基于16SrDNA基因高通量测序分析植烟土壤的细菌群落结构
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摘要
钾是影响烤烟品质的重要元素之一,为研究不同烤烟品质植烟区土壤的细菌群落,以期为提高烤烟品质提供依据,本研究通过对采取烤烟高钾植烟区的土样、烤烟低钾植烟区的土样,并通过宏基因组16SrDNA基因高通量测序,分析不同植烟区土壤细菌的群落结构,结果表明,高钾地区获得较多的有效序列。Shannon指数及Simpson指数共同表明高钾地区土样具有的细菌群落多样性最高。ACE指数与Chao1指数具有相同的趋势,都表明高钾地区土样具有的细菌群落丰富度最高。不同土壤样品细菌属水平的聚类分析显示把低钾地区的样品聚在一起,这些样品菌群分布比较相似。功能基因预测分析研究表明,高钾地区样品具有最多功能基因数量。
Potassium is one of the important elements that affect the quality of flue-cured tobacco. In this study,the bacterial community in tobacco planting soil with different quality of flue-cured were studied in order to provide a basis for improving the quality of flue-cured tobacco. Taking the soil samples in high potassium flue-cured tobacco planting area and in low potassium flue-cured tobacco planting area, we analyzed the bacterial community structure of the soil from different tobacco-growing areas through the high throughput sequencing of metagenome 16 SrDNA gene. The results showed that more efficient sequence of the community structure was obtained from the high potassium area. Then Shannon index and Simpson index both indicated that the soil samples in the high potassium area had the highest diversity of bacterial community. The ACE index and the Chao1 index had the same trend, indicating that the soil samples in the high potassium region had the highest bacterial community richness. Cluster analysis of bacterial levels in different soil samples demonstrated that samples from low potassium regions were clustered together, and the distribution of these samples was similar.Functional gene prediction analysis suggested that samples with high potassium had the largest number of functional genes.
Potassium is one of the important elements that affect the quality of flue-cured tobacco. In this study,the bacterial community in tobacco planting soil with different quality of flue-cured were studied in order to provide a basis for improving the quality of flue-cured tobacco. Taking the soil samples in high potassium flue-cured tobacco planting area and in low potassium flue-cured tobacco planting area, we analyzed the bacterial community structure of the soil from different tobacco-growing areas through the high throughput sequencing of metagenome 16 SrDNA gene. The results showed that more efficient sequence of the community structure was obtained from the high potassium area. Then Shannon index and Simpson index both indicated that the soil samples in the high potassium area had the highest diversity of bacterial community. The ACE index and the Chao1 index had the same trend, indicating that the soil samples in the high potassium region had the highest bacterial community richness. Cluster analysis of bacterial levels in different soil samples demonstrated that samples from low potassium regions were clustered together, and the distribution of these samples was similar.Functional gene prediction analysis suggested that samples with high potassium had the largest number of functional genes.
引文
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Cai H.,2013,Interaction between mycorrhizal fungi and phosphorus/potassium dissolved bacteria and effects of coinoculation on the seedings growth of Pinus sylvestnis var.mongolica Litv,Thesis for M.S.,Inner Mongolia Agricultural U-niversity,Supervisor:Yao Q.Z.,pp.29-42(彩花,2013,菌根真菌与解磷钾细菌的相互作用及共接种对樟子松幼苗生长的影响,硕士学位论文内蒙古农业大学,导师:姚庆智pp.29-42)
Cai H.L.,Wang L.D.,Sha H.J.,Liu H.L.,and Zhao H.W.,2016Effects of nitrogen fertilizing levels on nitrogen metabolism and grain protein content of japonica rice in cold region under cold water stress at tillering stage,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(9):2486-2493(蔡宏亮,王力冬,沙汉景,刘化龙,赵宏伟,2016分蘖期冷水胁迫下施氮量对寒地粳稻氮代谢和籽粒蛋白质含量的影响,基因组学与应用生物学,35(9):2486-2493)
Edgar R.C.,2010,Search and clustering orders of magnitude faster than BLAST,Bioinformatics,26(19):2460-2461
Fang G.W.,Hong X.M.,Cai L.X.,Peng K.,and Lin Y.,2005Preparation of metagenome from soil and analysis on the sequence of a bacteria 16SrDNA by culture-independent method,Jiangxi Nongye Daxue Xuebao(Acta Agriculturae Universitis Jiangxiensis),27(4):505-507(方光伟,洪雪梅,蔡丽希彭锟,林毅,2005,土壤宏基因组的提取及基于免培养技术分析细菌16SrDNA,江西农业大学学报,27(4):505-507)
Langille M.G.,Zaneveld J.,Caporaso J.G.,McDonald D.,Knights D.,Reyes J.A.,Clemente J.C.,Burkepile D.E.,Vega Thurber R.L.,Knight R.,Beiko R.G.,and Huttenhower C.,2013Predictive functional profiling of microbial communities using 16S r RNA marker gene sequences,Nat.Biotechnol.,31(9):814-821
Parks D.H.,Tyson G.W.,Hugenholtz P.,and Beiko R.G.,2014,STAMP:statistical analysis of taxonomic and functional profiles,Bioinformatics,30(21):3123-3124
Tian X.,Wei Q.R.,Liang X.L.,Qi C.H.,and Shi Y.,2015,Effects of nitrogen on yield and quality of potato variety Dongnong311,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(9):1975-1980(田洵,魏峭嵘,梁晓丽,祁驰恒,石瑛,2015,氮素对马铃薯品种东农311产量及品质的影响,基因组学与应用生物学,35(9):1975-1980)
Wang Q.,Garrity G.M.,Tiedje J.M.,and Cole J.R.,2007,Na觙ve Bayesian classifier for rapid assignment of r RNA sequences into the new bacterial taxonomy,Appl.Environ.Microbiol.,73(16):5261-5267
Yuan Z.H.,Wang J.,Yang W.J.,and Wu Y.Y.,2014,Progress in cultivation research on soil microbes,Turang Xuebao(Acta Pedologica Sinica),51(6):1183-1191(袁志辉,王健,杨文蛟,吴永尧,2014,土壤微生物分离新技术的研究进展,土壤学报,51(6):1183-1191)
Zhang J.,Kobert K.,Flouri T.,and Stamatakis A.,2014,PEAR:a fast and accurate Illumina Paired-End reAd mergeR,Bioinformatics,30(5):614-620
Zhang W.,Hu Y.G.,Huang G.H.,and Gao H.W.,2007,Soil microbial diversity of artificial peashrub plantation on North Loess Plateau of China,Weishengwu Xuebao(Acta Microbiologica Sinica),47(5):751-756(张薇,胡跃高,黄国和,高洪文,2007,西北黄土高原柠条种植区土壤微生物多样性分析,微生物学报,47(5):751-756)
Zhang Y.Y.,Dong J.D.,Yang Z.H.,Zhang S.,and Wang Y.S.,2008,Phylogenetic diversity of nitrogen-fixing bacteria in mangrove sediments assessed by PCR-denaturing gradient gel electrophoresis,Arch.Microbiol.,190(1):19-28
Zhao Y.C.,Liu X.W.,Li Y.,and Zhao D.G.,2016,Transcriptome data assembly and gene function annotation of Zanthoxylum piperitum DC var.inerme Makino,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(7):1805-1819(赵懿琛,刘雪微,李岩,赵德刚,2016,朝仓花椒幼芽转录组测序数据组装及基因功能注释,基因组学与应用生物学,35(7):1805-1819)
Cai H.,2013,Interaction between mycorrhizal fungi and phosphorus/potassium dissolved bacteria and effects of coinoculation on the seedings growth of Pinus sylvestnis var.mongolica Litv,Thesis for M.S.,Inner Mongolia Agricultural U-niversity,Supervisor:Yao Q.Z.,pp.29-42(彩花,2013,菌根真菌与解磷钾细菌的相互作用及共接种对樟子松幼苗生长的影响,硕士学位论文内蒙古农业大学,导师:姚庆智pp.29-42)
Cai H.L.,Wang L.D.,Sha H.J.,Liu H.L.,and Zhao H.W.,2016Effects of nitrogen fertilizing levels on nitrogen metabolism and grain protein content of japonica rice in cold region under cold water stress at tillering stage,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(9):2486-2493(蔡宏亮,王力冬,沙汉景,刘化龙,赵宏伟,2016分蘖期冷水胁迫下施氮量对寒地粳稻氮代谢和籽粒蛋白质含量的影响,基因组学与应用生物学,35(9):2486-2493)
Edgar R.C.,2010,Search and clustering orders of magnitude faster than BLAST,Bioinformatics,26(19):2460-2461
Fang G.W.,Hong X.M.,Cai L.X.,Peng K.,and Lin Y.,2005Preparation of metagenome from soil and analysis on the sequence of a bacteria 16SrDNA by culture-independent method,Jiangxi Nongye Daxue Xuebao(Acta Agriculturae Universitis Jiangxiensis),27(4):505-507(方光伟,洪雪梅,蔡丽希彭锟,林毅,2005,土壤宏基因组的提取及基于免培养技术分析细菌16SrDNA,江西农业大学学报,27(4):505-507)
Langille M.G.,Zaneveld J.,Caporaso J.G.,McDonald D.,Knights D.,Reyes J.A.,Clemente J.C.,Burkepile D.E.,Vega Thurber R.L.,Knight R.,Beiko R.G.,and Huttenhower C.,2013Predictive functional profiling of microbial communities using 16S r RNA marker gene sequences,Nat.Biotechnol.,31(9):814-821
Parks D.H.,Tyson G.W.,Hugenholtz P.,and Beiko R.G.,2014,STAMP:statistical analysis of taxonomic and functional profiles,Bioinformatics,30(21):3123-3124
Tian X.,Wei Q.R.,Liang X.L.,Qi C.H.,and Shi Y.,2015,Effects of nitrogen on yield and quality of potato variety Dongnong311,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(9):1975-1980(田洵,魏峭嵘,梁晓丽,祁驰恒,石瑛,2015,氮素对马铃薯品种东农311产量及品质的影响,基因组学与应用生物学,35(9):1975-1980)
Wang Q.,Garrity G.M.,Tiedje J.M.,and Cole J.R.,2007,Na觙ve Bayesian classifier for rapid assignment of r RNA sequences into the new bacterial taxonomy,Appl.Environ.Microbiol.,73(16):5261-5267
Yuan Z.H.,Wang J.,Yang W.J.,and Wu Y.Y.,2014,Progress in cultivation research on soil microbes,Turang Xuebao(Acta Pedologica Sinica),51(6):1183-1191(袁志辉,王健,杨文蛟,吴永尧,2014,土壤微生物分离新技术的研究进展,土壤学报,51(6):1183-1191)
Zhang J.,Kobert K.,Flouri T.,and Stamatakis A.,2014,PEAR:a fast and accurate Illumina Paired-End reAd mergeR,Bioinformatics,30(5):614-620
Zhang W.,Hu Y.G.,Huang G.H.,and Gao H.W.,2007,Soil microbial diversity of artificial peashrub plantation on North Loess Plateau of China,Weishengwu Xuebao(Acta Microbiologica Sinica),47(5):751-756(张薇,胡跃高,黄国和,高洪文,2007,西北黄土高原柠条种植区土壤微生物多样性分析,微生物学报,47(5):751-756)
Zhang Y.Y.,Dong J.D.,Yang Z.H.,Zhang S.,and Wang Y.S.,2008,Phylogenetic diversity of nitrogen-fixing bacteria in mangrove sediments assessed by PCR-denaturing gradient gel electrophoresis,Arch.Microbiol.,190(1):19-28
Zhao Y.C.,Liu X.W.,Li Y.,and Zhao D.G.,2016,Transcriptome data assembly and gene function annotation of Zanthoxylum piperitum DC var.inerme Makino,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(7):1805-1819(赵懿琛,刘雪微,李岩,赵德刚,2016,朝仓花椒幼芽转录组测序数据组装及基因功能注释,基因组学与应用生物学,35(7):1805-1819)