高通量测序技术在土壤微生物多样性研究中的应用

doi:10.11924/j.issn.1000-6850.2013-2513

摘要/Abstract

摘要： 为了阐明高通量测序技术在土壤微生物多样性研究中的应用前景，归纳介绍了Solexa、454和Ion Torrent等常用高通量测序技术的原理和优点，综述了近年高通量测序技术在土壤微生物物种多样性、结构多样性、功能多样性和遗传多样性四个方面应用的研究进展，总结了高通量测序技术应用中存在的问题，并分析展望了其在土壤微生物多样性研究中的发展趋势。

关键词: 稻瘟病, 稻瘟病, 化学防治, 抗性品种, 生物防治, 栽培措施

Abstract: In order to illuminate the application prospects of high-throughput sequencing techniques in soil microbial diversity, this article gave a summarization and introduction of principles and advantages of common high-throughput sequencing techniques, including Solexa, 454 and Ion Torrent. The latest research advances of high- throughput sequencing techniques applications were reviewed in soil microbial species diversity, structures diversity, functions diversity and genes diversity. Finally, the application problems and the development tendency of high- throughput sequencing techniques used in soil microbial studies were summarized and discussed.

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应用[J]. 中国农学通报, 2014, 30(15): 256-260.

Li Yan. Review of High-throughput Sequencing Techniques in Studies of Soil Microbial Diversity[J]. Chinese Agricultural Science Bulletin, 2014, 30(15): 256-260.

参考文献

[1] Whitman W B, Coleman D C, Wiebe W J. Prokaryotes: the unseen majority [J]. Proceedings of the National Academy of Sciences, 1998,95(12):6578-6583.
[2] Pace N R. A molecular view of microbial diversity and the biosphere [J]. Science, 1997, 276(5313):734-740.
[3] 刘国华,叶正芳,吴为中.土壤微生物群落多样性解析法:从培养到非培养[J].生态学报,2012,32(14):4421-4433.
[4] Gans J, Wolinsky M, Dunbar J. Computational improvements reveal great bacterial diversity and high metal toxicity in soil [J]. Science, 2005, 309(5739):1387-1390.
[5] 姚槐应,黄昌勇.土壤微生物生态学及其实验技术[M].北京:科学出版社,2006:8-8.
[6] 张旭霞,刘左军,陈正宏.土壤微生物多样性的研究方法[J].安徽农业科学,2007,35(32):1037-1037.
[7] 林先贵,胡君利.土壤微生物多样性的科学内涵及其生态服务功能[J].土壤学报,2008,45(5):892-900.
[8] 王保军,刘双江.环境微生物培养新技术的研究进展[J].微生物学通报,2013, 40(1):6-17.
[9] Torsvik V, Goksoyr J, Daae F L. High Diversity in DNA of Soil Bacteria [J]. Appl Environ Microb, 1990,56(3): 782-787.
[10] 张汉波,段昌群,屈良鹄.非培养方法在土壤微生物生态学研究中的应用[J].生态学杂志,2003,22(5):131-136.
[11] 秦楠,栗东芳,杨瑞馥.高通量测序技术及其在微生物学研究中的应用[J].微生物学报,2011,51(4):445-457.
[12] Quail M A, Kozarewa I, Smith F, et al. A large genome center's improvements to the Illumina sequencing system [J]. Nature methods, 2008,5(12):1005-1010.
[13] Meyer M, Stenzel U, Hofreiter M. Parallel tagged sequencing on the 454 platform [J]. Nature Protocols, 2008,3(2):267-278.
[14] Mardis E R. The impact of next-generation sequencing technology on genetics [J]. Trends in genetics, 2008, 24(3):133-141.
[15] Seo T S, Bai X, Kim D H, et al. Four-color DNA sequencing by synthesis on a chip using photocleavable fluorescent nucleotides [J]. Proceedings of the National Academy of Sciences, 2005, 102 (17):5926-5931.
[16] Quail M A, Smith M, Coupland P, et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers [J]. BMC genomics, 2012, 13(1):341.
[17] Perkel J. Is $1000 a cost, or a price? Chad Nusbaum—co-director of the Genome Sequencing and Analysis Program at the Broad Institute in Cambridge, MA—wants to know the true cost of sequencing, not just the outer pricetag. Photo credit: Len Rubenstein.(Click to enlarge) [J]. BioTechniques, 2013, 54(2):71- 74.
[18] Mason C E, Elemento O. Faster sequencers, larger datasets, new challenges [J]. Genome biology, 2012,13(3):314.
[19] Li R, Fan W, Tian G, et al. The sequence and de novo assembly of the giant panda genome [J]. Nature, 2009,463(7279):311-317.
[20] Margulies M, Egholm M, Altman W E, et al. Genome sequencing in microfabricated high- density picolitre reactors [J]. Nature, 2005, 437(7057):376-380.
[21] Carlton J M, Sullivan S A, Le Roch K G. Plasmodium Genomics and the Art of Sequencing Malaria Parasite Genomes [M]. Malaria Parasites: Comparative Genomics, Evolution and Molecular Biology. Norfolk: Caister Academic Press, 2013: 38-39.
[22] Ning J, Wang M, Li C, et al. Transcriptome Sequencing and De Novo Analysis of the Copepod Calanus sinicus Using 454 GS FLX [J]. PloS one, 2013, 8(5): e63741.
[23] Loman N J, Misra R V, Dallman T J, et al. Performance comparison of benchtop high- throughput sequencing platforms [J]. Nature biotechnology, 2012, 30(5):434-439.
[24] Toumazou C, Purushothaman S. Sensing apparatus and method: U. S. Pantent 7,686,929[P]. 2010.
[25] 杨霞,陈陆,王川庆.16S rRNA 基因序列分析技术在细菌分类中应用的研究进展[J].西北农林科技大学学报(自然科学版),2008,36 (2):55-60.
[26] Berbee M L, Taylor J W. Detecting morphological convergence in true fungi, using 18S rRNA gene sequence data [J]. Biosystems, 1992, 28(1):117-125.
[27] K?rén O, H?gberg N, Dahlberg A, et al. Inter- and intraspecific variation in the ITS region of rDNA of ectomycorrhizal fungi in Fennoscandia as detected by endonuclease analysis [J]. New Phytologist, 1997,136(2):313-325.
[28] Roesch L F, Fulthorpe R R, Riva A, et al. Pyrosequencing enumerates and contrasts soil microbial diversity [J]. The ISME Journal, 2007,1(4):283-290.
[29] Buee M, Reich M, Murat C, et al. 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity [J]. New Phytologist, 2009,184(2):449-456.
[30] Lauber C L, Hamady M, Knight R, et al. Pyrosequencing- based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale [J]. Appl Environ Microb, 2009,75 (15):5111-5120.
[31] Chu H, Fierer N, Lauber C L, et al. Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes [J]. Environmental Microbiology, 2010,12(11):2998-3006.
[32] Tripathi B M, Kim M, Lai-Hoe A, et al. pH dominates variation in tropical soil archaeal diversity and community structure [J]. FEMS Microbiology Ecology, 2013. DOI: 10.1111/1574-6941.12163.
[33] Moran M A. Metatranscriptomics: eavesdropping on complex microbial communities [J]. Issues, 2010.
[34] Damon C, Lehembre F, Oger-Desfeux C, et al. Metatranscriptomics reveals the diversity of genes expressed by eukaryotes in forest soils [J]. PloS one, 2012,7(1):e28967.
[35] Fleming J T, Yao W H, Sayler G S. Optimization of differential display of prokaryotic mRNA: application to pure culture and soil microcosms [J]. Appl Environ Microb, 1998, 64(10):3698-3706.
[36] Shrestha P M, Kube M, Reinhardt R, et al. Transcriptional activity of paddy soil bacterial communities [J]. Environmental microbiology, 2009,11(4):960-970.
[37] Chang B, Halgamuge S, Tang S- L. Analysis of SD sequences in completed microbial genomes: non-SD-led genes are as common as SD-led genes [J]. Gene, 2006, 373: 90-99.
[38] Van Elsas J, Boersma F. A review of molecular methods to study the microbiota of soil and the mycosphere [J]. European Journal of Soil Biology, 2011, 47(2): 77-87.
[39] Delmont T O, Robe P, Cecillon S, et al. Accessing the soil metagenome for studies of microbial diversity [J]. Appl Environ Microb, 2011,77(4):1315-1324.
[40] Gomez-Alvarez V, Teal T K, Schmidt T M. Systematic artifacts in metagenomes from complex microbial communities [J]. The ISME journal, 2009, 3(11):1314-1317.
[41] Chistoserdova L. Recent progress and new challenges in metagenomics for biotechnology [J]. Biotechnology letters, 2010, 32 (10):1351-1359.
[42] Lu J, Du L, Wei Y, et al. Expression and characterization of a novel highly glucose-tolerant β-glucosidase from a soil metagenome [J]. Acta biochimica et biophysica Sinica, 2013.
[43] Cheng G, Hu Y, Lu N, et al. Identification of a novel fosfomycinresistant UDP- N- acetylglucosamine enolpyruvyl transferase (MurA) from a soil metagenome [J]. Biotechnology letters, 2013, 35 (2):273-278.
[44] Mackelprang R, Waldrop M P, Deangelis K M, et al. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw [J]. Nature, 2011, 480(7377):368-371.
[45] Kelley D R, Liu B, Delcher A L, et al. Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering [J]. Nucleic acids research, 2012, 40(1):e9-e9.
[46] 张文力.高通量测序数据分析现状与挑战[J].集成技术,2012,1(3): 20-24.