基于高通量测序的藜麦连作根际土壤微生物多样性研究
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摘要
为了揭示连作藜麦土壤细菌群落结构和多样性的变化,采用高通量测序技术(Illumina-MiSeq)对不同处理(种植1 a、种植2 a)的连作藜麦根际土壤细菌进行16S rRNA基因V4区测序。结果表明,种植1 a较种植2 a的藜麦根际土壤细菌群落丰度和多样性指数都要高,其中,种植1 a较种植2 a的藜麦Chao1指数平均值增加16.4%,ACE指数平均值增加22.9%,Shannon指数平均值增加2.3%;菌群的分类学组成分析结果表明,重茬种植后,伦茨氏菌属、溶杆菌属、中慢生根瘤菌属、丛毛单菌属多样性增多;分枝杆菌属、藤黄单胞菌属、芽单胞菌属、浮霉状菌属等细菌多样性减少。功能预测分析表明,重茬种植后,编码细胞膜转运的功能基因、编码翻译、复制和修复的功能基因、编码外源性物质降解和代谢、多糖生物合成和代谢的功能基因大量减少,编码核苷酸代谢、萜类化合物的代谢、辅因子和维生素的代谢等功能基因少量减少;而编码信号转导和脂类代谢的功能基因有少量增加。
In order to reveal the changes of bacterial community structure and diversity in quinoa continuous cropping soil, the V4 aera of 16 S rRNA gene of bacteria from the quinoa rhizosphere soil with different treatments(planting for 1 a and for 2 a) was sequenced by high throughput sequencing. The results showed that the abundance and diversity index of the bacterial community in rhizosphere soil of planting quinoa for 1 a were higher than those of planting quinoa for 2 a, and the average values of Chao1, ACE and Shannon indexes increased by 16.4%, 22.9% and 2.3%, respectively. The taxonomic composition analysis of bacterial community showed that, after continuous cropping of quinoa, the bacterial diversity of Lentzea, Lysobacter, Mesorhizobium and Polaromonas increased, but the bacterial diversity of Mycobacterium, Luteimonas, Gemmatimonas and Planctomyces decreased. The analysis of functional prediction showed that the functional genes that code the membrane transport, the translation, copy and repair, the degradation and metabolism of exogenous substances and the biosynthesis and metabolism of polysaccharide decreased sigenificantly, and the functional genes coding the metabolism of nucleotide, steroids, cofactors and vitamin also decreased a little, but the functional genes of coding signal transduction and lipid metabolism increased in a small amount.
In order to reveal the changes of bacterial community structure and diversity in quinoa continuous cropping soil, the V4 aera of 16 S rRNA gene of bacteria from the quinoa rhizosphere soil with different treatments(planting for 1 a and for 2 a) was sequenced by high throughput sequencing. The results showed that the abundance and diversity index of the bacterial community in rhizosphere soil of planting quinoa for 1 a were higher than those of planting quinoa for 2 a, and the average values of Chao1, ACE and Shannon indexes increased by 16.4%, 22.9% and 2.3%, respectively. The taxonomic composition analysis of bacterial community showed that, after continuous cropping of quinoa, the bacterial diversity of Lentzea, Lysobacter, Mesorhizobium and Polaromonas increased, but the bacterial diversity of Mycobacterium, Luteimonas, Gemmatimonas and Planctomyces decreased. The analysis of functional prediction showed that the functional genes that code the membrane transport, the translation, copy and repair, the degradation and metabolism of exogenous substances and the biosynthesis and metabolism of polysaccharide decreased sigenificantly, and the functional genes coding the metabolism of nucleotide, steroids, cofactors and vitamin also decreased a little, but the functional genes of coding signal transduction and lipid metabolism increased in a small amount.
引文
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[14] 李俊锋.基于16S rRNA和宏基因组高通量测序的微生物多样性研究[D].北京:清华大学,2015.Li J F.Microbial diversity research based on high-throughput sequencing data of 16S rRNA and metagenome[D].Beijing:Tsinghua University,2015.
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[2] 李娜娜,裴艳婷,宫永超,蒲艳艳,刘保民,辛富刚,刘世华,丁汉凤.藜麦研究现状与发展前景[J].山东农业科学,2016,48(10):145-148.doi:10.14083 /j.issn.1001-4942.2016.10.033.Li N N,Pei Y T,Gong Y C,Pu Y Y,Liu B M,Xin F G,Liu S H,Ding H F.Research status and development prospect of Chenopodium quinoa Willd[J].Shandong Agricultural Sciences,2016,48(10):145-148.
[3] 马红梅,李小兵,符浩,符丽颜.灵芝连作障碍的土壤微生物种群特性及其生物防治初探[J].河南农业科学,2014,43(3):53-58.doi:10.15933/j.cnki.1004-3268.2014.03.002.Ma H M,Li X B,Fu H,Fu L Y.Preliminary study on microflora of Ganoderma lucidum continuous cropping obstacle soil and its biological control[J].Journal of Henan Agricultural Sciences,2014,43(3):53-58.
[4] 薛超,黄启为,凌宁,高雪莲,曹云,赵青云,何欣,沈其荣.连作土壤微生物区系分析、调控及高通量研究方法[J].土壤学报,2011,48(3):612-618.doi:10.11766/trxb201007120287.Xue C,Huang Q W,Ling N,Gao X L,Cao Y,Zhao Q Y,He X,Shen Q R.Analysis,regulation and high-throughput sequencing of soil microflora in mono-cropping system[J].Acta Pedologica Sinica,2011,48(3):612-618.
[5] Hiltner L.Uber neuere erfahrungen und probleme auf dem gebiete der bodenbakteriologie unter besonderer berück-sichtigung dergründ ngung und brache[J].Arbeiten der Deutschen Land-wirtschaftlichen Gesellschaft,1904,98:59-78.
[6] Morgan J A,Bending G D,White P J.Biological costs and benefits to plant-microbe interactions in the rhizosphere[J].Journal of Experimental Botany,2005,56(417):1729-1739.doi:10.1093/jxb/eri205.
[7] Berendsen R L,Pieterse C M J,Bakker P.The rhizosphere microbiome and plant health[J].Trends in Plant Science,2012,17(8):478-486.doi:10.1016/j.tplants.2012.04.001.
[8] 夏围围,贾仲君.高通量测序和DGGE分析土壤微生物群落的技术评价[J].微生物学报,2014,54(12):1489-1499.doi:10.13343/j.cnki.wsxb.2014.12.01.Xia W W,Jia Z J.Comparative analysis of soil microbial communities by pyrosequencing and dgge[J].Acta Microbiologica Sinica,2014,54(12):1489-1499.
[9] 徐雪雪.基于高通量测序的马铃薯沟垄覆膜连作土壤微生物多样性分析[D].兰州:甘肃农业大学,2016.Xu X X.Analysis of microbial diversity in potato continuous soil under different ridge-furrow film cropping patterns by high-throughput sequencing[D].Lanzhou:Gansu Agricultural University,2016.
[10] 李广宁,邓小丽,周丽沙,安海英,张海宏,徐慧.一株藤黄单胞菌属细菌HF-1127的分离与鉴定[J].生物技术,2009,19(5):43-46.doi:10.16519/j.cnki.1004-311x.2009.05.008.Li G N,Deng X L,Zhou L S,An H Y,Zhang H H,Xu H.Isolation and identification of A Luteimonas HF-1127 with antibacterial activity[J].Biotechnology,2009,19(5):43-46.
[11] 范晓阳.南太平洋沉积物深渊藤黄单胞菌(Luteimonasabyssisp.nov.etc.)等4个深海细菌新种的分类鉴定[D].青岛:中国海洋大学,2014.Fan X Y.Taxonomic analysis of four novel deep-sea bacteria species (Luteimonasabyssi sp.nov.etc.) Isolated from sediment of south pacific gyre[D].Qingdao:Ocean University of China,2014.
[12] 黄佩蓓,焦念志,冯洁,舒青龙.海洋浮霉状菌多样性与生态学功能研究进展[J].微生物学通报,2014,41(9):1891-1902.doi:10.13344/j.microbiol.china.130874.Huang P B,Jiao N Z,Feng J,Shu Q L.Research progress on planctomycetes′ diversity and ecological function in marine environments[J].Microbiology China,2014,41(9):1891-1902.
[13] Langille M G I,Zaneveld J,Caporaso J G,McDonald D,Knights D,Reyes J A,Clemente J C,Burkepile D E,Thurber R L V,Knight R,Beiko R G,Huttenhower C.Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences[J].Nat Biotechnol,2013,31(9):814-821.doi:10.1038/nbt.2676.
[14] 李俊锋.基于16S rRNA和宏基因组高通量测序的微生物多样性研究[D].北京:清华大学,2015.Li J F.Microbial diversity research based on high-throughput sequencing data of 16S rRNA and metagenome[D].Beijing:Tsinghua University,2015.
[15] Bais H P,Weir T L,Perry L G,Gilroy S,Vivanco J M.The roal of root exudates in rhizosphere interactions with plants and other organisms[J].Annaul Review of Plant Biology,2006,51(7):233-266.doi:10.1146/annurev.arplant.57.032905.105159.
[16] Bever J D,Westover K M,Antonovics J.Incroporating the soil community into plant populatindynamics:utility of the feedback approach[J].Journal of Ecology,1997,85(5):561-573.
[17] Christensen P,Cook F D.Lysobacter,a new genus of non-fruiting,gliding bacteria with a high base ratio[J].International Journal of Systematic and Bacteriology,1978,28:367-393.doi:10.1099/00207713-28-3-367.
[18] Li X G,Ding C F,Zhang T L,Wang X X.Fungal pathogen accumulation at the expense of plant-beneficial fungi as a consequence of consecutive peanut monoculturing[J].Soil Biology and Biochemistry,2014,72:11-18.doi:10.1016/j.soilbio.2014.01.019.