Multi-omic profiling of a novel activated sludge strain Sphingobacterium sp. WM1 reveals the mechanism of tetracycline biodegradation and its merits of potential application

Study on the biodegradation characteristics and mechanism of tetracycline by Serratia entomophila TC-1

Microbial degradation is an important solution for antibiotic pollution in livestock and poultry farming wastes. This study reports the isolation and identification of the novel bacterial strain Serratia entomophila TC-1, which can degrade 87.8 % of 200 mg/L tetracycline (TC) at 35 °C, pH 6.0, and an inoculation amount of 1 % (v/v). Based on the intermediate products, a possible biological transformation pathway was proposed, including dehydration, oxidation ring opening, decarbonylation, and deamination. Using Escherichia coli and Bacillus subtilis as biological indicators, TC degraded metabolites have shown low toxicity. Whole-genome sequencing showed that the TC-1 strain contained tet (d) and tet (34), which resist TC through multiple mechanisms. In addition, upon TC exposure, TC-1 participated in catalytic and energy supply activities by regulating gene expression, thereby playing a role in TC detoxification. We found that TC-1 showed less interference with changes in the bacterial community in swine wastewater. Thus, TC-1 provided new insights into the mechanisms responsible for TC biodegradation and can be used for TC pollution treatment.

Biodegradation and bioaugmentation of tetracycline by Providencia stuartii TX2: Performance, degradation pathway, genetic background, key enzymes, and application risk assessment

The antibiotic tetracycline (TC) is an emerging pollutant frequently detected in various environments. Biodegradation is a crucial approach for eliminating TC contamination. However, only a few efficient TC-degrading bacteria have been isolated, and the molecular mechanisms of TC degradation, as well as their application potential, remain poorly understood. This study isolated a novel TC-degrading bacterium, Providencia stuartii TX2, from the intestine of black soldier fly larvae. TX2 exhibited remarkable performance, degrading 72.17 % of 400 mg/L TC within 48 h. Genomic analysis of TX2 unveiled the presence of antibiotic resistance genes and TC degradation enzymes. Transcriptomic analysis highlighted the roles of proteins related to efflux pumps, enzymatic transformation, adversity resistance, and unknown functions. Three TC degradation pathways were proposed, with TC being transformed into 27 metabolites through epimerization, hydroxylation, oxygenation, ring opening, and de-grouping, reducing TC toxicity. Additionally, TX2 significantly enhanced TC biodegradation in four TC-contaminated environmental samples and reduced antibiotic resistance genes and mobile genetic elements in chicken manure. This research provides insights into the survival and biodegradation mechanisms of Providencia stuartii TX2 and evaluates its potential for environmental bioremediation.

Donor polarization engineering of conjugated microporous polymers to boost exciton dissociation for photocatalytic degradation of tetracycline

The misuse and inevitable release of antibiotics can cause significant harm to both human health and the environment, and the use of polymeric semiconductors for photodegradation of antibiotics in aqueous environments is one of the most effective strategies to alleviate the current dilemma. Nevertheless, the inherently high exciton binding energy (Eb) and low photogenerated carrier transfer efficiency for most photocatalysts results in unsatisfactory photodegradation performance. Hence, this work proposes a donor polarization strategy to regulate the exciton dissociation of conjugated microporous polymers (CMPs) by minimizing their Eb. Results exhibited that the introduction of the strong donor unit 3,4-ethylenedioxythiophene (EDOT) not only reduces the Eb and effectively promotes exciton dissociation, but also broadens the visible light absorption of CMP. Among them, EdtTz-CMP with the lowest Eb (99 meV) delivered an efficiency of 94.6% in photocatalytic degradation of tetracycline (TC) with in 90 min, significantly higher than those of its analogues. This work provides a viable approach to design CMPs by tuning the intrinsic dipole of the donor for efficient environmental purification.

Biochemical insights into the biodegradation mechanism of typical sulfonylureas herbicides and association with active enzymes and physiological response of fungal microbes: A multi-omics approach

The extensive use of sulfonylurea herbicides has raised major concerns regarding their long-term soil residues and agroecological risks despite their role in agricultural protection. Microbial degradation is an important approach to remove sulfonylureas, whereas understanding the associated biodegradation mechanisms, enzymes, and physiological responses remains incomplete. Based on the rapid biodegradation of nicosulfuron by typical fungal isolate Talaromyces flavus LZM1, the dependency on cellular accumulation and environmental conditions, e.g. pH and nutrient supplies, was shown in the study. The biodegradation of nicosulfuron occurred intracellularly and followed the cascade of reactions including hydrolysis, Smile contraction rearrangement, hydroxylation, and opening of the pyrimidine ring. Besides 2-amino-4,6-dimethoxypyrimidine (ADMP) and 2-aminosulfonyl-N,N-dimethylnicotinamide (ASDM), numerous products and intermediates were newly identified and the structural forms of methoxypyrimidine and sulfonylurea bridge contraction rearrangement are predicted to be more toxic than nicosulfuron. The biodegradation should be enzymatically regulated by glycosylphosphatidylinositol transaminase (GPI-T) and P450s, which were manifested with the significant upregulation in proteomics. It is the first time that the hydrolysis of nicosulfuron into ADMP and ASDM have been associated with GPI-T. The integrated pathways of biodegradation were further elucidated through the involvement of various active enzymes. Except for the enzymatic catalysis, the physiological responses verified by metabolo-proteomics were critical not only to regulate material synthesis, uptake, utilization, and energy transfer but also to maintain antioxidant homeostasis, biodegradability, and tolerance of nicosulfuron by the differentially expressed metabolites, such as acetolactate synthase and 3-isopropylmalate dehydratase. The obtained results would help understand the biodegradation mechanism of sulfonylurea from chemicobiology and enzymology and promote the use of fungal biodegradation in pollution rehabilitation.

Biodegradation characteristics of p-Chloroaniline and the mechanism of co-metabolism with aniline by Pseudomonas sp. CA-1

Co-metabolism is a promising method to optimize the biodegradation of p-Chloroaniline (PCA). In this study, Pseudomonas sp. CA-1 could reduce 76.57 % of PCA (pH = 8, 70 mg/L), and 20 mg/L aniline as the co-substrate improved the degradation efficiency by 12.50 %. Further, the response and co-metabolism mechanism of CA-1 to PCA were elucidated. The results revealed that PCA caused deformation and damage on the surface of CA-1, and the -OH belonging to polysaccharides and proteins offered adsorption sites for the contact between CA-1 and PCA. Subsequently, PCA entered the cell through transporters and was degraded by various oxidoreductases accompanied by deamination, hydroxylation, and ring-cleavage reactions. Thus, the key metabolite 4-chlorocatechol was identified and two PCA degradation pathways were proposed. Besides, aniline further enhanced the antioxidant capacity of CA-1, stimulated the expression of catechol 2,3-dioxygenase and promoted meta-cleavage efficiency of PCA. The findings provide new insights into the treatment of PCA-aniline co-pollution.

Microbial Degradation of Tetracycline Antibiotics: Mechanisms and Environmental Implications

The escalating global consumption of tetracyclines (TCs) as broad-spectrum antibiotics necessitates innovative approaches to mitigate their pervasive environmental persistence and associated risks. While initiatives such as China's antimicrobial reduction efforts highlight the urgency of responsible TC usage, the need for efficient degradation methods remains paramount. Microbial degradation emerges as a promising solution, offering novel insights into degradation pathways and mechanisms. Despite challenges, including the optimization of microbial activity conditions and the risk of antibiotic resistance development, microbial degradation showcases significant innovation in its cost-effectiveness, environmental friendliness, and simplicity of implementation compared to traditional degradation methods. While the published reviews have summarized some aspects of biodegradation of TCs, a systematic and comprehensive summary of all the TC biodegradation pathways, reactions, intermediates, and final products including ring-opening products involved with enzymes and mechanisms of each bacterium and fungus reported is necessary. This review aims to fill the current gap in the literature by offering a thorough and systematic overview of the structure, bioactivity mechanism, detection methods, microbial degradation pathways, and molecular mechanisms of all tetracycline antibiotics in various microorganisms. It comprehensively collects and analyzes data on the microbial degradation pathways, including bacteria and fungi, intermediate and final products, ring-opening products, product toxicity, and the degradation mechanisms for all tetracyclines. Additionally, it points out future directions for the discovery of degradation-related genes/enzymes and microbial resources that can effectively degrade tetracyclines. This review is expected to contribute to advancing knowledge in this field and promoting the development of sustainable remediation strategies for contaminated environments.

Integrative chemical and multiomics analyses of tetracycline removal mechanisms in Pseudomonas sp. DX-21

Tetracycline (TC), widely found in various environments, poses significant risks to ecosystems and human health. While efficient biodegradation removes TC, the mechanisms underlying this process have not been elucidated. This study investigated the molecular mechanisms underlying TC biosorption and transfer within the extracellular polymeric substances (EPS) of strain DX-21 and its biodegradation process using fourier transform infrared spectroscopy, molecular docking, and multiomics. Under TC stress, DX-21 increased TC biosorption by secreting more extracellular polysaccharides and proteins, particularly the latter, mitigating toxicity. Moreover, specialized transporter proteins with increased binding capacity facilitated TC movement from the EPS to the cell membrane and within the cell. Transcriptomic and untargeted metabolomic analyses revealed that the presence of TC led to the differential expression of 306 genes and significant alterations in 37 metabolites. Notably, genes related to key enzymes, such as electron transport, peroxidase, and oxidoreductase, exhibited significant differential expression. DX-21 combated and degraded TC by regulating metabolism, altering cell membrane permeability, enhancing oxidative defense, and enhancing energy availability. Furthermore, integrative omics analyses indicated that DX-21 degrades TC via various enzymes, reallocating resources from other biosynthetic pathways. These results advance the understanding of the metabolic responses and regulatory mechanisms of DX-21 in response to TC.

Elucidating doxycycline biotransformation mechanism by Chryseobacterium sp. WX1: Multi-omics insights

Doxycycline (DOX) represents a second-generation tetracycline antibiotic that persists as a challenging-to-degrade contaminant in environmental compartments. Despite its ubiquity, scant literature exists on bacteria proficient in DOX degradation. This study marked a substantial advancement in this field by isolating Chryseobacterium sp. WX1 from an activated sludge enrichment culture, showcasing its unprecedented ability to completely degrade 50 mg/L of DOX within 44 h. Throughout the degradation process, seven biotransformation products were identified, revealing a complex pathway that began with the hydroxylation of DOX, followed by a series of transformations. Employing an integrated multi-omics approach alongside in vitro heterologous expression assays, our study distinctly identified the tetX gene as a critical facilitator of DOX hydroxylation. Proteomic analyses further pinpointed the enzymes postulated to mediate the downstream modifications of DOX hydroxylation derivatives. The elucidated degradation pathway encompassed several key biological processes, such as the microbial transmembrane transport of DOX and its intermediates, the orchestration of enzyme synthesis for transformation, energy metabolism, and other gene-regulated biological directives. This study provides the first insight into the adaptive biotransformation strategies of Chryseobacterium under DOX-induced stress, highlighting the potential applications of this strain to augment DOX removal in wastewater treatment systems containing high concentrations of DOX.

Biotransformation characteristics of tetracycline by strain Serratia marcescens MSM2304 and its mechanism evaluation based on products analysis and genomics

Microbial biotransformation is a recommended and reliable method in face of formidable tetracycline (TC) with broad-spectrum antibacterial activity. Herein, comprehensive characteristics of a newfound strain and its molecular mechanism in process of TC bioremediation were involved in this study. Specifically, Serratia marcescens MSM2304 isolated from pig manure sludge grew well in presence of TC and achieved optimal removal efficiency of 61% under conditions of initial TC concentration of 10 mg/L, pH of 7.0, cell inoculation amount of 5%, and tryptone of 10 g/L as additional carbon. The pathways of biotransformation include EPS biosorption, cell surface biosorption and biodegradation, which enzymatic processes of biodegradation were occurred through TC adsorbed by biofilms was firstly broken down by extracellular enzymes and part of TC migrated towards biofilm interior and degraded by intracellular enzymes. Wherein extracellular polysaccharides in extracellular polymeric substances (EPS) from biofilm of strain MSM2304 mainly performed extracellular adsorption, and changes in position and intensity of CO, =CH and C-O-C/C-O of EPS possible further implied TC adsorption by it. Biodegradation accounting for 79.07% played a key role in TC biotransformation and could be fitted well by first-order model that manifesting rapid and thorough removal. Potential biodegradation pathway including demethylation, dihydroxylation, oxygenation, and ring opening possibly involved in TC disposal process of MSM2304, TC-degrading metabolites exhibited lower toxicity to indicator bacteria relative to parent TC. Whole genome sequencing as underlying molecular evidence revealed that TC resistance genes, dehydrogenases-encoding genes, monooxygenase-encoding genes, and methyltransferase-encoding genes of strain MSM2304 were positively related to TC biodegradation. Collectively, these results favored a theoretical evaluation for Serratia marcescens MSM2304 as a promising TC-control agent in environmental bioremediation processes.

Dimension-controlled synthesis of BiOI for efficient visible light photodegradation of tetracycline: role of pore structure

The transformation of photogenerated charge carriers (PC) in variable dimensional photocatalyst plays a pivotal role in unraveling the generation of reactive species (RS). However, the dimensional structure-activity relationship in photocatalysis remains elusive, with limited insights into its intricacies. Herein, we report a controlled synthesis strategy by using polyvinyl pyrrolidone (PVP)-assisted precipitation method for BiOI photocatalyst. Due to the steric hindrance of PVP, the 3D microsphere (3D-PVP0.5) and porous structure (3D-PVP1) of BiOI catalysts have been successfully prepared at room temperature. The 3D-PVP1 photocatalyst contains abundant mesopores and larger pores, which significantly shorten the diffusion distance of PC. Also, these PC in porous structure is beneficial for transferring from the inner phase to the surface of materials. Combined with optical property and radicals trapping experiments, the recombination rate of PC in porous structure performs a significant decrease, leading to the generation of more dominated ROS (•O2- and h+). The •O2- played a dominated role (86.98% of contribution rate) in photodegradation of tetracycline (TC) in 3D-PVP1 photocatalytic process. Compared with 2D nanosheet of BiOI (16.7% removal rate of TC), the as-prepared 3D porous structure of BiOI catalyst exhibits unique stable and high removal capacities (90.5%) for TC photodegradation under visible light irradiation. The kobs of 3D-PVP1 photocatalyst increased by 5.1 times than that of 2D nanosheet. To investigate its practical application, the effects of inorganic anions and pH have been systematically studied. This work sheds light on the design of variable dimension BiOI catalyst and provides more insight into the transfer mechanism of PC.

Highly efficient heterogeneous electro-Fenton reaction for tetracycline degradation by Fe-Ni LDH@ZIF-67 modified carbon cloth cathode: Mechanism and toxicity assessment

In this work, a novel and efficient Fe-Ni LDH@ZIF-67 catalyst modified carbon cloth (CC) cathode was developed for tetracycline (TC) degradation in heterogeneous electro-Fenton (Hetero-EF) process. Compared to Fe-Ni LDH/CC (75.7%), TC degradation rate of Fe-Ni LDH@ZIF-67/CC cathode increased to 95.6% within 60 min. The synergistic effect of hetero-EF and anodic oxidation process accelerated electron transfer, the maximum H2O2 production of Fe-Ni LDH@ZIF-67/CC electrode reached 264 mg/L, improving utilization efficiency of H2O2. The cathode possessing a satisfied TC degradation performance over a wide pH (3-9). Free radical capture experiment revealed the collaboration of ·O2-, ·OH, and 1O2 play a significant role in TC degradation. The 5 cycles experiment and metal ion leaching experiment showed that the proposed Fe-Ni LDH@ZIF-67/CC has good recyclability and stability. In addition, the proposed Fe-Ni LDH@ZIF-67/CC cathode achieved satisfying performance in real water (tap water: 97.3%, lake water: 97.7%), demonstrating the possibility for practical application. TC degradation pathways were proposed by theory analysis and experimental results. The toxicity of TC intermediates was reduced by Hetero-EF degradation according to Toxicity Estimation Software Tool and Escherichia coli growth inhibition experiments. This work provides a novel modified cathode to improve removal efficiency of antibiotics in wastewater.