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学者姓名：廖汉鹏
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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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本发明公开了一种噬菌体、噬菌体制剂及其在削减氧化亚氮排放中的应用，该噬菌体拉丁名为Shigella flexneri phage，被命名为B003，噬菌体B003于2024年7月1日保藏于中国典型培养物保藏中心，保藏编号为CCTCC NO：M 20241434；该噬菌体B003对福氏志贺菌具有较强的裂解作用，其噬菌体制剂可以有效削减堆肥产品储存过程中氧化亚氮的排放量，适用于各类有机废弃物的堆肥处理。通过接种福氏志贺菌噬菌体B003制剂，减少堆肥产品储存过程中的氧化亚氮排放，降低了堆肥产品排放温室气体的风险，提高了堆肥处理的安全性和环保性。
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| GB/T 7714 | 廖汉鹏 , 艾超凡 , 周顺桂 . 一种噬菌体、噬菌体制剂及其在削减氧化亚氮排放中的应用 : CN202411752296.2[P]. | 2024-12-02 . |
| MLA | 廖汉鹏 et al. "一种噬菌体、噬菌体制剂及其在削减氧化亚氮排放中的应用" : CN202411752296.2. | 2024-12-02 . |
| APA | 廖汉鹏 , 艾超凡 , 周顺桂 . 一种噬菌体、噬菌体制剂及其在削减氧化亚氮排放中的应用 : CN202411752296.2. | 2024-12-02 . |
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Bacteria play a pivotal role in nutrient turnover during the composting process. However, studies relying on total DNA analysis for bacterial community may be confounded by the presence of extracellular DNA from dead cells. In this study, ethidium monoazide (EMA) was employed to extract intracellular DNA from composting samples for amplicon and metagenomic sequencing, enabling the assessment of active bacterial community dynamics during cattle manure composting. The results revealed that total DNA-based 16S rRNA sequencing could only represent 36.9 %-81.6 % of the active bacterial communities. In contrast, EMA-based 16S rRNA sequencing identified Proteobacteria as the dominant active bacterial phylum throughout the composting process, with Actinobacteria exhibiting increased activity during the maturation phase. EMA-based metagenomic sequencing further showed that carbon and nitrogen metabolism genes showed the highest activity during the initial phase. Proteobacteria were identified as key functional bacteria in nutrient turnover, with its contribution reaching 55.4 % and participating in 82.1 % (23/28) of metabolic pathways. Meanwhile, Firmicutes (bin-23, g_Capillibacterium, bin-66, c_Bacilli) were the sole active nitrogen-fixing bacteria, harboring nitrogenase genes (nifH and nifD). This study offers novel understandings regarding the contribution of active bacteria in nutrient turnover and highlights the importance of distinguishing between active and total bacterial communities for a better understanding of microbial processes in composting systems.
Keyword ：
Active bacteria Active bacteria Metagenomic sequencing Metagenomic sequencing Nutrient cycling Nutrient cycling Thermophilic composting Thermophilic composting
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| GB/T 7714 | Ai, Chaofan , He, Yuqi , Cheng, Zhiwei et al. Unveiling of active bacteria associated with nutrient cycling during cattle manure composting [J]. | ENVIRONMENTAL RESEARCH , 2025 , 286 . |
| MLA | Ai, Chaofan et al. "Unveiling of active bacteria associated with nutrient cycling during cattle manure composting" . | ENVIRONMENTAL RESEARCH 286 (2025) . |
| APA | Ai, Chaofan , He, Yuqi , Cheng, Zhiwei , Wu, Jiawei , Liu, Chen , Wang, Na et al. Unveiling of active bacteria associated with nutrient cycling during cattle manure composting . | ENVIRONMENTAL RESEARCH , 2025 , 286 . |
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本发明属于微生物应用领域，公开了一种削减抗生素抗性基因的混合菌剂及其应用，该混合菌剂包括新芽孢杆菌(Neobacillus sedimentimangrovi)J35和土壤短波单胞菌(Brevundimonas terrae)KanS2，保藏编号分别为CCTCC NO：M 20241436和CCTCC NO：M 20241435。本发明的混合菌剂中两株细菌协同共生，分泌产生H2O2，利用所分泌H2O2的强氧化性高效降解堆肥中的ARGs，对ARGs的削减效率最高达到94.5％，能够有效控制ARGs在堆肥产品中传播，提高堆肥处理的安全性和环保性，简单易行、高效可靠，具有广阔的应用前景。
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| GB/T 7714 | 周顺桂 , 廖汉鹏 , 艾超凡 . 一种削减抗生素抗性基因的混合菌剂及其应用 : CN202411752292.4[P]. | 2024-12-02 . |
| MLA | 周顺桂 et al. "一种削减抗生素抗性基因的混合菌剂及其应用" : CN202411752292.4. | 2024-12-02 . |
| APA | 周顺桂 , 廖汉鹏 , 艾超凡 . 一种削减抗生素抗性基因的混合菌剂及其应用 : CN202411752292.4. | 2024-12-02 . |
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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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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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噬菌体通过自身的复制和裂解作用显著影响环境中微生物群落的丰度、种群组成和功能，在调控微食物网结构和生物地球化学循环中具有重要作用。相比于其他环境，土壤中噬菌体的数量更为庞大，功能可能更为重要。随着研究进展，土壤噬菌体的生态功能愈发得到关注，但土壤噬菌体对植物-微生物互作和根际微生物群落形成的关键作用及机制依然不清。本文综述了植物根际噬菌体生态的研究进展，总结了根际噬菌体的存在状态以及与微生物群落和环境因素间的关系，探讨了土壤噬菌体影响植物-微生物互作和根际微生物群落形成过程的作用机制，并对未来根际噬菌体生态研究的发展方向及对农业可持续发展的潜在贡献进行展望。
Keyword ：
定殖 定殖 有益微生物 有益微生物 根际细菌 根际细菌 植物-微生物互作 植物-微生物互作 溶原性转换 溶原性转换 病毒裂解 病毒裂解
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| GB/T 7714 | 钟玉君 , 梁小龙 , 王永峰 et al. 植物根际噬菌体生态研究进展 [J]. | 生态学杂志 , 2025 , 44 (11) : 3789-3800 . |
| MLA | 钟玉君 et al. "植物根际噬菌体生态研究进展" . | 生态学杂志 44 . 11 (2025) : 3789-3800 . |
| APA | 钟玉君 , 梁小龙 , 王永峰 , 朱冬 , 廖汉鹏 , 谢柠桧 et al. 植物根际噬菌体生态研究进展 . | 生态学杂志 , 2025 , 44 (11) , 3789-3800 . |
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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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