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690700.9933Deciphering the impact of organic loading rate and digestate recirculation on the occurrence patterns of antibiotics and antibiotic resistance genes in dry anaerobic digestion of kitchen waste. Organic loading rate (OLR) is crucial for determining the stability of dry anaerobic digestion (AD). Digestate recirculation contributes to reactor stability and enhances methane production. Nevertheless, the understanding of how OLR and digestate recirculation affect the abundance and diversity of antibiotics and antibiotic resistance genes (ARGs), as well as the mechanisms involved in the dissemination of ARGs, remains limited. This study thoroughly investigated this critical issue through a long-term pilot-scale experiment. The metabolome analyses revealed the enrichment of various antibiotics, such as aminoglycoside, tetracycline, and macrolide, under low OLR conditions (OLR ≤ 4.0 g·VS/L·d) and the reactor instability. Antibiotics abundance decreased by approximately 19.66-31.69 % during high OLR operation (OLR ≥ 6.0 g·VS/L·d) with digestate recirculation. The metagenome analyses demonstrated that although low OLR promoted reactor stability, it facilitated the proliferation of antibiotic-resistant bacteria, such as Pseudomonas, and triggered functional profiles related to ATP generation, oxidative stress response, EPS secretion, and cell membrane permeability, thereby facilitating horizontal gene transfer (HGT) of ARGs. However, under stable operation at an OLR of 6.0 g·VS/L·d, there was a decrease in ARGs abundance but a notable increase in human pathogenic bacteria (HPB) and mobile genetic elements (MGEs). Subsequently, during reactor instability, the abundance of ARGs and HPB increased. Notably, during digestate recirculation at OLR levels of 6.0 and 7.0 g·VS/L·d, the process attenuated the risk of ARGs spread by reducing the diversity of ARGs hosts, minimizing interactions among ARGs hosts, ARGs, and MGEs, and weakening functional profiles associated with HGT of ARGs. Overall, digestate recirculation aids in reducing the abundance of antibiotics and ARGs under high OLR conditions. These findings provide advanced insights into how OLR and digestate recirculation affect the occurrence patterns of antibiotics and ARGs in dry AD.202438968733
694010.9932Higher spreading risk of antibacterial biocide and heavy metal resistance genes than antibiotic resistance genes in aerobic granular sludge. Metagenomic approach was applied to simultaneously reveal the antibiotic resistance genes (ARGs) and antibacterial biocide & metal resistance genes (BMRGs), and the corresponding microbial hosts with high mobility during aerobic granular sludge (AGS) formation process. The results showed that the relative abundance of BMRGs was 88-123 times that of ARGs. AGS process was easier to enrich BMRGs, leading to a greater risk of drug resistance caused by BMRGs than that by ARGs. The enrichments of ARGs and BMRGs in AGS were closely related to several enhanced microbial metabolisms (i.e., cell motility, transposase and ATP-binding cassette transporters) and their corresponding regulatory genes. Several enhanced KEGG Orthologs (KO) functions, such as K01995, K01996, K01997 and K02002, might cause a positive impact on the spread of ARGs and BMRGs, and the main contributors were the largely enriched glycogens accumulating organisms. The first dominant ARGs (adeF) was carried by lots of microbial hosts, which might be enriched and propagated mainly through horizontal gene transfer. Candidatus Competibacter denitrificans simultaneously harbored ARG (cmx) and Cu related RGs (corR). Many enriched bacteria contained simultaneously multiple BMRGs (copR and corR) and mobile genetic elements (integrons and plasmids), granting them high mobility capabilities and contributing to the spread of BMRGs. This study might provide deeper understandings of the proliferation and mobility of ARGs and BMRGs, importantly, highlighted the status of BMRGs, which laid the foundation for the controlling widespread of resistance genes in AGS.202235489476
354820.9931From flagellar assembly to DNA replication: CJSe's role in mitigating microbial antibiotic resistance genes. The emergence of Antibiotic Resistance Genes (ARGs) in Campylobacter jejuni (CJ) poses a severe threat to food safety and human health. However, the specific impact of CJ and its variants on ARGs and other related factors remains to be further elucidated. Herein, integrated metagenomic sequencing and co-occurrence network analysis approach were employed to investigate the impact of CJ and CJ incorporated with biogenic selenium (CJSe) on ARGs, flagellar assembly pathways, microbial communities, and DNA replication pathways in chicken manure. Compared to the Control (CON) and CJ groups, the CJSe group exhibited 2.4-fold increase selenium levels (P < 0.01) in chicken manure. Notable differences were also observed between the CJ and CJSe groups, with sequence results showing a CJ > CJSe > CON trend in total ARG copy numbers. Furthermore, the CJSe group showed 31.6 % fewer flagellar assembly genes compared to the CJ group. Additionally, compared to the CJ group, CJSe inhibited pathways such as basal body/hook (e.g., FliH, FliO, FliQ reduced by 25-52 %) and stator (MotB downregulated by 42.3 %), suppressing flagellar assembly. We also found that both CJ and CJSe influenced bacterial DNA replication pathways, with the former increasing ARG-carrying bacteria and the latter, under selenium-induced selective pressure, reducing ARG-carrying bacteria. Moreover, compared to the CJ group, the CJSe group showed a significantly lower 9.72 % copy number of total archaeal DNA replication genes. Furthermore, through intricate co-occurrence network analysis, we discovered the complex interplay between changes in ARGs and bacterial and archaeal DNA replication dynamics within the microbial community. These findings indicate that CJSe mitigates the threat posed by CJ and reduces ARG prevalence, while its dual functionality enables applications in biofortified crop production and soil remediation in selenium-deficient regions, thereby advancing circular economy systems. While the current study demonstrates CJSe's dual functionality under controlled conditions, future work will implement a dedicated ecological risk assessment framework encompassing Se speciation/leaching tests and non-target organism assays to confirm environmental safety under field-relevant scenarios. This approach aligns with sustainable strategies for food security and public health safeguarding.202541108960
858330.9930Microplastics Enhance the Prevalence of Antibiotic Resistance Genes in Anaerobic Sludge Digestion by Enriching Antibiotic-Resistant Bacteria in Surface Biofilm and Facilitating the Vertical and Horizontal Gene Transfer. Antibiotic resistance genes (ARGs) and microplastics (MPs) are recognized as emerging contaminants and threats to global human health. Despite both of them being significantly detected in their "hotspots", i.e., waste activated sludge (WAS), rare studies on how MPs affect ARGs and antibiotic-resistant bacteria (ARB) in anaerobic sludge digestion are available. Herein, the fate of ARGs and ARB after exposure to MPs of three dosages (10, 30, and 80 particles/g-TS), three polymer types (LDPE, PET, and PS), and three branching extents (LDPE, LLDPE, and HDPE) in anaerobic sludge digestion was investigated. Metagenomic results indicated that all variants of MPs resulted in an increase of the relative abundance of ARGs in the digester compared to the control. The abundance of ARGs demonstrated a dosage-dependent relationship within the range from 10 to 80 particles/g-TS, resulting in an increase from 4.5 to 27.9% compared to the control. Branching structure and polymer type influence ARG level in the sludge digester as well. Mechanism studies revealed that LDPE selectively enriched potential ARB and ARGs in the surface biofilm, possibly creating a favorable environment for ARB proliferation and ARG exchange. Furthermore, vertical transfer of ARGs was facilitated by LDPE through increasing bacterial cell proliferation accompanied by the enhancement of relevant functional genes. The elevated abundance of mobile genetic elements (MGEs) and ARGs-carrying plasmids also demonstrated that MGE-mediated horizontal transfer was promoted by LDPE at 80 particles/g-TS. This effect was compounded by increased oxidative stress, cell membrane permeability, and cell cohesion, collectively facilitating horizontal ARG transfer. Consequently, both vertical and horizontal transfer of ARGs could be concurrently promoted by LDPE an in anaerobic sludge digester.202337733635
643440.9930Unraveling the role of microplastics in antibiotic resistance: Insights from long-read metagenomics on ARG mobility and host dynamics. As two emerging pollutants, microplastics (MPs) potentially serve as vectors for antibiotic resistance genes (ARGs) in aquatic environments, but the mechanisms driving ARG enrichment remain unclear. This study used long-read metagenomics to investigate ARG mobility and hosts dynamics within the biofilms of MPs and rocks in different water environments. We identified distinct enrichment patterns for microbial communities and ARGs, highlighting the significant role of horizontal gene transfer in ARG enrichment. Specifically, plasmid-encoded ARGs varied significantly among MP biofilms, rock biofilms, and water samples, while chromosome-encoded ARGs remained consistent across these environments, emphasizing the impact of plasmids on ARG enrichment. Despite this, 55.1 % of ARGs were on chromosomes, indicating that host organisms also play a crucial role. The related mechanisms driving ARG enrichment included enhanced cell adhesion, increased transmembrane transporter activity, and responses to environmental stressors, which led to an increased presence of plasmid-encoded ARGs on MP biofilms, facilitating more frequent horizontal gene transfer. Additionally, the diversity of hosts on MPs was notably lower compared to the water column, with specific bacteria, including Herbaspirillu, Limnohabitans, Polaromonas, Variovorax, Rubrivivax, and Thauera significantly driving ARG enrichment. This study highlights key mechanisms and bacterial taxa involved in ARG dynamics on MPs.202540056523
690650.9929Insights into the mobility and bacterial hosts of antibiotic resistance genes under dinotefuran selection pressure in aerobic granular sludge based on metagenomic binning and functional modules. Dinotefuran (DIN) is toxic to non-target organisms and accelerates the evolution of antibiotic resistance, which poses a problem for the stable operation of the activated sludge process in wastewater treatment plants (WWTPs). However, the emergence and the transfer mechanism of antibiotic resistance genes (ARGs) in activated sludge systems under DIN stress remains unclear. Thus, in the study, the potential impact of DIN on ARGs and virulence factor genes (VFGs) in aerobic granular sludge (AGS) was investigated in depth using metagenomic binning and functional modules. It was found that DIN stress increased the total abundance of ARGs, mobile genetic elements (MGEs), and VFGs in the AGS system, with the highest abundance of fabG (4.6%), tnpA (55.6%) and LPS (39.0%), respectively. The proliferation of the enteric pathogens Salmonella enterica and Escherichia coli in the system indicates that DIN induces exposure of harmless bacteria to the infected environment. The genera Nitrospira (1169 ARG subtypes) and Dechloromonas (663 ARG subtypes) were identified as the potentially antibiotic-resistant bacteria carrying the most ARGs and MGEs in the metagenome-assembled genomes. Co-localization patterns of some ARGs, MGEs, and the SOS response-related gene lexA were observed on metagenome-assembled contigs under high levels of DIN exposure, suggesting DIN stimulated ROS production (101.8% increase over control), altered cell membrane permeability, and increased the potential for horizontal gene transfer (HGT). Furthermore, the DNA damage caused by DIN in AGS led to the activation of the antioxidant system and the SOS repair response, which in turn promoted the expression of the type IV secretion system and HGT through the flagellar channel. This study extends the previously unappreciated DIN understanding of the spread and associated risks of ARGs and VFGs in the AGS system of WWTPs. It elucidates how DIN facilitates HGT, offering a scientific basis for controlling emerging contaminant-induced resistance.202539798650
866860.9928Globally Abundant "Candidatus Udaeobacter" Benefits from Release of Antibiotics in Soil and Potentially Performs Trace Gas Scavenging. Verrucomicrobia affiliated with "Candidatus Udaeobacter" belong to the most abundant soil bacteria worldwide. Although the synthesis of antibiotics presumably evolved in soil, and environmental pollution with antimicrobials increases, the impact of these complex molecules on "Ca Udaeobacter" remains to be elucidated. In this study, we demonstrate that "Ca. Udaeobacter" representatives residing in grassland as well as forest soil ecosystems show multidrug resistance and even take advantage of antibiotics release. Soils treated with up to six different antibiotics exhibited a higher "Ca. Udaeobacter" abundance than corresponding controls after 3, 8, and 20 days of incubation. In this context, we provide evidence that "Ca. Udaeobacter" representatives may utilize nutrients which are released due to antibiotic-driven lysis of other soil microbes and thereby reduce energetically expensive synthesis of required biomolecules. Moreover, genomic analysis revealed the presence of genes conferring resistance to multiple classes of antibiotics and indicated that "Ca. Udaeobacter" representatives most likely oxidize the trace gas H(2) to generate energy. This energy might be required for long-term persistence in terrestrial habitats, as already suggested for other dominant soil bacteria. Our study illustrates, for the first time, that globally abundant "Ca. Udaeobacter" benefits from release of antibiotics, which confers advantages over other soil bacteria and represents a so-far overlooked fundamental lifestyle feature of this poorly characterized verrucomicrobial genus. Furthermore, our study suggests that "Ca. Udaeobacter" representatives can utilize H(2) as an alternative electron donor.IMPORTANCE Soil bacteria have been investigated for more than a century, but one of the most dominant terrestrial groups on Earth, "Candidatus Udaeobacter," remains elusive and largely unexplored. Its natural habitat is considered a major reservoir of antibiotics, which directly or indirectly impact phylogenetically diverse microorganisms. Here, we found that "Ca. Udaeobacter" representatives exhibit multidrug resistance and not only evade harmful effects of antimicrobials but even benefit from antibiotic pressure in soil. Therefore, "Ca. Udaeobacter" evidently affects the composition of soil resistomes worldwide and might represent a winner of rising environmental pollution with antimicrobials. In addition, our study indicates that "Ca. Udaeobacter" representatives utilize H(2) and thereby contribute to global hydrogen cycling. The here-reported findings provide insights into elementary lifestyle features of "Ca. Udaeobacter," potentially contributing to its successful global dissemination.202032641424
680170.9928Persistent Risks in the Effluents of Wastewater Treatment Plants: Mobile Genetic Elements and Viral-Mediated Dissemination of Pathogenic Antibiotic-Resistant Bacteria. Wastewater treatment plants (WWTPs) are recognized as reservoirs of pathogenic antibiotic-resistant bacteria (PARB), yet their genomic risk dynamics remain unclear. This study recovered PARB genomes from 102 influent and effluent metagenomes from six countries; their activity and risk potential were then experimentally validated with metatranscriptomics on samples from a Shanghai WWTP. A total of 44 PARB genomes were reconstructed, which carried both antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), and they persisted in the effluent. Mobile genetic elements might mediate ARG transfer in 13 PARB genomes. Moreover, bacteriophages infecting PARB harbored and were transcribing ARGs/VFGs, and antiviral defense systems of PARB correlated with horizontal gene transfer (HGT). Evolutionary analyses indicated that influent PARB maintained high microdiversity via homologous recombination, while effluent populations underwent purifying selection, suggesting that wastewater treatment reduced the genetic diversity of PARB through purifying selection. However, the persistent accumulation of PARB as well as HGT might maintain the dissemination of ARGs. This study emphasized the necessity of selecting the PARB genomes for wastewater monitoring, thereby optimizing treatment strategies and mitigating the potential health risks posed by pathogenic bacteria.202541143557
682180.9928Mangrove plastisphere as a hotspot for high-risk antibiotic resistance genes and pathogens. Microplastics (MPs) are critical vectors for the dissemination of antibiotic resistance genes (ARGs); however, the prevalence and ecological risks of high-risk ARGs in mangrove ecosystems-globally vital yet understudied coastal habitats-remain poorly understood. To address this gap, this study investigated polyethylene, polystyrene, and polyvinyl chloride incubated in mangrove sediments for one month, focusing on high-risk ARGs, virulence gene (VGs), and pathogenic antibiotic-resistant bacteria within the mangrove plastisphere. High-throughput PCR and metagenomic analyses revealed that high-risk ARGs, VGs, and mobile genetic elements (MGEs) were significantly enriched on MPs compared to surrounding sediments. Pathogenic bacteria and MGEs were also more abundant in the plastisphere, highlighting its role as a hotspot for ARG dispersal. Metagenome-assembled genome analysis identified Pseudomonas and Bacillus as key hosts for ARGs, MGEs, and VGs, particularly multidrug resistance genes, integrase genes, and adherence factors. Notably, polystyrene harbored the highest abundance of pathogenic bacteria carrying ARGs, MGEs, and VGs, and mangrove root exudates were found to amplify horizontal gene transfer on MPs, uncovering a previously overlooked mechanism driving antibiotic resistance in coastal ecosystems. These findings not only elucidate how MPs accelerate the spread of ARGs, but also underscore the urgent need for targeted mitigation strategies to address the adverse impacts microplastic pollution on human, animal, and environmental health.202540043931
690490.9928Ionic Liquid Enriches the Antibiotic Resistome, Especially Efflux Pump Genes, Before Significantly Affecting Microbial Community Structure. An expanding list of chemicals may permeabilize bacterial cells and facilitate horizontal gene transfer (HGT), which enhances propagation of antibiotic resistance genes (ARGs) in the environment. Previous studies showed that 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]), an ionic liquid, can facilitate HGT of some ARGs among bacteria. However, the dynamic response of a wider range of ARGs and associated mobile genetic elements (MGEs) in different environments is unknown. Here, we used metagenomic tools to study shifts of the resistome and microbiome in both sediments and freshwater microcosms exposed to [BMIm][PF6]. Exposure for 16 h to 0.1 or 1.0 g/L significantly enriched more than 207 ARG subtypes primarily encoding efflux pumps in freshwater microcosms as well as cultivable antibiotic-resistant bacteria. This resistome enrichment was attributed to HGT facilitated by MGEs (428 plasmids, 61 integron-integrase genes, and 45 gene cassettes were enriched) as well as to HGT-related functional genes. Interestingly, resistome enrichment occurred fast (within 16 h) after [BMIm][PF6] exposure, before any significant changes in bacterial community structure. Similar ARG enrichment occurred in sediment microcosms exposed to [BMIm][PF6] for 28 d, and this longer exposure affected the microbial community structure (e.g., Proteobacteria abundance increased significantly). Overall, this study suggests that [BMIm][PF6] releases could rapidly enrich the antibiotic resistome in receiving environments by increasing HGT and fortuitously selecting for efflux pump genes, thus contributing to ARG propagation.202031944684
6426100.9928Deciphering the pathogenic risks of microplastics as emerging particulate organic matter in aquatic ecosystem. Microplastics are accumulating rapidly in aquatic ecosystems, providing habitats for pathogens and vectors for antibiotic resistance genes (ARGs), potentially increasing pathogenic risks. However, few studies have considered microplastics as particulate organic matter (POM) to elucidate their pathogenic risks and underlying mechanisms. Here, we performed microcosm experiments with microplastics and natural POM (leaves, algae, soil), thoroughly investigating their distinct effects on the community compositions, functional profiles, opportunistic pathogens, and ARGs in Particle-Associated (PA) and Free-Living (FL) bacterial communities. We found that both microplastics and leaves have comparable impacts on microbial community structures and functions, enriching opportunistic pathogens and ARGs, which may pose potential environmental risks. These effects are likely driven by their influences on water properties, including dissolved organic carbon, nitrate, DO, and pH. However, microplastics uniquely promoted pathogens as keystone species and further amplified their capacity as hosts for ARGs, potentially posing a higher pathogenic risk than natural POM. Our research also emphasized the importance of considering both PA and FL bacteria when assessing microplastic impacts, as they exhibited different responses. Overall, our study elucidates the role and underlying mechanism of microplastics as an emerging POM in intensifying pathogenic risks of aquatic ecosystems in comparison with conventional natural POM.202438805824
6823110.9927Metagenomic assembly and binning analyses the prevalence and spread of antibiotic resistome in water and fish gut microbiomes along an environmental gradient. The pristine river and urban river show an environmental gradient caused by anthropogenic impacts such as wastewater treatment plants and domestic wastewater discharges. Here, metagenomic and binning analyses unveiled antibiotic resistance genes (ARGs) profiles, their co-occurrence with metal resistance genes (MRGs) and mobile genetic elements (MGEs), and their host bacteria in water and Hemiculter leucisculus samples of the river. Results showed that the decrease of ARG abundances from pristine to anthropogenic regions was attributed to the reduction of the relative abundance of multidrug resistance genes in water microbiomes along the environmental gradient. Whereas anthropogenic impact contributed to the enrichment of ARGs in fish gut microbiomes. From pristine to anthropogenic water samples, the dominant host bacteria shifted from Pseudomonas to Actinobacteria. Potential pathogens Vibrio parahaemolyticus, Enterobacter kobei, Aeromonas veronii and Microcystis aeruginosa_C with multiple ARGs were retrieved from fish gut microbes in lower reach of Ba River. The increasing trends in the proportion of the contigs carrying ARGs (ARCs) concomitant with plasmids along environmental gradient indicated that plasmids act as efficient mobility vehicles to enhance the spread of ARGs under anthropogenic pressures. Moreover, the higher co-occurrence of ARGs and MRGs on plasmids revealed that anthropogenic impacts accelerated the co-transfer potential of ARGs and MRGs and the enrichment of ARGs. Partial least squares path modeling revealed anthropogenic contamination could shape fish gut antibiotic resistome mainly via affecting ARG host bacteria in water microbiomes, following by ARGs co-occurrence with MGEs and MRGs in gut microbiomes. This study enhanced our understanding of the mechanism of the anthropogenic activities on the transmission of antibiotic resistome in river ecosystem and emphasized the risk of ARGs and pathogens transferring from an aquatic environment to fish guts.202235716556
6819120.9927Risk characteristics of resistome coalescence in irrigated soils and effect of natural storage of irrigation materials on risk mitigation. Irrigation and fertilization are the routinely agricultural practices but also cause resistome coalescence, by which the entire microbiomes from irrigation materials invade soil microbial community, to transfer antibiotic resistance genes (ARGs) in the coalesced soils. Although studies have reported the effect of irrigation or fertilization on the prevalence and spread of ARGs in soils, risk characteristics of resistome coalescence in irrigation system remain to be demonstrated and few has shown whether natural storage of irrigation materials will reduce resistance risks. To fill the gaps, two microscopic experiments were conducted for deeply exploring resistance risks in the soils irrigated with wastewater and manure fertilizer from a perspective of community coalescence by metagenomic analysis, and to reveal the effect of natural storage of irrigation materials on the reduction of resistance risks in the coalesced soils. Results showed irrigation and coalescence significantly increased the abundance and diversity of ARGs in the soils, and introduced some emerging resistance genes into the coalesced community, including mcr-type, tetX, qacB, and an array of genes conferring resistance to carbapenem. Procrustes analysis demonstrated microbial community was significantly correlated with the ARGs in coalesced soils, and variance partitioning analysis quantified its dominant role on shaping resistome profile in the environment. Besides ARGs, abundant and diverse mobile genetic elements (MGEs) were also identified in the coalesced soils and co-existed on the ARG-carrying contigs, implying potential transfer risk of ARGs in the irrigation system. Further, the analysis of metagenome-assembled genomes (MAGs) confirmed the risk by recovering 358 ARGs-carrying MAGs and identifying the resistant bacteria that co-carried multiple ARGs and MGEs. As expected, the natural storage of irrigation water and manure fertilizer reduced about 27%-54% of ARGs, MGEs and virulence factors in the coalesced soils, thus caused the soils to move towards lower resistance risks to a certain extent.202337742860
7316130.9927Nanopore-based long-read metagenomics uncover the resistome intrusion by antibiotic resistant bacteria from treated wastewater in receiving water body. Wastewater treatment plant (WWTP) effluent discharge could induce the resistome enrichment in the receiving water environments. However, because of the general lack of a robust antibiotic-resistant bacteria (ARB) identification method, the driving mechanism for resistome accumulation in receiving environment is unclear. Here, we took advantage of the enhanced ARBs recognition by nanopore long reads to distinguish the indigenous ARBs and the accumulation of WWTP-borne ARBs in the receiving water body of a domestic WWTP. A bioinformatic framework (named ARGpore2: https://github.com/sustc-xylab/ARGpore2) was constructed and evaluate to facilitate antibiotic resistance genes (ARGs) and ARBs identification in nanopore reads. ARGs identification by ARGpore2 showed comparable precision and recall to that of the commonly adopt BLASTP-based method, whereas the spectrum of ARBs doubled that of the assembled Illumina dataset. Totally, we identified 33 ARBs genera carrying 65 ARG subtypes in the receiving seawater, whose concentration was in general 10 times higher than clean seawater's. Notably we report a primary resistome intrusion caused by the revival of residual microbes survived from disinfection treatment. These WWTP-borne ARBs, including several animal/human enteric pathogens, contributed up to 85% of the receiving water resistome. Plasmids and class 1 integrons were reckoned as major vehicles facilitating the persistence and dissemination of ARGs. Moreover, our work demonstrated the importance of extensive carrier identification in determining the driving force of multifactor coupled resistome booming in complicated environmental conditions, thereby paving the way for establishing priority for effective ARGs mitigation strategies.202236332295
6793140.9927Interplays between cyanobacterial blooms and antibiotic resistance genes. Cyanobacterial harmful algal blooms (cyanoHABs), which are a form of microbial dysbiosis in freshwater environments, are an emerging environmental and public health concern. Additionally, the freshwater environment serves as a reservoir of antibiotic resistance genes (ARGs), which pose a risk of transmission during microbial dysbiosis, such as cyanoHABs. However, the interactions between potential synergistic pollutants, cyanoHABs, and ARGs remain poorly understood. During cyanoHABs, Microcystis and high microcystin levels were dominant in all the nine regions of the river sampled. The resistome, mobilome, and microbiome were interrelated and linked to the physicochemical properties of freshwater. Planktothrix and Pseudanabaena competed with Actinobacteriota and Proteobacteria during cyanoHABs. Forty two ARG carriers were identified, most of which belonged to Actinobacteriota and Proteobacteria. ARG carriers showed a strong correlation with ARGs density, which decreased with the severity of cyanoHAB. Although ARGs decreased due to a reduction of ARG carriers during cyanoHABs, mobile gene elements (MGEs) and virulence factors (VFs) genes increased. We explored the relationship between cyanoHABs and ARGs for potential synergistic interaction. Our findings demonstrated that cyanobacteria compete with freshwater commensal bacteria such as Actinobacteriota and Proteobacteria, which carry ARGs in freshwater, resulting in a reduction of ARGs levels. Moreover, cyanoHABs generate biotic and abiotic stress in the freshwater microbiome, which may lead to an increase in MGEs and VFs. Exploration of the intricate interplays between microbiome, resistome, mobilome, and pathobiome during cyanoHABs not only revealed that the mechanisms underlying the dynamics of microbial dysbiosis but also emphasizes the need to prioritize the prevention of microbial dysbiosis in the risk management of ARGs.202337897871
6424150.9927Bacterium-Phage Symbiosis Facilitates the Enrichment of Bacterial Pathogens and Antibiotic-Resistant Bacteria in the Plastisphere. The plastisphere, defined as the ecological niche for microbial colonization of plastic debris, has been recognized as a hotspot of pathogenic and antibiotic-resistant bacteria. However, the interactions between bacteria and phages facilitated by the plastisphere, as well as their impact on microbial risks to public health, remain unclear. Here, we analyzed public metagenomic data from 180 plastisphere and environmental samples, stemming from four different habitats and two plastic types (biodegradable and nonbiodegradable plastics) and obtained 611 nonredundant metagenome-assembled genomes (MAGs) and 4061 nonredundant phage contigs. The plastisphere phage community exhibited decreased diversity and virulent proportion compared to those found in environments. Indexes of phage-host interaction networks indicated significant associations of phages with pathogenic and antibiotic-resistant bacteria (ARB), particularly for biodegradable plastics. Known phage-encoded auxiliary metabolic genes (AMGs) were involved in nutrient metabolism, antibiotic production, quorum sensing, and biofilm formation in the plastisphere, which contributed to enhanced competition and survival of pathogens and ARB hosts. Phages also carried transcriptionally active virulence factor genes (VFGs) and antibiotic resistance genes (ARGs), and could mediate their horizontal transfer in microbial communities. Overall, these discoveries suggest that plastisphere phages form symbiotic relationships with their hosts, and that phages encoding AMGs and mediating horizontal gene transfer (HGT) could increase the source of pathogens and antibiotic resistance from the plastisphere.202539836086
7721160.9927Unveiling plasmid diversity and functionality in pristine groundwater. BACKGROUND: Plasmids are key in creating a dynamic reservoir of genetic diversity, yet their impact on Earth's continental subsurface-an important microbial reservoir-remains unresolved. We analyzed 32 metagenomic samples from six groundwater wells within a hillslope aquifer system to assess the genetic and functional diversity of plasmids and to evaluate the role of these plasmids in horizontal gene transfer (HGT). RESULTS: Our results revealed 4,609 non-redundant mobile genetic elements (MGEs), with 14% (664) confidently classified as plasmids. These plasmids displayed well-specific populations, with fewer than 15% shared across wells. Plasmids were linked to diverse microbial phyla, including Pseudomonadota (42.17%), Nitrospirota (3.31%), Candidate Phyla Radiation (CPR) bacteria (2.56%), and Omnitrophota (2.11%). The presence of plasmids in the dominant CPR bacteria is significant, as this group remains underexplored in this context. Plasmid composition strongly correlated with well-specific microbial communities, suggesting local selection pressures. Functional analyses highlighted that conjugative plasmids carry genes crucial for metabolic processes, such as cobalamin biosynthesis and hydrocarbon degradation. Importantly, we found no evidence of high confidence emerging antibiotic resistance genes, contrasting with findings from sewage and polluted groundwater. CONCLUSIONS: Overall, our study emphasizes the diversity, composition, and eco-evolutionary role of plasmids in the groundwater microbiome. The absence of known antibiotic resistance genes highlights the need to preserve groundwater in its pristine state to safeguard its unique genetic and functional landscape.202540275408
7698170.9926Detecting horizontal gene transfer with metagenomics co-barcoding sequencing. Horizontal gene transfer (HGT) is the process through which genetic information is transferred between different genomes and that played a crucial role in bacterial evolution. HGT can enable bacteria to rapidly acquire antibiotic resistance and bacteria that have acquired resistance is spreading within the microbiome. Conventional methods of characterizing HGT patterns include short-read metagenomic sequencing (short-reads mNGS), long-read sequencing, and single-cell sequencing. These approaches present several limitations, such as short-read fragments, high amounts of input DNA, and sequencing costs, respectively. Here, we attempt to circumvent present limitations to detect HGT by developing a metagenomics co-barcode sequencing workflow (MECOS) and applying it to the human and mouse gut microbiomes. In addition to that, we have over 10-fold increased contig length compared to short-reads mNGS; we also obtained exceeding 30 million paired reads with co-barcode information. Applying the novel bioinformatic pipeline, we integrated this co-barcoding information and the context information from long reads, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Specifically, we detected approximately 3,000 HGT blocks in individual samples, encompassing ~6,000 genes and ~100 taxonomic groups, including loci conferring tetracycline resistance through ribosomal protection. MECOS provides a valuable tool for investigating HGT and advance our understanding on the evolution of natural microbial communities within hosts.IMPORTANCEIn this study, to better identify horizontal gene transfer (HGT) in individual samples, we introduce a new co-barcoding sequencing system called metagenomics co-barcoding sequencing (MECOS), which has three significant improvements: (i) long DNA fragment extraction, (ii) a special transposome insertion, (iii) hybridization of DNA to barcode beads, and (4) an integrated bioinformatic pipeline. Using our approach, we have over 10-fold increased contig length compared to short-reads mNGS, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Our results indicate the presence of approximately 3,000 HGT blocks, involving roughly 6,000 genes and 100 taxonomic groups in individual samples. Notably, these HGT events are predominantly enriched in genes that confer tetracycline resistance via ribosomal protection. MECOS is a useful tool for investigating HGT and the evolution of natural microbial communities within hosts, thereby advancing our understanding of microbial ecology and evolution.202438315121
3780180.9926Is ICE hot? A genomic comparative study reveals integrative and conjugative elements as "hot" vectors for the dissemination of antibiotic resistance genes. Different from other extensively studied mobile genetic elements (MGEs) whose discoveries were initiated decades ago (1950s-1980s), integrative and conjugative elements (ICEs), a diverse array of more recently identified elements that were formally termed in 2002, have aroused increasing concern for their crucial contribution to the dissemination of antibiotic resistance genes (ARGs). However, the comprehensive understanding on ICEs' ARG profile across the bacterial tree of life is still blurred. Through a genomic study by comparison with two key MGEs, we, for the first time, systematically investigated the ARG profile as well as the host range of ICEs and also explored the MGE-specific potential to facilitate ARG propagation across phylogenetic barriers. These findings could serve as a theoretical foundation for risk assessment of ARGs mediated by distinct MGEs and further to optimize therapeutic strategies aimed at restraining antibiotic resistance crises.202338032189
8603190.9926Ketoprofen promotes the conjugative transfer of antibiotic resistance among antibiotic resistant bacteria in natural aqueous environments. The emergence and spread of antibiotic resistance in the environment pose a serious threat to global public health. It is acknowledged that non-antibiotic stresses, including disinfectants, pharmaceuticals and organic pollutants, play a crucial role in horizontal transmission of antibiotic resistance genes (ARGs). Despite the widespread presence of non-steroidal anti-inflammatory drugs (NSAIDs), notably in surface water, their contributions to the transfer of ARGs have not been systematically explored. Furthermore, previous studies have primarily concentrated on model strains to investigate whether contaminants promote the conjugative transfer of ARGs, leaving the mechanisms of ARG transmission among antibiotic resistant bacteria in natural aqueous environments under the selective pressures of non-antibiotic contaminants remains unclear. In this study, the Escherichia coli (E. coli) K12 carrying RP4 plasmid was used as the donor strain, indigenous strain Aeromonas veronii containing rifampicin resistance genes in Taihu Lake, and E. coli HB101 were used as receptor strains to establish inter-genus and intra-genus conjugative transfer systems, examining the conjugative transfer frequency under the stress of ketoprofen. The results indicated that ketoprofen accelerated the environmental spread of ARGs through several mechanisms. Ketoprofen promoted cell-to-cell contact by increasing cell surface hydrophobicity and reducing cell surface charge, thereby mitigating cell-to-cell repulsion. Furthermore, ketoprofen induced increased levels of reactive oxygen species (ROS) production, activated the DNA damage-induced response (SOS), and enhanced cell membrane permeability, facilitating ARG transmission in intra-genus and inter-genus systems. The upregulation of outer membrane proteins, oxidative stress, SOS response, mating pair formation (Mpf) system, and DNA transfer and replication (Dtr) system related genes, as well as the inhibition of global regulatory genes, all contributed to higher transfer efficiency under ketoprofen treatment. These findings served as an early warning for a comprehensive assessment of the roles of NSAIDs in the spread of antibiotic resistance in natural aqueous environments.202439103039