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354800.9056From 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
354710.8984Occurrence of 40 sanitary indicators in French digestates derived from different anaerobic digestion processes and raw organic wastes from agricultural and urban origin. This study investigated the sanitary quality of digestates resulting from the mesophilic anaerobic digestion (AD) of urban and agricultural organic wastes (OWs). 40 sanitary indicators, including pathogenic bacteria, antimicrobial resistance genes, virulence factor genes, and mobile genetic elements were evaluated using real-time PCR and/or droplet digital PCR. 13 polycyclic aromatic hydrocarbons (PAHs) and 13 pharmaceutical products (PHPs) were also measured. We assessed agricultural OWs from three treatment plants to study the effect of different AD processes (feeding mode, number of stages, pH), and used three laboratory-scale reactors to study the effect of different feed-supplies (inputs). The lab-scale reactors included: Lab1 fed with 97% activated sludge (urban waste) and 3% cow manure; Lab2 fed with 85% sludge-manure mixture supplemented with 15% wheat straw (WS); and Lab3 fed with 81% sludge-manure mixture, 15% WS, and 4% zeolite powder. Activated sludge favored the survival of the food-borne pathogens Clostridium perfringens and Bacillus cereus, carrying the toxin-encoding genes cpe and ces, respectively. Globally, the reactors fed with fecal matter supplemented with straw (Lab2) or with straw and zeolite (Lab3) had a higher hygienization efficiency than the reactor fed uniquely with fecal matter (Lab1). Three pathogenic bacteria (Enterococcus faecalis, Enterococcus faecium, and Mycobacterium tuberculosis complex), a beta-lactam resistance gene (bla (TEM)), and three mobile genetic elements (intI1, intI2, and IS26) were significantly decreased in Lab2 and Lab3. Moreover, the concentrations of 11 PAHs and 11 PHPs were significantly lower in Lab2 and Lab3 samples than in Lab1 samples. The high concentrations of micropollutants, such as triclosan, found in Lab1, could explain the lower hygienization efficiency of this reactor. Furthermore, the batch-fed reactor had a more efficient hygienization effect than the semi-continuous reactors, with complete removal of the ybtA gene, which is involved in the production of the siderophore yersiniabactin, and significant reduction of intI2 and tetO. These data suggest that it is essential to control the level of chemical pollutants in raw OWs to optimize the sanitary quality of digestates, and that adding co-substrate, such as WS, may overcome the harmful effect of pollutants.202439165575
786920.8942Nano-CeO(2) activates physical and chemical defenses of garlic (Allium sativum L.) for reducing antibiotic resistance genes in plant endosphere. The transmission of manure- and wastewater-borne antibiotic-resistant bacteria (ARB) to plants contributes to the proliferation of antimicrobial resistance in agriculture, necessitating effective strategies for preventing the spread of antibiotic resistance genes (ARGs) from ARB in the environment to humans. Nanomaterials are potential candidates for efficiently controlling the dissemination of ARGs. The present study investigated the abundance of ARGs in hydroponically grown garlic (Allium sativum L.) following nano-CeO(2) (nCeO(2)) application. Specifically, root exposure to nCeO(2) (1, 2.5, 5, 10 mg L(-1), 18 days) reduced ARG abundance in the endosphere of bulbs and leaves. The accumulation of ARGs (cat, tet, and aph(3')-Ia) in garlic bulbs decreased by 24.2-32.5 % after nCeO(2) exposure at 10 mg L(-1). Notably, the lignification extent of garlic stem-disc was enhanced by 10 mg L(-1) nCeO(2), thereby accelerating the formation of an apoplastic barrier to impede the upward transfer of ARG-harboring bacteria to garlic bulbs. Besides, nCeO(2) upregulated the gene expression related to alliin biosynthesis and increased allicin content by 15.9-16.2 %, promoting a potent antimicrobial defense for reducing ARG-harboring bacteria. The potential exposure risks associated with ARGs and Ce were evaluated according to the estimated daily intake (EDI). The EDI of ARGs exhibited a decrease exceeding 95 %, while the EDI of Ce remained below the estimated oral reference dose. Consequently, through stimulating physical and chemical defenses, nCeO(2) contributed to a reduced EDI of ARGs and Ce, highlighting its potential for controlling ARGs in plant endosphere within the framework of nano-enabled agrotechnology.202438570269
690730.8933Deciphering 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
716140.8933Mitigating the risk of antibiotic resistance and pathogenic bacteria in swine waste: The role of ectopic fermentation beds. The ectopic fermentation bed (EFB) is used to recycle animal waste, but the fate and dynamic change of antibiotic resistance genes (ARGs) with biocide or heavy metal resistance genes (B/MRGs) and pathogens remain unclear. We performed metagenomic sequencing on 129 samples to study the resistome and bacteriome in pig feces from 24 farms, comparing these profiles with EFBs from five farms, and one farm's EFB was monitored for 154 days. Results showed pig feces from different cities (Chengdu, Meishan, and Chongqing) shared 284 of 311 ARG subtypes, with over 70 % being high-risk ARGs, and 106 of 114 pathogenic bacteria. Swine farms were heavily contaminated with co-occurrences of risky ARGs, B/MRGs, and pathogenic hosts, particularly Escherichia coli and Streptococcus suis being hosts of multidrug ARGs. The application of EFBs markedly mitigated these risks in feces, showing a 3.09-fold decrease in high-risk ARGs, a 72.22 % reduction in B/MRGs, a 3.95-fold drop in prioritized pathogens, an 89.09 % decline in the relative abundance of pig pathogens, and a simplification of their correlation networks and co-occurrence patterns. A mantel analysis revealed that metal contents (Fe, Mn, and Cu) and time influenced pathogen and ARG profiles. Pathogens, ARGs, and risk ARGs exhibited periodic variations, peaking at days 14, 84, and 154, with 70-day intervals. This study provides a comprehensive assessment of the risks associated with pig feces and EFBs and demonstrates that EFBs reduce ARG risks by inhibiting their associations with B/MRGs and pathogens. These findings can help guide and improve the management of antimicrobial resistance and pathogenic contaminants in EFB applications to reduce environmental pollution.202540220395
810550.8932Refluxing mature compost to replace bulking agents: A low-cost solution for suppressing antibiotic resistance genes rebound in sewage sludge composting. Antibiotic resistance genes (ARGs) rebounding during composting cooling phase is a critical bottleneck in composting technology that increased ARGs dissemination and application risk of compost products. In this study, mature compost (MR) was used as a substitute for rice husk (RH) to mitigate the rebound of ARGs and mobile genetic elements (MGEs) during the cooling phase of sewage sludge composting, and the relationship among ARGs, MGEs, bacterial community and environmental factors was investigated to explore the key factor influencing ARGs rebound. The results showed that aadD, blaCTX-M02, ermF, ermB, tetX and vanHB significantly increased 4.76-32.41 times, and the MGEs rebounded by 38.60% in the cooling phase of RH composting. Conversely, MR reduced aadD, tetM, ermF and ermB concentrations by 59.49-98.58%, and reduced the total abundance of ARGs in the compost product by 49.32% compared to RH, which significantly restrained ARGs rebound. MR promoted secondary high temperature inactivation of potential host bacteria, including Ornithinibacter, Rhizobiales and Caldicoprobacter, which could harbor aadE, blaCTX-M02, and blaVEB. It also reduced the abundance of lignocellulose degrading bacteria of Firmicutes, which were potential hosts of aadD, tetX, ermF and vanHB. Moreover, MR reduced moisture and increased oxidation reduction potential (ORP) that promoted aadE, tetQ, tetW abatement. Furthermore, MR reduced 97.36% of total MGEs including Tn916/1545, IS613, Tp614 and intI3, which alleviated ARGs horizontal transfer. Overall finding proposed mature compost reflux as bulking agent was a simple method to suppress ARGs rebound and horizontal transfer, improve ARGs removal and reduce composting plant cost.202539798649
871660.8932Organophosphorus mineralizing-Streptomyces species underpins uranate immobilization and phosphorus availability in uranium tailings. Phosphate-solubilizing bacteria (PSB) are important but often overlooked regulators of uranium (U) cycling in soil. However, the impact of PSB on uranate fixation coupled with the decomposition of recalcitrant phosphorus (P) in mining land remains poorly understood. Here, we combined gene amplicon sequencing, metagenome and metatranscriptome sequencing analysis and strain isolation to explore the effects of PSB on the stabilization of uranate and P availability in U mining areas. We found that the content of available phosphorus (AP), carbonate-U and Fe-Mn-U oxides in tailings was significantly (P < 0.05) higher than their adjacent soils. Also, organic phosphate mineralizing (PhoD) bacteria (e.g., Streptomyces) and inorganic phosphate solubilizing (gcd) bacteria (e.g., Rhodococcus) were enriched in tailings and soils, but only organic phosphate mineralizing-bacteria substantially contributed to the AP. Notably, most genes involved in organophosphorus mineralization and uranate resistance were widely present in tailings rather than soil. Comparative genomics analyses supported that organophosphorus mineralizing-Streptomyces species could increase soil AP content and immobilize U(VI) through organophosphorus mineralization (e.g., PhoD, ugpBAEC) and U resistance related genes (e.g., petA). We further demonstrated that the isolated Streptomyces sp. PSBY1 could enhance the U(VI) immobilization mediated by the NADH-dependent ubiquinol-cytochrome c reductase (petA) through decomposing organophosphorous compounds. This study advances our understanding of the roles of PSB in regulating the fixation of uranate and P availability in U tailings.202438908177
811170.8931Effect of alkaline-thermal pretreatment on biodegradable plastics degradation and dissemination of antibiotic resistance genes in co-compost system. Biodegradable plastics (BDPs) are an eco-friendly alternative to traditional plastics in organic waste, but their microbial degradation and impact on antibiotic resistance genes (ARGs) transmission during co-composting remain poorly understood. This study examines how alkaline-thermal pretreatment enhances BDPs degradation and influences the fate of ARGs and mobile genetic elements (MGEs) in co-composting. Pretreatment with 0.1 mol/L NaOH at 100℃ for 40 minutes increased the surface roughness and hydrophilicity of BDPs while reducing their molecular weight and thermal stability. Incorporating pretreated BDPs film (8 g/kg-TS) into the compost reduced the molecular weight of the BDPs by 59.70 % during the maturation stage, facilitating compost heating and prolonging the thermophilic stage. However, incomplete degradation of BDPs releases numerous smaller-sized microplastics, which can act as carriers for microorganisms, facilitating the dissemination of ARGs across environments and posing significant ecological and public health risks. Metagenomic analysis revealed that pretreatment enriched plastic-degrading bacteria, such as Thermobifida fusca, on BDPs surfaces and accelerated microbial plastic degradation during the thermophilic stage, but also increased ARGs abundance. Although pretreatment significantly reduced MGEs abundance (tnpA, IS19), the risk of ARGs dissemination remained. Three plastic-degrading bacteria (Pigmentiphaga sp002188465, Bacillus clausii, and Bacillus altitudinis) were identified as ARGs hosts, underscoring the need to address the risk of horizontal gene transfer of ARGs associated with pretreatment in organic waste management.202539970645
354680.8931Mitigation of tetracycline resistance genes in silage through targeted lactic acid bacteria inoculation. The dissemination of antibiotic resistance genes (ARGs) in silage ecosystems poses a critical challenge to ecological stability and public health security. This investigation focuses on tetracycline resistance genes (TRGs), the most prevalent subtype of ARGs in silage, employing a targeted selection strategy for lactic acid bacteria (LAB) inoculants. From 226 isolated LAB strains, four candidates (LP1-3: Lactiplantibacillus plantarum; LC1: Lacticaseibacillus paracasei) demonstrating superior growth kinetics (OD(600) > 1.6 within 24 h) and rapid acidification capacity (pH < 3.9 within 24 h) were selected. Strains LP3 and LC1 exhibited minimal intrinsic TRGs content. These four strains reduced (p < 0.001) pH, ammonia-N concentration, and coliform bacterial counts of stylo silage. Metagenomic analysis revealed that strains LP1-3 promoted Lactiplantibacillus dominance (0.709-0.975 vs. 0.379-0.509 in the control), while LC1 enhanced Lacticaseibacillus abundance (0.449-0.612 vs. 0.002-0.013 in the control). Ensiling process downregulated 367 and upregulated 227 ARGs. Inoculation with the four LAB strains further enhanced the suppression of ARGs. Among the top 30 TRGs, 22 were reduced by strains LP1-3 and 20 by LC1. Quantitative PCR results showed that strains LP1-3 decreased (p < 0.05) the contents of tetA and tetG during 30 days fermentation. Among the TRGs increased, tetA(60), tetB(58), tet(T) were positively correlated with Lactiplantibacillus spp., tetA(58), tetB(60), tetA(46), tetB(46), tet(43) were significantly correlated with Lacticaseibacillus spp. (R > 0.4, p < 0.001). In conclusion, the fermentation process induced substantial ARGs profile modifications, LAB-mediated microbiome engineering enables TRGs suppression, providing a scientific foundation for precision silage management strategies targeting antimicrobial resistance mitigation.202541038354
306490.8930High Diversity but Monodominance of Multidrug-Resistant Bacteria in Immunocompromised Pediatric Patients with Acute Lymphoblastic Leukemia Developing GVHD Are Not Associated with Changes in Gut Mycobiome. Graft-versus-host disease (GvHD) is a severe complication after hematopoietic stem cell transplantation (HSCT). Our study focused on identifying multidrug-resistant (MDR) gut bacteria associated with GvHD-prone guts and association with gut microbiota (GM) diversity, bacteriome, and mycobiome composition in post-HSCT patients. We examined 11 pediatric patients with acute lymphoblastic leukemia (ALL), including six with GvHD, within three time points: seven days pre-HSCT, seven days post-, and 28 days post-HSCT. The gut microbiome and its resistome were investigated using metagenomic sequencing, taxonomically classified with Kraken2, and statistically evaluated for significance using appropriate tests. We observed an increase in the abundance of MDR bacteria, mainly Enterococcus faecium strains carrying msr(C), erm(T), aac(6')-li, dfrG, and ant(6)-la genes, in GvHD patients one week post-HSCT. Conversely, non-GvHD patients had more MDR beneficial bacteria pre-HSCT, promoting immunosurveillance, with resistance genes increasing one-month post-HSCT. MDR beneficial bacteria included the anti-inflammatory Bacteroides fragilis, Ruminococcus gnavus, and Turicibacter, while most MDR bacteria represented the dominant species of GM. Changes in the gut mycobiome were not associated with MDR bacterial monodominance or GvHD. Significant α-diversity decline (Shannon index) one week and one month post-HSCT in GvHD patients (p < 0.05) was accompanied by increased Pseudomonadota and decreased Bacteroidota post-HSCT. Our findings suggest that MDR commensal gut bacteria may preserve diversity and enhance immunosurveillance, potentially preventing GvHD in pediatric ALL patients undergoing HSCT. This observation has therapeutic implications.202338136701
6834100.8930Landscape of antibiotic resistance genes and bacterial communities in groundwater on the Tibetan Plateau, and distinguishing their difference with low-altitude counterparts. Groundwater is a vital source of drinking water for Tibetans. Antibiotic resistance genes (ARGs) and bacterial communities in groundwater on the Tibetan Plateau remain unclear. Furthermore, the characterization of their differences between high-altitude and low-altitude groundwater is still unrevealed. Herein, 32 groundwater samples were collected on the plateau, and intra- and extracellular ARGs (iARGs and eARGs), and bacterial communities were characterised through qPCR assays to 19 ARGs and 16S rRNA sequencing. It showed top four abundant intra- and extracellular last-resort ARGs (LARGs) were bla(OXA-48), mcr-1, vanA, and vanB, whereas dominant common ARGs (CARGs) were tetA and ermB, respectively. CARGs had higher abundances than LARGs, and iARGs were more frequently detected than eARGs. Proteobacteria, an invasive resident phylum, and Firmicutes dominated eDNA release. Network analysis revealed all observed LARGs co-occurred with pathogenic and non-pathogenic bacteria. Community diversity was significantly associated with longitude and elevation, while nitrate correlated with ARGs. Comparative analysis demonstrated eARG frequencies and abundances were higher at high altitudes than at low altitudes. Additionally, Acinetobacter and Pseudomonas specifically dominated at high altitudes. This study reveals the widespread prevalence of ARGs, particularly LARGs, in groundwater on the less-disturbed Tibetan Plateau and underlines the potential risks associated with the LARG-carrying bacteria. ENVIRONMENTAL IMPLICATION: Antibiotic resistance genes (ARGs), which are defined as emerging environmental contaminants, are becoming a global concern due to their ability to confer antibiotic resistance to pathogens. Our findings highlight the prevalence of ARGs, particularly LARGs, in groundwater on the Tibetan Plateau, and the possibility that naturally-occurring pathogenic and non-pathogenic bacteria carry multiple LARGs. In addition, we further reveal differences in the distribution of ARGs and bacterial community between high-altitude and low-altitude groundwater. Collectively, our findings offer an important insight into the potential public risks related to groundwater on the Tibetan Plateau.202337595466
6381110.8930Occurrence and distribution of antibiotic resistance genes in Elymus nutans silage from different altitudes on the Qinghai-Tibetan Plateau. INTRODUCTION: Antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) have attracted more attentions in fermented feed recently. However, little information is available on the occurrence and distribution of ARGs in ensiled forages in the alpine region of the Qinghai-Tibetan plateau (QTP) with an extremely harsh environment. METHODS: The study investigated the distribution and spread mechanism of ARB and ARGs in Elymus nutans silage along 2600 m (low), 3600 m (medium) and 4600 m (high) altitude in the QTP. RESULTS: The major ARG types in Elymus nutans silage were multidrug, aminoglycoside, bacitracin, beta-lactam and polymyxin, while tnpA and IS91 were the dominant mobile genetic elements (MGEs) subtypes in the Elymus nutans silage. The dominant ARGs were mainly carried by Pantoea, Enterobacter, Serratia, and Lelliottia. Although altitudinal gradient had no influence on the diversity or abundance of other ARGs and MGEs in the Elymus nutans silage (p > 0.05), the network co-occurrence patterns among ARGs, MGEs, and bacteria in high-altitude silage were more complex than that in low- and medium-altitude silages. The dominant clinical ARGs in the alpine silage were bacA and acrF, and the abundance of clinical ARGs decreased with prolonged fermentation time. DISCUSSION: This study provides important data on the status of ARGs in ensiled forage from the alpine region of the QTP.202540458713
6905120.8928The hot air circulation ventilation composting system removes antibiotic resistance genes through competitive inhibition by core bacteria. Livestock manure is a significant reservoir of antibiotic resistance genes (ARGs). Aerobic composting technology can produce mature compost while effectively removing ARGs. In this study, we developed an energy-saving and emission-reducing hot air circulating ventilated composting technology (HACV), which had no adverse effects on the composting process or compost maturity. The HACV composting altered bacterial communities, primarily driven by heterogeneous selection among deterministic factors (65 %). Specifically, it increased the complexity of bacterial networks and promoted the colonization of high-temperature-tolerant bacteria, such as Erysipelothrix, Oceanobacillus and unclassified_f_Bacillaceae. Topological analysis revealed that core bacteria primarily functioned as connectors in composting, serving as important ARGs hosts and facilitating their spread in conventional composting. Among these, a core pathogenic bacterium (Corynebacterium) carried and transmitted ARGs with higher risks. In contrast, although the number of core bacteria (Bacillus, Oceanobacillus, Caldicoprobacter, Saccharomonospora, and Lactobacillus) increased during HACV composting, these bacteria were not potential hosts of the target ARGs. This contributed to the removal of aadE by 80.49 %. Consequently, compared to conventional composting, HACV composting was more effective at controlling risky ARGs, particularly aac(6')-Ib-cr and sul1. Furthermore, the ARGs removal mechanism primarily involved inhibiting horizontal gene transfer (HGT) in HACV composting, attributed to competition between core bacteria and ARGs hosts. In summary, HACV composting effectively promotes ARGs removal and reduces the risk of bacterial resistance. ENVIRONMENTAL IMPLICATION: In this study, we developed an energy-saving and emission-reducing hot air circulation ventilation composting technology (HACV), which effectively removes antibiotic resistance genes (ARGs). The HACV system maintained composting efficiency and maturity while driving bacterial community succession through deterministic processes (heterogeneous selection). HACV composting increased the colonization of core bacteria in the microbial network. Acting as connectors, the core bacteria are not hosts of ARGs in the HACV system, inhibiting horizontal gene transfer (HGT) and remove ARGs through competition with host bacteria.202540682888
8069130.8928Responsive change of crop-specific soil bacterial community to cadmium in farmlands surrounding mine area of Southeast China. In arable soils co-influenced by mining and farming, soil bacteria significantly affect metal (Cadmium, Cd) bioavailability and accumulation. To reveal the soil microecology response under this co-influence, three intersection areas (cornfield, vegetable field, and paddy field) were investigated. With a similar nutrient condition, the soils showed varied Cd levels (0.31-7.70 mg/kg), which was negatively related to the distance from mining water flow. Different soils showed varied microbial community structures, which were dominated by Chloroflexi (19.64-24.82%), Actinobacteria (15.49-31.96%), Acidobacteriota (9.46-20.31%), and Proteobacteria (11.88-14.57%) phyla. A strong correlation was observed between functional microbial taxon (e. g. Acidobacteriota), soil physicochemical properties, and Cd contents. The relative abundance of tolerant bacteria including Vicinamibacteraceae, Knoellia, Ardenticatenales, Lysobacter, etc. elevated with the increase of Cd, which contributed to the enrichment of heavy metal resistance genes (HRGs) and integration genes (intlI), thus enhancing the resistance to heavy metal pollution. Cd content rather than crop species was identified as the dominant factor that influenced the bacterial community. Nevertheless, the peculiar agrotype of the paddy field contributed to its higher HRGs and intlI abundance. These results provided fundamental information about the crop-specific physiochemical-bacterial interaction, which was helpful to evaluate agricultural environmental risk around the intersection of farmland and pollution sources.202235750128
7164140.8927Anthropogenic pressures amplify high-risk antibiotic resistome via co-selection among biocide resistance, virulence, and antibiotic resistance genes in the Ganjiang River basin: Drivers diverge in densely versus sparsely populated reaches. As the largest river in the Poyang Lake system, the Ganjiang River faces escalating anthropogenic pressures that amplify resistance gene dissemination. This study integrated antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and virulence factor genes (VFGs) to reveal their co-selection mechanisms and divergent environmental drivers between densely (DES) and sparsely populated (SPAR) regions of the Ganjiang River basin. The microbial and viral communities and structures differed significantly between the DES and SPAR regions (PERMANOVA, p < 0.001). Midstream DES areas were hotspots for ARGs/BRGs/VFGs enrichment, with peak enrichment multiples reaching 10.2, 5.7, and 5.9-fold respectively. Procrustes analysis revealed limited dependence of ARGs transmission on mobile genetic elements (MGEs) (p > 0.05). Separately, 74 % of dominant ARGs (top 1 %) showed strong correlations with BRGs (r(2) = 0.973, p < 0.01) and VFGs (r(2) = 0.966, p < 0.01) via co-selection. Pathogenic Pseudomonas spp. carrying multidrug-resistant ARGs, BRGs, and adhesion-VFGs were identified as high-risk vectors. In SPAR areas, anthropogenic pressure directly dominated ARGs risk (RC = 54.2 %, β = 0.39, p < 0.05), with biological factors as secondary contributors (RC = 45.8 %, β = 0.33, p < 0.05). In contrast, DES regions showed anthropogenic pressure exerting broader, enduring influences across microorganisms, physicochemical parameters, and biological factors, escalating ARGs risks through diverse pathways, with BRGs/VFGs acting as direct drivers. This study proposes establishing a risk prevention system using BRGs and pathogenic microorganisms as early-warning indicators.202540858019
8110150.8926Removal of chlortetracycline and antibiotic resistance genes in soil by earthworms (epigeic Eisenia fetida and endogeic Metaphire guillelmi). The impacts of two ecological earthworms on the removal of chlortetracycline (CTC, 0.5 and 15 mg kg(-1)) and antibiotic resistance genes (ARGs) in soil were explored through the soil column experiments. The findings showed that earthworm could significantly accelerate the degradation of CTC and its metabolites (ECTC) in soil (P < 0.05), with epigeic Eisenia fetida promoting degradation rapidly and endogeic Metaphire guillelmi exhibiting a slightly better elimination effect. Earthworms alleviated the abundances of tetR, tetD, tetPB, tetG, tetA, sul1, TnpA, ttgB and intI1 in soil, with the total relative abundances of ARGs decreasing by 35.0-44.2% in earthworm treatments at the 28th day of cultivation. High throughput sequencing results displayed that the structure of soil bacteria community was modified apparently with earthworm added, and some possible CTC degraders, Aeromonas, Flavobacterium and Luteolibacter, were promoted by two kinds of earthworms. Redundancy analysis demonstrated that the reduction of CTC residues, Actinobacteria, Acidobacteria and Gemmatimonadetes owing to earthworm stimulation was responsible for the removal of ARGs and intI1 in soil. Additionally, intI1 declined obviously in earthworm treatments, which could weaken the risk of horizontal transmission of ARGs. Therefore, earthworm could restore the CTC-contaminated soil via enhancing the removal of CTC, its metabolites and ARGs.202133798888
8066160.8925Inoculation of thermophilic bacteria from giant panda feces into cattle manure reduces gas emissions and decreases resistance gene prevalence in short-term composting. Here, thermophilic bacteria (TB) with cellulose degradation functions were screened from composting panda feces and applied to cattle manure composting. TB (Aeribacillus pallidus G5 and Parageobacillus toebii G12) inoculation led to remarkable improvement of the compost temperature, prolonging of the thermophilic stage and shortening of the composting process, resulting in increased manure harmlessness (GI ≥ 70%), compost humification, and greenhouse gas emission reduction (14.19%-22.57%), compared with the control compost, within 15 days of composting. In particular, G5 inoculation reduced NH(3) emissions by 41.97% relative to control composts over 15 days. G5 was capable of rapidly colonizing in the composts, and its inoculation immediately enriched the genera of Firmicutes, and simultaneously decreased the genera of Proteobacteria, contributing to the elimination of harmful microorganisms. Notably, this strain lacked antibiotic resistance genes, and the absolute abundances of resistance genes and mobile genetic genes (MGEs) decreased the most (by 80.84%). Metagenomic analysis revealed that enzymes capable of producing CO(2), N(2)O, and NH(3) were generally inhibited, while CO(2) fixation and N(2)O and NH(3) reduction enzymes were enriched in the G5 compost, since metagenome-assembled genomes of Proteobacteria harbored more key genes and enzymes in complete pathways for producing N(2)O, NH(3), and CO(2). Moreover, Proteobacteria, such as Pseudomonas and Halopseudomonas, were the main host of resistance genes and MGEs. Overall, the gas emission could be reduced, and more efficient control of resistance genes could be achieved by inhibited the abundance of Proteobacteria during composting. This study provides a safe and effective microbial agent (A. pallidus) for manure treatment.202539642832
3069170.8923The hospital sink drain biofilm resistome is independent of the corresponding microbiota, the environment and disinfection measures. In hospitals, the transmission of antibiotic-resistant bacteria (ARB) may occur via biofilms present in sink drains, which can lead to infections. Despite the potential role of sink drains in the transmission of ARB in nosocomial infections, routine surveillance of these drains is lacking in most hospitals. As a result, there is currently no comprehensive understanding of the transmission of ARB and the dissemination of antimicrobial resistance genes (ARGs) and associated mobile genetic elements (MGEs) via sink drains. This study employed a multifaceted approach to monitor the total aerobic bacteria as well as the presence of carbapenemase-producing Enterobacterales (CPEs), the microbiota and the resistome of sink drain biofilms (SDBs) and hospital wastewater (WW) of two separate intensive care units (ICUs) in the same healthcare facility in France. Samples of SDB and WW were collected on a monthly basis, from January to April 2023, in the neonatal (NICU) and the adult (AICU) ICUs of Grenoble Alpes University Hospital. In the NICU, sink drain disinfection with surfactants was performed routinely. In the AICU, routine disinfection is not carried out. Culturable aerobic bacteria were quantified on non-selective media, and CPEs were screened using two selective agars. Isolates were identified by MALDI-TOF MS, and antibiotic susceptibility testing (AST) was performed on Enterobacterales and P. aeruginosa. The resistome was analyzed by high-throughput qPCR targeting >80 ARGs and MGEs. The overall bacterial microbiota was assessed via full-length 16S rRNA sequencing. No CPEs were isolated from SDBs in either ICU by bacterial culture. Culture-independent approaches revealed an overall distinct microbiota composition of the SDBs in the two ICUs. The AICU SDBs were dominated by pathogens containing Gram-negative bacterial genera including Pseudomonas, Stenotrophomona, Klebsiella, and Gram-positive Staphylococcus, while the NICU SDBs were dominated by the Gram-negative genera Achromobacter, Serratia, and Acidovorax, as well as the Gram-positive genera Weisella and Lactiplantibacillus. In contrast, the resistome of the SDBs exhibited no significant differences between the two ICUs, indicating that the abundance of ARGs and MGEs is independent of microbiota composition and disinfection practices. The AICU WW exhibited more distinct aerobic bacteria than the NICU WW. In addition, the AICU WW yielded 15 CPEs, whereas the NICU WW yielded a single CPE. All the CPEs were characterized at the species level. The microbiota of the NICU and AICU WW samples differed from their respective SDBs and exhibited distinct variations over the four-month period:the AICU WW contained a greater number of genes conferring resistance to quinolones and integron integrase genes, whereas the NICU WW exhibited a higher abundance of streptogramin resistance genes. Our study demonstrated that the resistome of the hospital SDBs in the two ICUs of the investigated healthcare institute is independent of the microbiota, the environment, and the local disinfection measures. However, the prevalence of CPEs in the WW pipes collecting the waste from the investigated drains differed. These findings offer valuable insights into the resilience of resistance genes in SDBs in ICUs, underscoring the necessity for innovative strategies to combat antimicrobial resistance in clinical environments.202540483807
3497180.8923Biomarkers of antibiotic resistance genes during seasonal changes in wastewater treatment systems. To evaluate the seasonal distribution of antibiotic resistance genes (ARGs) and explore the reason for their patterns in different seasons and different systems, two wastewater treatment systems were selected and analyzed using high-throughput qPCR. Linear discriminant analysis (LDA) effect size (LEfSe) was used to discover the differential ARGs (biomarkers) and estimate the biomarkers' effect size. We found that the total absolute abundances of ARGs in inflows and excess sludge samples had no obvious seasonal fluctuations, while those in winter outflow samples decreased in comparison with the inflow samples. Eleven differentially abundant ARGs (biomarker genes, BmGs) (aadA5-02, aac-6-II, cmlA1-01, cmlA1-02, blaOXA10-02, aadA-02, tetX, aadA1, ereA, qacEΔ1-01, and blaTEM) in summer samples and 10 BmGs (tet-32, tetA-02, aacC2, vanC-03, aac-6-I1, tetE, ermB, mefA, tnpA - 07, and sul2) in winter samples were validated. According to 16S rRNA gene sequencing, the relative abundance of bacteria at the phylum level exhibited significant seasonal changes in outflow water (OW), and biomarker bacteria (BmB) were discovered at the family (or genus) level. Synechococcus and vadinCA02 are BmB in summer, and Trichococcus, Lactococcus, Pelosinus, Janthinobacterium, Nitrosomonadaceae and Sterolibacterium are BmB in winter. In addition, BmB have good correlations with BmGs in the same season, which indicates that bacterial community changes drive different distributions of ARGs during seasonal changes and that LEfSe is an acute and effective method for finding significantly different ARGs and bacteria between two or more classes. In conclusion, this study demonstrated the seasonal changes of BmGs and BmB at two wastewater treatment systems.201829169020
7745190.8923Iron-modified biochar boosts anaerobic digestion of sulfamethoxazole pharmaceutical wastewater: Performance and microbial mechanism. The accumulation of volatile fatty acids (VFAs) caused by antibiotic inhibition significantly reduces the treatment efficiency of sulfamethoxazole (SMX) wastewater. Few studies have been conducted to study the VFAs gradient metabolism of extracellular respiratory bacteria (ERB) and hydrogenotrophic methanogen (HM) under high-concentration sulfonamide antibiotics (SAs). And the effects of iron-modified biochar on antibiotics are unknown. Here, the iron-modified biochar was added to an anaerobic baffled reactor (ABR) to intensify the anaerobic digestion of SMX pharmaceutical wastewater. The results demonstrated that ERB and HM were developed after adding iron-modified biochar, promoting the degradation of butyric, propionic and acetic acids. The content of VFAs reduced from 1166.0 mg L(-1) to 291.5 mg L(-1). Therefore, chemical oxygen demand (COD) and SMX removal efficiency were improved by 22.76% and 36.51%, and methane production was enhanced by 6.19 times. Furthermore, the antibiotic resistance genes (ARGs) such as sul1, sul2, intl1 in effluent were decreased by 39.31%, 43.33%, 44.11%. AUTHM297 (18.07%), Methanobacterium (16.05%), Geobacter (6.05%) were enriched after enhancement. The net energy after enhancement was 0.7122 kWh m(-3). These results confirmed that ERB and HM were enriched via iron-modified biochar to achieve high efficiency of SMX wastewater treatment.202337030222