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微生物（英文）
微生物（英文）
微生物（英文）/Journal mLife
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    Unveiling the hidden world of microorganisms and their impact on the Earth's ecosystems

    Yunfeng YangJizhong Zhou
    339-340页
      原文链接:
    • NETL
    • NSTL
    • 万方数据

    Sequence-discrete species for prokaryotes and other microbes:A historical perspective and pending issues

    Konstantinos T.Konstantinidis
    341-349页
    查看更多>>摘要：Whether prokaryotes,and other microorganisms,form distinct clusters that can be recognized as species remains an issue of paramount theoretical as well as practical consequence in identifying,regulating,and communicating about these organisms.In the past decade,comparisons of thousands of genomes of isolates and hundreds of metagenomes have shown that prokaryotic diversity may be predominantly organized in such sequence-discrete clusters,albeit organisms of intermediate relatedness between the identified clusters are also frequently found.Accumulating evidence suggests,however,that the latter"intermediate"organisms show enough ecological and/or functional distinctiveness to be considered different species.No-tably,the area of discontinuity between clusters often-but not always-appears to be around 85％-95％genome-average nucleotide identity,consistently among different taxa.More recent studies have revealed remarkably similar diversity patterns for viruses and microbial eukaryotes as well.This high consistency across taxa implies a specific mechanistic process that underlies the maintenance of the clusters.The underlying mechanism may be a substantial reduction in the efficiency of homologous recombination,which mediates(successful)horizontal gene transfer,around 95％nucleotide identity.Deviations from the 95％threshold(e.g.,species showing lower intraspecies diversity)may be caused by ecological differentiation that imposes barriers to otherwise frequent gene transfer.While this hypothesis that clusters are driven by ecological differentiation coupled to recombination frequency(i.e.,higher recombination within vs.between groups)is appealing,the supporting evi-dence remains anecdotal.The data needed to rigorously test the hypothesis toward advancing the species concept are also outlined.
      原文链接:
    • NETL
    • NSTL
    • 万方数据

    Gut microbiota research nexus:One Health relationship between human,animal,and environmental resistomes

    Yuhao FuQingyuan DouKornelia SmallaYu Wang...
    350-364页
    查看更多>>摘要：The emergence and rapid spread of antimicrobial resistance is of global public health concern.The gut microbiota harboring diverse commensal and opportunistic bacteria that can acquire resistance via horizontal and vertical gene transfers is considered an important reservoir and sink of antibiotic resistance genes(ARGs).In this review,we describe the reservoirs of gut ARGs and their dynamics in both animals and humans,use the One Health perspective to track the transmission of ARG-containing bacteria between humans,animals,and the environment,and assess the impact of antimicrobial resistance on human health and socioeconomic development.The gut resistome can evolve in an environment subject to various selective pressures,including antibiotic administration and environmental and lifestyle factors(e.g.,diet,age,gender,and living con-ditions),and interventions through probiotics.Strategies to reduce the abundance of clinically relevant antibiotic-resistant bacteria and their resistance determinants in various environmental niches are needed to ensure the mitigation of acquired antibiotic resistance.With the help of effective measures taken at the national,local,personal,and intestinal management,it will also result in preventing or minimizing the spread of infectious diseases.This review aims to improve our understanding of the correlations between intestinal microbiota and antimicrobial resistance and provide a basis for the development of management strategies to mitigate the antimicrobial resistance crisis.
      原文链接:
    • NETL
    • NSTL
    • 万方数据

    The bZIP transcription factor ATF1 regulates blue light and oxidative stress responses in Trichoderma guizhouense

    Yifan LiYanshen LiHuanhong LuTingting Sun...
    365-377页
    查看更多>>摘要：In several filamentous fungi,incident light and environmental stress signaling share the mitogen-activated protein kinase(MAPK)HOG(SAK)pathway.It has been revealed that short-term illumination with blue light triggers the activation of the HOG pathway in Trichoderma spp.In this study,we demonstrate the crucial role of the basic leucine zipper transcription factor ATF1 in blue light responses and signaling downstream of the MAPK HOG1 in Trichoderma guizhouense.The lack of ATF1 severely impaired photoconidiation and delayed vegetative growth and conidial germination.Upon blue light or H2O2 stimuli,HOG1 interacted with ATF1 in the nucleus.Genome-wide transcriptome analyses revealed that 61.8％(509 out of 824)and 85.2％(702 out of 824)of blue light-regulated genes depended on ATF1 and HOG1,respectively,of which 58.4％(481 out of 824)were regulated by both of them.Our results also show that blue light promoted conidial germination and HOG1 and ATF1 played opposite roles in controlling conidial germination in the dark.Additionally,the lack of ATF1 led to reduced oxidative stress resistance,probably because of the downregulation of catalase-encoding genes.Overall,our results demonstrate that ATF1 is the downstream component of HOG1 and is responsible for blue light responses,conidial germination,vegetative growth,and oxidative stress resistance in T.guizhouense.
      原文链接:
    • NETL
    • NSTL
    • 万方数据

    Resilience and functional redundancy of methanogenic digestion microbiome safeguard recovery of methanogenesis activity under the stress induced by microplastics

    Jinting LiuGuofang XuSiyan ZhaoJianzhong He...
    378-388页
    查看更多>>摘要：Microplastics and nanoplastics are emerging pollutants that substantially influence biological element cycling in natural eco-systems.Plastics are also prevalent in sewage,and they accumulate in waste-activated sludge(WAS).However,the impacts of plastics on the methanogenic digestion of WAS and the underpinning microbiome remain underexplored,particularly during long-term operation.In this study,we found that short-term exposure to individual microplastics and nanoplastics(poly-ethylene,polyvinyl chloride,polystyrene,and polylactic acid)at a low concentration(10 particles/g sludge)slightly enhanced methanogenesis by 2.1％-9.0％,whereas higher levels(30-200 particles/g sludge)suppressed methanogenesis by 15.2％-30.1％.Notably,the coexistence of multiple plastics,particularly at low concentrations,showed synergistic sup-pression of methanogenesis.Unexpectedly,methanogenesis activity completely recovered after long-term exposure to plas-tics,despite obvious suppression of methanogenesis by initial plastic exposure.The inhibition of methanogenesis by plastics could be attributed to the stimulated generation of reactive oxygen species.The stress induced by plastics dramatically decreased the relative abundance of methanogens but showed marginal influence on putative hydrolytic and fermentation populations.Nonetheless,the digestion sludge microbiome exhibited resilience and functional redundancy,contributing to the recovery of methanogenesis during the long-term operation of digesters.Plastics also increased the complexity,modularity,and negative interaction ratios of digestion sludge microbiome networks,but their influence on community assembly varied.Interestingly,a unique plastisphere was observed,the networks and assembly of which were distinct from the sludge mi-crobiome.Collectively,the comprehensive evaluation of the influence of microplastics and nanoplastics on methanogenic digestion,together with the novel ecological insights,contribute to better understanding and manipulating this engineered ecosystem in the face of increasing plastic pollution.
      原文链接:
    • NETL
    • NSTL
    • 万方数据

    Climate warming suppresses abundant soil fungal taxa and reduces soil carbon efflux in a semi-arid grassland

    Yunpeng QiuKangcheng ZhangYunfeng ZhaoYexin Zhao...
    389-400页
    查看更多>>摘要：Soil microorganisms critically affect the ecosystem carbon(C)balance and C-climate feedback by directly controlling organic C decomposition and indirectly regulating nutrient availability for plant C fixation.However,the effects of climate change drivers such as warming,precipitation change on soil microbial communities,and C dynamics remain poorly understood.Using a long-term field warming and precipitation manipulation in a semi-arid grassland on the Loess Plateau and a complementary incubation experiment,here we show that warming and rainfall reduction differentially affect the abundance and composition of bacteria and fungi,and soil C efflux.Warming significantly reduced the abundance of fungi but not bacteria,increasing the relative dominance of bacteria in the soil microbial community.In particular,warming shifted the community composition of abundant fungi in favor of oligotrophic Capnodiales and Hypocreales over potential saprotroph Archaeorhizomycetales.Also,precipitation reduction increased soil total microbial biomass but did not significantly affect the abundance or diversity of bacteria.Furthermore,the community composition of abundant,but not rare,soil fungi was significantly correlated with soil CO2 efflux.Our findings suggest that alterations in the fungal community composition,in response to changes in soil C and moisture,dominate the microbial responses to climate change and thus control soil C dynamics in semi-arid grasslands.
      原文链接:
    • NETL
    • NSTL
    • 万方数据

    Variation in resource competition traits among Microcystis strains is affected by their microbiomes

    Dylan BakerCasey M.GodwinMuhtamim KhanamAshley M.Burtner...
    401-415页
    查看更多>>摘要：Freshwater harmful algal blooms are often dominated by Microcystis,a phylogenetically cohesive group of cyanobacteria marked by extensive genetic and physiological diversity.We have previously shown that this genetic diversity and the presence of a microbiome of heterotrophic bacteria influences competitive interactions with eukaryotic phytoplankton.In this study,we sought to explain these observations by characterizing Monod equation parameters for resource usage(maximum growth rateμmax,half-saturation value for growth Ks,and quota)as a function of N and P levels for four strains(NIES-843,PCC 9701,PCC 7806[WT],and PCC 7806 ΔmcyB)in presence and absence of a microbiome derived from Microcystis isolated from Lake Erie.Results indicated limited differences in maximum growth rates but more pronounced differences in half-saturation values among Microcystis strains.The largest impact of the microbiome was reducing the minimal nitrogen concentration sustaining growth and reducing half saturation values,with variable results depending on the Microcystis strain.Microcystis strains also differed from each other in their N and P quotas and the extent to which microbiome presence affected them.Our data highlight the importance of the microbiome in altering Microcystis-intrinsic traits,strain competitive hierarchies,and thus bloom dy-namics.As quota,μmax,and Ks are commonly used in models for harmful algal blooms,our data suggest that model im-provement may be possible by incorporating genotype dependencies of resource-use parameters.
      原文链接:
    • NETL
    • NSTL
    • 万方数据

    The diversity and ecological significance of microbial traits potentially involved in B12 biosynthesis in the global ocean

    Jiayin ZhouWei QinXinda LuYunfeng Yang...
    416-427页
    查看更多>>摘要：Cobalamin(B12),an essential nutrient and growth cofactor for many living organisms on Earth,can be fully synthesized only by selected prokaryotes in nature.Therefore,microbial communities related to B12 biosynthesis could serve as an example subsystem to disentangle the underlying ecological mechanisms balancing the function and taxonomic make-up of complex functional assemblages.By anchoring microbial traits potentially involved in B12 biosynthesis,we depict the biogeographic patterns of B12 biosynthesis genes and the taxa harboring them in the global ocean,despite the limitations of detecting de novo B12 synthesizers via metagenomes alone.Both the taxonomic and functional composition of B12 biosynthesis genes were strongly shaped by depth,differentiating the epipelagic zones from the mesopelagic layers.Functional genes related to B12 biosynthesis were relatively stably distributed across different oceans,but the taxa harboring them varied considerably,showing clear functional redundancy among microbial systems.Microbial taxa carrying B12 biosynthesis genes in the surface water were influenced by environmental factors such as temperature,oxygen,and nitrate.However,the composition of functional genes was only weakly associated with these environmental factors.Null model analyses demonstrated that determinism governed the variations in B12 biosynthesis genes,whereas a higher degree of stochasticity was associated with taxonomic variations.Significant associations were observed between the chlorophyll a concentration and B12 biosynthesis,confirming its importance in primary production in the global ocean.The results of this study reveal an essential ecological mechanism governing the assembly of microbes in nature:the environment selects for function rather than taxonomy;functional redundancy underlies stochastic community assembly.
      原文链接:
    • NETL
    • NSTL
    • 万方数据

    Engineering Nannochloropsis oceanica for the production of diterpenoid compounds

    Zhi-Yan DuWajid W.BhatEric PolinerSean Johnson...
    428-437页
    查看更多>>摘要：Photosynthetic microalgae like Nannochloropsis hold enormous potential as sustainable,light-driven biofactories for the pro-duction of high-value natural products such as terpenoids.Nannochloropsis oceanica is distinguished as a particularly robust host with extensive genomic and transgenic resources available.Its capacity to grow in wastewater,brackish,and sea waters,coupled with advances in microalgal metabolic engineering,genome editing,and synthetic biology,provides an excellent opportunity.In the present work,we demonstrate how N.oceanica can be engineered to produce the diterpene casbene-an important intermediate in the biosynthesis of pharmacologically relevant macrocyclic diterpenoids.Casbene accumulated after stably expressing and targeting the casbene synthase from Daphne genkwa(DgTPS1)to the algal chloroplast.The engineered strains yielded production titers of up to 0.12 mg g-1 total dry cell weight(DCW)casbene.Heterologous overexpression and chloroplast targeting of two upstream rate-limiting enzymes in the 2-C-methyl-D-erythritol 4-phosphate pathway,Coleus forskohlii 1-deoxy-D-xylulose-5-phosphate synthase and geranylgeranyl diphosphate synthase genes,further enhanced the yield of casbene to a titer up to 1.80 mg g-1 DCW.The results presented here form a basis for further development and production of complex plant diterpenoids in microalgae.
      原文链接:
    • NETL
    • NSTL
    • 万方数据

    The construction and optimization of engineered yeast chassis for efficient biosynthesis of 8-hydroxygeraniol

    Yu ZhangMengdi YuanXinxin WuQiuhui Zhang...
    438-449页
    查看更多>>摘要：Microbial production of monoterpenoid indole alkaloids(MIAs)provides a sustainable and eco-friendly means to obtain compounds with high pharmaceutical values.However,efficient biosynthesis of MIAs in heterologous microorganisms is hindered due to low supply of key precursors such as geraniol and its derivative 8-hydroxygeraniol catalyzed by geraniol 8-hydroxylase(G8H).In this study,we developed a facile evolution platform to screen strains with improved yield of geraniol by using the SCRaMbLE system embedded in the Sc2.0 synthetic yeast and confirmed the causal role of relevant genomic targets.Through genome mining,we identified several G8H enzymes that perform much better than the commonly used CrG8H for 8-hydroxygeraniol production in vivo.We further showed that the N-terminus of these G8H enzymes plays an important role in cellular activity by swapping experiments.Finally,the combination of the engineered chassis,optimized biosynthesis pathway,and utilization of G8H led to the final strain with more than 30-fold improvement in producing 8-hydroxygeraniol compared with the starting strain.Overall,this study will provide insights into the construction and opti-mization of yeast cells for efficient biosynthesis of 8-hydroxygeraniol and its derivatives.
      原文链接:
    • NETL
    • NSTL
    • 万方数据