根际促生解淀粉芽胞杆菌SQR9对香蕉根系分泌物响应的转录组分析
|
摘要
[目的]本文旨在阐明根系分泌物介导的植物根际促生细菌(plant growth-promoting rhizobacteria,PGPR)与宿主的互作机制。[方法]利用Illumina高通量测序技术研究促生解淀粉芽胞杆菌SQR9在体外振荡培养条件下对香蕉根系分泌物的转录响应特征,对显著差异表达基因的直系同源基因进行同源蛋白簇(COG)分析。通过Real-time PCR验证部分转录组测序结果,并研究分泌物代表性组分对部分差异基因表达的影响。[结果]香蕉根系分泌物可显著促进菌株SQR9在1/2MSgg培养基中的生长。转录组测序结果表明:根系分泌物处理6 h后菌株SQR9中共有764个基因的表达发生了显著变化,占其基因总数的18.7%,其中上调与下调基因数量分别为485和279。Real-time PCR验证获得的基因表达差异趋势与转录组测序结果一致,证明其结果可信。菌株SQR9中受根系分泌物显著调控的差异基因主要属于碳水化合物转运与代谢、氨基酸转运与代谢、能量产生与转化、转录调控、信号转导和细胞运动等;此外,与促生/生防活性物质合成相关的部分功能基因也被分泌物所诱导。根系分泌物中的葡萄糖、木糖、赤藓糖醇和硬脂酸可诱导SQR9中部分代表性差异基因的表达,但整体的转录组调控现象是分泌物中不同组分共同作用的结果。[结论]香蕉根系分泌物可促进菌株SQR9的生长代谢、信号响应、根际趋化和活性物质合成,这些都有利于SQR9在香蕉根际的存活定殖和促生/生防功能发挥,有助于其与香蕉合作关系的建立。
[Objectives]The purpose of this paper is to illustrate the mechanisms involved in root exudates-mediated interactions between hosts and plant growth-promoting rhizobacteria( PGPR). [Methods]The transcriptional profiling of PGPR strain Bacillus amyloliquefaciens SQR9 towards banana root exudates was analyzed by Illumina high-throughput transcriptome sequencing,genes with significantly different expression level in response to root exudates were examined by clusters of orthologous groups of proteins( COG)analysis. Real-time PCR was performed for validating partial of the sequencing results,as well as investigating the effects of the representative components in root exudates on the expression of several significant genes in SQR9. [Results]Banana root exudates significantly stimulate the growth of SQR9 in 1/2 MSgg medium. Transcriptome analysis indicated after treatment with root exudates by 6 h,764 genes of SQR9 were detected to be significantly regulated,which covered 18.7% of the whole genome of SQR9 and included 485 of up-regulated genes while 279 down-regulated. Real-time PCR validation showed that the expression patterns of the selected genes were in accordance with the results of transcriptional profiling analysis,suggesting that the transcriptome data was reliable. Genes that significantly regulated by root exudates mainly belonged to carbohydrate transport and metabolism,amino acid transport and metabolism,energy production and conversion,transcription,signal transduction mechanisms,and cell motility. Additionally,partial of the genes involved in biosynthesis of functional compounds relating to plant growth-promotion/biocontrol were also activated by root exudates.Glucose,xylose,erythritol,and stearic acid in root exudates could induce the expression of several representative significant genes in SQR9,while the overall regulation in response to root exudates revealed in transcriptomic profiling was the results of interaction among different components in root exudates. [Conclusions]In conclusion,banana root exudates can stimulate the growth and metabolism,signal response,rhizosphere chemotaxis,and biosynthesis of functional compounds of strain SQR9,which will facilitate its survival,root colonization,and exertion of growth-promotion/biocontrol,as well as establishment of the symbiosis between SQR9 and banana.
[Objectives]The purpose of this paper is to illustrate the mechanisms involved in root exudates-mediated interactions between hosts and plant growth-promoting rhizobacteria( PGPR). [Methods]The transcriptional profiling of PGPR strain Bacillus amyloliquefaciens SQR9 towards banana root exudates was analyzed by Illumina high-throughput transcriptome sequencing,genes with significantly different expression level in response to root exudates were examined by clusters of orthologous groups of proteins( COG)analysis. Real-time PCR was performed for validating partial of the sequencing results,as well as investigating the effects of the representative components in root exudates on the expression of several significant genes in SQR9. [Results]Banana root exudates significantly stimulate the growth of SQR9 in 1/2 MSgg medium. Transcriptome analysis indicated after treatment with root exudates by 6 h,764 genes of SQR9 were detected to be significantly regulated,which covered 18.7% of the whole genome of SQR9 and included 485 of up-regulated genes while 279 down-regulated. Real-time PCR validation showed that the expression patterns of the selected genes were in accordance with the results of transcriptional profiling analysis,suggesting that the transcriptome data was reliable. Genes that significantly regulated by root exudates mainly belonged to carbohydrate transport and metabolism,amino acid transport and metabolism,energy production and conversion,transcription,signal transduction mechanisms,and cell motility. Additionally,partial of the genes involved in biosynthesis of functional compounds relating to plant growth-promotion/biocontrol were also activated by root exudates.Glucose,xylose,erythritol,and stearic acid in root exudates could induce the expression of several representative significant genes in SQR9,while the overall regulation in response to root exudates revealed in transcriptomic profiling was the results of interaction among different components in root exudates. [Conclusions]In conclusion,banana root exudates can stimulate the growth and metabolism,signal response,rhizosphere chemotaxis,and biosynthesis of functional compounds of strain SQR9,which will facilitate its survival,root colonization,and exertion of growth-promotion/biocontrol,as well as establishment of the symbiosis between SQR9 and banana.
引文
[1] Lugtenberg B,Kamilova F. Plant-growth-promoting rhizobacteria[J]. Annual Review of Microbiology,2009,63(1):541-556.
[2] Borriss R. Use of plant-associated Bacillus strains as biofertilizers and biocontrol agents in agriculture[M]//Bacteria in Agrobiology:Plant Growth Responses. Heidelberg:Springer-Verlag,2011:41-76.
[3] Pii Y,Mimmo T,Tomasi N,et al. Microbial interactions in the rhizosphere:beneficial influences of plant growth-promoting rhizobacteria on nutrient acquisition process:a review[J]. Biology and Fertility of Soils,2015,51(4):403-415.
[4] Faure D,Vereecke D,Leveau J H J. Molecular communication in the rhizosphere[J]. Plant and Soil,2009,321(1/2):279-303.
[5] Parniske M. Arbuscular mycorrhiza:the mother of plant root endosymbioses[J]. Nature Reviews Microbiology,2008,6(10):763-775.
[6] de Weert S,Vermeiren H,Mulders I H,et al. Flagella-driven chemotaxis towards exudate components is an important trait for tomato root colonization by Pseudomonas fluorescens[J]. Molecular Plant-Microbe Interactions,2002,15(11):1173-1180.
[7] Sood S G. Chemotactic response of plant-growth-promoting bacteria towards roots of vesicular-arbuscular mycorrhizal tomato plants[J]. FEMS Microbiology Ecology,2003,45(3):219-227.
[8] Rudrappa T,Czymmek K J,Pare P W,et al. Root-secreted malic acid recruits beneficial soil bacteria[J]. Plant Physiology,2008,148(3):1547-1556.
[9] Chen Y,Cao S,Chai Y,et al. A Bacillus subtilis sensor kinase involved in triggering biofilm formation on the roots of tomato plants[J]. Molecular Microbiology,2012,85(3):418-430.
[10] Marguerat S,Bahler J. RNA-seq:from technology to biology[J]. Cellular and Molecular Life Sciences,2010,67(4):569-579.
[11] Balsanelli E,Tadra-Sfeir M Z,Faoro H,et al. Molecular adaptations of Herbaspirillum seropedicae during colonization of the maize rhizosphere[J].Environmental Microbiology,2016,18(8):2343-2356.
[12] Yi Y,de Jong A,Frenzel E,et al. Comparative transcriptomics of Bacillus mycoides strains in response to potato-root exudates reveals different genetic adaptation of endophytic and soil isolates[J]. Frontiers in Microbiology,2017,8:1487.
[13] Cao Y,Zhang Z H,Ling N,et al. Bacillus subtilis SQR9 can control Fusarium wilt in cucumber by colonizing plant roots[J]. Biology and Fertility of Soils,2011,47(5):495-500.
[14]张楠,吴凯,沈怡斐,等.根际益生菌解淀粉芽孢杆菌SQR9在香蕉根表的定殖行为研究[J].南京农业大学学报,2014,37(6):59-65.DOI:10.7685/j.issn.1000-2030.2014.06.009.Zhang N,Wu K,Shen Y F,et al. Investigation of the colonization patterns of plant growth-promoting rhizobacteria Bacillus amyloliquefaciens SQR9 on banana roots[J]. Journal of Nanjing Agricultural University,2014,37(6):59-65(in Chinese with English abstract).
[15] Tatusov R L,Fedorova N D,Jackson J D,et al. The COG database:an updated version includes eukaryotes[J]. BMC Bioinformatics,2003,4(1):41.
[16]冯海超.根系分泌物组分与SQR9基因转录的相关性分析及其趋化与成膜的影响[D].南京:南京农业大学,2015:17-24.Feng H C. Correlation of root exudates components and gene transcription of SQR9 and its effects on chemotaxis and biofilm formation[D].Nanjing:Nanjing Agricultural University,2015:17-24(in Chinese with English abstract).
[17] Chagas F O,de Pessotti R C,Caraballo-Rodríguez A M,et al. Chemical signaling involved in plant-microbe interactions[J]. Chemical Society Reviews,2018,47(5):1652-1704.
[18] Compant S,Clément C,Sessitsch A. Plant growth-promoting bacteria in the rhizo-and endosphere of plants:their role,colonization,mechanisms involved and prospects for utilization[J]. Soil Biology and Biochemistry,2010,42(5):669-678.
[19] Zhang N,Yang D,Wang D,et al. Whole transcriptomic analysis of the plant-beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 during enhanced biofilm formation regulated by maize root exudates[J]. BMC Genomics,2015,16(1):685.
[20] Xie S,Wu H,Chen L,et al. Transcriptome profiling of Bacillus subtilis OKB105 in response to rice seedlings[J]. BMC Microbiology,2015,15:21.
[21] Date R,Date A. Molecular mechanisms involved in Bacillus subtilis biofilm formation[J]. Environmental Microbiology,2015,17(3):555-565.
[22] Hamoen L W. Controlling competence in Bacillus subtilis:shared use of regulators[J]. Microbiology,2003,149(1):9-17.
[23] López D,Fischbach M A,Chu F,et al. Structurally diverse natural products that cause potassium leakage trigger multicellularity in Bacillus subtilis[J]. Proc Natl Acad Sci USA,2009,106(1):280-285.
[24] Chen Y,Yan F,Chai Y,et al. Biocontrol of tomato wilt disease by Bacillus subtilis isolates from natural environments depends on conserved genes mediating biofilm formation[J]. Environmental Microbiology,2013,15(3):848-864.
[25] Mwita L,Chan W Y,Pretorius T,et al. Gene expression regulation in the plant growth promoting Bacillus atrophaeus UCMB-5137 stimulated by maize root exudates[J]. Gene,2016,590(1):18-28.
[26] Shao J,Li S,Zhang N,et al. Analysis and cloning of the synthetic pathway of the phytohormone indole-3-acetic acid in the plant-beneficial Bacillus amyloliquefaciens SQR9[J]. Microbial Cell Factories,2015,14(1):130.
[27]邵佳慧.解淀粉芽孢杆菌SQR9吲哚乙酸合成途径及促生效应的研究[D].南京:南京农业大学,2014:13-14.Shao J H. Indole-3-acetic acid synthesis pathways and plant-growth-promotion effects of Bacillus amyloliquefaciens SQR9[D]. Nanjing:Nanjing Agricultural University,2014:13-14(in Chinese with English abstract).
[2] Borriss R. Use of plant-associated Bacillus strains as biofertilizers and biocontrol agents in agriculture[M]//Bacteria in Agrobiology:Plant Growth Responses. Heidelberg:Springer-Verlag,2011:41-76.
[3] Pii Y,Mimmo T,Tomasi N,et al. Microbial interactions in the rhizosphere:beneficial influences of plant growth-promoting rhizobacteria on nutrient acquisition process:a review[J]. Biology and Fertility of Soils,2015,51(4):403-415.
[4] Faure D,Vereecke D,Leveau J H J. Molecular communication in the rhizosphere[J]. Plant and Soil,2009,321(1/2):279-303.
[5] Parniske M. Arbuscular mycorrhiza:the mother of plant root endosymbioses[J]. Nature Reviews Microbiology,2008,6(10):763-775.
[6] de Weert S,Vermeiren H,Mulders I H,et al. Flagella-driven chemotaxis towards exudate components is an important trait for tomato root colonization by Pseudomonas fluorescens[J]. Molecular Plant-Microbe Interactions,2002,15(11):1173-1180.
[7] Sood S G. Chemotactic response of plant-growth-promoting bacteria towards roots of vesicular-arbuscular mycorrhizal tomato plants[J]. FEMS Microbiology Ecology,2003,45(3):219-227.
[8] Rudrappa T,Czymmek K J,Pare P W,et al. Root-secreted malic acid recruits beneficial soil bacteria[J]. Plant Physiology,2008,148(3):1547-1556.
[9] Chen Y,Cao S,Chai Y,et al. A Bacillus subtilis sensor kinase involved in triggering biofilm formation on the roots of tomato plants[J]. Molecular Microbiology,2012,85(3):418-430.
[10] Marguerat S,Bahler J. RNA-seq:from technology to biology[J]. Cellular and Molecular Life Sciences,2010,67(4):569-579.
[11] Balsanelli E,Tadra-Sfeir M Z,Faoro H,et al. Molecular adaptations of Herbaspirillum seropedicae during colonization of the maize rhizosphere[J].Environmental Microbiology,2016,18(8):2343-2356.
[12] Yi Y,de Jong A,Frenzel E,et al. Comparative transcriptomics of Bacillus mycoides strains in response to potato-root exudates reveals different genetic adaptation of endophytic and soil isolates[J]. Frontiers in Microbiology,2017,8:1487.
[13] Cao Y,Zhang Z H,Ling N,et al. Bacillus subtilis SQR9 can control Fusarium wilt in cucumber by colonizing plant roots[J]. Biology and Fertility of Soils,2011,47(5):495-500.
[14]张楠,吴凯,沈怡斐,等.根际益生菌解淀粉芽孢杆菌SQR9在香蕉根表的定殖行为研究[J].南京农业大学学报,2014,37(6):59-65.DOI:10.7685/j.issn.1000-2030.2014.06.009.Zhang N,Wu K,Shen Y F,et al. Investigation of the colonization patterns of plant growth-promoting rhizobacteria Bacillus amyloliquefaciens SQR9 on banana roots[J]. Journal of Nanjing Agricultural University,2014,37(6):59-65(in Chinese with English abstract).
[15] Tatusov R L,Fedorova N D,Jackson J D,et al. The COG database:an updated version includes eukaryotes[J]. BMC Bioinformatics,2003,4(1):41.
[16]冯海超.根系分泌物组分与SQR9基因转录的相关性分析及其趋化与成膜的影响[D].南京:南京农业大学,2015:17-24.Feng H C. Correlation of root exudates components and gene transcription of SQR9 and its effects on chemotaxis and biofilm formation[D].Nanjing:Nanjing Agricultural University,2015:17-24(in Chinese with English abstract).
[17] Chagas F O,de Pessotti R C,Caraballo-Rodríguez A M,et al. Chemical signaling involved in plant-microbe interactions[J]. Chemical Society Reviews,2018,47(5):1652-1704.
[18] Compant S,Clément C,Sessitsch A. Plant growth-promoting bacteria in the rhizo-and endosphere of plants:their role,colonization,mechanisms involved and prospects for utilization[J]. Soil Biology and Biochemistry,2010,42(5):669-678.
[19] Zhang N,Yang D,Wang D,et al. Whole transcriptomic analysis of the plant-beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 during enhanced biofilm formation regulated by maize root exudates[J]. BMC Genomics,2015,16(1):685.
[20] Xie S,Wu H,Chen L,et al. Transcriptome profiling of Bacillus subtilis OKB105 in response to rice seedlings[J]. BMC Microbiology,2015,15:21.
[21] Date R,Date A. Molecular mechanisms involved in Bacillus subtilis biofilm formation[J]. Environmental Microbiology,2015,17(3):555-565.
[22] Hamoen L W. Controlling competence in Bacillus subtilis:shared use of regulators[J]. Microbiology,2003,149(1):9-17.
[23] López D,Fischbach M A,Chu F,et al. Structurally diverse natural products that cause potassium leakage trigger multicellularity in Bacillus subtilis[J]. Proc Natl Acad Sci USA,2009,106(1):280-285.
[24] Chen Y,Yan F,Chai Y,et al. Biocontrol of tomato wilt disease by Bacillus subtilis isolates from natural environments depends on conserved genes mediating biofilm formation[J]. Environmental Microbiology,2013,15(3):848-864.
[25] Mwita L,Chan W Y,Pretorius T,et al. Gene expression regulation in the plant growth promoting Bacillus atrophaeus UCMB-5137 stimulated by maize root exudates[J]. Gene,2016,590(1):18-28.
[26] Shao J,Li S,Zhang N,et al. Analysis and cloning of the synthetic pathway of the phytohormone indole-3-acetic acid in the plant-beneficial Bacillus amyloliquefaciens SQR9[J]. Microbial Cell Factories,2015,14(1):130.
[27]邵佳慧.解淀粉芽孢杆菌SQR9吲哚乙酸合成途径及促生效应的研究[D].南京:南京农业大学,2014:13-14.Shao J H. Indole-3-acetic acid synthesis pathways and plant-growth-promotion effects of Bacillus amyloliquefaciens SQR9[D]. Nanjing:Nanjing Agricultural University,2014:13-14(in Chinese with English abstract).