Gene sequencing is a great way to interpret life, and high-throughput sequencing technology is a revolutionary technological innovation in gene sequencing researches. This technology is characterized by low cost and h...Gene sequencing is a great way to interpret life, and high-throughput sequencing technology is a revolutionary technological innovation in gene sequencing researches. This technology is characterized by low cost and high-throughput data. Currently, high-throughput sequencing technology has been widely applied in multi-level researches on genomics, transcriptomics and epigenomics. And it has fundamentally changed the way we approach problems in basic and translational researches and created many new possibilities. This paper presented a general description of high-throughput sequencing technology and a comprehensive review of its application with plain, concisely and precisely. In order to help researchers finish their work faster and better, promote science amateurs and understand it easier and better.展开更多
Switchgrass(Panicum virgatum L.)as a high-quality bioenergy crop that can effectively improve saline-alkali soil has strong resistance to stress and grows well in marginal soil and some abiotic stress environments.Thi...Switchgrass(Panicum virgatum L.)as a high-quality bioenergy crop that can effectively improve saline-alkali soil has strong resistance to stress and grows well in marginal soil and some abiotic stress environments.This study used alkali-sensitive genotype AM(AM-314/MS-155)and alkali-tolerant genotype ALA(Alamo)as experimental materials to investigate molecular mechanisms of switchgrass tolerance to alkali-salt stress.When the plants were grown to E5 stage,the alkali-salt stress treatment was carried out by soaking method(Na2CO3:NaHCO3=1:9,C(Na+)=150 mmol·L-1 and pH=9.0)and fresh root samples were taken after treatments for 0(CK),6 and 24 h,respectively,the differentially expressed microRNAs and their regulatory network were analyzed.A total of 1049 known miRNAs and 68 novel miRNAs were identified.Seventy-two differentially expressed miRNAs in ALA were more than three times higher than those in AM and 36.1%differentially expressed miRNAs was significantly down-regulated(p<0.05).Through analyses of differentially expressed miRNAs and their target genes,it was found that under alkali-salt stress,differentially expressed miRNAs in AM were mainly involved in the regulation of cellular ROS clearance,ethylene signal transduction,and root,leaf and flower development.MiRNAs in ALA were also involved in water transport,DNA methylation,response to high osmotic pressure,activation of stress-related genes and more complex responses to alkali-salt stress processes,but those in AM were not.ALA was significantly higher than AM in the number of microRNAs responding to alkali-salt stress and in the functional diversity of their regulatory target genes.展开更多
【Background】The application of beneficial-microbial seed soaking prior to sowing represents a novel technology that has not been employed in Lanzhou lily cultivation.We conducted an experiment to explore the impact ...【Background】The application of beneficial-microbial seed soaking prior to sowing represents a novel technology that has not been employed in Lanzhou lily cultivation.We conducted an experiment to explore the impact of this soaking method on the fungal and bacterial community structures using next-generation sequencing technology(NGS).【Methods】Lily bulbs were soaked in a seed treating agent containing beneficial microbes(SP treatment)for 4 hours.Subsequently,they were planted in soil in July and sampled in September to assess plant growth,rhizosphere soil physicochemical properties,and microorganism community structures.In addition,we employed the software PICRUSt and FUNGuild to predict bacterial pathways and fungal functions.【Results】Under SP treatment,there were significant alterations in fungi and bacteria community structures,accompanied by improved soil nutrient status.Notably,the relative abundance of dominant microorganism groups,such as the fungi Basidiomycota,Pseudeurotium,Cladophialophora,Microascus,and Dactylonectria,as well as the bacteria Proteobacteria,Chloroflexi,Ochrobactrium,Lysobacter,and RB41,underwent notable changes.Microorganism function prediction results indicated a reduction in pathotrophic fungi(including plant pathogens)and an increase in endophytic and saprotrophic fungi under SP treatment.Among the top 20 metabolism pathways,80%were upregulated in SP treatment compared to the CK.【Conclusions】Seed soaking with beneficial microbial strain promotes the growth of Lanzhou lily bulbs.The beneficial microorganisms play a crucial role in regulating soil microbial structures,enhancing the accumulation of endophytic fungi,reducing the abundance of pathogens,and improving soil functions.Furthermore,specific microbial groups are found to be involved in maintaining soil health.展开更多
12%difenoconazole+fluxapyroxad SC(commercial name:Jiangong)was first released by BASF in China in 2016.It has been registered to control many diseases,including pear scab,apple Alternaria leaf spot,tomato early blight...12%difenoconazole+fluxapyroxad SC(commercial name:Jiangong)was first released by BASF in China in 2016.It has been registered to control many diseases,including pear scab,apple Alternaria leaf spot,tomato early blight,cucumber powdery mildew,etc.This study evaluated the bioactivity of Jiangong against Alternaria alternata and explored variations of phyllosphere microorganisms in both asymptomatic and tobacco brown spot leaves at different persistence periods(0,5,10,and 15 days post-fungicide application)using high-throughput sequencing technology.The results indicated that Jiangong effectively inhibited mycelial growth(average EC_(50) value of 0.51μg/mL),conidia germination(average EC_(50) value of 3.47μg/mL),and the carbon metabolism of A.alternata.Both asymptomatic and symptomatic leaves presented complex microbial communities.Higher fungal diversity was noted in asymptomatic leaves,while higher bacterial diversity was found in symptomatic leaves.After application,the diversity and abundance of microbial community structures in both types of leaves changed over time.Fungal microbiome communities showed greater sensitivity than bacterial groups,with the microbiome communities of asymptomatic leaves being more affected than those of symptomatic leaves.Fungal community diversity decreased for both symptomatic and asymptomatic leaves after 5 days of application,while the diversity of fungal community in symptomatic leaves showed an upward trend after 10 days of application.Meanwhile,bacterial community diversity increased in both symptomatic and asymptomatic leaves after 5 days of application but then declined in asymptomatic leaves after 15 days.The abundance of the dominant function group of phyllosphere bacteria(metabolism,genetic information processing,environmental information processing)was not affected by the application of Jiangong.However,the abundance of the dominant function group of phyllosphere fungi(animal pathogen-endophyte-wood saprotroph,endophyte-plant pathogen,plant pathogen-undefined saprotroph)was significantly affected by the application of Jiangong,and high variation was found in symptomatic leaves than that of asymptomatic leaves.The application of Jiangong-induced alterations in the community structure of the tobacco phyllosphere microbiome provides a basis for future tobacco brown spot control strategies based on phyllospheric microecology.展开更多
The gut microbiota is a complex ecosystem composed of many bacteria and their metabolites.It plays an irreplaceable role in human digestion,nutrient absorption,energy supply,fat metabolism,immune regulation,and many o...The gut microbiota is a complex ecosystem composed of many bacteria and their metabolites.It plays an irreplaceable role in human digestion,nutrient absorption,energy supply,fat metabolism,immune regulation,and many other aspects.Exploring the structure and function of the gut microbiota,as well as their key genes and metabolites,will enable the early diagnosis and auxiliary diagnosis of diseases,new treatment methods,better effects of drug treatments,and better guidance in the use of antibiotics.The identification of gut microbiota plays an important role in clinical diagnosis and treatment,as well as in drug research and development.Therefore,it is necessary to conduct a comprehensive review of this rapidly evolving topic.Traditional identification methods cannot comprehensively capture the diversity of gut microbiota.Currently,with the rapid development of molecular biology,the classification and identification methods for gut microbiota have evolved from the initial phenotypic and chemical identification to identification at the molecular level.This review integrates the main methods of gut microbiota identification and evaluates their application.We pay special attention to the research progress on molecular biological methods and focus on the application of high-throughput sequencing technology in the identification of gut microbiota.This revolutionary method for intestinal flora identification heralds a new chapter in our understanding of the microbial world.展开更多
Microorganisms,one of the key factors affecting the bioleaching process,change the components of extracellular polymeric substance(EPS)and community structure to survive in leaching environments.In this work,Fourier t...Microorganisms,one of the key factors affecting the bioleaching process,change the components of extracellular polymeric substance(EPS)and community structure to survive in leaching environments.In this work,Fourier transform infrared(FTIR),X-ray powder diffraction(XRD)and 16S rDNA high-throughput sequence analyses were used to reveal the microbial changes in planktonic and sessile phases during bioleaching.The results showed the occupation of sessile cells decreased from 66.2%to(10±3)%.After bioleaching,the planktonic and sessile cells have similar EPS,but they are different from the original cells.Pyrite dissolution mainly occurs at the early and late stages with the decreasing of particle diameter,by 50%and 40%,respectively.The 16S rDNA gene based sequence analysis results in total of 1117420 Reads across the six samples,presented among 7 phyla,9 classes,17 orders,23 families and 31 genera.Genera Leptospirillum and Sulfobacillus are the main bacteria at the early and middle stages,and Leptospirillum is the main genus at the end of bioleaching.Aquabacterium and Acidovorax are special genera in sessile cells and Weissella is special in planktonic ones.展开更多
基金Supported by the National Natural Science Foundations of China(3127218631301791)
文摘Gene sequencing is a great way to interpret life, and high-throughput sequencing technology is a revolutionary technological innovation in gene sequencing researches. This technology is characterized by low cost and high-throughput data. Currently, high-throughput sequencing technology has been widely applied in multi-level researches on genomics, transcriptomics and epigenomics. And it has fundamentally changed the way we approach problems in basic and translational researches and created many new possibilities. This paper presented a general description of high-throughput sequencing technology and a comprehensive review of its application with plain, concisely and precisely. In order to help researchers finish their work faster and better, promote science amateurs and understand it easier and better.
基金Supported by the Natural Science Fund of Heilongjiang Province(LC2016009)(GH)U.S.Department of Energy and U.S.Department of Agricultural Plant Feedstocks Genomics for Bioenergy Program(DE-SC0008338 to XZ and BZ)。
文摘Switchgrass(Panicum virgatum L.)as a high-quality bioenergy crop that can effectively improve saline-alkali soil has strong resistance to stress and grows well in marginal soil and some abiotic stress environments.This study used alkali-sensitive genotype AM(AM-314/MS-155)and alkali-tolerant genotype ALA(Alamo)as experimental materials to investigate molecular mechanisms of switchgrass tolerance to alkali-salt stress.When the plants were grown to E5 stage,the alkali-salt stress treatment was carried out by soaking method(Na2CO3:NaHCO3=1:9,C(Na+)=150 mmol·L-1 and pH=9.0)and fresh root samples were taken after treatments for 0(CK),6 and 24 h,respectively,the differentially expressed microRNAs and their regulatory network were analyzed.A total of 1049 known miRNAs and 68 novel miRNAs were identified.Seventy-two differentially expressed miRNAs in ALA were more than three times higher than those in AM and 36.1%differentially expressed miRNAs was significantly down-regulated(p<0.05).Through analyses of differentially expressed miRNAs and their target genes,it was found that under alkali-salt stress,differentially expressed miRNAs in AM were mainly involved in the regulation of cellular ROS clearance,ethylene signal transduction,and root,leaf and flower development.MiRNAs in ALA were also involved in water transport,DNA methylation,response to high osmotic pressure,activation of stress-related genes and more complex responses to alkali-salt stress processes,but those in AM were not.ALA was significantly higher than AM in the number of microRNAs responding to alkali-salt stress and in the functional diversity of their regulatory target genes.
文摘【Background】The application of beneficial-microbial seed soaking prior to sowing represents a novel technology that has not been employed in Lanzhou lily cultivation.We conducted an experiment to explore the impact of this soaking method on the fungal and bacterial community structures using next-generation sequencing technology(NGS).【Methods】Lily bulbs were soaked in a seed treating agent containing beneficial microbes(SP treatment)for 4 hours.Subsequently,they were planted in soil in July and sampled in September to assess plant growth,rhizosphere soil physicochemical properties,and microorganism community structures.In addition,we employed the software PICRUSt and FUNGuild to predict bacterial pathways and fungal functions.【Results】Under SP treatment,there were significant alterations in fungi and bacteria community structures,accompanied by improved soil nutrient status.Notably,the relative abundance of dominant microorganism groups,such as the fungi Basidiomycota,Pseudeurotium,Cladophialophora,Microascus,and Dactylonectria,as well as the bacteria Proteobacteria,Chloroflexi,Ochrobactrium,Lysobacter,and RB41,underwent notable changes.Microorganism function prediction results indicated a reduction in pathotrophic fungi(including plant pathogens)and an increase in endophytic and saprotrophic fungi under SP treatment.Among the top 20 metabolism pathways,80%were upregulated in SP treatment compared to the CK.【Conclusions】Seed soaking with beneficial microbial strain promotes the growth of Lanzhou lily bulbs.The beneficial microorganisms play a crucial role in regulating soil microbial structures,enhancing the accumulation of endophytic fungi,reducing the abundance of pathogens,and improving soil functions.Furthermore,specific microbial groups are found to be involved in maintaining soil health.
基金Supported by China National Tobacco Corporation[No.110202101048(LS-08)]Hundred’Level Innovative Talent Foundation of Guizhou Province(No.GCC[2022]028-1,GCC[2023]108)+2 种基金Guizhou Science Technology Foundation(No.ZK[2021]Key036)the National Natural Science Foundation of China(No.32160522)Guizhou Province Applied Technology Research and Development Funding Post-subsidy Project and Guizhou Tobacco Company(No.2020XM03,2020XM22,2024XM06).
文摘12%difenoconazole+fluxapyroxad SC(commercial name:Jiangong)was first released by BASF in China in 2016.It has been registered to control many diseases,including pear scab,apple Alternaria leaf spot,tomato early blight,cucumber powdery mildew,etc.This study evaluated the bioactivity of Jiangong against Alternaria alternata and explored variations of phyllosphere microorganisms in both asymptomatic and tobacco brown spot leaves at different persistence periods(0,5,10,and 15 days post-fungicide application)using high-throughput sequencing technology.The results indicated that Jiangong effectively inhibited mycelial growth(average EC_(50) value of 0.51μg/mL),conidia germination(average EC_(50) value of 3.47μg/mL),and the carbon metabolism of A.alternata.Both asymptomatic and symptomatic leaves presented complex microbial communities.Higher fungal diversity was noted in asymptomatic leaves,while higher bacterial diversity was found in symptomatic leaves.After application,the diversity and abundance of microbial community structures in both types of leaves changed over time.Fungal microbiome communities showed greater sensitivity than bacterial groups,with the microbiome communities of asymptomatic leaves being more affected than those of symptomatic leaves.Fungal community diversity decreased for both symptomatic and asymptomatic leaves after 5 days of application,while the diversity of fungal community in symptomatic leaves showed an upward trend after 10 days of application.Meanwhile,bacterial community diversity increased in both symptomatic and asymptomatic leaves after 5 days of application but then declined in asymptomatic leaves after 15 days.The abundance of the dominant function group of phyllosphere bacteria(metabolism,genetic information processing,environmental information processing)was not affected by the application of Jiangong.However,the abundance of the dominant function group of phyllosphere fungi(animal pathogen-endophyte-wood saprotroph,endophyte-plant pathogen,plant pathogen-undefined saprotroph)was significantly affected by the application of Jiangong,and high variation was found in symptomatic leaves than that of asymptomatic leaves.The application of Jiangong-induced alterations in the community structure of the tobacco phyllosphere microbiome provides a basis for future tobacco brown spot control strategies based on phyllospheric microecology.
文摘The gut microbiota is a complex ecosystem composed of many bacteria and their metabolites.It plays an irreplaceable role in human digestion,nutrient absorption,energy supply,fat metabolism,immune regulation,and many other aspects.Exploring the structure and function of the gut microbiota,as well as their key genes and metabolites,will enable the early diagnosis and auxiliary diagnosis of diseases,new treatment methods,better effects of drug treatments,and better guidance in the use of antibiotics.The identification of gut microbiota plays an important role in clinical diagnosis and treatment,as well as in drug research and development.Therefore,it is necessary to conduct a comprehensive review of this rapidly evolving topic.Traditional identification methods cannot comprehensively capture the diversity of gut microbiota.Currently,with the rapid development of molecular biology,the classification and identification methods for gut microbiota have evolved from the initial phenotypic and chemical identification to identification at the molecular level.This review integrates the main methods of gut microbiota identification and evaluates their application.We pay special attention to the research progress on molecular biological methods and focus on the application of high-throughput sequencing technology in the identification of gut microbiota.This revolutionary method for intestinal flora identification heralds a new chapter in our understanding of the microbial world.
基金Project(U1608254)supported by the Special Fund for the National Natural Science Foundation of ChinaProjects(ZJKY2017(B)KFJJ01,ZJKY2017(B)KFJJ02)supported by the Zijin Mining Group Co.,Ltd.,China。
文摘Microorganisms,one of the key factors affecting the bioleaching process,change the components of extracellular polymeric substance(EPS)and community structure to survive in leaching environments.In this work,Fourier transform infrared(FTIR),X-ray powder diffraction(XRD)and 16S rDNA high-throughput sequence analyses were used to reveal the microbial changes in planktonic and sessile phases during bioleaching.The results showed the occupation of sessile cells decreased from 66.2%to(10±3)%.After bioleaching,the planktonic and sessile cells have similar EPS,but they are different from the original cells.Pyrite dissolution mainly occurs at the early and late stages with the decreasing of particle diameter,by 50%and 40%,respectively.The 16S rDNA gene based sequence analysis results in total of 1117420 Reads across the six samples,presented among 7 phyla,9 classes,17 orders,23 families and 31 genera.Genera Leptospirillum and Sulfobacillus are the main bacteria at the early and middle stages,and Leptospirillum is the main genus at the end of bioleaching.Aquabacterium and Acidovorax are special genera in sessile cells and Weissella is special in planktonic ones.
