Progress of Study on Extraction Methods of Environmental Microbial DNA

Authors

YANG Jing, College of Bioengineering, Sichuan University of Science & Engineering, Zigong, Sichuan 643000, China; Liquor Making Bio-Technology & Application of Key Laboratory of Sichuan Province, Zigong, Sichuan 643000, China
ZHANG Jing, College of Bioengineering, Sichuan University of Science & Engineering, Zigong, Sichuan 643000, China; Liquor Making Bio-Technology & Application of Key Laboratory of Sichuan Province, Zigong, Sichuan 643000, China
ZOU Wei, College of Bioengineering, Sichuan University of Science & Engineering, Zigong, Sichuan 643000, China; Liquor Making Bio-Technology & Application of Key Laboratory of Sichuan Province, Zigong, Sichuan 643000, China
ZHAO Xingxiu, College of Bioengineering, Sichuan University of Science & Engineering, Zigong, Sichuan 643000, China; Liquor Making Bio-Technology & Application of Key Laboratory of Sichuan Province, Zigong, Sichuan 643000, China
ZHAO Changqing, College of Bioengineering, Sichuan University of Science & Engineering, Zigong, Sichuan 643000, China; Liquor Making Bio-Technology & Application of Key Laboratory of Sichuan Province, Zigong, Sichuan 643000, China

Abstract

Environmental microbial DNA extraction is the foundation of microbial community research by molecular biology techniques, and its structural integrity and the purity of DNA extracted is directly related to the subsequent experiment results. DNA extraction method is not a unified standard because of various environmental samples, including water, soil and activated sludge, the traditional fermented food, liquor-making environment, etc. Now, there are many methods of DNA extraction, they can be divided into direct and indirect extraction ones. The direct extraction methods are simple, less time-consuming, while presenting impurities. However, complex indirect extraction operations are time-consuming, but the products are pure. Based on the comparison of the different DNA extraction methods, we focus on the research progress of DNA extractions of liquor brewing environment and the large fragments.

Publication Date

3-28-2017

First Page

207

Last Page

210,215

DOI

10.13652/j.issn.1003-5788.2017.03.043

Recommended Citation

Jing, YANG; Jing, ZHANG; Wei, ZOU; Xingxiu, ZHAO; and Changqing, ZHAO (2017) "Progress of Study on Extraction Methods of Environmental Microbial DNA," Food and Machinery: Vol. 33: Iss. 3, Article 42.
DOI: 10.13652/j.issn.1003-5788.2017.03.043
Available at: https://www.ifoodmm.cn/journal/vol33/iss3/42

References

[1] OGRAM A, SAYLER G S, BARKAY T. The extraction and purification of microbial DNA from sediments[J]. Microbio Methods, 1987, 7(2/3): 57-66.
[2] 陈竹, 陈元彩, 付时雨, 等. 环境样品中DNA提取方法的研究进展[J]. 环境污染与防治, 2007, 29(7): 537-540.
[3] TORSVIK V L, GOKSOY J. Determination of bacterial DNA in soil[J]. Soil Biology Biochemistry, 1978, 10(1): 7-12.
[4] 潘明, 袁城金, 王世宽. 浓香型大曲中微生物总DNA的PCR优化[J]. 中国酿造, 2012, 31(3): 108-110.
[5] GUTHRIE J N, MORIARTY D J W, BLACKALL L L. DNA extraction from coral reef sediment bacteria for the polymerase chain reaction[J]. Journal of Microbiological Methods, 2000, 43(2): 73-80．
[6] 王晓辉, 黄李淑馨, 白凤武, 等. 海洋底泥环境DNA提取与纯化方法比较研究[J]. 大连理工大学学报, 2014, 54(3): 272-277.
[7] MORE M I, HERRICK J B, SILVA M C, et al. Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment[J]. Appl Environ Microbiol, 1994, 60(5): 1 572-1 580.
[8] 李靖宇, 赵吉, 边玉, 等. 湿地土壤微生物DNA提取及其脱腐技术[J]. 微生物学通报, 2010, 37(8): 1 130-1 137.
[9] 崔彬彬, 李云, 冯大领, 等. 杨树叶绿体分离及叶绿体DNA提取方法的研究[J]. 保定学院学报, 2006, 19(2): 25-27.
[10] 傅莲英, 席峰, 袁建军, 等. 海水养殖沉积环境微生物总的提取方法研究[J]. 厦门大学学报: 自然科学版, 2006, 45(6): 841-846.
[11] FLORENCE Braun, JRME Hamelin, GALLE Gévaudan, et al. Development and Application of an Enzymatic and Cell Flotation Treatment for the Recovery of Viable Microbial Cells from Environmental Matrices Such as Anaerobic Sludge[J]. Applied and Environmental Microbiology, 2011, 77(24): 8 487-8 493.
[12] 席峰, 傅莲英, 王桂忠, 等. 海洋沉积物DNA 提取前的简易脱腐方法研究[J]. 高技术通讯, 2006, 16(5): 539-533.
[13] 宋培勇, 梁飞, 徐华谷, 等. 芬顿试剂在土壤DNA提取中的脱腐殖酸效果[J]. 腐殖酸, 2014(5): 20-23.
[14] 闫亮珍, 李晓然, 全哲学, 等. 汾酒大曲和酒醅样品DNA提取方法的优化[J]. 食品与发酵工业, 2011, 37(3): 32-36.
[15] 赵裕栋, 周俊, 何璟. 土壤微生物总DNA提取方法的优化[J]. 微生物学报, 2012, 52(9): 1 143-1 150.
[16] 万晶晶, 张汝嘉, 邢德峰, 等. 超声波破碎法提取活性污泥DNA及其DGGE分析[J]. 哈尔滨工业大学学报, 2008, 40(4): 559-562.
[17] 曲艳玲. 活性污泥DNA提取及其微生物群落分析研究[D]. 北京: 北京工商大学, 2007: 18-28.
[18] 吕新, 陈丽华, 李胡仁. 4种不同土壤微生物DNA提取方法对DGGE分析微生物群落的影响[J]. 福建农业学报, 2012, 27(4): 367-372.
[19] 郑璐, 高乃云. 环境样品中DNA提取方法的研究进展[J]. 给水排水, 2010, 46(5): 175-178.
[20] CHEN Hong, RANGASAMY Murugesan, TAN Sek Yee, et al. Evaluation of Five Methods for Total DNA Extraction from Western Corn Rootworm Beetles[J]. Plos One, 2010, 5(8): 1-6.
[21] FARIA Fatima, NEELAM Pathak, SMITA Rastogi Verma. An Improved Method for Soil DNA Extraction to Study the Microbial Assortment within Rhizospheric Region[J]. Molecular Biology International, 2014, doi:10.1155/2014/518960.
[22] BENJAMIN E R Rubin, JON G Sanders, JARRAD Hampton Marcell, et al. DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure[J]. Microbiology Open, 2014, 3(6): 910-921.
[23] KAZUYA Watanabe, SATOSHI Yamamoto, SANAE Hino, et al. Population Dynamics of Phenol-Degrading Bacteria in Activated Sludge Determined by gyrB-Targeted Quantitative PCR[J]. Applied And Environmental Microbiology, 1998(4): 1 203-1 209.
[24] EVGENIA Blagodatskaya, SERGEY Blagodatsky, TRAUTE-HEIDI Anderson, et al. Microbial Growth and Carbon Use Efficiency in the Rhizosphere and Root-Free Soil[J]. PLoS One, 2014, 9(4): 1-9.
[25] 张琳, 熊格生, 吴莎莎, 等. 沼气池污泥微生物总DNA提取方法的比较[J]. 激光生物学报, 2011, 20(6)： 847-854.
[26] 曲衍洪, 田琳, 李玉梅, 等. 环氧丙烷皂化废水活性污泥DNA提取方法的比较和优化[J]. 生物加工过程, 2015, 13(1): 42-46.
[27] 陈琰, 艾云灿. 大片段DNA提取和纯化的优化方案[J]. 安徽农业科学, 2011, 39(9): 5 096-5 097.
[28] 毛丹丹, 许培雅. 应用于PCR-DGGE分析的活性污泥微生物总DNA提取方法比较[J]. 环境工程学报, 2013, 7(3): 1 189-1 195.
[29] CULLEN D W, HIRSCH P R. Simple and rapid method for direct extraction of microbial DNA from soil for PCR[J]. Biochemistry, 1998, 30(8/9): 983-993.
[30] 闫建芳, 刘秋, 张璐, 等. 一种活性污泥总DNA 提取方法的优化[J]. 环境工程学报, 2012, 6(3): 1 000-1 004.
[31] 张春辉, 赵树欣, 梁慧珍. 高温大曲中细菌总DNA提取方法比较[J]. 酿酒科技, 2008(10): 54-56.
[32] ZHANG Xin, ZHANG He, PU Jin-ji, et al. Development of a Real-Time Fluorescence Loop-Mediated Isothermal Amplifica-tion Assay for Rapid and Quantitative Detection of Fusarium oxysporum f. sp. niveum in soil[J]. FEMS Microbiology, 2013, 349(2): 127-134.
[33] TANIMA Paul, SEMANTI Basu, KEKA Sarkar. SPION-mediated soil DNA extraction and comparative analysis with conventional and commercial kit-based protocol[J]. 3 Biotech. 2014, 4(6): 669-677.
[34] 谢军, 罗惠波, 边名鸿, 等. 酒曲中产香微生物的筛选及其生长特性研究[J]. 食品与机械, 2016, 32(1): 22-25, 86.
[35] 叶光斌,王彩虹,王毅, 等. 清香型大曲细菌群落结构的比较分析[J]. 食品与机械, 2015, 31(3): 11-15, 73.
[36] 甄攀. 窖泥微生态研究[D]. 自贡: 四川理工学院, 2010: 4-5.
[37] 李晓然. 基于核糖体RNA高通量测序分析微生物群落结构[D]. 上海: 复旦大学, 2011: 8.
[38] 沈才萍, 李德林, 沈才洪, 等. 酒醅微生物DNA提取预处理方法研究[J]. 四川理工学院学报, 2013, 26(3): 16-20.
[39] 李德林, 敖宗华, 邓波, 等. 酒醅微生物总DNA提取方法的研究[J]. 酿酒科技, 2014(1): 33-37.
[40] 汤斌, 刘金英, 周庆伍, 等. 浓香型白酒窖泥中细菌多样性的免培养技术分析[J]. 食品与发酵工业, 2012, 38(7): 43-47.
[41] 边名鸿, 叶光斌, 杨晓东, 等. 酱香型窖泥古菌群落结构的研究[J]. 酿酒科技, 2012(8): 51-53.
[42] 刘金英, 汤斌. 浓香型白酒窖泥中总DNA提取方法的研究[J]. 安徽工程大学学报[J], 2013, 28(3): 8-11.
[43] MARON P A, RANJARD L, MOUGEL C, et al. Metaproteomics: A New Approach for Studying Functional Microbial Ecology[J]. Microbiology Ecology, 2007, 53(3): 486-493.
[44] CULLIGAN E P, SLEATOR R D, MARCHESI J R, et al. Metagenomics and novel gene discovery Promise and pot ential for novel therapeutics[J]. Virulence, 2014, 5(3): 399-412.
[45] STREIT W R, SCHMITZ R A. Metagenomics-the key to the uncultured microbes[J]. Current Opinion in Microbiology, 2004, 7(5): 492-498.
[46] CHUNG E J, LIM H K, KIM J C, et al. Forest soil metagenome gene cluster involved in antifungal activity expression in Escherichia coli [J]. Applied and Environmental Microbiology, 2008, 74(3): 723-730.
[47] KAKIRDE K S, PARSLEY L C, LILES M R. Size Does Matter: Application-driven Approaches for Soil Metagenomics[J]. Soil Biol Biochem, 2010, 42(11): 1 911-1 923.
[48] 蒋云霞, 郑天凌. 天然红树林土壤微生物大片段宏基因组文库的构建[J]. 环境科学, 2007, 28(11): 2 609-2 614.
[49] KIM U J, BIRREN B W, SLEPAK T, et al. Construction and Characterization of a Human Bacterial Artificial Chromosome Library[J]. Genomics, 1996, 34(2): 213-218.
[50] 苟敏, 曲媛媛, 周集体, 等. 活性污泥宏基因组Fosmid文库的构建[J]. 华南理工大学学报: 自然科学版, 2012, 40(1): 120-124.