The Application of High-Throughput Sequencing Technologies in the Research of Wetland Microbiology

作者: 刘建丽 , 武琳慧 , 赵 吉 :内蒙古大学,环境与资源学院,呼和浩特; 杜瑞芳 :内蒙古大学,生命科学学院,呼和浩特;

关键词: 高通量测序湿地微生物生态功能High-Throughput Sequencing Wetland Microorganism Ecological Function


Abstract: Microbes play an important role in the wetland ecosystem, and DNA sequencing technology is one of the important tools to study microbes. Recently, the booming development of high-throughput sequencing technologies has made it possible for us to research more accurately about microor-ganisms in wetland ecosystem. In this review, the difference between high-throughput sequencing and other sequencing technologies is described. The applications of high-throughput sequencing in microbial community structures and diversities, functional bacteria and ecosystem functions, metagenomics are elaborated. Furthermore, the spatial heterogeneity of microorganism is also revealed. Finally, we prospect the development direction of this technology in the future.

文章引用: 刘建丽 , 武琳慧 , 杜瑞芳 , 赵 吉 (2014) 高通量测序技术在湿地微生物研究中的应用。 世界生态学, 3, 56-63. doi: 10.12677/IJE.2014.34009


[1] Leininger, S., Urich, T., Schloter, M., et al. (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature, 442, 806-809.

[2] 蔡燕飞, 廖宗文 (2002) 土壤微生物生态学研究方法进展. 土壤与环境, 2, 167-171.

[3] Matovelle, G. and Hernán, D. (2007) Comparison of the molecular methods, terminal restriction fragment length polymorphism and denaturant gradient gel electrophoresis, to characterize the microbiota in feces from breastfed infants. Tesis (Magíster en Microbiología), Universidad San Francisco de Quito, Colegio de Postgrados; Quito, Ecuador, Mayo.

[4] Sakata, S., Tonooka, T., Ishizeki, S., et al. (2005) Culture-independent analysis of fecal microbiota in infants, with special reference to Bifidobacterium species. FEMS Microbiology Letters, 243, 417-423.

[5] Polz, M.F. and Cavanaugh, C.M. (1998) Bias in Template-to-Product Ratios in Multitemplate PCR. Applied and Environmental Microbiology, 64, 3724-3730.

[6] Sergeant, M.J., Constantinidou, C., Cogan, C., et al. (2012) High-Throughput Sequencing of 16S rRNA Gene Amplicons: Effects of extraction Procedure, Primer Length and Annealing Temperature. PLOS ONE, 7.

[7] Niedringhaus, T.P., Milanova, D., Kerby, M.B., et al. (2011) Landscape of Next-Generation Sequencing Technologies. Analytical Chemistry, 83, 4327-4321.

[8] Schadt, E.E., Turner, S. and Kasarskis, A. (2010) A window into third-generation sequencing. Human Molecular Genetics, 19, 227-240.

[9] Kolb, S. and Stacheter, A. (2013) Prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment. Frontiers in Microbiology, 4, 1-12.

[10] Shokralla, S., Spall, J.L., Gibson, J.F., et al. (2012) Next-generation sequencing technologies for environmental DNA research. Molecular Ecology, 21, 1794-1805.

[11] Rothberg, J.M. and Leamon, J.H. (2008) The development and impact of 454 sequencing. Nature Biotechnology, 26, 1117-1124.

[12] Shendure, J., Porreca, G.J., Reppas, N.B., Lin, X.X., McCutcheon, J.P., Rosenbaum, A.M., et al. (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science, 309, 1728-1732.

[13] 郑春雨, 王光华 (2012) 湿地生态系统中主要功能微生物研究进展. 湿地科学, 2, 243-249.

[14] 孟晗 (2011) 长三角地区土壤不同发育阶段微生物群落结构的变化. 硕士论文, 复日大学, 上海.

[15] Arfi, Y., Buée, M., Marchand, C., Levasseur, A. and Record, E. (2012) Multiple markers pyrosequencing reveals highly diverse and host-specific fungal communities on the mangrove trees Avicennia marina and Rhizophora stylosa. FEMS Microbiology Ecology, 79, 433-444.

[16] Ligi, T., Oopkaup, K., Truu, M., Preem, J.K., Nõlvak, H., Mitsch, W.J., Mander, Ü. and Truu, J. (2013) Characterization of bacterial communities in soil and sediment of a created riverine wetland complex using high-throughput 16S rRNA amplicon sequencing. Ecological Engineering, in press.

[17] Ahn, C. and Peralta, R.M. (2009) Soil bacterial community structure and physicochemical properties in mitigation wetlands created in the Piedmont region of Virginia (USA). Ecological Engineering, 35, 1036-1042.

[18] 王玉 (2012) 基于BIPES分析三种沉积物的微生物群落多样性. 硕士论文, 南方医科大学, 广州.

[19] Peralta, R.M., Ahn, C. and Gillevet, P.M. (2013) Characterization of soil bacterial community structure and physicochemical properties in created and natural wetlands. Science of the Total Environment, 443, 725-732.

[20] Dentener, F., Stevenson, D., Ellingsen, K., van Noije, T., Schultz, M., Amann, M., et al. (2006) The global atmospheric environment for the next generation. Environmental Science & Technology, 40, 3586-3594.

[21] Medinger, R., Nolte, V., Pandey, R.V., Jost, S., Ottenwälder, B., Schlötterer, C. and Boenigk, J. (2010) Diversity in a hidden world: Potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms. Molecular Ecology, 19, 32-40.

[22] Taib, N., Mangot, J.F., Domaizon, I., Bronner, G. and Debroas, D. (2013) Phylogenetic affiliation of SSU rRNA genes generated by massively parallel sequencing: New insights into the freshwater protist diversity. PLoS ONE, 8, e58950.

[23] Feng, Y.Z., Lin, X.G., Yu, Y.C., Zhang, H.Y., Chu, H.Y. and Zhu, J.G. (2013) Elevated ground-level O3 negatively influences paddy methanogenic archaeal community. Scientific Reports, 3, Article Number: 3193.

[24] Kip, N., Dutilh, B.E., Pan, Y., Bodrossy, L., Neveling, K., Kwint, M.P., et al. (2011) Ultra-deep pyrosequencing of pmoA amplicons confirms the prevalence of Methylomonas and Methylocystis in sphagnum mosses from a Dutch peat bog. Environmental Microbiology Reports, 3, 667-673.

[25] Lüke, C. and Frenzel, P. (2011) Potential of pmoA amplicon pyrosequencing for methanotroph diversity studies. Applied and Environmental Microbiology, 77, 6305-6309.

[26] 郑燕, 贾仲君 (2013) 新一代高通量测序与稳定性同位素示踪DNA/RNA技术研究稻田红壤甲烷氧化的微生物过程. 微生物学报, 2, 173-184.

[27] De Boer, W. and Kowalchuk, G.A. (2001) Nitrification in acid soils: Micro-organisms and mechanisms. Soil Biology and Biochemistry, 33, 853-866.

[28] He, J.Z., Hu, H.W. and Zhang, L.M. (2012) Current insights into the autotrophic thaumarchaeal ammonia oxidation in acidic soils. Soil Biology and Biochemistry, 55, 146-154.

[29] Chariton, A.A., Court, L.N., Hartley, D.M., Colloff, M.J. and Hardy, C.M. (2010) Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA. Frontiers in Ecology and the Environment, 8, 233-238.

[30] Shange, R., Haugabrooks, E., Ankumah, R., Ibekwe, A.M., Smith, R.C. and Dowd, S. (2013) Assessing the diversity and composition of bacterial communities across a wetland, transition, upland gradient in Macon County Alabama. Diversity, 5, 461-478.

[31] Dos Santos, H.F., Cury, J.C., Do Carmo, F.L., dos Santos, A.L., Tiedje, J., van Elsas, J.D., et al. (2011) Mangrove bacterial diversity and the impact of oil contamination revealed by pyrosequencing: Bacterial proxies for oil pollution. PLoS ONE, 6, e16943.

[32] 贺纪正, 张丽梅, 沈菊培 (2008) 宏基因组学的研究现状和发展趋势. 环境科学学报, 2, 210-216.

[33] Cai, L., Yu, K., Yang, Y., Chen, B.W., Li, X.D. and Zhang, T. (2013) Metagenomic exploration reveals high levels of microbial arsenic metabolism genes in activated sludge and coastal sediments. Applied Microbiology and Biotechnology, 97, 9579-9588.

[34] Tveit, A., Schwacke, R., Svenning, M.M. and Urich, T. (2013) Organic carbon transformations in high-Arctic peat soils: Key functions and microorganisms. The ISME Journal, 7, 299-311.

[35] Svenning, M.M., Hestnes, A.G., Wartiainen, I., Stein, L.Y., Klotz, M.G., Kalyuzhnaya, M.G., et al. (2011) Genome sequence of the arctic methanotroph Methylobacter tundripaludum SV96. Journal of Bacteriology, 193, 6418-6419.

[36] Yeganeha, L.P., Azarbaijania, R., Sarikhan, S., Mousavi, H., Ramezani, M., Amoozegar, M.A., et al. (2012) Complete genome sequence of oceanimonas sp. GK1, a halotolerant acterium from Gavkhouni wetland in Iran. Journal of Bacteriology, 194, 2123-2124.

[37] 杨持 (2008) 生态学. 高等教育出版社, 北京.

[38] 陈玉福, 董鸣 (2003) 生态学系统的空间异质性. 生态学报, 2, 346-352.

[39] 王宪礼, 李秀珍 (1997) 湿地的国内外研究进展. 生态学杂志, 1, 58-62.

[40] Kanokratana, P., Uengwetwanit, T., Rattanachomsri, U., Bunterngsook, B., Nimchua, T., Tangphatsornruang, S., et al. (2011) Insights into the phylogeny and metabolic potential of a primary tropical peat swamp forest microbial community by metagenomic analysis. Microbial Ecology, 61, 518-528.

[41] 朱德锐, 刘建, 韩睿, 等 (2012) 青海湖嗜盐微生物系统发育与种群多样性. 生物多样性, 4, 495-504.

[42] 赵婉雨, 杨渐, 董海良, 等 (2013) 柴达木盆地达布逊盐湖微生物多样性研究. 地球与环境, 4, 398-405.

[43] 余悦 (2012) 黄河三角洲原生演替中土壤微生物多样性及其与土壤理化性质关系. 博士论文, 山东大学, 山东.

[44] Yu, Y., Wang, H., Liu, J., Wang, Q., Shen, T.L., Guo, W.H. and Wang, R.Q. (2012) Shifts in microbial community function and structure along the successional gradient of coastal wetlands in Yellow River Estuary. European Journal of Soil Biology, 49, 12-21.

[45] Jiang, X.T., Peng, X., Deng, G.H., Sheng, H.F., Wang, Y., Zhou, H.W. and Tam, N.F.Y. (2013) Illumina sequencing of 16S rRNA tag revealed spatial variations of bacterial communities in a mangrove wetland. Microbial Ecology, 66, 96-104.

[46] Thomas, P.N., Denitsa, M., Matthew, B.K., Snyder, M.P. and Barron, A.E. (2011) Landscape of next-generation sequencing technologies. Analytical Chemistry, 83, 4327-4341.

[47] Fonseca, N.A., Rung, J., Brazma, A. and Marioni, J.C. (2012) Tools for mapping high-throughput sequencing data. Bioinformatics, 28, 3169-3177.