Crops ›› 2017, Vol. 33 ›› Issue (1): 127-134.doi: 10.16035/j.issn.1001-7283.2017.01.023

Previous Articles     Next Articles

Effects of Water Conditions on Microbial Community in Maize Rhizosphere

Feng Shuai1,2,Liu Xiaoli1,2,Wu Xiaoli1,2,Jiang Shijie2,Zhou Zhengfu2,Zhang Wei2,Chen Ming2,Wang Jin1,2,Ke Xiubin2   

  1. 1Life Science and Engineering College,Southwest University of Science and Technology,Mianyang 621010,Sichuan
    2Biotechnology Research Institute,Chinese Academy of Agriculture Science,Beijing 100081,China
  • Received:2016-11-10 Revised:2016-12-18 Online:2017-02-15 Published:2018-08-26

RichHTML

7

PDF (PC)

193

Abstract:

Maize microcosms were constructed to investigate the dynamics of soil microbial community structure and population at different water treatments (20% and 80% WFPS) under greenhouse condition. We quantified the abundance and characterized the community structures based on the 16S rRNA gene of bacteria and archaea, using qPCR and barcoded pyrosequencing, by collecting the rhizosphere soil and surface soil at the 60th day of maize growth. Results showed that 41 546 OTUs of bacteria and 6 921 OTUs of archaea were obtained by high throughput sequencing. Higher diversity of bacteria was observed, and it was dominant by Proteobacteria and Acidobacteria. While the community structure of archaea was low, and it was predominant by Thaumarchaeota. Nonmetric Multidimensional Scaling (NMDS) analysis showed a significant difference in bacterium community pattern between rhizosphere soil and surface soil, but archaea community structure was not significantly affected. The abundances of bacterium and archaea were also significantly affected by “soil compartments”. Higher abundance of bacterium and archaea were found in surface soil than rhizosphere soil. In the rhizosphere soil, the abundance of bacterium and archaea under well-watered condition was significantly higher than those under drought condition. Besides, bacterium and archaea showed the similar trend in the surface soil. Our study indicates that soil compartments (niche differentiation) may be the most important factor affecting microbial community in agricultural soil.

Key words: Maize rhizosphere, Microbial community, Bacterium, Archaea, 16S rRNA pyrosequencing, Quantitative PCR

Fig.1

Maize productivity on the 60th day The values in the figure are the mean ±SE (n=3).Different letters indicate the significant difference (P<0.05), the same below"

Fig.2

Copy numbers of 16S rRNA genes of bacterium and archaea in rhizosphere soil and surface soil of maize on the 60th day"

Table 1

Variance analysis of the environmental factors on bacterium and archaea 16S rRNA gene copy number"

变异来源Source of variation 自由度
df		 细菌Bacterium 古菌Archaea
F值F-value P(>F) F值F-value P(>F)
土壤区域Soil compartment 1 87.39 <0.01 127.90 <0.01
水分条件Water treatment 1 54.21 <0.01 79.67 <0.01
土壤区域×水分条件Soil compartment×Water treatment 1 28.89 <0.01 50.79 <0.01

Table 2

Bacterium 16S rRNA diversity indices"

水分条件Water treatment 土壤区域Soil Compartment 操作分类单元OTUs 丰富度指数Chao1 多样性指数Shannon index 测序深度指数Coverage
干旱Water stress 根际土Rhizosphere soil 10 337 19 030.3±172.1 10.8±0.03 0.966
水充足Well-watered 根际土Rhizosphere soil 9 074 20 662.5±97.7 10.9±0.02 0.986
干旱Water stress 表层土Surface soil 9 839 20 438.0±546.3 10.7±0.06 0.994
水充足Well-watered 表层土Surface soil 12 296 16 311.5±815.2 10.1±0.14 0.995

Table 3

Archaea 16S rRNA diversity indices"

水分条件Water treatment 土壤区域Soil Compartment 操作分类单元OTUs 丰富度指数Chao1 多样性指数Shannon index 测序深度指数Coverage
干旱Water stress 根际土Rhizosphere soil 1 252 229.2±33.7 4.3±0.10 0.996
水充足Well-watered 根际土Rhizosphere soil 1 710 272.3±26.8 4.5±0.05 0.959
干旱Water stress 表层土Surface soil 2 320 300.7±29.3 4.8±0.03 0.979
水充足Well-watered 表层土Surface soil 1 639 186.2±16.2 4.5±0.05 0.979

Table 4

Identity and distribution of the 10 most abundant (core) OTUs (with 97% similarity as the cut off value) among all samples in bacterium 16S rRNA library collected from maize rhizosphere and surface soil"

OTU号码
OTU number		 分类Taxon 相对丰度 (%)
Relative abundance
OTU_18078 f_ Anaerolineaceae 3.85
OTU_24643 g_ Salinimicrobium 3.28
OTU_5453 f_ Cytophagaceae 1.86
OTU_26825 g_ Planktothrix 1.65
OTU_1926 f_ Anaerolineaceae 1.53
OTU_10853 s_ Arthrobacter globiformis 0.81
OTU_47774 g_ Flavisolibacter 0.65
OTU_35806 g_ Ramlibacter 0.63
OTU_43589 g_ Marmoricola 0.53
OTU_56073 c_ Acidobacteria 0.53

Table 5

Identity and distribution of the 10 most abundant (core) OTUs (with 95% similarity as the cut off value) among all samples in archaea 16S rRNA library collected from maize rhizosphere and surface soil"

OTU号码
OTU number		 分类Taxon 相对丰度(%)
Relative abundance
OTU_41732 c_ Soil Crenarchaeotic Group 31.89
OTU_18108 c_ Soil Crenarchaeotic Group 6.64
OTU_44564 c_ Soil Crenarchaeotic Group 5.79
OTU_48728 c_ Soil Crenarchaeotic Group 5.14
OTU_47697 c_ Soil Crenarchaeotic Group 4.31
OTU_53860 c_ Soil Crenarchaeotic Group 2.77
OTU_3112 c_ Soil Crenarchaeotic Group 1.54
OTU_3179 c_ Soil Crenarchaeotic Group 1.32
OTU_53911 c_ Soil Crenarchaeotic Group 1.25
OTU_28469 c_ Soil Crenarchaeotic Group 1.09

Fig.3

Community composition of bacterium and archaea in rhizosphere soil and surface at class level"

Fig.4

NMDS of bray-curtis similarity matrix analysis among 12 samples of bacterium and archaea from maize on the 60th day"

[1] Bastida F, Moreno J L, Nicolás C , et al. Soil metaproteomics:a review of an emerging environmental science.Significance,methodology and perspectives. European Journal of Soil Science, 2009,60(6):845-859.
doi: 10.1111/j.1365-2389.2009.01184.x
[2] Chaudary D R, Gautam R K, Yousuf B , et al. Nutrients,microbial community structure and functional gene abundance of rhizosphere and bulk soils of halophytes. Applied Soil Ecology, 2015,91:16-26.
doi: 10.1016/j.apsoil.2015.02.003
[3] Singh B K, Millard P, Whiteley A S , et al. Unravelling rhizosphere-microbial interactions:opportunities and limitations. Trends in Microbiology, 2004,12(8):386-393.
doi: 10.1016/j.tim.2004.06.008
[4] East R . Microbiome:Soil science comes to life. Nature, 2013,501(7468):18-19.
[5] Berendsen R L, Pieterse C M, Bakker P A . The rhizosphere microbiome and plant health. Trends in Plant Science, 2012,17(8):478-486.
doi: 10.1016/j.tplants.2012.04.001
[6] Bååth E, Berg B, Lohm U , et al. Effects of experimental acidification and liming on soil organisms and decomposition in a Scots pine forest. Pedobiologia, 1980,20:85-100.
[7] Bais H P, Weir T L, Perryl L G , et al. The role of root exudates in rhizosphere interations with plants and other organisms.Annual Review of Plant Biology.Palo Alto; Annual Reviews. 2006,57:233-266.
[8] Bardgett R, Mawdsley J, Edwards S , et al. Plant species and nitrogen effects on soil biological properties of temperate upland grasslands. Functional Ecology, 1999,13(5):650-660.
doi: 10.1046/j.1365-2435.1999.00362.x
[9] Berg G, Smalla K . Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiology Ecology, 2009,68(1):1-13.
doi: 10.1111/fem.2009.68.issue-1
[10] Cavaglieri L, Orlando J, Etcheverry M . Rhizosphere microbial community structure at different maize plant growth stages and root locations. Microbiological Research, 2009,164(4):391-399.
doi: 10.1016/j.micres.2007.03.006
[11] Castellanos T, Dohrmann A B, Imfeld G , et al. Search of environmental descriptors to explain the variability of the bacterial diversity from maize rhizospheres across a regional scale. European Journal of Soil Biology, 2009,45(5):383-393.
doi: 10.1016/j.ejsobi.2009.07.006
[12] Correa-galeote D, Bedmar E J, Fernández-González A J , et al. Bacterial communities in the rhizosphere of amilaceous maize (Zea mays L.) as assessed by pyrosequencing. Front Plant Science, 2016,7:1016.
[13] 覃潇敏, 郑毅, 汤利 , 等. 玉米与马铃薯间作对根际微生物群落结构和多样性的影响. 作物学报, 2015,41(6):919-928.
doi: 10.3724/SP.J.1006.2015.00919
[14] 叶慧香, 崔跃原, 宋新元 , 等. 转cry1Ie基因抗虫玉米对土壤中细菌群落结构的影响. 生物安全学报, 2015,24(1):64-71.
[15] van Dijk E L, Auger H, Jaszczyszyn Y , et al. Ten years of next-generation sequencing technology. Trends in Genetics, 2014,30(9):418-426.
doi: 10.1016/j.tig.2014.07.001
[16] Walker N J . Real-time and quantitative PCR:applications to mechanism-based toxicology. Journal of Biochemical and Molecular Toxicology, 2001,15(3):121-127.
doi: 10.1002/(ISSN)1099-0461
[17] Collavino M M, Tripp H J, Frank I E , et al. NifH pyrosequencing reveals the potential for location-specific soil chemistry to influence N2-fixing community dynamics. Environmental Microbiology, 2014,16(10):3211-3223.
doi: 10.1111/emi.2014.16.issue-10
[18] Chelius M, Triplett E . The Diversity of archaea and bacteria in association with the roots of Zea mays L. Microbial Ecology, 2001,41(3):252-263.
doi: 10.1007/s002480000087
[19] Peiffer J A, Spor A, Koren O , et al. Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proceedings of the Nationa Academy of Sciences of the United States of America, 2013,110(16):6548-6553.
doi: 10.1073/pnas.1302837110
[20] Cao P, Zhang L M, Shen J P , et al. Distribution and diversity of archaea communities in selected Chinese soils. FEMS Microbiology Ecology, 2012,80(1):146-158.
doi: 10.1111/j.1574-6941.2011.01280.x
[21] Atlas R M . Use of microbial diversity measurements to assess environmental stress.Current Perspectives in Microbial Ecology American Society for Microbiology,Washington,DC, 1984: 540-545.
[22] Schimel J . Ecosystem consequences of microbial diversity and community structure.Arctic and Alpine Biodiversity:Patterns, Causes and Ecosystem Consequences, 1995: 239-254.
[23] Uhlířová E, Elhottova E, Tříska J , et al. Physiology and microbial community structure in soil at extreme water content. Folia Microbiologica, 2005,50(2):161-166.
doi: 10.1007/BF02931466
[24] Valentine D L . Adaptations to energy stress dictate the ecology and evolution of the Archaea. Nature Reviews Microbiology, 2007,5(4):316-323.
doi: 10.1038/nrmicro1619
[25] Grinnell J . The niche-relationships of the California Thrasher. Auk, 1916,34(4):427-433.
[26] 杨万勤, 宋光煜 . 土壤生态位及其应用. 世界科技研究与发展, 2001,23(2):21-23.
[27] Grayston S J, Wang S, Campbell C D , et al. Selective influence of plant species on microbial diversity in the rhizosphere. Soil Biology and Biochemistry, 1998,30(3):369-378.
doi: 10.1016/S0038-0717(97)00124-7
[28] Li X, Rui J, Mao Y , et al. Dynamics of the bacterial community structure in the rhizosphere of a maize cultivar. Soil Biology and Biochemistry, 2014,68:392-401.
doi: 10.1016/j.soilbio.2013.10.017
[29] Garbeva P, Vanveen J A, Vanelsas J D . Microbial diversity in soil:Selection of microbial populations by plant and soil type and implications for disease suppressiveness. Phytopathology, 2004,42:243-270.
doi: 10.1146/annurev.phyto.42.012604.135455
[30] Brimecombe M J, Deleij F A, Lynch J M . The effect of root exudates on rhizosphere microbial populations.The Rhizosphere,Biochemistry and Organic Substances at the Soil-plant Interface,Marcel Dekker,Inc, 2000: 95-140.
[31] Ke X, Angel R, Lu Y , et al. Niche differentiation of ammonia oxidizers and nitrite oxidizers in rice paddy soil. Environmental Microbiology, 2013,15(8):2275-2292.
doi: 10.1111/emi.2013.15.issue-8
[32] Ke X, Lu Y, Conrad R . Different behaviour of methanogenic archaea and Thaumarchaeota in rice field microcosms. FEMS Microbiology Ecology, 2014,87(1):18-29.
doi: 10.1111/1574-6941.12188
[33] Uroz S, Bu E M, Murat C , et al. Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. Environmental Microbiology Reports, 2010,2(2):281-288.
doi: 10.1111/emi4.2010.2.issue-2
[1] Wei Zhang,Liangqun Wang,Yong Liu,Yanfang Hao,Wei Yang,Hongyan Bai,Bo Wu. Optimization of the Factors Related to the Efficiency of Agrobacterium-Mediated Transformation of Sorghum [J]. Crops, 2018, 34(1): 56-61.
[2] Jingang Liang,Zhengguang Zhang. Advance on Effects of Genetically ModifiedCrops on Soil Ecosystems [J]. Crops, 2017, 33(4): 1-6.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
[1] Guangcai Zhao,Xuhong Chang,Demei Wang,Zhiqiang Tao,Yanjie Wang,Yushuang Yang,Yingjie Zhu. General Situation and Development of Wheat Production[J]. Crops, 2018, 34(4): 1 -7 .
[2] Baoquan Quan,Dongmei Bai,Yuexia Tian,Yunyun Xue. Effects of Different Leaf-Peg Ratio on Photosynthesis and Yield of Peanut[J]. Crops, 2018, 34(4): 102 -105 .
[3] Xuefang Huang,Mingjing Huang,Huatao Liu,Cong Zhao,Juanling Wang. Effects of Annual Precipitation and Population Density on Tiller-Earing and Yield of Zhangzagu 5 under Film Mulching and Hole Sowing[J]. Crops, 2018, 34(4): 106 -113 .
[4] Wenhui Huang, Hui Wang, Desheng Mei. Research Progress on Lodging Resistance of Crops[J]. Crops, 2018, 34(4): 13 -19 .
[5] Yun Zhao,Cailong Xu,Xu Yang,Suzhen Li,Jing Zhou,Jicun Li,Tianfu Han,Cunxiang Wu. Effects of Sowing Methods on Seedling Stand and Production Profit of Summer Soybean under Wheat-Soybean System[J]. Crops, 2018, 34(4): 114 -120 .
[6] Mei Lu,Min Sun,Aixia Ren,Miaomiao Lei,Lingzhu Xue,Zhiqiang Gao. Effects of Spraying Foliar Fertilizers on Dryland Wheat Growth and the Correlation with Yield Formation[J]. Crops, 2018, 34(4): 121 -125 .
[7] Xiaofei Wang,Haijun Xu,Mengqiao Guo,Yu Xiao,Xinyu Cheng,Shuxia Liu,Xiangjun Guan,Yaokun Wu,Weihua Zhao,Guojiang Wei. Effects of Sowing Date, Density and Fertilizer Utilization Rate on the Yield of Oilseed Perilla frutescens in Cold Area[J]. Crops, 2018, 34(4): 126 -130 .
[8] Pengjin Zhu,Xinhua Pang,Chun Liang,Qinliang Tan,Lin Yan,Quanguang Zhou,Kewei Ou. Effects of Cold Stress on Reactive Oxygen Metabolism and Antioxidant Enzyme Activities of Sugarcane Seedlings[J]. Crops, 2018, 34(4): 131 -137 .
[9] Jie Gao,Qingfeng Li,Qiu Peng,Xiaoyan Jiao,Jinsong Wang. Effects of Different Nutrient Combinations on Plant Production and Nitrogen, Phosphorus and Potassium Utilization Characteristics in Waxy Sorghum[J]. Crops, 2018, 34(4): 138 -142 .
[10] Na Shang,Zhongxu Yang,Qiuzhi Li,Huihui Yin,Shihong Wang,Haitao Li,Tong Li,Han Zhang. Response of Cotton with Vegetative Branches to Plant Density in the Western of Shandong Province[J]. Crops, 2018, 34(4): 143 -148 .