基于整合宏组学技术认识腐生生境功能微生物区系
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摘要
微生物区系在天然生境中分布广泛,利用传统纯培养等方法无法全面认识其分布和功能,因此被认为是地球上的"暗物质"。随着新一代测序技术与高分辨率质谱技术的快速发展,研究者可以在非培养条件下全面快速分析天然生境中微生物组及其动态变化,这开启了微生物组时代,使得研究地球上"暗物质"成为可能,从而改变了微生物学研究的现状。腐生生境作为生物地球化学循环的重要推动部分,因其高效降解转化有机废弃物能力而被广泛关注。腐生生境由于原料多变、环境复杂等原因未能被全面深入研究,而整合宏组学技术则为解析相关生境微生物区系的多样性及其功能动态演替规律奠定了技术基础。基于整合宏组学数据分析与环境参数的优化,可以在认识微生物组及其功能的动态水平上,针对复杂物料建立高效降解转化的绿色转化工艺,促进农牧业废弃物无害化和资源化利用进程。
Microbiota is widely distributed in natural habitats and considered as "Dark Matter" because its distribution and function cannot be revealed by traditional culture-dependent methods. With the rapid development of next-generation sequencing technologies and high resolution mass spectrometric techniques, we can rapidly analyze the composition and dynamic changes of microbiome without culturing, which marks the beginning of new era of studying "Dark Matter", thus changing the status of microbiology research. As an important part of the biogeochemical cycle, saprophytic habitats have been widely concerned because of their ability to degrade organic wastes efficiently. However, the complex materials and environments hindered comprehensive studies on saprophytic habitats. With the advent of integrated meta-omic technologies, these problems could be addressed by analyzing diversity and dynamic succession of microbiota in saprophytic habitats. Therefore, based on the analysis of integrated meta-omic data and optimization of environmental parameters, we can learn about the dynamic changes and functions of microbiome, and then establish the green biotechnologies for efficient degradation of complex materials, which would promote the process of harmlessness and resource utilization of agricultural wastes.
Microbiota is widely distributed in natural habitats and considered as "Dark Matter" because its distribution and function cannot be revealed by traditional culture-dependent methods. With the rapid development of next-generation sequencing technologies and high resolution mass spectrometric techniques, we can rapidly analyze the composition and dynamic changes of microbiome without culturing, which marks the beginning of new era of studying "Dark Matter", thus changing the status of microbiology research. As an important part of the biogeochemical cycle, saprophytic habitats have been widely concerned because of their ability to degrade organic wastes efficiently. However, the complex materials and environments hindered comprehensive studies on saprophytic habitats. With the advent of integrated meta-omic technologies, these problems could be addressed by analyzing diversity and dynamic succession of microbiota in saprophytic habitats. Therefore, based on the analysis of integrated meta-omic data and optimization of environmental parameters, we can learn about the dynamic changes and functions of microbiome, and then establish the green biotechnologies for efficient degradation of complex materials, which would promote the process of harmlessness and resource utilization of agricultural wastes.
引文
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[34]Zainudin MHM,Hassan MA,Tokura M,et al.Indigenous cellulolytic and hemicellulolytic bacteria enhanced rapid co-composting of lignocellulose oil palm empty fruit bunch with palm oil mill effluent anaerobic sludge[J].Bioresource Technology,2013,147:632-635
[35]Storey S,Chualain DN,Doyle O,et al.Comparison of bacterial succession in green waste composts amended with inorganic fertiliser and wastewater treatment plant sludge[J].Bioresource Technology,2015,179:71-77
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[38]Partanen P,Hultman J,Paulin L,et al.Bacterial diversity at different stages of the composting process[J].BMC Microbiology,2010,10:94
[39]Wang C,Dong D,Wang HS,et al.Metagenomic analysis of microbial consortia enriched from compost:new insights into the role of Actinobacteria in lignocellulose decomposition[J].Biotechnology for Biofuels,2016,9(1):22
[40]Sun XM,Gong WL,Li X,et al.Omics analysis and industrial application prospects oflignocellulose-degrading actinomycetes[J].Scientia Sinica Vitae,2017,47(2):201-210(in Chinese)孙晓萌,公维丽,李欣,等.降解木质纤维素放线菌的功能组学分析及工业应用前景[J].中国科学:生命科学,2017,47(2):201-210
[41]Koeck DE,Pechtl A,Zverlov VV,et al.Genomics of cellulolytic bacteria[J].Current Opinion in Biotechnology,2014,29:171-183
[42]Jadhav AA,Ismail KS,Harale MA,et al.Study of protease enzyme from bacillus species and its application as a contact lens cleanser[J].British Biomedical Bulletin,2014,2(2):293-302
[43]Vranova V,Rejsek K,Formanek P.Proteolytic activity in soil:a review[J].Applied Soil Ecology,2013,70:23-32
[44]Heuer H,Schmitt H,Smalla K.Antibiotic resistance gene spread due to manure application on agricultural fields[J].Current Opinion in Microbiology,2011,14(3):236-243
[45]Hu YF,Yang X,Li J,et al.The bacterial mobile resistome transfer network connecting the animal and human microbiomes[J].Applied and Environmental Microbiology,2016,82(22):6672-6681
[46]Wang Y,Zhang RM,Li JY,et al.Comprehensive resistome analysis reveals the prevalence of NDM and MCR-1 in Chinese poultry production[J].Nature Microbiology,2017,2:16260
[47]Miyatake F,Iwabuchi K.Effect of compost temperature on oxygen uptake rate,specific growth rate and enzymatic activity of microorganisms in dairy cattle manure[J].Bioresource Technology,2006,97(7):961-965
[48]Martins LF,Antunes LP,Pascon RC,et al.Metagenomic analysis of a tropical composting operation at the S?o Paulo zoo park reveals diversity of biomass degradation functions and organisms[J].PLo S One,2013,8(4):e61928
[49]Wei H,Tucker MP,Baker JO,et al.Tracking dynamics of plant biomass composting by changes in substrate structure,microbial community,and enzyme activity[J].Biotechnology for Biofuels,2012,5:20
[2]Lungu MM,Bosancu A,Geman O.Mini-review:human microbiome project—recent trends and future challenges[A]//Proceedings of the E-Health and Bioengineering Conference(EHB)[C].Iasi:IEEE,2015:1-4
[3]Gilbert JA,Jansson JK,Knight R.The earth microbiome project:successes and aspirations[J].BMC Biology,2014,12(1):69
[4]Himmel ME,Ding SY,Johnson DK,et al.Biomass recalcitrance:engineering plants and enzymes for biofuels production[J].Science,2007,315(5813):804-807
[5]Wilson DB.Microbial diversity of cellulose hydrolysis[J].Current Opinion in Microbiology,2011,14(3):259-263
[6]Ma HX,Zhang LL,Sun XM,et al.Understanding microbial communities and their functions by meta-omics approaches[J].Microbiology China,2015,42(5):902-912(in Chinese)马海霞,张丽丽,孙晓萌,等.基于宏组学方法认识微生物群落及其功能[J].微生物学通报,2015,42(5):902-912
[7]Grimes DJ,Atwell RW,Brayton PR,et al.The fate of enteric pathogenic bacteria in estuarine and marine environments[J].Microbiological Sciences,1986,3(11):324-329
[8]Torsvik V,?vre?s L.Microbial diversity and function in soil:from genes to ecosystems[J].Current Opinion in Microbiology,2002,5(3):240-245
[9]Barer MR,Harwood CR.Bacterial viability and culturability[J].Advances in Microbial Physiology,1999,41:93-137
[10]Hassen A,Belguith K,Jedidi N,et al.Microbial characterization during composting of municipal solid waste[J].Bioresource Technology,2001,80(3):217-225
[11]Katayama A,Hu HY,Nozawa M,et al.Changes in the microbial community structure in soils treated with a mixture of glucose and peptone with reference to the respiratory quinone profile[J].Soil Science and Plant Nutrition,2002,48(6):841-846
[12]Kurisu F,Satoh H,Mino T,et al.Microbial community analysis of thermophilic contact oxidation process by using ribosomal RNA approaches and the quinone profile method[J].Water Research,2002,36(2):429-438
[13]Tang JC,Kanamori T,Inoue Y,et al.Changes in the microbial community structure during thermophilic composting of manure as detected by the quinone profile method[J].Process Biochemistry,2004,39(12):1999-2006
[14]Klamer M,B??th E.Microbial community dynamics during composting of straw material studied using phospholipid fatty acid analysis[J].FEMS Microbiology Ecology,1998,27(1):9-20
[15]Head IM,Saunders JR,Pickup RW.Microbial evolution,diversity,and ecology:a decade of ribosomal RNA analysis of uncultivated microorganisms[J].Microbial Ecology,1998,35(1):1-21
[16]Alfreider A,Peters S,Tebbe CC,et al.Microbial community dynamics during composting of organic matter as determined by16S ribosomal DNA analysis[J].Compost Science&Utilization,2002,10(4):303-312
[17]Zhang LL,Ma HX,Zhang HQ,et al.Thermomyces lanuginosusis the dominant fungus in maize straw composts[J].Bioresource Technology,2015,197:266-275
[18]Antunes LP,Martins LF,Pereira RV,et al.Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics[J].Scientific Reports,2016:6:38915
[19]Cui EP,Wu Y,Zuo YR,et al.Effect of different biochars on antibiotic resistance genes and bacterial community during chicken manure composting[J].Bioresource Technology,2016,203:11-17
[20]Zhang LL,Zhang HQ,Wang ZH,et al.Dynamic changes of the dominant functioning microbial community in the compost of a90-m3 aerobic solid state fermentor revealed by integrated meta-omics[J].Bioresource Technology,2016,203:1-10
[21]Guo Y,Zhang JL,Yan YF,et al.Molecular phylogenetic diversity and spatial distribution of bacterial communities in cooling stage during swine manure composting[J].Asian-Australasian Journal of Animal Sciences,2015,28(6):888-895
[22]Hess M,Sczyrba A,Egan R,et al.Metagenomic discovery of biomass-degrading genes and genomes from cow rumen[J].Science,2011,331(6016):463-467
[23]Warnecke F,Luginbühl P,Ivanova N,et al.Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite[J].Nature,2007,450(7169):560-565
[24]Shokralla S,Spall JL,Gibson JF,et al.Next-generation sequencing technologies for environmental DNA research[J].Molecular Ecology,2012,21(8):1794-1805
[25]Leininger S,Urich T,Schloter M,et al.Archaea predominate among ammonia-oxidizing prokaryotes in soils[J].Nature,2006,442(7104):806-809
[26]Turnbaugh PJ,Ley RE,Hamady M,et al.Feature the human microbiome project[J].Nature,2007,449(7164):804-810
[27]Urich T,Lanzén A,Stokke R,et al.Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta-omics[J].Environmental Microbiology,2014,16(9):2699-2710
[28]Lv BY,Xing MY,Yang J,et al.Pyrosequencing reveals bacterial community differences in composting and vermicomposting on the stabilization of mixed sewage sludge and cattle dung[J].Applied Microbiology and Biotechnology,2015,99(24):10703-10712
[29]Qin JJ,Li RQ,Raes J,et al.A human gut microbial gene catalogue established by metagenomic sequencing[J].Nature,2010,464(7285):59-65
[30]Hettich RL,Sharma R,Chourey K,et al.Microbial metaproteomics:identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities[J].Current Opinion in Microbiology,2012,15(3):373-380
[31]Zubarev RA,Makarov A.Orbitrap mass spectrometry[J].Aanlytical Chemistry Publications.2013,85(11):5288-5296
[32]Lundgren DH,Hwang SI,Wu LF,et al.Role of spectral counting in quantitative proteomics[J].Expert Review of Proteomics,2010,7(1):39-53
[33]Poulsen PHB,Al-Soud WA,Bergmark L,et al.Effects of fertilization with urban and agricultural organic wastes in a field trial-Prokaryotic diversity investigated by pyrosequencing[J].Soil Biology and Biochemistry,2013,57:784-793
[34]Zainudin MHM,Hassan MA,Tokura M,et al.Indigenous cellulolytic and hemicellulolytic bacteria enhanced rapid co-composting of lignocellulose oil palm empty fruit bunch with palm oil mill effluent anaerobic sludge[J].Bioresource Technology,2013,147:632-635
[35]Storey S,Chualain DN,Doyle O,et al.Comparison of bacterial succession in green waste composts amended with inorganic fertiliser and wastewater treatment plant sludge[J].Bioresource Technology,2015,179:71-77
[36]Tian W,Sun Q,Xu DB,et al.Succession of bacterial communities during composting process as detected by 16S r RNA clone libraries analysis[J].International Biodeterioration&Biodegradation,2013,78:58-66
[37]Math RK,Islam SMA,Hong SJ,et al.Metagenomic characterization of oyster shell dump reveals predominance of Firmicutes bacteria[J].Microbiology,2010,79(4):509-519
[38]Partanen P,Hultman J,Paulin L,et al.Bacterial diversity at different stages of the composting process[J].BMC Microbiology,2010,10:94
[39]Wang C,Dong D,Wang HS,et al.Metagenomic analysis of microbial consortia enriched from compost:new insights into the role of Actinobacteria in lignocellulose decomposition[J].Biotechnology for Biofuels,2016,9(1):22
[40]Sun XM,Gong WL,Li X,et al.Omics analysis and industrial application prospects oflignocellulose-degrading actinomycetes[J].Scientia Sinica Vitae,2017,47(2):201-210(in Chinese)孙晓萌,公维丽,李欣,等.降解木质纤维素放线菌的功能组学分析及工业应用前景[J].中国科学:生命科学,2017,47(2):201-210
[41]Koeck DE,Pechtl A,Zverlov VV,et al.Genomics of cellulolytic bacteria[J].Current Opinion in Biotechnology,2014,29:171-183
[42]Jadhav AA,Ismail KS,Harale MA,et al.Study of protease enzyme from bacillus species and its application as a contact lens cleanser[J].British Biomedical Bulletin,2014,2(2):293-302
[43]Vranova V,Rejsek K,Formanek P.Proteolytic activity in soil:a review[J].Applied Soil Ecology,2013,70:23-32
[44]Heuer H,Schmitt H,Smalla K.Antibiotic resistance gene spread due to manure application on agricultural fields[J].Current Opinion in Microbiology,2011,14(3):236-243
[45]Hu YF,Yang X,Li J,et al.The bacterial mobile resistome transfer network connecting the animal and human microbiomes[J].Applied and Environmental Microbiology,2016,82(22):6672-6681
[46]Wang Y,Zhang RM,Li JY,et al.Comprehensive resistome analysis reveals the prevalence of NDM and MCR-1 in Chinese poultry production[J].Nature Microbiology,2017,2:16260
[47]Miyatake F,Iwabuchi K.Effect of compost temperature on oxygen uptake rate,specific growth rate and enzymatic activity of microorganisms in dairy cattle manure[J].Bioresource Technology,2006,97(7):961-965
[48]Martins LF,Antunes LP,Pascon RC,et al.Metagenomic analysis of a tropical composting operation at the S?o Paulo zoo park reveals diversity of biomass degradation functions and organisms[J].PLo S One,2013,8(4):e61928
[49]Wei H,Tucker MP,Baker JO,et al.Tracking dynamics of plant biomass composting by changes in substrate structure,microbial community,and enzyme activity[J].Biotechnology for Biofuels,2012,5:20