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Pedosphere 2018年第2期28卷 261-268页

作者： LIU Hongjun ZHONG Xi HUANG Yan QIAO Cece SHAO Cheng LI Rong SHEN Qirong jiangsu provincial Key Lab for solid organic waste utilization Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization National Engineering Research Center for Organic-based Fertilizers Nanjing Agricultural University

Free amino acids and short peptides(FAPS)that play an important role in plant nutrition can be extracted from rapeseed meal(RSM)by microbial *** enzymolytic activity of one bacterial strain isolated from RSM for the production of FAPS fertilizer(FAPSF)via solid-state fermentation,as well as its detoxification activity for isothiocyanates and oxazolidinethione,was investigated in this *** strain NJNPD41 isolated from RSM piled-soil possessed effective proteolytic activity and was identified as Bacillus flexus on the basis of its morphological,physiological,and biochemical properties,as well as 16S rDNA *** to the uninoculated control,inoculation with the strain NJNPD41 significantly increased the yield of total free amino acids and short peptides by 115%and decreased the content of isothiocyanates and oxazolidinethione by 53%and 60%,respectively,after solid-state *** pot and field experiments showed that FAPSF significantly promoted eggplant growth and enhanced the fruit yield and quality of eggplant compared to the *** conclusion,this study provided a novel method for the high-value utilization of RSM to produce high-quality and low-toxicity FAPSF using the newly isolated strain *** NJNPD41.

关键词： bacterial strain detoxification activity isothiocyanate microbial enzymolysis N pool organic fertilizer solid-statefermentation oxazolidinethione

Coupling of the chemical niche and microbiome in the rhizosphere:implications from watermelon grafting

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Frontiers of Agricultural Science and Engineering 2016年第3期3卷 249-262页

作者： Yang SONG Chen ZHU Waseem RAZA Dongsheng WANG Qiwei HUANG Shiwei GUO Ning LING Qirong SHEN jiangsu provincial coordinated research center for organic solid waste utilization Nanjing Agricultural University Nanjing Institute of Vegetable Science

Grafting is commonly used to overcome soilborne diseases. However, its effects on the rhizodeposits as well as the linkages between the rhizosphere chemical niche and microbiome remained unknown. In this paper,significant negative correlations between the bacterial alpha diversity and both the disease incidence(r = – 0.832,P = 0.005) and pathogen population(r = – 0.786, P = 0.012)were detected. Moreover, our results showed that the chemical diversity not only predicts bacterial alpha diversity but also can impact on overall microbial community structure(beta diversity) in the ***, some anti-fungal compounds including heptadecane and hexadecane were identified in the rhizosphere of grafted watermelon. We concluded that grafted watermelon can form a distinct rhizosphere chemical niche and thus recruit microbial communities with high diversity. Furthermore, the diverse bacteria and the antifungal compounds in the rhizosphere can potentially serve as biological and chemical barriers, respectively, to hinder pathogen invasion. These results not only lead us toward broadening the view of disease resistance mechanism of grafting, but also provide clues to control the microbial composition by manipulating the rhizosphere chemical niche.

关键词： rhizodeposits rhizosphere microbiome diversity Mi Seq sequencing watermelon grafting

Effect of bacterial intra-species community interactions on the production and activity of volatile organic compounds

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Soil Ecology Letters 2021年第1期3卷 32-41页

作者： Jianing Wang Xinlan Mei Zhong Wei Waseem Raza Qirong Shen jiangsu provincial Key Lab for organic solid waste utilization National Engineering Research Center for Organic-based FertilizersJiangsu Collaborative Innovation Center for Solid Organic Waste Resource UtilizationNanjing Agricultural UniversityNanjing 210095China

Microorganisms experience intra-and inter-species interactions in the soil,and how these interactions affect the production of microbial volatile organic compounds(VOCs)is still not *** we evaluated the production and activity of microbial VOCs as driven by bacterial intra-species community *** set up bacterial communities of increasing biodiversity out of 1–4 strains each of the Gram-positive Bacillus and Gram-negative Pseudomonas *** evaluated the ability of each community to provide two VOCmediated services,pathogen suppression and plant-growth promotion and then correlated these services to the production of VOCs by each *** results showed that an increase in community richness from 1 to 4 strains of both genera increased VOC-mediated pathogen suppression and plant-growth promotion on agar medium and in the soil,which was positively correlated with the production of pathogen suppressing and plant growth-promoting *** strains maintained while Bacillus strains reduced community productivity with an increase in community richness and produced eight novel VOCs compared with the *** results revealed that intra-species interactions may vary between Gram-negative and Gram-positive species but improved VOC-mediated functioning with respect to pathogen suppression and plant-growth promotion by affecting the amount and diversity of produced VOCs potentially affecting plant disease outcomes.

关键词： Biodiversity Community richness Ecosystem functioning Intra-species interactions Plant-microbe interactions

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

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mLife 2023年第4期2卷 365-377页

作者： Yifan Li Yanshen Li Huanhong Lu Tingting Sun Jia Gao Jian Zhang Qirong Shen Zhenzhong Yu Nanjing Agricultural University Jiangsu Provincial Key Lab for Organic Solid Waste UtilizationNational Engineering Research Center for Organic-based FertilizersJiangsu Collaborative Innovation Center for Solid Organic Waste Resource UtilizationAgricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu ProvinceNanjingChina Department of Microbiology Karlsruhe Institute of Technology(KIT)—South CampusInstitute for Applied BiosciencesKarlsruheGermany

In several filamentous fungi,incident light and environmental stress signaling share the mitogen-activated protein kinase(MAPK)HOG(SAK)*** has been revealed that short-term illumination with blue light triggers the activation of the HOG pathway in Trichoderma *** 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 *** lack of ATF1 severely impaired photoconidiation and delayed vegetative growth and conidial *** blue light or H2O2 stimuli,HOG1 interacted with ATF1 in the ***-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 *** results also show that blue light promoted conidial germination and HOG1 and ATF1 played opposite roles in controlling conidial germination in the ***,the lack of ATF1 led to reduced oxidative stress resistance,probably because of the downregulation of catalase-encoding ***,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 ***.

关键词： bZiP transcription factor ATF1 light responses MAPK HOG1 oxidative stress Trichoderma guizhouense

Enrichment of beneficial cucumber rhizosphere microbes mediated by organic acid secretion

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Horticulture research 2020年第1期7卷 662-674页

作者： Tao Wen Jun Yuan Xiaoming He Yue Lin Qiwei Huang Qirong Shen jiangsu provincial Key Lab for organic solid waste utilization Key Laboratory of Plant ImmunityJiangsu Collaborative Innovation Center for Solid Organic WastesEducational Ministry Engineering Center of Resource-saving FertilizersNanjing Agricultural University210095 NanjingChina Vegetable research Institute Guangdong Academy of Agricultural SciencesGuangzhou510640 GuangdongChina

Resistant cultivars have played important roles in controlling Fusarium wilt disease,but the roles of rhizosphere interactions among different levels of resistant cultivars are still ***,two phenotypes of cucumber,one resistant and one with increased susceptibility to Fusarium oxysporum ***(Foc),were grown in the soil and hydroponically,and then 16S rRNA gene sequencing and nontargeted metabolomics techniques were used to investigate rhizosphere microflora and root exudate *** high microbial community evenness for the Foc-susceptible cultivar was detected,and the relative abundances of Comamonadaceae and Xanthomonadaceae were higher for the Foc-susceptible cultivar than for the other *** analysis revealed that specific functional traits,such as protein synthesis and secretion,bacterial chemotaxis,and small organic acid metabolism pathways,were significantly upregulated in the rhizobacterial community of the Foc-susceptible cultivar.A machinelearning approach in conjunction with FishTaco plus metabolic pathway analysis revealed that four organic acids(citric acid,pyruvate acid,succinic acid,and fumarate)were released at higher abundance by the Foc-susceptible cultivar compared with the resistant cultivar,which may be responsible for the recruitment of Comamonadaceae,a potential beneficial microbial *** validation demonstrated that Comamonadaceae can be“cultured”by these organic ***,compared with the resistant cultivar,the susceptible cucumber tends to assemble beneficial microbes by secreting more organic acids.

关键词： group susceptibility synthesis

Strategies for timing nitrogen fertilization of pear trees based on the distribution, storage, and remobilization of ^(15)N from seasonal application of (^(15)NH_4)_2SO_4

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Journal of Integrative Agriculture 2020年第5期19卷 1340-1353页

作者： JIANG Hai-bo LI Hong-xu ZHAO Ming-xin MEI Xin-lan KANG Ya-long DONG Cai-xia XU Yang-chun jiangsu provincial Key Lab of solid organic waste utilization/jiangsu Collaborative Innovation center of solid organic wastes/Educational Ministry Engineering center of Resource-saving Fertilizers Nanjing Agricultural UniversityNanjing 210095P.R.China Institute of Fruit and Floriculture Gansu Academy of Agricultural SciencesLanzhou 730070P.R.China

In order to improve the management of nitrogen(N) fertilization in pear orchards, we investigated the effects of application timing on the distribution, storage, and remobilization of N in mature pear trees in a field experiment at Jingtai County, Gansu Province, China. Nine trees were selected for the experiment and each received equal aliquots of 83.33 g N in the autumn, spring, and summer, with ^(15)N-labeled(NH_4)_2SO_4 used in one of the aliquots each season. Results showed that the(^(15)NH_4)_2SO_4 applied in the autumn remained in the soil during the winter. In the following spring this N was absorbed and rapidly remobilized into each organ, especially new organs(leaves, fruit and new shoots). The ^(15)N supplied in spring was rapidly transported to developing fruit between the young fruit and fruit enlargement stages. ^(15)N from the summer application of fertilizer was mainly stored in the coarse roots over the winter, then was mobilized to support growth of new organs in spring. In conclusion, for pear trees we recommend that the autumn application of N-fertilizer be soon after fruit harvest in order to increase N stores in fine roots. Spring application should be between full bloom and the young fruit stages to meet the high N demands of developing fruit. Summer application of fertilizer at the fruit enlargement stage does not contemporaneously affect the growth of pears, but increases the N stored in coarse roots, and in turn the amount available for remobilization in spring.

关键词： fertilization time N distribution N storage N remobilization Pear(Pyrus bretschneideri Rehd cv.Huangguan)

Root exudates mediate plant defense against foliar pathogens by recruiting beneficial microbes

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Soil Ecology Letters 2021年第1期3卷 42-51页

作者： Tao Wen Mengli Zhao Jun Yuan George A.Kowalchuk Qirong Shen jiangsu provincial Key Lab for organic solid waste utilization National Engineering Research Center for Organic-based FertilizersJiangsu Collaborative Innovation Center for Solid Organic Waste Resource UtilizationNanjing Agricultural UniversityNanjing 210095China Ecology and Biodiversity Group Department of BiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 83584 CH UtrechtThe Netherlands

Plants are capable of releasing specific root exudates to recruit beneficial rhizosphere microbes upon foliar pathogen invasion attack,including long-chain fatty acids,amino acids,short-chain organic acids and *** long-chain fatty acids and amino acids application have been linked to soil legacy effects that improve future plant performance in the presence of the pathogen,the precise mechanisms involved are to a large extent still ***,we conditioned soils with long-chain fatty acids and amino acids application(L+A)or short-chain organic acids and sugars(S+S)to examine the direct role of such exudates on soil microbiome structure and *** L+A treatment recruited higher abundances of Proteobacteria which were further identified as members of the genera Sphingomonas,Pseudomonas,Roseiflexus,and *** then isolated the enriched bacterial strains from these groups,identifying ten Pseudomonas strains that were able to help host plant to resist foliar pathogen *** investigation showed that the L+A treatment resulted in growth promotion of these Pseudomonas ***,our data suggest that long-chain fatty acids and amino acids stimulated by foliar pathogen infection can recruit specific Pseudomonas populations that can help protect the host plant or future plant generations.

关键词： Foliar pathogen resistance Pseudomonas Recruitment Root exudates

The best practice for microbiome analysis using R

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Protein & Cell 2023年第10期14卷 713-725页

作者： Tao Wen Guoqing Niu Tong Chen Qirong Shen Jun Yuan Yong-Xin Liu Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China The Key Laboratory of Plant Immunity jiangsu provincial Key Lab for organic solid waste utilization jiangsu Collaborative Innovation center for solid organic waste Resource utilization National Engineering Research Center for Organic-based FertilizersNanjing Agricultural UniversityNanjing 210095China National Resource center for Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing 100700China

With the gradual maturity of sequencing technology,many microbiome studies have published,driving the emergence and advance of related analysis tools.R language is the widely used platform for microbiome data analysis for powerful ***,tens of thousands of R packages and numerous similar analysis tools have brought major challenges for many researchers to explore microbiome *** to choose suitable,efficient,convenient,and easy-to-learn tools from the numerous R packages has become a problem for many microbiome *** have organized 324 common R packages for microbiome analysis and classified them according to application categories(diversity,difference,biomarker,correlation and network,functional prediction,and others),which could help researchers quickly find relevant R packages for microbiome ***,we systematically sorted the integrated R packages(phyloseq,microbiome,MicrobiomeAnalystR,Animalcules,microeco,and amplicon)for microbiome analysis,and summarized the advantages and limitations,which will help researchers choose the appropriate ***,we thoroughly reviewed the R packages for microbiome analysis,summarized most of the common analysis content in the microbiome,and formed the most suitable pipeline for microbiome *** paper is accompanied by hundreds of examples with 10,000 lines codes in GitHub,which can help beginners to learn,also help analysts compare and test different *** paper systematically sorts the application of R in microbiome,providing an important theoretical basis and practical reference for the development of better microbiome tools in the *** the code is available at GitHub ***/taowenmicro/EasyMicrobiomeR.

关键词： R package microbiome data analysis visualization amplicon metagenome

Functions of silicon in plant drought stress responses

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Horticulture research 2021年第1期8卷 3425-3437页

作者： Min Wang Ruirui Wang Luis Alejandro Jose Mur Jianyun Ruan Qirong Shen Shiwei Guo jiangsu provincial Key Lab of solid organic waste utilization Jiangsu Collaborative Innovation Center of Solid Organic WastesThe Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjing 210095 JiangsuChina Institute of Biological Environmental and Rural SciencesAberystwyth UniversityAberystwyth SY233DAUK Key Laboratory of Tea Plant Biology and Resources utilization(Ministry of Agriculture) Tea Research InstituteChinese Academy of Agricultural SciencesHangzhou 310008 ZhejiangChina

Silicon(Si),the second most abundant element in Earth’s crust,exerts beneficial effects on the growth and productivity of a variety of plant species under various environmental ***,the benefits of Si and its importance to plants are controversial due to differences among the species,genotypes,and the environmental *** Si has been widely reported to alleviate plant drought stress in both the Si-accumulating and nonaccumulating plants,the underlying mechanisms through which Si improves plant water status and maintains water balance remain *** aim of this review is to summarize the morphoanatomical,physiological,biochemical,and molecular processes that are involved in plant water status that are regulated by Si in response to drought stress,especially the integrated modulation of Si-triggered drought stress responses in Si accumulators and intermediate-and excluder-type *** key mechanisms influencing the ability of Si to mitigate the effects of drought stress include enhancing water uptake and transport,regulating stomatal behavior and transpirational water loss,accumulating solutes and osmoregulatory substances,and inducing plant defense-associated with signaling events,consequently maintaining whole-plant water *** study evaluates the ability of Si to maintain water balance under drought stress conditions and suggests future research that is needed to implement the use of Si in *** the complex relationships between Si and different plant species,genotypes,and the environment,detailed studies are needed to understand the interactions between Si and plant responses under stress conditions.

关键词： drought stress maintain

Interspecific plant interaction via root exudates structures the disease suppressiveness of rhizosphere microbiomes

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Molecular Plant 2023年第5期16卷 849-864页

作者： Xingang Zhou Jingyu Zhang Muhammad Khashi u Rahman Danmei Gao Zhong Wei Fengzhi Wu Francisco Dini-Andreote Key Laboratory of Biology and Genetic Improvement of Horticultural Crops(Northeast Region) Ministry of Agriculture and Rural AffairsDepartment of HorticultureNortheast Agricultural UniversityChangjiang 600Harbin 150030P.R.China jiangsu provincial Key Lab for organic solid waste utilization National Engineering Research Center for Organic-based FertilizersJiangsu Collaborative Innovation Center for Solid Organic Waste Resource UtilizationNanjing Agricultural UniversityWeigang No.1Nanjing 210095P.R.China Department of Plant Science&Huck Institutes of the Life Sciences The Pennsylvania State UniversityUniversity ParkPAUSA

Terrestrial plants can affect the growth and health of adjacent plants via interspecific ***,we studied the mechanism by which plant root exudates affect the recruitment of the rhizosphere microbiome in adjacent plants—with implications for plant protection—using a tomato(Solanum lycopersicum)–potatoonion(Allium cepa ***)intercropping ***,we showed that the intercropping system results in a disease-suppressive rhizosphere microbiome that protects tomato plants against Verticillium wilt disease caused by the soilborne pathogen Verticillium ***,16S rRNA gene sequencing revealed that intercropping with potatoonion altered the composition of the tomato rhizosphere microbiome by promoting the colonization of specific Bacillus *** taxon was isolated and shown to inhibit *** growth and induce systemic resistance in tomato ***,a belowground segregation experiment found that root exudates mediated the interspecific interaction between potatoonion and ***,experiments using split-root tomato plants found that root exudates from potatoonion,especially taxifolin—a flavonoid compound—stimulate tomato plants to recruit plant-beneficial bacteria,such as Bacillus ***,ultra-high-pressure liquid chromatography–mass spectrometry analysis found that taxifolin alters tomato root exudate chemistry;thus,this compound acts indirectly in modulating root colonization by Bacillus *** results revealed that this intercropping system can improve tomato plant fitness by changing rhizosphere microbiome recruitment via the use of signaling chemicals released by root exudates of *** study revealed a novel mechanism by which interspecific plant interaction modulates the establishment of a disease-suppressive microbiome,thus opening up new avenues of research for precision plant microbiome manipulations.

关键词： intercropping microbiome rhizosphere root exudates soilborne disease