Metagenomic approach reveals the fates and mechanisms of antibiotic resistance genes exposed to allicins during waste activated sludge fermentation: Insight of the microbial community, cellular status and gene regulation

Underrated risk of antibiotic resistance genes dissemination mediated by bioaerosols released from anaerobic biological wastewater treatment system

Antibiotic resistance has been recognized as one of the most prevalent public health problems. The bioaerosol-mediated spread of antibiotic resistance genes (ARGs) is an important but underrated pathway. Therefore, this work investigated the comprehensive resistome and pathogen-induced risk in bioaerosols released from anaerobic ammonium oxidation (anammox) process under antibiotic stress. The results showed that the bioaerosol oxidation potential increased by 2.7 times after the addition of sulfamethoxazole (SMX) into the anammox system. Based on the metagenomic analyses, abundant ARGs were enriched in bioaerosols, especially novA, olec, msbA and patA. There were many antibiotic resistance contigs carrying at least two mobile genetic elements (MGEs) in bioaerosols. Compared to the control, SMX caused the significant increase in ARGs proportion in plasmids from 11.4 % to 19.4 %. Similarly, the abundance of the type IV secretion system protein encoding genes (mtrA and mtrB) increased by 30.2 % and 31.5 %, respectively, which was conducive to gene transfer between bacteria. In addition, SMX stress induced the reactive oxygen species (ROS) production and the upregulation of genes related to membrane protein and DNA replication, further facilitating ARGs transfer. The co-occurrence networks showed that Aquamicrobium and Microbacterium probably were the hosts of most ARGs. Notably, four abundant human pathogens were detected in bioaerosols from the anammox system, which raised concerns on the health risk of resistant bioaerosol diffusion. These findings reveal the potential of horizontal gene transfer through bioaerosols and provide a guidance for systematically assessing the risk of environmental antibiotic resistance and relevant pathogens.

The synergistic antibacterial effects of allicin nanoemulsion and ε-polylysine against Escherichia coli in both planktonic and biofilm forms

The synergistic effects of allicin nanoemulsion (AcN) and ε-polylysine (ε-PL) against Escherichia coli were investigated in this study. The combination of AcN and ε-PL synergistically inhibited the planktonic growth of E. coli, with a low fractional inhibitory concentration index of 0.252. AcN/ε-PL treatment remarkably promoted the agent-cell contacts compared to AcN or ε-PL treatment, as evidenced by the larger cellular size and lower absolute zeta potential value. Analysis of membrane potential, intracellular ATP and superoxide dismutase activity revealed that the co-treatment induced membrane depolarization and intracellular metabolic disorders. Laser scanning confocal microscope, flow cytometer, and scanning electron microscope revealed that the membrane integrity and cell structure were severely degraded. Further, biofilm formation, cluster motility, and mature biofilm of E. coli were disrupted substantially by AcN/ε-PL. Finally, the application of AcN/ε-PL in raw beef preservation verified the synergy. Therefore, AcN/ε-PL can be used as a potential bacteriostatic agent in food preservation.

Signaling molecule alleviates inhibitory impacts of surfactant on methane production during sludge and food waste co-digestion: Insights of electron bifurcation and quorum sensing

Anaerobic co-digestion of food waste (FW) and waste-activated sludge (WAS) is increasingly recognized as a viable solution for managing organic wastes. However, emerging contaminants (ECs), such as surfactant like sodium dodecylbenzene sulfonate (SDBS), can severely inhibit methane production. This study explores the potential of C6-HSL, a quorum sensing (QS) signaling molecule, to mitigate inhibitory effects of SDBS during FW and WAS co-digestion. Results demonstrated that SDBS reduced methane yields from 122.2 mL/g VSS in the control to 18.5 mL/g VSS, but supplementation with C6-HSL alleviated this inhibition, increasing yields to 115.4 mL/g VSS. C6-HSL not only restored suppressed methanogen populations but also promoted bacteria-archaea mutualisms, enhancing system resilience and stability. Additionally, C6-HSL enhanced key electron bifurcation pathways critical for overcoming thermodynamic barriers in methane metabolism, increasing the relative abundance of functional genes involved in four methane metabolism modules. Moreover, C6-HSL enhanced QS system (e.g., SecY and trpE), prompting microorganisms to activate adaptive mechanisms, such as DNA replication (e.g., rfcL and rfcS), efflux pumps (e.g., mdlA and mdlB), and bacterial chemotaxis (e.g., cheB and cheD), to counter SDBS toxicity. Correspondingly, TCA cycle (e.g., fumA and fumB) was also upregulated to ensure sufficient energy and electrons for methane production and microbial adaptation.

Metagenomic analysis reveals the effects of potassium ferrate and steel slag on fate of ARGs in anaerobic sludge digestion system

Waste activated sludge (WAS) pose a potential risk for the spread of antibiotic resistance genes (ARGs). This study estimated the effect of sludge on antibiotic resistance genes (ARGs) in anaerobic sludge digestion process. Metagenomic analysis revealed anaerobic sludge with potassium ferrate (PF) and the modified PF loaded steel slag (MPF-SS) brought an increase of ARGs during digestion process. PF was found to effectively reduce most of the high-risk ARGs (i.e., acrB and mexW). Furthermore, network and correlation analysis among ARGs and genera verified that PF significantly increased the potential ARGs hosts. Mechanistic analysis revealed that PF induced oxidative stress behavior of anaerobic digestion microorganisms, and observably upregulated the relative genes about SOS response-related. These findings provide insights into the mechanism underlining PF for ARGs fate and its risk during anaerobic sludge digestion, which could offer practical guidance on the sustainable management of WAS.

Development of oriented microbial consortium-based compound enzyme strengthens food waste hydrolysis and antibiotic resistance genes removal: Deciphering of performance, metabolic pathways and microbial communities

Enzymatic hydrolysis has been considered as an eco-friendly pretreatment method for enhancing bioconversion process of food waste (FW). However, existing commercial enzymes and microbial monomer-based compound enzymes (MME) have the issues of uneven distribution of enzymatic activity and low matching degree with the components of FW, leading to low efficiency with enzymatic hydrolysis and removal of antibiotic resistance genes (ARGs). This study used FW as the substrate, under the co-culture system, produced a microbial consortium-based compound enzymes (MCE) with oriented and well-matching degree for FW hydrolysis and ARGs removal, of which the performance, metabolic pathways and microbial communities were also investigated in depth. Results showed that the best performance for ARGs was achieved by the MCE prepared by mixing 1:5 of Aspergillus oryzae and Aspergillus niger after 12 days fermentation. The highest soluble chemical oxygen demand (SCOD) concentration and ARGs removal could respectively reach 83.90 ± 1.67 g/L and 45.95% after MCE pretreatment. The analysis of metabolic pathways revealed that 1:5 MCE pretreatment strengthened the catalytic activity of carbohydrate-active enzymes, increased the abundances of genes involved in cellulose and starch degradation, polysaccharide synthesis, ATP binding cassette (ABC) transporters and global regulation, while decreased the abundances of genes involved in mating pair formation system, two-component regulatory systems and quorum sensing, thereby enhanced FW hydrolysis and restrained ARGs dissemination. Microbial community analysis further indicated that the 1:5 MCE pretreatment promoted growth, metabolism and richness of functional microbes, while inhibited the host microbes of ARGs. It is expected that this study can provide useful insights into understanding the fate of ARGs in food waste during MCE pretreatment process.

Hydraulic conditions control the abundance of antibiotic resistance genes and their potential host microorganisms in a frequently regulated river-lake system

Antibiotic resistance genes (ARGs) are a growing problem that is widespread in river-lake ecosystems, where they pose a threat to the aquatic environment's health and public safety. These systems serve as critical nodes in water management, as they facilitate the equitable allocation of water resources through long-term and frequent water diversions. However, hydrological disturbances associated with water-regulation practices can influence the dynamics of their potential host microorganisms and associated resistance genes. Consequently, identifying the key ARGs and their resistance mechanisms in heavily regulated waters is vital for safeguarding human health and that of river-lake ecosystems. In this study, we examined the impact of water-regulation factors on ARGs and their hosts within a river-lake continuum using 16S rRNA and metagenomic sequencing. We found that a significant increase in ARG abundance during regulation periods (p < 0.05), especially in the aquatic environment. Key resistance genes were macB, tetA, evgS, novA, and msbA, with increased efflux pinpointed as their principal resistance mechanism. Network analysis identified Flavobacteriales, Acinetobacter, Pseudomonas, Burkholderiaceae, and Erythrobacter as key potential host microorganisms, which showed increased abundance within the water column during regulation periods (p < 0.05). Flow velocity and water depth both drove the host microorganisms and critical ARGs. Our findings underscore the importance of monitoring and mitigating the antibiotic resistance risk during water transfers in river-lake systems, thereby supporting informed management and conservation strategies.

Parachlorometaxylenol stress caused multidrug-type antibiotic resistance genes proliferation via simultaneously reshaping microbial community and interfering metabolic traits during wastewater treatment process

Despite biological wastewater treatment processes (e.g., sequencing batch reactors (SBR)) being able to reduce the dissemination of antibiotic resistance genes (ARGs), the variation of ARGs under exogenous pollutant stress is an open question. This work investigated the impacts of para-chloro-meta-xylenol (PCMX, typical antibacterial contaminants) on ARGs spread in long-term SBR operation. Although the SBR process inherently decreased ARGs abundance, the presence of PCMX substantially amplified both the prevalence (mainly multidrug) and abundance of total ARGs (1.17-fold of the control). Further analysis demonstrated that PCMX disintegrated sludge structures as well as increased membrane permeability, facilitating the release of mobile genetic elements and subsequent horizontal transfer of ARGs. In addition, PCMX selectively enriched potential ARG hosts, notably Nitrospira and Candidatus Accumulibacter, which predominantly served as multidrug ARG hosts. Concurrently, the self-adaptive functions of ARGs hosts in the PCMX-exposed SBR system were activated via quorum sensing, two-component regulatory system, ATP-binding cassette transporters, and bacterial secretion system. The upregulation of these metabolic pathways also contributed to the dissemination of ARGs.

Untangling the interplay of dissolved organic matters variation with microbial symbiotic network in sludge anaerobic fermentation triggered by various pretreatments

Various pretreatments are commonly adopted to facilitate dissolved organic matter (DOM) release from waste activated sludge (WAS) for high-valued volatile fatty acids (VFAs) promotion, while the interplay impact of DOM dynamics transformation on microbial population and metabolic function traits is poorly understood. This work constructed "DOM-microorganisms-metabolism-VFAs" symbiotic ecologic networks to disclose how DOM dynamics variation intricately interacts with bacterial community networks, assembly processes, and microbial traits during WAS fermentation. The distribution of DOM was altered by different pretreatments, triggering the release of easily biodegradable compounds (O/C ratio > 0.3) and protein-like substance. This alteration greatly improved the substrates biodegradability (higher biological index) and upregulated microbial metabolism capacity (e.g., hydrolysis and fatty acid synthesis). In turn, microbial activity modifications augment substance metabolism level and expedite the conversion of highly reactive compounds (proteins-like DOM) to VFAs, leading to 1.6-4.2 fold rise in VFAs generation. Strong correlations were found between proteins-like DOM and topological properties of DOM-bacteria associations, suggesting that high DOM availability leads to more intricate ecological networks. A change in the way communities assemble, shifting from stronger uniform selection in pH10 and USp reactors to increased randomness in heat reactor, was linked to DOM composition alterations. The ecologic networks further revealed metabolic synergy between hydrolytic-acidogenic bacteria (e.g., Bacteroidota and Firmicutes) and biodegradable DOM (e.g., proteins and amino sugars) leading to higher VFAs generation. This study provides a deeper knowledge of the inherent connections between DOM and microbial traits for efficient VFAs biosynthesis during WAS anaerobic fermentation, offering valuable insights for effective WAS pretreatment strategies.

Mechanism of self-supporting montmorillonite composite material for bio-enhanced degradation of chlorotetracycline: Electron transfer and microbial response

The efficient degradation of antibiotics holds significant implications for mitigating environmental pollution. This study synthesized a montmorillonite chitosan composite material (MMT-CS) using the gel template method. Subsequently, a bio-enhanced reactor was constructed to facilitate the degradation of chlorotetracycline (CTC). The addition of MMT-CS composite material enables the degradation of different concentrations of CTC. MMT-CS, a conductive carrier, effectively promotes microbial adhesion and boosts the metabolic activity of functional microorganisms. Additionally, it facilitates the maintenance of microbial activity under CTC pressure by promoting the secretion of extracellular polymeric substances, increasing critical enzyme activity, and enhancing the electron transfer capacity within the system. In this MMT-CS bio-enhanced process, Paracoccus (11.4%) and Bacillus (3.9%) are utilized as essential bacteria genes. The results of metabolic pathways prediction indicated significant enhancements in membrane-transport, nucleotide-metabolism, replication-repair, and lipid-metabolism. Thus, the developed self-supporting MMT-CS bio-enhanced process ensured the stability of the system during the removal of antibiotics.

A systematic review of antibiotics and antibiotic resistance genes (ARGs) in mariculture wastewater: Antibiotics removal by microalgal-bacterial symbiotic system (MBSS), ARGs characterization on the metagenomic

Antibiotic residues in mariculture wastewater seriously affect the aquatic environment. Antibiotic Resistance Genes (ARGs) produced under antibiotic stress flow through the environment and eventually enter the human body, seriously affecting human health. Microalgal-bacterial symbiotic system (MBSS) can remove antibiotics from mariculture and reduce the flow of ARGs into the environment. This review encapsulates the present scenario of mariculture wastewater, the removal mechanism of MBSS for antibiotics, and the biomolecular information under metagenomic assay. When confronted with antibiotics, there was a notable augmentation in the extracellular polymeric substances (EPS) content within MBSS, along with a concurrent elevation in the proportion of protein (PN) constituents within the EPS, which limits the entry of antibiotics into the cellular interior. Quorum sensing stimulates the microorganisms to produce biological responses (DNA synthesis - for adhesion) through signaling. Oxidative stress promotes gene expression (coupling, conjugation) to enhance horizontal gene transfer (HGT) in MBSS. The microbial community under metagenomic detection is dominated by aerobic bacteria in the bacterial-microalgal system. Compared to aerobic bacteria, anaerobic bacteria had the significant advantage of decreasing the distribution of ARGs. Overall, MBSS exhibits remarkable efficacy in mitigating the challenges posed by antibiotics and resistant genes from mariculture wastewater.

Simultaneous volatile fatty acids promotion and antibiotic resistance genes reduction in fluoranthene-induced sludge alkaline fermentation: Regulation of microbial consortia and cell functions

The impact and mechanism of fluoranthene (Flr), a typical polycyclic aromatic hydrocarbon highly detected in sludge, on alkaline fermentation for volatile fatty acids (VFAs) recovery and antibiotic resistance genes (ARGs) transfer were studied. The results demonstrated that VFAs production increased from 2189 to 4272 mg COD/L with a simultaneous reduction of ARGs with Flr. The hydrolytic enzymes and genes related to glucose and amino acid metabolism were provoked. Also, Flr benefited for the enrichment of hydrolytic-acidifying consortia (i.e., Parabacteroides and Alkalibaculum) while reduced VFAs consumers (i.e., Rubrivivax) and ARGs potential hosts (i.e., Rubrivivax and Pseudomonas). Metagenomic analysis indicated that the genes related to cell wall synthesis, biofilm formation and substrate transporters to maintain high VFAs-producer activities were upregulated. Moreover, cell functions of efflux pump and Type IV secretion system were suppressed to inhibit ARGs proliferation. This study provided intrinsic mechanisms of Flr-induced VFAs promotion and ARGs reduction during alkaline fermentation.

Analysis of extracellular and intracellular antibiotic resistance genes in commercial organic fertilizers reveals a non-negligible risk posed by extracellular genes

Livestock manure is known to be a significant reservoir of antibiotic resistance genes (ARGs), posing a major threat to human health and animal safety. ARGs are found in both intracellular and extracellular DNA fractions. However, there has been no comprehensive analysis of these fractions in commercial organic fertilizers (COFs). The present study conducted a systematic survey of the profiles of intracellular ARGs (iARGs) and extracellular ARGs (eARGs) and their contributing factor in COFs in Northern China. Results showed that the ARG diversity in COFs (i.e., 57 iARGs and 53 eARGs) was significantly lower than that in cow dung (i.e., 68 iARGs and 69 eARGs). The total abundance of iARGs and eARGs decreased by 85.7% and 75.8%, respectively, after compost processing, and there were no significant differences between iARGs and eARGs in COFs (P > 0.05). Notably, the relative abundance of Campilobacterota decreased significantly (99.1-100.0%) after composting, while that of Actinobacteriota and Firmicutes increased by 21.1% and 29.7%, respectively, becoming the dominant bacteria in COFs. Co-occurrence analysis showed that microorganisms and mobile genetic elements (MGEs) were more closely related to eARGs than iARGs in COFs. And structural equation models (SEMs) further verified that microbial community was an essential factor regulating iARGs and eARGs variation in COFs, with a direct influence (λ = 0.74 and 0.62, P < 0.01), following by similar effects of MGEs (λ = 0.59 and 0.43, P < 0.05). These findings indicate the need to separate eARGs and iARGs when assessing the risk of dissemination and during removal management in the environment.

Carbamazepine facilitated horizontal transfer of antibiotic resistance genes by enhancing microbial communication and aggregation

Antimicrobial resistance is a global health security issue of widespread concern. Recent studies have unveiled the potential contribution of non-antibiotics to the emergence of antimicrobial resistance. This study investigated the effect of carbamazepine, a non-antibiotic pharmaceutical, on the fate of antibiotic resistance genes (ARGs) during anaerobic digestion. The results, as revealed by both metagenomic sequencing and absolute quantification, demonstrated that carbamazepine induced the enrichment of ARGs and increased the abundance of ARGs hosts by 1.2-2.1 times. Carbamazepine facilitated microbial aggregation and intercellular communication by upregulating functional genes associated with two-component systems, quorum sensing and type IV secretion systems, thereby increasing the frequency of ARGs conjugation. Furthermore, carbamazepine induced the acquisition of ARGs by pathogens and elevated the overall pathogenic abundance. This study revealed the mechanisms of microbial self-regulation and ARGs transmission under carbamazepine stress, highlighting the potential health risks posed by non-antibiotic pharmaceuticals during the safe disposal of sludge.

Non-Invasive Detection of Biomolecular Abundance from Fermentative Microorganisms via Raman Spectra Combined with Target Extraction and Multimodel Fitting

Biomolecular abundance detection of fermentation microorganisms is significant for the accurate regulation of fermentation, which is conducive to reducing fermentation costs and improving the yield of target products. However, the development of an accurate analytical method for the detection of biomolecular abundance still faces important challenges. Herein, we present a non-invasive biomolecular abundance detection method based on Raman spectra combined with target extraction and multimodel fitting. The high gain of the eXtreme Gradient Boosting (XGBoost) algorithm was used to extract the characteristic Raman peaks of metabolically active proteins and nucleic acids within E. coli and yeast. The test accuracy for different culture times and cell cycles of E. coli was 94.4% and 98.2%, respectively. Simultaneously, the Gaussian multi-peak fitting algorithm was exploited to calculate peak intensity from mixed peaks, which can improve the accuracy of biomolecular abundance calculations. The accuracy of Gaussian multi-peak fitting was above 0.9, and the results of the analysis of variance (ANOVA) measurements for the lag phase, log phase, and stationary phase of E. coli growth demonstrated highly significant levels, indicating that the intracellular biomolecular abundance detection was consistent with the classical cell growth law. These results suggest the great potential of the combination of microbial intracellular abundance, Raman spectra analysis, target extraction, and multimodel fitting as a method for microbial fermentation engineering.

Disinfectant sodium dichloroisocyanurate synergistically strengthened sludge acidogenic process and pathogens inactivation: Targeted upregulation of functional microorganisms and metabolic traits via self-adaptation

Harmless and resourceful treatment of waste activated sludge (WAS) have been the crucial goal for building environmental-friendly and sustainable society, while the synergistic realization approach is currently limited. This work skillfully utilized the disinfectant sodium dichloroisocyanurate (NaDCC) to simultaneously achieve the pathogenic potential inactivation (decreased by 60.1 %) and efficient volatile fatty acids (VFAs) recovery (increased by 221.9 %) during WAS anaerobic fermentation in rather cost-effective way (Chemicals costs:0.4 USD/kg VFAs versus products benefits: 2.68 USD/kg chemical). Mechanistic analysis revealed that the C=O and NCl bonds in NaDCC could spontaneously absorb sludge (binding energy -4.9 kJ/mol), and then caused the sludge disintegration and organic substrates release for microbial utilization due to the oxidizability of NaDCC. The disruption of sludge structure along with the increase of bioavailable fermentation substrates contributed to the selectively regulation of microbial community via enriching VFAs-forming microorganisms (e.g., Pseudomonas and Streptomyces) and reducing VFAs-consuming microorganisms, especially aceticlastic methanogens (e.g., Methanothrix and Methanospirillum). Correspondingly, the metabolic functions of membrane transport, substrate metabolism, pyruvate metabolism, and fatty acid biosynthesis locating in the central pathway of VFAs production were all upregulated while the methanogenic step was inhibited (especially acetate-type methanogenic pathway). Further exploration unveiled that for those enriched functional anaerobes were capable to activate the self-adaptive systems of DNA replication, SOS response, oxidative stress defense, efflux pump, and energy metabolism to counteract the unfavorable NaDCC stress and maintain high microbial activities for efficient VFAs yields. This study would provide a novel strategy for synergistic realization of harmless and resourceful treatment of WAS, and identify the interrelations between microbial metabolic regulations and adaptive responses.

Insights into antibiotic resistance gene abundances and regulatory mechanisms induced by ionic liquids during composting

This study investigated the regulatory mechanism of the evolution of antibiotic resistance genes (ARGs) during the composting process with sawdust and cow manure as raw materials using ionic liquids (ILs) pretreatment. The results showed that genes of MLS, chloramphenicol, tetracycline, beta - lactam as composting gradually decreased. From day0 to day3, MLS in control group (CK) and experimental group (T) decreased by 25.62% and 26.66%, respectively. Tetracycline decreased by 7.21% in CK and by 7.86% in T. Chloramphenicol decreased by 2.85% in CK and 3.34% in T. Beta-lactam decreased by 1.95% in Ck and by 3.69% in T. Mechanism studies have shown that ILs can effectively decompose extracellular polymeric substances (EPS) and enhance lactose dehydrogenase (LDH) release, resulting in ARGs release and elimination. Meanwhile, ILs pretreatment can inhibit growth of some ARGs hosts, especially Firmicutes, resulting in decreased ARGs. Moreover, metabolic pathways and related genes take part in ARGs transmission were down regulated, leading to decreased ARGs.

Artificial Sweetener Enhances the Spread of Antibiotic Resistance Genes During Anaerobic Digestion

Artificial sweeteners have been frequently detected in the feedstocks of anaerobic digestion. As these sweeteners can lead to the shift of anaerobic microbiota in the gut similar to that caused by antibiotics, we hypothesize that they may have an antibiotic-like impact on antibiotic resistance genes (ARGs) in anaerobic digestion. However, current understanding on this topic is scarce. This investigation aimed to examine the potential impact of acesulfame, a typical artificial sweetener, on ARGs in anaerobic digestion by using metagenomics sequencing and qPCR. It was found that acesulfame increased the number of detected ARG classes and the abundance of ARGs during anaerobic digestion. The abundance of typical mobile genetic elements (MGEs) and the number of potential hosts of ARGs also increased under acesulfame exposure, suggesting the enhanced potential of horizontal gene transfer of ARGs, which was further confirmed by the correlation analysis between absolute abundances of the targeted ARGs and MGEs. The increased horizontal dissemination of ARGs may be associated with the SOS response induced by the increased ROS production, and the increased cellular membrane permeability. These findings indicate that artificial sweeteners may accelerate ARG spread through digestate disposal, thus corresponding strategies should be considered to prevent potential risks in practice.

Ultrasonic-assisted hypochlorite activation accelerated volatile fatty acids production during sewage sludge fermentation: Critical insights on solubilization/hydrolysis stages and microbial traits

The effective disruption of extracellular polymeric substances using appropriate pretreatment is critical to achieving resource recovery from sewage sludge (SS) by anaerobic fermentation. This work proposed an ultrasonic-assisted hypochlorite activation strategy for enhanced production of volatile fatty acids (VFAs) during SS fermentation. The results demonstrated that after individual ultrasonic and hypochlorite pretreatment, the maximum VFAs yield improved by 8 and 107% with that in control, respectively, while a combination of both techniques led to an improvement of 119%, indicating their synergistic effects on SS fermentation. This method enhanced the solubilization and hydrolysis efficiencies and contributed to the increased biodegradable substrates, which would be beneficial in enhancing microbial activity for VFAs production. The functional anaerobes, metabolic pathways, and gene expressions involved in VFAs biosynthesis were effectively improved. This work would bring a novel insight into the disposal of municipal solid waste for resource recovery.

Insights into the Occurrence, Fate, Impacts, and Control of Food Additives in Food Waste Anaerobic Digestion: A Review

The recovery of biomass energy from food waste through anaerobic digestion as an alternative to fossil energy is of great significance for the development of environmental sustainability and the circular economy. However, a substantial number of food additives (e.g., salt, allicin, capsaicin, allyl isothiocyanate, monosodium glutamate, and nonnutritive sweeteners) are present in food waste, and their interactions with anaerobic digestion might affect energy recovery, which is typically overlooked. This work describes the current understanding of the occurrence and fate of food additives in anaerobic digestion of food waste. The biotransformation pathways of food additives during anaerobic digestion are well discussed. In addition, important discoveries in the effects and underlying mechanisms of food additives on anaerobic digestion are reviewed. The results showed that most of the food additives had negative effects on anaerobic digestion by deactivating functional enzymes, thus inhibiting methane production. By reviewing the response of microbial communities to food additives, we can further improve our understanding of the impact of food additives on anaerobic digestion. Intriguingly, the possibility that food additives may promote the spread of antibiotic resistance genes, and thus threaten ecology and public health, is highlighted. Furthermore, strategies for mitigating the effects of food additives on anaerobic digestion are outlined in terms of optimal operation conditions, effectiveness, and reaction mechanisms, among which chemical methods have been widely used and are effective in promoting the degradation of food additives and increasing methane production. This review aims to advance our understanding of the fate and impact of food additives in anaerobic digestion and to spark novel research ideas for optimizing anaerobic digestion of organic solid waste.

Distinct effects of typical sludge pretreatment approaches on the antibiotic resistance genes variations, associated bacterial community dynamics and metabolic activities during anaerobic fermentation process

Anaerobic fermentation is effective for waste activated sludge (WAS) disposal to realize resource generation and pollutants reduction, and various pretreatments were commonly applied to improve the performance. This work mainly investigated the effects of typical WAS pretreatment approaches on the antibiotic resistance genes (ARGs, as emerging contaminants) removal during anaerobic fermentation processes and unveiled the underlying mechanisms. The results indicated that all the pretreatment strategies exhibited evident effects on the overall ARGs removal with the order of Fe²⁺ activated persulfate (PS/Fe²⁺) > pH 10 > Ultrasonication > Heat, and showed selective removal tendency for the specific ARGs (namely easily removed (aadA1 and sul1) and persistent ARGs). Mechanistic analysis demonstrated that the pretreatments disrupted the extracellular polymeric substances (EPS) and rose the cell membrane permeability (particularly for PS/Fe²⁺ and Heat). Then the increased ARGs release benefitted the subsequent reduction of mobile genetic elements (MGEs) and extracellular ARGs (especially for PS/Fe²⁺ and pH10), resulting the ARGs attenuation. Pretreatments significantly shifted the microbial community structure and the abundances of potential ARGs hosts (i.e., Sulfuritalea, and Denitratisoma). Also, the different pretreatments exhibited distinct effects on the microbial metabolic traits related with ARGs proliferation (i.e., ABC transporters, two-component system and bacterial secretion systems), which also contributed to the ARGs attenuations during WAS fermentation. The partial least-squares path modeling (PLS-PM) analysis indicated that the bacterial community (total effects = 0.968) was key factor determining ARGs fates.

Para-chloro-meta-xylenol reshaped the fates of antibiotic resistance genes during sludge fermentation: Insights of cell membrane permeability, bacterial structure and biological pathways

The occurrence of para-chloro-meta-xylenol (PCMX, as largely consumed antimicrobial chemicals) in waste activated sludge (WAS) would pose environmental risks for WAS utilization. This study revealed that PCMX principally prompted the abundances and diversity of antibiotic resistance genes (ARGs), particularly for the multidrug- genes (i.e., acrB and mexW), and reshaped the resistance mechanism categories during WAS fermentation process. The genotype and phenotype results indicated that PCMX upregulated abundances of transposase and increased cell permeability via disrupting WAS structure, which further facilitated the horizontal transfer of ARGs. The network and correlation analysis among ARGs, mobile genetic elements (MGEs) and genera (i.e., Sphingopyxis and Pseudoxanthomonas) verified that PCMX enriched the potential ARGs hosts associated with multidrug resistance mechanism. Also, PCMX upregulated the genes involved in ARGs-associated metabolic pathways, such as two-component (i.e., phoP and vcaM) and quorum sensing systems (i.e., lasR and cciR), which determined the ARGs proliferation via multidrug efflux pump and outer membrane proteins, and facilitated the recognition between ARGs hosts. Variance partitioning analysis (VPA) implied that the shift of microbial community contributed predominantly to the dissemination of ARGs. These findings unveiled the environmental behaviors and risks of exogenous pollutants in WAS with insightful understanding, which could guide the WAS utilization for resource recovery.

Potassium ferrate pretreatment promotes short chain fatty acids yield and antibiotics reduction in acidogenic fermentation of sewage sludge

During the acidogenic fermentation converting waste activated sludge (WAS) into short-chain fatty acids (SCFA), hydrolysis of complex organic polymers is a limiting step and the transformation of harmful substances (such as antibiotics) during acidogenic fermentation is unknown. In this study, potassium ferrate (K₂FeO₄) oxidation was used as a pretreatment strategy for WAS acidogenic fermentation to increase the hydrolysis of sludge and destruct the harmful antibiotics. Pretreatment with K₂FeO₄ can effectively increase the SCFA production during acidogenic fermentation and change the distribution of SCFA components. With the dosage of 0.2 g/g TS, the maximum SCFA yield was 4823 mg COD/L, which is 28.3 times that of the control group; acetic acid accounts for more than 90% of the total SCFA. The higher dosage (0.5 g/g TS) can further increase the proportion of acetic acid, but inhibit the overall performance of SCFA production. Apart from the promotion of hydrolysis and acidogenesis, K₂FeO₄ pretreatment can also simultaneously oxidizes and degrades part of the antibiotics in the sludge. When the dosage is 0.5 g/g TS, the degradation efficacy of antibiotics is the most significant, and the contents of ofloxacin, azithromycin, and tetracycline in the sludge are reduced by 69%, 42%, and 50%, respectively. In addition, K₂FeO₄ pretreatment can also promote the release of antibiotics from sludge flocs, which is conducive to the simultaneous degradation of antibiotics in the subsequent biological treatment process.

Deciphering the role of extracellular polymeric substances in the regulation of microbial extracellular electron transfer under low concentrations of tetracycline exposure: Insights from transcriptomic analysis

Low concentrations of antibiotics can regulate the formation of electroactive biofilms, however, the underlying mechanisms, especially the composition and spatial distribution of extracellular polymeric substances (EPS) and their effects on extracellular electron transfer (EET) process, have not been fully deciphered. Here, the response of EPS of Geobacter sulfurreducens biofilm to low concentrations of tetracycline (μg L^-1 to mg L^-1) was explored, and the impact of such EPS variations on EET efficiency was further elucidated by transcriptomic analysis. Results showed that 0.05 mg L^-1 of tetracycline achieved both beneficial quantitative and spatial regulation of redox-active proteins and non-conducting exopolysaccharides in EPS, while higher concentrations induced negative effects. Moreover, 1 mg L^-1 of tetracycline upregulated multiple exopolysaccharide biosynthesis-related genes, indicating a stress response for cell-protection, while 0.05 mg L^-1 of tetracycline upregulated most direct EET-related gene expressions, resulting in the promoted EET efficiency. Furthermore, 0.05 mg L^-1 of tetracycline selectively enriched Geobacter (45.55% vs 19.55% in control, respectively) from mixed inoculum. This research provides a new insight of how antibiotics at low concentrations regulated EET process through modulation of EPS.

Detection and various environmental factors of antibiotic resistance gene horizontal transfer

Bacterial antibiotic resistance in water environments is becoming increasingly severe, and new antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) have also attracted the attention of researchers. The horizontal transfer of ARGs in water environments is considered one of the main sources of bacterial resistance in the natural environment. Horizontal gene transfer (HGT) mainly includes conjugation, natural transformation, and transduction, and conjugation has been investigated most. Several studies have shown that there are a large number of environmental factors that might affect the horizontal transfer of ARGs in water environments, such as nanomaterials, various oxidants, and light; however, there is still a lack of systematic and comprehensive reviews on the detection and the effects of the influence factors of on ARG horizontal transfer. Therefore, this study introduced three HGT modes, analysed the advantages and disadvantages of current methods for monitoring HGT, and then summarized the influence and mechanism of various factors on ARG horizontal transfer, and the possible reasons for the different effects caused by similar factors were mainly critically discussed. Finally, existing research deficiencies and future research directions of ARG horizontal transfer in water environments were discussed.

Deciphering changes in the abundance of intracellular and extracellular antibiotic resistance genes and mobile genetic elements under anaerobic fermentation: Driven by bacterial community

Antibiotic resistance genes (ARGs) are considered to be a new environmental pollutant and the removal of ARGs from swine manure by anaerobic fermentation was a crucial topic. This research discusses effects of initial pH values (3, 5, 7, 11) on intracellular and extracellular ARGs (iARGs and eARGs) as well as mobile genetic elements (MGEs) during anaerobic fermentation of swine manure had been examined. The initial pH during fermentation was found to be acidic (pH 3 and 5) in results, which was conducive to the removal of six eARGs and seven iARGs. Similarly, intracellular and extracellular MGEs were effectively eliminated with an initial pH of 3 and 5. The abundance of MGEs and four ARGs were enriched with an initial pH of 7 and 11. Acidic conditions can greatly deduce the diversity as well as abundance of the microbial community, ensuing removal of MEGs and ARGs. These findings are critical for risk assessment and management of ARGs.

Chloroxylenol at environmental concentrations can promote conjugative transfer of antibiotic resistance genes by multiple mechanisms

The intergeneric conjugative transfer of antibiotic resistance genes (ARGs) is recognized as an important way to the dissemination of antibiotic resistance. However, it is unknown whether the extensive use of chloroxylenol (para-chloro-meta-xylenol, PCMX) in many pharmaceutical personal care products will lead to the spread of ARGs. In this study, the abilities and mechanisms of PCMX to accelerate the intergeneric conjugative transfer were investigated. Results showed that exposure of bacteria to environmental concentrations of PCMX (0.20-1.00 mg/L) can significantly stimulate the increase of conjugative transfer by 8.45-9.51 fold. The phenotypic experiments and genome-wide RNA sequencing revealed that 0.02-5.00 mg/L PCMX exposure could increase the content of alkaline phosphatase and malondialdehyde, which are characteristic products of cell wall and membrane damage. In addition, PCMX could lead to excessive production of reactive oxygen species (ROS) by 1.26-2.00 times, the superoxide dismutase and catalase produced by bacteria in response to oxidative stress were not enough to neutralize the damage of ROS, thus promoting the conjugative transfer. Gene Ontology enrichment analysis indicated that cell membrane permeability, pili, some chemical compounds transport and energy metabolism affected conjugative transfer. This study deepened the understanding of PCMX in promoting propagation of ARGs, and provided new perspectives for use and treatment of personal care products.

Metagenomic assembly deciphered the type-dependent effects of surfactants on the fates of antibiotics resistance genes during sludge fermentation and the underlying mechanisms

Waste activated sludge (WAS) is an important reservoir of antibiotic resistance genes (ARGs). However, the interactive effects of co-existed substances in WAS on ARGs fates have yet to be disclosed. This study demonstrated the type-dependent effects of surfactants (potentially effective chemicals for WAS disposal) on the reduction of ARGs during WAS fermentation, which followed the order of linear alkylbenzene sulphonates (LAS) > alkyl polyglucoside (APG) > hexadecyl trimethyl ammonium bromide (HTAB). Interestingly, the ratio of ARGs affiliated to efflux pump showed an upward trend in the surfactant-treated reactor. Mechanistic investigations revealed that the extracellular polymeric substances (EPS) destruction induced by surfactants increased the permeability of bacterial cells and caused the ARGs being released and susceptible for subsequent elimination. Besides, the surfactants significantly altered the microbial community, resulting in the ARGs reduction via changing the potential hosts. Also, the metabolic pathways participated in the dissemination of ARGs were remarkably down-regulated, thereby resulting in the reduction of ARGs abundances. This work broadened the understanding of ARGs fates during WAS fermentation and provided insights on the interactive functions of exogenous chemicals in multiple matrics.

Effects of persulfate treatment on the fates of antibiotic resistance genes in waste activated sludge fermentation process and the underlying mechanism

The occurrence of antibiotic resistance genes (ARGs) in waste activated sludge (WAS) fermentation was investigated with persulfate (PS)-based treatment. ARGs affiliated with multidrug (mexP), macrolide (bla_OXA-129), tetracycline (tetB), sulfonamide (sul1), and vancomycin (vanRG) types were significantly decreased by PS/Fe treatment. Mechanistic investigations revealed that PS/Fe possessed oxidating potential and exhibited devastating effects on WAS fermentation. First, PS/Fe promoted cell structure damage, which facilitated ARGs release from potential hosts. A co-occurrence network analysis indicated that Fe/PS suppressed the proliferation of potential host bacteria. In addition, the PS/Fe treatment induced the decreased abundance of certain functional genes involved in pathways associated with ARGs dissemination. Finally, variation partitioning analysis demonstrated that the microbial community structure exhibited more vital effects on ARGs fates than physicochemical factors (i.e., pH and ORP) and gene expression (i.e., two-component system). This work provided a deeper understanding of the critical factors used to determine ARGs fates during WAS fermentation.