Review of High-throughput Sequencing Techniques in Studies of constructedwetland Microbial Diversity

doi:10.11924/j.issn.1000-6850.casb15090065

Abstract

Abstract: The paper aims to explain the theory of purifying the water body with wetland from the perspective of microbial diversity. The process and principle of the next- generation sequencing technology—highthroughput sequencing technology was analyzed, the advantages and disadvantages of high- throughput sequencing technology applications and the high-throughput sequencing technology application in wetland microbial diversity were summarized in this paper. Meanwhile the broad application value of high-throughput sequencing technology in the diversity and dynamics of the microbial community of artificial wetland was obtained, the high-throughput sequencing results in huge data processing and other issues were pointed out in this paper. Because the high- throughput sequencing technology has unique advantages, it has a great application prospect in the study of wetland microbial diversity.

CLC Number:

Q331

References

[1]Liu D, Wu X, Chang J, et al. Constructed wetlands as biofuel production systems[J].Nature Climate Change,2012.2(3):190-194.
[2]吴晓磊.人工湿地废水处理机理[J].环境科学,1994.16(3):83-87.
[3] Liu D, Ge Y, Chang J, et al. Constructed wetlands in China: recent developments and future challenges[J].Frontiers in Ecology and the Environment,2009.7(5):261-268.
[4]GREENWAY M.Suitability of macrophytes for nutrient removal from surface flow constructed wetlands receiving secondary treated sewage effluent in Queensland,Australia[J].Wat Sci Tech,2003,48(2)：121-128.
[5]陈长太,王雪,祁继英.国外人工湿地技术的应用及研究进展[J].中国给水排水,2003,19(12)：105-106.
[6]范志峰,李平,王丽卿等.复合型人工湿地系统在农业面源污染水处理以上的应用[J].上海海洋大学学报,2010,19(2)：259-264.
[7]Verhoeven J T A, Meuleman A F M. Wetlands for waste water treatment: opportunities and limitations[J] .Ecol. Eng. 1999(12): 5-12.
[8]Vrhosek D, Kukanja V, Bulc T. Constructed wetlands(CW) for industrial waste water treatment[J]. Ecol. Eng. 1996(30): 2287-2292.
[9]李晓,李冰,朱健.变性梯度凝胶电泳技术及其在人工湿地及养殖水体中应用的研究进展[J]．江苏农业科学,2013,41( 7) : 7 － 12．
[10]Faulwetter J L,Gagnon V,Sundberg C, et al． Microbial processes influencing performance of treatment wetlands: A eview[J]． Ecological Engineering,2009,35( 6) : 987 － 1004．
[11]周元清,李秀珍,李淑英等.不同类型人工湿地微生物群落的研究进展[J].生态学杂志, 2011, 30( 6) : 1251 － 1257.
[12]Sultan M,Schulz M H,Richard H,et al． A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome． Science,2008,321( 5891) : 956-960．
[13]Schuster S C． Next-generation sequencing transforms today’s biology． Nat Methods,2008,5( 1) : 16-18．
[14]王兴春,杨致荣,王敏等.高通量测序技术及其应用[J].中国生物工程杂志China Biotechnology,2012, 32( 1) : 109-114.
[15]Margulies M,Egholm M, Altman W E, et al． Genomesequencing in microfabricated high-density picolitre reactors．Nature,2005,437( 7057) : 376-380．
[16]Porreca G J,Zhang K,Li J B,et al． Multiplex amplification oflarge sets of human exons． Nat Methods,2007,4 ( 11 ) : 931-936．
[17]Ondov B D,Varadarajan A,Passalacqua K D,et al． Efficient mapping of Applied Biosystems SOLiD sequence data to aReference genome for functional genomic applications．Bioinformatics,2008,24( 23) : 2776-2777．
[18]Harris T D,Buzby PR,Babcock H,et al． Single-molecule DNA sequencing of a viral genome． Science,2008,320( 5872) : 106-109．
[19]Wheeler D A,Srinivasan M,Egholm M,et al． The complete genome of an individual by massively parallel DNA sequencing． Nature,2008,452( 7189) : 872-876．
[20]Gilad Y,Pritchard J K,Thornton K． Characterizing natural Variation using next-generation sequencing technologies． Trends in Genetics,2009 25( 10) : 463-471．
[21]李晓,李冰,董玉峰等.精养团头鲂池塘沉积物微生物群落的结构特征及组成多样性分析[J].2014,38(2)：218-227.
[22]雷旭,李冰,李晓等.复合垂直流人工湿地系统中不同植物根际微生物群落结构[J].生态学杂志Chinese Journal of Ecology 2015, 34( 5) : 1373－1381.
[23]Duncan CP,Groffman PM.1994.Comparing microbial parameters in natural and constructed wetlands.Journal of Environmental Quality,23: 298 － 305．
[24]Ibekwe AM,Grieve CM,Lyon SR． 2003． Characterization of microbial communities and composition in constructed dairy wetland wastewater effluent.Applied and Environmental Microbiology,69: 5060 － 5069．
[25]Walsh KA,Hill TC,Moffett BF,et al． 2002． Molecular characterisation of bacteria in a wetland used to remove ammoniacal-N from landfill leachate． Waste Management ＆ Research,20: 529 － 535．
[26]Ibekwe AM,Lyon SR,Leddy M,et al． 2007． Impact of plant density and microbial composition on water quality from a free water surface constructed wetland.Journal of Applied Microbiology,102: 921－936．
[27]Ahn C,Gillevet PM,Sikaroodi M． 2007． Molecular characterization of microbial communities in treatment microcosmwetlands as influenced by macrophytes and phosphorus loading． Ecological Indicators,7: 852 － 863．
[28]Shipin O,Koottatep T,Khanh NT,et al． 2005． Integrated natural treatment systems for developing communities: Lowtech N-removal through the fluctuating microbial pathways．Water Science and Technology,51: 299 － 306．
[29]Baptista JD,Davenport RJ,Donnelly T,et al.2008.The microbialdiversity of laboratory-scale wetlands appears to be randomly assembled． Water Research,42: 3182 － 3190．
[30]冯冲凌,李科林,李芸.人工湿地中微生物群落特征及其净化机理[J].中南林业科技大学学报Journal of Central South University of Forestry Technology,2012,32(12)：42-45.
[31]王绍祥,杨洲祥,孙真等.高通量测序技术在水环境微生物群落多样性中的应用[J].化学通报,2014,77(3):196-203.
[32]张瑞福,崔中利,李顺鹏.土壤,2004,36: 476 ～ 480．
[33]S E Leckie.Forset Ecol.Manage．2005,220: 88 ～ 106．
[34]Polz, M.F. and Cavanaugh, C.M. (1998) Bias in Template-to-Product Ratios in Multitemplate PCR. Applied and Environmental Microbiology, 64, 3724-3730.
[35]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.
[36]Niedringhaus, T.P., Milanova, D., Kerby, M.B., et al. (2011) Landscape of Next-Generation Sequencing Technologies.Analytical Chemistry, 83, 4327-4321.
[37]杜刚,黄磊,高旭等.人工湿地中微生物数量与污染物去除的关系[J].湿地科学,2013,11(1)：13-20
[38]Ligi, T., Oopkaup, K., Truu, M., Preem, J.K., N?lvak, H., Mitsch, W.J., Mander, ü. and Truu, J. (2013) Characterizationof bacterial communities in soil and sediment of a created riverine wetland complex using high-throughput 16S rRNA amplicon sequencing. Ecological Engineering, in press.
[39]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.
[40]Kadlec RH,Knight RL． 1996． Treatment Wetlands． Boca Raton,FL: CRC Press．
[41]龙丽珠,阮晓红,赵振华.组合人工湿地工艺微生物群落结构及脱氮效果研究.环境污染与防治,2008,30(6):75－77．
[42]曹笑笑,吕宪国,张仲胜等.人工湿地设计研究进展[J].湿地科学,2013,11(1)：121-128.
[43] 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.
[44]Medinger,R.,Nolte,V.,Pandey,R.V.,Jost,S.,Ottenw?lder, B., Schl?tterer,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.
[45]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.
[46]Dos Santos, H.F., Cury, J.C., Do Carmo, F.L., dos Santos, A.L., Tiedje, J., van Elsas, J.D., et al. (2011) Mangrovebacterial diversity and the impact of oil contamination revealed by pyrosequencing: Bacterial proxies for oil pollution.PLoS ONE, 6, e16943.
[47] 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.
[48] 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.
[49]刘建丽,武琳慧,赵吉等.高通量测序技术在湿地微生物研究中的应用[J].世界生态学, 2014, 3, 56-63.
[50] 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.
[51] 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.
[52]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研究进展[J].中国农学通报,2014,30(15):256-260.