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微生物（英文）
微生物（英文）/Journal mLife
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    A successful start for mLife

    Li HuangJizhong Zhou
    1页
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    Ecosystem Microbiome Science

    Yong-Guan ZhuDong ZhuMatthias C.RilligYunfeng Yang...
    2-10页
    查看更多>>摘要：The microbiome contributes to multiple ecosystem functions and services through its interactions with a complex environment and other organisms.To date,however,most microbiome studies have been carried out on individual hosts or particular environmental compartments.This greatly limits a comprehensive understanding of the processes and functions performed by the microbiome and its dynamics at an ecosystem level.We propose that the theory and tools of ecosystem ecology be used to investigate the connectivity of microorganisms and their interactions with the biotic and abiotic environment within entire ecosystems and to examine their contributions to ecosystem services.Impacts of natural and anthropogenic stressors on ecosystems will likely cause cascading effects on the microbiome and lead to unpredictable outcomes,such as outbreaks of emerging infectious diseases or changes in mutualistic interactions.Despite enormous advances in microbial ecology,we are yet to study microbiomes of ecosystems as a whole.Doing so would establish a new framework for microbiome study:Ecosystem Microbiome Science.The advent and application of molecular and genomic technologies,together with data science and modeling,will accelerate progress in this field.
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    The archaeal KEOPS complex possesses a functional Gon7 homolog and has an essential function independent of the cellular t6A modification level

    Pengju WuQi GanXuemei ZhangYunfeng Yang...
    11-27页
    查看更多>>摘要：Kinase,putative Endopeptidase,and Other Proteins of Small size(KEOPS)is a multisubunit protein complex conserved in eukaryotes and archaea.It is composed of Pcc1,Kae1,Bud32,Cgi121,and Gon7 in eukaryotes and is primarily involved in N6-threonylcarbamoyl adenosine(t6A)modification of transfer RNAs(tRNAs).Recently,it was reported that KEOPS par-ticipates in homologous recombination(HR)repair in yeast.To characterize the KEOPS in archaea(aKEOPS),we conducted genetic and biochemical analyses of its encoding genes in the hyperthermophilic archaeon Saccharolobus islandicus.We show that aKEOPS also possesses five subunits,Pcc1,Kae1,Bud32,Cgi121,and Pcc1-like(or Gon7-like),just like eukaryotic KEOPS.Pcc1-like has physical interactions with Kae1 and Pcc1 and can mediate the monomerization of the dimeric sub-complex(Kae1-Pcc1-Pcc1-Kae1),suggesting that Pcc1-like is afunctional homolog of the eukaryotic Gon7 subunit.Strikingly,none of the genes encoding aKEOPS subunits,including Pcc1 and Pcc1-like,can be deleted in the wild type and in a t6A modification complementary strain named TsaKI,implying that the aKEOPS complex is essential for an additional cellular process in this archaeon.Knock-down of the Cgi121 subunit leads to severe growth retardance in the wild type that is partially rescued in TsaKI.These results suggest that aKEOPS plays an essential role independent of the cellular t6A modification level.In addition,archaeal Cgi121 possesses dsDNA-binding activity that relies on its tRNA 3'CCA tail binding module.Our study clarifies the subunit organization of archaeal KEOPS and suggests an origin of eukaryotic Gon7.The study also reveals a possible link between the function in t6A modification and the additional function,presumably HR.
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    Cell division factor ZapE regulates Pseudomonas aeruginosa biofilm formation by impacting the pqs quorum sensing system

    Xi LiuMinlu JiaJing WangHang Cheng...
    28-42页
    查看更多>>摘要：Pseudomonas aeruginosa is one of the leading nosocomial pathogens that causes both severe acute and chronic infections.The strong capacity of P.aeruginosa to form biofilms can dramatically increase its antibiotic resistance and lead to treatment failure.The biofilm resident bacterial cells display distinct gene expression profiles and phenotypes compared to their free-living counterparts.Elucidating the genetic determinants of biofilm formation is crucial for the development of antibiofilm drugs.In this study,a high-throughput transposon-insertion site sequencing(Tn-seq)approach was employed to identify novel P.aeruginosa biofilm genetic determinants.When analyzing the novel biofilm regulatory genes,we found that the cell division factor ZapE(PA4438)controls the P.aeruginosa pqs quorum sensing system.The ΔzapE mutant lost fitness against the wild-type PAO1 strain in biofilms and its production of 2-heptyl-3-hydroxy-4(1 H)-quinolone(PQS)had been reduced.Further biochemical analysis showed that ZapE interacts with PqsH,which encodes the synthase that converts 2-heptyl-4-quinolone(HHQ)to PQS.In addition,site-directed mutagenesis of the ATPase active site of ZapE(K72A)abolished the positive regulation of ZapE on PQS signaling.As ZapE is highly conserved among the Pseudomonas group,our study suggests that it is a potential drug target for the control of Pseudomonas infections.
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    Regulation of RNase E during the UV stress response in the cyanobacterium Synechocystis sp.PCC 6803

    Satoru WatanabeDamir StazicJens GeorgShota Ohtake...
    43-57页
    查看更多>>摘要：Endoribonucleases govern the maturation and degradation of RNA and are indispensable in the posttranscriptional regulation of gene expression.A key endoribonuclease in Gram-negative bacteria is RNase E.To ensure an appropriate supply of RNase E,some bacteria,such as Escherichia coli,feedback-regulate RNase E expression via the rne 5'-untranslated region(5'UTR)in cis.However,the mechanisms involved in the control of RNase E in other bacteria largely remain unknown.Cyanobacteria rely on solar light as an energy source for photosynthesis,despite the inherent ultraviolet(UV)irradiation.In this study,we first investigated globally the changes in gene expression in the cyanobacterium Synechocystis sp.PCC 6803 after a brief exposure to UV.Among the 407 responding genes 2h after UV exposure was a prominent upregulation of rne mRNA level.Moreover,the enzymatic activity of RNase E rapidly increased as well,although the protein stability decreased.This unique response was underpinned by the increased accumulation of full-length rne mRNA caused by the stabilization of its 5'UTR and suppression of premature transcriptional termi-nation,but not by an increased transcription rate.Mapping of RNA 3'ends and in vitro cleavage assays revealed that RNase E cleaves within a stretch of six consecutive uridine residues within the rne 5'UTR,indicating autoregulation.These observations suggest that RNase E in cyanobacteria contributes to reshaping the transcriptome during the UV stress response and that its required activity level is secured at the RNA level despite the enhanced turnover of the protein.
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    LipR functions as an intracellular pH regulator in Bacillus thuringiensis under glucose conditions

    Xia CaiJiaxin QinXuelian LiTaoxiong Yuan...
    58-72页
    查看更多>>摘要：Intracellular pH critically affects various biological processes,and an appropriate cytoplasmic pH is essential for ensuring bacterial growth.Glucose is the preferred carbon source for most heterotrophs;however,excess glucose often causes the accumulation of acidic metabolites,lowering the intracellular pH and inhibiting bacterial growth.Bacillus thuringiensis can effectively cope with glucose-induced stress;unfortunately,little is known about the regulators involved in this process.Here,we document that the target of the dual-function sRNA YhfH,the lipR gene,encodes a Lacl-family transcription factor LipR as an intracellular pH regulator when B.thuringiensis BMB171 is suddenly exposed to glucose.Under glucose conditions,lipR deletion leads to early growth arrest by causing a rapid decrease in intracellular pH(～5.4).Then,the direct targets and a binding motif(GAWAWCRWTWTCAT)of LipR were identified based on the electrophoretic mobility shift assay,the DNase-l footprinting assay,and RNA sequencing,and the gapN gene encoding a key enzyme in glycolysis was directly inhibited by LipR.Fur-thermore,Ni2+is considered a possible effector for LipR.In addition to YhfH,the lipR expression was coregulated by itself,CcpA,and AbrB.Our study reveals that LipR plays a balancing role between glucose metabolism and intracellular pH in B.thuringiensis subjected to glucose stress.
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    Assembly processes underlying bacterial community differentiation among geographically close mangrove forests

    Lu LiuNan WangMin LiuZixiao Guo...
    73-88页
    查看更多>>摘要：Bacterial communities play pivotal roles in nutrient cycling in mangrove forests.The assembly of mangrove microbial com-munities has been found to be influenced by complex factors,such as geographic distance,physicochemical conditions,and plant identity,but the relative importance of these factors and how these factors shape the assembling process remain elusive.We analyzed the bacterial communities sampled from three mangrove species(Aegiceras corniculatum,Bruguiera sexangula,and Kandelia obovata)at three locations along the estuarine Dongzhai Harbor in Hainan,China.We revealed larger differences in rhizosphere bacterial communities among geographical locations than among plant species,indicated by differences in diversity,composition,and interaction networks.We found that dispersal limitation and homogeneous selection have substantial contributions to the assembly of mangrove rhizosphere bacterial communities in all three locations.Following the phylogenetic-bin-based null model analysis(iCAMP)framework,we also found dispersal limitation and homogeneous selection showing dominance in some bins.The greater differences among geographic locations may be mainly attributed to the larger proportions of dispersal limitation even at such a short geographic distance.We also found that beta diversity was positively correlated with environmental distances,implying that the more similar environmental conditions(such as rich carbon and nitrogen contents)among plant species may have shaped similar bacterial communities.We concluded that the geographic distances,which are associated with dispersal limitation,played a key role in assembling mangrove rhizosphere bacterial communities,while physicochemical conditions and plant identity contributed less.
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    Beyond biogeographic patterns:Processes shaping the microbial landscape in soils and sediments along the Yangtze River

    Wenjie WanGeoffrey M.GaddJi-Dong GuWenzhi Liu...
    89-100页
    查看更多>>摘要：Deciphering biogeographic patterns of microorganisms is important for evaluating the maintenance of microbial diversity with respect to the ecosystem functions they drives.However,ecological processes shaping distribution patterns of micro-organisms across large spatial-scale watersheds remain largely unknown.Using Illumina sequencing and multiple statistical methods,we characterized distribution patterns and maintenance diversity of microorganisms(i.e.,archaea,bacteria,and fungi)in soils and sediments along the Yangtze River.Distinct microbial distribution patterns were found between soils and sediments,and microbial community similarity significantly decreased with increasing geographical distance.Physicochemical properties showed a larger effect on microbial community composition than geospatial and climatic factors.Archaea and fungi displayed stronger species replacements and weaker environmental constraints in soils than that in sediments,but opposite for bacteria.Archaea,bacteria,and fungi in soils showed broader environmental breadths and stronger phylogenetic signals compared to those in sediments,suggesting stronger environmental adaptation.Stochasticity dominated community as-semblies of archaea and fungi in soils and sediments,whereas determinism dominated bacterial community assembly.Our results have therefore highlighted distinct microbial distribution patterns and diversity maintenance mechanisms between soils and sediments,and emphasized important roles of species replacement,environmental adaptability,and ecological assembly processes on microbial landscape.Our findings are helpful in predicting loss of microbial diversity in the Yangtze River Basin,and might assist the establishment of environmental policies for protecting fragile watersheds.
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    Design of microaerobically inducible miniR1 plasmids

    Fabiola IslasAndrea SabidoJuan-Carlos SigalaAlvaro R.Lara...
    101-104页
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