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

Effects of nitrogen fertilization on antibiotic resistance gene spread from soil to floodwater in paddy fields

The environmental risks associated with antibiotic resistance genes (ARGs) have drawn increasing attention. Here, we investigated the spread of ARGs from soil to floodwater in paddy fields by conducting 5-year field experiments having four treatments: control, reduced N fertilization, conventional N fertilization (CN) and plant-based organic N fertilization (ON). In comparison to the control treatment, CN and ON treatments significantly increased the total N content by 26.8%-36.6% in soil and 42.7%-67.4% in floodwater, respectively. Additionally, ON treatments increased the concentrations of free-floating and particle-attached mobile gene elements in floodwater by 78.6% and 32.7%, respectively. Redundancy and linear regression analyses indicated that total N and NH4+ in soil and mobile gene elements in floodwater were closely connected with the levels of ARGs in floodwater. Correspondingly, CN and ON treatments increased total abundances of ARGs in floodwater to 1.26 and 1.46 times, respectively. The network analysis further revealed that ARGs, such as MexW, tetAB and optrA, could be carried by the hosts of ARGs (such as Chloroflexi, Gemmatimonadetes and Nitrospirae) and spread from soil to particle-attached floodwater fractions through suspended solids. Moreover, structure equation models indicated that the evolution of ARGs in free-floating fractions could dominate the propagation of ARGs in floodwater. These findings provide valuable insights into the propagation of ARGs in paddy fields and highlight nutrient management in paddy field floodwater as a potentially effective strategy to mitigate the spread of ARGs.

Thermophilic degradation of sulfamethazine by Geobacillus sp. S-07: pathway and mechanism

Biodegradation is crucial for the removal and remediation of sulfonamide antibiotic (SA) contamination. Comprehensively understanding the thermophilic degradation mechanism is essential for the application of SA-biodegrading isolates in engineered systems, such as composting. In this study, we explored the thermophilic biodegradation mechanism of Geobacillus sp. S-07 on sulfamethazine (SMZ). Targeted metabolite analysis unveiled that strain S-07 effectively detoxifies SMZ by modifying the amino moiety and disassembling the sulfonamide bridge moiety. By integrating genomic and proteomic analysis, enzymes potentially involved in the SMZ biotransformation were further proposed, including an adenine deaminase, a dimethylsulfone monooxygenase, and a putative heme-containing peroxidase. Genomic analysis indicated that S-07 carries five antibiotic resistance genes, presenting a low mobility in horizontal transfer, implying its low resistance pollution risk in bioremediation application. This study offers novel insights into the thermophilic SA biodegradation mechanism, and provides biological resources for the development of thermophilic bioremediation technologies aimed at enhanced SA removal.

A new strategy for removing insecticide etoxazole from soil using a combination of a novel Paracoccus versutus Y4 and a fungal mycelium carrier

Etoxazole is a widely used insecticide that poses a serious threat to both ecosystems and human health. In present study, a novel strain Paracoccus versutus Y4 was isolated and identified. More than 98 % of the etoxazole (10 mg/L) was degraded as the sole carbon source within 8 d by strain Y4 in liquid culture. HPLCMS/MS analysis revealed three possible intermediates, and a novel metabolic pathway of etoxazole including oxidation, dehydrogenation, and hydrolysis reactions was proposed. The Toxicity Estimation Software Tool suggests that the biodegradation intermediates were less harmful than etoxazole. Whole-genome sequencing revealed that the genome size of P. versutus Y4 was 5320,902 bp containing 5187 coding sequences. Among them, the gene coding monooxygenase, dehydrogenase and hydrolase may be responsible for etoxazole biodegradation. The results of molecular docking analysis suggested that the monooxygenase, dehydrogenase, and hydrolase from strain Y4 may facilitate catalytic degradation through efficient substrate binding. Compared with diatomite carrier, fungal mycelium carrier can promote the growth of strain Y4. In the soil degradation experiments, the fungal mycelium carrier promoted etoxazole degradation by strain Y4 in both fresh and sterilized soil. Treatment with Y4 +fungal mycelium significantly reduced the half-life of etoxazole in fresh soil from 24.2 to 6.3 d. Our study is the first to isolate etoxazole-degrading bacteria and provides a new strategy for the bioremediation of pesticide pollution by combining degrading microbes and fungal mycelium carriers.

The treated wastewater enhances the biodegradation of sulfonamide antibiotics in biofilm-sediment downstream of the receiving river outlet

Although the treated wastewater meets the discharge standards, it can still become a potential transmitted stressor that affects aquatic organisms in receiving rivers. Biofilms and sediments as the main solid-phase substances in natural aquatic environments can biodegrade micropollutants. However, most of the current studies have selected a single solid-phase material, and there are relatively few studies that comprehensively consider the effect of treated wastewater on the dissipation of micropollutants in a composite biofilm-sediment system. Therefore, this study investigated the dissipation pathways of six sulfonamide antibiotics (SAs) in biofilm-sediment and the effect of treated wastewater on SAs dissipation. The results showed that biodegradation was the main pathway for SAs dissipation in biofilm-sediment. The input of treated wastewater increased the abundance of dominant degradation bacteria Burkholderiales and Pseudomonadale, thereby improving the biodegradation rate of SAs (approximately 1.5 times higher than upstream degradation rate). These genera could also be further integrated into downstream communities to continuously mediate the biodegradation of SAs. Through mass spectrometry and metagenomic sequencing analysis, it was found that the common degradation pathways of SAs in biofilm-sediment affected by treated wastewater are acetylation, formylation, hydroxylation, and bond cleavage. Acetyltransferase played an important role in the biodegradation of SAs. In addition, the enrichment of antibiotic resistant genes during biodegradation increased the risk of their spread in the aquatic environment. These findings provide new insights into the fate of antibiotics in aquatic environments and the impact of treated wastewater on downstream bacterial communities.

Pathway Elucidation and Key Enzymatic Processes in the Biodegradation of Difenoconazole by Pseudomonas putida A-3

The extensive agricultural use of the fungicide difenoconazole (DIF) and its associated toxicity increasingly damage ecosystems and human health. Thus, an urgent need is to develop environmentally friendly technological approaches capable of effectively removing DIF residues. In this study, strain Pseudomonas putida A-3 was isolated for the first time which can degrade DIF efficiently. After optimization of the degradation conditions, the degradation rate reached 75.98%. Moreover, a new DIF degradation pathway, including hydroxylation, hydrolysis, dechlorination, and ether bond breaking. The acute and chronic toxicity of DIF degradation products assessed using ECOSAR software showed lower toxicity than the parent compound. Furthermore, strain A-3 remarkably accelerated the degradation of DIF in contaminated water-sediment systems. We successfully predicted six potential key enzymes for DIF degradation based on the results of whole genome sequencing, RT-qPCR, and molecular docking. Overall, the results revealed novel pathways for DIF biodegradation and provide a strong candidate for bioremediation of DIF residue-polluted environments.

Dirammox (direct ammonia oxidation) to nitrogen (N2): discovery, current status, and perspectives

Microbial ammonia oxidation plays an important role in nitrogen (N2) cycling in natural and man-made systems. Heterotrophic microorganisms that oxidize ammonia were observed more than a century ago; however, the underlying molecular mechanism of ammonia oxidation is still mysterious. Dirammox (direct ammonia oxidation to N2) is a newly described heterotrophic ammonia oxidation process in which ammonia or its organic amine is oxidized into hydroxylamine and then directly converted to N2 gas without the involvement of nitrite and nitrate. As demonstrated with Alcaligenes species, the conversion of ammonia to hydroxylamine is mediated by the dnf genes, and hydroxylamine conversion to N2 is considered both a biotic and abiotic process. Dirammox is different from the N2-producing processes of nitrification-denitrification and anaerobic ammonia oxidation (anammox), in which nitrite or nitrate is involved. Here, we review the discovery of dirammox, progress toward understanding its genetics, biochemistry, physiology, and ecology, and future perspectives and directions.

Characterization and degradation mechanism of a newly isolated hydrolyzed polyacrylamide-degrading bacterium Alcaligenes faecalis EPDB-5 from the oilfield sludge

Hydrolyzed polyacrylamide (HPAM) is posing serious threats to ecosystems. However, biodegradation is an effective method to remove HPAM owing to its low cost and environmental friendliness. In this study, Alcaligenes faecalis EPDB-5 was isolated as a highly efficient HPAM degrading strain from sludge contaminated with polymerized produced water from Daqing oilfield. Under the optimal conditions, the strain EPDB-5 demonstrated an impressive HPAM degradation rate of 86.05%, the total nitrogen (TN) removal of 71.96% and chemical oxygen demand (COD) removal of 67.98%. Meanwhile, it can maintain a stable degradation rate higher than 75% under different pH and temperature conditions. 27 genes that play a key role in HPAM degradation were annotated by metagenomics sequencing. The key genes were involved in multiple KEGG pathways, including biofilm formation, biosynthesis secondary metabolites, and metabolic pathways. SEM, GPC, and FTIR analyses revealed that the structure of HPAM after biodegradation showed pores, a significant decrease in molecular weight, -NH2 detachment, and carbon chain breakage. Particularly, we propose a possible mechanism of biofilm formation - HPAM degradation - biofilm disappearance and reorganization. Moreover, the degradation rate of strain EPDB-5 on real wastewater containing HPAM was 29.97% in only three days. This work expands our knowledge boundary about the HPAM degradation mechanism at the functional gene level, and supports the potential of strain EPDB-5 as a novel auxiliary microbial resource for the practical application of HPAM.

Comprehensive analysis of biotransformation pathways and products of chloramphenicol by Raoultella Ornithinolytica CT3: Pathway elucidation and toxicity assessment

Microbial degradation of chloramphenicol (CAP) has become important for reducing the adverse impact of environmental pollution with antibiotics. Although several pathways for CAP degradation have been identified in various bacteria, multiple metabolic pathways and their respective intermediate metabolites within a single strain are rarely reported. Here, Raoultella ornithinolytica CT3 was first isolated from silkworm excrement using CAP as the sole carbon source, and 100 mg/L CAP was almost completely degraded within 48 h. The biodegradation type of CAP followed first-order kinetics. Twenty-two CAP biotransformation products were identified using high-performance liquid chromatography and ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry. The CAP biotransformation pathways were predicted mainly in the acetylation and auxiliary pathways of propionylation and butyrylation. The toxicity of CAP biotransformation products was evaluated using the ecological structure-activity relationship (ECOSAR) model and biological indicators. The results showed that the toxicity of the intermediate metabolites changed slightly, but the final metabolite was harmless to the environment. Genomic analysis predicted that genes encoding acetyltransferase, amido-linkage hydrolase, nitroreductase, haloacetate dehalogenase, and protocatechuate 3,4-dioxygenase were associated with CAP biodegradation. This study provides new insights into the microbial degradation pathway of CAP and constitutes an ecological safety assessment for CAP-contaminated environments.

A newly NH2-UiO-66 composite functionalized by molecularly imprinted polymer for selective and rapid removal of sulfamethoxazole

Metal-organic frameworks (MOFs) are used as novel adsorption materials owing to their large surface area and tunable pore size. However, the lack of selectivity considerably limits their application. Consequently, designing functionalized MOFs with specific recognition abilities is essential for enhancing their adsorption performance. Herein, we synthesized a functionalized NH2-UiO-66 composite modified by molecularly imprinted polymers (MIP@NH2-UiO-66) via a one-step polymerization process in which NH2-UiO-66 and MIP were formed simultaneously. Results demonstrate that MIP@NH2-UiO-66 effectively recognized sulfamethoxazole (SMX) in complex matrices. The adsorption equilibrium was reached in only 30 min, and this fast SMX adsorption on MIP@NH2-UiO-66 was described by the Avrami kinetic model, which indicates a spontaneous and exothermic adsorption process. Within the pH range of 3.0-10.0, MIP@NH2-UiO-66 exhibited an optimal binding capacity for SMX, and the maximum adsorption of SMX was 68.36 mg g-1 at 25°C, which exceeded those of existing adsorption materials (< 60.10 mg g-1). Additionally, MIP@NH2-UiO-66 was regenerated for ∼17 cycles compared to less than eight cycles for the other adsorbents. MIP@NH2-UiO-66 effectively removed 90.58%-99.60% of SMX from river water, rainwater, soil, sediment, chicken, pork, and milk samples, with a relative standard deviation of less than 4.43%. The superior adsorption of SMX on MIP@NH2-UiO-66 was primarily driven by the synergistic effects of the imprinting sites, hydrogen bonding, and electrostatic forces. The one-step polymerization method substantially simplified the synthesis process and reduced the costs, which are promising factors for the synthesis of MOFs with high selectivity.

Development and detailed investigation of metal nanoparticles decorated carbon black/sodium alginate composite beads for catalytic reduction of environmental toxicants and hydrogen production

The discharge of environmental pollutants requires intellectual and rapid solutions to convert them into safer products. Simultaneously, the high energy demands underscore the imperative importance of generating sufficient green energy to fulfill human needs. This study focused on metal nanoparticles (MNPs) decoration on polymeric beads (BDs), employing orange peel derived carbon black (OrP) and sodium alginate polymer (Alg). The resulting Alg-OrP-BDs serve as a versatile platform for the adsorption of different metal ions and their treatment with a potent reducing agent (NaBH4) yielding modified BDs catalysts: Ag0@Alg-OrP-BDs, Ni0@Alg-OrP-BDs, Co0@Alg-OrP-BDs, Fe0@Alg-OrP-BDs, and Cu0@Alg-OrP-BDs. These synthesized nanocomposite catalysts were characterized and exhibit remarkable catalytic reduction capabilities against various nitrophenols and dyes. Notably, Cu0@Alg-OrP-BDs emerges as an outstanding catalyst, demonstrating high efficiency in the (>98 %) reduction of 4-nitrophenol and methyl orange with the rates of 1.568 min-1 and 2.185 min-1, respectively. Furthermore, its parametric study was investigated to explore the efficiency of the selected catalyst in detail. Similarly, the Cu0@Alg-OrP-BDs also enhance hydrogen gas production in various conditions, achieving a rate of 1620.37 mL g-1 of catalyst min-1. The purity of the hydrogen was determined using a GC-TCD system. Hence, this study pioneers the development and thorough examination of the Cu0@Alg-OrP-BDs catalyst, showcasing its exceptional activity and recyclability.

Hydrogel based on M1 macrophage lysate and alginate loading with oxaliplatin for effective immunomodulation to inhibit melanoma progression, recurrence and metastasis

Despite the monumental success of immunotherapy in treating melanoma clinically, it still confronts significant challenges, chiefly that singular immunomodulatory tactics are insufficient to suppress the recurrence and metastasis of melanoma. Herein, these challenges are addressed by a hydrogel based on M1 macrophage lysate and alginate (M1LMHA) loaded with oxaliplatin (OXA), named M1LMHA@OXA.The results obtained from scanning electron microscopy and confocal microscopy indicate that the structure and morphology of M1LMHA@OXA remain unchanged. Flow cytometry results reveal that M1LMHA@OXA significantly promotes the maturation of dendritic cells (DCs) and enhances the proliferation of T lymphocytes. In a subcutaneous melanoma transplant model, M1LMHA@OXA effectively suppressed tumor growth in comparison to OXA alone and M1LMHA alone. Flow cytometry demonstrated that M1LMHA@OXA markedly increased the number of mature DCs and CD8+ T cells at the tumor site, while significantly reducing the quantity of M2-like tumor-associated macrophages (TAM) and enhancing the presence of M1 macrophages. Enzyme-linked immunosorbent assay (ELISA) results indicated that following treatment with M1LMHA@OXA, the levels of interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-α) in the bloodstream of mice were significantly elevated, whereas interleukin-10 (IL-10) exhibited no significant difference. This outcome further corroborates the ability of M1LMHA@OXA to substantially bolster the immune capability of mice. Similar results have also been observed in a melanoma subcutaneous transplantation recurrence model, and optical imaging of the lungs of mice revealed that M1LMHA@OXA inhibited tumor metastasis to the lungs. Notably, M1LMHA@OXA exhibits an exceptional therapeutic effect on the growth, post-surgical recurrence, and metastasis of the B16F10 melanoma. Therefore, this study provides a straightforward strategy that leverages the cooperative regulation of multiple immune cells to thwart the proliferation, recurrence, and spread of melanoma.

Functionalization of MXene using iota-carrageenan, maleic anhydride, and N,N'-methylene bis-acrylamide for high-performance removal of thorium (IV), uranium (IV), sulfamethoxazole, and levofloxacin

An increasing quantity of pollutants has been discharged into the aquatic media, posing a serious hazard to public health. To address this issue, a new sorbent material, MXene@i.Carr@MaMb, was developed through the functionalization of the MXene surface using iota-carrageenan (i.Carr), maleic anhydride, and N, N'-methylene bis-acrylamide. This sorbent material was designed to remove thorium (Th (IV)) effectively, uranium (U (IV)), sulfamethoxazole (SMX), and levofloxacin (LEV) from wastewater. The MXene@i.Carr@MaMb composite incorporated significant functional groups, including OH, F, and O from MXene, oxygen and ester sulfate groups from iota-carrageenan (i.Carr), and OH, NH, and CO groups from N, N'-methylene bis-acrylamide, and maleic anhydride, which interacted with the UV (IV), Th (IV), SMX, and LEV pollutants through electrostatic interaction, complexation, and hydrogen bonding. MXene@i.Carr@MaMb composite exhibited excellent sorption capacities for Th (IV) (3.6 ± 0.03 mmol g-1), U (IV) (3.7 ± 0.09 mmol g-1), SMX (5.8 ± 0.03 mmol g-1), and LEV (5.9 ± 0.05 mmol g-1) at 323.15 K. The sorption kinetics and isotherms of radioactive metals and antibiotics can be well-described using pseudo-first-order kinetic models and Langmuir and Sips isothermal equations. This study presented a novel sorbent material for efficiently removing radioactive metals and antibiotics from wastewater.

Empowering agriculture: The promise of zinc biofortification in rice

Zinc (Zn) plays a crucial role in metabolism in both plant and animal life. Zn deficiency is a worldwide problem that has recently gotten worse. This micronutrient shortage can be largely attributed to eating foods that are poor in zinc. If biofortification methods were widely used, Zn enrichment of the organ or tissue of interest would increase dramatically. However, Zn absorption mechanisms in rice plants must be understood on a fundamental level before these methods can be used effectively. Plant systems' Zn transporters and metal chelators play a major role in regulating this intricate physiological characteristic. The Zn efficiency of specific species is affected by a variety of factors, including the plant's growth stage, edaphic conditions, the time of year, and more. Both old and new ways of breeding plants can be used for biofortification. We have highlighted the significance of recombinant and genetic approaches to biofortifying in rice. In this review, we have the metabolic role of zinc in rice, and the different transporter families involved in the transportation of zinc in rice. We have also discussed the combined approaches of agronomic and genetic in zinc biofortification in rice and potential outcomes and future predictions.

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.

Microbial degradation of contaminants of emerging concern: metabolic, genetic and omics insights for enhanced bioremediation

The perpetual release of natural/synthetic pollutants into the environment poses major risks to ecological balance and human health. Amongst these, contaminants of emerging concern (CECs) are characterized by their recent introduction/detection in various niches, thereby causing significant hazards and necessitating their removal. Pharmaceuticals, plasticizers, cyanotoxins and emerging pesticides are major groups of CECs that are highly toxic and found to occur in various compartments of the biosphere. The sources of these compounds can be multipartite including industrial discharge, improper disposal, excretion of unmetabolized residues, eutrophication etc., while their fate and persistence are determined by factors such as physico-chemical properties, environmental conditions, biodegradability and hydrological factors. The resultant exposure of these compounds to microbiota has imposed a selection pressure and resulted in evolution of metabolic pathways for their biotransformation and/or utilization as sole source of carbon and energy. Such microbial degradation phenotype can be exploited to clean-up CECs from the environment, offering a cost-effective and eco-friendly alternative to abiotic methods of removal, thereby mitigating their toxicity. However, efficient bioprocess development for bioremediation strategies requires extensive understanding of individual components such as pathway gene clusters, proteins/enzymes, metabolites and associated regulatory mechanisms. "Omics" and "Meta-omics" techniques aid in providing crucial insights into the complex interactions and functions of these components as well as microbial community, enabling more effective and targeted bioremediation. Aside from natural isolates, metabolic engineering approaches employ the application of genetic engineering to enhance metabolic diversity and degradation rates. The integration of omics data will further aid in developing systemic-level bioremediation and metabolic engineering strategies, thereby optimising the clean-up process. This review describes bacterial catabolic pathways, genetics, and application of omics and metabolic engineering for bioremediation of four major groups of CECs: pharmaceuticals, plasticizers, cyanotoxins, and emerging pesticides.

Biosorption of thorium onto Chlorella Vulgaris microalgae in aqueous media

Thorium biosorption by a green microalga, Chlorella Vulgaris, was studied in a stirred batch reactor to investigate the effect of initial solution pH, metal ion concentration, biomass dosage, contact time, kinetics, equilibrium and thermodynamics of uptake. The green microalgae showed the highest Th adsorption capacity at 45 °C for the solution with a thorium concentration of 350 mg L-1 and initial pH of 4. The amount of uptake raised from 84 to 104 mg g-1 as the temperature increased from 15 to 45 °C for an initial metal concentration of 75 mg L-1 at pH 4. Transformation Infrared Spectroscopy (FTIR) was employed to characterize the vibrational frequency changes for peaks related to surface functional groups. Also, the scanning electron microscope (SEM) and energy-dispersive X-ray spectroscopy (EDX) were used to determine the morphological changes and elemental analysis of the biosorbent before and after the sorption process. The Langmuir isotherm was in perfect agreement with the equilibrium empirical data of thorium biosorption and the highest sorption capacity of the Chlorella Vulgaris microalgae was determined as 185.19 mg g-1. Also, the results of kinetic studies show that the thorium biosorption process follows a pseudo-second-order kinetic model. The negative value of ΔG0 indicates spontaneity and the positive values of ΔH0 indicate the endothermic nature of the adsorption process.

Sulfadiazine degradation by Bjerkandera adusta DH0817 at low temperatures and its cold-adaptation mechanisms

The prolonged period of low temperatures in northern China poses a significant challenge to the bioremediation of antibiotic pollution. This study reports that a white-rot fungus Bjerkandera adusta DH0817, isolated from a poultry farm in Liaoning Province, can remove 60 % of SDZ within 20 days at 10°C and reduce the biotoxicity of SDZ. Six degradation pathways were proposed. SDZ biodegradation was primarily driven by cytochrome P450. Transcriptome analysis revealed that DH0817 upregulated genes associated with cell membrane, transcription factors and soluble sugars in response to low temperatures. Subsequently, genes associated with fatty acid, proteins and enzymes were upregulated to remove SDZ at low temperatures. This study provides valuable microbial resources and serves as a theoretical reference for addressing antibiotic pollution in livestock and poultry farms under low temperature conditions.

Cultivating resilience in wheat: mitigating arsenic toxicity with seaweed extract and Azospirillum brasilense

Arsenic (As) toxicity is a serious hazard to agricultural land due to growing industrialization, which has a negative effect on wheat crop yields. To address this issue, using seaweed extract and Azospirillum brasilense has emerged as an effective strategy for improving yield under stress conditions. However, the combined application of A. brasilense and seaweed extract in wheat crops under As toxicity has not been fully explored. The effectiveness of combining A. brasilense and seaweed extract in reducing As toxicity in wheat production was examined in this study through a 2-year pot experiment with nine treatments. These treatments included a control with no additives and two As concentrations (50 and 70 μM). At 50 and 70 μM, As was tested alone, with seaweed extract, with A. brasilense, and both. Significant results were achieved in reducing As toxicity in wheat crops. Arsenic at 70 μM proved more harmful than at 50 μM. The application of A. brasilense and seaweed extract was more effective in improving crop growth rates, chlorophyll levels, and stomatal conductance. The combined application notably decreased As concentration in wheat plants. It was concluded that applying A. brasilense and seaweed extract not only improves wheat growth but can also improve soil parameters under As toxicity conditions by increasing organic matter contents, boosting nutrient availability, and increasing the production of antioxidant enzymes.

Biodegradable Acid-Based Fe2MnO4 Nanoparticles for Water Remediation

This study demonstrated the synthesis of Fe2MnO4 modified by citric acid, a biodegradable acid, using a simple co-precipitation method. Characterization was performed using qualitative analysis techniques such as Fourier-transformed infrared spectroscopy, scanning electron microscopy equipped with energy-dispersive X-ray spectroscopy, X-ray diffraction, selected-area electron diffraction, N2 adsorption-desorption, and zero-point charge. The prepared nanoparticles had a rough and porous surface, and contained oxygenous (-OH, -COOH, etc.) functional groups. The specific surface area and average pore size distribution were 83 m2/g and 5.17 nm, respectively. Net zero charge on the surface of the prepared nanoparticles was observed at pH 7.5. The prepared nanoparticles were used as an adsorbent to remove methylene blue dye from water under various conditions. Using small amounts of the adsorbent (2.0 g/L), even a high concentration of MB dye (60 mg/L) could be reduced by about ~58%. Exothermic, spontaneous, feasible, and monolayer adsorption was identified based on thermodynamics and isotherm analysis. Reusability testing verified the stability of the adsorbent and found that the reused adsorbent performed well for up to three thermal cycles. Comparative analysis revealed that the modified adsorbent outperformed previously reported adsorbents and unmodified Fe2MnO4 in terms of its partition coefficient and equilibrium adsorption capacity under different experimental conditions.

Biochar is an organomineral tool for mitigation of Cd toxicity in rice embedded soil and plant

Cadmium (Cd) contamination poses a significant threat to plants and human, as it can easily accumulate in plant tissues, leading to biochemical and physiological disorders. There is a growing interest in using biochar to mitigate the absorption of heavy metals by rice plants. This study tested peach biochar (PB) and its various levels of applications to evaluate the promising level for Cd remediation in contaminated soil. The application of PB3 had a significant impact on Cd mitigation, with extractable Cd (AB-DTPA) in soil decreasing from 66 mg kg-1 to 18 mg kg-1. Cd content in shoots decreased from 2.5 mg kg-1 to 0.9 mg kg-1, and in grains decreased from 1.1 mg kg-1 to 0.5 mg kg-1. Moreover, the PB treatment led to increased rice yield, from 4.9 to 10 g pot-1, and biological yield, from 4 to 20 g pot-1. The soil also showed improved organic matter content, increasing from 0.4% to 0.7%, and enhanced levels of nitrogen (N), phosphorus (P), and potassium (K), by increases from 2.1 g pot-1 to 5 g pot-1, 58 mg kg-1 to 83 mg kg-1, and 40 mg kg-1 to 63 mg kg-1, respectively. These findings demonstrate the potential of PB in mitigating Cd contamination in soil and reducing its uptake by rice plants.

Polyethylene and sulfa antibiotic remediation in soil using a multifunctional degrading bacterium

To obtain a multifunctional bacterium that can effectively degrade polyethylene (PE) and sulfonamide antibiotics (SAs), PE and SAs were selected as the primary research objects. Multifunctional degrading bacteria were isolated and screened from an environment in which plastics and antibiotics have existed for a long time. An efficient degrading strain, Raoultella sp., was screened by measuring the degradation performance of PE and SAs. We analyzed the changes in the microbial community of indigenous bacteria using 16S rRNA. After 60 d of degradation at 28 °C, the Raoultella strain to PE degradation rate was 4.20 %. The SA degradation rates were 96 % (sulfonathiazole, (ST)), 86 % (sulfamerazine, (SM)), 72 % (sulfamethazine, (SM2)) and 64 % (sulfamethoxazole, (SMX)), respectively. This bacterium increases the surface roughness of PE plastic films and produces numerous gullies, pits, and folds. In addition, after 60 d, the contact angle of the plastic film decreased from 92.965° to 70.205°, indicating a decrease in hydrophobicity. High-throughput sequencing analysis of the degrading bacteria revealed that the Raoultella strain encodes enzymes involved in PE and SA degradation. The results of this study not only provide a theoretical basis for further study of the degradation mechanism of multifunctional and efficient degrading bacteria but also provide potential strain resources for the biodegradation of waste plastics and antibiotics in the environment.

Molecular insights into the catabolism of dibutyl phthalate in Pseudomonas aeruginosa PS1 based on biochemical and multi-omics approaches

A comprehensive understanding of the molecular mechanisms underlying microbial catabolism of dibutyl phthalate (DBP) is still lacking. Here, we newly isolated a bacterial strain identified as Pseudomonas aeruginosa PS1 with high efficiency of DBP degradation. The degradation ratios of DBP at 100-1000 mg/L by this strain reached 80-99 % within 72 h without a lag phase. A rare DBP-degradation pathway containing two monobutyl phthalate-catabolism steps was proposed based on intermediates identified by HPLC-TOF-MS/MS. In combination with genomic and transcriptomic analyses, we identified 66 key genes involved in DBP biodegradation and revealed the genetic basis for a new complete catabolic pathway from DBP to Succinyl-CoA or Acetyl-CoA in the genus Pseudomonas for the first time. Notably, we found that a series of homologous genes in Pht and Pca clusters were simultaneously activated under DBP exposure and some key intermediate degradation related gene clusters including Pht, Pca, Xyl, Ben, and Cat exhibited a favorable coexisting pattern, which contributed the high-efficient DBP degradation ability and strong adaptability to this strain. Overall, these results broaden the knowledge of the catabolic diversity of DBP in microorganisms and enhance our understanding of the molecular mechanism underlying DBP biodegradation.

Biodegradation of ciprofloxacin using machine learning tools: Kinetics and modelling

Recently, the rampant administration of antibiotics and their synthetic organic constitutes have exacerbated adverse effects on ecosystems, affecting the health of animals, plants, and humans by promoting the emergence of extreme multidrug-resistant bacteria (XDR), antibiotic resistance bacterial variants (ARB), and genes (ARGs). The constraints, such as high costs, by-product formation, etc., associated with the physico-chemical treatment process limit their efficacy in achieving efficient wastewater remediation. Biodegradation is a cost-effective, energy-saving, sustainable alternative for removing emerging organic pollutants from environmental matrices. In view of the same, the current study aims to explore the biodegradation of ciprofloxacin using microbial consortia via metabolic pathways. The optimal parameters for biodegradation were assessed by employing machine learning tools, viz. Artificial Neural Network (ANN) and statistical optimization tool (Response Surface Methodology, RSM) using the Box-Behnken design (BBD). Under optimal culture conditions, the designed bacterial consortia degraded ciprofloxacin with 95.5% efficiency, aligning with model prediction results, i.e., 95.20% (RSM) and 94.53% (ANN), respectively. Thus, befitting amendments to the biodegradation process can augment efficiency and lead to a greener solution for antibiotic degradation from aqueous media.

Biodegradation of penicillin G sodium by Sphingobacterium sp. SQW1: Performance, degradation mechanism, and key enzymes

Biodegradation is an efficient and cost-effective approach to remove residual penicillin G sodium (PGNa) from the environment. In this study, the effective PGNa-degrading strain SQW1 (Sphingobacterium sp.) was screened from contaminated soil using enrichment technique. The effects of critical operational parameters on PGNa degradation by strain SQW1 were systematically investigated, and these parameters were optimized by response surface methodology to maximize PGNa degradation. Comparative experiments found the extracellular enzyme to completely degrade PGNa within 60 min. Combined with whole genome sequencing of strain SQW1 and LC-MS analysis of degradation products, penicillin acylase and β-lactamase were identified as critical enzymes for PGNa biodegradation. Moreover, three degradation pathways were postulated, including β-lactam hydrolysis, penicillin acylase hydrolysis, decarboxylation, desulfurization, demethylation, oxidative dehydrogenation, hydroxyl reduction, and demethylation reactions. The toxicity of PGNa biodegradation intermediates was assessed using paper diffusion method, ECOSAR, and TEST software, which showed that the biodegradation products had low toxicity. This study is the first to describe PGNa-degrading bacteria and detailed degradation mechanisms, which will provide new insights into the PGNa biodegradation.

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.

Unraveling how Fe-Mn modified biochar mitigates sulfamonomethoxine in soil water: The activated biodegradation and hydroxyl radicals formation

This study indicated that the application of a novel Fe-Mn modified rice straw biochar (Fe/Mn-RS) as soil amendment facilitated the removal of sulfamonomethoxine (SMM) in soil water microcosms, primarily via activating degradation mechanism rather than adsorption. The similar enhancement on SMM removal did not occur using rice straw biochar (RS). Comparison of Fe/Mn-RS with RS showed that Fe/Mn-RS gains new physic-chemical properties such as abundant oxygenated C-centered persistent free radicals (PFRs). In the Fe/Mn-RS microcosms, the degradation contributed 79.5-83.8% of the total SMM removal, which was 1.28-1.70 times higher than that in the RS microcosms. Incubation experiments using sterilized and non-sterilized microcosms further revealed that Fe/Mn-RS triggered both the biodegradation and abiotic degradation of SMM. For abiotic degradation of SMM, the abundant •OH generation, induced by Fe/Mn-RS, was demonstrated to be the major contributor, according to EPR spectroscopy and free radical quenching experiments. Fenton-like bio-reaction occurred in this process where Fe (Ⅲ), Mn (Ⅲ) and Mn (Ⅳ) gained electrons, resulting in oxidative hydroxylation of SMM. This work provides new insights into the impacts of biochar on the fates of antibiotics in soil water and a potential solution for preventing antibiotic residues in agricultural soil becoming a non-point source pollutant.

Complete biodegradation of fungicide carboxin and its metabolite aniline by Delftia sp. HFL-1

Fungicide carboxin was commonly used in the form of seed coating for the prevention of smut, wheat rust and cotton damping-off, leading carboxin and its probable carcinogenic metabolite aniline to directly enter the soil with the seeds, causing residual pollution. In this study, a novel carboxin degrading strain, Delftia sp. HFL-1, was isolated. Strain HFL-1 could use carboxin as the carbon source for growth and completely degrade 50 mg/L carboxin and its metabolite aniline within 24 h. The optimal temperatures and pH for carboxin degrading by strain HFL-1 were 30 to 42 °C and 5 to 9, respectively. Furthermore, the complete mineralization pathway of carboxin by strain HFL-1 was revealed by High Resolution Mass Spectrometer (HRMS). Carboxin was firstly hydrolyzed into aniline and further metabolized into catechol through multiple oxidation processes, and finally converted into 4-hydroxy-2-oxopentanoate, a precursor of the tricarboxylic acid cycle. Genome sequencing revealed the corresponding degradation genes and cluster of carboxin. Among them, amidohydrolase and dioxygenase were key enzymes involved in the degradation of carboxin and aniline. The discovery of transposons indicated that the aniline degradation gene cluster in strain HFL-1 was obtained via horizontal transfer. Furthermore, the degradation genes were cloned and overexpressed. The in vitro test showed that the expressed degrading enzyme could efficiently degrade aniline. This study provides an efficient strain resource for the bioremediation of carboxin and aniline in contaminated soil, and further revealing the molecular mechanism of biodegradation of carboxin and aniline.

The connection between the antibiotic resistome and nitrogen-cycling microorganisms in paddy soil is enhanced by application of chemical and plant-derived organic fertilizers

Antibiotic resistant genes (ARGs) present significant risks to environments and public health. In particular, there is increasing awareness of the role of soil nitrogen in ARG dissemination. Here, we investigated the connections between antibiotic resistome and nitrogen-cycling microbes in paddy soil by performing five-year field experiments with the treatments of no nitrogen fertilization (CK), reduced chemical nitrogen fertilization (LN), conventional chemical nitrogen fertilization (CN) and plant-derived organic nitrogen fertilization (ON). Compared with CK treatment, CN and ON treatments significantly increased soil NH4+ and TN concentrations by 25.4%-56.5% and 10.4%-20.1%, respectively. Redundancy analysis revealed significantly positive correlation of NH4+ with most ARGs, including tetA, macB and barA. Correspondingly, CN and ON treatments enhanced ARG abundances by 21.9%-23.2%. Moreover, CN and ON treatments promoted nitrate/nitrite-reducing bacteria and linked the corresponding N-cycling functional genes (narG, narH, nirK and nrfA) with most ARGs. Metagenomic binning was performed and identified Gemmatimonadaceae, Caulobacteraceae, Ilumatobacteraceae and Anaerolineaceae as hosts for both ARGs and nitrate/nitrite reduction genes that were enriched by CN and ON treatments. Soil resistome risk score analysis indicated that, although there was increased relation of ARG to nitrogen-cycling microorganisms with nitrogen fertilizer application, the environmental risk of ARGs was not increased due to the lower distribution of ARGs in pathogens. This study contributed to a deeper understanding of the role of soil nitrogen in shaping ARG profiles and controlling soil resistome risk.

The Growth Yield of Aminobacter niigataensis MSH1 on the Micropollutant 2,6-Dichlorobenzamide Decreases Substantially at Trace Substrate Concentrations

2,6-Dichlorobenzamide (BAM) is an omnipresent micropollutant in European groundwaters. Aminobacter niigataensis MSH1 is a prime candidate for biologically treating BAM-contaminated groundwater since this organism is capable of utilizing BAM as a carbon and energy source. However, detailed information on the BAM degradation kinetics by MSH1 at trace concentrations is lacking, while this knowledge is required for predicting and optimizing the degradation process. Contaminating assimilable organic carbon (AOC) in media makes the biodegradation experiment a mixed-substrate assay and hampers exploration of pollutant degradation at trace concentrations. In this study, we examined how the BAM concentration affects MSH1 growth and BAM substrate utilization kinetics in a AOC-restricted background to avoid mixed-substrate conditions. Conventional Monod kinetic models were unable to predict kinetic parameters at low concentrations from kinetics determined at high concentrations. Growth yields on BAM were concentration-dependent and decreased substantially at trace concentrations; i.e., growth of MSH1 diminished until undetectable levels at BAM concentrations below 217 μg-C/L. Nevertheless, BAM degradation continued. Decreasing growth yields at lower BAM concentrations might relate to physiological adaptations to low substrate availability or decreased expression of downstream steps of the BAM catabolic pathway beyond 2,6-dichlorobenzoic acid (2,6-DCBA) that ultimately leads to Krebs cycle intermediates for growth and energy conservation.

Reusable and Practical Biocomposite Based on Sphingopyxis sp. YF1 and Polyacrylonitrile-Based Carbon Fiber for the Efficient Bioremediation of Microcystin-LR-Contaminated Water

Microbial degradation is a cost-effective and environmentally friendly method for removing microcystin-LR (MC-LR). However, the application of free bacteria has limitations due to low operational stability and difficulties in recovery. In a previous study, our group successfully isolated a highly efficient MC-LR-degrading bacterium, Sphingopyxis sp. YF1, from Taihu. To enhance its practical potential in addressing MC-LR-contaminated water pollution, a novel biological material named polyacrylonitrile-based carbon fiber @Sphingopyxis sp. YF1 (PAN-CF@YF1) was synthesized. The immobilization conditions of strain Sphingopyxis sp. YF1 on PAN-CF surfaces were optimized using Box-Behnken design and response surface methodology (RSM), which turned out to be an optimal pH of 7.6 for the culture medium, a ratio of 0.038 g of supporting materials per 100 mL of culture media, and an incubation time of 53.4 h. The resultant PAN-CF@YF1 showed a great degradation effect both for low and high concentrations of MC-LR and exhibited satisfactory cyclic stability (85.75% after six cycles). Moreover, the application of PAN-CF@YF1 in the bioreactors demonstrated effective and sustainable MC-LR removal, with a removal efficiency of 78.83% after three consecutive treatments. Therefore, PAN-CF@YF1 with high degradation activity, environmental compatibility, straightforward preparation, and recyclability shows significant application potential for the bioremediation of MC-LR-contaminated water bodies.

Chemistry of soil-type dependent soil matrices and its influence on behaviors of pharmaceutical compounds (PCs) in soils

Behaviors of pharmaceutical compounds (PCs) in soil are usually determined by experimental extrapolation of results from separate constitutes to the soil, or from a special soil to other regional soil conditions. However, such extrapolation is problematic due to variations in soil clay mineral and organic matter (OM) compositions with soil types, which dominate the interaction mechanisms of PCs in soil. It is essential to review current literature to enhance our understanding of the soil-type dependent surface chemistry of soil matrices and the environmental behavior of PCs in different soil types. Major types of soils occur globally in parallel to the latitudinal or altitudinal zonation due to regional climate conditions with distinct clay mineral and OM compositions. The soil-type dependent surface chemistry results in variations in retention, distribution, transport, and transformation PCs in soil. The mixture of PCs of different classes usually exhibited enhanced sorption due to the cooperative multilayer sorption on soil constituents, and that of the same class often caused differential adsorption capacity compared to the sorption from single compound due to competitive sorption. PCs preferentially adsorb to a soil component, or to a special soil type, and exhibit notably soil-type dependent sorption affinity, mobility, and dissipation. The soil-dependent surface chemistry of soil is critical to predict the persistence and bioavailability of PCs in soil. In the future, more detailed studies of influence of individual soil factor on the behaviors of PCs and especially the practical field site investigation are required to better understand the sorption, transport, transformation, and ecotoxicology of PCs in typical soil types.

Biotransformation of sulfamethoxazole by newly isolated surfactant-producing strain Proteus mirabilis sp. ZXY4: Removal efficiency, pathways, and mechanisms

In this study, the SMX degrading strain Proteus mirabilis sp. ZXY4 with surfactant manufacturing potential was isolated from sludge utilizing blood agar and CTAB agar plate. FTIR analysis indicated that the biosurfactant generated by strain ZXY4 was glycolipid. 3D-EEM demonstrated that SMX biodegradation was strongly connected to biosurfactants, the synergistic effect of biodegradation and biosurfactant made strain ZXY4 have excellent SMX degradation performance. Under the optimal conditions of inoculation dosage of 15%, temperature of 30 ℃, pH of 7 and initial SMX concentration of 5 mg L^-1, strain ZXY4 could completely degrade SMX within 24 h. SMX biodegrades at low concentrations (less than5 mg L^-1) followed by the zero-order kinetic model, high concentration (>5 mg L^-1) is more consistent with the first-order kinetic model. LC-MS analysis revealed 14 SMX degradation intermediates, and five potential biodegradation mechanisms were postulated. The findings provide new insights into the biodegradation of SMX.

A dual bacterial alliance removed erythromycin residues by immobilizing on activated carbon

Removing erythromycin from the environment is a major challenge. In this study, a dual microbial consortium (Delftia acidovorans ERY-6A and Chryseobacterium indologenes ERY-6B) capable of degrading erythromycin was isolated, and the erythromycin biodegradation products were studied. Coconut shell activated carbon was modified and its adsorption characteristics and erythromycin removal efficiency of the immobilized cells were studied. It was indicated that alkali-modified and water-modified coconut shell activated carbon and the dual bacterial system had excellent erythromycin removal ability. The dual bacterial system follows a new biodegradation pathway to degrade erythromycin. The immobilized cells removed 95% of erythromycin at a concentration of 100 mg L^-1 within 24 h through pore adsorption, surface complexation, hydrogen bonding, and biodegradation. This study provides a new erythromycin removal agent and for the first time describes the genomic information of erythromycin-degrading bacteria, providing new clues regarding bacterial cooperation and efficient erythromycin removal.