|本期目录/Table of Contents|

 HU Shaoda,GUO Jin,ZOU Shaolan,et al.Application of metaproteomics in study of activated sludge*[J].Chinese Journal of Applied & Environmental Biology,2016,22(22卷04):725-731.[doi:10.3724/SP.J.1145.2015.11009]

宏蛋白质组学在活性污泥研究中的应用 ()




Application of metaproteomics in study of activated sludge*
1天津大学化工学院 天津 300072 2天津市职业与环境危害防制重点实验室,中国人民武装警察部队后勤学院 天津 300309
HU Shaoda1 GUO Jin2 ZOU Shaolan1 LI Dejin2 LI Huaying2 & ZHAO Huabing2**
1School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China 2Tianjin Key Laboratory for Prevention and Control of Occupational and Environmental Hazards, Logistics University of People’s Armed Police Force, Tianjin 300309, China
metaproteomics activated sludge microbial community protein extraction protein identification
Q93-31 : X172
宏蛋白质组学作为研究微生物群落的一种新兴技术,主要是对特定微生物群落所表达的全部蛋白进行宏观、高通量的分析研究. 本文综述了宏蛋白质组学研究的技术路线,主要包括蛋白的提取和纯化、分离和鉴定,以及宏蛋白质组学在强化生物除磷的活性污泥、活性污泥胞外多聚物和比较不同处理工艺活性污泥的差异等方面的研究. 活性污泥的宏蛋白质组学研究完善了强化生物除磷活性污泥的厌氧和好氧阶段的代谢模型,揭示了活性污泥胞外多聚物在污染物降解过程中的主要作用和表现,阐述了不同活性污泥在污水处理过程中宏观特性与微观功能之间的关系,对于污水的生物处理有着重要的指导意义. 宏蛋白质组学在活性污泥研究领域仍处于起步阶段,没有统一、有效的蛋白提取方法,数据库匮乏,成为活性污泥宏蛋白质组学发展的主要阻碍. 随着各种新兴仪器、方法的应用以及数据库的不断完善,活性污泥宏蛋白质组学将会在污染物生物降解机制分析、鉴定功能蛋白等方面展现其巨大的优势. (表2参47)
Activated sludge is widely used as an effective and stable method in wastewater treatment. However a deep insight into the microbial communities and components of activated sludge is still a great challenge. The rapidly growing number of metagenomic sequences together with revolutionary advances in bioinformatics and protein analyses have opened completely new horizons to investigate the molecular basis of such complex communities. Metaproteomics, a new approach for studying functional microbial ecology, is mainly applied for macroscopical and high-throughput analysis of total proteins expressed by a specific microbial community. The research approach of metaproteomic is similar to the classical approach in proteomic analysis, including protein extraction and purification, separation and identification. Currently, activated sludge metaproteomics has made a great progress in research on enhanced biological phosphorus removal sludge, activated sludge extracellular polymeric substances and comparison of wastewater treatment processes. However, compared with the rapid development in bio-medical field, the research on activated sludge by metaproteomics is still in its infancy. The lack of a common effective protein extraction method and the imperfection of environmental microbial database became the biggest obstacle of the the application of metaproteomics in studies of activated sludge. This review summarizes the recent research advances both domestic and overseas, and compares the different methods of activated sludge metaproteomics. With the development of the new instruments and corresponding technologies, activated sludge metaproteomics will show its great advantages in study on the pollutant biodegradation mechanism and the proteins function identification.


1 陈世霞, 王雷, 韩志英. 宏蛋白质组学技术在废水生物处理工艺研究领域中的应用[J]. 应用生态学报, 2014, 25 (10): 3056-3066 [Chen SX, Wang L, Han ZY. Applications of metaproteomics in the study of wastewater biotreatment process [J]. Chin J Appl Ecol, 2014, 25 (10): 3056-3066] 2 金浩, 李柏林, 欧杰, 陈兰明. 污水处理活性污泥微生物群落多样性研究[J]. 微生物学杂志, 2012, 32 (4): 1-5 [Jin H, Li BL, Ou J, Chen LM. Microbial population diversity of activated sludge for wastewater treatment [J]. Chin J Micobiol, 2012, 32 (4): 1-5] 3 于仁涛, 高培基, 韩黎, 黄留玉. 宏蛋白质组学研究策略及应用 [J]. 生物工程学报, 2009, 25 (7): 961-967 [Yu RT, Gao PJ, Han L, Huang LY. Strategy and application of metaproteomics [J]. Chin J Biotechnol, 2009, 25 (7): 961-967] 4 Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM. Molecular biological access to the chemistry of unknown soil microbes a new frontier for natural products [J]. Chem Biol, 1998, 5 (10): 245-249 5 Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNeil IA, Minor C, Tiong CL, Gilman M, Osburne MS, Clardy J, Handelsman J, Goodman RM. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms [J]. Appl Environ Microbiol, 2000, 66 (6): 2541-2547 6 刘虎虎, 田云, 卢向阳, 方俊. 宏蛋白质组学:研究微生物群落的一种新策略[J]. 微生物学杂志, 2010, 30 (5): 88-92 [Liu HH, Tian Y, Lu XY, Fang J. Metaproteomics: a new strategy for studying microbial community [J]. Chin J Micobiol, 2010, 30 (5): 88-92] 7 Rodr??guez-Valera F. Environmental genomics, the big picture? [J]. FEMS Microbiol Lett, 2004, 231 (2): 153-158 8 郝纯, 刘庆华, 杨俊仕, 李旭东. 宏蛋白质组学:探索环境微生态系统的功能[J]. 应用与环境生物学报, 2008, 14 (2): 270-275 [Hao C, Liu QH, Yang SJ, Li XD. Metaproteomics: exploration of the functions of microbial ecosystems [J]. Chin J Appl Environ Biol, 2008, 14 (2): 270-275] 9 Wilmes P, Bond PL. Metaproteomics: studying functional gene expression in microbial ecosystems [J]. Trends Microbiol, 2006, 14 (2): 92-97 10 王小丽, Pablo GP, 叶俊, 黄丹枫. 土壤宏蛋白质组学蛋白质提取方法及其应用 [J]. 应用与环境生物学报, 2012, 18 (4): 691-696 [Wang XL, Pablo GP, Ye J, Huang DF. Methods of protein extraction from soil and their potential application in study of soil metaproteome [J]. Chin J Appl Environ Biol, 2012, 18 (4): 691-696] 11 Schneider T, Riedel K. Environmental proteomics: analysis of structure and function of microbial communities [J]. Proteomics, 2010, 10: 785-798 12 Wilmes P, Bond PL. The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms [J]. Environ Microbiol, 2004, 6 (9): 911-920 13 Kuhn R, Benndorf D, Rapp E, Reichl U, Palese LL, Pollice A. Metaproteome analysis of sewage sludge from membrane bioreactors [J]. Proteomics, 2011, 11: 2738-2744 14 Benndorf D, Balcke GU, Harms H, von Bergen M. Functional metaproteome analysis of protein extracts from contaminated soil and groundwater [J]. ISME J , 2007, 1: 224-234 15 Hansen SH, Stensballe A, Nielsen PH, Herbst FA. Metaproteomics: evaluation of protein extraction from activated sludge [J]. Proteomics, 2014, 14: 2535-2539 16 Lacerda C, Choe LH, Reardon KF. Metaproteomic analysis of a bacterial community response to cadmium exposure [J]. J Proteome Res, 2007, 6: 1145-1152 17 Silva AF, Carvalho G, Soares R, Coelho AV, Barreto Crespo MT. Step-by-step strategy for protein enrichment and proteome characterisation of extracellular polymeric substances in wastewater treatment systems [J]. Appl Microbiol Biotechnol, 2012, 95: 767-776 18 Collado N, Buttiglieri G, Kolvenbach BA, Comas J, Corvini PF, Rodriguez-Roda I. Exploring the potential of applying proteomics for tracking bisphenol A and nonylphenol degradation in activated sludge [J]. Chemosphere, 2013, 90: 2309-2314 19 Abram F, Gunnigle E, O’Flaherty V. Optimisation of protein extraction and 2-DE for metaproteomics of microbial communities from anaerobic wastewater treatment biofilms [J]. Electrophoresis, 2009, 30: 4149-4151 20 O’Farrell PH. High resolution two-dimensional electrophoresis of proteins [J]. J Biol Chem, 1975, 250: 4007-4021 21 Klose J. Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals [J]. Humangenetik, 1975, 26: 231-243 22 ?nlü M, Morgan ME, Minden JS. Difference gel electrophoresis: a single gel method for detecting changes in protein extracts [J]. Electrophoresis, 1997, 18: 2071-2077 23 Timms JF, Cramer R. Differential gel electrophoresis [J]. Proteomics, 2008, 8: 4886-4897 24 Lane CS. Mass spectrometry-based proteomics in the life sciences [J]. Cell Mol Life Sci, 2005, 62: 848-869 25 Motoyama A, Yates JR. Multidimensional LC separations in shotgun proteomics [J]. Anal Chem, 2008, 80: 7187-7193 26 Peng J, Gygi SP. Proteomics: the move to mixtures [J]. J Mass Spectrom, 2001, 36: 1083-1091 27 Shevchenko A, Wilm M, Vorm O, Mann M. Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels [J]. Anal Chem, 1996, 68: 850-858 28 Puttker S, Kohrs F, Benndorf D, Heyer R, Rapp E, Reichl U. Metaproteomics of activated sludge from a wastewater treatment plant - A pilot study [J]. Proteomics, 2015, 15: 3596-3601 29 Kohrs F, Heyer R, Magnussen A, Benndorf D, Muth T, Behne A, Rapp E, Kausmann R, Heiermann M, Klocke M, Reichl U. Sample prefractionation with liquid isoelectric focusing enables in depth microbial metaproteome analysis of mesophilic and thermophilic biogas plants [J]. Anaerobe, 2014, 29: 59-67 30 Kan JJ, Hanson TE, Ginter JM, Wang K, Chen F. Metaproteomic analysis of Chesapeake Bay microbial communities [J]. Saline Sys, 2005, 1: 7 31 杨倩, 王丹, 常丽丽, 孙勇, 靳翔, 王旭初. 生物质谱技术研究进展及其在蛋白质组学中的应用 [J]. 中国农学通报, 2015, 31 (1): 239-246 [Yang Q, Wang D, Chang LL,Sun Y, Jin X, Wang XC. Progress in mass spectrometry and its application in proteomics. Chin Agric Sci Bull, 2015, 31 (1): 239-246] 32 Wilmes P, Wexler M, Bond PL. Metaproteomics provides functional insight into activated sludge wastewater treatment [J]. PLoS ONE, 2008, 3: e1778 33 Martin HG, Ivanova N, Kunin V, Warnecke F, Barry KW, McHardy AC, Yeates C, He S, Salamov AA, Szeto E, Dalin E, Putnam NH, Shapiro HJ, Pangilinan JL, Rigoutsos I, Kyrpides NC, Blackall LL, McMahon KD, Hugenholtz P. Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities [J]. Nat Biotechnol, 2006, 24: 1263-1269 34 Wilmes P, Andersson AF, Lefsrud MG, Wexler M, Shah M, Zhang B, Hettich RL, Bond PL, VerBerkmoes NC, Banfield JF. Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal [J]. ISME J, 2008, 2: 853-864 35 Park C, Helm RF. Application of metaproteomic analysis for studying extracellular polymeric substances (EPS) in activated sludge flocs and their fate in sludge digestion [J]. Water Sci Technol, 2008, 57: 2009-2015 36 Seifert J, Herbst FA, Nielsen PH, Planes FJ, Jehmlich N, Ferrer M, Bergen M. Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities [J]. Proteomics, 2013, 13: 2786-2804 37 Ehlers MM, Cloete TE. Direct extractions of proteins to monitor an activated sludge system on a weekly basis for 34 weeks using SDS-page [J]. Water SA, 1999, 25: 57-62 38 Park C, Novak JT, Helm RF, Ahn YO, Esen A. Evaluation of the extracellular proteins in full-scale activated sludges [J]. Water Res, 2008, 42: 3879-3889 39 Zhang P, Guo JS, Shen Y, Yan P, Chen YP, Wang H, Yang JX, Fang F, Li C. Microbial communities, extracellular proteomics and polysaccharides: a comparative investigation on biofilm and suspended sludge [J]. Bioresour technol, 2015, 190: 21-28 40 Zhang P, Shen Y, Guo JS, Li C, Wang H, Chen YP, Yan P, Yang JX, Fang F. Extracellular protein analysis of activated sludge and their functions in wastewater treatment plant by shotgun proteomics [J]. Sci Rep, 2015, 5: 12041 41 Gunnigle E, Nielsen JL, Fuszard M, Botting CH, Sheahan J, O’Flaherty V, Abram F. Functional responses and adaptation of mesophilic microbial communities to psychrophilic anaerobic digestion [J]. FEMS Microbiol Ecol, 2015, 91 (12):132 42 Wexler M, Richardson DJ, Bond PL. Radiolabelled proteomics to determine differential functioning of Accumulibacter during the anaerobic and aerobic phases of a bioreactor operating for enhanced biological phosphorus removal [J]. Environ Microbiol, 2009, 11: 3029-3044 43 Markert S, Arndt C, Felbeck H, Becher D, Sievert SM, Hugler M, Albrecht D, Robidart J, Bench S, Feldman RA, Hecker M, Schweder T. Physiological proteomics of the uncultured endosymbiont of Riftia pachyptila [J]. Science, 2007, 315: 247-250 44 Klaassens ES, de Vos WM, Vaughan EE. Metaproteomics approach to study the functionality of the microbiota in the human infant gastrointestinal tract [J]. Appl Environ Microbiol, 2007, 73: 1388-1392 45 Gilchrist A, Au CE, Hiding J, Bell AW, Fernandez-Rodriguez J, Lesimple S, Nagaya H, Roy L, Gosline SJ, Hallett M, Paiement J, Kearney RE, Nilsson T, Bergeron JJ. Quantitative proteomics analysis of the secretory pathway [J]. Cell, 2006, 127: 1265-1281 46 Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents [J]. Mol Cell Proteomics, 2004, 3: 1154-1169 47 Wilmes P, Heintz-Buschart A, Bond PL. A decade of metaproteomics: Where we stand and what the future holds [J]. Proteomics, 2015, 15: 3409-3417


 GAO Pingping,et al..Isolation of novel phenoldegrading bacteria from activated sludge using feed water medium (FWM)[J].Chinese Journal of Applied & Environmental Biology,2003,9(22卷04):189.
 ZHOU Kexin,et al..Dynamics of Protozoa Diversity and Their Relationship with Performance of Activated Sludge System[J].Chinese Journal of Applied & Environmental Biology,2007,13(22卷04):840.
 JIN Min,ZHAO Zuguo,WANG Jingfeng,et al.DNA Extraction from Activated Sludge for Metagenomic Array[J].Chinese Journal of Applied & Environmental Biology,2009,15(22卷04):245.[doi:10.3724/SP.J.1145.2009.00245]
[4]王小丽,GONZALEZ PEREZ Pablo,叶俊,等.土壤宏蛋白质组学蛋白质提取方法及其应用[J].应用与环境生物学报,2012,18(04):691.[doi:10.3724/SP.J.1145.2012.00691]
 WANG Xiaoli,GONZALEZ PEREZ Pablo,YE Jun,et al.Methods of Protein Extraction from Soil and Their Potential Application in Study of Soil Metaproteome[J].Chinese Journal of Applied & Environmental Biology,2012,18(22卷04):691.[doi:10.3724/SP.J.1145.2012.00691]
 MA Li,JIA Hui,YIN Xiuqin,et al.Growth and Propagation of Earthworm in Activated Sewage Sludge Treatment[J].Chinese Journal of Applied & Environmental Biology,2013,19(22卷04):147.[doi:10.3724/SP.J.1145.2013.00147]
 ZHAI Siyuan,WANG Yae WEI Zhiyong,LI Jie.Effects of pH and Temperature on the Dissimilatory Reduction of Fe(Ⅲ) by Activated Sludge under Anoxic/anaerobic Condition[J].Chinese Journal of Applied & Environmental Biology,2013,19(22卷04):1040.[doi:10.3724/SP.J.1145.2013.01040]

更新日期/Last Update: 2016-08-25