. This study demonstrated that earthworms could remediate SMX-contaminated soil by enhancing the removal of SMX and ARGs.

Ecological Aerobic Ammonia and Methane Oxidation Involved Key Metal Compounds, Fe and Cu

Interactions between metals and microbes are critical in geomicrobiology and vital in microbial ecophysiological processes. Methane-oxidizing bacteria (MOB) and ammonia-oxidizing microorganisms (AOM) are key members in aerobic environments to start the C and N cycles. Ammonia and methane are firstly oxidized by copper-binding metalloproteins, monooxygenases, and diverse iron and copper-containing enzymes that contribute to electron transportation in the energy gain pathway, which is evolutionally connected between MOB and AOM. In this review, we summarized recently updated insight into the diverse physiological pathway of aerobic ammonia and methane oxidation of different MOB and AOM groups and compared the metabolic diversity mediated by different metalloenzymes. The elevation of iron and copper concentrations in ecosystems would be critical in the activity and growth of MOB and AOM, the outcome of which can eventually influence the global C and N cycles. Therefore, we also described the impact of various concentrations of metal compounds on the physiology of MOB and AOM. This review study could give a fundamental strategy to control MOB and AOM in diverse ecosystems because they are significantly related to climate change, eutrophication, and the remediation of contaminated sites for detoxifying pollutants.

Role of ammonia-oxidizing microorganisms in the removal of organic micropollutants during simulated riverbank filtration

Biodegradation plays an important role in the removal of organic micropollutants (OMPs) during riverbank filtration (RBF) for drinking water production. The ability of ammonia-oxidizing microorganisms (AOM) to remove OMPs has attracted increasing attention. However, the distribution of AOM in RBF and its role in the degradation of OMPs remains unknown. In this study, the behavior of 128 selected OMPs and the distribution of AOM and their roles in the degradation of OMPs in RBF were explored by column and batch experiments simulating the first meter of the riverbank. The results showed that the selected OMPs were effectively removed (82/128 OMPs, >70% removal) primarily by biodegradation and partly by adsorption. Inefficiently removed OMPs tended to have low molecular weights, low log P, and contain secondary amides, secondary sulfonamides, secondary ketimines, and benzyls. In terms of the microbial communities, the relative abundance of AOM increased from 0.1%-0.2% (inlet_-sand) to 5.3%-5.9% (outlet_-sand), which was dominated by ammonia-oxidizing archaea whose relative abundance increased from 23%-72% (inlet_-sand) to 97% (outlet_-sand). Comammox accounted for 23%-64% in the inlet_-sand and 1% in the outlet_-sand. The abundances of AOM amoA genes kept stable in the inlet_-sand of control columns, while decreased by 78% in the treatment columns, suggesting the inhibition effect of allylthiourea (ATU) on AOM. It is observed that AOM played an important role in the degradation of OMPs, where its inhibition led to the corresponding inhibition of 32 OMPs (5/32 were completely suppressed). In particular, OMPs with low molecular weights and containing primary amides, secondary amides, benzyls, and secondary sulfonamides were more likely to be removed by AOM. This study reveals the vital role of AOM in the removal of OMPs, deepens our understanding of the degradation of OMPs in RBF, and offers valuable insights into the physiochemical properties of OMPs and their AOM co-metabolic potential.

Free Nitrous Acid Inhibits Atenolol Removal during the Sidestream Partial Nitritation Process through Regulating Microbial-Induced Metabolic Types

Limited studies have attempted to evaluate pharmaceutical removal during the sidestream partial nitritation (PN) process. In this work, atenolol biodegradation by PN cultures was investigated by maintaining ammonium and pH at different levels. For the first time, free nitrous acid (FNA), other than ammonium, pH, and free ammonia, was demonstrated to inhibit atenolol removal, with biodegradation efficiencies of ∼98, ∼67, and ∼28% within 6 days at average FNA levels of 0, 0.03, and 0.19 mg-N L^-1, respectively. Ammonia-oxidizing bacteria (AOB)-induced metabolism was predominant despite varying FNA concentrations. In the absence of ammonium/FNA, atenolol was mostly biodegraded via AOB-induced metabolism (65%) and heterotroph-induced metabolism (33%). AOB-induced metabolism was largely inhibited (down to 29%) at 0.03 mg-N L^-1 FNA, while ∼27 and ∼11% were degraded via heterotroph-induced metabolism and AOB-induced cometabolism, respectively. Higher FNA (0.19 mg-N L^-1) substantially reduced atenolol biodegradation via heterotroph-induced metabolism (4%), AOB-induced metabolism (16%), and AOB-induced cometabolism (8%). Newly identified products and pathways were related to metabolic types and FNA levels: (i) deamination and decarbonylation (AOB-induced cometabolism, 0.03 mg-N L^-1 FNA); (ii) deamination from atenolol acid (heterotrophic biodegradation); and (iii) nitro-substitution (reaction with nitrite). This suggests limiting FNA to realize simultaneous nitrogen and pharmaceutical removal during the sidestream process.

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.

Microbial Defluorination of Unsaturated Per- and Polyfluorinated Carboxylic Acids under Anaerobic and Aerobic Conditions: A Structure Specificity Study

The recently discovered microbial reductive defluorination of two C₆ branched and unsaturated fluorinated carboxylic acids (FCAs) provided valuable insights into the environmental fate of per- and polyfluoroalkyl substances (PFASs) and potential bioremediation strategies. However, a systematic investigation is needed to further demonstrate the role of C═C double bonds in the biodegradability of unsaturated PFASs. Here, we examined the structure-biodegradability relationships of 13 FCAs, including nine commercially available unsaturated FCAs and four structurally similar saturated ones, in an anaerobic defluorinating enrichment and an activated sludge community. The anaerobic and aerobic transformation/defluorination pathways were elucidated. The results showed that under anaerobic conditions, the α,β-unsaturation is crucial for FCA biotransformation via reductive defluorination and/or hydrogenation pathways. With sp² C-F bonds being substituted by C-H bonds, the reductive defluorination became less favorable than hydrogenation. Moreover, for the first time, we reported enhanced degradability and defluorination capability of specific unsaturated FCA structures with trifluoromethyl (-CF₃) branches at the α/β-carbon. Such FCA structures can undergo anaerobic abiotic defluorination in the presence of reducing agents and significant aerobic microbial defluorination. Given the diverse applications and emerging concerns of fluorochemicals, this work not only advances the fundamental understanding of the fate of unsaturated PFASs in natural and engineered environments but also may provide insights into the design of readily degradable fluorinated alternatives to existing PFAS compounds.

Exploring the Distinct Distribution of Archaeal Communities in Sites Contaminated with Explosives

Most of the research on bioremediation and estimation of microbial diversity in waste contaminated sites is focused on the domain Bacteria, whereas details on the relevance of Archaea are still lacking. The present study examined the archaeal diversity and predicted metabolic pathways in two discrete sites (SITE1 and SITE2) contaminated with explosives (RDX and HMX) by amplicon-targeted sequencing of 16S rRNA genes. In total, 14 soil samples were processed, and 35,758 OTUs were observed, among which 981 OTUs were classified as Archaea, representing ~2.7% of the total microbial diversity in our samples. The majority of OTUs belonged to phyla Euryarchaeota (~49%), Crenarchaeota (~24%), and Thaumarchaeota (~23%), while the remaining (~4%) OTUs were affiliated to Candidatus Parvarchaeota, Candidatus Aenigmarchaeota, and Candidatus Diapherotrites. The comparative studies between explosives contaminated and agricultural soil samples (with no history of explosives contamination) displayed significant differences between the compositions of the archaeal communities. Further, the metabolic pathways pertaining to xenobiotic degradation were presumably more abundant in the contaminated sites. Our data provide a first comprehensive report of archaeal communities in explosives contaminated sites and their putative degradation role in such ecosystems which have been as yet unexplored.

Determination of the lower limits of antibiotic biodegradation and the fate of antibiotic resistant genes in activated sludge: Both nitrifying bacteria and heterotrophic bacteria matter

Antibiotics can be biodegraded in activated sludge via co-metabolism and metabolism. In this study, we investigated the biodegradation pathways of sulfamethoxazole (SMX) and antibiotic resistant genes' (ARGs) fate in different autotrophic and heterotrophic microorganisms, by employing aerobic sludge, mixed sludge, and nitrifying sludge. A threshold concentration of SMX activating the degradation pathways in the initial stage of antibiotics degradation was found and proved in different activated sludge systems. Heterotrophic bacteria played an important role in SMX biodegradation. However, ammonia-oxidizing bacteria (AOB) had a faster metabolic rate, which was about 15 times higher than heterotrophic bacteria, contributing much to SMX removal via co-metabolism. As SMX concentration increases, the amoA gene and AOB relative abundance decreased in aerobic sludge due to the enrichment of functional heterotrophic bacteria, while it increased in nitrifying sludge. Microbial community analysis showed that functional bacteria which possess the capacity of SMX removal and antibiotic resistance were selected by SMX pressure. Potential ARGs hosts could increase their resistance to the biotoxicity of SMX and maintain system performance. These findings are of practical significance to guide antibiotic biodegradation and ARGs control in wastewater treatment plants.

Effect of pig manure-derived sulfadiazine on species distribution and bioactivities of soil ammonia-oxidizing microorganisms after fertilization

To evaluate the effect of pig manure-derived sulfadiazine (SDZ) on the species distribution and bioactivities of ammonia-oxidizing microorganisms (AOMs), ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and complete ammonia oxidizer (comammox) within the soil were investigated pre- and post-fertilization. Kinetic modeling and linear regression results demonstrated that the DT₅₀ value of different SDZ fractions under initial SDZ concentrations of 50 and 100 mg·kg^-1 exhibited the following trend: total SDZ>CaCl₂-extractable SDZ>MeOH-extractable SDZ, whereas their inhibiting effect on AOMs showed an opposite trend. qPCR analysis suggested that comammox was the predominant ammonia oxidizer in soils regardless of SDZ addition, accounting for as much as 77.2-94.7% of the total amoA, followed by AOA (5.3-22.5%), whereas AOB (<0.5%) was the lowest. The SDZ exhibited a significant effect on the AOM abundance. Specifically, SDZ exerted the highest inhibitory effect on comammox growth, followed by AOA, whereas negligible for AOB. The community diversity of AOMs within the pig manure-fertilized soils was affected by SDZ, and AOA Nitrososphaera cluster 3 played a key role in potential ammonia oxidation capacity (PAO) maintenance. This study provides new insights into the inhibition mechanisms of pig manure-derived antibiotics on AOMs within the fertilized soil.

Toward Characterizing the Genetic Basis of Trace Organic Contaminant Biotransformation in Activated Sludge: The Role of Multicopper Oxidases as a Case Study

Activated sludge treatment leverages the ability of microbes to uptake and (co)-metabolize chemicals and has shown promise in eliminating trace organic contaminants (TrOCs) during wastewater treatment. However, targeted interventions to optimize the process are limited as the fundamental drivers of the observed reactions remain elusive. In this work, we present a comprehensive workflow for the identification and characterization of key enzymes involved in TrOCs biotransformation pathways in complex microbial communities. To demonstrate the applicability of the workflow, we investigated the role of the enzymatic group of multicopper oxidases (MCOs) as one putatively relevant driver of TrOCs biotransformation. To this end, we analyzed activated sludge metatranscriptomic data and selected, synthesized, and heterologously expressed three phylogenetically distinct MCO-encoding genes expressed in communities with different TrOCs oxidation potentials. Following the purification of the encoded enzymes, we screened their activities against different substrates. We saw that MCOs exhibit significant activities against selected TrOCs in the presence of the mediator compound 2,2'-azino-bis-3-ethylbenzthiazoline-6-sulfonic acid and, in some cases, also in the presence of the wastewater contaminant 4'-hydroxy-benzotriazole. In the first case, we identified oxidation products previously reported from activated sludge communities and concluded that in the presence of appropriate mediators, bacterial MCOs could contribute to the biological removal of TrOCs. Similar investigations of other key enzyme systems may significantly advance our understanding of TrOCs biodegradation and assist the rational design of biology-based water treatment strategies in the future.

Temperature, phytoplankton density and bacteria diversity drive the biotransformation of micropollutants in a lake ecosystem

For most micropollutants (MPs) present in surface waters, such as pesticides and pharmaceuticals, the contribution of biotransformation to their overall removal from lake ecosystems is largely unknown. This study aims at empirically determining the biotransformation rate constants for 35 MPs at different periods of the year and depths of a meso-eutrophic lake. We then tested statistically the association of environmental parameters and microbial community composition with the biotransformation rate constants obtained. Biotransformation was observed for 14 out of 35 studied MPs for at least one sampling time. Large variations in biotransformation rate constants were observed over the seasons and between compounds. Overall, the transformation of MPs was mostly influenced by the lake's temperature, phytoplankton density and bacterial diversity. However, some individual MPs were not following the general trend or association with microorganism biomass. The antidepressant mianserin, for instance, was transformed in all experiments and depths, but did not show any relationship with measured environmental parameters, suggesting the importance of specific microorganisms in its transformation. The results presented here contribute to our understanding of the fate of MPs in surface waters and thus support improved risk assessment of contaminants in the environment.

Heterotrophic enzymatic biotransformations of organic micropollutants in activated sludge

While heterotrophic microorganisms constitute the major fraction of activated sludge biomass, the role of heterotrophs in the biotransformation of organic micropollutants (OMPs) has not been fully elucidated. Yet, such knowledge is essential, particularly when conceiving novel wastewater treatment plants based on a two-stage process including an A-stage under heterotrophic conditions and a B-stage based on anammox activity. Biotransformation of OMPs in activated sludge is thought to mostly occur cometabolically thanks to the action of low specificity enzymes involved in the metabolism of the primary substrates. For a better understanding of the process, it is important to determine such enzymatic activities and the underlying mechanisms involved in OMPs biotransformation. This task has proven to be difficult due to the lack of information about the enzymatic processes and the complexity of the biological systems present in activated sludge. In this paper, a continuous aerobic heterotrophic reactor following 20 OMPs at environmental concentrations was operated to (i) assess the potential of heterotrophs during the cometabolic biotransformation of OMPs, (ii) identify biotransformation reactions catalyzed by aerobic heterotrophs and (iii) predict possible heterotrophic enzymatic activities responsible for such biotransformations. Contradicting previous reports on the dominant role of nitrifiers in OMPs removal during activated sludge treatment, the heterotrophic population proved its capacity to biotransform the OMPs to extents equivalent to reported values in nitrifying activated sludge plants. Besides, 12 transformation products potentially formed through the activity of several enzymes present in heterotrophs, including monooxygenases, dioxygenases, hydrolases and transferases, were identified.

Responses of aerobic granular sludge to fluoroquinolones: Microbial community variations, and antibiotic resistance genes

In this study, aerobic granular sludge (AGS) was operated under high levels of ammonium for removing three fluoroquinolones (FQs), i.e., ciprofloxacin (CFX), ofloxacin (OFX), and norfloxacin (NFX) at 3, 300, and 900 µg/L, respectively. Two key objectives were to investigate the differential distribution of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in sludge fractions and to evaluate correlations between ARGs and MGEs to nitrifying and denitrifying bacteria. AGS showed excellent stability under the exposure of FQs, with nitrite-oxidizing bacteria (NOB) more sensitive to FQs than ammonium-oxidizing bacteria (AOB). Specific oxygen utilization rates (SOUR) showed a reduction of 26.9% for NOB but only 4.0% of the reduced activity of AOB by 3 μg/L FQs. AGS performed better removal efficiencies for CFX and NFX than OFX, and the efficiencies increased with their elevated concentrations, except at 900 μg/L FQs. The elevated FQ concentrations led to a significant enrichment of intI1 and genus Thauera, while qnrD and qnrS showed no accumulation. Compared to nitrifiers, FQs relevant ARGs and the intI1 gene preferred to exist in denitrifiers, and the abundance of denitrifiers behaved a decreasing trend with the sludge size. Two quinoline-degrading bacteria were found in the AGS system, i.e., Alicycliphilus and Brevundimonas, possibly carrying qnrS and qnrD, respectively. Their relative abundance increased with the sludge size, which was 2.18% in sludge <0.5 mm and increased to 3.70% in sludge >2.0 mm, suggesting that the AGS may be a good choice in treating FQs-containing wastewater.

An integrated approach to MS-based identification and risk assessment of pharmaceutical biotransformation in wastewater

The omnipresence of pharmaceuticals at relatively high concentrations (μg/L) in environmental compartments indicated their inadequate removal by wastewater treatment plants. As such, batch reactors seeded with activated sludge were set up to assess the biotransformation of metformin, ranitidine, lidocaine and atorvastatin. The main objective was to identify transformation products (TPs) through the establishment of an integrated workflow for suspect and non-target screening based on reversed phase liquid chromatography quadrupole-time-of-flight mass spectrometry. To support the identification, hydrophilic interaction liquid chromatography (HILIC) was used as a complementary tool, in order to enhance the completeness of the developed workflow by identifying the more polar TPs. The structure assignment/elucidation of the candidate TPs was mainly based on interpretation of MS/MS spectra. Twenty-two TPs were identified, with fourteen of them reaching high identification confidence levels (level 1: confirmed structure by reference standards and level 2: probable structure by library spectrum match and diagnostic evidence). Finally, retrospective analysis in influent and effluent wastewater was performed for the TPs for four consecutive years in wastewater sampled in Athens, Greece. The potential toxicological threat of the compounds to the aquatic environment was assessed and atorvastatin with two of its TPs showed a potential risk to the aquatic organisms.

Biotransformation of lincomycin and fluoroquinolone antibiotics by the ammonia oxidizers AOA, AOB and comammox: A comparison of removal, pathways, and mechanisms

In this study, we evaluated the biotransformation mechanisms of lincomycin (LIN) and three fluoroquinolone antibiotics (FQs), ciprofloxacin (CFX), norfloxacin (NFX), and ofloxacin (OFX), which regularly enter aquatic environments through human activities, by different ammonia-oxidizing microorganisms (AOM). The organisms included a pure culture of the complete ammonia oxidizer (comammox) Nitrospira inopinata, an ammonia oxidizing archaeon (AOA) Nitrososphaera gargensis, and an ammonia-oxidizing bacterium (AOB) Nitrosomonas nitrosa Nm90. The removal of these antibiotics by the pure microbial cultures and the protein-normalized biotransformation rate constants indicated that LIN was significantly co-metabolically biotransformed by AOA and comammox, but not by AOB. CFX and NFX were significantly co-metabolized by AOA and AOB, but not by comammox. None of the tested cultures transformed OFX effectively. Generally, AOA showed the best biotransformation capability for LIN and FQs, followed by comammox and AOB. The transformation products and their related biotransformation mechanisms were also elucidated. i) The AOA performed hydroxylation, S-oxidation, and demethylation of LIN, as well as nitrosation and cleavage of the piperazine moiety of CFX and NFX; ii) the AOB utilized nitrosation to biotransform CFX and NFX; and iii) the comammox carried out hydroxylation, demethylation, and demethylthioation of LIN. Hydroxylamine, an intermediate of ammonia oxidation, chemically reacted with LIN and the selected FQs, with removals exceeding 90%. Collectively, these findings provide important fundamental insights into the roles of different ammonia oxidizers and their intermediates on LIN and FQ biotransformation in nitrifying environments including wastewater treatment systems.

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

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

Removal of pharmaceutical and personal care products (PPCPs) from wastewater using microalgae: A review

Pharmaceuticals and personal care products (PPCPs) are a group of emerging micro-pollutants causing detrimental effects on living organisms even at low doses. Previous investigations have confirmed the presence of PPCPs in the environment at hazardous levels, mainly due to the inefficiency of conventional wastewater treatment plants (CWWTPs). Their stable structure induces longer persistence in the environment. Microalgae are currently used to bioremediate numerous pollutants of different characteristics and properties released from the domestic, industrial, agricultural, and farm sectors. CO₂ mitigation during culture and the use of biomass as feedstock for biodiesel or biofuel production are, briefly, other benefits of microalgae-mediated treatment over CWWTPs. This review provides a comprehensive summary of recent literature, an overview of approaches and treatment systems, and breakthrough in the field of algal-mediated removal of PPCPs in wastewater treatment processes. The mechanisms involved in phycoremediation, along with their experimental approaches, have been discussed in detail. Factors influencing the removal of PPCPs from aqueous media are comprehensively described and assessed. A comparative study on microalgal strains is analyzed for a more efficient implementation of future processes. The role of microalgae to mitigate the most severe environmental impacts of PPCPs and the generation of antibiotic-resistant bacteria is discussed. Also, a detailed assessment of recent research on potential toxic effects of PPCPs on microalgae was conducted. The current review highlights microalgae as a promising and sustainable approach to efficiently bio-transform or bio-adsorb PPCPs.

Removal of pharmaceuticals by ammonia oxidizers during nitrification

The adverse effect of pharmaceuticals on ecosystem and human health raises great interest for the removal of pharmaceuticals in wastewater treatment plants (WWTPs). Enhanced removal of pharmaceuticals by ammonia oxidizers (AOs) has been observed during nitrification. This review provides a comprehensive summary on the removal of pharmaceuticals by AOs-ammonia oxidizing bacteria (AOB), ammonia oxidizing archaea (AOA), and complete ammonia oxidizer (comammox) during nitrification in pure ammonia oxidizing culture and mixed microbes systems. The superior removal of pharmaceuticals by AOs in conditions with nitrifying activity compared with the conditions without nitrifying activity was proposed. The contribution of AOs on pharmaceuticals removal in pure and mixed microbe systems was discussed and activated sludge modeling was suggested as the proper measure on assessing the contribution of AOs on the removal of pharmaceuticals in mixed microbe culture. Three transformation processes and the involved reaction types of pharmaceuticals transformation during nitrification were reviewed. The present paper provides a systematical summary on pharmaceuticals removal by different AOs across pure and mixed microbes culture during nitrification, which opens up the opportunity to optimize the wastewater biological treatment systems for enhanced removal of pharmaceuticals. KEY POINTS: • The superior removal of pharmaceuticals by ammonia oxidizers (AOs) was summarized. • The removal contribution of pharmaceuticals attributed by AOs was elucidated. • The transformation processes and reaction types of pharmaceuticals were discussed.

Enhanced removal of cephalexin and sulfadiazine in nitrifying membrane-aerated biofilm reactors

Nitrification process has been reported to be capable of degrading various pharmaceuticals due to the cometabolism of ammonia-oxidizing bacteria (AOB). The membrane aerated biofilm reactor (MABR) is an emerging configuration in wastewater treatment with advantages of high nitrification rate and low energy consumption. However, there are very few studies investigating the degradation of antibiotics at environmentally relevant levels in nitrifying MABR systems. In this study, the removal of two widely used antibiotics, cephalexin (CFX) and sulfadiazine (SDZ), was evaluated in two independent MABRs with nitrifying biofilms. The impacts of CFX and SDZ exposure on the nitrification performance and microbial community structure within biofilms were also investigated. The results showed that nitrifying biofilms were very efficient in removing CFX (94.6%) and SDZ (75.4%) with an initial concentration of 100 μg/L when hydraulic retention time (HRT) was 4 h in the reactors. When HRT decreased from 4 h to 3 h, the removal rates of CFX and SDZ increased significantly from 23.4 ± 1.0 μg/(L·h) and 18.7 ± 1.1 μg/(L·h), respectively, to 27.7 ± 1.3 μg/(L·h) (p＜0.01) and 20.8 ± 2.4 μg/(L·h) (p＜0.05), while the removal efficiencies decreased to 86.0% and 61.5%, respectively. Despite the exposure to CFX and SDZ, the nitrification performance was not affected, and microbial community structure within biofilms also remained relatively stable. This study shows that nitrifying MABR process is a promising option for the efficient removal of antibiotics from domestic wastewater.

The role of mobile genetic elements in organic micropollutant degradation during biological wastewater treatment

Wastewater treatment plants (WWTPs) are crucial for producing clean effluents from polluting sources such as hospitals, industries, and municipalities. In recent decades, many new organic compounds have ended up in surface waters in concentrations that, while very low, cause (chronic) toxicity to countless organisms. These organic micropollutants (OMPs) are usually quite recalcitrant and not sufficiently removed during wastewater treatment. Microbial degradation plays a pivotal role in OMP conversion. Microorganisms can adapt their metabolism to the use of novel molecules via mutations and rearrangements of existing genes in new clusters. Many catabolic genes have been found adjacent to mobile genetic elements (MGEs), which provide a stable scaffold to host new catabolic pathways and spread these genes in the microbial community. These mobile systems could be engineered to enhance OMP degradation in WWTPs, and this review aims to summarize and better understand the role that MGEs might play in the degradation and wastewater treatment process. Available data about the presence of catabolic MGEs in WWTPs are reviewed, and current methods used to identify and measure MGEs in environmental samples are critically evaluated. Finally, examples of how these MGEs could be used to improve micropollutant degradation in WWTPs are outlined. In the near future, advances in the use of MGEs will hopefully enable us to apply selective augmentation strategies to improve OMP conversion in WWTPs.

Microbial Cleavage of C-F Bonds in Two C6 Per- and Polyfluorinated Compounds via Reductive Defluorination

The C-F bond is one of the strongest single bonds in nature. Although microbial reductive dehalogenation is well known for the other organohalides, no microbial reductive defluorination has been documented for perfluorinated compounds except for a single, nonreproducible study on trifluoroacetate. Here, we report on C-F bond cleavage in two C₆ per- and polyfluorinated compounds via reductive defluorination by an organohalide-respiring microbial community. The reductive defluorination was demonstrated by the release of F^- and the formation of the corresponding product when lactate was the electron donor, and the fluorinated compound was the sole electron acceptor. The major dechlorinating species in the seed culture, Dehalococcoides, were not responsible for the defluorination as no growth of Dehalococcoides or active expression of Dehalococcoides-reductive dehalogenases was observed. It suggests that minor phylogenetic groups in the community might be responsible for the reductive defluorination. These findings expand our fundamental knowledge of microbial reductive dehalogenation and warrant further studies on the enrichment, identification, and isolation of responsible microorganisms and enzymes. Given the wide use and emerging concerns of fluorinated organics (e.g., per- and polyfluoroalkyl substances), particularly the perfluorinated ones, the discovery of microbial defluorination under common anaerobic conditions may provide valuable insights into the environmental fate and potential bioremediation strategies of these notorious contaminants.

Comparison of diclofenac transformation in enriched nitrifying sludge and heterotrophic sludge: Transformation rate, pathway, and role exploration

The adverse effects of diclofenac (DCF) on ecosystems and human health have induced increasing interest in its elimination in environment. DCF can be removed to some extent by nitrifying and heterotrophic microbes during wastewater treatment process. However, the actual roles of nitrifying and heterotrophic microbes in the transformation of DCF remain unclear. In this study, batch experiments were conducted to explore the biological transformation of DCF in enriched nitrifying sludge (NS), heterotrophic sludge (HS) and activated sludge (AS) systems. DCF was removed three times faster in enriched NS than in HS. Three transformation pathways of DCF in enriched NS, HS, and AS were proposed and compared. Hydroxylation was the crucial transformation step in the three transformation pathways. A faster hydroxylation reaction contributed to the faster removal of DCF in enriched NS. More transformation products (TPs) and reaction types (i.e. reductive dechlorination, sulphidation and methylation reactions) were observed in HS. Furthermore, some TPs that were resistant to degrade in enriched NS, such as DCF-benzoic acid, could be further transformed in HS. Accordingly, enriched NS could remove DCF more rapidly while HS could further transform some TPs resistant to degrade in enriched NS. Nitrifying and heterotrophic microbes may cooperatively and rapidly eliminate not only DCF, but also its TPs.

Achieving simultaneous nitrogen and antibiotic removal in one-stage partial nitritation-Anammox (PN/A) process

Partial nitritation-Anammox (PN/A) process has been recognized as a sustainable process for biological nitrogen removal. Although various antibiotics have been ubiquitously detected in influent of wastewater treatment plants, little is known whether functional microorganisms in the PN/A process are capable of biodegrading antibiotics. This study aimed to investigate simultaneous nitrogen and antibiotic removal in a lab-scale one-stage PN/A system treating synthetic wastewater containing a widely-used antibiotic, sulfadiazine (SDZ). Results showed that maximum total nitrogen (TN) removal efficiency of 86.1% and SDZ removal efficiency of 95.1% could be achieved when treating 5 mg/L SDZ under DO conditions of 0.5-0.6 mg/L. Compared to anammox bacteria, ammonia-oxidizing bacteria (AOB) made a major contribution to SDZ degradation through their cometabolic pathway. A strong correlation between amoA gene and SDZ removal efficiency was found (p < 0.01). In addition, the degradation products of SDZ did not exhibit any inhibitory effects on Escherichia coli. The findings suggest that it is promising to apply the PN/A process to simultaneously remove antibiotics and nitrogen from contaminated wastewater.

Inhibition of Ammonia Monooxygenase from Ammonia-Oxidizing Archaea by Linear and Aromatic Alkynes

Ammonia monooxygenase (AMO) is a key nitrogen-transforming enzyme belonging to the same copper-dependent membrane monooxygenase family (CuMMO) as the particulate methane monooxygenase (pMMO). The AMO from ammonia-oxidizing archaea (AOA) is very divergent from both the AMO of ammonia-oxidizing bacteria (AOB) and the pMMO from methanotrophs, and little is known about the structure or substrate range of the archaeal AMO. This study compares inhibition by C2 to C8 linear 1-alkynes of AMO from two phylogenetically distinct strains of AOA, "Candidatus Nitrosocosmicus franklandus" C13 and "Candidatus Nitrosotalea sinensis" Nd2, with AMO from Nitrosomonas europaea and pMMO from Methylococcus capsulatus (Bath). An increased sensitivity of the archaeal AMO to short-chain-length alkynes (≤C5) appeared to be conserved across AOA lineages. Similarities in C2 to C8 alkyne inhibition profiles between AMO from AOA and pMMO from M. capsulatus suggested that the archaeal AMO has a narrower substrate range than N. europaea AMO. Inhibition of AMO from "Ca Nitrosocosmicus franklandus" and N. europaea by the aromatic alkyne phenylacetylene was also investigated. Kinetic data revealed that the mechanisms by which phenylacetylene inhibits "Ca Nitrosocosmicus franklandus" and N. europaea are different, indicating differences in the AMO active site between AOA and AOB. Phenylacetylene was found to be a specific and irreversible inhibitor of AMO from "Ca Nitrosocosmicus franklandus," and it does not compete with NH3 for binding at the active site.IMPORTANCE Archaeal and bacterial ammonia oxidizers (AOA and AOB, respectively) initiate nitrification by oxidizing ammonia to hydroxylamine, a reaction catalyzed by ammonia monooxygenase (AMO). AMO enzyme is difficult to purify in its active form, and its structure and biochemistry remain largely unexplored. The bacterial AMO and the closely related particulate methane monooxygenase (pMMO) have a broad range of hydrocarbon cooxidation substrates. This study provides insights into the AMO of previously unstudied archaeal genera, by comparing the response of the archaeal AMO, a bacterial AMO, and pMMO to inhibition by linear 1-alkynes and the aromatic alkyne, phenylacetylene. Reduced sensitivity to inhibition by larger alkynes suggests that the archaeal AMO has a narrower hydrocarbon substrate range than the bacterial AMO, as previously reported for other genera of AOA. Phenylacetylene inhibited the archaeal and bacterial AMOs at different thresholds and by different mechanisms of inhibition, highlighting structural differences between the two forms of monooxygenase.

Unravelling kinetic and microbial responses of enriched nitrifying sludge under long-term exposure of cephalexin and sulfadiazine

Wastewater treatment plants (WWTPs) have been identified as one of the reservoirs of antibiotics. Although nitrifying bacteria have been reported to be capable of degrading various antibiotics, there are very few studies investigating long-term effects of antibiotics on kinetic and microbial responses of nitrifying bacteria. In this study, cephalexin (CFX) and sulfadiazine (SDZ) were selected to assess chronic impacts on nitrifying sludge with stepwise increasing concentrations in two independent bioreactors. The results showed that CFX and SDZ at an initial concentration of 100 μg/L could be efficiently removed by enriched nitrifying sludge, as evidenced by removal efficiencies of more than 88% and 85%, respectively. Ammonia-oxidizing bacteria (AOB) made a major contribution to the biodegradation of CFX and SDZ via cometabolism, compared to limited contributions from heterotrophic bacteria and nitrite-oxidizing bacteria. Chronic exposure to CFX (≥30 μg/L) could stimulate ammonium oxidation activity in terms of a significant enhancement of ammonium oxidation rate (p < 0.01). In contrast, the ammonium oxidation activity was inhibited due to exposure to 30 μg/L SDZ (p < 0.01), then it recovered after long-term adaption under exposure to 50 and 100 μg/L SDZ. In addition, 16S rRNA gene amplicon sequencing revealed that the relative abundance of AOB decreased distinctly from 23.8% to 28.8% in the control phase (without CFX or SDZ) to 14.2% and 10.8% under exposure to 100 μg/L CFX and SDZ, respectively. However, the expression level of amoA gene was up-regulated to overcome this adverse impact and maintain a stable and efficient removal of both ammonium and antibiotics. The findings in this study shed a light on chronic effects of antibiotic exposure on kinetic and microbial responses of enriched nitrifying sludge in WWTPs.

New perspectives on microbial communities and biological nitrogen removal processes in wastewater treatment systems

Biological nitrogen removal (BNR) is a critical process in wastewater treatment. Recently, there have new microbial communities been discovered to be capable of performing BNR with novel metabolic pathways. This review presents the up-to-date status on these microorganisms, including ammonia oxidizing archaea (AOA), complete ammonia oxidation (COMAMMOX) bacteria, anaerobic ammonium oxidation coupled to iron reduction (FEAMMOX) bacteria, anaerobic ammonium oxidation (ANAMMOX) bacteria and denitrifying anaerobic methane oxidation (DAMO) microorganism. Their metabolic pathways and enzymatic reactions in nitrogen cycle are demonstrated. Generally, these novel microbial communities have advantages over canonical nitrifiers or denitrifiers, such as higher substrate affinities, better physicochemical tolerances and/or less greenhouse gas emission. Also, their recent development and/or implementation in BNR is discussed and outlook. Finally, the key implications of coupling these microbial communities for BNR are identified. Overall, this review illustrates novel microbial communities that could provide new possibilities for high-performance and energy-saving nitrogen removal from wastewater.

Insight into the nitrification kinetics and microbial response of an enriched nitrifying sludge in the biodegradation of sulfadiazine

The intensive use of antibiotics results in the continuous release of antibiotics into wastewater treatment systems, leading to the spread of antibiotic resistance. Nitrifying system is reported to be capable of degrading antibiotics, yet few studies have systematically investigated the inherent correlation among ammonium oxidation rate, antibiotic degradation and genetic expression of nitrifying bacteria along the process. This study selected a widely used sulfonamide antibiotic, sulfadiazine (SDZ), to investigate its biodegradation potential by an enriched nitrifying culture and the response of nitrifying bacteria against antibiotic exposure. Our results demonstrated that SDZ degradation was mainly contributed by cometabolism of ammonia-oxidizing bacteria (AOB), rather than biomass adsorption. The quantitative reverse transcription PCR (RT-qPCR) analysis revealed that the expression level of amoA gene was down-regulated due to the SDZ exposure. In addition, the degradation products of SDZ did not exhibit inhibitory effect on Escherichia coli K12, indicating the biotoxicity of SDZ could be mitigated after biodegradation. The findings offer insights regarding the biodegradation process of sulfonamide antibiotics via cometabolism by AOB.

Archaeal nitrification is constrained by copper complexation with organic matter in municipal wastewater treatment plants

Consistent with the observation that ammonia-oxidizing bacteria (AOB) outnumber ammonia-oxidizing archaea (AOA) in many eutrophic ecosystems globally, AOB typically dominate activated sludge aeration basins from municipal wastewater treatment plants (WWTPs). In this study, we demonstrate that the growth of AOA strains inoculated into sterile-filtered wastewater was inhibited significantly, in contrast to uninhibited growth of a reference AOB strain. In order to identify possible mechanisms underlying AOA-specific inhibition, we show that complex mixtures of organic compounds, such as yeast extract, were highly inhibitory to all AOA strains but not to the AOB strain. By testing individual organic compounds, we reveal strong inhibitory effects of organic compounds with high metal complexation potentials implying that the inhibitory mechanism for AOA can be explained by the reduced bioavailability of an essential metal. Our results further demonstrate that the inhibitory effect on AOA can be alleviated by copper supplementation, which we observed for pure AOA cultures in a defined medium and for AOA inoculated into nitrifying sludge. Our study offers a novel mechanistic explanation for the relatively low abundance of AOA in most WWTPs and provides a basis for modulating the composition of nitrifying communities in both engineered systems and naturally occurring environments.

Specific Micropollutant Biotransformation Pattern by the Comammox Bacterium Nitrospira inopinata

The recently discovered complete ammonia-oxidizing (comammox) bacteria occur in various environments, including wastewater treatment plants. To better understand their role in micropollutant biotransformation in comparison with ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), we investigated the biotransformation capability of Nitrospira inopinata (the only comammox isolate) for 17 micropollutants. Asulam, fenhexamid, mianserin, and ranitidine were biotransformed by N. inopinata, Nitrososphaera gargensis (AOA), and Nitrosomonas nitrosa Nm90 (AOB). More distinctively, carbendazim, a benzimidazole fungicide, was exclusively biotransformed by N. inopinata. The biotransformation of carbendazim only occurred when N. inopinata was supplied with ammonia but not nitrite as the energy source. The exclusive biotransformation of carbendazim by N. inopinata was likely enabled by an enhanced substrate promiscuity of its unique AMO and its much higher substrate (for ammonia) affinity compared with the other two ammonia oxidizers. One major plausible transformation product (TP) of carbendazim is a hydroxylated form at the aromatic ring, which is consistent with the function of AMO. These findings provide fundamental knowledge on the micropollutant degradation potential of a comammox bacterium to better understand the fate of micropollutants in nitrifying environments.

Cometabolic biotransformation and microbial-mediated abiotic transformation of sulfonamides by three ammonia oxidizers

The abilities of three phylogenetically distant ammonia oxidizers, Nitrososphaera gargensis, an ammonia-oxidizing archaeon (AOA); Nitrosomomas nitrosa Nm90, an ammonia-oxidizing bacterium (AOB); and Nitrospira inopinata, the only complete ammonia oxidizer (comammox) available as a pure culture, to biotransform seven sulfonamides (SAs) were investigated. The removals and protein-normalized biotransformation rate constants indicated that the AOA strain N. gargensis exhibited the highest SA biotransformation rates, followed by N. inopinata and N. nitrosa Nm90. The transformation products (TPs) of sulfadiazine (SDZ), sulfamethazine (SMZ) and sulfamethoxazole (SMX) and the biotransformation mechanisms were evaluated. Based on the analysis of the TP formulas and approximate structures, it was found that during biotransformation, i) the AOA strain carried out SA deamination, hydroxylation, and nitration; ii) the AOB strain mainly performed SA deamination; and iii) the comammox isolate participated only in deamination reactions. It is proposed that deamination was catalyzed by deaminases while hydroxylation and nitration were mediated by nonspecific activities of the ammonia monooxygenase (AMO). Additionally, it was demonstrated that among the three ammonia oxidizers, only AOB contributed to the formation of pterin-SA conjugates. The biotransformation of SDZ, SMZ and SMX occurred only when ammonia oxidation was active, suggesting a cometabolic transformation mechanism. Interestingly, SAs could also be transformed by hydroxylamine, an intermediate of ammonia oxidation, suggesting that in addition to enzymatic conversions, a microbially induced abiotic mechanism contributes to SA transformation during ammonia oxidation. Overall, using experiments with pure cultures, this study provides important insights into the roles played by ammonia oxidizers in SA biotransformation.

Cometabolic biodegradation of cephalexin by enriched nitrifying sludge: Process characteristics, gene expression and product biotoxicity

The nitrifying systems have been reported to be able to biodegrade micropollutants, yet it is still unclear about the cometabolism of ammonia-oxidizing bacteria (AOB) towards micropollutants, in particular their enzyme and transcriptional responses under exposure of micropollutants. This study investigated cometabolic biodegradation of a selected antibiotic, cephalexin (CFX), by an enriched nitrifying culture through a series of batch experiments, together with the assessments of enzymatic activity, key gene expression, and biotoxicity of the degradation products. More than 99% CFX with an initial concentration of 50 μg/L could be removed with the presence of ammonium, while <44% of CFX removal was observed in the absence of ammonium, suggesting the cometabolic degradation of CFX by ammonia-oxidizing bacteria (AOB). After the addition of 50 μg/L CFX, the ammonia oxidizing rate (AOR) decreased from 36.6 to 11.0 mg N/(L·h·g VSS), followed by a slight recovery when CFX concentration decreased to below 8 μg/L. Ammonia monooxygenase (AMO) activity showed a similar trend with that of AOR. The quantitative reverse transcription PCR assay indicated that the expression level of amoA gene was significantly upregulated (up to 3-fold, p < 0.05) due to the addition of CFX, while decreased to the normal level once CFX was degraded, suggesting a mechanism of AOB to neutralize the toxicity of CFX by metabolizing ammonia more effectively. Meanwhile, the biotoxicity test showed the degradation products of CFX did not exhibit any antibacterial impacts in terms of cell viability, compared to the parent compounds. Our finding shed a light on AMO-mediated cometabolic biodegradation of antibiotics in nitrifying cultures.

Diverse aromatic-degrading bacteria present in a highly enriched autotrophic nitrifying sludge

Biotransformation of refractory organics by ammonia-oxidizing microorganisms in nitrifying sludge have been widely reported, while the contribution of heterotrophic bacteria in nitrifying sludge in the biotransformation and degradation process might be overlooked. Here, we provide metagenomic and metatranscriptomic evidences showing that heterotrophic bacteria in a highly enriched autotrophic nitrifying sludge could significantly contribute to the aromatic biotransformation and biodegradation. Diverse genes encoding enzymes for aromatic degradation were observed in an enriched autotrophic nitrifying sludge. These genes are involved in the degradation of at least 15 complex aromatics. Genome binning results showed that these genes were mainly carried by species in Bacteroidetes (Flavobacteriaceae and Sphingobacteriales), Alphaproteobacteria (Rhodobacter) and Betaproteobacteria (Bordetella, Acidovorax, Ramlibacter and Pusillimonas). According to the metatranscriptomic analysis, the overall expression of the potential aromatic-degrading genes was significantly upregulated, and almost all genes involved in phenol degradation were over expressed after the nitrifying sludge was exposed to phenol. Overall, our results suggest that certain heterotrophs in nitrifying sludge are involved aromatic biotransformation and biodegradation and advance our knowledge of the underlying properties and metabolic mechanisms of the nitrifying sludge.

Effects of antibiotic residuals in dewatered sludge on the behavior of ammonia oxidizers during vermicomposting maturation process

Antibiotics existed in dewatered sludge may affect the organic decomposition and nitrification efficiency of vermicomposting process, and thus lowering the agricultural value of sludge vermicompost. However, few studies have focused on the effects of antibiotics during vermicomposting process of sludge, notably for the maturated phage. Hence, this study aimed to investigate the effects of antibiotics on the nitrification rate and the features of ammonia oxidizing archaea (AOA) and bacteria (AOB) during vermicomposting maturated phage of sludge. The treatments including the additions of tetracycline and ofloxacin with high and low concentrations were compared with the control without adding antibiotics. The results showed the antibiotics enhanced the nitrification rate of 15.8%-42% in vermicomposting maturated phage compared with the counterpart, with a better stimulating effect in the low concentration of tetracycline. The population of amoA genes increased in antibiotic treatments with low concentrations but decreased in these with high concentrations. In addition, high through-put sequencing results revealed that the tetracycline had a stronger influence on the α and β diversities of AOA and AOB, relative to the ofloxacin. In contrast to the AOB, the AOA played a more important role in ammonia oxidization, in the presence of antibiotics. This study suggests that the antibiotics of dewatered sludge can strongly affect the ammonia oxidization process through modifying the numbers and community structures of AOA and AOB during vermicomposting and these effects are associated with the types and concentrations of antibiotics.

Overview of sulfonamide biodegradation and the relevant pathways and microorganisms

Sulfonamide antibiotics have aroused increasing concerns due to their ability to enhance the resistance of pathogenic bacteria and promote the spread of antibiotic resistance. Biodegradation plays an important role in sulfonamide dissipation in both natural and engineered ecosystems. In this article, we provided an overview of sulfonamide biodegradation in different systems and summarized the relevant sulfonamide-degrading species and metabolic pathways. The removal of sulfonamides depends on a variety of factors, such as the type and initial concentration of sulfonamides, the properties of water or soil, and treatment process. The removal efficiency of sulfonamides by engineered ecosystems can be improved by optimizing their operating conditions. Much higher sulfonamide removal was also observed in upgraded or advanced treatment systems than in conventional activated sludge systems. Ammonia oxidation might promote sulfonamide biodegradation. In addition, sulfonamide-degraders from different bacterial genera have been isolated and classified, but no bioaugmentation practice has been reported. Different pathways have been detected in sulfonamide biodegradation. Further efforts will be necessary to elucidate in-situ degraders and the metabolic pathways and functional genes of sulfonamide biodegradation.

Trends in Micropollutant Biotransformation along a Solids Retention Time Gradient

For many polar organic micropollutants, biotransformation by activated sludge microorganisms is a major removal process during wastewater treatment. However, our current understanding of how wastewater treatment operations influence microbial communities and their micropollutant biotransformation potential is limited, leaving major parts of observed variability in biotransformation rates across treatment facilities unexplained. Here, we present biotransformation rate constants for 42 micropollutants belonging to different chemical classes along a gradient of solids retention time (SRT). The geometric mean of biomass-normalized first-order rate constants shows a clear increase between 3 and 15 d SRT by 160% and 87%, respectively, in two experiments. However, individual micropollutants show a variety of trends. Rate constants of oxidative biotransformation reactions mostly increased with SRT. Yet, nitrifying activity could be excluded as primary driver. For substances undergoing other than oxidative reactions, i.e., mostly substitution-type reactions, more diverse dependencies on SRT were observed. Most remarkably, characteristic trends were observed for groups of substances undergoing similar types of initial transformation reaction, suggesting that shared enzymes or enzyme systems that are conjointly regulated catalyze biotransformation reactions within such groups. These findings open up opportunities for correlating rate constants with measures of enzyme abundance such as genes or gene products, which in turn should help to identify enzymes associated with the respective biotransformation reactions.

Ammonia Monooxygenase-Mediated Cometabolic Biotransformation and Hydroxylamine-Mediated Abiotic Transformation of Micropollutants in an AOB/NOB Coculture

Biotransformation of various micropollutants (MPs) has been found to be positively correlated with nitrification in activated sludge communities. To further elucidate the roles played by ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), we investigated the biotransformation capabilities of an NOB pure culture ( Nitrobacter sp.) and an AOB ( Nitrosomonas europaea)/NOB ( Nitrobacter sp.) coculture for 15 MPs, whose biotransformation was reported previously to be associated with nitrification. The NOB pure culture did not biotransform any investigated MP, whereas the AOB/NOB coculture was capable of biotransforming six MPs (i.e., asulam, bezafibrate, fenhexamid, furosemide, indomethacin, and rufinamide). Transformation products (TPs) were identified, and tentative structures were proposed. Inhibition studies with octyne, an ammonia monooxygenase (AMO) inhibitor, suggested that AMO was the responsible enzyme for MP transformation that occurred cometabolically. For the first time, hydroxylamine, a key intermediate of all aerobic ammonia oxidizers, was found to react with several MPs at concentrations typically occurring in AOB batch cultures. All of these MPs were also biotransformed by the AOB/NOB coculture. Moreover, the same asulam TPs were detected in both biotransformation and hydroxylamine-treated abiotic transformation experiments, whereas rufinamide TPs formed from biological transformation were not detected during hydroxylamine-mediated abiotic transformation, which was consistent with the inability of rufinamide abiotic transformation by hydroxylamine. Thus, in addition to cometabolism likely carried out by AMO, an abiotic transformation route indirectly mediated by AMO might also contribute to MP biotransformation by AOB.

Modeling of Pharmaceutical Biotransformation by Enriched Nitrifying Culture under Different Metabolic Conditions

Pharmaceutical removal could be significantly enhanced through cometabolism during nitrification processes. To date, pharmaceutical biotransformation models have not considered the formation of transformation products associated with the metabolic type of microorganisms. Here we report a comprehensive model to describe and evaluate the biodegradation of pharmaceuticals and the formation of their biotransformation products by enriched nitrifying cultures. The biotransformation of parent compounds was linked to the microbial processes via cometabolism induced by ammonium-oxidizing bacteria (AOB) growth, metabolism by AOB, cometabolism by heterotrophs (HET) growth, and metabolism by HET in the model framework. The model was calibrated and validated using experimental data from pharmaceutical biodegradation experiments at realistic levels, taking two pharmaceuticals as examples, i.e., atenolol and acyclovir. Results demonstrated the good predictive performance of the established biotransformation model under different metabolic conditions, as well as the reliability of the established model in predicting different pharmaceutical biotransformations. The linear positive correlation between ammonia oxidation rate and pharmaceutical degradation rate confirmed the major role of cometabolism induced by AOB in the pharmaceutical removal. Dissolved oxygen was also revealed to be capable of regulating the pharmaceutical biotransformation cometabolically, and the substrate competition between ammonium and pharmaceuticals existed especially at high ammonium concentrations.