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学者姓名：杨秋娥
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Abstract ：
The COVID-19 pandemic had a profound impact on the environment due to the extensive use of disinfectants to control the virus. While the dramatic increase in the use of disinfectants during the COVID-19 pandemic has been shown to affect antibiotic resistome in rivers, the impact on soils remains underexplored. Here, we collected 332 metagenomic farm soil samples across China before (2017-2019) and during (2020-2022) the COVID-19 pandemic and compared differences in antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial community characteristics. Our results revealed a significant increase in the abundance of ARGs and MGEs during the COVID-19 pandemic compared to the pre-pandemic period. Additionally, we observed a significant rise in the abundance of potentially pathogenic bacteria during the pandemic, including Pseudomonas, Salmonella, and Vibrio, while changes in human activities during the COVID-19 pandemic significantly impacted the composition of soil bacterial communities. Partial Least Squares Path Modeling indicated that the use of disinfectants increased the dissemination of ARGs by elevating the abundance of MGEs. Collectively, these findings suggest that the increased use of disinfectants to control the SARS-CoV-2 virus, likely contributed the spread of ARGs in soils during the COVID-19 pandemic. © 2024, The Authors. All rights reserved.
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| GB/T 7714 | Wu, Jiawei , Liao, Hanpeng , Liu, Chen et al. The Covid-19 Pandemic is Associated with the Spread of Antibiotic Resistance Genes in Soils Across China [J]. | SSRN , 2025 . |
| MLA | Wu, Jiawei et al. "The Covid-19 Pandemic is Associated with the Spread of Antibiotic Resistance Genes in Soils Across China" . | SSRN (2025) . |
| APA | Wu, Jiawei , Liao, Hanpeng , Liu, Chen , Ai, Chaofan , Guan, Yanlong , Yang, Qiu E. et al. The Covid-19 Pandemic is Associated with the Spread of Antibiotic Resistance Genes in Soils Across China . | SSRN , 2025 . |
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Two facultatively aerobic strains, designated SGZ-02(T) and SGZ-792(T), were isolated from plant Pennisetum sp., exhibiting the highest 16S rRNA gene sequence similarities with the type strains of Sphingomonas zeae LMG 28739(T) (98.6%) and Massilia forsythiae NBRC 114511(T) (98.4%), respectively. SGZ-02(T) grew between 5 and 45 degrees C, pH 5.0-11.0 and tolerated NaCl concentrations of 0-4% (w/v), whereas SGZ-792(T) thrived at 5-40 degrees C, pH 5.0-11.0 and NaCl tolerance to 0-3.5% (w/v). The major quinone of SGZ-02(T) was ubiquinone-10, with the dominant fatty acids being C-16:0 (13.5%), Summed Feature 3 (6.3%), C-14:02-OH (5.3%) and Summed Feature 8 (66.3%). SGZ-792(T) predominantly contained ubiquinone-8, with major fatty acids being C-16:0 (20.3%), Summed Feature 3 (5.0%) and Summed Feature 8 (54.7%). Average nucleotide identity and digital DNA-DNA hybridization values between two strains and their closest references strains were below the bacterial species threshold. Based on genotypic and phenotypic characteristics, strains SGZ-02(T) and SGZ-792(T) are proposed as novel species within the genera Sphingomonas and Massilia, respectively. The suggested names for the new species are Sphingomonas fuzhouensis sp. nov. (SGZ-02(T) = GDMCC 1.4033(T) = JCM 36769(T)) and Massilia phyllosphaerae sp. nov. (SGZ-792(T) = GDMCC 1.4211(T) = JCM 36643(T)), respectively.
Keyword ：
Massilia phyllosphaerae sp. nov. Massilia phyllosphaerae sp. nov. Plant growth-promoting Plant growth-promoting Polyphasic taxonomy Polyphasic taxonomy Sphingomonas fuzhouensis sp. nov. Sphingomonas fuzhouensis sp. nov.
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| GB/T 7714 | Yao, Ling , Liu, Guo-Hong , Zhang, Shu-Yi et al. Genome-based taxonomy and functional prediction of Sphingomonas fuzhouensis sp. nov. and Massilia phyllosphaerae sp. nov. isolated from Pennisetum sp. with plant growth-promoting potential [J]. | ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY , 2025 , 118 (1) . |
| MLA | Yao, Ling et al. "Genome-based taxonomy and functional prediction of Sphingomonas fuzhouensis sp. nov. and Massilia phyllosphaerae sp. nov. isolated from Pennisetum sp. with plant growth-promoting potential" . | ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY 118 . 1 (2025) . |
| APA | Yao, Ling , Liu, Guo-Hong , Zhang, Shu-Yi , Gao, Peng , Rensing, Christopher , Yang, Qiu-E et al. Genome-based taxonomy and functional prediction of Sphingomonas fuzhouensis sp. nov. and Massilia phyllosphaerae sp. nov. isolated from Pennisetum sp. with plant growth-promoting potential . | ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY , 2025 , 118 (1) . |
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The COVID-19 pandemic has profoundly impacted the environment due to changes in human activities, including the widespread use of disinfectants. While previous studies have shown that increased disinfectant use during the pandemic affected the antibiotic resistome in aquatic environments, its impact on soils remains largely unexplored. In this study, we analyzed 332 soil metagenomic samples collected across China before (2017-2019) and during (2020-2022) the pandemic to assess the effects on antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and the soil bacterial community. Our results revealed a significant increase in the abundance of ARGs and MGEs in farmland soils during the COVID-19 pandemic. Moreover, the abundance of potentially pathogenic bacteria, such as Pseudomonas, Salmonella, and Vibrio, increased significantly during the pandemic. Partial least squares path modeling indicated that disinfectant use was a key factor associated with the spread of ARGs, primarily by enhancing MGE-mediated gene transfer. These findings suggest that shifts in human activity during the pandemic have contributed to the dissemination of soil ARGs and underscore the importance of managing microbial resistance within the One Health framework.
Keyword ：
Antibiotic resistance genes Antibiotic resistance genes COVID-19 COVID-19 Human activity Human activity Mobile genetic elements Mobile genetic elements Soil bacterial communities Soil bacterial communities
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| GB/T 7714 | Wu, Jiawei , He, Yuqi , Liao, Hanpeng et al. Human activities accelerated the spread of antibiotic resistance in farmland soils across China during the COVID-19 pandemic [J]. | ENVIRONMENTAL TECHNOLOGY & INNOVATION , 2025 , 40 . |
| MLA | Wu, Jiawei et al. "Human activities accelerated the spread of antibiotic resistance in farmland soils across China during the COVID-19 pandemic" . | ENVIRONMENTAL TECHNOLOGY & INNOVATION 40 (2025) . |
| APA | Wu, Jiawei , He, Yuqi , Liao, Hanpeng , Liu, Chen , Ai, Chaofan , Guan, Yanlong et al. Human activities accelerated the spread of antibiotic resistance in farmland soils across China during the COVID-19 pandemic . | ENVIRONMENTAL TECHNOLOGY & INNOVATION , 2025 , 40 . |
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BackgroundAntimicrobial resistance poses a substantial and growing threat to global health. While antibiotic resistance genes (ARGs) are tracked most closely in clinical settings, their spread remains poorly understood in non-clinical environments. Mitigating the spread of ARGs in non-clinical contexts such as soil could limit their enrichment in food webs.ResultsMulti-omics (involving metagenomics, metatranscriptomics, viromics, and metabolomics) and direct experimentation show that targeting keystone bacterial taxa by phages can limit ARG maintenance and dissemination in natural soil environments. Based on the metagenomic analysis, we first show that phages from activated sludge can regulate soil microbiome composition and function in terms of reducing ARG abundances and changing the bacterial community composition. This effect was mainly driven by a reduction in the abundance and activity of Streptomyces genus, which is well known for encoding both antibiotic resistance and synthesis genes. To validate the significance of this keystone species for the loss of ARGs, we enriched phage consortia specific to Streptomyces and tested their effect on ARG abundances on 48 soil samples collected across China. We observed a consistent reduction in ARG abundances across all soils, confirming that Streptomyces-enriched phages could predictably change the soil microbiome resistome and mitigate the prevalence of ARGs. This study highlights that phages can be used as ecosystem engineers to control the spread of antibiotic resistance in the environment.ConclusionOur study demonstrates that some bacterial keystone taxa are critical for ARG maintenance and dissemination in soil microbiomes, and opens new ecological avenues for microbiome modification and resistome control. This study advances our understanding of how metagenomics-informed phage consortia can be used to predictably regulate soil microbiome composition and functioning by targeting keystone bacterial taxa.3cmU8RStwhfZ94ahX7b_G7Video AbstractConclusionOur study demonstrates that some bacterial keystone taxa are critical for ARG maintenance and dissemination in soil microbiomes, and opens new ecological avenues for microbiome modification and resistome control. This study advances our understanding of how metagenomics-informed phage consortia can be used to predictably regulate soil microbiome composition and functioning by targeting keystone bacterial taxa.3cmU8RStwhfZ94ahX7b_G7Video Abstract
Keyword ：
Antibiotic resistance Antibiotic resistance Farmland soil Farmland soil Keystone taxa Keystone taxa Metagenomics and viromics Metagenomics and viromics Phage community Phage community
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| GB/T 7714 | Liao, Hanpeng , Wen, Chang , Huang, Dan et al. Harnessing phage consortia to mitigate the soil antibiotic resistome by targeting keystone taxa Streptomyces [J]. | MICROBIOME , 2025 , 13 (1) . |
| MLA | Liao, Hanpeng et al. "Harnessing phage consortia to mitigate the soil antibiotic resistome by targeting keystone taxa Streptomyces" . | MICROBIOME 13 . 1 (2025) . |
| APA | Liao, Hanpeng , Wen, Chang , Huang, Dan , Liu, Chen , Gao, Tian , Du, Qiyao et al. Harnessing phage consortia to mitigate the soil antibiotic resistome by targeting keystone taxa Streptomyces . | MICROBIOME , 2025 , 13 (1) . |
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The plasmid-mediated transfer of antibiotic resistance genes (ARGs) in complex recent technological advancements that have enabled us to move beyond the limitations of culture-dependent detection of conjugation and have enhanced our ability to track and understand the movement of ARGs in real-world scenarios. We critically assess the applications of single-cell sequencing, fluorescencebased techniques and advanced high-throughput chromatin conformation capture (Hi-C) approaches in elucidating plasmid-host interactions at unprecedented resolution. We also evaluate emerging techniques such as CRISPR-based phage engineering and discuss their potential for developing targeted strategies to curb ARG dissemination. Emerging data derived from these technologies have challenged our previous paradigms on plasmid-host compatibility and an awareness of an emerging uncharted realm for ARGs.
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| GB/T 7714 | Yang, Qiu E. , Gao, Jiang Tao , Zhou, Shun Gui et al. Cutting-edge tools for unveiling the dynamics of plasmid-host interactions [J]. | TRENDS IN MICROBIOLOGY , 2025 , 33 (5) : 496-509 . |
| MLA | Yang, Qiu E. et al. "Cutting-edge tools for unveiling the dynamics of plasmid-host interactions" . | TRENDS IN MICROBIOLOGY 33 . 5 (2025) : 496-509 . |
| APA | Yang, Qiu E. , Gao, Jiang Tao , Zhou, Shun Gui , Walsh, Timothy R. . Cutting-edge tools for unveiling the dynamics of plasmid-host interactions . | TRENDS IN MICROBIOLOGY , 2025 , 33 (5) , 496-509 . |
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Antimicrobial resistance (AMR) and environmental degradation are existential global public health threats. Linking microplastics (MPs) and AMR is particularly concerning as MPs pollution would have significant ramifications on controlling of AMR; however, the effects of MPs on the spread and genetic mechanisms of AMR bacteria remain unclear. Herein, we performed Simonsen end-point conjugation to investigate the impact of four commonly used MPs on transfer of clinically relevant plasmids. The transfer breadth of a representative pA/ C_MCR-8 plasmid across bacterial communities was confirmed by the cell sorting and 16S rRNA gene amplicon sequencing. Our study shows that exposure to four commonly found MPs promotes the conjugation rates of four clinically relevant AMR plasmids by up to 200-fold, when compared to the non-exposed group and that the transfer rates are MP concentrations demonstrate a positive correlation with higher transfer rates. Furthermore, we show that MPs induce the expression of plasmid-borne conjugal genes and SOS-linked genes such as recA, lexA, dinB and dinD. High-throughput sequencing of the broad transmission of plasmid pA/C_MCR-8, shows distribution over two main phyla, Pseudomonadota (50.0 %-95.0 %) and Bacillota (0.4 %-2.0 %). These findings definitively link two global health emergencies - AMR and environmental degradation via MPs, and to tackle global AMR, we must also now consider plastic utilisation and waste management.
Keyword ：
Antimicrobial resistance Antimicrobial resistance Conjugation Conjugation Horizontal gene transfer Horizontal gene transfer Microplastics Microplastics Plasmids Plasmids
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| GB/T 7714 | Yang, Qiu E. , Lin, Zhenyan , Gan, Dehao et al. Microplastics mediates the spread of antimicrobial resistance plasmids via modulating conjugal gene expression [J]. | ENVIRONMENT INTERNATIONAL , 2025 , 195 . |
| MLA | Yang, Qiu E. et al. "Microplastics mediates the spread of antimicrobial resistance plasmids via modulating conjugal gene expression" . | ENVIRONMENT INTERNATIONAL 195 (2025) . |
| APA | Yang, Qiu E. , Lin, Zhenyan , Gan, Dehao , Li, Minchun , Liu, Xuedan , Zhou, Shungui et al. Microplastics mediates the spread of antimicrobial resistance plasmids via modulating conjugal gene expression . | ENVIRONMENT INTERNATIONAL , 2025 , 195 . |
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Klebsiella pneumoniae is widely recognized as a pathogen responsible for hospital-acquired infections and community-acquired invasive infections. It has rapidly become a significant global public health threat due to the emergence of hypervirulent and multidrug-resistant strains, which have increased the challenges associated with treating life-threatening infections. Tellurium resistance genes are widespread on virulence plasmids in K. pneumoniae isolates. However, the core function of the ter operon (terZABCDEF) in K. pneumoniae remains unclear. In this study, the multidrug-resistant K. pneumoniae P1927 strain was isolated from the sputum of a hospitalized pneumonia patient. The ter operon, along with antimicrobial resistance and virulence genes, was identified on a large hybrid plasmid in K. pneumoniae P1927. We generated a terC deletion mutant and demonstrated that this mutant exhibited reduced virulence in a Galleria mellonella larva infection model. Further physiological functional analysis revealed that terC is not only important for Te(IV) resistance but also for resistance to Zn(II), Mn(II), and phage infection. All genes of the ter operon were highly inducible by Zn(II), which is a stronger inducer than Te(IV), and the terBCDE genes were also induced by Mn(II). Collectively, our study demonstrates novel physiological functions of TerC in Zn(II) resistance and virulence in K. pneumoniae.IMPORTANCEKlebsiella pneumoniae has rapidly become a global threat to public health. Although the ter operon is widely identified in clinical isolates, its physiological function remains unclear. It has been proposed that proteins encoded by the ter operon form a multi-site metal-binding complex, but its exact function is still unknown. TerC, a central component of the tellurium resistance determinant, was previously shown to interact with outer membrane proteins OmpA and KpsD in Escherichia coli, suggesting potential changes in outer membrane structure and properties. Here, we report that TerC confers resistance to Zn(II), Mn(II), and phage infection, and Zn(II) was shown to be a strong inducer of the ter operon. Furthermore, TerC was identified as a novel virulence factor. Taken together, our results expand our understanding of the physiological functions encoded by the ter operon and its role in the virulence of K. pneumoniae, providing deeper insights into the link between heavy metal(loid) resistance determinants and virulence in pathogenic bacteria.
Keyword ：
Klebsiella pneumoniae Klebsiella pneumoniae TerC TerC virulence virulence zinc detoxification zinc detoxification
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| GB/T 7714 | Yang, Ruixiang , Han, Shuang , Yu, Yanshuang et al. The Klebsiella pneumoniae tellurium resistance gene terC contributes to both tellurite and zinc resistance [J]. | MICROBIOLOGY SPECTRUM , 2025 , 13 (5) . |
| MLA | Yang, Ruixiang et al. "The Klebsiella pneumoniae tellurium resistance gene terC contributes to both tellurite and zinc resistance" . | MICROBIOLOGY SPECTRUM 13 . 5 (2025) . |
| APA | Yang, Ruixiang , Han, Shuang , Yu, Yanshuang , Li, Hongru , Helmann, John D. , Schaufler, Katharina et al. The Klebsiella pneumoniae tellurium resistance gene terC contributes to both tellurite and zinc resistance . | MICROBIOLOGY SPECTRUM , 2025 , 13 (5) . |
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Understanding the extraordinary environmental adaptability of prokaryotes is crucial for manipulating microbial communities, as their adaptive mechanisms drive community dynamics, resilience and functional responses to interventions like bioremediation. Microbial adaptation to the environment is shaped not only by their intrinsic characteristics but also by interactions with other microorganisms. Among them, temperate phages, which reside alongside cellular microorganisms across diverse ecosystems, are emerging as key players in microbial adaptation. This review delves into the contribution of temperate phages to microbial adaptation across multiple levels. It begins with a survey of culture-dependent studies that reveal the complex mechanisms by which temperate phages facilitate adaptation at the individual and population levels. The review then explores how temperate phage-host symbioses interact with selection pressures in complex environments, assessing both the influence of these pressures on lysogeny at the community level and how prophages respond. Finally, building on established concepts and recent scientific advances, this review outlines the potential for harnessing temperate phages to help address major societal challenges. This synthesis underscores the importance of temperate phages and encourages further exploration in phage ecology.
Keyword ：
auxiliary metabolic genes (AMGs) auxiliary metabolic genes (AMGs) microbial adaptation microbial adaptation prophage prophage temperate phage temperate phage
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| GB/T 7714 | Tang, Xiang , Liao, Han-Peng , Gao, Jiang-Tao et al. Omnipresent Allies: The Role of Temperate Phages in Microbial Adaptation Across Ecosystems [J]. | ENVIRONMENTAL MICROBIOLOGY , 2025 , 27 (11) . |
| MLA | Tang, Xiang et al. "Omnipresent Allies: The Role of Temperate Phages in Microbial Adaptation Across Ecosystems" . | ENVIRONMENTAL MICROBIOLOGY 27 . 11 (2025) . |
| APA | Tang, Xiang , Liao, Han-Peng , Gao, Jiang-Tao , Yang, Qiu-E , Rensing, Christopher , Zhou, Shun-Gui . Omnipresent Allies: The Role of Temperate Phages in Microbial Adaptation Across Ecosystems . | ENVIRONMENTAL MICROBIOLOGY , 2025 , 27 (11) . |
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Hyperthermophilic composting (HTC) is a promising strategy for the treatment of organic solid waste, leveraging extreme thermophilic conditions (up to 90 degrees C) driven by specialized microbial communities. While microbial community composition and succession have been previously described during HTC, the metabolic activity and adaptation of thermophilic microbiomes remain largely unexplored. In this study, we conducted time-series metagenomic and metatranscriptomic analyses on samples from a full-scale HTC system to characterize the composition, functional potential, and metabolic activity of thermophilic bacteria. A total of 227 non-redundant metagenome-assembled genomes (MAGs) were recovered, including 45 thermophilic MAGs (optimal growth temperatures > 45 degrees C). Metatranscriptomic profiling revealed that thermophilic taxa-such as Thermus thermophilus, Planifilum fulgidum, and Thermaerobacter spp.-were highly transcriptionally active and played vital roles in heat generation through the upregulation of energy production and carbohydrate metabolism pathways. Additionally, these thermophiles exhibited survival and adaptation strategies involving physiological changes (e.g., spore formation, enhanced motility, and genome streamlining) and the induction of thermal resistance mechanisms (e.g., DNA repair systems, heat-shock proteins, and synthesis of compatible solutes). Overall, this study provides novel insights into the diverse survival strategies of thermophilic microbiomes in HTC and suggests potential avenues for optimizing thermophilic biotreatment processes for solid waste management. IMPORTANCE Despite increasing interest in hyperthermophilic composting as a sustainable waste treatment strategy, the mechanisms by which microbial communities both tolerate and drive extreme thermal conditions remain unclear. This study fills a critical knowledge gap by identifying a small group of highly active thermophilic bacteria that dominate during peak composting temperatures and orchestrate endogenous heat production. Using genome-resolved multi-omics, we demonstrate that these thermophiles couple high metabolic output with specialized survival strategies-such as genome streamlining, thermotolerance systems, and adaptive motility systems. These findings advance our understanding of microbial function under extreme conditions and provide a framework for optimizing thermophilic microbiome performance in engineered ecosystems.
Keyword ：
hyperthermophilic composting hyperthermophilic composting metabolic activities metabolic activities metagenomics metagenomics metatranscriptomics metatranscriptomics microbiome microbiome
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| GB/T 7714 | Liu, Chen , He, Yuqi , Zhang, Hongbo et al. Metabolic activity and survival strategies of thermophilic microbiomes during hyperthermophilic composting [J]. | MSYSTEMS , 2025 , 10 (11) . |
| MLA | Liu, Chen et al. "Metabolic activity and survival strategies of thermophilic microbiomes during hyperthermophilic composting" . | MSYSTEMS 10 . 11 (2025) . |
| APA | Liu, Chen , He, Yuqi , Zhang, Hongbo , Zhang, Dong , Ai, Chaofan , Tang, Xiang et al. Metabolic activity and survival strategies of thermophilic microbiomes during hyperthermophilic composting . | MSYSTEMS , 2025 , 10 (11) . |
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The horizontal transfer of plasmids has been recognized as one of the key drivers for the worldwide spread of antimicrobial resistance (AMR) across bacterial pathogens. However, knowledge remain limited about the contribution made by environmental stress on the evolution of bacterial AMR by modulating horizontal acquisition of AMR plasmids and other mobile genetic elements. Here we combined experimental evolution, whole genome sequencing, reverse genetic engineering, and transcriptomics to examine if the evolution of chromosomal AMR to triclosan (TCS) disinfectant has correlated effects on modulating bacterial pathogen (Klebsiella pneumoniae) permissiveness to AMR plasmids and phage susceptibility. Herein, we show that TCS exposure increases the evolvability of K. pneumoniae to evolve TCS-resistant mutants (TRMs) by acquiring mutations and altered expression of several genes previously associated with TCS and antibiotic resistance. Notably, nsrR deletion increases conjugation permissiveness of K. pneumoniae to four AMR plasmids, and enhances susceptibility to various Klebsiella-specific phages through the downregulation of several bacterial defense systems and changes in membrane potential with altered reactive oxygen species response. Our findings suggest that unrestricted use of TCS disinfectant imposes a dual impact on bacterial antibiotic resistance by augmenting both chromosomally and horizontally acquired AMR mechanisms. In this work, Yang et al. provide evidence of triclosan exposure resulting in increased evolvability of K. pneumoniae in experimental evolution studies. They utilize sequencing and transcriptomics to explore the chromosomally and horizontally acquired antimicrobial resistance mechanisms.
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| GB/T 7714 | Yang, Qiu E. , Ma, Xiaodan , Li, Minchun et al. Evolution of triclosan resistance modulates bacterial permissiveness to multidrug resistance plasmids and phages [J]. | NATURE COMMUNICATIONS , 2024 , 15 (1) . |
| MLA | Yang, Qiu E. et al. "Evolution of triclosan resistance modulates bacterial permissiveness to multidrug resistance plasmids and phages" . | NATURE COMMUNICATIONS 15 . 1 (2024) . |
| APA | Yang, Qiu E. , Ma, Xiaodan , Li, Minchun , Zhao, Mengshi , Zeng, Lingshuang , He, Minzhen et al. Evolution of triclosan resistance modulates bacterial permissiveness to multidrug resistance plasmids and phages . | NATURE COMMUNICATIONS , 2024 , 15 (1) . |
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