FMNH2-dependent monooxygenases initiate catabolism of sulfonamides in Microbacterium sp. strain BR1 subsisting on sulfonamide antibiotics

Sulfamethoxazole is Metabolized and Mineralized at Extremely Low Concentrations

The presence of organic micropollutants in water and sediments motivates investigation of their biotransformation at environmentally low concentrations, usually in the range of μg L-1. Many are biotransformed by cometabolic mechanisms; however, there is scarce information concerning their direct metabolization in this concentration range. Threshold concentrations for microbial assimilation have been reported in both pure and mixed cultures from different origins. The literature suggests a range value for bacterial growth of 1-100 μg L-1 for isolated aerobic heterotrophs in the presence of a single substrate. We aimed to investigate, as a model case, the threshold level for sulfamethoxazole (SMX) metabolization in pure cultures of Microbacterium strain BR1. Previous research with this strain has covered the milligram L-1 range. In this study, acclimated cultures were exposed to concentrations from 0.1 to 25 μg L-1 of 14C-labeled SMX, and the 14C-CO2 produced was trapped and quantified over 24 h. Interestingly, SMX removal was rapid, with 98% removed within 2 h. In contrast, mineralization was slower, with a consistent percentage of 60.0 ± 0.7% found at all concentrations. Mineralization rates increased with rising concentrations. Therefore, this study shows that bacteria are capable of the direct metabolization of organic micropollutants at extremely low concentrations (sub μg L-1).

Isolation, identification and whole-genome analysis of an Achromobacter strain with a novel sulfamethazine resistance gene and sulfamethazine degradation gene cluster

A sulfamethazine (SM2) degrading strain, Achromobacter mucicolens JD417, was isolated from sulfonamide-contaminated sludge using gradient acclimation. Optimal SM2 degradation conditions were pH 7, 36 °C, and 5 % inoculum, achieving a theoretical maximum degradation rate of 48 % at 50 ppm SM2. Cell growth followed the Haldane equation across different SM2 concentrations. Whole-genome sequencing of the strain revealed novel functional annotations, including a sulfonamide resistance gene (sul4) encoding dihydropteroate synthase, two flavin-dependent monooxygenase genes (sadA and sadB) crucial for SM2 degradation, and unique genomic islands related to metabolism, pathogenicity, and resistance. Comparative genomics analysis showed good collinearity and homology with other Achromobacter species exhibiting organics resistance or degradation capabilities. This study reveals the novel molecular resistance and degradation mechanisms and genetic evolution of an SM2-degrading strain, providing insights into the bioremediation of sulfonamide-contaminated environments.

Natural attenuation of sulfonamides and metabolites in contaminated groundwater - Review, advantages and challenges of current documentation techniques

Sulfonamides are applied worldwide as antibiotics. They are emerging contaminants of concern, as their presence in the environment may lead to the spread of antibiotic resistance genes. Sulfonamides are present in groundwater systems, which suggest their persistence under certain conditions, highlighting the importance of understanding natural attenuation processes in groundwater. Biodegradation is an essential process, as degradation of sulfonamides reduces the risk of antibiotic resistance spreading. In this review, natural attenuation, and in particular assessment of biodegradation, is evaluated for sulfonamides in groundwater systems. The current knowledge level on biodegradation is reviewed, and a scientific foundation is built based on sulfonamide degradation processes, pathways, metabolites and toxicity. An overview of bacterial species and related metabolites is provided. The main research effort has focused on aerobic conditions while investigations under anaerobic conditions are lacking. The level of implementation in research is laboratory scale; here we strived to bridge towards field application and assessment, by assessing approaches commonly used in monitored natural attenuation. Methods to document contaminant mass loss are assessed to be applicable for sulfonamides, while the approach is limited by a lack of reference standards for metabolites. Furthermore, additional information is required on relevant metabolites in order to improve risk assessments. Based on the current knowledge on biodegradation, it is suggested to use the presence of substituent-containing metabolites from breakage of the sulfonamide bridge as specific indicators of degradation. Microbial approaches are currently available for assessment of microbial community's capacities, however, more knowledge is required on indigenous bacteria capable of degrading sulfonamides and on the impact of environmental conditions on biodegradation. Compound specific stable isotope analysis shows great potential as an additional in situ method, but further developments are required to analyse for sulfonamides at environmentally relevant levels. Finally, in a monitored natural attenuation scheme it is assessed that approaches are available that can uncover some processes related to the fate of sulfonamides in groundwater systems. Nevertheless, there are still unknowns related to relevant bacteria and metabolites for risk assessment as well as the effect of environmental settings such as redox conditions. Alongside, uncovering the fate of sulfonamides in future research, the applicability of the natural attenuation documentation approaches will advance, and provide a step towards in situ remedial concepts for the frequently detected sulfonamides.

How data on transformation products can support the redesign of sulfonamides towards better biodegradability in the environment

Sulfonamide antibiotics (SUAs) released into the environment can affect environmental und human health, e.g., by accelerating the development and selection of antimicrobial resistant bacteria. Benign by Design (BbD) of SUAs is an effective risk prevention approach. BbD principles aim for fast and complete mineralization or at least deactivation of the SUA after release into the aquatic environment. Main objective was to test if mixtures of transformation products (TPs) generated via photolysis of SUAs can be used as an efficient way to screen for similarly effective but better biodegradable SUA alternatives. Six SUAs were photolyzed (Hg ultraviolet (UV) light), and generated UV-mixtures analysed by high performance liquid chromatography coupled to an UV and tandem mass spectrometry detector. UV-mixtures were screened for antibiotic activity (luminescence bacteria test, LBT, on luminescence and growth inhibition of Aliivibrio Fischeri) and environmental biodegradability (manometric respirometry test, MRT, OECD 301F) using untreated parent SUAs in comparison. Additionally, ready environmental biodegradability of three commercially available hydroxylated sulfanilamide derivatives was investigated. SUA-TPs contributed to acute and chronic bacterial luminescence inhibition by UV-mixtures. LBT's third endpoint, growth inhibition, was not significant for UV-mixtures. However, it cannot be excluded for tested TPs as concentrations were lower than parents' concentrations and inhibition by most parental concentrations tested was also not significant. HPLC analysis of MRT samples revealed that one third of SUA-TPs was reduced during incubation. Three of these TPs, likely OH-SIX, OH-SMX and OH-STZ, were of interest for BbD because the sulfonamide moiety is still present. However, hydroxylated sulfanilamide derivatives, tested to investigate the effect of hydroxylation on biodegradability, were not readily biodegraded. Thus, improving mineralization through hydroxylation as a general rule couldn't be confirmed, and no BbD candidate could be identified. This study fills data gaps on bioactivity and environmental biodegradability of SUAs' TP-mixtures. Findings may support new redesign approaches.

A novel enrofloxacin-degrading fungus, Humicola sp. KC0924g, isolated from the rhizosphere sediment of the submerged macrophyte Vallisneria spiralis L

A novel enrofloxacin-degrading fungus was isolated from a rhizosphere sediment of the submerged macrophyte Vallisneria spiralis L.. The isolate, designated KC0924g, was identified as a member of the genus Humicola based on morphological characteristics and tandem conserved sequence analysis. The optimal temperature and pH for enrofloxacin degradation by strain KC0924g were 28 °C and 9.0, respectively. Under such condition, 98.2% of enrofloxacin with an initial concentration of 1 mg L-1 was degraded after 72 h of incubation, with nine possible degradation products identified. Four different metabolic pathways were proposed, which were initiated by cleavage of the piperazine moiety, hydroxylation of the aromatic ring, oxidative decarboxylation, or defluorination. In addition to enrofloxacin, strain KC0924g also degraded other fluoroquinolone antibiotics (ciprofloxacin, norfloxacin, and ofloxacin), malachite green (an illegal additive in aquaculture), and leucomalachite green. Pretreatment of cells of strain KC0924g with Cu2+ accelerated ENR degradation. Furthermore, it was speculated that a flavin-dependent monooxygenase was involved in ENR degradation, based on the increased transcriptional levels of these two genes after Cu2+ induction. This work enriches strain resources for enrofloxacin remediation and, more importantly, would facilitate studies on the molecular mechanism of ENR degradation with degradation-related transcriptome available.

Identification of sulfamethazine degraders in swine farm-impacted river and farmland: A comparative study of aerobic and anaerobic environments

Sulfonamides (SAs) are extensively used antibiotics in the prevention and treatment of animal diseases, leading to significant SAs pollution in surrounding environments. Microbial degradation has been proposed as a crucial mechanism for removing SAs, but the taxonomic identification of microbial functional guilds responsible for SAs degradation in nature remain largely unexplored. Here, we employed 13C-sulfamethazine (SMZ)-based DNA-stable isotope probing (SIP) and metagenomic sequencing to investigate SMZ degraders in three distinct swine farm wastewater-receiving environments within an agricultural ecosystem. These environments include the aerobic riparian wetland soil, agricultural soil, and anaerobic river sediment. SMZ mineralization activities exhibited significant variation, with the highest rate observed in aerobic riparian wetland soil. SMZ had a substantial impact on the microbial community compositions across all samples. DNA-SIP analysis demonstrated that Thiobacillus, Auicella, Sphingomonas, and Rhodobacter were dominant active SMZ degraders in the wetland soil, whereas Ellin6067, Ilumatobacter, Dongia, and Steroidobacter predominated in the agricultural soil. The genus MND1 and family Vicinamibacteraceae were identified as SMZ degrader in both soils. In contrast, anaerobic SMZ degradation in the river sediment was mainly performed by genera Microvirga, Flavobacterium, Dechlorobacter, Atopostipes, and families Nocardioidaceae, Micrococcaceae, Anaerolineaceae. Metagenomic analysis of 13C-DNA identified key SAs degradation genes (sadA and sadC), and various of dioxygenases, and aromatic hydrocarbon degradation-related functional genes, indicating their involvement in degradation of SMZ and its intermediate products. These findings highlight the variations of indigenous SAs oxidizers in complex natural habitats and emphasize the consideration of applying these naturally active degraders in future antibiotic bioremediation.

Biodegradation strategies of veterinary medicines in the environment: Enzymatic degradation

One Health closely integrates healthy farming, human medicine, and environmental ecology. Due to the ecotoxicity and risk of transmission of drug resistance, veterinary medicines (VMs) are regarded as emerging environmental pollutants. To reduce or mitigate the environmental risk of VMs, developing friendly, safe, and effective removal technologies is an important means of environmental remediation for VMs. Many previous studies have proved that biodegradation has significant advantages in removing VMs, and biodegradation based on enzyme catalysis presents higher operability and specificity. This review focused on biodegradation strategies of environmental pollutants and reviewed the enzymatic degradation of VMs including antimicrobial drugs, insecticides, and disinfectants. We reviewed the sources and catalytic mechanisms of peroxidase, laccase, and organophosphorus hydrolases, and summarized the latest research status of immobilization methods and bioengineering techniques in improving the performance of degrading enzymes. The mechanism of enzymatic degradation for VMs was elucidated in the current research. Suggestions and prospects for researching and developing enzymatic degradation of VMs were also put forward. This review will offer new ideas for the biodegradation of VMs and have a guide significance for the risk mitigation and detoxification of VMs in the environment.

Performance and mechanism of SMX removal by an electrolysis-integrated ecological floating bed at low temperatures: A new perspective of plant activity, iron plaque, and microbial functions

Improvements in plant activity and functional microbial communities are important to ensure the stability and efficiency of pollutant removal measures in cold regions. Although electrochemistry is known to accelerate pollutant degradation, cold stress acclimation of plants and the stability and activity of plant-microbial synergism remain poorly understood. The sulfamethoxazole (SMX) removal, iron plaque morphology, plant activity, microbial community, and function responses were investigated in an electrolysis-integrated ecological floating bed (EFB) at 6 ± 2 ℃. Electrochemistry significantly improved SMX removal and plant activity. Dense and uniform iron plaque was found on root surfaces in L-E-Fe which improved the plant adaptability at low temperatures and provided more adsorption sites for bacteria. The microbial community structure was optimized and the key functional bacteria for SMX degradation (e.g., Actinobacteriota, Pseudomonas) were enriched. Electrochemistry improves the relative abundance of enzymes related to energy metabolism, thereby increasing energy responses to SMX and low temperatures. Notably, electrochemistry improved the expression of target genes (sadB and sadC, especially sadC) involved in SMX degradation. Electrochemistry enhances hydrogen bonding and electrostatic interactions between SMX and sadC, thereby enhancing SMX degradation and transformation. This study provides a deeper understanding of the electrochemical stability of antibiotic degradation at low temperatures.

Promising bioprocesses for the efficient removal of antibiotics and antibiotic-resistance genes from urban and hospital wastewaters: Potentialities of aerobic granular systems

The use, overuse, and improper use of antibiotics have resulted in higher levels of antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs), which have profoundly disturbed the equilibrium of the environment. Furthermore, once antibiotic agents are excreted in urine and feces, these substances often can reach wastewater treatment plants (WWTPs), in which improper treatments have been highlighted as the main reason for stronger dissemination of antibiotics, ARB, and ARGs to the receiving bodies. Hence, achieving better antibiotic removal capacities in WWTPs is proposed as an adequate approach to limit the spread of antibiotics, ARB, and ARGs into the environment. In this review, we highlight hospital wastewater (WW) as a critical hotspot for the dissemination of antibiotic resistance due to its high level of antibiotics and pathogens. Hence, monitoring the composition and structure of the bacterial communities related to hospital WW is a key factor in controlling the spread of ARGs. In addition, we discuss the advantages and drawbacks of the current biological WW treatments regarding the antibiotic-resistance phenomenon. Widely used conventional activated sludge technology has proved to be ineffective in mitigating the dissemination of ARB and ARGs to the environment. However, aerobic granular sludge (AGS) technology is a promising technology-with broad adaptability and excellent performance-that could successfully reduce antibiotics, ARB, and ARGs in the generated effluents. We also outline the main operational parameters involved in mitigating antibiotics, ARB, and ARGs in WWTPs. In this regard, WW operation under long hydraulic and solid retention times allows better removal of antibiotics, ARB, and ARGs independently of the WW technology employed. Finally, we address the current knowledge of the adsorption and degradation of antibiotics and their importance in removing ARB and ARGs. Notably, AGS can enhance the removal of antibiotics, ARB, and ARGs due to the complex microbial metabolism within the granular biomass.

Binding order of substrate and cofactor in sulfonamide monooxygenase during sulfa drug degradation: in silico studies

For decades, sulfonamide antibiotics have been used across industries such as agriculture and animal husbandry. However, the use and inadvertent misuse of these antibiotics have resulted in the advent of sulfonamide-drug-resistant strains due to antibiotic pollution. Enzymatic bioremediation of antibiotics remains a potential emerging solution to combat antibiotic pollution. Here, we propose an enzymatic model for the degradation of sulfonamides by Microbacterium sp. We have employed a multi-pronged computational strategy involving - protein structure modelling, ligand docking and molecular dynamics simulations to decipher a plausible binding order for the enzymatic degradation of sulfonamides by the bacterial sulfonamide monooxygenase, SulX. Our results enable us to predict that this degradation is achieved through the sequential binding of the antibiotic sulfonamide followed by the reduced flavin cofactor FMNH2, thereby laying the computational foundation for further advancements in enzyme-mediated degradation of the antibiotic. We also provide a list of experiments which may be performed to verify and follow-up on our in-silico studies.Communicated by Ramaswamy H. Sarma.

Strain-level diversity in sulfonamide biodegradation: adaptation of Paenarthrobacter to sulfonamides

The widespread occurrence of sulfonamides raises significant concerns about the evolution and spread of antibiotic resistance genes. Biodegradation represents not only a resistance mechanism but also a clean-up strategy. Meanwhile, dynamic and diverse environments could influence the cellular function of individual sulfonamide-degrading strains. Here, we present Paenarthrobacter from different origins that demonstrated diverse growth patterns and sulfonamide-degrading abilities. Generally, the degradation performance was largely associated with the number of sadA gene copies and also relied on its genotype. Based on the survey of sad genes in the public database, an independent mobilization of transposon-borne genes between chromosome and plasmid was observed. Insertions of multiple sadA genes could greatly enhance sulfonamide-degrading performance. Moreover, the sad gene cluster and sadA transposable element showed phylogenetic conservation currently, being identified only in two genera of Paenarthrobacter (Micrococcaceae) and Microbacterium (Microbacteriaceae). Meanwhile, Paenarthrobacter exhibited a high capacity for genome editing to adapt to the specific environmental niche, opening up new opportunities for bioremediation applications.

Simulated-sunlight enhances membrane aerated biofilm reactor performance in sulfamethoxazole removal and antibiotic resistance genes reduction

Membrane aerated biofilm reactors (MABRs) can be used to treat domestic wastewater containing sulfamethoxazole (SMX) because of their favorable performance in the treatment of refractory pollutants. However, biologics are generally subjected to antibiotics stress, which induces the production of antibiotic resistance genes (ARGs). In this study, a simulated-sunlight assisted MABR (L-MABR) was used to promote SMX removal and reduce ARGs production. The SMX removal efficiency of the l-MABR system was 9.62 % superior to that of the MABR system (83.13 %). In contrast from MABR, in the l-MABR, only 28.75 % of SMX was removed through microbial activity because functional bacteria were inactivated through radiation by simulated sunlight. In addition, photolysis (64.61 %) dominated SMX removal, and the best performing indirect photolysis process was the excited state of effluent organic matters (3EfOMs*). Through photolysis, ultraviolet (UV) and reactive oxygen species (ROS) enriched the SMX removal route, resulting in the SMX removal pathway in the l-MABR no longer being limited by enzyme catalysis. More importantly, because of the inactivation of functional bacteria, whether in the effluent or biofilm, the copy number of ARGs in the l-MABR was 1-3 orders of magnitude lower than that in the MABR. Our study demonstrates the feasibility of utilizing simulated-sunlight to enhance the antibiotic removal efficiency while reducing ARG production, thus providing a novel idea for the removal of antibiotics from wastewater.

Isolation and characterization of polyhydroxyalkanoate-degrading bacteria in seawater at two different depths from Suruga Bay

IMPORTANCE

Polyhydroxyalkanoate (PHA) is a highly biodegradable microbial polyester, even in marine environments. In this study, we incorporated an enrichment culture-like approach in the process of isolating marine PHA-degrading bacteria. The resulting 91 isolates were suggested to fall into five genera (Alloalcanivorax, Alteromonas, Arenicella, Microbacterium, and Pseudoalteromonas) based on 16S rRNA analysis, including two novel genera (Arenicella and Microbacterium) as marine PHA-degrading bacteria. Microbacterium schleiferi (DSM 20489) and Alteromonas macleodii (NBRC 102226), the type strains closest to the several isolates, have an extracellular poly(3-hydroxybutyrate) [P(3HB)] depolymerase homolog that does not fit a marine-type domain composition. However, A. macleodii exhibited no PHA degradation ability, unlike M. schleiferi. This result demonstrates that the isolated Alteromonas spp. are different species from A. macleodii. P(3HB) depolymerase homologs in the genus Alteromonas should be scrutinized in the future, particularly about which ones work as the depolymerase.

From micro to macro: The role of seawater in maintaining structural integrity and bioactivity of granules in treating antibiotic-laden mariculture wastewater

Granular sludge (GS) has superior antibiotic removal ability to flocs, due to GS's layered structure and rich extracellular polymeric substances. However, prolonged exposure to antibiotics degrades the performance and stability of GS. This study investigated how a seawater matrix might help maintain the structural integrity and bioactivity of granules. The results demonstrated that GS had better sulfadiazine (SDZ) removal efficiency in a seawater matrix (85.6 %) than in a freshwater matrix (57.6 %); the multiple ions in seawater enhanced boundary layer diffusion (kiR1 = 0.0805 mg·g-1·min-1/2 and kiR2 = 0.1112 mg·g-1·min-1/2) and improved adsorption performance by 15 % (0.123 mg/g-SS freshwater vs. 0.141 mg/g-SS seawater). Moreover, multiple hydrogen bonds (1-3) formed between each SDZ and lipid bilayer fortified the adsorption. Beyond S-N and S-C bond hydrolyses that took place in freshwater systems, there was an additional biodegradation pathway for GS to be cultivated in a saltwater system that involved sulfur dioxide extrusion. This additional pathway was attributable to the greater microbial diversity and larger presence of sulfadiazine-degrading bacteria containing SadAC genes, such as Leucobacter and Arthrobacter, in saltwater wastewater. The findings of this study elucidate how seawater influences GS properties and antibiotic removal ability.

Monooxygenases and Antibiotic Resistance: A Focus on Carbapenems

Carbapenems are a group of broad-spectrum beta-lactam antibiotics that in many cases are the last effective defense against infections caused by multidrug-resistant bacteria, such as some strains of Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii. Resistance to carbapenems has emerged and is beginning to spread, becoming an ongoing public-health problem of global dimensions, causing serious outbreaks, and dramatically limiting treatment options. This paper reviews the role of flavin monooxygenases in antibiotic resistance, with a specific focus on carbapenem resistance and the recently discovered mechanism mediated by Baeyer-Villiger monooxygenases. Flavin monooxygenases are enzymes involved in the metabolism and detoxification of compounds, including antibiotics. Understanding their role in antibiotic resistance is crucial. Carbapenems are powerful antibiotics used to treat severe infections caused by multidrug-resistant bacteria. However, the rise of carbapenem-resistant strains poses a significant challenge. This paper explores the mechanisms by which flavin monooxygenases confer resistance to carbapenems, examining molecular pathways and genetic factors. Additionally, this paper highlights the discovery of Baeyer-Villiger monooxygenases' involvement in antibiotic resistance. These enzymes catalyze the insertion of oxygen atoms into specific chemical bonds. Recent studies have revealed their unexpected role in promoting carbapenem resistance. Through a comprehensive analysis of the literature, this paper contributes to the understanding of the interplay between flavin monooxygenases, carbapenem resistance, and Baeyer-Villiger monooxygenases. By exploring these mechanisms, it aims to inform the development of strategies to combat antibiotic resistance, a critical global health concern.

Metabolic engineering of Paracoccus denitrificans for dual degradation of sulfamethoxazole and ammonia nitrogen

Sulfamethoxazole (SMX), as one of the most widely used sulfonamide antibiotics, has been frequently detected in the aqueous environment, posing potential risks to the environment and human health. Although microbial degradation methods have been widely applied, some issues remain, including low degradation efficiency and poor environmental adaptability. In this regard, constructing efficient degrading bacteria by metabolic engineering is an ideal solution to these challenges. In this study, we used Paracoccus denitrificans DYTN-1, a superior nitrogen removal environment strain, as chassis to construct an SMX degradation pathway, obtaining a new bacteria for simultaneous degradation of SMX and removal of ammonia nitrogen. In doing this, we first identified and characterized four native promoters of P. denitrificans DYTN-1 with gradient strength to control the expression of the SMX degradation pathway. After degradation pathway expression level optimization and FMN reductase optimization, SMX degradation efficiency was significantly improved. The constructed P. d-pIAB4-PCS-sutR strain exhibited superior co-degradation of SMX and ammonia nitrogen contaminants with degradation rates of 44% and 71%, respectively. This study could pave the way for SMX degradation engineered strain design and evolution of environmental bioremediation. IMPORTANCE The abuse of sulfamethoxazole (SMX) had led to an increased accumulation in the environment, resulting in the disruption of the structure of microbial communities, further disrupting the bio-degradation process of other pollutants, such as ammonia nitrogen. To solve this challenge, we first identified and characterized four native promoters of Paracoccus denitrificans DYTN-1 with gradient strength to control the expression of the SMX degradation pathway. Then SMX degradation efficiency was significantly improved with degradation pathway expression level optimization and FMN reductase optimization. Finally, the superior nitrogen removal environment strain, P. denitrificans DYTN-1, obtained an SMX degradation function. This pioneering study of metabolic engineering to enhance the SMX degradation in microorganisms could pave the way for designing the engineered strains of SMX and nitrogen co-degradation and the environmental bioremediation.

The sulfonamide-resistance dihydropteroate synthase gene is crucial for efficient biodegradation of sulfamethoxazole by Paenarthrobacter species

Sulfonamide antibiotics (SAs) are serious pollutants to ecosystems and environments. Previous studies showed that microbial degradation of SAs such as sulfamethoxazole (SMX) proceeds via a sad-encoded oxidative pathway, while the sulfonamide-resistant dihydropteroate synthase gene, sul, is responsible for SA resistance. However, the co-occurrence of sad and sul genes, as well as how the sul gene affects SMX degradation, was not explored. In this study, two SMX-degrading bacterial strains, SD-1 and SD-2, were cultivated from an SMX-degrading enrichment. Both strains were Paenarthrobacter species and were phylogenetically identical; however, they showed different SMX degradation activities. Specifically, strain SD-1 utilized SMX as the sole carbon and energy source for growth and was a highly efficient SMX degrader, while SD-2 did could not use SMX as a sole carbon or energy source and showed limited SMX degradation when an additional carbon source was supplied. Genome annotation, growth, enzymatic activity tests, and metabolite detection revealed that strains SD-1 and SD-2 shared a sad-encoded oxidative pathway for SMX degradation and a pathway of protocatechuate degradation. A new sulfonamide-resistant dihydropteroate synthase gene, sul918, was identified in strain SD-1, but not in SD-2. Moreover, the lack of sul918 resulted in low SMX degradation activity in strain SD-2. Genome data mining revealed the co-occurrence of sad and sul genes in efficient SMX-degrading Paenarthrobacter strains. We propose that the co-occurrence of sulfonamide-resistant dihydropteroate synthase and sad genes is crucial for efficient SMX biodegradation. KEY POINTS: • Two sulfamethoxazole-degrading strains with distinct degrading activity, Paenarthrobacter sp. SD-1 and Paenarthrobacter sp. SD-2, were isolated and identified. • Strains SD-1 and SD-2 shared a sad-encoded oxidative pathway for SMX degradation. • A new plasmid-borne SMX resistance gene (sul918) of strain SD-1 plays a crucial role in SMX degradation efficiency.

Iron-modified biochar boosts anaerobic digestion of sulfamethoxazole pharmaceutical wastewater: Performance and microbial mechanism

The accumulation of volatile fatty acids (VFAs) caused by antibiotic inhibition significantly reduces the treatment efficiency of sulfamethoxazole (SMX) wastewater. Few studies have been conducted to study the VFAs gradient metabolism of extracellular respiratory bacteria (ERB) and hydrogenotrophic methanogen (HM) under high-concentration sulfonamide antibiotics (SAs). And the effects of iron-modified biochar on antibiotics are unknown. Here, the iron-modified biochar was added to an anaerobic baffled reactor (ABR) to intensify the anaerobic digestion of SMX pharmaceutical wastewater. The results demonstrated that ERB and HM were developed after adding iron-modified biochar, promoting the degradation of butyric, propionic and acetic acids. The content of VFAs reduced from 1166.0 mg L^-1 to 291.5 mg L^-1. Therefore, chemical oxygen demand (COD) and SMX removal efficiency were improved by 22.76% and 36.51%, and methane production was enhanced by 6.19 times. Furthermore, the antibiotic resistance genes (ARGs) such as sul1, sul2, intl1 in effluent were decreased by 39.31%, 43.33%, 44.11%. AUTHM297 (18.07%), Methanobacterium (16.05%), Geobacter (6.05%) were enriched after enhancement. The net energy after enhancement was 0.7122 kWh m^-3. These results confirmed that ERB and HM were enriched via iron-modified biochar to achieve high efficiency of SMX wastewater treatment.

Biodegradation of sulfametoxydiazine by Alcaligenes aquatillis FA: Performance, degradation pathways, and mechanisms

This study reports the isolation and characterization of a novel bacterial strain Alcaligenes aquatillis FA with the ability to degrade sulfametoxydiazine (SMD), a commonly used sulfonamide antibiotic (SA) in livestock and poultry production. The biodegradation kinetics, pathways, and genomic background of SMD by FA were investigated. The results showed that strain FA had high specificity to degrade SMD, and was unable to effectively degrade its isomer, sulfamonomethoxine. The SMD biodegradation followed a first-order kinetic model with a rate constant of 27.39 mg·L^-1·day^-1 and a half-life of 5.98 days. The biodegradation pathways and detoxification processes of SMD were proposed based on the identification of its biodegradation byproducts and the biotoxicity assessment using both the ecological structure-activity relationship (ECOSAR) model and biological indicator. The involvement of novel degrading enzymes, such as dimethyllsulfone monooxygenase, 4-carboxymuconolactone decarboxylase, and 1,4-benzoquinone reductase, was inferred in the SMD biodegradation process. The presence of sul2 and dfrA genes in strain FA, which were constitutively expressed in its cells, suggests that multiple mechanisms were employed by the strain to resist SMD. This study provides new insights into the biodegradation of sulfonamide antibiotics (SAs) as it is the first to describe an SMD-degrading bacterium and its genetic information.

Deciphering of sulfonamide biodegradation mechanism in wetland sediments: from microbial community and individual populations to pathway and functional genes

Figuring out the comprehensive metabolic mechanism of sulfonamide antibiotics (SA) is critical to improve and optimize SA removal in the bioremediation process, but relevant studies are still lacking. Here, an approach integrating metagenomic analysis, degraders' isolation, reverse transcriptional quantification and targeted metabolite determination was used to decipher microbial interactions and functional genes' characteristics in SA-degrading microbial consortia enriched from wetland sediments. The SA-degrading consortia could rapidly catalyze ipso-hydroxylation and subsequent reactions of SA to achieve the complete mineralization of sulfadiazine and partial mineralization of the other two typical SA (sulfamethoxazole and sulfamethazine). Paenarthrobacter, Achromobacter, Pseudomonas and Methylobacterium were identified as the primary participants for the initial transformation of SA. Among them, Methylobacterium could metabolize the heterocyclic intermediate of sulfadiazine (2-aminopyrimidine), and the owning of sadABC genes (SA degradation genes) made Paenarthrobacter have relatively higher SA-degrading activity. Besides, the coexistence of sadABC genes and sul1 gene (SA resistance gene) gave Paenarthrobacter a dual resistance mechanism to SA. The results of reverse transcription quantification further demonstrated that the activity of sadA gene was related to the biodegradation of SA. Additionally, sadABC genes were relatively conserved in a few Microbacteriaceae and Micrococcaceae SA-degraders, but the multiple recombination events caused by densely nested transposase encoding genes resulted in the differential sequence of sadAB genes in Paenarthrobacter genome. These new findings provide valuable information for the selection and construction of engineered microbiomes.

Critical review of phytoremediation for the removal of antibiotics and antibiotic resistance genes in wastewater

Antibiotics in wastewater are a growing environmental concern. Increased prescription and consumption rates have resulted in higher antibiotic wastewater concentration. Conventional wastewater treatment methods are often ineffective at antibiotic removal. Given the environmental risk of antibiotics and associated antibiotic resistant genes (ARGs), finding methods of improving antibiotic removal from wastewater is of great importance. Phytoremediation of antibiotics in wastewater, facilitated through constructed wetlands, has been explored in a growing number of studies. To assess the removal efficiency and treatment mechanisms of plants and microorganisms within constructed wetlands for specific antibiotics of major antibiotic classes, the present review paper considered and evaluated data from the most recent published research on the topics of bench scale hydroponic, lab and pilot scale constructed wetland, and full scale constructed wetland antibiotic remediation. Additionally, microbial and enzymatic antibiotic degradation, antibiotic-ARG correlation, and plant effect on ARGs were considered. It is concluded from the present review that plants readily uptake sulfonamide, macrolide, tetracycline, and fluoroquinolone antibiotics and that constructed wetlands are an effective applied phytoremediation strategy for the removal of antibiotics from wastewater through the mechanisms of microbial biodegradation, root sorption, plant uptake, translocation, and metabolization. More research is needed to better understand the effect of plants on microbial community and ARGs. This paper serves as a synthesis of information that will help guide future research and applied use of constructed wetlands in the field antibiotic phytoremediation and wastewater treatment.

Sulfamethoxazole degradation by Aeromonas caviae and co-metabolism by the mixed bacteria

Sulfamethoxazole (SMX) is a frequently detected antibiotic in the environment and has attracted much attention. Aeromonas caviae strain GLB-10 was isolated, which could degrade SMX to Aniline and 3-Amino-5-methylisoxazole. Compared to the single bacteria, the mixed bacteria including stain GLB-10, Vibrio diabolicus strain L2-2, Zobellella taiwanensis, Microbacterium testaceum, Methylobacterium, etc, had an ultrahigh degradation efficiency to SMX, with 250 mg/L SMX being degraded in 3 days. In addition to bioproducts of single bacteria, SMX bioproducts by the mixed bacteria also included acetanilide and hydroquinone which were not detected in the single bacteria. The SMX degradation mechanism of the mixed bacteria was more complicated including acetylation, sulfur reduction 4S pathway, and ipso-hydrolysis. The molecular mechanism of the mixed bacteria degrading SMX was also investigated, revealing that the resistance mechanism related to protein outer membrane protein and catalase peroxidase were overexpressed, meanwhile, 6-hydroxynicotinate 3-monooxygenase and ammonia monooxygenase might be the key proteins in SMX degradation. The mixed bacteria could efficiently degrade SMX in different real environments including tap water, river water, artificial lake water, estuary, and, marine water, and have very great research value in bacterial co-metabolism and biodegradation of sulfonamides antibiotics in the environment.

Insight into sulfamethoxazole effects on aerobic denitrification by strain Pseudomonas aeruginosa PCN-2: From simultaneous degradation performance to transcriptome analysis

It is a well-established fact that aerobic denitrifying strains are profoundly affected by antibiotics, but bacterium performing simultaneous aerobic denitrification and antibiotic degradation is hardly reported. Here, a typical aerobic denitrifying bacterium Pseudomonas aeruginosa PCN-2 was discovered to be capable of sulfamethoxazole (SMX) degradation. The results showed that nitrate removal efficiency was decreased from 100% to 88.12%, but the resistance of strain PCN-2 to SMX stress was enhanced with the increment of SMX concentration from 0 to 100 mg/L. Transcriptome analysis revealed that the down-regulation of energy metabolism pathways rather than the denitrifying functional genes was responsible for the suppressed nitrogen removal, while the up-regulation of antibiotic resistance pathways (e.g., biofilm formation, multi-drug efflux system, and quorum sensing) ensured the survival of bacterium and the carrying out of aerobic denitrification. Intriguingly, strain PCN-2 could degrade SMX during aerobic denitrification. Seven metabolites were identified by the UHPLC-MS, and three degradation pathways (which includes a new pathway that has never been reported) was proposed combined with the expressions of drug metabolic genes (e.g., cytP450, FMN, ALDH and NAT). This work provides a mechanistic understanding of the metabolic adaption of strain PCN-2 under SMX stress, which provided a broader idea for the treatment of SMX-containing wastewater.

Analysis of the Comparative Growth Kinetics of Paenarthrobacter ureafaciens YL1 in the Biodegradation of Sulfonamide Antibiotics Based on Substituent Structures and Substrate Toxicity

The high consumption and emission of sulfonamide antibiotics (SAs) have a considerable threat to humans and ecosystems, so there is a need to develop safer and more effective methods than conventional strategies for the optimal removal of these compounds. In this study, four SAs with different substituents, sulfadiazine (SDZ), sulfamerazine (SMR), sulfamethoxazole (SMX), and sulfamethazine (SMZ) were removed by a pure culture of Paenarthrobacter ureafaciens YL1. The effect of the initial SAs concentration on the growth rate of strain YL1 was investigated. The results showed that the strain YL1 effectively removed various SAs in the concentration range of 0.05–2.4 mmol·L−1. The Haldane model was used to perform simulations of the experimental data, and the regression coefficient of the model indicated that the model had a good predictive ability. During SAs degradation, the maximum specific growth rate of strain YL1 was ranked as SMX > SDZ > SMR > SMZ with constants of 0.311, 0.304, 0.302, and 0.285 h−1, respectively. In addition, the biodegradation of sulfamethoxazole (SMX) with a five-membered substituent was the fastest, while the six-membered substituent of SMZ was the slowest based on the parameters of the kinetic equation. Also, density functional theory (DFT) calculations such as frontier molecular orbitals (FMOs), and molecular electrostatic potential map analysis were performed. It was evidenced that different substituents in SAs can affect the molecular orbital distribution and their stability, which led to the differences in the growth rate of strain YL1 and the degradation rate of SAs. Furthermore, the toxicity of P. ureafaciens is one of the crucial factors affecting the biodegradation rate: the more toxic the substrate and the degradation product are, the slower the microorganism grows. This study provides a theoretical basis for effective bioremediation using microorganisms in SAs-contaminated environments.

Pharmaceutical Biotransformation is Influenced by Photosynthesis and Microbial Nitrogen Cycling in a Benthic Wetland Biomat

In shallow, open-water engineered wetlands, design parameters select for a photosynthetic microbial biomat capable of robust pharmaceutical biotransformation, yet the contributions of specific microbial processes remain unclear. Here, we combined genome-resolved metatranscriptomics and oxygen profiling of a field-scale biomat to inform laboratory inhibition microcosms amended with a suite of pharmaceuticals. Our analyses revealed a dynamic surficial layer harboring oxic-anoxic cycling and simultaneous photosynthetic, nitrifying, and denitrifying microbial transcription spanning nine bacterial phyla, with unbinned eukaryotic scaffolds suggesting a dominance of diatoms. In the laboratory, photosynthesis, nitrification, and denitrification were broadly decoupled by incubating oxic and anoxic microcosms in the presence and absence of light and nitrogen cycling enzyme inhibitors. Through combining microcosm inhibition data with field-scale metagenomics, we inferred microbial clades responsible for biotransformation associated with membrane-bound nitrate reductase activity (emtricitabine, trimethoprim, and atenolol), nitrous oxide reduction (trimethoprim), ammonium oxidation (trimethoprim and emtricitabine), and photosynthesis (metoprolol). Monitoring of transformation products of atenolol and emtricitabine confirmed that inhibition was specific to biotransformation and highlighted the value of oscillating redox environments for the further transformation of atenolol acid. Our findings shed light on microbial processes contributing to pharmaceutical biotransformation in open-water wetlands with implications for similar nature-based treatment systems.

Rhodococcus strains as a good biotool for neutralizing pharmaceutical pollutants and obtaining therapeutically valuable products: Through the past into the future

Active pharmaceutical ingredients present a substantial risk when they reach the environment and drinking water sources. As a new type of dangerous pollutants with high chemical resistance and pronounced biological effects, they accumulate everywhere, often in significant concentrations (μg/L) in ecological environments, food chains, organs of farm animals and humans, and cause an intense response from the aquatic and soil microbiota. Rhodococcus spp. (Actinomycetia class), which occupy a dominant position in polluted ecosystems, stand out among other microorganisms with the greatest variety of degradable pollutants and participate in natural attenuation, are considered as active agents with high transforming and degrading impacts on pharmaceutical compounds. Many representatives of rhodococci are promising as unique sources of specific transforming enzymes, quorum quenching tools, natural products and novel antimicrobials, biosurfactants and nanostructures. The review presents the latest knowledge and current trends regarding the use of Rhodococcus spp. in the processes of pharmaceutical pollutants’ biodegradation, as well as in the fields of biocatalysis and biotechnology for the production of targeted pharmaceutical products. The current literature sources presented in the review can be helpful in future research programs aimed at promoting Rhodococcus spp. as potential biodegraders and biotransformers to control pharmaceutical pollution in the environment.

Microbial degradation of antibiotic: future possibility of mitigating antibiotic pollution

Antibiotics are the major pharmaceutical wastes that are being exposed to the environment from the pharmaceutical industries and for the anthropogenic activities. The use of antibiotics for disease prevention and treatment in humans has been surpassed by the amount used in agriculture, particularly on livestock. It is stipulated that the overuse of antibiotics is the single largest reason behind the rise of bacterial anti-microbial resistance (AMR). The development of alternative therapy, like gene therapy, immunotherapy, use of natural products, and various nanoparticles, to control bacterial pathogens might be an alternative of antibiotics for mankind but the remediation of already exposed antibiotics from the lithosphere and hydrosphere needs to be envisioned with priority. The ever-increasing release of antibiotics in the environment makes it one of the major emerging contaminants (ECs). Decomposition of such antibiotic contaminants is a great challenge to get a cleaner environment. There are reports describing the degradation of antibiotics by photolysis, hydrolysis, using cathode and metal salts, or by degradation via microbes. Antimicrobials like sulfonamides are recalcitrant to natural biodegradation, exhibiting high thermal stability. There are recent reports on microbial degradation of a few common antibiotics and their derivatives but their applications in waste management are scanty. It could however be a major concern to the scientists whether to use the antibiotic degradation traits of a microbe for the removal of antibiotic wastes. The complexity of the genetic clusters of a microbe that are responsible for degradation is crucial, as a small genetic cluster might have higher chance of horizontal transfer into sensitive species of the normal microbial flora that in turn triggers the rise of antimicrobial resistance.

Occurrence of antibiotics and bacterial resistance genes in wastewater: resistance mechanisms and antimicrobial resistance control approaches

Antimicrobial pharmaceuticals are classified as emergent micropollutants of concern, implying that even at low concentrations, long-term exposure to the environment can have significant eco-toxicological effects. There is a lack of a standardized regulatory framework governing the permissible antibiotic content for monitoring environmental water quality standards. Therefore, indiscriminate discharge of antimicrobials at potentially active concentrations into urban wastewater treatment facilities is rampant. Antimicrobials may exert selective pressure on bacteria, leading to resistance development and eventual health consequences. The emergence of clinically important multiple antibiotic-resistant bacteria in untreated hospital effluents and wastewater treatment plants (WWTPs) has been linked to the continuous exposure of bacteria to antimicrobials. The levels of environmental exposure to antibiotics and their correlation to the evolution and spread of resistant bacteria need to be elucidated to help in the formulation of mitigation measures. This review explores frequently detected antimicrobials in wastewater and gives a comprehensive coverage of bacterial resistance mechanisms to different antibiotic classes through the expression of a wide variety of antibiotic resistance genes either inherent and/or exchanged among bacteria or acquired from the reservoir of antibiotic resistance genes (ARGs) in wastewater systems. To complement the removal of antibiotics and ARGs from WWTPs, upscaling the implementation of prospective interventions such as vaccines, phage therapy, and natural compounds as alternatives to widespread antibiotic use provides a multifaceted approach to minimize the spread of antimicrobial resistance.

Sulfonamide-metabolizing microorganisms and mechanisms in antibiotic-contaminated wetland sediments revealed by stable isotope probing and metagenomics

Sulfonamide (SA) antibiotics are ubiquitous pollutants in livestock breeding and aquaculture wastewaters, which increases the propagation of antibiotic resistance genes. Microbes with the ability to degrade SA play important roles in SA dissipation, but their diversity and the degradation mechanism in the field remain unclear. In the present study, we employed DNA-stable isotope probing (SIP) combined with metagenomics to explore the active microorganisms and mechanisms of SA biodegradation in antibiotic-contaminated wetland sediments. DNA-SIP revealed various SA-assimilating bacteria dominated by members of Proteobacteria, such as Bradyrhizobium, Gemmatimonas, and unclassified Burkholderiaceae. Both sulfadiazine and sulfamethoxazole were dissipated mainly through the initial ipso-hydroxylation, and were driven by similar microbes. sadA gene, which encodes an NADH-dependent monooxygenase, was enriched in the ¹³C heavy DNA, confirming its catalytic capacity for the initial ipso-hydroxylation of SA in sediments. In addition, some genes encoding dioxygenases were also proposed to participate in SA hydroxylation and aromatic ring cleavage based on metagenomics analysis, which might play an important role in SA metabolism in the sediment ecosystem when Proteobacteria was the dominant active bacteria. Our work elucidates the ecological roles of uncultured microorganisms in their natural habitats and gives a deeper understanding of in-situ SA biodegradation mechanisms.

Bibliometric analysis of microbial sulfonamide degradation: Development, hotspots and trend directions

Microbial sulfonamide degradation (MSD) is an efficient and safe treatment in both natural and engineered ecosystems. In order to systematically understand the research status and frontier trends of MSD, this study employed CiteSpace to conduct a bibliometric analysis of data from the Web of Science (WoS) and the China National Knowledge Infrastructure (CNKI) published from 2000 to 2021. During this time, China, Germany, Spain, the United States and Australia played leading roles by producing numerous high impact publications, while the Chinese Academy of Sciences was the leading research institution in this interdisciplinary research category. The Chemosphere was the top journal in terms of the number of citations. MSD research has gradually progressed from basic laboratory-based experiments to more complex environmental microbial communities and finally to deeper research on molecular mechanisms and engineering applications. Although multi-omics and synthetic community are the key techniques in the frontier research, they are also the current challenges in this field. A summary of published articles shows that Proteobacteria, Gammaproteobacteria, Burkholderiales and Alcaligenaceae are the most frequently observed MSD phylum, class, order and family, respectively, while Bacillus, Pseudomonas and Achromobacter are the top three MSD genera. To our knowledge, this study is the first to investigate the development and current challenges of MSD research, put forward future perspective, and form a relatively complete list of sulfonamide-degrading microorganisms for reference.

Microbial Community Structure and Bacterial Lineages Associated with Sulfonamides Resistance in Anthropogenic Impacted Larut River

Anthropogenic activities often contribute to antibiotic resistance in aquatic environments. Larut River Malaysia is polluted with both organic and inorganic pollutants from domestic and industrial wastewater that are probably treated inadequately. The river is characterized by high biochemical oxygen demand, chemical oxygen demand, total suspended solids, ammonia, and heavy metals. In our previous study, sulfonamides (SAs) and sulfonamide resistance genes (sul) were detected in the Larut River. Hence, in this study, we further examined the microbial community structure, diversity of sulfonamide-resistant bacteria (SARB), and their resistance genes. The study also aimed at identifying cultivable bacteria potential carriers of sul genes in the aquatic environment. Proteobacteria (22.4–66.0%), Firmicutes (0.8–41.6%), Bacteroidetes (2.0–29.4%), and Actinobacteria (5.5–27.9%) were the most dominant phyla in both the effluents and river waters. SARB isolated consisted only 4.7% of the total genera identified, with SAR Klebsiella as the most dominant (38.0–61.3%) followed by SAR Escherichia (0–22.2%) and Acinetobacter (3.2–16.0%). The majority of the SAR Klebsiella isolated from the effluents and middle downstream were positive for sul genes. Sul genes-negative SAR Escherichia and Acinetobacter were low (<20%). Canonical-correlation analysis (CCA) showed that SAs residues and inorganic nutrients exerted significant impacts on microbial community and total sul genes. Network analysis identified 11 SARB as potential sul genes bacterial carriers. These findings indicated that anthropogenic activities exerted impacts on the microbial community structure and SAs resistance in the Larut River.

Harnessing Paenarthrobacter ureafaciens YL1 and Pseudomonas koreensis YL2 Interactions to Improve Degradation of Sulfamethoxazole

Sulfamethoxazole (SMX) is a widespread and persistent pollutant in the environment. Although the screening and analysis of SMX-degrading bacteria have been documented, the interaction mechanisms of functional microorganisms are still poorly understood. This study constructed a consortium with strain YL1 and YL2 supplied with SMX as the sole carbon and energy source. The coexisting mechanism and the removal of SMX of the consortium were investigated. The total oxidizable carbon (TOC) removal rate of the combined bacterial system was 38.94% compared to 29.45% for the single bacterial system at the same biomass. The mixed bacterial consortium was able to resist SMX at concentrations up to 400 mg/L and maintained a stable microbial structure at different culture conditions. The optimum conditions found for SMX degradation were 30 °C, pH 7.0, a shaking speed of 160 r·min⁻¹, and an initial SMX concentration of 200 mg·L⁻¹. The degradation of SMX was accelerated by the addition of YL2 for its ability to metabolize the key intermediate, 4-aminophenol. The removal rate of 4-aminophenol by strain YL2 reached 19.54% after 5 days. Genome analysis revealed that adding riboflavin and enhancing the reducing capacity might contribute to the degradation of SMX. These results indicated that it is important for the bioremediation of antibiotic-contaminated aquatic systems to understand the metabolism of bacterial communities.

Biological removal of sulfamethoxazole enhanced by S. oneidensis MR-1 via promoting NADH generation and electron transfer and consumption

The bio-removal efficiency of sulfamethoxazole (SMX) from wastewater is usually very poor. In this paper a new efficient method to biodegrade SMX was reported. The SMX biodegradation efficiency by Paracoccus denitrificans was observed to be remarkably enhanced from 48.9% to 94.2% after Shewanella oneidensis MR-1 addition. The mechanisms investigation revealed that P. denitrificans was the dominant microbe for SMX biodegradation. Although SMX biodegradation by S. oneidensis MR-1 alone was negligible, its presence advanced NADH generation. The proteomics assay revealed that the expression of key proteins relevant with complex I and III and cytochrome c in electron transfer chain were increased due to P. denitrificans acquiring iron from periplasm to cytoplasm being improved. In addition, the extracellular electron transfer capability was enhanced as S. oneidensis MR-1 not only produced flavin, but caused P. denitrificans to secret more extracellular polymeric substances. Further investigation indicated that the expression of key enzymes related to electron consumption in SMX biodegradation was up-regulated. Based on these findings, the pathways of S. oneidensis MR-1 promoting SMX biodegradation were proposed. As all nitrate could be removed with almost no nitrite accumulation, this study would also provide an attractive way for simultaneous bio-removal of multiple pollutants from wastewater.

Complete genome sequences of the antibiotic sulfamethoxazole-mineralizing bacteria Paenarthrobacter sp. P27 and Norcardiodes sp. N27

Sulfonamide antibiotics (SAs) have been produced and consumed on a large scale over the last few decades. SAs are a typical class of refractory contaminants that are omnipresent in various environments. Although several [phenyl]-SA-degrading bacteria and their corresponding genomes have been documented, limited genetic information is available for the degraders of heterocyclic products (e.g., 3-amino-5-methylisoxazole [3A5MI] produced via sulfamethoxazole [SMX] catabolism). In this study, the previously isolated SMX-mineralizing bacterial partners, Paenarthrobacter sp. P27 (responsible for the initial cleavage of the -C-S-N- bond of SMX and further degradation of [phenyl]-SMX) and Norcardiodes sp. N27 (responsible for 3A5MI catabolism), were further studied and their complete genomes were sequenced. Complete degradation and bacterial growth were verified by pure-culture experiments with SMX or 3A5MI as the sole carbon, nitrogen, and energy source. By cross-feeding strains P27 and N27, complete catabolism of SMX could be achieved over a wide range of initial SMX concentrations. Moreover, strain P27 was capable of transforming the additional nine SA representatives into their corresponding nitrogen-containing heterocyclic products, strongly indicating the broad substrate spectrum and marked bioremediation potential of strain P27. The genome of strain P27 contained the highly homologous monooxygenase gene cluster, sadABC, which initially attacked the sulfonamide molecules. The complete genome sequences of the two important degraders will benefit future research centering on the molecular mechanism underlying advanced SMX mineralization and will aid in further understanding the interspecific interactions and metabolite exchanges for the optimization of artificially constructed synthetic functional microbiomes.

Mechanism for biodegradation of sulfamethazine by Bacillus cereus H38

Degradation of sulfonamides (SAs) by microorganisms has become a focus of current research. Sulfamethazine (SMZ) is a type of SA widely used in the livestock and poultry industry. However, understanding the intermediate products, degradation pathways and mechanism of SMZ biodegradation is limited at present. In this study, a SMZ degrading bacterium Bacillus cereus H38, which can use SMZ as its only carbon source, was isolated from farmland soil. The bacterium was gram-positive with rod-shaped cells. The effects of initial SMZ concentration, pH, temperature and amount of inoculation on the biodegradation of SMZ were investigated by a single factor experiment. The results showed that the maximum degradation rate of SMZ was achieved in the environmental conditions at an initial SMZ concentration of 5 mg/L, pH of 7.0, temperature of 25 °C and inoculation amount of 5%. Under these optimum degradation conditions, strain H38 can completely degrade SMZ within 3 days. The effects of intracellular enzymes, extracellular enzymes and periplasmic enzymes on the SMZ degradation process were compared. It was found that intracellular enzymes contributed the most to the biodegradation of SMZ, and the degradation rate approached 70%. Three possible intermediates were identified by LC-MS/MS, and two degradation pathways were proposed. Whole genome sequencing results showed that the genome size of strain H38 was 5,477,631 bp, including 5599 coding sequences (CDSs), and the GC content was 35.21%. In addition, functional annotation of CDSs was performed to analyze the metabolic pathways of nitrogen and sulfur in strain H38 combining genomics and bioinformatics. This study proposes new insights into the mechanism for biodegradation of SAs and will inform future research.

Comparison of chemical and biological degradation of sulfonamides: Solving the mystery of sulfonamide transformation

Sulfonamides (SAs) are widespread in aquatic environments and pose serious environmental risks. The removal efficiencies and degradation mechanisms of SAs in both chemical and biological degradation systems were comprehensively reviewed. Density functional theory (DFT) was utilized to decipher the reaction types and reactive sites of both degradation mechanisms at the electron level. In chemical degradation, the rate of the reactive oxidants to degrade SAs follows the order SO₄•^- ≈ •OH > O₃ > ¹O₂ > ClO₂ ≈ Fe(VI) ≈ HOCl > peroxymonosulfate. pH affects the oxidation-reduction potentials of oxidants, the reactivity of SAs, and the intermolecular force between oxidants and SAs, thereby affecting the chemical degradation efficiencies and mechanisms. In biological degradation, oxidoreductase produced by bacteria, fungi, algae, and plants can degrade SAs. The catalytic activity of the enzyme is affected by the enzyme system, reaction conditions, and type of SAs. Despite the different reaction modes and removal efficiencies of SAs in chemical degradation and biological degradation, the transformation pathways and products show commonalities. Modification of the amino (N¹H₂-) moiety and destruction of sulfonamide bridge (-SO₂-N¹¹H-) moiety are the main pathways for both chemical and biological degradation of SAs. Most oxidants or enzymes can react with the N¹H₂- moiety. Reactions of the -SO₂-N¹¹H- moiety are mainly initiated by the cleavage of S-N bonds for five-membered heterocyclic ring-substituted SAs, and by SO₂ extrusion for six-membered heterocyclic ring-substituted SAs. Chlorine substitution and coupling on the N¹H₂- moiety, hydroxylation of the benzene moiety, oxidation of methyl, and isomerization of the R substituents are the transformation pathways unique to chemical degradation. Formylation/acetylation, glycosylation, pterin conjugation, and deamination of the N¹H₂- moiety are the transformation pathways unique to biological degradation. DFT studies revealed the same reaction types and the same reactive sites of SAs in chemical and biological degradation. Electrophiles are mostly prone to attack the N¹ atom on the amino moiety of neutral SAs and the N¹¹ atom on the sulfonamide bridge moiety of anionic SAs, leading to nitration or electrophilic substitution of the amino moiety and the cleavage of S-N bonds or SO₂ extrusion of the sulfonamide bridge moiety. Reactions on the -SO₂-N¹¹H- moiety eliminate antibacterial activity in the SA degradation process. This review elucidated SA transformation by comparing the chemical and biological degradation of SAs. This could provide theoretical guidance for the development of more efficient and economical treatment technologies for SAs.

Profiling microbial removal of micropollutants in sand filters: Biotransformation pathways and associated bacteria

Although there is growing evidence that micropollutants can be microbially converted in rapid sand filters of drinking water treatment plants (DWTPs), little is known about the biotransformation pathways and associated microbial strains in this process. Here, we constructed sand filter columns filled with manganese or quartz sand obtained from full-scale DWTPs to explore the biotransformation of eight micropollutants. Under seven different empty bed contact times (EBCTs), the column experiments showed that caffeine and atenolol were easily removed (up to 92.1% and 97.6%, respectively) with adsorption and microbial biotransformation of the filters. In contrast, the removal of other six micropollutants (i.e., naproxen, carbamazepine, atrazine, trimethoprim, sulfamethoxazole, and sulfadiazine) in the filters were less than 27.1% at shorter EBCTs, but significantly increased at EBCT = 4 h, indicating the dominant role of microbial biotransformation in these micropollutants removal. Integrated analysis of metagenomic reads and transformation products of micropollutants showed a shift in caffeine oxidation and demethylation pathways at different EBCTs, simultaneous occurrence of atrazine hydrolysis and oxidation pathways, and sulfadiazine and sulfamethoxazole oxidation in the filters. Furthermore, using genome-centric analysis, we observed previously unidentified degrading strains, e.g., Piscinibacter, Hydrogenophaga, and Rubrivivax for caffeine transformation, and Methylophilus and Methyloversatilis for atenolol transformation.

Microbiome assembly for sulfonamide subsistence and the transfer of genetic determinants

Antibiotic subsistence in bacteria represents an alternative resistance machinery, while paradoxically, it is also a cure for environmental resistance. Antibiotic-subsisting bacteria can detoxify antibiotic-polluted environments and prevent the development of antibiotic resistance in environments. However, progress toward efficient in situ engineering of antibiotic-subsisting bacteria is hindered by the lack of mechanistic and predictive understanding of the assembly of the functioning microbiome. By top-down manipulation of wastewater microbiomes using sulfadiazine as the single limiting source, we monitored the ecological selection process that forces the wastewater microbiome to perform efficient sulfadiazine subsistence. We found that the community-level assembly selects for the same three families rising to prominence across different initial pools of microbiomes. We further analyzed the assembly patterns using a linear model. Detailed inspections of the sulfonamide metabolic gene clusters in individual genomes of isolates and assembled metagenomes reveal limited transfer potential beyond the boundaries of the Micrococcaceae lineage. Our results open up new possibilities for engineering specialist bacteria for environmental applications.

Biotransformation mechanism of Vibrio diabolicus to sulfamethoxazole at transcriptional level

Sulfamethoxazole (SMX) has attracted much attention due to its high probability of detection in the environment. Marine bacteria Vibrio diabolicus strain L2-2 has been proven to be able to transform SMX. In this study, the potential resistance and biotransformation mechanism of strain L2-2 to SMX, and key genes responses to SMX at environmental concentrations were researched. KEGG pathways were enriched by down-regulated genes including degradation of L-Leucine, L-Isoleucine, and fatty acid metabolism. Resistance mechanism could be concluded as the enhancement of membrane transport, antioxidation, response regulator, repair proteins, and ribosome protection. Biotransformation genes might involve in arylamine N-acetyltransferases (nat), cytochrome c553 (cyc-553) and acyl-CoA synthetase (acs). At the environmental concentration of SMX (0.1-10 μg/L), nat was not be activated, which meant the acetylation of SMX might not occur in the environment; however, cyc-553 was up-regulated under SMX stress of 1 μg/L, which indicated the hydroxylation of SMX could occur in the environment. Besides, the membrane transport and antioxidation of strain L2-2 could be activated under SMX stress of 10 μg/L. The results provided a better understanding of resistance and biotransformation of bacteria to SMX and would support related researches about the impacts of environmental antibiotics.

Various strategies applied for the removal of emerging micropollutant sulfamethazine: a systematic review

Pharmaceutical active drug(s) especially sulfamethazine (SMZ) is considered as one of the major emerging microcontaminants due its long-term existence in the environmental system and that can influence on the developmental of antibacterial resistance genes. Because of this region it has a great concern in the aquatic system. Moreover, the vast utilization of SMZ, excretion of undigested portion by animals and also through dumping or mishandling, SMZ is frequently detected in various samples (including water) of different places and its surroundings. Additionally, reports shown it has toxic effect against microalgae and mice. Thus, that can lead to several investigators, focusing on removal of SMZ alone or in combination of other drugs in wastewater treatment plants (WWTPs) either by abiotic and/or biotic treatment methods. The present review provides an overview of the toxic effect of SMZ and SMZ degradation/removal in abiotic and biotic processes. Finally, reveals the need of further implication of integrated treatments (including engineered biological mediators) to understand ideal biological approaches for the mineralization of SMZ.

Acquisition and Spread of Antimicrobial Resistance: A tet(X) Case Study

Understanding the mechanisms leading to the rise and dissemination of antimicrobial resistance (AMR) is crucially important for the preservation of power of antimicrobials and controlling infectious diseases. Measures to monitor and detect AMR, however, have been significantly delayed and introduced much later after the beginning of industrial production and consumption of antimicrobials. However, monitoring and detection of AMR is largely focused on bacterial pathogens, thus missing multiple key events which take place before the emergence and spread of AMR among the pathogens. In this regard, careful analysis of AMR development towards recently introduced antimicrobials may serve as a valuable example for the better understanding of mechanisms driving AMR evolution. Here, the example of evolution of tet(X), which confers resistance to the next-generation tetracyclines, is summarised and discussed. Initial mechanisms of resistance to these antimicrobials among pathogens were mostly via chromosomal mutations leading to the overexpression of efflux pumps. High-level resistance was achieved only after the acquisition of flavin-dependent monooxygenase-encoding genes from the environmental microbiota. These genes confer resistance to all tetracyclines, including the next-generation tetracyclines, and thus were termed tet(X). ISCR2 and IS26, as well as a variety of conjugative and mobilizable plasmids of different incompatibility groups, played an essential role in the acquisition of tet(X) genes from natural reservoirs and in further dissemination among bacterial commensals and pathogens. This process, which took place within the last decade, demonstrates how rapidly AMR evolution may progress, taking away some drugs of last resort from our arsenal.

Antibiotrophy: Key Function for Antibiotic-Resistant Bacteria to Colonize Soils-Case of Sulfamethazine-Degrading Microbacterium sp. C448

Chronic and repeated exposure of environmental bacterial communities to anthropogenic antibiotics have recently driven some antibiotic-resistant bacteria to acquire catabolic functions, enabling them to use antibiotics as nutritive sources (antibiotrophy). Antibiotrophy might confer a selective advantage facilitating the implantation and dispersion of antibiotrophs in contaminated environments. A microcosm experiment was conducted to test this hypothesis in an agroecosystem context. The sulfonamide-degrading and resistant bacterium Microbacterium sp. C448 was inoculated in four different soil types with and without added sulfamethazine and/or swine manure. After 1 month of incubation, Microbacterium sp. (and its antibiotrophic gene sadA) was detected only in the sulfamethazine-treated soils, suggesting a low competitiveness of the strain without antibiotic selection pressure. In the absence of manure and despite the presence of Microbacterium sp. C448, only one of the four sulfamethazine-treated soils exhibited mineralization capacities, which were low (inferior to 5.5 ± 0.3%). By contrast, manure addition significantly enhanced sulfamethazine mineralization in all the soil types (at least double, comprised between 5.6 ± 0.7% and 19.5 ± 1.2%). These results, which confirm that the presence of functional genes does not necessarily ensure functionality, suggest that sulfamethazine does not necessarily confer a selective advantage on the degrading strain as a nutritional source. 16S rDNA sequencing analyses strongly suggest that sulfamethazine released trophic niches by biocidal action. Accordingly, manure-originating bacteria and/or Microbacterium sp. C448 could gain access to low-competition or competition-free ecological niches. However, simultaneous inputs of manure and of the strain could induce competition detrimental for Microbacterium sp. C448, forcing it to use sulfamethazine as a nutritional source. Altogether, these results suggest that the antibiotrophic strain studied can modulate its sulfamethazine-degrading function depending on microbial competition and resource accessibility, to become established in an agricultural soil. Most importantly, this work highlights an increased dispersal potential of antibiotrophs in antibiotic-polluted environments, as antibiotics can not only release existing trophic niches but also form new ones.

Microbial Interactions Drive the Complete Catabolism of the Antibiotic Sulfamethoxazole in Activated Sludge Microbiomes

Microbial communities are believed to outperform monocultures in the complete catabolism of organic pollutants via reduced metabolic burden and increased robustness to environmental challenges; however, the interaction mechanism in functional microbiomes remains poorly understood. Here, three functionally differentiated activated sludge microbiomes (S1: complete catabolism of sulfamethoxazole (SMX); S2: complete catabolism of the phenyl part of SMX ([phenyl]-SMX) with stable accumulation of its heterocyclic product 3-amino-5-methylisoxazole (3A5MI); A: complete catabolism of 3A5MI rather than [phenyl]-SMX) were enriched. Combining time-series cultivation-independent microbial community analysis, DNA-stable isotope probing, molecular ecological network analysis, and cultivation-dependent function verification, we identified key players involved in the SMX degradation process. Paenarthrobacter and Nocardioides were primary degraders for the initial cleavage of the sulfonamide functional group (-C-S-N- bond) and 3A5MI degradation, respectively. Complete catabolism of SMX was achieved by their cross-feeding. The co-culture of Nocardioides, Acidovorax, and Sphingobium demonstrated that the nondegraders Acidovorax and Sphingobium were involved in the enhancement of 3A5MI degradation. Moreover, we unraveled the internal labor division patterns and connections among the active members centered on the two primary degraders. Overall, the proposed methodology is promisingly applicable and would help generate mechanistic, predictive, and operational understanding of the collaborative biodegradation of various contaminants. This study provides useful information for synthetic activated sludge microbiomes with optimized environmental functions.

Sulfadiazine dissipation as a function of soil bacterial diversity

Antibiotic residues in the environment are concerning since results in dispersion of resistance genes. Their degradation is often closely related to microbial metabolism. However, the impacts of soil bacterial community on sulfadiazine (SDZ) dissipation remains unclear, mainly in tropical soils. Our main goals were to evaluate effects of long-term swine manure application on soil bacterial structure as well as effects of soil microbial diversity depletion on SDZ dissipation, using "extinction dilution approach" and ¹⁴C-SDZ. Manure application affected several soil attributes, such as pH, organic carbon (OC), and macronutrient contents as well as bacterial community structure and diversity. Even minor bacterial diversity depletion impacted SDZ mineralization and non-extractible residue (NER) formation rates, but NER recovered along 42 d likely due to soil diversity recovery. However, this period may be enough to spread resistance genes into the environment. Surprisingly, the non-manured natural soil (NS-S1) showed faster SDZ dissipation rate (DT₉₀ = 2.0 versus 21 d) and had a great number of bacterial families involved in major SDZ dissipation pathways (mineralization and mainly NER), such as Isosphaeraceae, Ktedonobacteraceae, Acidobacteriaceae_(Subgroup_1), Micromonosporaceae, and Sphingobacteriaceae. This result is unique and contrasts our hypothesis that long-term manured soils would present adaptive advantages and, consequently, have higher SDZ dissipation rates. The literature suggests instantaneous chemical degradation of SDZ in acidic soils responsible to the fast formation of NER. Our results show that if chemical degradation happens, it is soon followed by microbial metabolism (biodegradation) performed by a pool of bacteria and the newly formed metabolites should favors NER formation since SDZ presented low sorption. It also showed that SDZ mineralization is a low redundancy function.

Flavoprotein monooxygenases: Versatile biocatalysts

Flavoprotein monooxygenases (FPMOs) are single- or two-component enzymes that catalyze a diverse set of chemo-, regio- and enantioselective oxyfunctionalization reactions. In this review, we describe how FPMOs have evolved from model enzymes in mechanistic flavoprotein research to biotechnologically relevant catalysts that can be applied for the sustainable production of valuable chemicals. After a historical account of the development of the FPMO field, we explain the FPMO classification system, which is primarily based on protein structural properties and electron donor specificities. We then summarize the most appealing reactions catalyzed by each group with a focus on the different types of oxygenation chemistries. Wherever relevant, we report engineering strategies that have been used to improve the robustness and applicability of FPMOs.

New frontiers in flavin-dependent monooxygenases

Flavin-dependent monooxygenases catalyze a wide variety of redox reactions in important biological processes and are responsible for the synthesis of highly complex natural products. Although much has been learned about FMO chemistry in the last ~80 years of research, several aspects of the reactions catalyzed by these enzymes remain unknown. In this review, we summarize recent advancements in the flavin-dependent monooxygenase field including aspects of flavin dynamics, formation and stabilization of reactive species, and the hydroxylation mechanism. Novel catalysis of flavin-dependent N-oxidases involving consecutive oxidations of amines to generate oximes or nitrones is presented and the biological relevance of the products is discussed. In addition, the activity of some FMOs have been shown to be essential for the virulence of several human pathogens. We also discuss the biomedical relevance of FMOs in antibiotic resistance and the efforts to identify inhibitors against some members of this important and growing family enzymes.

Living with sulfonamides: a diverse range of mechanisms observed in bacteria

Sulfonamides are the oldest class of synthetic antibiotics still in use in clinical and veterinary settings. The intensive utilization of sulfonamides has been leading to the widespread contamination of the environment with these xenobiotic compounds. Consequently, in addition to pathogens and commensals, also bacteria inhabiting a wide diversity of environmental compartments have been in contact with sulfonamides for almost 90 years. This review aims at giving an overview of the effect of sulfonamides on bacterial cells, including the strategies used by bacteria to cope with these bacteriostatic agents. These include mechanisms of antibiotic resistance, co-metabolic transformation, and partial or total mineralization of sulfonamides. Possible implications of these mechanisms on the ecosystems and dissemination of antibiotic resistance are also discussed. KEY POINTS: • Sulfonamides are widespread xenobiotic pollutants; • Target alteration is the main sulfonamide resistance mechanism observed in bacteria; • Sulfonamides can be modified, degraded, or used as nutrients by some bacteria.

Subsistence and complexity of antimicrobial resistance on a community-wide level

There are a multitude of resistance strategies that microbes can apply to avoid inhibition by antimicrobials. One of these strategies is the enzymatic modification of the antibiotic, in a process generally termed inactivation. Furthermore, some microorganisms may not be limited to the mere inactivation of the antimicrobial compounds. They can continue by further enzymatic degradation of the compounds' carbon backbone, taking nutritional and energetic advantage of the former antibiotic. This driving force to harness an additional food source in a complex environment adds another level of complexity to the reasonably well-understood process of antibiotic resistance proliferation on a single cell level: It brings bioprotection into play at the level of microbial community. Despite the possible implications of a resistant community in a host and a lurking antibiotic failure, knowledge of degradation pathways of antibiotics and their connections is scarce. Currently, it is limited to only a few families of antibiotics (e.g. β-lactams and sulfonamides). In this article, we discuss the fluctuating nature of the relationship between antibiotic resistance and the biodegradation of antibiotics. This distinction mainly depends on the genetic background of the microbe, as general resistance genes can be recruited to function in a biodegradation pathway.

Biodiversity, isolation and genome analysis of sulfamethazine-degrading bacteria using high-throughput analysis

Sulfamethazine (SM2) is one of the sulfonamide antibiotics that is frequently detected in aquatic environment. Given the complex structure of SM2 and its potential threat to the environment, it is necessary to determine the degradation behavior of high-concentration SM2. The mechanisms of community structure and diversity of activated sludge were analyzed. A novel SM2-degrading strain YL1 was isolated which can degrade SM2 with high concentration of 100 mg L^-1. Strain YL1 was identified as Paenarthrobacter ureafaciens and there was also a significant increase in the genus during acclimation. Additional SM2 metabolic mechanisms and genomic information of YL1 were analyzed for further research. The succession of the community structure also investigated the effect of SM2 on the activated sludge. This result not only advances the current understanding of microbial ecology in activated sludge, but also has practical implications for the design and operation of the environmental bioprocesses for treatment of antimicrobial-bearing waste streams.