高原作物青稞根及根际内生细菌群落结构的高通量分析

doi:10.16035/j.issn.1001-7283.2016.06.009

作物杂志,2016, 第6期: 49–52 doi: 10.16035/j.issn.1001-7283.2016.06.009

• 遗传育种·种质资源·生物技术 • 上一篇下一篇

高原作物青稞根及根际内生细菌群落结构的高通量分析

刘振东¹,王波²,薛蓓¹,王强锋³,侯磊¹

1 西藏农牧学院,860000,西藏林芝
2 西藏自治区农牧科学院农业研究所,850032,西藏拉萨
3 四川省农业科学院生物技术核技术研究所,610061,四川成都

收稿日期:2016-08-27 修回日期:2016-10-18 出版日期:2016-12-15 发布日期:2018-08-26
作者简介:刘振东,讲师,研究方向为微生物资源的发掘与利用
基金资助:
西藏自治区自然科学基金(2015212-14-23);西藏自治区青年教师创新计划项目(QCZ2016-45);国家现代农业(大麦青稞)产业技术体系加工试验站(CARS-05)

High Throughput Analysis of the Endophytic Bacterial Community Structure in Roots and Rhizosphere of Highland Barley of Tibetan Plateau

Liu Zhendong¹,Wang Bo²,Xue Bei¹,Wang Qiangfeng³,Hou Lei¹

1 Tibet Agricultural and Animal Husbandry College,Nyingchi 860000,Tibet,China
2 Agricultural Institute,Tibet Academy of Agricultural and Animal Husbandry Sciences,Lhasa 850032,Tibet,China
3 Institute of Biological & Nuclear Technology,Sichuan Academy of Agricultural Sciences,Chengdu 610061,Sichuan,China;

Received:2016-08-27 Revised:2016-10-18 Online:2016-12-15 Published:2018-08-26

摘要/Abstract

摘要：

利用高通量测序技术分析了西藏青稞主栽品种藏青2000根及根际内生细菌的16S V4变异区序列,同时应用UparseRON、KA等软件整理和统计样品序列数和操作分类单元（OTU）数,分析物种丰度及Alpaha多样性等指标。获得的用于分析青稞根部内生细菌的有效序列和OTUs为55 192/3 613,用于分析青稞根际土壤内生细菌的有效序列和OTUs为62 181/4 399;根部及根际土壤Chao1指数分别为3 443.4290和4 632.5820,shannon多样性指数分别为8.542和9.967。在门水平对代表性OTU进行注释发现,青稞根及根际土壤内生细菌主要是变形菌门（Proteobacteria）、拟杆菌门（Bacteroidetes）、放线菌门（Actinobacteria）、酸杆菌门（Acidobacteria）、厚壁菌门（Firmicutes）。在属水平上主要是假单胞菌属（Pseudomonas）、链霉菌属（Streptomyces）、土地杆菌属（Pedobacter）、黄杆菌属（Flavobacterium）、红游动菌属（Rhodoplanes）。结果显示,青稞根及根际内生细菌具有丰富的多样性,且二者的优势菌属一致。

关键词: 青稞, 根, 根际, 内生细菌, 种类, 丰度

Abstract:

High-throughput sequencing technology has been applied to the determination of 16S V4 variation sequences of the endophytic bacteria in roots and rhizosphere of the main cultivar of highland barley (Zangqing 2000) in Tibetan Plateau. The number of sample sequences and operational taxonomic units (OTUs) were sorted and calculated and the species richness and alpha diversity index were analyzed by Uparse and KRONA. The results showed that the useful sequences and OTUs of the endophytic bacteria in roots were 55 192/3 613, while the useful sequences and OTUs of the endophytic bacteria in rhizosphere were 62 181/4 399. The Chao1 indices of the endophytic bacteria in roots and rhizosphere were 3 443.4290 and 4 632.5820, respectively, and the Shannon diversity indices were 8.542 and 9.967, respectively. The endophytic bacteria in roots and rhizosphere of highland barley were mainly included in Pseudomonas, Streptomyces, Pedobacter, Flavobacterium and Rhodoplanes. These results indicate that the endophytic bacteria in roots and rhizosphere of highland barley ZQ2000 have rich diversity and the dominant genera of the bacteria in both roots and rhizosphere.

Key words: Highland barley, Root, Rhizosphere, Endophytic bacteria, Species, Richness

刘振东,王波,薛蓓,王强锋,侯磊. 高原作物青稞根及根际内生细菌群落结构的高通量分析[J]. 作物杂志, 2016 (6): 49–52

Zhendong Liu,Bo Wang,Bei Xue,Qiangfeng Wang,Lei Hou. High Throughput Analysis of the Endophytic Bacterial Community Structure in Roots and Rhizosphere of Highland Barley of Tibetan Plateau[J]. Crops, 2016(6): 49–52

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参考文献 11

[1]	Schulz B, Boyle C . What are endophytes?// Schulz B J E, Boyle C J C, Sieber T N. Microbial Root Endophytes.Berlin Heidelberg:Springer-Verlag, 2006: 1-13.
[2]	Ryan R P, Germaine K, Franks A , et al. Bacterial endophytes:recent developments and applications. FEMS Microbiology Letters, 2008,278(1):1-9. doi: 10.1111/j.1574-6968.2007.00918.x pmid: 18034833
[3]	Reinhold-Hurek B, Hurek T . Life in grasses diazotrophic endophytes. Trends in Microbiology, 1998,6(4):139-144. doi: 10.1016/S0966-842X(98)01229-3 pmid: 9587190
[4]	Sturz A V, Christie B R, Matheson B G , et al. Biodiversity of endophy-tic bacteria which colonize red clover nodules,roots,stems and folia-ges and their influence on host growth. Biology & Fertillity of Soils, 1997,25(1):13-19.
[5]	Fendrik I, Gallo M D, Vanderleyden ,et al.Azospirillum VI and Related Microorganisms:Genetics-Physiology-Ecology. Heidelberg:Springer, 1995: 169-187.
[6]	杨慧林, 张志斌, 颜日明 , 等. 东乡野生稻内生放线菌Streptomyces sp.PRh5的全基因组测序及序列分析. 微生物学通报, 2015,42(4):801-809. doi: 10.13344/j.microbiol.china.140615
[7]	Lupwayi N Z, Clayton G W, Hanson K G , et al. Endophytic rhizobia in barley,wheat and canola roots. Canadian Journal of Plant Science, 2004,84(1):37-45. doi: 10.4141/P03-087
[8]	Wipps J M . Carbon utilization. UK:The rhizosphere, 1990: 59-97.
[9]	Niedringhaus T P, Milanova D, Kerby M B , et al. Landscape of next-generation sequencing technologies. Analytical Chemistry, 2011,83(12):4327-4341. doi: 10.1021/ac2010857 pmid: 3437308
[10]	Ligi T, Oopkaup K, Truu M , et al. Characterization of bacterial communities in soil and sediment of a created riverine wetland complex using high-throughput 16S rRNA amplicon sequencing. Ecological Engineering, 2014,72:56-66. doi: 10.1016/j.ecoleng.2013.09.007
[11]	Akinsanya M A, Goh J K, Lim S P , et al. Metagenomics study of endophytic bacteria in Aloe vera using next-generation technology. Genomics Data, 2015,6:159-163. doi: 10.1016/j.gdata.2015.09.004 pmid: 26697361

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样品sample	Total tag	Taxon tag	Unclassified Mitochondria Chloroplast tag	Unique tag	OTU number
ZQ2000.1.r	67 671	54 226	9 896	3 549	3 669
ZQ2000.2.r	63 671	51 708	8 406	3 557	3 588
ZQ2000.3.r	67 264	59 643	4 372	3 249	3 583
平均值Mean	66 202	55 192	7 558	3 452	3 613
ZQ2000.1.s	59 159	53 413	164	5 582	4 009
ZQ2000.2.s	75 030	69 298	87	5 645	4 930
ZQ2000.3.s	69 506	63 832	255	5 419	4 257
平均值Mean	67 898	62 181	169	5 547	4 399

样品Sample	Proteobacteria	Bacteroidetes	Actinobacteria	Acidobacteria	Firmicutes	Others
ZQ2000.1.r	61.1	14.1	13.6	2.9	0.8	21.6
ZQ2000.2.r	63.8	14.6	9.8	3.1	0.8	22.5
ZQ2000.3.r	70.0	11.8	8.6	2.7	0.6	18.1
平均值Mean	64.9	13.5	10.6	2.9	0.7	20.9
ZQ2000.1.s	47.3	11.9	8.8	7.4	0.4	36.1
ZQ2000.2.s	40.0	7.9	8.5	11.9	0.5	39.1
ZQ2000.3.s	52.5	9.7	9.2	7.6	0.7	30.0
平均值Mean	46.6	9.8	8.8	8.9	0.5	35.2

样品Sample	Pseudomonas	Streptomyces	Pedobacter	Flavobacterium	Rhodoplanes	Others
ZQ2000.1.r	1.7	2.5	0.8	0.6	0.8	93.6
ZQ2000.2.r	1.4	1.5	0.9	0.4	0.8	95.0
ZQ2000.3.r	3.1	1.0	0.8	1.2	0.7	93.2
平均值Mean	2.1	1.7	0.8	0.7	0.8	93.9
ZQ2000.1.s	0.6	0.5	0.5	0.6	1.2	96.6
ZQ2000.2.s	0.4	0.4	0.1	0.1	2.4	96.6
ZQ2000.3.s	0.6	0.5	0.4	0.5	1.8	96.2
平均值Mean	0.5	0.5	0.3	0.4	1.8	96.5

样品Sample	Shannon	Chao 1	物种数Observed species
ZQ2000.1.r	8.0860	3 495.1635	2 997
ZQ2000.2.r	8.7512	3 397.1178	2 933
ZQ2000.3.r	8.0134	3 438.0043	2 888
平均值Mean	8.2835	3 443.4290	2 939
ZQ2000.1.s	9.9022	3 911.0820	3 448
ZQ2000.2.s	10.1277	5 361.9856	4 077
ZQ2000.3.s	9.8716	4 624.6773	3 582
平均值Mean	9.9672	4 632.5820	3 702

高原作物青稞根及根际内生细菌群落结构的高通量分析

High Throughput Analysis of the Endophytic Bacterial Community Structure in Roots and Rhizosphere of Highland Barley of Tibetan Plateau

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