Influence on denitrifying community performance by the long-term exposure to sulfamethoxazole and chlortetracycline in the continuous-flow EGSB reactors

Transcriptional and molecular simulation analysis of the response mechanism of anammox bacteria to 3,4-dimethylpyrazole phosphate stress

Anaerobic ammonium oxidation (anammox) and nitrification are two vital biological pathways for ammonium oxidation, pivotal in microbial nitrogen cycling. 3,4-Dimethylpyrazole phosphate (DMPP) is commonly used as inhibitors in agricultural soils to reduce nitrogen losses from farmland, while whether it affect anammox is an open question. Acute inhibition tests revealed that 53.5 mg·L-1 DMPP caused 50 % reduction in anammox bacteria. After 36 days of prolonged exposure to 5 mg·L-1 DMPP, the ammonium(nitrite) removal rate of endnote decreased from 78.39(94.78) to 13.57(15.28) mgN·gVSS-1·d-1. Additionally, the abundance of Ca. Kuenenia decreased from 36.5 % to 6.06 %. Transcriptomic analysis revealed that the mRNA levels of ammonium transport genes (amt_1 and amt_4), and hydrazine synthase (hzs) were significantly downregulated. Molecular docking simulations indicated that DMPP bound with ammonium transport and hydrazine synthesis. This interaction hindered the transcriptional levels of genes encoding ammonium transporters and hzs. The study has guiding value to reduce the nitrogen loss involved in anammox bacteria in agricultural soils under the application of DMPP.

Metagenomic analysis reveals abundance of mixotrophic, heterotrophic, and homoacetogenic bacteria in a hydrogen-based membrane biofilm reactor

Heterotrophic microorganisms are frequently observed in hydrogenotrophic denitrification systems and are presumed to contribute to their improved performance. However, their roles and metabolic pathways in the hydrogen-based membrane biofilm reactor (H2-MBfR) system remain unclear. The objective of this study was to elucidate the underlying mechanisms driving heterotrophic denitrification. For this purpose, metagenomic analysis was conducted on an H2-MBfR showing higher denitrification performance, focusing on the metabolic function of the microbial community. Functional genes related to H2 oxidation, organic carbon metabolism, and denitrification were the major targets of interest. This analysis revealed a substantial number of genes associated with the oxidation of organic carbon compounds in the biofilm, suggesting its potential for heterotrophic denitrification. Investigation of the genes of interest in metagenome-assembled genomes (MAGs) has demonstrated a predominance of mixotrophs or heterotrophs rather than obligate autotrophs. Notably, MAGs exhibiting the highest abundance of genes of interest were affiliated with Hydrogenophaga and Thauera, implying their significant role in denitrifying the H2-MBfR as mixotrophs utilizing both H2 and organic substrates. The identification of 11 MAGs, presumed to originate from homoacetogens suggested that acetate might contribute to the proliferation of heterotrophs. Based on these metagenomic findings, possible metabolic pathways were identified to explain heterotrophic denitrification within the H2-MBfR biofilms.

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.

Influence of Four Veterinary Antibiotics on Constructed Treatment Wetland Nitrogen Transformation

The use of wetlands as a treatment approach for nitrogen in runoff is a common practice in agroecosystems. However, nitrate is not the sole constituent present in agricultural runoff and other biologically active contaminants have the potential to affect nitrate removal efficiency. In this study, the impacts of the combined effects of four common veterinary antibiotics (chlortetracycline, sulfamethazine, lincomycin, monensin) on nitrate-N treatment efficiency in saturated sediments and wetlands were evaluated in a coupled microcosm/mesocosm scale experiment. Veterinary antibiotics were hypothesized to significantly impact nitrogen speciation (e.g., nitrate and ammonium) and nitrogen uptake and transformation processes (e.g., plant uptake and denitrification) within the wetland ecosystems. To test this hypothesis, the coupled study had three objectives: 1. assess veterinary antibiotic impact on nitrogen cycle processes in wetland sediments using microcosm incubations, 2. measure nitrate-N reduction in water of floating treatment wetland systems over time following the introduction of veterinary antibiotic residues, and 3. identify the fate of veterinary antibiotics in floating treatment wetlands using mesocosms. Microcosms containing added mixtures of the veterinary antibiotics had little to no effect at lower concentrations but stimulated denitrification potential rates at higher concentrations. Based on observed changes in the nitrogen loss in the microcosm experiments, floating treatment wetland mesocosms were enriched with 1000 μg L-1 of the antibiotic mixture. Rates of nitrate-N loss observed in mesocosms with the veterinary antibiotic enrichment were consistent with the microcosm experiments in that denitrification was not inhibited, even at the high dosage. In the mesocosm experiments, average nitrate-N removal rates were not found to be impacted by the veterinary antibiotics. Further, veterinary antibiotics were primarily found in the roots of the floating treatment wetland biomass, accumulating approximately 190 mg m-2 of the antibiotic mixture. These findings provide new insight into the impact that veterinary antibiotic mixtures may have on nutrient management strategies for large-scale agricultural operations and the potential for veterinary antibiotic removal in these wetlands.

Effects of Antibiotics on the DAMO Process and Microbes in Cattle Manure

Denitrifying anaerobic methane oxidation (DAMO) can mitigate methane emissions; however, this process has not been studied in cattle manure, an important source of methane emissions in animal agriculture. The objective of this study was to investigate the occurrence of DAMO microbes in cattle manure and examine the impacts of veterinary antibiotics on the DAMO process in cattle manure. Results show that DAMO archaea and bacteria consistently occur at high concentrations in beef cattle manure. During the long-term operation of a sequencing batch reactor seeded with beef cattle manure, the DAMO activities intensified, and DAMO microbial biomass increased. Exposure to chlortetracycline at initial concentrations up to 5000 μg L-1 did not inhibit DAMO activities or affect the concentrations of the 16S rRNA gene and functional genes of DAMO microbes. In contrast, exposure to tylosin at initial concentrations of 50 and 500 μg L-1 increased the activities of the DAMO microbes. An initial concentration of 5000 μg L-1 TYL almost entirely halted DAMO activities and reduced the concentrations of DAMO microbes. These results show the occurrence of DAMO microbes in cattle manure and reveal that elevated concentrations of dissolved antibiotics could inhibit the DAMO process, potentially affecting net methane emissions from cattle manure.

Impact of sulfamethoxazole and organic supplementation on mixotrophic denitrification process: Nitrate removal efficiency and the response of functional microbiota

Recirculating aquaculture systems (RAS) effluent is characterized by low COD to total inorganic nitrogen ratio (C/N), excessive nitrate, and the presence of traces of antibiotics. Hence, it urgently needs to be treated before recycling or discharging. In this study, four denitrification bioreactors at increasing C/N ratios (0, 0.7, 2, and 5) were started up to treat mariculture wastewater under the sulfamethoxazole (SMX) stress, during which the bioreactors performance and the shift of mixotrophic microbial communities were explored. The result showed that during the SMX exposure, organic supplementation enhanced nitrate and thiosulfate removal, and eliminated nitrite accumulation. The denitrification rate was accelerated by increasing C/N from 0 to 2, while it declined at C/N of 5. The decline was ascribed to which SMX reduced the relative abundance of denitrifiers, but improved the capability of dissimilatory nitrogen reduction to ammonia (DNRA) and sulfide production. The direct evidence was the relative abundance of sulfidogenic populations, such as Desulfuromusa, Desulfurocapsa, and Desulfobacter increased under the SMX stress. Moreover, high SMX (1.5 mg L^-1) caused the obvious accumulation of ammonia at C/N of 5 due to the high concentration of sulfide (3.54 ± 1.08 mM) and the enhanced DNRA process. This study concluded that the mixotrophic denitrification process with the C/N of 0.7 presented the best performance in nitrate and sulfur removal and indicated the maximum resistance to SMX.

Antibiotics in anaerobic digestion: Investigative studies on digester performance and microbial diversity

The ever-increasing consumption of antibiotics in both humans and animals has increased their load in municipal and pharmaceutical industry waste and may cause serious damage to the environment. Impact of antibiotics on the performance of commercially used anaerobic digesters in terms of bioenergy output, antibiotics' removal and COD removal have been compared critically with a few studies indicating >90% removal of antibiotics. AnMBR performed the best in terms of antibiotic removal, COD removal and methane yield. Most of the antibiotics investigated have adverse effects on microbiome associated with different stages and methane generation pathways of AD which has been assessed using high throughput technologies like metatranscriptomics, metaproteomics and flow cytometry. Perspectives have been given for understanding the fate and elimination of antibiotics from AD. The challenge of optimization and process improvement needs to be addressed to increase efficiency of the anaerobic digesters.

Deciphering the Inhibition of Ethane on Anaerobic Ammonium Oxidation

Anaerobic ammonium oxidation (anammox) and nitrification, two common biological ammonium oxidation pathways, are critical for the microbial nitrogen cycle. Short chain alkanes (C₂-C₈) have been well-known as inhibitors for nitrification through interaction with the ammonia monooxygenase, while whether these alkanes affect anammox is an open question. Here, this work demonstrated significant inhibition of ethane on anammox and revealed the inhibitory mechanism. The acute inhibition of ethane on anammox was concentration-dependent and reversible; 0.86 mM dissolved ethane caused 50% inhibition (IC₅₀), and 1.72 mM ethane almost completely inhibited anammox. After long-term exposure to 0.09 mM ethane for 30 days, the ammonium (nitrite) removal rate dropped from 202 (267) mg N L^-1 d^-1 to 1 (1) mg N L^-1 d^-1, and the abundance of anammox bacteria decreased from 61.9% to 9.5%. The intercellular ammonium concentration of anammox bacteria decreased after ethane exposure, while metatranscriptome analysis showed significant upregulation of genes for ammonium transport of anammox bacteria. Thus, ethane could suppress ammonium uptake resulting in the inhibition of anammox activities. As ethane is the second most prevalent alkane after methane in various anoxic environments, ethane may have an important effect on the nitrogen cycle driven by anammox that should be investigated in future research.

Enhanced removal of fluoride, nitrate, and calcium using self-assembled fungus-flexible fiber composite microspheres combined with microbially induced calcium precipitation

Self-assembled fungus-flexible fiber composite microspheres (SFFMs) were firstly combined with microbially induced calcium precipitation (MICP) in a continuous-flow bioreactor and achieved the efficient removal of fluoride (F^-), nitrate (NO₃^-), and calcium (Ca²⁺). Under the influent F^- of 3.0 mg L^-1, pH of 7.0, and HRT of 8 h, the average removal efficiencies reached 77.54%, 99.39%, and 67.25% (0.29, 2.03, and 8.34 mg L^-1 h^-1), respectively. Fluorescence spectrum and flow cytometry analyses indicated that F^- content significantly affected the metabolism and viability of bacteria. SEM images showed that flexible fibers and intertwined hyphae provided effective locations for bacterial colonization in SFFMs. The precipitated products were characterized by XRD and FTIR, which revealed that F^- was mainly removed in the form of calcium fluoride and calcium fluorophosphate (CaF₂ and Ca₅(PO₄)₃F). High-throughput analysis at different levels demonstrated that Pseudomonas sp. WZ39 acted as the core strain, which played a crucial role in the bioreactor. The mechanism of enhanced denitrification was attributed to minor F^- stress and bioaugmentation technology. This study highlighted the superiorities of SFFMs and MICP combined remediation and documented a promising option for F^-, NO₃^-, and Ca²⁺ removal.

Sulfonamide antibiotics alter gaseous nitrogen emissions in the soil-plant system: A mesocosm experiment and meta-analysis

Veterinary antibiotics are widely used in many countries worldwide to treat diseases and protect the health of animals. However, the effects of sulfonamide antibiotics introduced via manure and wastewater irrigation on nitrogen (N) loss in the soil-plant system remain poorly understood. Here, we conducted a pot experiment to assess the effects of sulfamethazine (SMZ) and its degradation product (2-amino-4,6-dimethylpyrimidine, ADPD) at four concentration gradients (i.e., 0, 1, 10, 100 mg kg^-1) on nitrous oxide (N₂O) and ammonia (NH₃) emissions, and the abundances of N-cycling functional genes and sulfonamide resistance genes. We also collated 350 observations from 62 published papers and performed a meta-analysis of antibiotic addition effects on N₂O emission and soil net nitrification and denitrification. Antibiotics additions showed an inhibitory effect on N₂O emissions, which accords with the trend of our meta-analysis showing a significant decrease of 32%. The decreased N₂O emissions were attributed to the significant reduction in the abundances of total bacterial communities, ammonia oxidizers, and nir-type denitrifiers and to the resultant changes in soil inorganic N. N₂O emissions did not differ between non-environmentally relevant concentrations for SMZ but lowered with increasing ADPD concentrations. This discrepancy can be explained by differential responses of the gene abundances of ammonia oxidizers and nirK-type denitrifiers and the development of antibiotic resistance genes in the highest concentration following antibiotic additions. Antibiotic additions increased soil NH₃ volatilization but did not affect vegetable yield. Therefore, these findings provide insight into how the prevalence of antibiotics in soils could alter the N-cycling process and associated gas emissions, with implications for understanding the ecological risks of antibiotics in agriculture.