首页期刊导航|微生物（英文）
期刊信息/Journal information
微生物（英文）
微生物（英文）
微生物（英文）/Journal mLife
正式出版
收录年代

    Cultivating the unseen:Lessons from James Tiedje

    Yoichi Kamagata
    217-223页
      原文链接:
    • NETL
    • NSTL
    • 万方数据

    Roadmap to tackle antibiotic resistance in the environment under the One Health framework

    Liguan LiTong Zhang
    224-228页
    查看更多>>摘要：Antibiotic resistance has been recognized as a major challenge worldwide for humans."One Health"has been recognized as a key concept for containment of antibiotic resistance.Under the framework,the role of the environment in the development of antibiotic resistance genes(ARGs)has become increasingly obvious.Despite numerous efforts,response to antibiotic re-sistance is considered to be inadequate,which is probably due to the lack of a clear roadmap.Here,we propose a"One Health"roadmap to combat antibiotic resistance in the environment through(1)understanding environmental resistome.The environmental gene pool has long been recognized as the single largest reservoir of both known and novel ARGs.(2)Standardizing ARG quantification.Systematic joint efforts based on standardized quantification are urgently needed to un-derstand the true tempospatial profiles of the environmental resistome.(3)Identifying mechanisms of resistome development.Horizontal gene transfer and co-selection have been recognized as the two main mechanisms contributing to the environmental resistome.(4)Establishing a risk-assessment framework.The first critical step for large-scale cost-effective targeted ARG management in the environment is the risk assessment to identify the priority ARGs for control.(5)Formulating regulatory standards.By correlating the environmental ARG profile with public health,we may identify the indicator ARGs that can be integrated into current environmental quality standards.(6)Developing control strategies.Systematic analysis of available control technologies is required to identify the most feasible ones to curtail the spread of ARGs in the environment.The proposed roadmap under the"One Health"framework provides a guide to tackle antibiotic resistance in the environment.
      原文链接:
    • NETL
    • NSTL
    • 万方数据

    Denitrification and the challenge of scaling microsite knowledge to the globe

    G.Philip Robertson
    229-238页
    查看更多>>摘要：Our knowledge of microbial processes—who is responsible for what,the rates at which they occur,and the substrates consumed and products produced—is imperfect for many if not most taxa,but even less is known about how microsite processes scale to the ecosystem and thence the globe.In both natural and managed environments,scaling links funda-mental knowledge to application and also allows for global assessments of the importance of microbial processes.But rarely is scaling straightforward:More often than not,process rates in situ are distributed in a highly skewed fashion,under the infiuence of multiple interacting controls,and thus often difficult to sample,quantify,and predict.To date,quantitative models of many important processes fail to capture daily,seasonal,and annual fiuxes with the precision needed to effect meaningful management outcomes.Nitrogen cycle processes are a case in point,and denitrification is a prime example.Statistical models based on machine learning can improve predictability and identify the best environmental predictors but are—by themselves—insufficient for revealing process-level knowledge gaps or predicting outcomes under novel environmental conditions.Hybrid models that incorporate well-calibrated process models as predictors for machine learning algorithms can provide both improved understanding and more reliable forecasts under environmental conditions not yet experienced.Incorporating trait-based models into such efforts promises to improve predictions and understanding still further,but much more development is needed.
      原文链接:
    • NETL
    • NSTL
    • 万方数据

    Assessing mechanisms for microbial taxa and community dynamics using process models

    Linwei WuYunfeng YangDaliang NingQun Gao...
    239-252页
    查看更多>>摘要：Disentangling the assembly mechanisms controlling community composition,structure,distribution,functions,and dynamics is a central issue in ecology.Although various approaches have been proposed to examine community assembly mechanisms,quanti-tative characterization is challenging,particularly in microbial ecology.Here,we present a novel approach for quantitatively delineating community assembly mechanisms by combining the consumer-resource model with a neutral model in stochastic differential equations.Using time-series data from anaerobic bioreactors that target microbial 16S rRNA genes,we tested the applicability of three ecological models:the consumer-resource model,the neutral model,and the combined model.Our results revealed that model performances varied substantially as a function of population abundance and/or process conditions.The combined model performed best for abundant taxa in the treatment bioreactors where process conditions were manipulated.In contrast,the neutral model showed the best performance for rare taxa.Our analysis further indicated that immigration rates decreased with taxa abundance and com-petitions between taxa were strongly correlated with phylogeny,but within a certain phylogenetic distance only.The determinism underlying taxa and community dynamics were quantitatively assessed,showing greater determinism in the treatment bioreactors that aligned with the subsequent abnormal system functioning.Given its mechanistic basis,the framework developed here is expected to be potentially applicable beyond microbial ecology.
      原文链接:
    • NETL
    • NSTL
    • 万方数据

    Environmental selection and evolutionary process jointly shape genomic and functional profiles of mangrove rhizosphere microbiomes

    Xiaoli YuQichao TuJihua LiuYisheng Peng...
    253-266页
    查看更多>>摘要：Mangrove reforestation with introduced species has been an important strategy to restore mangrove ecosystem functioning.However,how such activities affect microbially driven methane(CH4),nitrogen(N),and sulfur(S)cycling of rhizosphere microbiomes remains unclear.To understand the effect of environmental selection and the evolutionary process on microbially driven biogeochemical cycles in native and introduced mangrove rhizospheres,we analyzed key genomic and functional profiles of rhizosphere microbiomes from native and introduced mangrove species by metagenome sequencing technologies.Compared with the native mangrove(Kandelia obovata,KO),the introduced mangrove(Sonneratia apetala,SA)rhizosphere microbiome had significantly(p＜0.05)higher average genome size(AGS)(5.8 vs.5.5 Mb),average 16S ribosomal RNA gene copy number(3.5 vs.3.1),relative abundances of mobile genetic elements,and functional diversity in terms of the Shannon index(7.88 vs.7.84)but lower functional potentials involved in CH4 cycling(e.g.,mcrABCDG and pmoABC),N2 fixation(nifHDK),and inorganic S cycling(dsrAB,dsrC,dsrMKJOP,soxB,sqr,and fccAB).Similar results were also observed from the recovered Proteobacterial metagenome-assembled genomes with a higher AGS and distinct functions in the introduced mangrove rhizosphere.Additionally,salinity and ammonium were identified as the main environmental drivers of functional profiles of mangrove rhizosphere microbiomes through deterministic processes.This study advances our understanding of microbially mediated biogeochemical cycling of CH4,N,and S in the mangrove rhizosphere and provides novel insights into the infiuence of environmental selection and evolutionary processes on ecosystem functions,which has important implications for future mangrove reforestation.
      原文链接:
    • NETL
    • NSTL
    • 万方数据

    A small,polyphyletic group of Firmicutes synthesizes trimethylamine from L-carnitine

    Marius VitalYlenia Heinrich-Sanchez
    267-271页
      原文链接:
    • NETL
    • NSTL
    • 万方数据

    Widespread Bathyarchaeia encode a novel methyltransferase utilizing lignin-derived aromatics

    Tiantian YuHaining HuXianhong ZengYinzhao Wang...
    272-282页
    查看更多>>摘要：Lignin degradation is a major process in the global carbon cycle across both terrestrial and marine ecosystems.Bathyarchaeia,which are among the most abundant microorganisms in marine sediment,have been proposed to mediate anaerobic lignin degradation.However,the mechanism of bathyarchaeial lignin degradation remains unclear.Here,we report an enrichment culture of Bathy-archaeia,named Candidatus Baizosediminiarchaeum ligniniphilus DL1YTT001(Ca.B.ligniniphilus),from coastal sediments that can grow with lignin as the sole organic carbon source under mesophilic anoxic conditions.Ca.B.ligniniphilus possesses and highly expresses novel methyltransferase 1(MT1,mtgB)for transferring methoxyl groups from lignin monomers to cob(I)alamin.MtgBs have no homology with known microbial methyltransferases and are present only in bathyarchaeial lineages.Heterologous expression of the mtgB gene confirmed O-demethylation activity.The mtgB genes were identified in metagenomic data sets from a wide range of coastal sediments,and they were highly expressed in coastal sediments from the East China Sea.These findings suggest that Bathyarchaeia,capable of O-demethylation via their novel and specific methyltransferases,are ubiquitous in coastal sediments.
      原文链接:
    • NETL
    • NSTL
    • 万方数据

    Dual functions:A coumarin-chalcone conjugate inhibits cyclic-di-GMP and quorum-sensing signaling to reduce biofilm formation and virulence of pathogens

    Yu ZhangPramod BhasmeDinesh S.ReddyDejian Liu...
    283-294页
    查看更多>>摘要：Antibiotic resistance or tolerance of pathogens is one of the most serious global public health threats.Bacteria in biofilms show extreme tolerance to almost all antibiotic classes.Thus,use of antibiofilm drugs without bacterial-killing effects is one of the strategies to combat antibiotic tolerance.In this study,we discovered a coumarin-chalcone conjugate C9,which can inhibit the biofilm formation of three common pathogens that cause nosocomial infections,namely,Pseudomonas aeruginosa,Staph-ylococcus aureus,and Escherichia coli,with the best antibiofilm activity against P.aeruginosa.Further investigations indicate that C9 decreases the synthesis of the key biofilm matrix exopolysaccharide Psl and bacterial second messenger cyclic-di-GMP.Meanwhile,C9 can interfere with the regulation of the quorum sensing(QS)system to reduce the virulence of P.aeruginosa.C9 treatment enhances the sensitivity of biofilm to several antibiotics and reduces the survival rate of P.aeruginosa under starvation or oxidative stress conditions,indicating its excellent potential for use as an antibiofilm-forming and anti-QS drug.
      原文链接:
    • NETL
    • NSTL
    • 万方数据

    Identification of atypical T4SS effector proteins mediating bacterial defense

    Xi ShenZixiang YangZihan LiDan Xiong...
    295-307页
    查看更多>>摘要：To remain competitive,proteobacteria use various contact-dependent weapon systems to defend against microbial com-petitors.The bacterial-killing type IV secretion system(T4SS)is one such powerful weapon.It commonly controls the killing/competition between species by secreting the lethal T4SS effector(T4E)proteins carrying conserved XVIPCD domains into competing cells.In this study,we sought knowledge to understand whether the bacterial-killing T4SS-producing bacteria encode T4E-like proteins and further explore their biological functions.To achieve this,we designed a T4E-guided approach to discover T4E-like proteins that are designated as atypical T4Es.Initially,this approach required scientists to perform simple BlastP search to identify T4E homologs that lack the XVIPCD domain in the genomes of T4SS-producing bacteria.These homologous genes were then screened in Escherichia coli to identify antibacterial candidates(atypical T4Es)and their neighboring detoxification proteins,followed by testing their gene cotranscription and validating their physical interactions.Using this approach,we did discover two atypical T4E proteins from the plant-beneficial Lysobacter enzymogenes and the phytopathogen Xanthomonas citri.We also provided substantial evidence to show that the atypical T4E protein Le1637-mediated bacterial defense in interspecies interactions between L.enzymogenes and its competitors.Therefore,the newly designed T4E-guided approach holds promise for detecting functional atypical T4E proteins in bacterial cells.
      原文链接:
    • NETL
    • NSTL
    • 万方数据

    Protective efficacy of a universal influenza mRNA vaccine against the challenge of H1 and H5 influenza A viruses in mice

    Yulei LiXi WangXi ZengWenbo Ren...
    308-316页
    查看更多>>摘要：Current infiuenza vaccines need to be updated annually owing to constant antigenic drift in the globular head of the viral surface hemagglutinin(HA)glycoprotein.The immunogenic subdominant stem domain of HA is highly conserved and can be recognized by antibodies capable of binding multiple HA subtypes.Therefore,the HA stem antigen is a promising target for the design of universal infiuenza vaccines.On the basis of an established lipid nanoparticle-encapsulated mRNA vaccine platform,we designed and developed a novel universal infiuenza mRNA vaccine(mHAs)encoding the HA stem antigen of the infiuenza A(H1N1)virus.We tested the efficacy of the mHAs vaccine using a mouse model.The vaccine induced robust humoral and specific cellular immune responses against the stem region of HA.Importantly,two doses of the mHAs vaccine fully protected mice from lethal challenges of the heterologous H1N1 and heterosubtypic H5N8 infiuenza viruses.Vacci-nated mice had less pathological lung damage and lower viral titers than control mice.These results suggest that an mRNA vaccine using the conserved stem region of HA may provide effective protection against seasonal and other possible infiuenza variants.
      原文链接:
    • NETL
    • NSTL
    • 万方数据