轮作和连作对胡萝卜根际和非根际细菌多样性的影响
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摘要
细菌是土壤最重要的组成部分,土壤细菌的群落结构对土壤的健康至关重要,可以直接影响植物的生长。胡萝卜的长年连作导致其产量低、质量差等一系列问题的发生,连作问题已成为不可忽视的问题。本研究通过HiSeq PE250高通量测序和生物信息学方法获得了玉米胡萝卜轮作种植和胡萝卜连作种植中胡萝卜根际和非根际土壤细菌的组成结构。研究结果表明,相较于胡萝卜连作,玉米胡萝卜轮作种植改变了胡萝卜根际土壤细菌的组成和群落多样性。RM.M (玉米胡萝卜轮作根际土壤样品)样品中的优势菌门为放线菌门和厚壁菌门,RM.R (胡萝卜连作根际土壤样品)的优势菌门是变形菌门;有益菌如芽孢杆菌属和根瘤菌属在玉米胡萝卜轮作种植中的胡萝卜根际富集。RM.M与RM.R的细菌类群差异显著,群落多样性较低;NRM.M(玉米胡萝卜轮作非根际土壤样品)和NRM.R (胡萝卜连作非根际土壤样)的细菌类群差异不明显,群落多样性较高。与连作根际土壤相比,轮作根际土壤中有益菌的相对丰度较大,细菌相对丰度明显增加。本研究结果对通过调节根际土壤细菌组成来保证胡萝卜产量和质量的稳定,解决连作问题具有重要的意义。
Bacteria are the most important part of soil. The community structure of soil bacteria is very important for soil health and can directly affect the growth of plants. Continuous cropping of carrot leads to a series of problems such as low yield and poor quality. Obviously, continuous cropping in carot production has become a problem that cannot be ignored. The bacterial composition in rhizosphere and non-rhizosphere soil in rotation of maize and carrot and carrot continuous cropping were analyzed based on HiSeq PE250 and bioinformatics. The results illustrated that compared with consecutive cropping of carrot, the rotation of maize and carrot shifted the diversity and composition of bacteria community in rhizosphere of carrot. The dominant phyla of RM.M(the bacteria in carrot soil rhizosphere of rotation of maize and carrot) sample was Actinobacteria and Firmicutes. The dominant phyla of RM.R(the bacteria in carrot soil rhizosphere of carrot continuous cropping) sample was Proteobacteria. The bacteria population increased such as Bacillus and Rhizobium in the bacteria in carrot soil rhizosphere of rotation of maize and carrot. The community composition of soil bacteria was significantly different in RM.R and RM.M, the diversity were showed lower. The community composition of soil bacteria was not obviously different in NRM.M(The bacteria in soil non-rhizosphere of rotation of maize and carrot) and NRM.R(The bacteria in soil non-rhizosphere of carrot continuous cropping), the diversity were showed higher. Compared with the consecutive cropping rhizosphere soil, the relative abundance of the beneficial bacteria was higher, and the relative abundance of the bacteria increased obviously in the rotation cropping rhizosphere soil. It is the key to solve the continuous cropping problem by regulating the composition of rhizosphere soil bacteria to ensure the stable yield and quality of carrot. The results had great significance to regulate the yield and quality of carrots by adjusting the composition of rhizosphere soil bacteria and solve the problem of continuous cropping.
Bacteria are the most important part of soil. The community structure of soil bacteria is very important for soil health and can directly affect the growth of plants. Continuous cropping of carrot leads to a series of problems such as low yield and poor quality. Obviously, continuous cropping in carot production has become a problem that cannot be ignored. The bacterial composition in rhizosphere and non-rhizosphere soil in rotation of maize and carrot and carrot continuous cropping were analyzed based on HiSeq PE250 and bioinformatics. The results illustrated that compared with consecutive cropping of carrot, the rotation of maize and carrot shifted the diversity and composition of bacteria community in rhizosphere of carrot. The dominant phyla of RM.M(the bacteria in carrot soil rhizosphere of rotation of maize and carrot) sample was Actinobacteria and Firmicutes. The dominant phyla of RM.R(the bacteria in carrot soil rhizosphere of carrot continuous cropping) sample was Proteobacteria. The bacteria population increased such as Bacillus and Rhizobium in the bacteria in carrot soil rhizosphere of rotation of maize and carrot. The community composition of soil bacteria was significantly different in RM.R and RM.M, the diversity were showed lower. The community composition of soil bacteria was not obviously different in NRM.M(The bacteria in soil non-rhizosphere of rotation of maize and carrot) and NRM.R(The bacteria in soil non-rhizosphere of carrot continuous cropping), the diversity were showed higher. Compared with the consecutive cropping rhizosphere soil, the relative abundance of the beneficial bacteria was higher, and the relative abundance of the bacteria increased obviously in the rotation cropping rhizosphere soil. It is the key to solve the continuous cropping problem by regulating the composition of rhizosphere soil bacteria to ensure the stable yield and quality of carrot. The results had great significance to regulate the yield and quality of carrots by adjusting the composition of rhizosphere soil bacteria and solve the problem of continuous cropping.
引文
Berendsen R.L.,Pieterse C.M.J.,and Bakker P.A.H.M.,2012,The rhizosphere microbiome and plant health,Trends in Plant Science,17(8):478-486
Bokulich N.A.,Subramanian S.,Faith J.J.,Gevers D.,Gordon J.I.Knight R.,Mills D.A.,and Caporaso J.G.,2012,Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing,Nature Methods,10(1):57-59
Caporaso J.G.,Kuczynski J.,Stombaugh J.,Bittinger K.,Bushman F.D.,Costello E.K.,Fierer N.,Pe觡a A.G.,Goodrich JK.,Gordon J.I.,Huttley G.A.,Kelley S.T.,Knights D.Koenig J.E.,Ley R.E.,Lozupone C.A.,McDonald D.Muegge B.D.,Pirrung M.,Reeder J.,Sevinsky J.R.,Turnbaugh P.J.,Walters W.A.,Widmann J.,Yatsunenko T.,Zaneveld J.,and Knight R.,2010,QIIME allows analysis of high-throughput community sequencing data,Nature Methods,7(5):335-336
Edgar R.C.,2013,UPARSE:highly accurate OTU sequences from microbial amplicon reads,Nature Methods,10(10):996-998
Edgar R.C.,Haas B.J.,Clemente J.C.,Quince C.,and Knight R.2011,Uchime improves sensitivity and speed of chimera detection,Bioinformatics,27(16):2194-200
Gao Z.Q.,and Zhang S.X.,1998,Continuous cropping obstacle and rhizospheric microecology I.root exudates and their ecological effects,Yingyong Shengtai Xuebao(Chinese Journal of Applied Ecology),9(5):549-554(高子勤,张淑香,1998连作障碍与根际微生态研究I.根系分泌物及其生态效应应用生态学报,9(5):549-554)
Haas B.J.,Gevers D.,Earl A.M.,Feldgarden M.,Ward D.V.,Giannoukos G.,Ciulla D.,Tabbaa D.,Highlander S.K.,Soder gren E.,MethéB.,DeSantis T.Z.,Consortium H.M.,Petrosino J.F.,Knight R.,and Birren B.W.,2011,Chimeric 16S r RNAsequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons,Genome Research,21(3):494-504
Jin L.,Gao X.M.,Du J.H.,Wang H.X.,Guan L.M.,Wang J.C.Wei G.W.,and Qiu X.Z.,2016,Peat bacterial diversity and community structure in Gahai Lake wetlandin Gan'nan Weishengwuxue Tongbao(Microbiology China),43(11):2396-2404(靳亮,高学梅,杜建华,王洪秀,关丽梅,王金昌魏国汶,邱小忠,2016,尕海湖湿地泥炭细菌多样性分析微生物学通报,43(11):2396-2404)
Li C.G.,Li X.M.,and Wang J.G.,2006,Effect of soybean continuous cropping on bulk and rhizosphere soil microbial community function,Shengtai Xuebao(Acta Ecologica Sinica),26(4):1144-1150(李春格,李晓鸣,王敬国,2006,大豆连作对土体和根际微生物群落功能的影响,生态学报,26(4):1144-1150)
Li K.F.,Yang B.N.,Yang W.,Shang S.Q.,Li J.D.,Yang D.Q.and Jia J.X.,2015,Planting status and research progress on seeding machine of carrot at home and abroad,Nongye Gongcheng(Agricultural Engineering),5(1):1-5(李凯锋,杨炳南,杨薇,尚书旗,李建东,杨德秋,贾晶霞,2015,国内外胡萝卜种植现状及播种机研究进展,农业工程,5(1):1-5)
Li X.Z.,Rui J.P.,Mao Y.J.,Yannarell A.,and Mackie R.,2014,Dynamics of the bacterial community structure in the rhizosphere of a maize cultivar,Soil Biology and Biochemistry,68(68):392-401
Li Z.F.,Yang Y.Q.,Xie D.F.,Zhu L.F.,Zhang Z.G.,and Lin W.X.,2012,Identification of autotoxic compounds in fibrous roots of rehmannia(rehmannia glutinosa libosch.),PLoS One,7(1):e28806
Luby C.H.,Maeda H.A.,and Goldman I.L.,2014,Genetic and phenological variation of tocochromanol(vitamin E)content in wild(Daucus carota L.var.carota)and domesticated car rot(D.carota L.var.sativa),Horticulture Research,1(15):1-6
Ma L.,Ma K.,Yang G.L.,Niu H.X.,and Dai X.H.,2015,Effects of continuous potato cropping on the diversity of soil microorganisms,Zhongguo Shengtai Nongye Xuebao(Chinese Journal of Eco-Agriculture),23(5):225-232(马玲,马琨,杨桂丽,牛红霞,代晓华,2015,马铃薯连作栽培对土壤微生物多样性的影响,中国生态农业学报,23(5):225-232)
Magoc T.,and Salzberg S.L.,2011,FLASH:fast length adjustment of short reads to improve genome assemblies,Bioinformatics,27(21):2957-2963
Mendes R.,Kruijt M.,De B.I.,Dekkers E.,Van D.V.M.,Schneider J.H.,Piceno Y.M.,DeSantis T.Z.,Andersen G.L.,Bakker P.A.,and Raaijmakers J.M.,2011,Deciphering the rhizosphere microbiome for disease-suppressive bacteria,Science,332(6033):1097-1100
Mendes R.,and Raaijmakers J.M.,2015,Cross-kingdom similarities in microbiome functions,ISME J.,9:1905-1907
Quast C.,Pruesse E.,Yilmaz P.,Gerken J.,Schweer T.,Yarza P.,Peplies J.,and Gl?ckner F.O.,2013,The SILVA ribosomal RNA gene database project:improved data processing and web-based tools,Nucleic Acids Res.,41(D1):590-596
Trivedi P.,He Z.,Nostrand J.D.V.,Albrigo G.,Zhou J.,and Wang N.,2012,Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere,Isme Journal,6(2):363-383
Wei G.H.,and Ma Z.Q.,2010,Application of rhizobia-legume symbiosis for remediation of heavy-metal contaminated soils,Weishengwu Xuebao(Acta Microbiologica Sinica),50(11):1421-1430(韦革宏,马占强,2010,根瘤菌-豆科植物共生体系在重金属污染环境修复中的地位,应用及潜力,微生物学报,50(11):1421-1430)
Wu L.,Wang H.,Zhang Z.,Lin R.,Zhang Z.,and Lin W.,2011,Comparative metaproteomic analysis on consecutively rehmannia glutinosa-monocultured rhizosphere soil,PLoS One,6(5):9055-9059
Xu H.G.,Ai Q.H.,Mai K.S.,Xu W.,and Liu F.Z.G.,2011,Effects of dietary administration of bacillus subtilis and chitooligosaccharide on serum immune parameters of juvenile large croaker Pseudosciaena crocea,Zhongguo Haiyang Daxue Xuebao(Periodical of Ocean University of China),41(7):42-47(徐后国,艾庆辉,麦康森,徐玮,刘付志国,2011饲料中添加枯草芽孢杆菌和壳寡糖对大黄鱼幼鱼血清免疫指标的影响,中国海洋大学学报,41(7):42-47)
Yuan Z.,Druzhinina I.S.,LabbéJ.,Redman R.,Qin Y.,Rodriguez R.,Zhang C.,Tuskan G.A.,and Lin F.,2016,Specialized microbiome of a halophyte and its role in helping non-host plants to withstand salinity,Scientific Reports,6:32467
Zhao Y.P.,Lin S.,Chu L.,Lin S.,Chu L.X.,Gao J.T.,Azeem S.,and Lin W.X.,2016,Insight into structure dynamics of soil microbiota mediated by the richness of replanted Pseudostellaria heterophylla,Scientific Reports,6:26175
Bokulich N.A.,Subramanian S.,Faith J.J.,Gevers D.,Gordon J.I.Knight R.,Mills D.A.,and Caporaso J.G.,2012,Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing,Nature Methods,10(1):57-59
Caporaso J.G.,Kuczynski J.,Stombaugh J.,Bittinger K.,Bushman F.D.,Costello E.K.,Fierer N.,Pe觡a A.G.,Goodrich JK.,Gordon J.I.,Huttley G.A.,Kelley S.T.,Knights D.Koenig J.E.,Ley R.E.,Lozupone C.A.,McDonald D.Muegge B.D.,Pirrung M.,Reeder J.,Sevinsky J.R.,Turnbaugh P.J.,Walters W.A.,Widmann J.,Yatsunenko T.,Zaneveld J.,and Knight R.,2010,QIIME allows analysis of high-throughput community sequencing data,Nature Methods,7(5):335-336
Edgar R.C.,2013,UPARSE:highly accurate OTU sequences from microbial amplicon reads,Nature Methods,10(10):996-998
Edgar R.C.,Haas B.J.,Clemente J.C.,Quince C.,and Knight R.2011,Uchime improves sensitivity and speed of chimera detection,Bioinformatics,27(16):2194-200
Gao Z.Q.,and Zhang S.X.,1998,Continuous cropping obstacle and rhizospheric microecology I.root exudates and their ecological effects,Yingyong Shengtai Xuebao(Chinese Journal of Applied Ecology),9(5):549-554(高子勤,张淑香,1998连作障碍与根际微生态研究I.根系分泌物及其生态效应应用生态学报,9(5):549-554)
Haas B.J.,Gevers D.,Earl A.M.,Feldgarden M.,Ward D.V.,Giannoukos G.,Ciulla D.,Tabbaa D.,Highlander S.K.,Soder gren E.,MethéB.,DeSantis T.Z.,Consortium H.M.,Petrosino J.F.,Knight R.,and Birren B.W.,2011,Chimeric 16S r RNAsequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons,Genome Research,21(3):494-504
Jin L.,Gao X.M.,Du J.H.,Wang H.X.,Guan L.M.,Wang J.C.Wei G.W.,and Qiu X.Z.,2016,Peat bacterial diversity and community structure in Gahai Lake wetlandin Gan'nan Weishengwuxue Tongbao(Microbiology China),43(11):2396-2404(靳亮,高学梅,杜建华,王洪秀,关丽梅,王金昌魏国汶,邱小忠,2016,尕海湖湿地泥炭细菌多样性分析微生物学通报,43(11):2396-2404)
Li C.G.,Li X.M.,and Wang J.G.,2006,Effect of soybean continuous cropping on bulk and rhizosphere soil microbial community function,Shengtai Xuebao(Acta Ecologica Sinica),26(4):1144-1150(李春格,李晓鸣,王敬国,2006,大豆连作对土体和根际微生物群落功能的影响,生态学报,26(4):1144-1150)
Li K.F.,Yang B.N.,Yang W.,Shang S.Q.,Li J.D.,Yang D.Q.and Jia J.X.,2015,Planting status and research progress on seeding machine of carrot at home and abroad,Nongye Gongcheng(Agricultural Engineering),5(1):1-5(李凯锋,杨炳南,杨薇,尚书旗,李建东,杨德秋,贾晶霞,2015,国内外胡萝卜种植现状及播种机研究进展,农业工程,5(1):1-5)
Li X.Z.,Rui J.P.,Mao Y.J.,Yannarell A.,and Mackie R.,2014,Dynamics of the bacterial community structure in the rhizosphere of a maize cultivar,Soil Biology and Biochemistry,68(68):392-401
Li Z.F.,Yang Y.Q.,Xie D.F.,Zhu L.F.,Zhang Z.G.,and Lin W.X.,2012,Identification of autotoxic compounds in fibrous roots of rehmannia(rehmannia glutinosa libosch.),PLoS One,7(1):e28806
Luby C.H.,Maeda H.A.,and Goldman I.L.,2014,Genetic and phenological variation of tocochromanol(vitamin E)content in wild(Daucus carota L.var.carota)and domesticated car rot(D.carota L.var.sativa),Horticulture Research,1(15):1-6
Ma L.,Ma K.,Yang G.L.,Niu H.X.,and Dai X.H.,2015,Effects of continuous potato cropping on the diversity of soil microorganisms,Zhongguo Shengtai Nongye Xuebao(Chinese Journal of Eco-Agriculture),23(5):225-232(马玲,马琨,杨桂丽,牛红霞,代晓华,2015,马铃薯连作栽培对土壤微生物多样性的影响,中国生态农业学报,23(5):225-232)
Magoc T.,and Salzberg S.L.,2011,FLASH:fast length adjustment of short reads to improve genome assemblies,Bioinformatics,27(21):2957-2963
Mendes R.,Kruijt M.,De B.I.,Dekkers E.,Van D.V.M.,Schneider J.H.,Piceno Y.M.,DeSantis T.Z.,Andersen G.L.,Bakker P.A.,and Raaijmakers J.M.,2011,Deciphering the rhizosphere microbiome for disease-suppressive bacteria,Science,332(6033):1097-1100
Mendes R.,and Raaijmakers J.M.,2015,Cross-kingdom similarities in microbiome functions,ISME J.,9:1905-1907
Quast C.,Pruesse E.,Yilmaz P.,Gerken J.,Schweer T.,Yarza P.,Peplies J.,and Gl?ckner F.O.,2013,The SILVA ribosomal RNA gene database project:improved data processing and web-based tools,Nucleic Acids Res.,41(D1):590-596
Trivedi P.,He Z.,Nostrand J.D.V.,Albrigo G.,Zhou J.,and Wang N.,2012,Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere,Isme Journal,6(2):363-383
Wei G.H.,and Ma Z.Q.,2010,Application of rhizobia-legume symbiosis for remediation of heavy-metal contaminated soils,Weishengwu Xuebao(Acta Microbiologica Sinica),50(11):1421-1430(韦革宏,马占强,2010,根瘤菌-豆科植物共生体系在重金属污染环境修复中的地位,应用及潜力,微生物学报,50(11):1421-1430)
Wu L.,Wang H.,Zhang Z.,Lin R.,Zhang Z.,and Lin W.,2011,Comparative metaproteomic analysis on consecutively rehmannia glutinosa-monocultured rhizosphere soil,PLoS One,6(5):9055-9059
Xu H.G.,Ai Q.H.,Mai K.S.,Xu W.,and Liu F.Z.G.,2011,Effects of dietary administration of bacillus subtilis and chitooligosaccharide on serum immune parameters of juvenile large croaker Pseudosciaena crocea,Zhongguo Haiyang Daxue Xuebao(Periodical of Ocean University of China),41(7):42-47(徐后国,艾庆辉,麦康森,徐玮,刘付志国,2011饲料中添加枯草芽孢杆菌和壳寡糖对大黄鱼幼鱼血清免疫指标的影响,中国海洋大学学报,41(7):42-47)
Yuan Z.,Druzhinina I.S.,LabbéJ.,Redman R.,Qin Y.,Rodriguez R.,Zhang C.,Tuskan G.A.,and Lin F.,2016,Specialized microbiome of a halophyte and its role in helping non-host plants to withstand salinity,Scientific Reports,6:32467
Zhao Y.P.,Lin S.,Chu L.,Lin S.,Chu L.X.,Gao J.T.,Azeem S.,and Lin W.X.,2016,Insight into structure dynamics of soil microbiota mediated by the richness of replanted Pseudostellaria heterophylla,Scientific Reports,6:26175