宏基因组学在植物病害研究中的应用

doi:10.13560/j.cnki.biotech.bull.1985.2020-0207

摘要/Abstract

摘要：

随着测序技术的不断发展,宏基因组学已成为当前研究热点,是研究植物病害的重要手段之一。植物病害影响了植物的正常生长和发育,甚至导致植物死亡。大部分植物病害是由致病微生物或病毒引起。与传统微生物组研究方法相比,宏基因组可通过高通量测序和后续的生物信息学分析,探明样品中的物种组成和功能基因,研究物种多样性。总结并比较了当前宏基因组学的分析策略以及在植物根际微生物和植物病毒研究中的应用,并对今后的发展趋势进行了展望,以期为宏基因组学在植物病害的相关研究中提供方法上的参考。

关键词: 宏基因组学, 高通量测序, 生物信息学, 植物病害

Abstract:

With the continuous development of sequencing technology,metagenomics has become a current research hotspot and is one of the important approaches of studying plant diseases. Plant disease affects plant normal growth and development,even leads to the death of a plant. Most plant diseases result from pathogenic microorganisms or viruses. In contrast to traditional research methods on microbes,metagenomics can be used to investigate species composition and functional genes in samples by high-throughput sequencing and subsequent bioinformatics analysis,i.e. studying the species diversity. This paper summarizes and compares the analytical strategies of current metagenomics,and its applications in the study of plant rhizosphere microorganisms and plant viruses,and also provides an outlook on future trends,aiming at providing methodological reference in the study of plant diseases.

Key words: metagenomics, high-throughput sequencing, bioinformatics, plant diseases

汪盼盼, 杨野, 刘迪秋, 崔秀明, 刘源. 宏基因组学在植物病害研究中的应用[J]. 生物技术通报, 2020, 36(12): 146-154.

WANG Pan-pan, YANG Ye, LIU Di-qiu, CUI Xiu-ming, LIU Yuan. Application of Metagenomics in Plant Diseases Research[J]. Biotechnology Bulletin, 2020, 36(12): 146-154.

图/表 2

参考文献 64

[1]	Clark MF, Adams AN. Characteristics of the microplate method of enzyme-linked immunosorbent assay for the detection of plant viruses[J]. J Gen Virol, 1977,34(3):475-83. URL pmid: 323416
[2]	Candresse T, Cambra M, Dallot S, et al. Comparison of monoclonal antibodies and polymerase chain reaction assays for the typing of isolates belonging to the D and M serotypes of plum pox potyvirus[J]. Phytopathology, 1998,88:198-204. URL pmid: 18944965
[3]	Martin RM, James D, Levesque CA. Impacts of molecular diagnostic technologies on plant disease management[J]. Annual Review of Phytopathology, 2000,38:207-239. doi: 10.1146/annurev.phyto.38.1.207 URL pmid: 11701842
[4]	Amann RI, Ludwig W, Schleifer KH. Phylogenetic identification of individual microbial cells without cultivation[J]. Microbiol Review, 1995,59(1):143-169.
[5]	Handelsman J, Rondon MR, Brady SF, et al. Molecular biological access to the chemistry of unknown soil microbes:a new frontier for natural products[J]. Chem Biological, 1998,5(10):245-249.
[6]	Ian PA, Rachel HG, Wendy AM, et al. Next-generation sequencing and metagenomic analysis:a universal diagnostic tool in plant virology[J]. Molecular Plant Pathology, 2009,10(4), 537-545. URL pmid: 19523106
[7]	Chen K, Pachter L. Bioinformatics for whole-genome shotgun sequencing of microbial communities[J]. PLoS Computational Biology, 2005,1(2):e24.
[8]	周华, 张新, 刘腾云, 等. 高通量转录组测序的数据分析与基因挖掘[J]. 江西科学, 2012,30(5):607-611.
	Zhou H, Zhang X, Liu TY, et al. Data processing and gene discovery of high-throughput transcriptome sequencing[J]. Jiangxi Science, 2012,30(5):607-611.
[9]	Seeman T. Prokka:rapid prokaryotic genome annotation[J]. Bioinformatics, 2014,30(14):2068-2069. URL pmid: 24642063
[10]	田李, 张颖, 赵云峰. 新一代测序技术的发展和应用[J]. 生物技术通报, 2015,31(11):1-8.
	Tian L, Zhang Y, Zhao YF. The next generation sequencing technology and its applications[J]. Biotechnology Bulletin, 2015,31(11):1-8.
[11]	Raaijmakers JM, Paulitz TC, Steinberg C, et al. The rhizosphere:a playground and battlefield for soilborne pathogens and beneficial microorganisms[J]. Plant and Soil, 2009,321:341-361.
[12]	Marcel GA. Van DH, Richard D, et al. The unseen majority:soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems[J]. Ecology Letters, 2007,11(3):296-310. URL pmid: 18047587
[13]	Schnitzer SA, Klironomos JN, HilleRisLambers J, et al. Soil microbes drive the classic plant diversity-productivity pattern[J]. Ecology, 2011,92(2):296-303. URL pmid: 21618909
[14]	Wagg C, Jansa J, Schmid B, et al. Belowground biodiversity effects of plant symbionts support aboveground productivity[J]. Ecology Letters, 2011,14(10):1001-1009. doi: 10.1111/ele.2011.14.issue-10 URL
[15]	Maurhofer M, Keel C, Schnider U, et al. Influence of enhanced antibiotic production in Pseudomonas fluorescens strain CHA0 on its disease suppressive capacity[J]. Phytopathology, 1992,82:190-195.
[16]	Tian BY, Cao Y, Zhang KQ. Metagenomic insights into communities, functions of endophytes, and their associates with infection by root-knot nematode, Meloidogyne incognita, in tomato roots[J]. Scientific Reports, 2015,5:17087. doi: 10.1038/srep17087 URL pmid: 26603211
[17]	Dnceppe MO, Kimoto T, Lemieux C, et al. Screening for exotic forest pathogens to increase survey capacity using metagenomics[J]. Phytopathology, 2018,108(2):1509-1521.
[18]	欧小宏, 刘迪秋, 王麟猛, 等. 土壤熏蒸处理对连作三七生长发育及土壤理化性状的影响[J]. 中国现代中药, 2018,20(7):842-849.
	Ou XH, Liu DQ, Wang LM, et al. Effects of soil fumigant chlorpicrin on the growth development and soil physico-chemical properties of continuous cropping panax notoginseng[J]. Modern Chinese Medicine, 2018,20(7):842-849.
[19]	王峰, 吕艺, 刘洋, 等. 氯化苦土壤消毒对三七种植后细菌群落多样性及烤烟轮作的影响[J]. 昆明理工大学学报:自然科学版, 2019,4(44):90-96.
	Wang F, LÜ Y, Liu Y, et al. Effects of fumigation with chloropicrin on soil fungal composition and diversity after continuous cropping of Panax notoginseng[J]. Journal of Kunming University of Science and Technology:Natural Science, 2019,4(44):90-96.
[20]	Van LL. Plant responses to plant growth-promoting rhizobacteria[J]. European Journal of Plant Pathology, 2007,119:243-254. doi: 10.1007/s10658-007-9165-1 URL
[21]	Tyler HL, Triplett EW. Plants as a habitat for beneficial and/or human pathogenic bacteria[J]. Annual Review of Phytopathology, 2008,46:53-73. URL pmid: 18680423
[22]	Holden N, Pritchard L, Toth I. Colonization outwith the colon:plants as an alternative environmental reservoir for human pathogenic enterobacteria[J]. FEMS Microbiol Rev, 2009,33(4):689-703.
[23]	Teplitski M, Warriner K, Bartz J, et al. Untangling metabolic and communication networks:interactions of enterics with phytobacteria and their implications in produce safety[J]. Trends in Microbiology, 2011,19(3):121-127. URL pmid: 21177108
[24]	Pierret A, Doussan C, Capowiez Y, et al. Root functional architecture:A framework for modeling the interplay between roots and soil[J]. Vadose Zone Journal, 2007,6(2):269-281.
[25]	Goss EM, Tabima JF, Cooke DE, et al. The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes[J]. Proc Natl Inst Sci USA, 2014,111(24):8791-8796.
[26]	Punja ZK. Fungal pathogens of American ginseng(Panax quinquefolium)in British Columbia[J]. Canadian Journal of Plant Pathology, 1997,19(3):301-306.
[27]	Gaulin E, Jacquet C, Bottin A, et al. Root rot disease of legumes caused by Aphanomyces euteiches[J]. Molecular Plant Pathology, 2007,8(5):539-548. doi: 10.1111/j.1364-3703.2007.00413.x URL pmid: 20507520
[28]	Chatterton S, Gossen B, McLaren D, et al. Metagenomic analysis of oomycete communities from the rhizosphere of field pea on the Canadian prairies[J]. Canadian Journal of Microbiology, 2017, 63(9). https://doi.org/10.1139/cjm-2017-0099. doi: 10.1139/cjm-2017-0221 URL pmid: 28521110
[29]	Duan Y, Zhou L, Hall DG, et al. Complete genome sequence of citrus huanglongbing bacterium, ‘Candidatus Liberibacter asiaticus’ obtained through metagenomics[J]. Microbiology Resource Announcements Starting, 2009,22(8):1011-1020.
[30]	Cook RJ, Thomashow LS, Weller DM, et al. Molecular mechanisms of defense by rhizobacteria against root disease[J]. Proc Natl Acad Sci USA, 1995,92(10):4197-4201. URL pmid: 11607544
[31]	Rudrappa T, Czymmek KJ, Pare PW, et al. Root-secreted malic acid recruits beneficial soil bacteria[J]. Plant Physiology, 2008,148(3):1547-1556. URL pmid: 18820082
[32]	Carrión VJ, Perez-Jaramillo J, Cordovez V, et al. Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome[J]. Science, 2019,366(6465):606-612. URL pmid: 31672892
[33]	Manoj K, George M, Rony S. Metagenomic insights of the root colonizing microbiome associated with symptomatic and non-symptomatic bananas in Fusarium wilt infected fields[J]. Plants, 2020,18, 9(2):263.
[34]	Insam H, Seewald MSA. Volatile organic compounds(VOCs)in soils[J]. Biology and Fertility of Soils, 2010,46(3):199-213.
[35]	Vespermann A, Kai M, Piechulla B. Rhizobacterial volatiles affect the growth of fungi and Arabidopsis thaliana[J]. Appl Environ Microbiol, 2007,73(17):5639-5641. URL pmid: 17601806
[36]	Marilyn JR. Plant virus metagenomics:biodiversity and ecology[J]. Annual Review of Genetics, 2012,46:359-369. URL pmid: 22934641
[37]	Xiao HG, Li CH, Rwahnih MA, et al. Metagenomic analysis of riesling grapevine reveals complex virome including two new and divergent variants of Grapevine leafroll associated virus 3[J]. Plant Disease, 2019,103(6):1275-1285. doi: 10.1094/PDIS-09-18-1503-RE URL pmid: 30932733
[38]	Zhou J, Cao K, Zhang ZX, et al. Identification and characterization of a novel rhabdovirus infecting peach in China[J]. Virus Res, 2020,280:197905. URL pmid: 32105763
[39]	Héctor SO, Rodolfo DLTA, Jesús ÁSN, et al. Identification and genomic characterization of a novel tobamovirus from prickly pear cactus[J]. Arch Virol, 2020,165(3):781-784. URL pmid: 31980940
[40]	Susi H, Denis F, Mikko JF, et al. Diverse and variable virus communities in wild plant populations revealed by metagenomic tools[J]. PeerJ, 2019,7:e6140. URL pmid: 30648011
[41]	Susi H, Laine AL, Filloux D, et al. Genome sequences of a capulavirus infecting Plantago lanceolata in the land archipelago of Finland[J]. Archives of Virology, 2017,162:2041-2045. URL pmid: 28283818
[42]	Power AG, Borer ET, Hosseini P, et al. The community ecology of barley/cereal yellow dwarf viruses in Western US grasslands[J]. Virus Res, 2011,159:95-100. URL pmid: 21641945
[43]	Moore SM, Borer ET. The influence of host diversity and composition on epidemiological patterns at multiple spatial scales[J]. Ecology, 2012,93:1095-1105. URL pmid: 22764495
[44]	Malmstrom CM, Hughes CC, Newton LA, et al. Virus infection in remnant native bunchgrasses from invaded California grasslands[J]. New Phytol, 2005,168:217-230. URL pmid: 16159335
[45]	Malmstrom CM, McCullough AJ, Johnson HA, et al. Invasive annual grasses indirectly increase virus incidence in California native perennial bunchgrasses[J]. Oecologia, 2005,145:153-164. URL pmid: 15875144
[46]	Marilyn JR. Plants, viruses and the environment：Ecology and mutualism[J]. Virology, 2015,479-480:271-277. URL pmid: 25858141
[47]	Márquez LM, Redman RS, Rodriguez RJ, et al. A virus in a fungus in a plant:Three-way symbiosis required for thermal tolerance[J]. Science, 2007,315(5811):513-515. URL pmid: 17255511
[48]	Staginnus C. Endogenous pararetroviral sequences in tomato(Solanum lycopersicum)and related species[J]. BMC Plant Biology, 2007,7:24. doi: 10.1186/1471-2229-7-24 URL pmid: 17517142
[49]	Xu P, Fang C, Jonathan P, et al. Virus infection improves drought tolerance[J]. New Phytologist, 2008,180(4):911-921.
[50]	Nuss DL. Encyclopedia of virology[M]. Academic Press, 2008.
[51]	VanMolken T, DeCaluwe H, Hordijk CA, et al. Virus infection decreases the attractiveness of white clover plants for a non-vectoring herbivore[J]. Oecologia, 2012,170(2):433-444. doi: 10.1007/s00442-012-2322-z URL pmid: 22526939
[52]	Eilenberg J, Hajek A, Lomer C. Suggestions for unifying the terminology in biological control[J]. BioControl, 2001,46(4):387-400. doi: 10.1023/A:1014193329979 URL
[53]	Xu XM, Jeffries P, Pautasso M, et al. Combined use of biocontrol agents to manage plant diseases in theory and practice[J]. Phytopathology, 2011,101(9):1024-1031. doi: 10.1094/PHYTO-08-10-0216 URL
[54]	Blagodatskaya E, Blagodatsky S, Kuzyakov Y, et al. Microbial growth and carbon use efficiency in the rhizosphere and root free soil[J]. PLoS One, 2014,9(4):e93282. URL pmid: 24722409
[55]	Timm CM, Campbell AG, Uttukar SM, et al. Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment[J]. Front in Microbiol, 2015,6:1118.
[56]	Inch S, Leder J, Taylor A, et al. Evaluation of microbials using comparative genomics and high-throughput assays as a method to reduce product development time[J]. Phytopathology, 2016,106:168.
[57]	Scheffler RJ, Colmer S, Tynan H, et al. Antimicrobials, drug discovery and genome mining[J]. Applied Microbiology Biotechnology, 2013,97(3):969-978. URL pmid: 23233204
[58]	Bhattacharyya PN, Jha DK. Plant growth-promoting rhizobacteria(PGPR):Emergence in agriculture[J]. World Journal of Microbiology Biotechnology, 2012,28(4):1327-1350. URL pmid: 22805914
[59]	Brodeur J. Host specificity in biological control:insights from opportunistic pathogens[J]. Evol Appl, 2012,5, 470-480. URL pmid: 22949922
[60]	Alvarez B, Biosca EG. Bacteriophage-based bacterial wilt biocontrol for an environmentally sustainable agriculture[J]. Front Plant Sci, 2017,8:1218. URL pmid: 28769942
[61]	Wang XF, Wei Z, Yang KM, et al. Phage combination therapies for bacterial wilt disease in tomato[J]. Nature Biotechnology, 2019,37:1513-1520. doi: 10.1038/s41587-019-0328-3 URL pmid: 31792408
[62]	田荣欢, 刘迪秋, 葛峰, 等. 植物病毒基因沉默抑制子研究进展[J]. 生物技术通报, 2010(4):11-15.
	Tian RH, Liu DQ, Ge F, et al. Approach of research on gene silencing suppressors of plant virus[J]. Biotechnology Bulletin, 2010(4):11-15.
[63]	Heinlein M. Plant virus replication and movement[J]. Virology, 2015, 479-480:657-671. doi: 10.1016/j.virol.2015.01.025 URL pmid: 25746797
[64]	Berg G, Eberl L, Hartmann A. The rhizosphere as a reservoir for opportunistic human pathogenic bacteria[J]. Environmental Microbiology, 2005,7(11):1673-1685. doi: 10.1111/j.1462-2920.2005.00891.x URL pmid: 16232283

宿主	病毒	互惠关系	参考文献
真菌内生植物	Curvularia thermal tolerance virus	赋予共生植物热耐受性,耐受温度可达65℃	[47]
番茄	Tomato endogenous pararetroviral	保护番茄免受外源性LycePRV和其他相关病毒的感染	[48]
植物	Cytomegalo	提高植物耐旱和耐寒的特性	[49]
栗子	Cryphonectria parasitica	当真菌感染Cryphonectria parasitica后,植株的病理影响大大降低	[50]
白三叶草植物	White clover mosaic virus	白三叶草植物感染WCIMV后对真菌性蚊虫的吸引力降低	[51]

宿主	病毒	互惠关系	参考文献
真菌内生植物	Curvularia thermal tolerance virus	赋予共生植物热耐受性,耐受温度可达65℃	[47]
番茄	Tomato endogenous pararetroviral	保护番茄免受外源性LycePRV和其他相关病毒的感染	[48]
植物	Cytomegalo	提高植物耐旱和耐寒的特性	[49]
栗子	Cryphonectria parasitica	当真菌感染Cryphonectria parasitica后,植株的病理影响大大降低	[50]
白三叶草植物	White clover mosaic virus	白三叶草植物感染WCIMV后对真菌性蚊虫的吸引力降低	[51]