基于高通量测序技术分析使它隆对玉米根系内生菌多样性的影响

doi:10.16035/j.issn.1001-7283.2018.01.026

摘要/Abstract

摘要：

利用Illumina Miseq高通量测序技术,对玉米根系内生菌16S rRNA的V4~V5可变区序列进行测定,分析不同时期有杂草生长（长草组）与使用使它隆除草对玉米根系内生菌群落组成的影响。从5个玉米根系样品共得到166 647条有效序列、145 298条优质序列和4 464个细菌OTUs。Alpha多样性分析结果表明,玉米根系内生菌的群落多样性随玉米植株的生长而增加;使用使它隆除草后,群落的丰富度和均匀度在花期下降,在成熟期下降明显。对群落组成分析发现,使用使它隆除草后,与长草组相比,花期和成熟期的内生菌在门及属水平上的分布均发生较大变化。内生菌的基因功能分析表明,使用使它隆除草后,花期根系内生菌的异型生物质的降解代谢通路丰度高于未喷施使它隆的长草组样品;成熟期糖代谢通路丰度高于长草组。结果表明,喷施使它隆能降低玉米根系内生菌的多样性,并使内生菌的组成比例发生变化。花期根系内生假单胞菌属等比例的增加与异型生物质的降解代谢有关;成熟期肠杆菌属、芽孢杆菌属等比例的增加与糖代谢功能的提高有关。

关键词: 高通量测序, 使它隆, 玉米, 根部内生菌, 细菌多样性

Abstract:

The Illumina Miseq high-throughput sequencing technology was used to determine the V4-V5 variable region sequence of 16S rRNA and the effect of growing weed or weeding control with starane on the composition of the community structure of maize root endophytes in different periods. The research received a total of 166 647 effective sequences, 145 298 high-quality sequences, 4 464 OTUs from 5 maize root samples. The results of the analysis of Alpha diversity showed that the community diversity of maize root endophytes increased with the growth of maize plants. By weeding control with starane, the richness and evenness of the root community were decreased slightly at florescence stage, and obviously at maturation stage. Community composition analysis showed that by weeding control with starane, the distribution of bacteria in phylum and genus level changed greatly at florescence and maturation stages compared with the grass groups. The analysis of the gene function of endophytes showed that by weeding control with starane, the abundance of xenobiotics biodegradation metabolism was higher than the group of growing weed at florescence stage, and the abundance of carbohydrate metabolism increased at maturation stage. In brief, the result indicated that the spraying starane reduced the diversity of bacteria in maize roots, and the proportion of endophytic bacteria changed. The increase in the proportion of Pseudomonas was relevant with the xenobiotics biodegradation metabolism at florescence stage, and the increase in proportion of Enterobacter and Bacillus was relevant with the increase of carbohydrate metabolism.

Key words: High-throughput sequencing, Starane, Maize, Roots endophytes, Bacterial diversity

王春蕾,方志军,许艳蕊,卢晓平,穆春华,单凯,郝鲁江. 基于高通量测序技术分析使它隆对玉米根系内生菌多样性的影响[J]. 作物杂志, 2018 (1): 160–165

Chunlei Wang,Zhijun Fang,Yanrui Xu,Xiaoping Lu,Chunhua Mu,Kai Shan,Lujiang Hao. Effects of Starane on the Community Diversity of Maize Root Endophytes Analyzed Using High-Throughput Sequencing Technology[J]. Crops, 2018(1): 160–165

图/表 7

表1

表2

图1

表3

表4

表5

图2

参考文献 16

[1]	李绍强 . 玉米田化学除草试验. 长江蔬菜, 2013(4):68-69.
[2]	董莉环 . 使它隆、烟嘧磺隆防除玉米田杂草的药效试验. 吉林农业, 2015(17):75. doi: 10.14025/j.cnki.jlny.2015.17.028
[3]	喻江 . 玉米和大豆根内生细菌多样性及促生细菌鉴定评价. 哈尔滨:东北农业大学, 2016.
[4]	楼骏, 柳勇, 李延 . 高通量测序技术在土壤微生物多样性研究中的研究进展. 中国农学通报, 2014,30(15):256-260.
[5]	喻江, 于镇华 , Ikenaga M, 等. 施用有机肥对侵蚀黑土玉米苗期根内生细菌多样性的影响. 应用生态学报, 2016,27(8):2663-2669. doi: 10.13287/j.1001-9332.201608.012
[6]	Magoc T, Salzberg S L . FLASH:fast length adjustment of short reads to improve genome assemblies. Bioinformatics, 2011,27(21):2957-2963. doi: 10.1093/bioinformatics/btr507 pmid: 21903629
[7]	Caporaso J G, Kuczynski J, Stombaugh J , et al. QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 2010,7(5):335-336. doi: 10.1038/nmeth.f.303
[8]	Blaxter M, Mann J, Chapman T , et al. Defining operational taxonomic units using DNA barcode data. Philosophical Transactions of the Royal Society B -Biological Sciences, 2005,360(1462):1935-1943. doi: 10.1098/rstb.2005.1725 pmid: 1609233
[9]	Pitta D W, Parmar N, Patel A K , et al. Bacterial diversity dynamics associated with different diets and different primer pairs in the rumen of Kankrej cattle. PLoS ONE, 2014,9(11):e111710. doi: 10.1371/journal.pone.0111710
[10]	夏金兰, 刘鹏, 万民熙 . Chlorella Sorokiniana rbcL基因的克隆与序列分析及其与18S rRNA基因在分类学上的比较. 现代生物医学进展, 2010,24(10):4601-4605.
[11]	孙淑清, 刘限, 姚远 , 等. 莠去津和烟嘧磺隆对玉米田土壤微生物的影响. 农药, 2014,53(4):276-279.
[12]	黄顶成, 尤民生, 侯有明 , 等. 化学除草剂对农田生物群落的影响. 生态学报, 2005,25(6):1452-1458. doi: 10.3321/j.issn:1000-0933.2005.06.033
[13]	Hallmann J, Quadt-Hallmann A, Mahaffee W F , et al. Bacterial endophytes in agricultural crops. Canadian Journal of Microbiology, 1997,43(10):895-914. doi: 10.1139/m97-131
[14]	Ramesh R, Joshi A A, Ghanekar M P . Pseudomonads:major antagonistic endophytic bacteria to suppress bacterial wilt pathogen,Ralstonia solanacearum in the eggplant (Solanum melongena L.). World Journal of Microbiology and Biotechnology, 2009,25(1):47-55. doi: 10.1007/s11274-008-9859-3
[15]	杨海君, 谭周进, 肖启明 , 等. 假单胞菌的生物防治作用研究. 中国生态农业学报, 2004,12(3):158-161.
[16]	Tian B Y, Zhang C J, Ye Y , et al. Beneficial traits of bacterial endophytes belonging to the core communities of the tomato root microbiome. Agriculture, Ecosystems and Environment, 2017,247:149-156. doi: 10.1016/j.agee.2017.06.041

相关文章 15

[1]	陈广周王广福渠建洲司雷勇金岩徐淑兔薛吉全路海东. 不同玉米自交系子粒脱水速率及其#br# 与主要影响性状的相关分析[J]. 作物杂志, 2018, (5): 33–39
[2]	苏桂华李春雷, 苏义臣. 吉林省22 份主推玉米品种区域试验评价[J]. 作物杂志, 2018, (5): 63–70
[3]	吴荣华庄克章刘鹏张春艳. 鲁南地区夏玉米产量对气象因子的响应[J]. 作物杂志, 2018, (5): 104–109
[4]	李少昆张万旭, 王克如韩冬生杨小霞陈永生. 北疆玉米大田机械粒收质量调查[J]. 作物杂志, 2018, (5): 127–131
[5]	高文俊杨国义高新中玉柱许庆方原向阳孙耀武. 氮磷钾肥对青贮玉米产量和品质的影响[J]. 作物杂志, 2018, (5): 144–149
[6]	李红燕,王永宏,赵如浪,张文杰,明博,谢瑞芝,王克如,李璐璐,高尚,李少昆. 宁夏引/扬黄灌区玉米子粒脱水模型的构建与应用[J]. 作物杂志, 2018, (4): 149–153
[7]	李少昆,张万旭,王克如,俞万兵,陈永生,韩冬生,杨小霞,刘朝巍,张国强,王浥州,柳枫贺,陈江鲁,杨京京,谢瑞芝,侯鹏,明博. 北疆玉米密植高产宜粒收品种筛选[J]. 作物杂志, 2018, (4): 62–68
[8]	樊艳丽,董会,卢柏山,史亚兴,高宁,史亚民,徐丽,席胜利,张翠芬,刘焱辉. 播期对不同糯玉米品种淀粉糊化特性的影响[J]. 作物杂志, 2018, (4): 79–83
[9]	杨京京,陈江鲁,谢瑞芝,张小伟,丁变红,吴新明,李少昆,李东方. 玉米种子粒重差异对相关发芽指标整齐度的影响[J]. 作物杂志, 2018, (3): 180–184
[10]	李少昆,王克如,王延波,赵海岩,沈玉忠,蔡丹丹,肖万欣,姜文野,黄兆福,翟立超,谢瑞芝,侯鹏,明博. 辽宁中部地区玉米机械粒收质量及其限制因素研究[J]. 作物杂志, 2018, (3): 162–167
[11]	史磊,王国宏,王延波,王大为,赵海岩. 玉米杂交种及其亲本子粒脱水速率初步研究[J]. 作物杂志, 2018, (3): 84–89
[12]	王克如,李少昆,王延波,赵海岩,沈玉忠,蔡丹丹,肖万欣,姜文野,黄兆福,翟立超,李璐璐,谢瑞芝,侯鹏,明博. 辽宁中部适宜机械粒收玉米品种的筛选[J]. 作物杂志, 2018, (3): 97–102
[13]	李璐璐,谢瑞芝,王克如,明博,侯鹏,李少昆. 去苞叶对玉米子粒脱水过程的影响[J]. 作物杂志, 2018, (2): 114–117
[14]	李锐,白建荣,王秀红,张丛卓,张效梅,闫蕾,杨瑞娟. 144份甜玉米群体的遗传多样性分析[J]. 作物杂志, 2018, (2): 17–24
[15]	李忠南,王越人,邬生辉,曲海涛,许正学,李光发. 玉米主要性状GCA效应值的因子分析[J]. 作物杂志, 2018, (2): 25–29

Metrics

Viewed

Full text

Abstract

Cited

Shared

Discussed

编号 Number	使它隆处理 Starane treatment	采集时期 Collection stage	采集日期 Collection date
LR81CK	-	苗期Seedling	2016-06-24
LR82	+	花期Florescence	2016-08-24
LR82CK	-	花期Florescence	2016-08-24
LR83	+	成熟期Maturation	2016-09-17
LR83CK	-	成熟期Maturation	2016-09-17

样品 Sample	有效序列数 Effective sequence number	高质量序列 High quality sequence	比例(%) Ratio	OTU数 OTUs
LR81CK	28 916	27 226	94.16	485
LR82	36 203	31 590	87.26	924
LR82CK	34 414	27 056	78.62	958
LR83	32 665	29 873	91.45	805
LR83CK	34 449	29 553	85.79	1 292
合计Total	166 647	145 298	87.19	4 464

样品Sample	Chao1	ACE	Simpson	Shannon
LR81CK	279.00	379.60	0.60	2.34
LR82	711.00	852.91	0.96	6.07
LR82CK	736.00	839.58	0.96	6.59
LR83	620.00	714.06	0.93	5.50
LR83CK	1 120.00	1 194.33	0.96	6.77

门Phylum	LR81CK	LR82	LR82CK	LR83	LR83CK
变形菌门Proteobacteria	30.022	48.047	40.834	51.995	50.362
厚壁菌门Firmicutes	3.133	25.657	29.960	29.889	17.223
蓝藻菌门Cyanobacteria	60.596	10.908	12.934	5.843	9.915
放线菌门Actinobacteria	5.030	7.649	6.444	5.046	7.445
拟杆菌门Bacteroidetes	0.570	5.365	7.321	4.392	2.861
酸杆菌门Acidobacteria	0.328	1.694	1.275	1.894	5.546
绿弯菌门Chloroflexi	0.119	0.065	0.126	0.133	1.809
芽单胞菌门Gemmatimonadetes	0.041	0.026	0.008	0.102	1.559
浮霉菌门Planctomycetes	0.019	0.132	0.126	0.164	0.966
硝化螺旋菌门Nitrospirae	0.034	0.006	0.008	0.034	0.825
柔膜菌门Tenericutes	0.067	0.239	0.333	0.102	0.116
疣微菌门Verrucomicrobia	0.019	0.052	0.463	0.048	0.119
泉古菌门Crenarchaeota	0.007	0.013	0.015	0.055	0.470
装甲菌门Armatimonadetes	0.000	0.000	0.000	0.102	0.260
梭杆菌门Fusobacteria	0.000	0.023	0.031	0.024	0.029
广古菌门Euryarchaeota	0.000	0.013	0.008	0.014	0.022
迷踪菌门Elusimicrobia	0.000	0.000	0.000	0.000	0.033
螺旋体门Spirochaetes	0.000	0.000	0.011	0.000	0.000
互养菌门Synergistetes	0.000	0.000	0.011	0.000	0.000
绿菌门Chlorobi	0.000	0.000	0.000	0.000	0.011

属Genus	LR81CK	LR82	LR82CK	LR83	LR83CK
链球菌属Streptococcus	6.835	17.833	14.959	23.453	16.950
肠杆菌属Enterobacter	40.055	6.388	15.440	21.940	4.577
莫拉氏菌属Moraxella	4.062	10.714	1.402	5.535	17.210
丛毛单胞菌属Comamonas	3.620	6.897	5.556	5.044	5.525
根瘤菌属Rhizobium	0.059	5.943	5.248	4.353	14.549
拟诺卡菌属Nocardiopsis	23.537	5.726	4.835	0.258	0.141
假单胞菌属Pseudomonas	1.505	4.390	3.334	4.751	4.144
黄单胞菌属Xanthomonas	3.194	6.593	4.105	2.145	2.662
芽孢杆菌属Bacillus	1.586	2.879	2.236	4.353	2.765
曼嗜甲壳菌属Chitinophaga	1.867	4.161	2.619	3.550	2.702
诺卡氏菌属Nocardia	1.327	2.113	1.933	3.132	2.411
慢生根瘤菌属Bradyrhizobium	0.825	1.664	0.810	1.888	2.089
动性球菌属Planococcus	3.436	1.637	2.231	0.402	0.338
草酸杆菌属Oxalobacter	1.084	4.563	4.601	1.517	1.385
鞘脂单胞菌属Sphingomonas	0.200	1.490	1.739	0.820	1.198
伯克氏菌属Burkholderia	0.944	1.136	2.033	1.899	1.000
毛螺菌属Lachnospira	0.987	1.704	4.706	0.452	0.630
布鲁氏菌属Brucella	0.583	0.927	0.810	1.006	1.271
生丝微菌属Hyphomicrobium	0.081	0.659	0.850	1.311	1.426
其他Others (128)	4.213(15)	12.584(48)	20.553(47)	12.192(53)	17.027(102)