QKSAN: A Quantum Kernel Self-Attention Network.

The Self-Attention Mechanism (SAM) excels at distilling important information from the interior of data to improve the computational efficiency of models. Nevertheless, many Quantum Machine Learning (QML) models lack the ability to distinguish the intrinsic connections of information like SAM, which limits their effectiveness on massive high-dimensional quantum data. To tackle the above issue, a Quantum Kernel Self-Attention Mechanism (QKSAM) is introduced to combine the data representation merit of Quantum Kernel Methods (QKM) with the efficient information extraction capability of SAM. Further, a Quantum Kernel Self-Attention Network (QKSAN) framework is proposed based on QKSAM, which ingeniously incorporates the Deferred Measurement Principle (DMP) and conditional measurement techniques to release half of quantum resources by mid-circuit measurement, thereby bolstering both feasibility and adaptability. Simultaneously, the Quantum Kernel Self-Attention Score (QKSAS) with an exponentially large characterization space is spawned to accommodate more information and determine the measurement conditions. Eventually, four QKSAN sub-models are deployed on PennyLane and IBM Qiskit platforms to perform binary classification on MNIST and Fashion MNIST, where the QKSAS tests and correlation assessments between noise immunity and learning ability are executed on the best-performing sub-model. The paramount experimental finding is that the QKSAN subclasses possess the potential learning advantage of acquiring impressive accuracies exceeding 98.05% with far fewer parameters than classical machine learning models. Predictably, QKSAN lays the foundation for future quantum computers to perform machine learning on massive amounts of data while driving advances in areas such as quantum computer vision.

Occurrence and risks of PPCPs of a typical mountainous region: Implications for sustainable urban water systems.

Urban wastewater treatment plants (WWTPs) and drinking water treatment plants (DWTPs) play vital roles in the urban water cycle, ensuring access to safe drinking water and maintaining aquatic ecosystems. This study comprehensively assessed the occurrence and risks of pharmaceuticals and personal care products (PPCPs) in urban WWTPs and DWTPs. Our findings revealed widespread PPCPs presence, with concentrations ranging from <1 ng/L to several thousand ng/L. Significant regional disparities in occurrence and composition were observed linked to population types and economic structures. Furthermore, strong correlations were observed between DWTPs and WWTPs indicating consistent transport and transformation patterns of PPCPs within the urban water cycle. Approximately two-thirds of PPCPs were degraded post-WWTP treatment, with about one-tenth persisting in drinking water following surface water dilution and purification processes. Thus, we suggested that controlling the total concentration of the five priority PPCPs in the effluent from the WWTP to <1100 ng/L have potential to reduce the environmental and health risk of PPCPs. Additionally, this research identified influential water quality parameters, such as pH, dissolved oxygen, and temperature, through redundancy analysis. This research underscores the importance of establishing emission standards to mitigate PPCP-related risks and supports sustainable urban water system advancement.

Decrypting the viral community in aerobic activated sludge reactors treating antibiotic production wastewater.

Viruses are the most abundant yet understudied members that may influence microbial metabolism in activated sludge treating antibiotic production wastewater. This study comprehensively investigated virome community characteristics under the selection pressure of nine types and different concentrations of antibiotics using a metagenomics approach. Of the 15,514 total viral operational taxonomic units (tOTUs) recovered, only 37.5 % were annotated. Antibiotics altered the original viral community structure in activated sludge. The proportion of some pathogenic viral families, including Herpesviridae_like, increased significantly in reactors treating erythromycin production wastewater. In total, 16.5 % of the tOTUs were associated with two or more hosts. tOTUs rarely carried antibiotic resistance genes (ARGs), and the ARG types in the tOTUs did not match the ARGs carried by the bacterial hosts. This suggests that transduction contributes little to the horizontal ARG transfer. Auxiliary metabolic genes (AMGs) were prevalent in tOTUs, and those involved in folate biosynthesis were particularly abundant, indicating their potential to mitigate antibiotic-induced host damage. This study provides comprehensive insights into the virome community in activated sludge treating antibiotic production wastewater and sheds light on the potential role of viral AMGs in mitigating antibiotic-induced stress.

Bacterial assembly and succession patterns in conventional and advanced drinking water systems: From source to tap.

Bacteria are pivotal to drinking water treatment and public health. However, the mechanisms of bacterial assembly and their impact on species coexistence remain largely unexplored. This study explored the assembly and succession of bacterial communities in two full-scale drinking water systems over one year. We observed a decline in bacterial biomass, diversity, and co-occurrence network complexity along the treatment processes, except for the biological activated carbon filtration stage. The conventional plant showed higher bacterial diversity than the advanced plant, despite similar bacterial concentrations and better removal efficiency. The biological activated carbon filter exhibited high phylogenetic diversity, indicating enhanced bacterial metabolic functionality for organic matter removal. Chlorination inactivated most bacteria but favored some chlorination-resistant and potentially pathogenic species, such as Burkholderia, Bosea, Brevundimonas, and Acinetobacter. Moreover, the spatiotemporal dynamics of the bacterial continuum were primarily driven by stochastic processes, explaining more than 78% of the relative importance. The advanced plant's bacterial community was less influenced by dispersal limitation and more by homogeneous selection. The stochastic process regulated bacterial diversity and influenced the complexity of the species co-occurrence network. These findings deepen our understanding of microbial ecological mechanisms and species interactions, offering insights for enhancing hygienic safety in drinking water systems.

Metagenomic surveillance of antibiotic resistome in influent and effluent of wastewater treatment plants located on the Qinghai-Tibetan Plateau.

As hotspots for the dissemination of antibiotic resistance genes (ARGs), wastewater treatment plants (WWTPs) have attracted global attention. However, there lacks a sufficient metagenomic surveillance of antibiotic resistome in the WWTPs located on the Qinghai-Tibet Plateau. Here, metagenomic approaches were used to comprehensively investigate the occurrence, mobility potential, and bacterial hosts of ARGs in influent and effluent of 18 WWTPs located on the Qinghai-Tibet Plateau. The total ARG relative abundances and diversity were significantly decreased from influent to effluent across the WWTPs. Multidrug, bacitracin, sulfonamide, aminoglycoside, and beta-lactam ARGs generally consisted of the main ARG types in effluent samples, which were distinct from influent samples. A group of 72 core ARGs accounting for 61.8-95.8 % of the total ARG abundances were shared by all samples. Clinically relevant ARGs mainly conferring resistance to beta-lactams were detected in influent (277 ARGs) and effluent (178 ARGs). Metagenomic assembly revealed that the genetic location of an ARG on a plasmid or a chromosome was related to its corresponding ARG type, demonstrating the distinction in the mobility potential of different ARG types. The abundance of plasmid-mediated ARGs accounted for a much higher proportion than that of chromosome-mediated ARGs in both influent and effluent. Moreover, the ARGs co-occurring with diverse mobile genetic elements in the effluent exhibited a comparable mobility potential with the influent. Furthermore, 137 metagenome-assembled genomes (MAGs) assigned to 13 bacterial phyla were identified as the ARG hosts, which could be effectively treated in most WWTPs. Notably, 46 MAGs were found to carry multiple ARG types and the potential pathogens frequently exhibited multi-antibiotic resistance. Some ARG types tended to be carried by certain bacteria, showing a specific host-resistance association pattern. This study highlights the necessity for metagenomic surveillance and will facilitate risk assessment and control of antibiotic resistome in WWTPs located on the vulnerable area.

Ecological risks induced by consumption and emission of Pharmaceutical and personal care products in Qinghai-Tibet Plateau: Insights from the polar regions.

As the third pole of the world and Asia's water tower, the Tibetan Plateau experiences daily release of pharmaceutical and personal care products (PPCPs) due to increasing human activity. This study aimed to explore the potential relationship between the concentration and composition of PPCPs and human activity, by assessing the occurrence of PPCPs in areas of typical human activity on the Qinghai-Tibet Plateau and evaluating their ecological risk. The results indicate that 28 out of 30 substances were detected in concentrations ranging from less than 1 ng/L to hundreds of ng/L, with the average concentration of most PPCPs in the Tibet Autonomous Region being higher than that in Qinghai Province. Among the detected substances, CAF, NOR, CTC, CIP, TCN, OTC, AZN, and DOX accounted for over 90% of the total concentration. The emission sources of PPCPs were identified by analyzing the correlation coefficients of soil and water samples, with excess PPCPs used by livestock breeding discharged directly into soil and then into surface water through leaching or runoff. By comparing the concentration and composition of PPCPs with those in other regions, this study found that CIP, ENR, LOM, NOR, CTC, DOX, OTC, and TCN were the most commonly used PPCPs in the Qinghai-Tibet Plateau. To assess the ecological risk of PPCPs, organisms at different trophic levels, including algae, crustaceans, fish, and insects, were selected. The prediction of the no effect concentration of each PPCP showed that NOR, CTC, TCN, CAF, and CBZ may have deleterious effects on water biota. This study can assist in identifying the emission characteristics of PPCPs from different types and intensities of human activities, as well as their occurrence and fate during the natural decay of aquatic systems.

New insights into lincomycin biodegradation by Conexibacter sp. LD01: Genomics characterization, biodegradation kinetics and pathways.

The aerobic, lincomycin-degrading bacterial strain Conexibacter sp. LD01, belonging to the phylum Actinobacteria, was isolated from activated sludge. Both second- and third-generation sequencing technologies were applied to uncover the genomic characterization and high-quality genome with 99.2% completeness and 2.2% contamination was obtained. The biodegradation kinetics of lincomycin fit well with the modified Gompertz model (R2 > 0.97). Conexibacter sp. LD01 could subsist with lincomycin as the sole source of carbon, nitrogen, and energy. When 500 mg/L of glucose was added as a co-substrate, the biodegradation rate improved significantly, whereas the addition of 500 mg/L sodium pyruvate had a slight inhibitory effect. Ammonia nitrogen was the best nitrogen source for Conexibacter sp. LD01 when growing and degrading lincomycin. In total, 17 metabolic products consisting of nine novel products were detected, and five biodegradation pathways, including N-demethylation, breakage of the amido bond, sulfoxidation, and oxidation of the pyrrolidine ring and propylamino chain, were proposed. This study significantly expands our understanding of the functional microorganisms and mechanism involved in lincomycin biodegradation at the phylum level.

Genome-centric metagenomics provides new insights into metabolic pathways of polyhydroxyalkanoates biosynthesis and functional microorganisms subsisting on municipal organic wastes.

The microbial community of a sequencing batch reactor operated under feast and famine conditions for production of polyhydroxyalkanoates (PHAs) was characterized through high-throughput sequencing and metagenomic analysis. The fermented food waste and chemically-enhanced primary sludge was fed in this bioreactor. After acclimation, the PHA yield achieved as high as 0.60-0.69 g CODPHA/g CODS. The complete changes of microbial community structure were found during shifts of feedstock. A synthesis of SCL/MCL-PHAs pathway was established for PHA-producing bioreactor in this mixed-culture system. The structure-performance relationship of PHA-producing microbial community and feedstock composition was investigated. The results showed that microbial community tends to be decentralized and prefer team work for PHA synthesis to consume the multiple substrates and digest inevitable non-VFA contents in fermented liquor. This study also discovered unreported potential PHA producers (e.g., genera Tabrizicola, Nannocystis, Ga0077539, Ga0077559, JOSHI-001, SNC69-320 and UBA2334) subsisting on municipal organic wastes and expands the current knowledge about mixed-culture system that the PHA synthesis pathway is widely existed in activated sludge.

New insights into thiamphenicol biodegradation mechanism by Sphingomonas sp. CL5.1 deciphered through metabolic and proteomic analysis.

Biological treatment is an efficient and economical process to remove thiamphenicol (TAP) residues from the environment. The discovery of TAP-degrading bacteria and the decryption of its biodegradation mechanism will be beneficial to enhance the biological removal of TAP. In this study, Sphingomonas sp. CL5.1 was found to be capable of catabolizing TAP as the sole carbon, nitrogen, and energy source. This strain could degrade 93.9% of 25 mg/L TAP in 36 h, and remove about 11.9% of the total organic carbon of TAP. A novel metabolism pathway of TAP was constructed, and the enzymes involved in TAP metabolism in strain CL5.1 were predicted via proteomic and metabolic analysis. TAP was proposed to be transformed to O-TAP via oxidation of C3-OH and DD-TAP via dehydration of C3-OH and dehydrogenation of C1-OH. A novel glucose-methanol-choline (GMC) family oxidoreductase CapO was predicted to be involved in the oxidation of C3-OH. O-TAP was supposed to be further cleaved into DCA, glycine, and PMB. Glycine might be a pivotal direct nitrogen source for strain CL5.1, and it could be involved in nitrogen metabolism through the glycine cleavage system or directly participate in the biosynthetic processes.

Estuarine salinity gradient governs sedimentary bacterial community but not antibiotic resistance gene profile.

Antibiotic resistance gene (ARG) pollution in estuarine environment has drawn great attention, and it is not clear if the physical and chemical parameters such as salinity, total organic carbon, total nitrogen, total phosphorus and antibiotics affects the distribution of ARGs. Herein, we deciphered the ARG profiles and microbial community compositions in sediments from Jiulong River Estuary (JRE) and Min River Estuary (MRE) of China using high-throughput sequencing-based metagenomics analysis. Furthermore, we explored the influence of salinity on bacterial community and ARG profiles. The results showed that Proteobacteria, Chloroflexi, and Acidobacteria were the dominant phyla in these two estuaries. The abundance of ARGs ranged from 1.05 × 10-1 to 2.93 × 10-1 copy of ARG per copy of 16S rRNA gene in all the sediment samples and the profiles of ARGs presented similar patterns in two estuaries. Multidrug resistance genes were the dominant ARG types in both estuaries, with an overall abundance of 2.39 × 10-2-1.07 × 10-1 copy of ARG per copy of 16S rRNA gene, followed by genes conferring resistance to bacitracin and macrolide-lincosamide-streptogramin. Salinity was an important influencing factor on the bacterial community but not on the ARG profiles. Instead, stochastic processes exerted the main influence on the distribution of ARGs. The comparison of ARG profiles among estuary sediments, marine sediments, and samples from anthropogenic pollution environments revealed remarkable similarity of ARG profiles between samples from estuary sediments and those from municipal wastewater treatment plants. These results suggested that the complex emission of anthropogenic pollution could cause the stochastic ecological pattern of ARGs.

Genome-centric metagenomics provides new insights into the microbial community and metabolic potential of landfill leachate microbiota.

Landfills are important sources of microorganisms associated with anaerobic digestion. However, the knowledge on microbiota along with their functional potential in this special habitat are still lacking. In this study, we recovered 1168 non-redundant metagenome-assembled genomes (MAGs) from nine landfill leachate samples collected from eight cities across China, spanning 42 phyla, 73 classes, 114 orders, 189 families, and 267 genera. Totally, 74.1% of 1168 MAGs could not be classified to any known species and 5.9% of these MAGs belonged to microbial dark matter phyla. Two putative novel classes were discovered from landfill leachate samples. The identification of thousands of novel carbohydrate-active enzymes showed similar richness level compared to the cow rumen microbiota. The methylotrophic methanogenic pathway was speculated to contribute significantly to methane production in the landfill leachate because of its co-occurrence with the acetoclastic and hydrogenotrophic methanogenic pathways. The genetic potential of dissimilatory nitrate reduction to ammonium (DNRA) was observed, implying DNRA may play a role in ammonium generation in landfill leachate. These findings implied that landfill leachate might be a valuable microbial resource repository and filled the previous understanding gaps for both methanogenesis and nitrogen cycling in landfill leachate microbiota. Our study provides a comprehensive genomic catalog and substantially provides unprecedented taxonomic and functional profiles of the landfill leachate microbiota.

Selective enrichment of comammox from activated sludge using antibiotics.

While the ubiquitous presence of comammox in engineered systems provides the foundation of developing a novel biological nitrogen removal process, factors contributing to the comammox dynamics in engineered systems have not been well resolved. Here, we investigate the long-term effects of ten different antibiotics on microbial community dynamics in activated sludge and the results show that both types and concentrations of antibiotics affect the taxonomic composition of nitrifiers, including comammox, ammonia-oxidizing bacteria, and canonical nitrite-oxidizing bacteria. Specifically, phylogenetically different comammox Nitrospira were selectively enriched by four types of antibiotics (i.e., ampicillin, kanamycin, lincomycin, and trimethoprim). Comparative genomic analysis of the four newly identified comammox clade A Nitrospira revealed that the comammox enriched by antibiotics shared the conserved key metabolic potentials, such as carbon fixation, complete ammonia oxidation, and utilization of hydrogen as alternative electron donors, among the known comammox organisms. Comammox strains enriched in this study also encoded genes involved in formate and cyanate metabolism that were recently reported in comammox clade A organisms from wastewater treatment systems. Our findings highlight that the comammox in activated sludge ecosystems possess high metabolic versatility than previously recognized and could be selectively enriched by some antibiotics.

Microbial community composition and metabolic functions in landfill leachate from different landfills of China.

Landfill leachate usually harbors complex microbial communities responsible for the decomposition of municipal solid waste. However, the diversity and metabolic functions of the microbial communities in landfill leachate as well as the factors that influence them are still not well understood. In this study, Illumina MiSeq high-throughput sequencing was used to investigate the microbial community composition and metabolic functions in landfill leachate from 11 cities in China. The microbial diversity and structure of different leachate samples exhibited obvious differences. In general, Bacteroidetes, Firmicutes and Proteobacteria were the three dominant microbial communities among the 26 bacterial phyla identified in landfill leachate, regardless of the geographical locations. Diverse bacterial genera associated with various functions such as cellulolytic bacteria (e.g., Sphaerochaeta and Defluviitoga), acidifying bacteria (e.g., Prevotella and Trichococcus) and sulfate-reducing bacteria (e.g., Desulfuromonas and Desulfobacterium) were detected abundantly in the landfill leachate. Moreover, the archaeal community in all leachate samples was dominated by the orders Methanomicrobiales and Methanosarcinales belonging to the Euryarchaeota phylum. Notably, the archaea-specific primer pair covered more diverse archaeal communities than the universal bacteria-archaea primer pair. Seventeen archaeal genera belonging to acetoclastic, hydrogenotrophic, and methylotrophic methanogens were identified, and the composition of the dominant genera in these samples varied greatly. The canonical correlation analysis indicated that landfill age, electrical conductivity, ammonia nitrogen, and total nitrogen were significantly correlated with the microbial community structure. Based on PICRUSt2, a total of 41 metabolic pathways belonging to six metabolic pathway groups were predicted, and the KEGG pathway Metabolism was the most abundant group across all leachate samples. This study provides an important insight into the composition and functional characteristics of the microbial communities in landfill leachate.

Reponses of microbial community and antibiotic resistance genes to the selection pressures of ampicillin, cephalexin and chloramphenicol in activated sludge reactors.

High concentrations of antibiotics can exert strong selection pressures on the microbial community and promote the emergence and dissemination of antibiotic resistance genes (ARGs). The activated sludge reactors treating ampicillin, cephalexin and chloramphenicol production wastewater were established to investigate the responses of microbial community, ARGs and mobile genetic elements (MGEs) to antibiotics. Antibiotic selection pressures significantly declined the microbial diversity and changed microbial community structures. Based on metagenomic analysis, a total of 500 ARG subtypes affiliated with 18 ARG types were identified and 63 ARGs were shared by all samples. The substantial increase of ARG abundance and the shifts of ARG profiles were significantly correlated with antibiotic types and concentrations. The evident enrichment of non-corresponding ARG types suggested the strong co-selection effects of the target antibiotics. Additionally, metagenomic analysis revealed the occurrence of 104 MGEs belonging to various types and the five dominant MGEs were tnpA, intI1, tniA, tniB and IS91. The ARG-MGE co-occurrence associations implied the potential mobility of ARGs. Network analysis also demonstrated that five ARG types (aminoglycoside, beta-lactam, chloramphenicol, multidrug and tetracycline resistance genes) tended to co-occur internally and the obvious co-occurrence patterns among different ARG types indicated the potential for resistance co-selection. Moreover, 15 bacterial genera were speculated as the hosts of diverse ARGs. This study provides a comprehensive overview of the occurrence of ARGs and MGEs and is valuable for the risk assessment and management of antibiotic resistance.

Metagenomic analysis reveals the fate of antibiotic resistance genes in two-stage and one-stage anaerobic digestion of waste activated sludge.

Waste activated sludge (WAS) from wastewater treatment plants is an important reservoir of antibiotic resistance genes (ARGs). The fate of ARGs in this process was not revealed previously. The present study applied metagenomic approach to examine the occurrence and fate of ARGs in thermophilic alkaline fermentation followed by mesophilic anaerobic digestion (TM), by comparison with mesophilic alkaline fermentation followed by mesophilic anaerobic digestion (MM) and one-stage mesophilic anaerobic digestion (M) process. The removal efficiency of two-stage anaerobic digestion (AD) to total ARGs is higher than that of one-stage AD. The hydrogen and methane production stages of two-stage AD processes have dissimilar impact on the fate of ARGs. Macrolide, lincosamide, and streptogramin (MLS) resistance genes were enriched, especially in the hydrogen production reactors of TM and MM processes. Statistical analysis of metagenomic profiles analysis suggested that bacA may be the differential ARG subtype of two-stage AD process. ARG-like sequences encoding antibiotic efflux pump, antibiotic inactivation and antibiotic target alteration mechanisms were identified as the dominant ARGs resistance mechanisms in all samples. Procrustes analysis showed that microbial community composition structured the resistome. Co-occurrence patterns between ARGs and microbial phylogeny revealed that 26 bacterial species might be potential hosts of 94 ARG subtypes.

Metagenomics analysis revealing the occurrence of antibiotic resistome in salt lakes.

Although antimicrobial resistance genes (ARGs) in dozens of environments have been well documented, the distribution of ARGs in salt lake ecosystems has been less intensively investigated. In this study, the broad-spectrum ARG profiles, microbial community composition and the comprehensive associations between microbiome and antimicrobial resistome in four salt lakes were investigated using a metagenomic approach. A total of 175 ARG subtypes affiliated with 19 ARG types were detected, and ARGs conferring resistance to multidrug, bacitracin, and macrolide-lincosamide-streptogramin (MLS) accounted for 71.2% of the total ARG abundance. However, the abundance of ARGs significantly decreased with the increasing salinity in the lakes. Both ARG profiles and microbial community structure presented remarkable discrepancies in different lakes, as well as in different sample types. Microbes such as genera Azoarcus, Aeromonas, Pseudomonas, and Kocuria, significantly co-occurred with multiple ARGs, indicating that these bacteria are potential ARG hosts in salt lake ecosystems. Collectively, this work provides new insights into the occurrence and distribution of ARGs in salt lake ecosystems.

Metagenomic and network analyses decipher profiles and co-occurrence patterns of antibiotic resistome and bacterial taxa in the reclaimed wastewater distribution system.

Metagenomic and network analyses were applied to decipher the profiles and co-occurrence of resistome and microbial taxa in the reclaimed wastewater distribution system, including reclaimed wastewater and two types of biofilms, i.e., surface layer biofilms and inner layer biofilms. The effects of chlorination, UV irradiation and no disinfection treatment on ARG relative abundance and composition were systemically investigated. The reclaimed wastewater possesses more diverse and abundant ARGs than biofilms and total ARG relative abundance followed the order of reclaimed wastewater samples > surface layer biofilms > inner layer biofilms. Multidrug, bacitracin, sulfonamide, aminoglycoside, beta-lactam, and macrolide-lincosamide-streptogramin resistance genes were the six most dominant ARG types and their sum accounted for 90.1 %-96.0 % of the total ARG relative abundance in different samples. Beta-lactam resistance gene was the discriminative ARG type for reclaimed wastewater. Bacitracin resistance gene and bacA were the discriminative ARG type and subtype for biofilms. Chlorination significantly reduced ARG relative abundance in the reclaimed wastewater. Nevertheless, it could not reduce ARG relative abundance in biofilms. Regarding to the total ARG profiles, there were no obvious increasing or decreasing trends over time during one year period. Co-occurrence results revealed twenty-six genera were deduced as the potential hosts of twenty-two ARG subtypes.

High-efficiency biodegradation of chloramphenicol by enriched bacterial consortia: Kinetics study and bacterial community characterization.

The risk of environmental pollution caused by chloramphenicol has necessitated special attention. Biodegradation has tremendous potential for chloramphenicol removal in the environment. Six chloramphenicol-degrading consortia were acclimated under different culture conditions to investigate their chloramphenicol biodegradation behaviors, and the bacterial community structures were comprehensively characterized. The enriched consortia CL and CH which utilized chloramphenicol as their sole carbon and energy source could thoroughly degrade 120 mg/L chloramphenicol within 5 days, and the mineralization rate reached up to 90%. Chloramphenicol biodegradation kinetics by different enriched consortia fit the modified Gompertz model or the first-order decay model (R2≥0.97). Consortia CL could almost completely degrade 1-500 mg/L CAP with a final mineralization rate of 87.8-91.7%. Chloramphenicol 3-acetate was identified to be a major intermediate of CAP biodegradation by metabolite analysis and enzyme activity assay. 16S rRNA sequencing analysis revealed that the diversities and abundances of the main genera in the enriched consortia were distinct from each other. Forty-one core OTUs belonging to 18 genera were the core bacteria which might be related to chloramphenicol biodegradation. Among them, the genera Sphingomonas, Chryseobacterium, Cupriavidus, Bradyrhizobium, Burkholderia, and Afipia with high abundance may play potential roles for chloramphenicol biodegradation.

Chloramphenicol biodegradation by enriched bacterial consortia and isolated strain Sphingomonas sp. CL5.1: The reconstruction of a novel biodegradation pathway.

Figuring out the comprehensive metabolic mechanism of chloramphenicol (CAP) is critical to improving CAP removal in the bioremediation process. In this study, CAP biodegradation by six consortia and isolated Sphingomonas sp. CL5.1 were systematically investigated using the combination of high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry, second-generation, and third-generation sequencing technologies. The CAP-degrading capability of six consortia was enhanced while CAP mineralization rate declined after long-term enrichment. The microbial community structures of six consortia were all simplified with 69%-82% decline in species richness after continuous passages for one year. The core genera of consortia CL and CH included Sphingomonas, Cupriavidus, Burkholderia, Chryseobacterium, and Pigmentiphaga, which accounted for over 98% of the total population. Sphingomonas was discovered as a new CAP degrader that could subsist on CAP as the sole carbon, nitrogen, and energy sources. Sphingomonas sp. CL5.1 was able to completely remove 120 mg/L CAP within 48 hours with a mineralization rate of 50.4%. The presence of acetate or nitrite could inhibit CAP metabolization by strain CL5.1. Four CAP metabolic pathways were constructed, including modification of the C3 hydroxyl group of CAP via acetylation, oxidization, dehydration and the bond cleavage between C1 and C2. C3 hydroxyl group dehydration and C1-C2 bond-cleavage were first reported regarding to CAP biotransformation. Strain CL5.1 played a core role in the consortia and was responsible for C3 hydroxyl oxidation, C3 dehydration, and C1-C2 bond cleavage. Genomic information of strain CL5.1 revealed the further mineralization pathways of downstream product p-nitrobenzoic acid via ortho- and meta-cleavage.

Deciphering the mobility and bacterial hosts of antibiotic resistance genes under antibiotic selection pressure by metagenomic assembly and binning approaches.

The presence of antibiotics can exert significant selection pressure on the emergence and spread of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB). However, co-selection effects for ARGs, the mobility of ARGs and the identification of ARG hosts under high antibiotic selection pressures are poorly understood. Here, metagenomic assembly and binning approaches were used to comprehensively decipher the prevalence of ARGs and their potential mobility and hosts in activated sludge reactors treating antibiotic production wastewater. We found the abundance of different ARG types in antibiotic treatments varied greatly and certain antibiotic pressure promoted the co-selection for the non-corresponding types of ARGs. Antibiotic selection pressures significantly increased the abundance and proportions of ARGs mediated by plasmids (57.9%), which were more prevalent than those encoded in chromosomes (19.2%). The results indicated that plasmids and chromosomes had a tendency to carry different types of ARGs. Moreover, higher co-occurrence frequency of ARGs and MGEs revealed that antibiotics enhanced the mobility potential of ARGs mediated by both plasmids and integrative and conjugative elements. Among the 689 metagenome-assembled genomes (MAGs) with high estimated quality, 119 MAGs assigning to nine bacterial phyla were identified as the ARG hosts and 33 MAGs exhibited possible multi-resistance to antibiotics. Some ARG types tended to be carried by certain bacteria (e.g. bacitracin resistance genes carried by the family Burkholderiaceae) and thus showed a pronounced host-specific pattern. This study enhances the understanding of the mobility and hosts of ARGs and provides important insights into the risk assessment and management of antibiotic resistance.