Antibiotics sulfamethoxazole alter nitrous oxide production and pathways in estuarine sediments: Evidenced by the N15-O18 isotopes tracing

Assessing foodborne health risks from dietary exposure to antibiotic resistance genes and opportunistic pathogens in three types of vegetables: An in vitro simulation of gastrointestinal digestion

Foodborne health risks posed by antibiotic resistant genes (ARGs) and pathogenic bacteria have garnered increasing global attention. However, the patterns of their propagation and reduction, as well as the resulting health risks in the human gastrointestinal tract, remain unknown. We employed leafy vegetables (water spinach), solanaceous vegetables (pepper), and root vegetables (radish) to investigate the propagation and reduction patterns of ARGs and pathogenic bacteria within an in vitro simulated digestion system. This system mimicked the soil-vegetable-stomach-small intestine (SVSTI) transmission chain. We found that kan, oqxA, and multidrug resistance genes were enriched by 1.10-fold, 11.2-fold, and 2.21-fold, respectively, along the transmission chain. The succession of bacterial communities and horizontal gene transfer mediated by intl1 were identified as the primary drivers of ARG accumulation. Notably, certain pathogenic bacteria (Bacillus cereus, Klebsiella pneumoniae) accumulated in the intestinal environment. According to our proposed health risk assessment system, Bacillus species, as potential ARG hosts, and multidrug ARGs are at a higher risk of exposure to intestinal environment through the transmission chain. Our findings highlight the significant health risks associated with the intake of ARGs and pathogenic bacteria carried by vegetables, emphasizing an urgent need to implement effective biological control measures in vegetable production and consumption.

Efficient simultaneous degradation of multiple sulfonamide antibiotics in soil using biocarbon-based nanomaterials as catalysts for persulfate activation

There is an urgent need to develop effective and sustainable methods to decrease sulfonamide (SA) contamination of soil. Herein, a non-homogeneous system of zero-valent metal-biochar-based composites was proposed and tested for persulfate (PS) activation. This system employed zero-valent iron (Fe0) as an electron donor to catalyze the cleavage of the OO bond in PS, thereby generating reactive oxygen species (ROS) that degrade SAs. Notably, the incorporation of elemental sulfur (S) significantly mitigated the passivation of Fe0, leading to an enhanced degradation capability of the system. The system decomposes 84-97 % of SAs at their concentration in soil suspension 10 mg/kg in 3 h. Among the coexistence of several SAs, the system showed the fastest degradation rate of sulfisoxazole with a kobs of 0.0305 min-1, nearing complete removal within 3 h. The system is resistant to the impact of organic matter in soil. It allows to decrease concentration of sulfadiazine in actual contaminated soil on 73 % in 2 h. The system remains effective with decreasing concentrations of PS from 20 mM to 2.5 mM, which lowered the operating cost. T.E.S.T software evaluation showed a significant reduction in the bioaccumulation toxicity and developmental toxicity of the degradation products, suggesting that the system is environmentally friendly. The high efficiency of the catalytic system, the simplicity and economy of the manufacturing process, the resistance to interference in real soil, and the environmental friendliness make this technology promising for mitigating the problem of the environment contamination by SAs.

Removal and ecological impact of sulfamethoxazole and N-acetyl sulfamethoxazole in mesocosmic wetlands dominated by submerged plants: Plant tolerance, microbial response, and nitrogen transformation

Sulfamethoxazole (SMX) and its human metabolite N-acetylsulfamethoxazole (N-SMX) are frequently detected in aquatic environments, posing potential threats to freshwater ecosystem health. Constructed wetlands are pivotal for wastewater treatment, with plant species serving as key determinants of pollutant removal efficiency. In this study, wetlands dominated by three submerged plants (Myriophyllum verticillatum, Vallisneria spiralis, Hydrilla verticillata) were respectively constructed to investigate the removal of SMX and N-SMX, and the impact on wetland ecology regarding plant tolerance, microbial response, and nitrogen transformation. Results showed that wetlands removed N-SMX (82.3-99.8 %) more effectively than SMX (54.3-80.2 %), with the wetland dominated by Myriophyllum verticillatum showing the highest removal efficiency. However, high concentrations (5 mg/L) of SMX and N-SMX significantly reduced NH4+-N and TN removal (p < 0.05), accompanied by shifts in microbial communities, especially a decreased abundance of Proteobacteria and key nitrogen-transforming genes. A total of 22 different ARGs (antibiotic resistance genes) were detected. SMX significantly increased the relative abundance of sulfonamide resistance genes (sul1, sul2) (p < 0.05), while major denitrifying genera, such as Thiobacillus, which were not the primary hosts of these genes, showed a significant negative correlation with sul1 and sul2 (p < 0.05). This study provides a reference for ecological remediation of wetlands in response to antibiotic contamination.

Selective increase of antibiotic-resistant denitrifiers drives N2O production in ciprofloxacin-contaminated soils

Agricultural systems significantly contribute to global N2O emissions, which is intensified by excessive fertilization and antibiotic residues, attracting global concerns. However, the dynamics and pathways of antibiotics-induced soil N2O production coupled with microbial metabolism remain controversial. Here, we explored the pathways of N2O production in agricultural soils exposed to ciprofloxacin (CIP), and revealed the underlying mechanisms of CIP degradation and the associated microbial metabolisms using 15N-isotope labeling and molecular techniques. CIP exposure significantly increases the total soil N2O production rate. This is attributed to an unexpected shift from heterotrophic and autotrophic nitrification to denitrification and an increased abundance of denitrifiers Methylobacillus members under CIP exposure. The most striking strain M. flagellatus KT is further discovered to harbor N2O-producing genes but lacks a N2O-reducing gene, thereby stimulating denitrification-based N2O production. Moreover, this denitrifying strain is probably capable of utilizing the byproducts of CIP as carbon sources, evidenced by genes associated with CIP resistance and degradation. Molecular docking further shows that CIP is well ordered in the catalytic active site of CotA laccase, thus affirming the potential for this strain to degrade CIP. These findings advance the mechanistic insights into N2O production within terrestrial ecosystems coupled with the organic contaminants degradation.

Effects of antibiotics on microbial nitrogen cycling and N2O emissions: A review

Sulfonamides, quinolones, tetracyclines, and macrolides are the most prevalent classes of antibiotics used in both medical treatment and agriculture. The misuse of antibiotics leads to their extensive dissemination in the environment. These antibiotics can modify the structure and functionality of microbial communities, consequently impacting microbial-mediated nitrogen cycling processes including nitrification, denitrification, and anammox. They can change the relative abundance of nirK/norB contributing to the emission of nitrous oxide, a potent greenhouse gas. This review provides a comprehensive examination of the presence of these four antibiotic classes across different environmental matrices and synthesizes current knowledge of their effects on the nitrogen cycle, including the underlying mechanisms. Such an overview is crucial for understanding the ecological impacts of antibiotics and for guiding future research directions. The presence of antibiotics in the environment varies widely, with significant differences in concentration and type across various settings. We conducted a comprehensive review of over 70 research articles that compare various aspects including processes, antibiotics, concentration ranges, microbial sources, experimental methods, and mechanisms of influence. Antibiotics can either inhibit, have no effect, or even stimulate nitrification, denitrification, and anammox, depending on the experimental conditions. The influence of antibiotics on the nitrogen cycle is characterized by dose-dependent responses, primarily inhibiting nitrification, denitrification, and anammox. This is achieved through alterations in microbial community composition and diversity, carbon source utilization, enzyme activities, electron transfer chain function, and the abundance of specific functional enzymes and antibiotic resistance genes. These alterations can lead to diminished removal of reactive nitrogen and heightened nitrous oxide emissions, potentially exacerbating the greenhouse effect and related environmental issues. Future research should consider diverse reaction mechanisms and expand the scope to investigate the combined effects of multiple antibiotics, as well as their interactions with heavy metals and other chemicals or organisms.

Revealing discrepancies and drivers in the impact of lomefloxacin on groundwater denitrification throughout microbial community growth and succession

The coexistence of antibiotics and nitrates has raised great concern about antibiotic's impact on denitrification. However, conflicting results in these studies are very puzzling, possibly due to differences in microbial succession stages. This study investigated the effects of the high-priority urgent antibiotic, lomefloxacin (LOM), on groundwater denitrification throughout microbial growth and succession. The results demonstrated that LOM's impact on denitrification varied significantly across three successional stages, with the most pronounced effects exhibited in the initial stage (53.8% promotion at 100 ng/L-LOM, 84.6% inhibition at 100 μg/L-LOM), followed by the decline stage (13.3-18.2% inhibition), while no effect in the stable stage. Hence, a distinct pattern encompassing susceptibility, insusceptibility, and sub-susceptibility in LOM's impact on denitrification was discovered. Microbial metabolism and environment variation drove the pattern, with bacterial numbers and antibiotic resistance as primary influencers (22.5% and 15.3%, p < 0.01), followed by carbon metabolism and microbial community (5.0% and 3.68%, p < 0.01). The structural equation model confirmed results reliability. Bacterial numbers and resistance influenced susceptibility by regulating compensation and bacteriostasis, while carbon metabolism and microbial community impacted energy, electron transfer, and gene composition. These findings provide valuable insights into the complex interplay between antibiotics and denitrification patterns in groundwater.

Natural chalcopyrite mitigates nitrous oxide emissions in sediment from coastal wetlands

Coastal wetlands are one of the most important natural sources of nitrous oxide (N2O). Previous studies have shown that copper-containing chemicals are able to reduce N2O emissions from these ecosystems. However, these chemicals may harm organisms present in coastal waters and sediment, and disturb the ecological balance of these areas. Here, we first investigated the physiological characteristics and genetic potential of denitrifying bacteria isolated from coastal wetlands. Based on an isolated denitrifier carrying a complete denitrification pathway, we tested the effect of the natural mineral chalcopyrite on N2O production by the bacteria. The results demonstrated that chalcopyrite addition lowers N2O emissions from the bacteria while increasing its N2 production rate. Among the four denitrification genes of the isolate, only nosZ gene expression was significantly upregulated following the addition of 2 mg L-1 chalcopyrite. Furthermore, chalcopyrite was applied to coastal wetland sediments. The N2O flux was significantly reduced in 50-100 mg L-1 chalcopyrite-amended sets relative to the controls. Notably, the dissolved Cu concentration in chalcopyrite-amended sediment remained within the limit set by the National Sewage Treatment Discharge Standard. qPCR and metagenomic analysis revealed that the abundance of N2O-reducing bacteria with the nosZ or nirK + nosZ genotype increased significantly in the chalcopyrite-amended groups relative to the controls, suggesting their active involvement in the reduction of N2O emissions. Our findings offer valuable insights for the use of natural chalcopyrite in large-scale field applications to reduce N2O emissions.

Seasonal changes in N-cycling functional genes in sediments and their influencing factors in a typical eutrophic shallow lake, China

N-cycling processes mediated by microorganisms are directly linked to the eutrophication of lakes and ecosystem health. Exploring the variation and influencing factors of N-cycling-related genes is of great significance for controlling the eutrophication of lakes. However, seasonal dynamics of genomic information encoding nitrogen (N) cycling in sediments of eutrophic lakes have not yet been clearly addressed. We collected sediments in the Baiyangdian (BYD) Lake in four seasons to explore the dynamic variation of N-cycling functional genes based on a shotgun metagenome sequencing approach and to reveal their key influencing factors. Our results showed that dissimilatory nitrate reduction (DNRA), assimilatory nitrate reduction (ANRA), and denitrification were the dominant N-cycling processes, and the abundance of nirS and amoC were higher than other functional genes by at least one order of magnitude. Functional genes, such as nirS, nirK and amoC, generally showed a consistent decreasing trend from the warming season (i.e., spring, summer, fall) to the cold season (i.e., winter). Furthermore, a significantly higher abundance of nitrification functional genes (e.g., amoB, amoC and hao) in spring and denitrification functional genes (e.g., nirS, norC and nosZ) in fall were observed. N-cycling processes in four seasons were influenced by different dominant environmental factors. Generally, dissolved organic carbon (DOC) or sediment organic matter (SOM), water temperature (T) and antibiotics (e.g., Norfloxacin and ofloxacin) were significantly correlated with N-cycling processes. The findings imply that sediment organic carbon and antibiotics may be potentially key factors influencing N-cycling processes in lake ecosystems, which will provide a reference for nitrogen management in eutrophic lakes.

Effects of microplastics on denitrification and associated N2O emission in estuarine and coastal sediments: insights from interactions between sulfate reducers and denitrifiers

Global estuarine and coastal zones are facing severe microplastics (MPs) pollution. Sulfate reducers (SRB) and denitrifiers (DNB) are two key functional microorganisms in these zones, exhibiting intricate interactions. However, whether and how MPs modulate the interactions between SRB and DNB, with implications for denitrification and associated N2O emissions, remains poorly understood. Here, we simultaneously investigated the spatial response patterns of SRB-DNB interactions and denitrification and associated N2O emissions to different MPs exposure along an estuarine gradient in the Yangtze Estuary. Spatial responses of denitrification to polyvinyl chloride (PVC) and polyadipate/butylene terephthalate (PBAT) MPs exposure were heterogeneous, while those of N2O emissions were not. Gradient-boosted regression tree and multiple regression model analyses showed that sulfide, followed by nitrate (NO3-), controlled the response patterns of denitrification to MPs exposure. Further mechanistic investigation revealed that exposure to MPs resulted in a competitive and toxic (sulfide accumulation) inhibition of SRB on DNB, ultimately inhibiting denitrification at upstream zones with high sulfide but low NO3- levels. Conversely, MPs exposure induced a competitive inhibition of DNB on SRB, generally promoting denitrification at downstream zones with low sulfide but high NO3- levels. These findings advance the current understanding of the impacts of MPs on nitrogen cycle in estuarine and coastal zones, and provide a novel insight for future studies exploring the response of biogeochemical cycles to MPs in various ecosystems.

Reclamation of tidal flats to paddy soils reshuffles the soil microbiomes along a 53-year reclamation chronosequence: Evidence from assembly processes, co-occurrence patterns and multifunctionality

Coastal soil microbiomes play a key role in coastal ecosystem functioning and are intensely threatened by land reclamation. However, the impacts of coastal reclamation on soil microbial communities, particularly on their assembly processes, co-occurrence patterns, and the multiple soil functions they support, remain poorly understood. This impedes our capability to comprehensively evaluate the impacts of coastal reclamation on soil microbiomes and to restore coastal ecosystem functions degraded by reclamation. Here, we investigated the temporal dynamics of bacterial and fungal communities, community assembly processes, co-occurrence patterns, and ecosystem multifunctionality along a 53-year chronosequence of paddy soil following reclamation from tidal flats. Reclamation of tidal flats to paddy soils resulted in decreased β-diversity, increased homogeneous selection, and decreased network complexity and robustness of both bacterial and fungal communities, but caused contrasting α-diversity response patterns of them. Reclamation of tidal flats to paddy soils also decreased the multifunctionality of coastal ecosystems, which was largely associated with the fungal network complexity and α-diversity. Collectively, this work demonstrates that coastal reclamation strongly reshaped the soil microbiomes at the level of assembly mechanisms, interaction patterns, and functionality level, and highlights that soil fungal community complexity should be considered as a key factor in restoring coastal ecosystem functions deteriorated by land reclamation.

Permeability decides the effect of antibiotics on sedimentary nitrogen removal in Jiulong River Estuary

Sedimentary denitrification takes place beneath the oxic layer at the sediment-water interface, where nitrate and antibiotics need to diffuse through the overlying water. However, the antibiotics' effect on sedimentary N removal and associated N2O production has not been adequately investigated under in situ conditions. Here, isotope pairing techniques, including slurry incubations (potential) and intact core incubations (in situ), combined with metagenomic analysis were applied to investigate the impacts of two protein-inhibiting antibiotics (oxytetracycline and thiamphenicol) on sediment nitrogen removal in a subtropical estuary. Slurry incubations showed that the two antibiotics significantly inhibited denitrification (67-98%) and anammox (49-99%), while intact core incubations presented no antibiotic effect at upstream but significant inhibition (23%-52%) at downstream. Meanwhile, N2O yields were stimulated up to 20 folds in slurry incubations yet showing insignificant response in intact cores. Such contrasting results between up- and down-stream and between slurry and intact core incubations strongly indicated that permeability, which determines diffusion of antibiotics to microbes, is the key to exert the effect of antibiotics on in situ sedimentary nitrogen removal processes regardless the existence of antibiotics resistance genes. This diffusive obstruction may mitigate the toxic effect of antibiotics on nitrogen removal related microbes in natural environments.

Structure and function response of bacterial communities towards antibiotic contamination in hyporheic zone sediments

Bacterial communities are crucial for processing and degrading contaminants in hyporheic zones (HZ). However, the effects of antibiotics on HZ bacterial communities have seldom been addressed. Here, using MiSeq 16S amplicon sequencing technology, the effects of acute exposure to Enrofloxacin, Sulfathiazole, Tetracycline hydrochloride, and Penicillin V potassium on HZ bacterial communities were investigated. Results revealed that HZ sediment communities responded differently to different classes of antibiotics, reflecting the distinct selection stress of antibiotics on HZ bacterial communities. Besides, HZ communities from the locations with more severe antibiotic contamination backgrounds (∼150 μg kg^-1) were more resistant towards antibiotic treatment. Compared with small/non-significant changes in HZ community diversity and composition treated with ng L^-1∼ug L^-1 level antibiotics compared to the control group, treatments with antibiotics over mg L^-1 level significantly reduced the diversity and changed the structures of HZ bacterial communities, and enhanced the resistance of the community to antibiotics by enriching antibiotic resistant bacteria. The exposure to mg L^-1 level antibiotics also changed community functions by restricting the growth of functional bacteria, such as ammonia oxidizing bacteria (AOB) Nitrosomonas, resulting in ammonia accumulation in sediments. The results implied that at field-relevant concentrations, there was no or minor effect of antibiotics on HZ bacterial community structure and functions, and only those areas with high antibiotic concentrations would have effects.