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Advances in Nanomaterial-microbe Coupling System for Removal of Emerging Contaminants

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Chemical Research in Chinese Universities 2023年第3期39卷 389-394页

作者： REN Chongyuan BAI Rui CHEN Wei LI Junpeng ZHOU Xudong TIAN Xiaochun ZHAO Feng CAS Key Laboratory of Urban Pollutant Conversion Institute of Urban EnvironmentChinese Academy of SciencesXiamen361021P.R.China University of Chinese Academy of Sciences Beijing100049P.R.China College of Life Sciences Fujian Agriculture and Forestry UniversityFuzhou350002P.R.China

Emerging contaminants are characterized by toxicity,environmental durability,and bioaccumulation.How to effectively remove them has attracted tremendous attention in the field of environmental science and engineering.Nanomaterial-microbe coupling systems driven by photo-electrochemistry have high degradation efficiency and low cost by combining the advantages of nanomaterials and microorganisms in pollutant treatment.This review summarizes the recent development of the nanomaterial-microbe system for the removal of emerging contaminants,which is divided into exogenous nanomaterial-microbe and endogenous nanomaterial-microbe.The interaction mechanism of materials and microorganisms is addressed from the particular perspective of extracellular electron transfer and redox reactions,and the advantages and challenges of the pollutants treatment are analyzed.Furthermore,future applications in the degradation of emerging contaminants in environmental fields have been prospected.

关键词： Emerging contaminant Nanomaterial microbe Extracellular electron transfer

Modeling methane dynamics in three wetlands in Northeastern China by using the CLM-microbe model

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Ecosystem Health and Sustainability 2022年第1期8卷 109-122页

作者： Yunjiang Zuo Yihui Wang Liyuan He Nannan Wang Jianzhao Liu Fenghui Yuan Kexin Li Ziyu Guo Ying Sun Xinhao Zhu Lihua Zhang Changchun Song Li Sun Xiaofeng Xu Key Laboratory of Wetland Ecology and Environment Northeast Institute of Geography and AgroecologyChinese Academy of SciencesChangchunJilinChina University of the Chinese Academy of Sciences BeijingChina Biology Department San Diego State UniversitySan DiegoCAUSA Key Laboratory of Forest Ecology and Management Institute of Applied EcologyChinese Academy of SciencesShenyangLiaoningChina Department of Soil Waterand ClimateUniversity of MinnesotaSaint PaulMNUSA College of Life and Environmental Sciences Minzu University of ChinaBeijingChina

Wetlands account for up to 70%of the natural source of methane(CH_(4))in terrestrial ecosystems on a global scale.Soil microbes are the ultimate producers and biological consumers of CH_(4)in wetlands.Therefore,simulating microbial mechanisms of CH_(4)production and consumptionwould improve the predictability of CH_(4)flux in wetland ecosystems.In this study,we applied a microbial-explicit model,the CLM-microbe,to simulate CH_(4)flux in three major natural wetlands in northeastern China.The CLM-microbe model was able to capture the seasonal variation of gross primary productivity(GPP),dissolved organic carbon(DOC),and CH_(4)flux.The CLM-microbe model explained more than 40%of the variation in GPP and CH_(4)flux across sites.Marsh wetlands had higher CH_(4)flux than mountain peatlands.Ebullition dominated the CH_(4)transport pathway in all three wetlands.The methanogenesis dominates while methanotroph makes a minor contribution to the CH_(4)flux,making all wetlands a CH_(4)source.Sensitivity analysis indicated that microbial growth and death rates are the key factors governing CH_(4)emission and vegetation physiological properties(flnr)and maintenance respiration predominate GPP variation.Explicitly simulating microbial processes allows genomic information to be incorporated,laying a foundation for better predicting CH_(4)dynamics under the changing environment.

关键词： CH_(4)flux microbe CLMmicrobe model wetlands

microbe-Mediated Mineral Transformation of Montmorillonite by a Strain of Bacillus Mucilaginosus 3027

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矿物学报 2013年第S1期33卷 126-126页

作者： YANG Xiaoxue LU Anhuai LI Yan WANG Haoran ZHU Yun DING Hongrui Key Laboratory of Orogenic Belts and Crustal Evolution School of Earth and Space Sciences National Research Centre for Geoanalysis

Clay minerals are ubiquitous on epigeosphere, especially in soils and sediments where microbes thrive. The clay-microbe interactions are common in these geological media and greatly contribute to accelerating the mineral transformation process, e.g. the illitization of nontronite (a Fe-rich smectite) catalyzed by microbes under anoxic atmosphere in 2 weeks. However, few has considered montmorillonite, a Fe-poor smectite more typical in natural environments than nontronite. This study therefore focuses on the interaction between montmorillonite and bacteria under conditions relevant to those in natural soils and sediments.

关键词： smectite kaolinite microbe transformation

PathogenTrack and Yeskit:tools for identifying intracellular pathogens from single-cell RNA-sequencing datasets as illustrated by application to COVID-19

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Frontiers of Medicine 2022年第2期16卷 251-262页

作者： Wei Zhang Xiaoguang Xu Ziyu Fu Jian Chen Saijuan Chen Yun Tan Shanghai Institute of Hematology State Key Laboratory of Medical GenomicsNational Research Center for Translational Medicine at ShanghaiRuijin Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai 200025China School of Life Sciences and Biotechnology Shanghai Jiao Tong UniversityShanghai 200240China Department of Thoracic Surgery Shanghai Pulmonary HospitalTongji University School of MedicineShanghai 200433China

Pathogenic microbes can induce cellular dysfunction,immune response,and cause infectious disease and other diseases including cancers.However,the cellular distributions of pathogens and their impact on host cells remain rarely explored due to the limited methods.Taking advantage of single-cell RNA-sequencing(scRNA-seq)analysis,we can assess the transcriptomic features at the single-cell level.Still,the tools used to interpret pathogens(such as viruses,bacteria,and fungi)at the single-cell level remain to be explored.Here,we introduced PathogenTrack,a python-based computational pipeline that uses unmapped scRNA-seq data to identify intracellular pathogens at the single-cell level.In addition,we established an R package named Yeskit to import,integrate,analyze,and interpret pathogen abundance and transcriptomic features in host cells.Robustness of these tools has been tested on various real and simulated scRNA-seq datasets.PathogenTrack is competitive to the state-of-the-art tools such as Viral-Track,and the first tools for identifying bacteria at the single-cell level.Using the raw data of bronchoalveolar lavage fluid samples(BALF)from COVID-19 patients in the SRA database,we found the SARS-CoV-2 virus exists in multiple cell types including epithelial cells and macrophages.SARS-CoV-2-positive neutrophils showed increased expression of genes related to type I interferon pathway and antigen presenting module.Additionally,we observed the Haemophilus parahaemolyticus in some macrophage and epithelial cells,indicating a co-infection of the bacterium in some severe cases of COVID-19.The PathogenTrack pipeline and the Yeskit package are publicly available at GitHub.

关键词： scRNA-seq intracellular pathogen microbe COVID-19 SARS-CoV-2

Advances in fungal-assisted phytoremediation of heavy metals:A review

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Pedosphere 2021年第3期31卷 475-495页

作者： Muhammad KHALID Saeed UR-RAHMAN Danial HASSANI Kashif HAYAT Pei ZHOU Nan HUI Key Laboratory of Urban Agriculture School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240China Joint International Research Laboratory of Metabolic&Developmental Sciences Key Laboratory of Urban Agriculture(South)of Ministry of AgriculturePlant Biotechnology Research CenterFudan-SJTU-Nottingham Plant Biotechnology R&D CenterSchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240China

Trace metals such as manganese(Mn),copper(Cu),zinc(Zn),and iron(Fe)are essential for many biological processes in plant life cycles.However,in excess,they can be toxic and disrupt plant growth processes,which is economically undesirable for crop production.For this reason,processes such as homeostasis and transport control of these trace metals are of constant interest to scientists studying heavily contaminated habitats.Phytoremediation is a promising cleanup technology for soils polluted with heavy metals.However,this technique has some disadvantages,such as the slow growth rate of metal-accumulating plant species,low bioavailability of heavy metals,and long duration of remediation.Microbial-assisted phytoremediation is a promising strategy for hyperaccumulating,detoxifying,or remediating soil contaminants.Arbuscular mycorrhizal fungi(AMF)are found in association with almost all plants,contributing to their healthy performance and providing resistance against environmental stresses.They colonize plant roots and extend their hyphae to the rhizosphere region,assisting in mineral nutrient uptake and regulation of heavy metal acquisition.Endophytic fungi exist in every healthy plant tissue and provide enormous services to their host plants,including growth enhancement by nutrient acquisition,detoxification of heavy metals,secondary metabolite regulation,and enhancement of abiotic/biotic stress tolerance.The aim of the present work is to review the recent literature regarding the role of AMF and endophytic fungi in plant heavy metal tolerance in terms of its regulation in highly contaminated conditions.

关键词： arbuscular mycorrhizal fungi bioremediation endophytic fungi environmental stress metal tolerance microbe plant transporter soil contaminant

USING NUTRITIONAL STRATEGIES TO MITIGATE RUMINAL METHANE EMISSIONS FROM RUMINANTS

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Frontiers of Agricultural Science and Engineering 2023年第3期10卷 390-402页

作者： Jian SUN Guangyong ZHAO Meng M.LI State Key Laboratory of Animal Nutrition China Agricultural UniversityBeijing 100193China

Within the agricultural sector,animal production contributes to 14.5%of global anthropogenic greenhouse gas emissions and produces around 37%of global CH_(4) emissions,mainly due to ruminal fermentation in ruminants.Over 90%of CH_(4) is synthesized by methanogens in the rumen during carbohydrate fermentation.According to different substrates,methanogenesis pathways can be divided into four categories:(1)hydrogenotrophic pathway;(2)acetoclastic pathway;(3)methyl dismutation pathway;and(4)methylreducing pathway.Based on the principle of biochemical reactions in the methanogenesis pathways,this paper reviews the latest publications on CH_(4) decreases in ruminants and described three nutritional strategies in terms of dietary nutrient manipulation(feeding management,feed composition,forage quality and lipids),microbial manipulation(ionophore,defaunation,methanogen inhibitors and probiotics),and chemical manipulation(nitrate,organic acids,plant secondary metabolites and phlorotannins,or halides in seaweeds).For each mitigation strategy,the review discusses effectiveness for decreasing CH_(4) emissions,application prescription,and feed safety based on results from in vitro and in vivo studies.This review summarizes different nutritional strategies to mitigate CH_(4) emissions and proposed comprehensive approaches for future feeding interventions and applications in the livestock industry.

关键词： nutritional strategy mitigation microbe methane ruminant

Deployment of Pre-Industrial Autonomous microbe Sensor in Saudi Arabia’s Injection Seawater System

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Journal of Sensor Technology 2018年第1期8卷 1-17页

作者： Mohammed A.Al-Moniee Xiangyang Zhu Rikke Markfoged Aabdullah H.Al-Wadei Poul L.Pedersen Anders K.Tuxen Fuad I.Al-Nuwaiser Lone Tang Tinna Staghoj Roesen Thomas Lundgaard Saudi Arabian Oil Company(Saudi Aramco) DhahranSaudi Arabia Danish Technological Institute(DTI) AarhusDenmark

Microbial growth in water injection systems can lead to many problems, including biofouling, water quality deterioration, injectivity loss, microbial corrosion, and reservoir formation damage. Monitoring of microbial activities is required in any mitigation strategy, enabling operators to apply and adjust countermeasures properly and in due time. In this study, the pre-industrial autonomous microbe sensor (AMS) was constructed with technical improvements from the prototype for increased sensitivity, durability, robustness, and maintainability. The pre-industrial AMS was lab validated, field proven, and deployed at critical locations of seawater injection network for automated detection of microorganisms under the Saudi Arabia’s harsh environment. An excellent correlation between AMS measurement data (fluorescence count) and actual count of microbial cell number under microscope was established (coefficient of determination, R2 > 0.99) for converting AMS fluorescence count to cell numbers (cell mL-1) in the injection seawater. The pre-industrial AMS only required monthly maintenance with solutions refill, and was able to cope with hot summer months even without protection in an air-conditioned shelter. The study team recommended wider deployment of the online AMS for real-time monitoring of bacteria numbers in the various strategic locations in Saudi Aramco’s complex seawater injection network, as an integral component of pipeline corrosion and leak mitigation program.

关键词： Automated Monitoring Autonomous microbe Sensor Microbial Sensor DNA Staining Injection Seawater

Cell Host & microbe:给蚊子注射细菌可阻断寨卡病毒传播

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现代生物医学进展 2016年第15期 3004-3004页

近日,来自巴西的研究人员通过研究表示,感染沃尔巴克氏体或许可以明显降低蚊子传播寨卡病毒的风险,相关研究刊登于国际杂志Cell Host&microbe上,而这一研究为开发新型方法来阻断寨卡病毒的感染和传播提供希望。如今在诸如澳大利亚、巴... 详细信息

近日,来自巴西的研究人员通过研究表示,感染沃尔巴克氏体或许可以明显降低蚊子传播寨卡病毒的风险,相关研究刊登于国际杂志Cell Hostµbe上,而这一研究为开发新型方法来阻断寨卡病毒的感染和传播提供希望。如今在诸如澳大利亚、巴西、印度尼西亚及越南等国家中研究者已经大量释放沃尔巴克氏体来感染蚊子作为抑制登革热的新型策略,而如今

关键词：沃尔巴克氏体研究者 Cell Host 蚊子 microbe 细菌病毒传播

New evidence of microbe origin for ferromanganese nodules from the East Pacific deep sea floor

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Science China Earth Sciences 2000年第2期43卷 187-192页

作者：胡文宣周怀阳顾连兴张文兰陆现彩符琦潘建明张海生 Department of Earth Sciences State Key Laboratory of Mineral Deposit Research Nanjing University Nanjing China Second Institute of Oceanography State Oceanic Administration Hangzhou China State Key Laboratory of Mineral Deposit Research Nanjing University Nanjing China

Using a fluorescence microscope and EPMA, abundant microbe "bodies" and clear mi-crobic fluorescent microstructure are determined in the ferromanganese nodules recently collected from the East Pacific deep sea floor. The microbic fluorescent structure shows a close relation to the formation of the ferromanganese nodules. According to their morphological features, the microbes are classified into two types: one is named clumpy microbe, which takes a bar-shaped manganese mineral as a pillar and grows like fasciculate coral, resulting in irregular cauliflorate nodules with rough surfaces; the other is called filamentous microbe, which grows in very thin arcuate and/or concentric circular laminae composed of a microbe layer and a metal (manganese and iron)-rich layer, leading to potato-shaped nodules with relatively smooth surfaces. It also can be seen that the two types of microbes are intergrown together, resulting in nodules complicated in compositions and shapes.

关键词： ferromanganese nodule microbic fluorescent microstructure clumpy microbe filamentous microbe.