Sludge anaerobic digestion with high concentrations of tetracyclines and sulfonamides: Dynamics of microbial communities and change of antibiotic resistance genes

Comparative efficacy of anaerobic digestion systems in removing antimicrobial resistance genes from swine wastewater

Swine farm wastewater is a major reservoir of antimicrobial resistance genes (ARGs). Anaerobic digestion (AD), widely implemented in farms, has been extensively studied for ARG removal. However, a comparative study on ARG removal efficiency across the four principal AD systems - up-flow anaerobic sludge blanket (UASB), continuous stirred tank reactor (CSTR), buried biogas digester (BBD), and septic tank (SPT) - is lacking. Herein, we employed metagenomic sequencing, ultra-performance liquid chromatography-tandem mass spectrometry, as well as atomic absorption spectrometry/atomic fluorescence spectrophotometry, and revealed that UASB and CSTR achieved higher removal efficiencies for both ARGs (67% and 57%) and antibiotic residues (100% and 90%) compared to BBD and SPT. Acinetobacter, Escherichia, Pseudomonas and Streptococcus were the primary ARG hosts, comprising over 65% of the total abundance in influent samples. UASB and CSTR systems demonstrated superior removal efficiencies for both mobile genetic elements (MGEs) and antibiotic residues, both of which had essential impacts on ARG profiles. In addition, heavy metals might contribute to variation in ARGs through horizontal gene transfer. Collectively, the variation in microbial communities and better removal of both MGEs and antibiotic residues contribute to the remarkable ARG removal efficiency of UASB and CSTR, therefore, advocating for the widespread adoption of these two AD systems in swine farms.

Antibiotic resistance genes in anaerobic digestion: Unresolved challenges and potential solutions

Antimicrobial resistance (AMR) threatens public health, necessitating urgent efforts to mitigate the global impact of antibiotic resistance genes (ARGs). Anaerobic digestion (AD), known for volatile solid reduction and energy generation, also presents a feasible approach for the removal of ARGs. This review encapsulates the existing understanding of ARGs and antibiotic-resistant bacteria (ARB) during the AD process, highlighting unresolved challenges pertaining to their detection and quantification. The questions raised and discussed include: Do current ARGs detection methods meet qualitative and quantitative requirements? How can we conduct risk assessments of ARGs? What happens to ARGs when they come into co-exposure with other emerging pollutants? How can the application of internal standards bolster the reliability of the AD resistome study? What are the potential future research directions that could enhance ARG elimination? Investigating these subjects will assist in shaping more efficient management strategies that employ AD for effective ARG control.

Determinants of antimicrobial resistance in biosolids: A systematic review, database, and meta-analysis

Biosolids can provide a nutrient rich soil amendment, particularly for poor soils and semi-arid or drought-prone areas. However, there are concerns that sludge and biosolids could be a source of propagation and exposure to AMR determinants such as antibiotic resistant bacteria (ARB), and antibiotic resistance genes (ARGs). To inform risk assessment efforts, a systematic literature review was performed to build a comprehensive spreadsheet database of ARB and ARG concentrations in biosolids (and some sludges specified as intended for land application), along with 69 other quantitative and qualitative meta-data fields from 68 published studies describing sampling information and processing methods that can be used for modeling purposes. Mean ARG concentrations per gram in positive samples of biosolids ranged from -5.7 log10(gene copies [gc]/g) to 12.92 log10(gc/g) (with these range values reported per dry weight), and aqueous concentrations ranged from 0.9 log10(gc/L) to 14.6 log10(gc/L). Mean ARB concentrations per gram of biosolids ranged from 2.02 log10 (colony forming units [CFU]/g) to 9.00 log10 (CFU/g) (dry weight), and aqueous concentrations ranged from 3.23 log10 (CFU/L) to 12.0 log10 (CFU/L). ARG log removal values (LRVs) during sewage sludge stabilization were calculated from a meta-analysis of mean concentrations before and after stabilization from 31 studies, ranging from -2.05 to 5.52 logs. The classes of resistance most relevant for a risk assessment corresponded to sulfonamide (sul1 and sul2), tetracycline (tetZ, tetX, tetA and tetG), beta-lactam (blaTEM), macrolide (ermB and ermF), aminoglycoside (strA and aac(6')-Ib-cr), and integron-associated (intI1). The resistance classes most relevant for ARB risk assessment included sulfonamides (sulfamethoxazole and sulfamethazine), cephalosporin (cephalothin and cefoxitin), penicillin (ampicillin), and ciprofloxin (ciprofloxacin). Considerations for exposure assessment are discussed to highlight risk assessment needs relating to antimicrobial resistance (AMR) associated with biosolids application. This study aids in prioritization of resources for reducing the spread of AMR within a One Health framework.

Occurrence, fate and control strategies of heavy metals and antibiotics in livestock manure compost land application: A review

Composting is a sustainable method for managing livestock manure, but the residual heavy metals and antibiotics in the compost pose can pose environmental risks when applied to land. Although many studies focus on occurrence and risk mitigation of heavy metals and antibiotics in manure compost land application, there is a lack of systematic analysis covering the entire chain from source to process and final disposal. Given this, this article provides a comprehensive review of the sources, migration, fate, risk assessment, and risk reduction of heavy metals and antibiotics contamination in land application of livestock manure compost for the first time. The main pollutants of concern are heavy metals, particularly Cu and Zn, and antibiotics such as quinolones, tetracyclines, and sulfonamides. The coexistence of these contaminants can easily trigger co-contamination, threatening soil ecosystems and human health. Risk reduction strategies, emphasizing the use of additives during composting and phytoremediation after land application, are discussed. Challenges remain in understanding the interactions between heavy metals and antibiotics and developing effective strategies for mitigating co-contamination. Furthermore, the paper proposes the future prospects on the interactions study and the simultaneous control strategy of heavy metals and antibiotics contamination. It is expected to promote the whole process management of livestock manure and the control of heavy metal-antibiotic co-contamination in the future.

Investigating the robustness of microbial communities in municipal sludge anaerobic digestion under organic loading rate disturbance

Anaerobic digestion (AD) frequently encounters disturbances due to variations in organic loading rates (OLRs), which can result in the failure of the sludge treatment process. However, there is a lack of comprehensive studies on the robustness of AD systems against OLR disturbances and the underlying mechanisms. In this study, the responses of reactor performance and active microbial communities in mesophilic AD were investigated and compared under conditions of OLR shock and OLR fluctuation. Statistical analysis confirmed that all reactors recovered from both types of OLR disturbance, indicating both functional and structural robustness of the mesophilic community. Based on metagenomics and metatranscriptomics analyses, it was observed that high diversity within the microbial community led to functional redundancy, which appears to be a key mechanism contributing to the robustness against OLR disturbances. Additionally, for the first time, the potential metabolic diversity of aerobic autotrophy bacteria in AD reactors was identified, including their roles in the utilization of glucose and acetate. Furthermore, the analysis of topological properties within the microbial interaction network was conducted, and the robustness of the community network was verified through the application of random node deletion attacks. The findings from this study provide valuable information for the effective regulation of microbial communities and the design of practical AD systems.

Fabrication and characterization of magnetic mesoporous nanoparticles for efficient determination and magnetic separation of sulfonamides in food samples

A magnetic, mesoporous core/shell structured Fe3O4@SiO2@mSiO2 nanocomposite was synthesized and employed as a magnetic solid phase extraction (MSPE) sorbent for the determination of trace sulfonamides (SAs) in food samples. The synthesized nanocomposite was characterized by transmission electron microscopy, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, thermogravimetric analysis, X-ray diffraction, N2 sorption analysis and vibrating sample magnetometry. The results showed that Fe3O4@SiO2@mSiO2 possessed a mesoporous structure with a large surface area. Batch experiments were carried out to investigate the adsorption ability for SAs. Fe3O4@SiO2@mSiO2 showed fast kinetics and high adsorption capacity, and the pseudo-second-order model and Langmuir adsorption isotherm are well fitted with the experimental data, indicating that chemical adsorption might be the rate-limiting step. Moreover, the high adsorption capacity can be maintained for at least 8 runs, indicating excellent stability and reusability. The proposed method exhibited good linearity in the range of 0.2-500 μg L-1, the R2 values of all the analytes were greater than 0.99 and the LODs were all lower than 0.2 μg L-1. Furthermore, real food samples were successfully analyzed with Fe3O4@SiO2@mSiO2 and high recoveries varying from 89.7% and 110.6% were obtained with low relative standard deviations ranging from 1.78% to 6.91%. The Fe3O4@SiO2@mSiO2 magnetic nanocomposite is a promising sorbent for the efficient extraction of SAs from complex food samples.

An overview of the occurrence, impact of process parameters, and the fate of antibiotic resistance genes during anaerobic digestion processes

Antibiotic resistance genes (ARGs) have emerged as a significant global health threat, contributing to fatalities worldwide. Wastewater treatment plants (WWTPs) and livestock farms serve as primary reservoirs for these genes due to the limited efficacy of existing treatment methods and microbial adaptation to environmental stressors. Anaerobic digestion (AD) stands as a prevalent biological treatment for managing sewage sludge and manure in these settings. Given the agricultural utility of AD digestate as biofertilizers, understanding ARGs' fate within AD processes is essential to devise effective mitigation strategies. However, understanding the impact of various factors on ARGs occurrence, dissemination, and fate remains limited. This review article explores various AD treatment parameters and correlates to various resistance mechanisms and hotspots of ARGs in the environment. It further evaluates the dissemination and occurrence of ARGs in AD feedstocks and provides a comprehensive understanding of the fate of ARGs in AD systems. This review explores the influence of key AD parameters such as feedstock properties, pretreatments, additives, and operational strategies on ARGs. Results show that properties such as high solid content and optimum co-digestion ratios can enhance ARG removal, while the presence of heavy metals, microplastics, and antibiotics could elevate ARG abundance. Also, operational enhancements, such as employing two-stage digestion, have shown promise in improving ARG removal. However, certain pretreatment methods, like thermal hydrolysis, may exhibit a rebounding effect on ARG levels. Overall, this review systematically addresses current challenges and offers future perspectives associated with the fate of ARGs in AD systems.

External carbon source as a viable tool for controlling antibiotics and antibiotic resistance genes (ARGs) in effluent: Influence on antibiotic removal and ARGs dissemination

Fluoroquinolone antibiotics and antibiotic resistance genes (ARGs) regarded as emerging contaminants were poorly removed in conventional wastewater treatment plants (WWTPs). Nitrogen-containing heterocyclic organics were found to be biodegraded through denitrification co-metabolism. The feasibility to enhance antibiotics removal efficiency in WWTPs through denitrification co-metabolism needs to be further verified. Meanwhile, due to significant correlation between ARGs profiles and nitrogen removal that was previously observed, the dissemination of ARGs during denitrification was worthy of in-depth understanding. Herein, the antibiotic removal and ARGs dissemination in denitrification co-metabolism condition were investigated with different denitrifying consortiums that acclimated under different conditions in terms of carbon source and the exposure of Ofloxacin (OFL). The results suggest that the removal of OFL can be enhanced by the denitrification co-metabolism. The tolerance to OFL is different among various denitrifying communities. For the denitrifying consortiums acclimated with methanol, long-term exposure to trace OFL (1 μg/L) could reduce the capabilities of removal and tolerance to OFL. On the contrary, those acclimated with sodium acetate (NaAc), the capabilities of removal and tolerance to OFL, were enhanced by long-term exposure to trace OFL. According to the quantitative determination to 384 target genes with high-throughput quantitative PCR, the abundance of ARGs in consortiums greatly increased when exposed to OFL at the concentration of comparable to sewage, which was also much larger than that acclimated with methanol. It can be confirmed and supported by DNA sequencing results that the antibiotic removal and the dissemination of ARGs were determined by microbial community that could be shaped with carbon source. These conclusions suggest that selecting the right external carbon source can be a useful strategy for WWTPs to control antibiotics and ARGs in the effluent. From a new perspective on mitigating ARGs dissemination, NaAc was not an appropriate carbon source.

Underlying the inhibition mechanisms of sulfate and lincomycin on long-term anaerobic digestion: Microbial response and antibiotic resistance genes distribution

This study evaluated the resilience of a long-term anaerobic treatment system exposed to sulfate, lincomycin (LCM) and their combined stress. LCM was found to impede anaerobic propionate degradation, while sulfate for restraining methanogenic acetate utilization. The combined stress, with influent LCM of 200 mg/L and sulfate of 1404 mg/L, revealed severer inhibition on anaerobic digestion than individual inhibition, leading to 73.9 % and 38.5 % decrease in methane production and sulfate removal, respectively. Suppression on propionate-oxidizing bacteria like unclassified_f__Anaerolineae and unclassified_f__Syntrophaceae further demonstrated LCM's inhibitory effect on propionate degradation. Besides, the down-regulation of genes encoding dissimilatory sulfate reduction enzymes caused by LCM triggered great inhibition on sulfate reduction. A notable increase in ARGs was detected under sulfate-stressed condition, owing to its obvious enrichment of tetracycline-resistant genes. Genera including unclassified_f__Syntrophaceae, unclassified_f__Geobacteraceae and unclassified_f__Anaerolineaceae were identified as dominant host of ARGs and enriched by sulfate addition. Overall, these results could provide the theoretical basis for further enhancement on anaerobic digestion of pharmaceutical wastewater containing sulfate and lincomycin.

New insights into antibiotic stimulation of methane production during anaerobic digestion

Residual antibiotics in swine wastewater pose a critical challenge for stable anaerobic digestion (AD). This study offers fresh insights into the anaerobic treatment of swine wastewater. The results showed that the presence of three typical antibiotics (sulfamethoxazole (SMX), oxytetracycline (OTC) and ciprofloxacin (CIP)) in swine wastewater could promote methane production by stimulating the production and conversion of ethanol. Among them, SMX exhibited the strongest methane promotion effect, with the cumulative methane production increasing from 138.47 to 2204.19 mL/g VS. According to the microbial community structure, antibiotics could promote the growth of Corynebacterium, Lutispora and hydrogenotrophic methanogens (Methanosassiliicoccus, Methanobrevibacter, and Methanobacterium), but inhibit the enrichment of acetoclastic methanogen (Methanosaeta). The relative abundance of Methanosaeta decreased from 2.93-19.80% to 0.52-2.58% under antibiotic stress. Furthermore, there were significant differences in the influence of different antibiotic types on methanogenic pathways. Specifically, OTC and CIP promoted the acetoclastic and hydrogenotrophic pathways, respectively, to enhance methane production. However, SMX could promote both acetoclastic and hydrogenotrophic pathways.

Variations in antibiotic resistance genes during long-term operation of an upflow anaerobic sludge blanket reactor

Antibiotic resistance genes (ARGs) have been widely detected in the environment. Anaerobic digestion (AD) has the potential ability to remove ARGs, and a comprehensive study is needed on the variations in ARGs during AD. In this study, variations in antibiotic resistance genes (ARGs) and microbial communities were investigated during the long-term operation of an upflow anaerobic sludge blanket (UASB) reactor. An antibiotic mixture of erythromycin, sulfamethoxazole and tetracycline was added to the UASB influent and the operation period was 360 days. The abundances of 11 ARGs and class 1 integron-integrase gene were detected in the UASB reactor, and the correlation between the ARGs and the microbial community was analyzed. The composition of ARGs indicated that the main ARGs in the effluent were sul1, sul2, and sul3, whereas the main ARG in the sludge was tetW. Correlation analysis indicated a negative correlation between microorganisms and ARGs in the UASB. In addition, most of ARGs showed a positive correlation with norank_f_Propionibacteriaceae and Clostridum_sensu_stricto_6, which were identified as potential hosts. These findings may help develop a feasible strategy for removing ARGs from aquatic environments during anaerobic digestion.

Metagenomic insights into the nitrogen metabolism, antioxidant pathway, and antibiotic resistance genes of activated sludge from a sequencing batch reactor under tetracycline stress

Tetracycline is prevalent in wastewater treatment plants and poses a potential threat to biological nitrogen removal under long-term exposure. In the present study, the influence of different tetracycline concentrations on the nitrogen removal, bioactivity response, and the spread of antibiotic resistance genes (ARGs) was assessed in sequencing batch reactor (SBR). The nitrogen removal efficiency, nitrification rate, and denitrification rate and their corresponding enzymatic activities gradually decreased with an increase in tetracycline concentration from 0.5 to 15 mg/L. The remarkable toxicity induced by tetracycline led to a significant increase in the peroxidation and the response of antioxidant system, as evidenced by strengthened antioxidant enzymatic activity and abundant genes (SOD12, katG, PXDN, gpx, and apx). Tetracycline addition significantly inhibited the ammonia-oxidizing bacterium Nitrosomonas and functional genes (amoA, amoB, and amoC). The presence of tetracycline decreased the abundance of citrate synthase and genes (CS, IDH3, and acnA) and interfered with carbon source metabolism, leading to impaired bioactivity and treatment performance. In addition, the presence of tetracycline induces diversity and differences in ARGs. The results provide reliable basic data for a deeper understanding of the effects of tetracycline on the nitrogen removal performance of bioreactors and provide a theoretical basis to build a promising strategy for relieving antibiotic-caused process fluctuations.

Copper in different forms and tetracycline affect behavior and risk of antibiotic resistome in thermophilic anaerobic digestion of cattle manure

The metagenomics-based behavior and risk of antibiotic resistance genes (ARGs) were investigated during cattle manure thermophilic anaerobic digestion with tetracycline and copper, namely, bulk-copper oxide, nano-copper oxide, and copper sulfate, which are common feed additives. Although bulk-copper oxide reduced ARGs' diversity, it enriched high-risk ARGs the most than the other two copper species, while copper sulfate could strongly mitigate the ARG risk by decreasing their abundances. Compared to corresponding individual effects, copper and tetracycline combinations may decrease ARGs' co-occurrence potential by 22.0%, and particularly, tetracycline combined separately with copper sulfate and nano-copper oxide reduces the ARGs' risk in abundance (by 7.2%) and human health (by 4.0%). These were mainly driven by bioavailable copper, volatile fatty acids, and pH, as well as the main potential hosts in phyla Firmicutes, Coprothermobacterota, and Euryarchaeota. Notably, the twin risks of pathogenicity and ARGs should be emphasized due to the ARGs' positive correlation with human pathogens of Clostridioides difficile and Arcobacter peruensis. These findings are important for understanding the potential ARGs' risk in treatments of livestock wastes containing feed additives of different sizes and speciation.

Dissemination of sulfonamide resistance genes in digester microbiome during anaerobic digestion of food waste leachate

The preeminence of sulfonamide drug resistance genes in food waste (FW) and the increased utilization of high-strength organic FW in anaerobic digestion (AD) to enhance methane production have raised severe public health concerns in wastewater treatment plants worldwide. In this regard, the dissemination patterns of different sulfonamide resistance genes (sul1 and sul2) and their impact on the digester core microbiota during AD of FW leachate (FWL) were evaluated. The presence of various sulfonamide antibiotics (SAs) in FWL digesters improved the final methane yield by 37 % during AD compared with FWL digesters without SAs. Microbial population shifts towards hydrolytic, acidogenic, and acetogenic bacteria in the phyla Actinobacteriota, Bacteroidota, Chloroflexi, Firmicutes, Proteobacteria, and Synergistota occurred due to SA induced substrate digestion and absorption through active transport; butanoate, propanoate, and pyruvate metabolism; glycolysis; gluconeogenesis; the citrate cycle; and pentose phosphate pathway. The initial dominance of Methanosaeta (89-96 %) declined to 47-53 % as AD progressed and shifted towards Methanosarcina (40 %) in digesters with the highest SA concentrations at the end of AD. Dissemination of sul1 depended on class 1 integron gene (intl1)-based horizontal gene transfer to pathogenic members of Chloroflexi, Firmicutes, and Patescibacteria, whereas sul2 was transmitted to Synergistota independent of intl1. Low susceptibility and ability to utilize SAs during methanogenesis shielded methanogenic archaea against selection pressure, thus preventing them from interacting with sul or intl1 genes, thereby minimizing the risk of antibiotic resistance development. The observed emergence of cationic antimicrobial peptide, vancomycin, and β-lactam resistance in the core microbiota during AD of FWL in the presence of SAs suggests that multidrug resistance caused by bacterial transformation could lead to an increase in the environmental resistome through wastewater sludge treatment.

Risk control of antibiotics, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) during sewage sludge treatment and disposal: A review

Sewage sludge is an important reservoir of antibiotics, antibiotic resistance genes (ARGs), and antibiotic resistant bacteria (ARB) in wastewater treatment plants (WWTPs), and the reclamation of sewage sludge potentially threats human health and environmental safety. Sludge treatment and disposal are expected to control these risks, and this review summarizes the fate and controlling efficiency of antibiotics, ARGs, and ARB in sludge involved in different processes, i.e., disintegration, anaerobic digestion, aerobic composting, drying, pyrolysis, constructed wetland, and land application. Additionally, the analysis and characterization methods of antibiotics, ARGs, and ARB in complicate sludge are reviewed, and the quantitative risk assessment approaches involved in land application are comprehensively discussed. This review benefits process optimization of sludge treatment and disposal, with regard to environmental risks control of antibiotics, ARGs, and ARB in sludge. Furthermore, current research limitations and gaps, e.g., the antibiotic resistance risk assessment in sludge-amended soil, are proposed to advance the future studies.

Deciphering risks of resistomes and pathogens in intensive laying hen production chain

Antimicrobial resistance (AMR) and pathogens derived from food animals and their associated environments have emerged as challenging threats to humans from a health perspective, but our understanding of these risks and their key prevention and control points in the current intensive breeding industry remains poor. By creating an integral composition and risk profile of the resistome and microbiome through metagenomics in feces, flies, dust, sewage, and soil along the four-stage laying hen production chain, we found that the whole production chain is a hotspot for antimicrobial resistance genes (ARGs) with 374 known subtypes and pathogens, including 157 human pathogenic bacteria (HPB). Feces and flies were identified as major risk sources for these contaminations. Also, we confirmed a twin-risk of AMR and pathogenicity prevailing throughout the chain, but with different frequencies in each stage; thus, high-risk ARGs in the young chicken stage and highly prioritized HPB in the chick stage contributed 37.33 % to the total AMR risk and 36.36 % to the pathogenic risks, respectively, thus rendering the two stages to be the key prevention points. Moreover, the prevalence of 112 binned ARG supercarriers (for example, Klebsiella pneumoniae harboring 20 ARGs) was unraveled along the production chain, especially in feces, flies, and dust, and 87 potential hosts exhibited high pathogenic risk, high-risk AMR, or both, with 262 ARGs and 816 virulence factor genes. Overall, this study provides first-hand comprehensive data on high-risk ARGs and their pathogenic hosts in the intensive laying hen production chain, and thus is fundamentally important for developing new measures to help control the global AMR crisis induced through the animal-environment-human pathway.

Detailed investigation of catalytically important residues of class A β-lactamase

An increasing global health challenge is antimicrobial resistance. Bacterial infections are often treated by using β-lactam antibiotics. But several resistance mechanisms have evolved in clinically mutated bacteria, which results in resistance against such antibiotics. Among which production of novel β-lactamase is the major one. This results in bacterial resistance against penicillin, cephalosporin, and carbapenems, which are considered to be the last resort of antibacterial treatment. Hence, β-lactamase enzymes produced by such bacteria are called extended-spectrum β-lactamase and carbapenemase enzymes. Further, these bacteria have developed resistance against many β-lactamase inhibitors as well. So, investigation of important residues that play an important role in altering and expanding the spectrum activity of these β-lactamase enzymes becomes necessary. This review aims to gather knowledge about the role of residues and their mutations in class A β-lactamase, which could be responsible for β-lactamase mediated resistance. Class A β-lactamase enzymes contain most of the clinically significant and expanded spectrum of β-lactamase enzymes. Ser70, Lys73, Ser130, Glu166, and Asn170 residues are mostly conserved and have a role in the enzyme's catalytic activity. In-depth investigation of 69, 130, 131, 132, 164, 165, 166, 170, 171, 173, 176, 178, 179, 182, 237, 244, 275 and 276 residues were done along with its kinetic analysis for knowing its significance. Further, detailed information from many previous studies was gathered to know the effect of mutations on the kinetic activity of class A β-lactamase enzymes with β-lactam antibiotics.Communicated by Ramaswamy H. Sarma.

The responses of mesophilic and thermophilic anaerobic digestion of municipal sludge to periodic fluctuation disturbance of organic loading rate

Fluctuation disturbance of organic loading rate (OLR) is common in actual anaerobic digestion (AD), but its effects on AD of municipal sludge gets little attention. This study investigated the responses of reactor performance and active microbial community in mesophilic and thermophilic AD of municipal sludge before, during and after OLR periodic fluctuation disturbance. The performance of both reactors were similar before and after disturbance although some parameter values changed during the disturbance, which indicated their enough buffer capacity to OLR periodic fluctuation. Different microbial community at RNA level was observed in the two reactors. When the OLR disturbance commenced, the microbial community changed greatly in thermophilic AD. Error and attack tolerance of the microbial network was analyzed in order to learn the response mechanisms to OLR disturbance. The results assisted that the thermophilic microbial community was more vulnerable, but the reactor performance of which could be maintained using the functional redundancy strategy under OLR fluctuation disturbance.

Effect of minute amounts of arsenic on the sulfamethoxazole removal and microbial community structure via the SBR system

In this study, the effect of arsenic on the sulfamethoxazole (SMX) removal efficiency and microbial community structure was investigated over 60 days using the SBR process. The results showed that the presence of arsenic had no significant impact on the system performance, the removal efficiencies of two reactors, R1 (the control test) and R2 (with the addition of arsenic), were 13.36 ± 5.71 and 14.20 ± 5.27%, which were attributed to the adsorption of SMX by fulvic acid-like substances and tryptophan-like proteins of extracellular polymeric substances. Compared to the seed sludge, the species number indicated that R2 possessed the richer diversity, while R1 possessed the lower diversity on day 60, which might be relative to the transferring of antibiotic resistance genes (ARGs) in sludge bacterial communities; the minute amounts of arsenic could make the relative levels of Sul1 and Sul2 genes which encode ARGs of sulfonamides in R2 (2.07 and 2.47%) be higher than that in R1 (1.65 and 1.27%), which made the bacterial community of the R2 system more adaptable to SMX stress. Therefore, the minute amounts of arsenic weakened the effect of SMX on the system and enhanced the stability of the microbial community structure.

Antimicrobial Resistance Profile of Common Foodborne Pathogens Recovered from Livestock and Poultry in Bangladesh

Multidrug-resistant (MDR) foodborne pathogens have created a great challenge to the supply and consumption of safe & healthy animal-source foods. The study was conducted to identify the common foodborne pathogens from animal-source foods & by-products with their antimicrobial drug susceptibility and resistance gene profile. The common foodborne pathogens Escherichia coli (E. coli), Salmonella, Streptococcus, Staphylococcus, and Campylobacter species were identified in livestock and poultry food products. The prevalence of foodborne pathogens was found higher in poultry food & by-product compared with livestock (p < 0.05). The antimicrobial drug susceptibility results revealed decreased susceptibility to penicillin, ampicillin, amoxicillin, levofloxacin, ciprofloxacin, tetracycline, neomycin, streptomycin, and sulfamethoxazole-trimethoprim whilst gentamicin was found comparatively more sensitive. Regardless of sources, the overall MDR pattern of E. coli, Salmonella, Staphylococcus, and Streptococcus were found to be 88.33%, 75%, 95%, and 100%, respectively. The genotypic resistance showed a prevalence of blaTEM, blaSHV, blaCMY, tetA, tetB, sul1, aadA1, aac(3)-IV, and ereA resistance genes. The phenotype and genotype resistance patterns of isolated pathogens from livestock and poultry had harmony and good concordance, and sul1 & tetA resistance genes had a higher prevalence. Good agricultural practices along with proper biosecurity may reduce the rampant use of antimicrobial drugs. In addition, proper handling, processing, storage, and transportation of foods may decline the spread of MDR foodborne pathogens in the food chain.

Effects of antibiotics on anaerobic digestion of sewage sludge: Performance of anaerobic digestion and structure of the microbial community

As a common biological engineering technology, anaerobic digestion can stabilize sewage sludge and convert the carbon compounds into renewable energy (i.e., methane). However, anaerobic digestion of sewage sludge is severely affected by antibiotics. This review summarizes the effects of different antibiotics on anaerobic digestion of sewage sludge, including production of methane and volatile fatty acids (VFAs), and discusses the impact of antibiotics on biotransformation processes (solubilization, hydrolysis, acidification, acetogenesis and methanogenesis). Moreover, the effects of different antibiotics on microbial community structure (bacteria and archaea) were determined. Most of the research results showed that antibiotics at environmentally relevant concentrations can reduce biogas production mainly by inhibiting methanogenic processes, that is, methanogenic archaea activity, while a few antibiotics can improve biogas production. Moreover, the combination of multiple environmental concentrations of antibiotics inhibited the efficiency of methane production from sludge anaerobic digestion. In addition, some lab-scale pretreatment methods (e.g., ozone, ultrasonic combined ozone, zero-valent iron, Fe³⁺ and magnetite) can promote the performance of anaerobic digestion of sewage sludge inhibited by antibiotics.

The responses of marine anammox bacteria-based microbiome to multi-antibiotic stress in mariculture wastewater treatment

Saline mariculture wastewater containing multi-antibiotics poses a challenge to anaerobic ammonia oxidation (anammox) process. Herein, the halophilic marine anammox bacteria (MAB)-based microbiome was used for treating mariculture wastewater (35‰ salinity) under multi-antibiotics (enrofloxacin + oxytetracycline + sulfamethoxazole, EOS) stress. And the main focus of this study lies in the response of MAB-based microbiome against multi-antibiotics stress. It is found that MAB-based microbiome shows stable community structure and contributes high nitrogen removal efficiency (>90%) even under high stress of EOS (up to 4 mg·L^-1). The relative abundance of main functional genus Candidatus Scalindua, responsible for anammox, had little change while controlling the influent EOS concentration within 4 mg·L^-1, whereas, significantly decreased to 2.23% at EOS concentration of as high as 24 mg·L^-1. As an alternative, antibiotic resistance bacteria (ARB) species Rheinheimera dominated the microbial community of MAB-based biological reactor under extremely high EOS stress (e.g. 24 mg·L^-1 in influent). The response mechanism of MAB-based microbiome consists of extracellular and intracellular defenses with dependence of EOS concentration. For example, while EOS within 4 mg·L^-1 in this study, most of the antibiotics were retained by extracellular polymeric substances (EPS) via adsorption; If increasing the EOS concentration to 8 and even 24 mg·L^-1, part of antibiotics could intrude into the cells and cause the intracellular accumulation of antibiotic resistance genes (ARGs) (total abundance up to 2.44 × 10^-1 copies/16S rRNA) for EOS response. These new understandings will facilitate the practical implementation of MAB-based bioprocess for saline nitrogen- and antibiotics-laden wastewater treatment.

Effects of g-C3N4 on bacterial community and tetracycline resistance genes in two typical sediments in tetracycline pollution remediation

Photocatalysis, as a novel technique, has been widely used for antibiotic pollution remediation in wastewater. In the processes of degradation and removal of antibiotics, the impact of photocatalysts on microenvironment is very important but remains poorly understood. In the present study, the effect of typical photocatalyst g-C3N4 (Graphitic carbon nitride) on microbial community was investigated in two sediment types (riverbed sediment and pig-farm sediment) polluted by tetracycline (TC) in central southern China. The riverbed sediment and pig farm sediment samples were respectively exposed to g-C3N4 (25, 75, 125 mg⋅kg-1) and TC (60, 120, 180 mg⋅L-1) treatments alone or combination for 30 days, respectively. The bacterial community and antibiotic resistance genes (ARGs) of the treated sediments were analyzed by Illumina sequencing and metagenomic sequencing. Studies had shown that: TC, g-C3N4, and TC/g-C3N4 have significant effects on the changes of microbial communities and components in riverbed sediment, but they do not exist in pig farm sediment. The most alterations of microbial taxa were Acidobacteriota, Actinobacteriota, and Desulfobacterota in riverbed sediment, and Elusimicrobiota in the pig farm sediment under various treatments. Through network analysis, it was found that the distribution of microorganisms in the pig farm sediment is more complex and more stable. The addition of g-C3N4 reduced the absolute abundance of ARGs in the two examined sediments, but not significantly changed their relative abundance of ARGs. The g-C3N4 application was beneficial to the removal of TC residues and to the prevention of the generation and transmission of ARGs in sediments. Our results suggested that g-C3N4 was a suitable photocatalyst with excellent application prospect for the removal of TC residues and the control of ARGs in environment.

Dissecting the roles of conductive materials in attenuating antibiotic resistance genes: Evolution of physiological features and bacterial community

Supplying conductive materials (CMs) into anaerobic bioreactors is considered as a promising technology for antibiotic wastewater treatment. However, whether and how CMs influence antibiotic resistance genes (ARGs) spread remains poorly known. Here, we investigated the effects of three CMs, i.e., magnetite, activated carbon (AC), and zero valent iron (ZVI), on ARGs dissemination during treating sulfamethoxazole wastewater, by dissecting the shifts of physiological features and microbial community. With the addition of magnetite, AC, and ZVI, the SMX removal was improved from 49.05 to 71.56-92.27 %, while the absolute abundance of ARGs reducing by 26.48 %, 61.95 %, 48.45 %, respectively. The reduced mobile genetic elements and antibiotic resistant bacteria suggested the inhibition of horizontal and vertical transfer of ARGs. The physiological features, including oxidative stress response, quorum sensing, and secretion system may regulate horizontal transfer of ARGs. The addition of all CMs relieved oxidative stress compared with no CMs, but ZVI may cause additional free radicals that needs to be concerned. Further, ZVI and AC also interfered with cell communication and secretion system. This research deepens the insights about the underlying mechanisms of CMs in regulating ARGs, and is expected to propose practical ways for mitigating ARGs proliferation.

Exploration of machine learning algorithms for predicting the changes in abundance of antibiotic resistance genes in anaerobic digestion

The land application of digestate from anaerobic digestion (AD) is considered a significant route for transmitting antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) to ecosystems. To date, efforts towards understanding complex non-linear interactions between AD operating parameters with ARG/MGE abundances rely on experimental investigations due to a lack of mechanistic models. Herein, three different machine learning (ML) algorithms, Random Forest (RF), eXtreme Gradient Boosting (XGBoost), and Artificial Neural Network (ANN), were compared for their predictive capacities in simulating ARG/MGE abundance changes during AD. The models were trained and cross-validated using experimental data collected from 33 published literature. The comparison of model performance using coefficients of determination (R²) and root mean squared errors (RMSE) indicated that ANN was more reliable than RF and XGBoost. The mode of operation (batch/semi-continuous), co-digestion of food waste and sewage sludge, and residence time were identified as the three most critical features in predicting ARG/MGE abundance changes. Moreover, the trained ANN model could simulate non-linear interactions between operational parameters and ARG/MGE abundance changes that could be interpreted intuitively based on existing knowledge. Overall, this study demonstrates that machine learning can enable a reliable predictive model that can provide a holistic optimization tool for mitigating the ARG/MGE transmission potential of AD.

Effect of g-C3N4 on biodiversity and structure of bacterial community in sediment of Xiangjiang River under tetracycline pressure

Photocatalysts have been widely prepared and used in wastewater treatment. Although the influence of photocatalyst application on survival and activity of organisms has been examined, its impact on composition and diversity of microbial community is not fully understood. In this study, the impact of photocatalyst g-C₃N₄ (Graphitic carbon nitride) on microbial communities in riverbed sediments polluted by antibiotic tetracycline (TC) was investigated. The sediment samples collected from the Xiangjiang River of China were exposed to different concentrations of TC, g-C₃N₄ and TC/g-C₃N₄ and the bacterial community were analyzed by Illumina sequencing. The results showed that the dominant bacterial phyla were Acidobacteriota, Proteobacteria, Actinobacteriota, and Chloroflexi in the study site. When compared to the control treatments, the application of TC, g-C₃N₄ and TC/g-C₃N₄ exhibited distinguishable effects on bacterial community structure in sediments. The presence of TC had greater influence on bacterial composition, while g-C₃N₄ and TC/g-C₃N₄ had less influence on bacteria. The diversity and richness of microorganisms in sediment increased under g-C₃N₄ application and reached the highest values when g-C₃N₄ was 75 mg/kg. The photocatalyst g-C₃N₄ restored bacterial community diversity affected by TC, reduced the TC residues in aquatic environment, and eliminated the side effects of TC application in sediments. Our study indicated that g-C₃N₄ was an environmentally friendly photocatalyst with lightly negative effects on microbial community in riverbed sediments, and could be used for effective remediation of TC-contaminated environments.

Effect of sulfamethoxazole on nitrate removal by simultaneous heterotrophic aerobic denitrification

The increase in mariculture activities worldwide has not only led to a rise of nitrogen compounds in the ecosystem but has also intensified the accumulation of antibiotics in both terrestrial and marine environments. This study focused on the effect of typical antibiotics, specifically sulfamethoxazole (SMX) on nitrate removal from mariculture wastewater by aerobic denitrification process; an aerobic denitrification system feeding with 148.2 mg/L COD, 8.59 mg/L nitrate, 0.72 mg/L nitrite, and 4.75 mg/L ammonium was set up. The hydraulic retention time (HRT) was 8 h. As the aerobic bioreactor started up successfully without SMX dosage, an excellent removal of ammonium, nitrite, and nitrate was achieved at 91.35%, 93.33%, and 88.51%, respectively; the corresponding effluent concentrations were 0.41 mg/L, 0.048 mg/L, and 0.96 mg/L. At the influent SMX doses of 0, 1, 5, and 10 mg/L, the COD removal reached 96.91%, 96.27%, 88.69%, and 85.89%, resulting in effluent concentrations of 4.53, 5.45, 17.38, and 20.6 mg/L, respectively. Nitrification was not inhibited by SMX dosage. However, aerobic denitrification was inhibited by 10 mg/L SMX. Proteobacteria was the most abundant phylum, and surprisingly its abundance increased with the increase in SMX concentration. An excellent SMX degradation was noted at initial SMX dosages of 1, 5, and 10 mg/L; the removal rate was 100%,100%, and 99.8%, respectively. The SMX degrading genera Comamonas sp., Acinetobacter sp., and Thauera sp. are of great validity to wastewater engineers because they have demonstrated efficiency in simultaneous heterotrophic aerobic denitrification and antibiotic degradation as well as COD removal. PRACTITIONER POINTS: Nitrification was not inhibited by increase in SMX dosage. An increase in SMX dosage inhibited aerobic denitrification. COD removal was not affected by increased SMX dosage. Comamonas, Acinetobacter, and Thauera had high efficiency in COD removal and SMX degradation.

Do microplastic biofilms promote the evolution and co-selection of antibiotic and metal resistance genes and their associations with bacterial communities under antibiotic and metal pressures?

Microplastic (MP) biofilms with heterogeneous bacterial compositions and structure have become a hotspot of antibiotic resistance genes (ARGs) in aquatic environments. The evolutionary features of ARGs and their related factors including class 1 integron (intI1), metal resistance genes (MRGs), and bacterial communities in MP biofilms under exogenous pressures and how they compared with natural substrates (NS) are unclear. The individual and combined pressures of sulfamethoxazole, tetracycline, and zinc were used to drive the dynamic evolution of ARGs, intI1, MRGs, and bacterial communities in the MP and NS biofilms. The exogenous pressures from the combined selection of sulfamethoxazole, tetracycline, and zinc and their increasing concentrations both significantly enhanced the abundances of ARGs on the MP compared to the NS. Meanwhile, the selective pressures resulted in obvious dissimilarities between the MP and NS bacterial communities. The core bacterial taxa and the co-occurrence patterns of ARGs and bacterial genera in the biofilms of MP and NS were obviously different, and more potential ARG host bacteria selectively colonized the MP. Metal pressure also enhanced the enrichment of ARGs in the MP biofilms by promoting the spread of intI1 via the co-selection mechanism.

Metatranscriptomic insight into the effects of antibiotic exposure on performance during anaerobic co-digestion of food waste and sludge

Antibiotics are inevitably entered into anaerobic co-digestion (AcoD) system of food waste (FW) and sludge along with the addition of abundant antibiotic-containing activated sludge. However, the in-depth insights into antibiotics affecting AcoD performance have not comprehensively studied. In present study, the results showed that tetracycline (TC), sulfamethoxazole (SMZ) and erythromycin (ERY) inhibited and delayed methane production except for 5 mg/L ERY. By comparison, TC and SMZ significantly inhibited the cumulative methane yields (one-way ANOVA, p < 0.01), and the inhibition effects were magnified as the antibiotic level increased. Physicochemical and methane yield analysis indicated antibiotics inhibited hydrolysis process and delayed methanogenesis process, which was in line with the declined abundance of acetogenic Proteiniphilum and hydrogenotrophic Methanobacterium during AcoD. Furthermore, metatranscriptomic analysis demonstrated the microbial activities of major organic and energy metabolism were down-regulated under antibiotics exposure, thereby down-regulating the expressions of key coenzymes (coenzymes M, F420, methanofuran) biosynthesis for methanogenesis and methane metabolism. The declined methanogenesis activity was completely consistent with the inhibited activity of dominant Methanosarcina and methane production, proving the importance of Methanosarcina on methane production. This study provides new metatranscriptomic evidence into the effects of antibiotics on methanogenesis during AcoD.

Bioaugmentation with syntrophic volatile fatty acids-oxidizing consortia to alleviate the ammonia inhibition in continuously anaerobic digestion of municipal sludge

Ammonia inhibition easily affects the performance of anaerobic digestion (AD) for municipal sludge and the oxidization of volatile fatty acids (VFAs) is the rate-limiting step of this process. Bioaugmentation is considered to be an effective method to alleviate ammonia inhibition of AD, but most study used the hydrogenotrophic methanogens as the bioaugmentation culture. In this study, bioaugmentation of mesophilic AD (MAD) and thermophilic AD (TAD) under ammonia inhibition with syntrophic acetate and propionate oxidizing consortia was investigated. The results showed that the bioaugmented reactors recovered earlier than control reactors with 20 (MAD) and 8 (TAD) days, respectively. The high-throughput 16S rRNA gene sequencing indicated that the relative abundance of carbohydrates fermenter (Lentimicrobium), syntrophic VFAs-oxidizing bacteria (Rikenellaceae_DMER64, Smithella and Syntrophobacter) and acetoclastic and hydrogenotrophic methanogens (Methanosaeta, Methanolinea and Methanospirillum) increased in MAD after bioaugmentation. However, part of the bioaugmentation culture could not adapt to the high free ammonia (FAN) concentration in MAD and the effect was weakened. In TAD, proteolytic bacteria (Keratinibaculum and Tepidimicrobium), syntrophic VFAs-oxidizing bacteria (Syntrophomonas) and hydrogenotrophic methanogen (Methanosarcina) were strengthened. The effect of bioaugmentation in TAD was durable even at higher organic loading rate (OLR), due to its positive influence on microbial community. These results suggested that the different bioaugmentation mechanism occurred in MAD and TAD, which are derived from the synergetic effects of ammonia tolerance and microbial interactions. Our study revealed the VFAs-oxidizing consortia as bioaugmented culture could be the potential strategy to alleviate the ammonia stress of AD.

Deciphering the transfers of antibiotic resistance genes under antibiotic exposure conditions: Driven by functional modules and bacterial community

Antibiotics can exert selective pressures on sludge as well as affect the emergence and spread of antibiotic resistance genes (ARGs). However, the underlying mechanisms of ARGs transfers are still controversial and not fully understood in sludge system. In present study, two anaerobic sequence batch reactors (ASBR) were constructed to investigate the development of ARGs exposed to two sulfonamide antibiotics (SMs, sulfadiazine SDZ and sulfamethoxazole SMX) with increasing concentrations. The abundance of corresponding ARGs and total ARGs obviously increased with presence of SMs. Functional analyses indicated that oxidative stress response, signal transduction and type IV secretion systems were triggered by SMs, which would promote ARGs transfers. Network analysis revealed 18 genera were possible hosts of ARGs, and their abundances increased with SMs. Partial least-squares path modeling suggested functional modules directly influenced mobile genetic elements (MGEs) as well as the ARGs might be driven by both functional modules and bacteria community, while bacteria community composition played a more key role. Sludge with refractory antibiotics (SDZ) may stimulate the relevant functions and shift the microbial composition to a greater extent, causing more ARGs to emerge and spread. The mechanisms of ARGs transfers are revealed from the perspective of functional modules and bacterial community in sludge system for the first time, and it could provide beneficial directions, such as oxidative stress reduction, cellular communication control, bacterial composition directional regulation, for ARGs spread controlling in the future.

The impact of antimicrobials on the efficiency of methane fermentation of sewage sludge, changes in microbial biodiversity and the spread of antibiotic resistance

The study was designed to simultaneously evaluate the influence of high doses (512-1024 µg/g) the most commonly prescribed antimicrobials on the efficiency of anaerobic digestion of sewage sludge, qualitative and quantitative changes in microbial consortia responsible for the fermentation process, the presence of methanogenic microorganisms, and the fate of antibiotic resistance genes (ARGs). The efficiency of antibiotic degradation during anaerobic treatment was also determined. Metronidazole, amoxicillin and ciprofloxacin exerted the greatest effect on methane fermentation by decreasing its efficiency. Metronidazole, amoxicillin, cefuroxime and sulfamethoxazole were degraded in 100%, whereas ciprofloxacin and nalidixic acid were least susceptible to degradation. The most extensive changes in the structure of digestate microbiota were observed in sewage sludge exposed to metronidazole, where a decrease in the percentage of bacteria of the phylum Bacteroidetes led to an increase in the proportions of bacteria of the phyla Firmicutes and Proteobacteria. The results of the analysis examining changes in the concentration of the functional methanogen gene (mcrA) did not reflect the actual efficiency of methane fermentation. In sewage sludge exposed to antimicrobials, a significant increase was noted in the concentrations of β-lactam, tetracycline and fluoroquinolone ARGs and integrase genes, but selective pressure was not specific to the corresponding ARGs.

The variation of antibiotic resistance genes and their links with microbial communities during full-scale food waste leachate biotreatment processes

The prevalence of antibiotic resistance genes (ARGs) has been widely reported in various environments. However, little is known of them in food waste (FW) leachate with high organic content and how their distribution is influenced by biotreatment processes. Here, twelve ARGs, two integrase genes and bacterial communities were investigated during two full-scale FW biotreatment processes. High ARGs abundances (absolute: 1.03 × 10⁷-2.82 × 10⁹copies/mL; relative: 0.076-2.778copies/16S rRNA) were observed across all samples. Although biotreatment effectively reduced absolute abundance of ARGs, additional bacteria acquiring ARGs caused an increase in their relative abundance, which further increased the transmission risk of ARGs. mexF, blaCTX-M, sul1 played crucial roles and sul1 might be considered as an indicator for the prediction of total ARGs. It is worrying that the discharge (effluent and sludge) included highly abundant ARGs (5.09 × 10¹⁴-4.83 × 10¹⁵copies/d), integrons (1.11 × 10¹⁴-6.04 × 10¹⁴copies/d) and potential pathogens (such as Pseudomonas and Streptococcus), which should be given more attentions. blaCTX-M and tetQ possessed most potential hosts, Proteobacteria-L and Firmicutes-W were predominant contributors of ARGs-hosts at genus level. This study suggested FW leachate biotreatment systems could be reservoirs of ARGs and facilitated the proliferation of them. The exploration of effective removal methods and formulation of emission standard are necessary for future ARGs mitigation.

A review targeting veterinary antibiotics removal from livestock manure management systems and future outlook

Veterinary antibiotics (VAs) contamination has been considered as a worldwide environmental and health concern in recent decades. This paper reviewed the variability of contents of VAs and their release from the animal breeding industry into the surrounding environment along with the performance of the manure treatment technologies. The data collected revealed that VAs were mostly excreted in animal feces and observed in manure, soil, water, and sediment. The findings illustrate the disparity of VAs in excretion rates, consumption, and their residues in the environment with relatively high distribution for tetracyclines, fluoroquinolones, and sulfonamides. Anaerobic digestion has a capacity to remove of 73% VAs while manure composting and constructed wetlands can remove 84.7%, and 90% VAs. Due to the profound effect of antibiotics on the environment, further research and intensive management strategies for livestock manure need to be designed to improve the removal efficiency and manure management technologies.

Responses of bacterial and bacteriophage communities to long-term exposure to antimicrobial agents in wastewater treatment systems

The occurrence of antibacterial agents has received increasing concern due to their possible threats to human health. However, the effects of antibacterial residues on the evolution and dynamics between bacteria and bacteriophages in wastewater treatment systems have seldom been researched. Especially for phages, little is known about their response to antimicrobial exposure. In this study, two identical anoxic-aerobic wastewater treatment systems were established to evaluate the responses of bacterial and phage communities to long-term exposure to antimicrobial agents. The results indicated simultaneous exposure to combined antimicrobials significantly inhibited (p < 0.05) the abundance of phages and bacteria. Metagenomic sequencing analysis indicated the community of bacteria and phages changed greatly at the genus level due to combined antibacterial exposure. Additionally, long-term exposure to antimicrobial agents promoted the attachment of receptor-binding protein genes to Klebsiella, Escherichia and Salmonella (which were all members of Enterobacteriaceae). Compared to that in the control system, the numbers of receptor-binding protein genes on their possible phages (such as Lambdalikevirus and P2likevirus) were also obviously higher when the microorganisms were exposed to antimicrobials. The results are helpful to understanding the microbial communities and tracking the relationship of phage-bacterial host systems, especially under the pressure of antimicrobial exposure.

A systematic review of antibiotics and antibiotic resistance genes in estuarine and coastal environments

Antibiotics and antibiotic resistance genes (ARGs) are prevalent in estuarine and coastal environments due to substantial terrestrial input, aquaculture effluent, and sewage discharge. In this article, based on peer-reviewed papers, the sources, spatial patterns, driving factors, and environmental implications of antibiotics and ARGs in global estuarine and coastal environments are discussed. Riverine runoff, WWTPs, sewage discharge, and aquaculture, are responsible for the prevalence of antibiotics and ARGs. Geographically, pollution due to antibiotics in low- and middle-income countries is higher than that in high-income countries, and ARGs show remarkable latitudinal variations. The distribution of antibiotics is driven by antibiotic usage and environmental variables (heavy metals, nutrients, organic pollutants, etc.), while ARGs are affected by antibiotics residues, environmental variables, microbial communities, and mobile genetic elements (MGEs). Antibiotics and ARGs alter microbial communities and biogeochemical cycles, as well as pose threats to marine organisms and human health. Our results provide comprehensive insights into the transport and environmental behaviors of antibiotics and ARGs in global estuarine and coastal environments.

Fate of antibiotic resistance genes during temperature-changed psychrophilic anaerobic digestion of municipal sludge

The effects of anaerobic digestion (AD) on the abundance of antibiotic resistance genes (ARGs) are highly related to operational temperature. However, the removal performance of ARGs in psychrophilic AD and changed temperatures simulating variable seasonal temperatures is poorly understood. Herein, we investigated the fate of ARGs, correlated bacterial communities and physicochemical properties of AD operation at psychrophilic (15 ℃), mesophilic (35 ℃), and temperature changed conditions (15 to 35 ℃ and 35 to 15 ℃). The results indicated that ammonia release was positively correlated with temperature. The mesophilic AD facilitated phosphorous intake and ARGs proliferation and selection with oxytetracycline (OTC), while psychrophilic AD was conducive to the removal and control of ARGs if no OTC existed. The diversity and composition of AD bacterial communities were influenced more by temperature than OTC. The dominant genera like Candidatus_Microthrix and Acinetobacter had dramatical abundance discrepancies at different temperatures and were obviously positively correlated with ARGs (tet39, tetC and mexD), mobile genetic elements (MGEs) intI, insert sequences (IS) and plasmid. The physicochemical properties of AD influenced the bacterial richness, which in turn significantly correlated with the ARGs abundances. Therefore, ARGs removal could be potentially optimized by eliminating bacterial hosts with deteriorated living conditions and decreased nutrients. This study clarified the response of antibiotic resistome to different temperature variation and highlighted the potential strategies for improved ARGs removal in AD.

The impact and fate of clarithromycin in anaerobic digestion of waste activated sludge for biogas production

Clarithromycin retained in waste activated sludge (WAS) inevitably enters the anaerobic digestion system. So far, the complex impacts and fate of clarithromycin in continuous operated WAS anaerobic digestion system are still unclear. In this study, two semi-continuous long-term reactors were set up to investigate the effect of clarithromycin on biogas production and antibiotic resistance genes (ARGs) during WAS anaerobic digestion, and a batch test was carried out to explore the potential metabolic mechanism. Experimental results showed that clarithromycin at lower concentrations (i.e., 0.1 and 1.0 mg/L) did not affect biogas production, whereas the decrease in biogas production was observed when the concentration of clarithromycin was further increased to 10 mg/L. Correspondingly, the relative abundance of functional bacteria in WAS anaerobic digestion (i.e., Anaerolineaceae and Microtrichales) was reduced with long-term clarithromycin exposure. The investigation of ARGs suggested that the effect of methylation belonging to the target site modification played a critical role for the anaerobic microorganisms in the expression of antibiotic resistance, and ermF, played dominated ARGs, presented the most remarkable proliferation. In comparison, the role of efflux pump was weakened with a significant decrease of two detected efflux genes. During WAS anaerobic digestion, clarithromycin could be partially degraded into metabolites with lower antimicrobial activity including oleandomycin and 5-O-desosaminyl-6-O-methylerythronolide and other metabolites without antimicrobial activity.

Feed-additive of bioengineering strain with surface-displayed laccase degrades sulfadiazine in broiler manure and maintains intestinal flora structure

Sulfonamide antibiotics (SAs) are excreted into the ecosystem unchanged through feces and urine because of their low adsorption and degradation in the guts of humans and animals. In this study, a novel whole-cell biocatalyst with fungal laccase on the cell surface of Escherichia coli Nissle 1917 was developed to degrade sulfadiazine (SDZ). Engineered strain EcN-IL showed laccase enzyme activity of 2 ± 1 U/mg dry weight of cell and degraded 37 ± 1% of SDZ at temperature 40 °C and pH 5 within 3 h in vitro. Strain EcN-IL with 500 mg/kg of SDZ was employed as a food supplement to feed chicken broilers, which can reduce the residue of SDZ in broiler manure by 58 ± 2% and also reduced dysbiosis of the gut microbiota due to overuse of antibiotics. The genetically engineered EcN-IL has laid a foundation for degrading SDZ in broilers and their manure.

Two-dimension N-doped nanoporous carbon from KCl thermal exfoliation of Zn-ZIF-L: Efficient adsorption for tetracycline and optimizing of response surface model

N-doped nanoporous carbon (NC) with two-dimensional structure derived from Zn-ZIF-L via KCl exfoliation and carbonization at different temperature were prepared for adsorptive removal of tetracycline (TC). Characterizations revealed the effective dopant of N atoms and low degree of graphitization with more defects related to the enhanced adsorption capacity of the NC materials. Benefiting from the huge surface area (2195.57 m² g^-1), high porosity (1.34 cm³ g^-1) and accessible sheeting structure, the NC-800 exhibited its fast and efficient adsorption of TC in 60 min. Meantime, the maximum adsorption of TC could reach 347.06 mg g^-1. Effects of pH, humic acid (HA) and ionic strength (Na⁺, Ca²⁺) were studied along with the interactions among influencing factors investigated by response surface model (RSM). By optimizing experimental conditions from RSM, the adsorption capacity could increase to 427.41 mg g^-1. Additionally, electrostatic interaction and hydrogen bond interaction might play a dominating role in adsorption reaction. The NC-800 could maintain a high adsorption level after four cycles. Therefore, the NC-800 with great adsorptive property and reusability could be considered as an effective adsorbent with promising potential in applications for water treatment.

Heterogeneous activation of peroxymonosulfate by cobalt-doped MIL-53(Al) for efficient tetracycline degradation in water: Coexistence of radical and non-radical reactions

Compared with the transition metal induced homogeneous catalytic system, the heterogeneous catalytic system based on transition metal-doped metal organic frameworks (MOFs) were stable for the efficient utilization of transition metal and avoiding the metal leaching. The aim of this work is to synthesize Co-doped MIL-53(Al) by one-step solvent thermal method and use it to activate peroxymonosulfate (PMS) to remove tetracycline (TC) in water. The successful synthesis of Co-MIL-53(Al) samples was demonstrated by XDR, SEM and FTIR characterizations. The 25% Co-MIL-53(Al)/PMS system showed the optimal TC removal effect compared to the PMS alone and MIL-53(Al)/PMS system. The catalytic performances of Co-MIL-53(Al)/PMS system in conditions of different pH, co-existing substances and water bodies were investigated. Quenching experiment and electron paramagnetic resonance (EPR) showed that the degradation mechanism by Co-MIL-53(Al) activation PMS was mainly attributed to sulfate radical (SO₄^•-) and singlet oxygen (¹O₂) non-radical. The degradation intermediates of TC were also identified and the possible degradation pathways were proposed. Co-MIL-53(Al) showed good activity after four cycles. These findings demonstrated that Co-MIL-53(Al) can be a promising heterogeneous catalyst for activating PMS to degrade TC.

One-step synthesis of Mn-doped MIL-53(Fe) for synergistically enhanced generation of sulfate radicals towards tetracycline degradation

Herein, Mn-doped MIL-53(Fe) were fabricated via one-pot solvothermal method and used for peroxymonosulfate (PMS) activation towards tetracycline (TC) degradation from aqueous solution. The characterizations of SEM, FTIR and XRD were utilized to reveal the morphology and structure of the materials. The results showed that Mn-MIL-53(Fe)-0.3 displayed the optimal catalytic performance, the removal efficiency of TC could reach 93.2%. Moreover, the catalytic activity of Mn-MIL-53(Fe) towards TC under different initial pH values, co-existing anions (Cl^-,CO₃^2- and SO₄^2-) and humic acid (HA) were investigated. The results of thermodynamic experiment suggested that the catalytic process was endothermic. In addition, integrated with capture experiments results and the characterization results of electron paramagnetic resonance (EPR), which revealed that SO₄^·- and HO^- were the reactive radicals involving in the reaction. More importantly, the possible activation mechanism was discussed in detail based on the X-ray photoelectron spectroscopy results. The active species were generated by the active sites of Fe(II) and Mn(II) on Mn-MIL-53(Fe) effectively activated PMS. Furthermore, the degradation intermediates and possible degradation pathway were investigated by LC-MS. Finally, the catalyst also showed good performance in actual wastewater and demonstrated good recyclability. The Mn-MIL-53(Fe)/PMS system exhibited a promising application prospect for antibiotic-containing waste water treatment.

Microbial adaptation in vertical soil profiles contaminated by an antimony smelting plant

Antimony mining has resulted in considerable pollution to the soil environment. Although studies on antinomy contamination have been conducted, its effects on vertical soil profiles and depth-resolved microbial communities remain unknown. The current study selected three vertical soil profiles (0–2 m) from the world's largest antimony mining area to characterize the depth-resolved soil microbiota and investigate the effects of mining contamination on microbial adaptation. Results demonstrated that contaminated soil profiles showed distinct depth-resolved effects when compared to uncontaminated soil profiles. As soil depth increased, the concentrations of antimony and arsenic gradually declined in the contaminated soil profiles. Acidobacteria, Chloroflexi, Proteobacteria and Thaumarchaeota were the most variable phyla from surface to deep soil. The co-occurrence networks were loosely connected in surface soil, but obviously recovered and were well-connected in deep soil. The metagenomic results indicated that microbial metabolic potential also changed with soil depth. Genes encoding C metabolism pathways were negatively correlated with antimony and arsenic concentrations. Abundances of arsenic-related genes were enriched by severe contamination, but reduced with soil depth. Overall, soil depth-resolved characteristics are often many meters deep and such effects affected the indigenous microbial communities, as well as their metabolic potential due to different contaminants along vertical depths.

Effect of extracellular polymer substances on the tetracycline removal during coagulation process

In this study, the effect of extracellular polymer substances on the tetracycline removal under hydroxyl aluminium treatment was investigated, and the molecular mechanisms of extracellular polymeric substances mediated coagulation of tetracycline were also explored. The results show that the presence of extracellular polymeric substances could significantly enhance the removal efficiency of tetracycline in hydroxyl aluminium coagulation. Findings suggest that tyrosine and tryptophan in extracellular proteins acted as binding sites to capture tetracycline. Evidences provided by the density functional theory calculations in combination with spectroscopy analysis indicated that two main mechanisms accounted for tetracycline removal in the presence of extracellular polymeric substances and polyaluminum chloride: (1) amino group in proteins and carbonyl in tetracycline were bridged by Al³⁺; (2) benzene rings in tryptophan and tyrosine were π-π stacked with tetracycline, and the amino group in complexes were further coordinated with Al³⁺.

Chemically Stressed Bacterial Communities in Anaerobic Digesters Exhibit Resilience and Ecological Flexibility

Anaerobic digestion is a technology known for its potential in terms of methane production. During the digestion process, multiple metabolites of high value are synthesized. However, recent works have demonstrated the high robustness and resilience of the involved microbiomes; these attributes make it difficult to manipulate them in such a way that a specific metabolite is predominantly produced. Therefore, an exact understanding of the manipulability of anaerobic microbiomes may open up a treasure box for bio-based industries. In the present work, the effect of nalidixic acid, γ-aminobutyric acid (GABA), and sodium phosphate on the microbiome of digested sewage sludge from a water treatment plant fed with glucose was investigated. Despite of the induced process perturbations, high stability was observed at the phylum level. However, strong variations were observed at the genus level, especially for the genera Trichococcus, Candidatus Caldatribacterium, and Phascolarctobacterium. Ecological interactions were analyzed based on the Lotka–Volterra model for Trichococcus, Rikenellaceae DMER64, Sedimentibacter, Candidatus Cloacimonas, Smithella, Cloacimonadaceae W5 and Longilinea. These genera dynamically shifted among positive, negative or no correlation, depending on the applied stressor, which indicates a surprisingly dynamic behavior. Globally, the presented work suggests a massive resilience and stability of the methanogenic communities coupled with a surprising flexibility of the particular microbial key players involved in the process.

Co-composting of sewage sludge and Phragmites australis using different insulating strategies

Insulating strategies are indispensable for laboratory-scale composting reactors, however, current insulation methods interfere with the aerobic fermentation behaviors related to composting. To address this issue, a centre-oriented real-time temperature compensation strategy was designed in this study. Five 9 L reactors (R1-R5) with different insulation strategies were used for the co-composting of dewatered sludge and Phragmites australis and compared. The process performance was assessed by monitoring the temperature, O₂ and CO₂ emissions, the physical-chemical properties of the composting materials were evaluated by measuring the organic matter (OM), carbon nitrogen ratio (C/N), pH, electrical conductivity (EC), and fluorescence excitation-emission matrix (EEM) spectra. And a 16S rDNA analysis was used to quantify the evolution of bacterial community. The main findings are as follows. Compared with R1 as a control, the insulating strategies can increase the maximum temperature and prolong the thermophilic phase of composting. Comparing R1 and R3 showed that real-time temperature compensation can better restore the real fermentation of the compost. The results showed that R5 had the best composting effect, reaching 69.8 °C, which was 25.1%, 29.7%, 19.3%, and 17.3% higher than R1, R2, R3, and R4, respectively, and remaining in the thermophilic phase for 4.24 d, which is 1.4, 1.5, 1.3, and 0.2 times longer than R1, R2, R3, and R4, respectively. Furthermore, it can significantly reduce the temperature difference between the centre and edge of the reactor, which improved the composting material allocation efficiency and composting process control accuracy, further providing a basis for the actual full-scale composting operation.

Temporal dynamics of antibiotic resistant genes and their association with the bacterial community in a water-sediment mesocosm under selection by 14 antibiotics

Antibiotics in aquatic environments at high concentrations and sub-inhibitory concentrations potentially select for the evolution of antibiotic resistant genes (ARGs), posing a potential risk to aquatic ecological safety. Our knowledge of the temporal and successive dynamics of ARGs and bacterial community under the selective pressure of antibiotics in natural water-sediment system was limited. This study used a 120-d operating hydrodynamic mesocosm to explore the temporal dynamics of ARGs in water-sediment systems, and the main selective mechanisms following the attenuation and transport of 14 commonly used antibiotics. Under the selective pressures by antibiotics, ARGs propagated transiently, and persisted after antibiotic removal; the bacterial community structures likewise changed. Mantel test and network analysis indicated that ARGs significantly correlated with the bacterial community in the water and surface sediments. Structural equation model (SEM) further revealed that the evolution of ARGs was mainly due to the direct effect of the change in bacterial community and horizontal gene transfer (HGT) via the class 1 integron-integrase gene (intI1), but antibiotics indirectly influenced ARG profiles. The migration of ARGs in deep layer sediments was not related to the bacterial community and intI1, but may be explained by antibiotic selective effects and ARG transformation.