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[1]黄祖新,黄镇,叶冰莹,等.宿根甘蔗根际土壤细菌多样性分析中培养法与非培养法比较研究[J].应用与环境生物学报,2011,17(05):742-746.[doi:10.3724/SP.J.1145.2011.00742]
 HUANG Zuxin,HUANG Zhen,YE Bingying,et al.Comparison of Culture-dependent and -independent Approaches for Diversity Analysis of Soil Bacteria in the Rhizosphere of Sugarcane[J].Chinese Journal of Applied & Environmental Biology,2011,17(05):742-746.[doi:10.3724/SP.J.1145.2011.00742]
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宿根甘蔗根际土壤细菌多样性分析中培养法与非培养法比较研究()
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《应用与环境生物学报》[ISSN:1006-687X/CN:51-1482/Q]

卷:
17卷
期数:
2011年05期
页码:
742-746
栏目:
技术与方法
出版日期:
2011-10-24

文章信息/Info

Title:
Comparison of Culture-dependent and -independent Approaches for Diversity Analysis of Soil Bacteria in the Rhizosphere of Sugarcane
作者:
黄祖新黄镇叶冰莹陈由强陈如凯
(1农业部甘蔗遗传改良重点实验室 福州 350108)
(2福建师范大学生命科学学院 福州 350108)
(3教育部工业微生物工程研究中心 福州 350108)
Author(s):
HUANG ZuxinHUANG ZhenYE BingyingCHEN YouqiangCHEN Rukai
(1Key Laboratory of Genetics Improvement for Sugarcane, Ministry of Agriculture, Fuzhou 350108, China)
(2College of Life Sciences, Fujian Normal University, Fuzhou 350108, China)
(3Engineering Research Center of Industrial Microbiology, Ministry of Education, Fuzhou 350108, China)
关键词:
甘蔗根际土壤微生物细菌群落ARDRA多样性分析
Keywords:
sugarcane rhizospheric soil microorganism bacterial community ARDRA diversity analysis
分类号:
Q938.1 : Q93-335
DOI:
10.3724/SP.J.1145.2011.00742
文献标志码:
A
摘要:
采用培养法和非培养法提取甘蔗根际土壤微生物的总DNA,基于通用引物PCR扩增构建两种方法的细菌16S rDNA文库,并进行核糖体DNA扩增片段限制性内切酶分析(ARDRA),通过部分克隆序列测定构建细菌克隆文库的系统发育树,进而对基于传统的细菌平板培养法和直接提取总细菌DNA的非培养法进行比较分析. 结果显示,非培养法文库的香侬–威纳指数、辛普森指数、丰富度分别为4.94、0.998、28.91,均高于培养法文库中相应的多样性参数(分别为4.27、0.996、16.79),均一度数值都>0.95. 结合统计学数据和序列测定信息,反映出甘蔗根际土壤存在着丰富的细菌多样性,但平板培养法所展现的多样性低于直接提取法,表明前者存在着很大的局限性,而非培养法文库中主要是未培养微生物的 16S rDNA序列,这从一个侧面反映了土壤样品中未培养微生物占很大比例. 因此,在土壤微生物群落研究中,必须结合新的分子生态学技术手段,如采用直接提取总DNA的方法进行研究,才能比较全面地认识土壤微生物多样性. 图3 表3 参18
Abstract:
The total DNA of soil microorganisms in the rhizosphere of sugarcane was extracted by the cultivation method or the uncultivation method. Based on general primer PCR, the 16S rDNA library was constructed and the Amplified Ribosomal DNA Restriction Analysis (ARDRA) was conducted. Ultimately the phylogenetic tree was constructed based on the cloning sequences and the comparison between the cultivation and the uncultivation approaches was investigated. For the uncultivation method, the diversity indexes of Shannon-Wienner (H), Simpson (D) and Richness (R) were 4.94, 0.998 and 28.91, respectively, all higher than those of the cultivation method (H: 4.27, D: 0.996, R: 16.79). The evenness indexes (E) of both approaches were higher than 0.95. With the analysis of ARDRA and sequences of 44 clones, the results revealed that the microbes in the rhizospheric soil of sugarcane had huge structural, functional and genetic diversity. Because of the limitations of the cultivation method, the uncultivation method along with the techniques of molecular ecology would more appropriate for analyzing the diversity of the microbial community in the soil. Fig 3, Tab 3, Ref 18

参考文献/References:

1 Luo J (罗俊), Yuan ZN (袁照年), Zhang H (张华), Chen YQ (陈由强), Chen RK (陈如凯). Stability analysis on yield characters of sugarcane ratoon. Chin J Appl Environ Biol (应用与环境生物学报), 2009, 15 (4): 488~494
2 Zheng C (郑超), Tan ZW (谭中文), Liu KX (刘可星), Liao ZW (廖宗文), Liu YL (刘月廉), Liao YL (廖愉朗). Study on soil micro-organism community of sugarcane field under different mulch conditions. J South China Agric Univ (华南农业大学学报), 2004, 25 (2): 5~9
3 Riesenfeld CS, Schloss PD, Handelsman J. Metagenomics: Genomic analysis of microbial communities. Annu Rev Geneti, 2004, 38: 525
4 Gich FB, Amer E, Figueras JB, Abella CA, Balaguer MD, Poch M. Assessment of microbial community structure changes by amplified ribosomal DNA restriction analysis (ARDRA). Int Microbiol, 2000, 3 (2): 103~106
5 Mazo JZ, Dinon AZ, Tagliari C, Ilha EC, Sant, Anna ES, Arisi ACM. Amplified ribosomal DNA restriction analysis (ARDRA) of new isolated strains of bifidobacteria from newborn babies microbiota. Af J Microbiol Res, 2010, 4 (22): 2339~2342
6 Hao XG (郝旭光), Sun YJ (孙寓姣), Wang HQ (王红旗). Application of PCR-ARDRA technology in screening and identifiying oil degrading strains. Chin J Environ Engin (环境工程学报), 2010, 4 (2): 449~452
7 Zhang RF (张瑞福), Cao H (曹慧), Cui ZL (崔中利), Li SP (李顺鹏), Fan B (樊奔). Extraction and purification of soil microbial total DNA. Acta Microbiol Sin (微生物学报), 2003, 43 (2): 276~282
8 Zhou J, Bruns MA, Tiedje JM. DNA recovery from soils of diverse composition. Appl Environ Microbiol, 1996, 62 (2): 316~322
9 Lu XF (芦晓飞), Zhao ZX (赵志祥), Xie BY (谢丙炎), Yang YH (杨宇红), Feng DX (冯东昕). DNA extraction and construction of a metagenomic fosmid library of alpine meadow soil from the Mila Mountains in Tibet, China. Chin J Appl Environ Biol (应用与环境生物学报), 2009, 15 (6): 824~829
10 Cheng HR, Jiang N. Extremely rapid extraction of DNA from bacteria and yeasts. Biotechnol Lett, 2006, 28 (1): 55~59
11 Peralta AL, Matthews JW, Kent AD. Microbial community structure and denitrification in a wetland mitigation bank. Appl & Environ Microbiol, 2010, 76 (13): 4207~4215
12 Zhang XM (张雪梅), She YH (佘跃惠), Huang JF (黄金凤), Zhang F (张凡), Wang J (王靖), Wang WJ (王文军), Wang HZ (王洪志), Wang ZL (王正良). Microbial diversity of the Daqing Oilfield after polymer flooding. Chin J Appl Environ Biol (应用与环境生物学报), 2008, 14 (5): 668~672
13 DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl & Environ Microbiol, 2006, 72 (7): 5069~5072
14 Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol & Evol, 2007, 24: 1596~1599
15 Tamaki H, Sekiguchi Y, Hanada S, Nakamura K, Nomura N, Matsumura M, Kamagata Y. Comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivation-based techniques. Appl & Environ Microbiol, 2005, 71 (4): 2162~2169
16 Luo YC (罗远婵), Xie GL (谢关林). Burkholderia cepacia: Our enemy or friend? Acta Microbiol Sin (微生物学报), 2005, 45 (4): 647~652
17 Cui ZL (崔中利), Liu J (刘娟), Cao H (曹慧), Luo YM (骆永明), Zhao QG (赵其国). Comparison of bacterial diversity from a rice soil in Jiangxi Province by cultivation and uncultivation method. Soils (土壤), 2008, 40 (6): 903~908
18 Quaiser A, Ochsenreiter T, Lanz C, Schuster SC, Treusch AH, Jürgen Eck, Schleper C. Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Mol Microbiol, 2003, 50 (2): 563~575

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备注/Memo

备注/Memo:
农业部现代农业产业技术体系建设专项资金(No. CARS-20-4-4)、农业部公益性行业(农业)科研专项(No. nyhyzx07-019)、农业部“968”项目(No. 2006-G37)和福建省教育厅B类项目(No. 03BC727)资助
更新日期/Last Update: 2011-10-25