基于高通量测序研究草莓根际微生物群落结构和多样性
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摘要
研究草莓根际土壤微生物群落组成和结构,对健康草莓土壤生态系统的构建和保持具有重要意义。以不同地区草莓根际土壤为研究样本,利用MiSeq平台Illumina第二代高通量测序技术并结合相关生物信息学分析土壤细菌16S rRNA基因V4+V5区域和真菌ITS1+ITS2区域的丰富度和多样性指数以及群落结构。结果表明:从15个草莓根际土壤样本中获得4554个细菌分类操作单元OTU和1298个真菌OTU,草莓根际土壤的优势细菌门为变形菌门、厚壁菌门、放线菌门、酸杆菌门和绿弯菌门,主要的优势细菌属有16种;优势真菌门为子囊菌门、接合菌门和担子菌门,主要的优势真菌属有8种。冗余分析(RDA)显示,全氮和pH对土壤微生物群落结构的影响最大,共解释了61%的群落变化,各因子的贡献率大小依次为土壤全氮>pH>有效磷>全钾>全磷>有机质>速效钾>碱解氮;相关性分析也表明,土壤理化指标均与不同优势菌门存在密切的相关关系。本研究结果加深了对草莓根际微生物群落结构和多样性的认识,为深入研究草莓根际微生物多样性及功能与环境因子之间的关系提供了借鉴。
It is important for constructing and maintaining a healthy soil ecosystem to explore microbial community composition and structure in strawberry rhizosphere soil. Strawberry rhizosphere soils in different places were collected and used as study targets, the 16 S rRNA genes of V4+V5 regions of soil bacteria and of ITS1+ITS2 regions of soil fungi were sequenced and analyzed by Illumina high-throughput sequencing technology on MiSeq platform combined with related bioinformatics analysis to explore the changes of abundances, diversities and structures of soil bacteria and fungi. Results showed that a total of4 554 bacterial operational taxonomic units(OTUs) and 1 298 fungal OTUs were obtained from 15 strawberry rhizosphere soil samples. At phylum level, dominant bacteria were Proteobacteria, Firmicutes, Actinobacteria, Acidobacteria and Chloroflexi,dominant fungi were Ascomycota, Zygomycota and Basidiomycota. At genera level, there were 16 genera of dominant bacteria and 8 genera of dominant fungi. Redundancy analysis(RDA) showed that total nitrogen and pH had the greatest effect on soil microbial community structure, explaining 61% of the community changes. The order of contribution rate was total nitrogen > pH> available phosphorus > total potassium > total phosphorus > organic matter > available potassium > alkali-hydrolyzable nitrogen. Correlation analysis also showed that soil physiochemical characteristics were significantly correlated with different dominant microbial community. This study deepens the understanding on microbial community in strawberry rhizosphere and provides references for the relation between microbial composition and diversity with environmental factors.
It is important for constructing and maintaining a healthy soil ecosystem to explore microbial community composition and structure in strawberry rhizosphere soil. Strawberry rhizosphere soils in different places were collected and used as study targets, the 16 S rRNA genes of V4+V5 regions of soil bacteria and of ITS1+ITS2 regions of soil fungi were sequenced and analyzed by Illumina high-throughput sequencing technology on MiSeq platform combined with related bioinformatics analysis to explore the changes of abundances, diversities and structures of soil bacteria and fungi. Results showed that a total of4 554 bacterial operational taxonomic units(OTUs) and 1 298 fungal OTUs were obtained from 15 strawberry rhizosphere soil samples. At phylum level, dominant bacteria were Proteobacteria, Firmicutes, Actinobacteria, Acidobacteria and Chloroflexi,dominant fungi were Ascomycota, Zygomycota and Basidiomycota. At genera level, there were 16 genera of dominant bacteria and 8 genera of dominant fungi. Redundancy analysis(RDA) showed that total nitrogen and pH had the greatest effect on soil microbial community structure, explaining 61% of the community changes. The order of contribution rate was total nitrogen > pH> available phosphorus > total potassium > total phosphorus > organic matter > available potassium > alkali-hydrolyzable nitrogen. Correlation analysis also showed that soil physiochemical characteristics were significantly correlated with different dominant microbial community. This study deepens the understanding on microbial community in strawberry rhizosphere and provides references for the relation between microbial composition and diversity with environmental factors.
引文
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[28]张向民.镰刀菌属分类学研究历史与现状[J].菌物研究,2005,3(2):59-62
[29]杨瑞红,赵成义,王新军,等.梭梭和柽柳土壤微生物多样性初步分析[J].土壤,2016,48(6):1120-1130
[30]Liu J,Sui Y,Yu Z,et al.High throughput sequencing analysis of biogeographical distribution of bacterial communities in the black soils of northeast China[J].Soil Biology&Biochemistry,2014,70(2):113-122
[31]Fierer N,Lauber C L,Ramirez K S,et al.Comparative metagenomic,phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients[J].The Isme Journal,2012,6(5):1007
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[33]Paterson E,Gebbing T,Abel C,et al.Rhizodeposition shapes rhizosphere microbial community structure in organic soil[J].New Phytologist,173,600-610
[34]Kitazawa H,Asao T,Ban T,et al.Autotoxicity of root exudates from strawberry in hydroponic culture[J].The Journal of Horticultural Science and Biotechnology,2005,80(6):677-680
[35]侯慧,董坤,杨智仙,等.连作障碍发生机理研究进展[J].土壤,2016,48(6):1068-1076
[36]Qi J J,Yao H Y,Ma X J,et al.Soil microbial community composition and diversity in the rhizosphere of a Chinese medicinal plant[J].Communications in Soil Science and Plant Analysis,2009,40(9/10):1462-1482
[37]吴林坤,林向民,林文雄.根系分泌物介导下植物-土壤-微生物互作关系研究进展与展望[J].植物生态学报,2014,38(3):298-310
[2]汪其同,朱婉芮,刘梦玲,等.基于高通量测序的杨树人工林根际和非根际细菌群落结构比较[J].应用与环境生物学报,2015,21(5):967-973
[3]Aira M,Bybee S,Domínguez J.Carnivory does not change the rhizosphere bacterial community of the plant Drosera intermedia[J].Applied Soil Ecology,2015(92):14-17
[4]Acosta-martinez V,Burow G,Zobeck T M,et al.Soil microbial communities and function in alternative systems to continuous cotton[J].Soil Science Society of America Journal[J],2010,74(4):1181-1192
[5]Nayyar A,Hamel C,Lafond G,et al.Soil microbial quality associated with yield reduction in continuous-pea[J].Appl Soil Ecology,2009,43(1):115
[6]Schirmer M,Ijaz U Z,D'Amore R,et al.Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform[J].Nucleic Acids Research,2015,43(6):e37
[7]Williams S T,Foster P G,Littlewood D T J.The complete mitochondrial genome of a turbinid vetigastropod from MiSeq Illumina sequencing of genomic DNA and steps towards a resolved gastropod phylogeny[J].Gene,2014,533(1):38-47
[8]Sogin M L,Morrison H G,Huber J A,et al.Microbial diversity in the deep sea and the underexplored“rare biosphere”[J].Proceeding of the National Academy of Sciences of the United States of America,2006,103(32):12115-12120
[9]Konstantinidis K T,Tiedje J M.Genomic insights that advance the species definition for prokaryotes[J].Proceeding of the National Academy of Sciences of the United States of America,2005,102(7):2567-2572
[10]Elad Y,Chet I,Henis Y.Biological control of Rhizoctonia solani in strawberry fields by Trichoderma harzianum[J].Plant and Soil,1981,60(2):245-254
[11]杨剑虹.土壤农化分析与环境监测[M].北京:中国大地出版社,2008.pp 26-75
[12]Kozich J J,Westcott S L,Baxter N T,et al.Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform[J].Applied and Environmental Microbiology,2013,79(17):5112-5120
[13]Amato K R,Yeoman C J,Kent A,et al.Habitat degradation impacts black howler monkey(Alouatta pigra)gastrointestinal microbiomes[J].The ISME Journal,2013,7(7):1344-1353
[14]Romaniuk R,GiuffréL,Costantini A,et al.Assessment of soil microbial diversity measurements as indicators of soil functioning in organic and conventional horticulture systems[J].Ecological Indicators,2011,11(5):1345-1353
[15]陈秀蓉,南志标.细菌多样性及其在农业生态系统中的作用[J].草业科学,2002,19(9):34-38
[16]Kennedy A C.Bacterial diversity in agroecosystems[J].Agriculture,Ecosystems and Environment,1999,74:65-76
[17]Fierer N,Bradford M A,Jackson R B.Toward an ecological classification of soil bacteria[J].Ecology,2007,88(6):1354-1364
[18]Peiffer J A,Spor A,Koren O,et al.Diversity and heritability of the maize rhizosphere microbiome under field conditions[J].Proceedings of the National Academy of Sciences,2013,110(16):6548-6553
[19]纳小凡,郑国琦,彭励,等.不同种植年限宁夏枸杞根际微生物多样性变化[J].土壤学报,2016,53(1):241-252
[20]柳春林,左伟英,赵增阳,等.鼎湖山不同演替阶段森林土壤细菌多样性[J].微生物学报,2012,52(12):1489-1496
[21]Peralta R M,Ahn C,Gillevet P M.Characterization of soil bacterial community structure and physicochemical properties in created and natural wetlands[J].Science of the Total Environment,2013,443(3):725-732
[22]Lynd L R,Weimer P J,VanZyl W H,et al.Microbial cellulose utilization:Fundamentals and biotechnology[J].Microbiology and Molecular Biology Reviews,2002,66(3):506-577
[23]Pankratov T A,Ivanova A O,Dedysh S N,et al.Bacterial populations and environmental factors controlling cellulose degradation in an acidic Sphagnum peat[J].Environmental Microbiology,2011,13(7):1800-1814
[24]Lopez-Mondejar R,Voriskova J,Vetrovsky T,et al.The bacterial community inhabiting temperate deciduous forests is vertically stratified and undergoes seasonal dynamics[J].Soil Biology and Biochemistry,2015,87:43-50
[25]赵吉,廖仰南.羊草草地分解者亚系统的特性及作用[J].生态学报,1995,15(4):359-364
[26]Yelle D J,Ralph J,Lu F C,et al.Evidence for cleavage of lignin by a brown rot basidiomycete[J].Environmental Microbiology,2008,10(7):1844-1849
[27]Beimforde C,Feldberg K,Nylinder S,et al.Estimating the phanerozoic history of the ascomycota lineages:Combining fossil and molecular data[J].Molecular Phylogenetics and Evolution,2014,78:386-398
[28]张向民.镰刀菌属分类学研究历史与现状[J].菌物研究,2005,3(2):59-62
[29]杨瑞红,赵成义,王新军,等.梭梭和柽柳土壤微生物多样性初步分析[J].土壤,2016,48(6):1120-1130
[30]Liu J,Sui Y,Yu Z,et al.High throughput sequencing analysis of biogeographical distribution of bacterial communities in the black soils of northeast China[J].Soil Biology&Biochemistry,2014,70(2):113-122
[31]Fierer N,Lauber C L,Ramirez K S,et al.Comparative metagenomic,phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients[J].The Isme Journal,2012,6(5):1007
[32]纳小凡,郑国旗,邢正操,等.连作对再植枸杞根际细菌群落多样性和群落结构的影响[J].土壤学报,2017,54(5):1280-1292
[33]Paterson E,Gebbing T,Abel C,et al.Rhizodeposition shapes rhizosphere microbial community structure in organic soil[J].New Phytologist,173,600-610
[34]Kitazawa H,Asao T,Ban T,et al.Autotoxicity of root exudates from strawberry in hydroponic culture[J].The Journal of Horticultural Science and Biotechnology,2005,80(6):677-680
[35]侯慧,董坤,杨智仙,等.连作障碍发生机理研究进展[J].土壤,2016,48(6):1068-1076
[36]Qi J J,Yao H Y,Ma X J,et al.Soil microbial community composition and diversity in the rhizosphere of a Chinese medicinal plant[J].Communications in Soil Science and Plant Analysis,2009,40(9/10):1462-1482
[37]吴林坤,林向民,林文雄.根系分泌物介导下植物-土壤-微生物互作关系研究进展与展望[J].植物生态学报,2014,38(3):298-310
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