基于高通量测序分析大豆和油菜根际微生物群落结构的差异
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摘要
根肿病是由芸薹根肿菌侵染引起的专性寄生性土传病害,严重制约着油菜等十字花科作物的可持续生产.前期研究发现,大豆作为前茬作物可以显著降低后茬油菜根肿病的发生和危害,"豆-油轮作"模式是一种值得探索和应用的根肿病防治新途径.为了解开大豆作为前茬防治根肿病发生的机理,本研究基于扩增子测序技术探究大豆与油菜根际土壤微生物的群落结构差异.结果表明:大豆和油菜根际土壤微生物类群在门水平的优势类群相同,包括变形菌门、拟杆菌门、酸杆菌门、放线菌门、子囊菌门、接合菌门、担子菌门和壶菌门等丰度都较高.但相比于油菜根际土壤,大豆根际土壤富含具有生防作用和促进植物生长的微生物,如黄杆菌属、鞘脂单胞菌属、芽孢杆菌属、链霉菌属、假单胞菌属、木霉属和盾壳霉属等;而一些植物病原细菌(如肠杆菌、黄单胞菌)和真菌(炭疽菌和尾孢菌)含量则低于油菜根际土壤;另外,大豆根际土壤中还富含具有固氮功能的根瘤菌属、慢生根瘤菌属和丛枝菌根真菌(如球囊霉属).可见,大豆根际土壤利于有益微生物生长并可抑制病原菌繁殖.大豆和油菜根际微生物组差异为大豆-油菜轮作防治根肿病提供了理论依据,并为根肿病的防治提供了一些潜在的生物防治资源.
Clubroot, caused by the soil-borne obligate pathogen Plasmodiophora brassicae, is one of the most severe disease in cruciferous crops. Previous studies showed that when oilseed rape was planted after soybean(namely soybean-oilseed rotation), the incidence and severity of clubroot of oilseed rape could be significantly reduced, compared with that with oilseed rape-oilseed rape conti-nuous cropping. Therefore, the soybean-oilseed rape rotation is a good way to suppress clubroot of oilseed rape. In this study, we compared the rhizosphere microbiome of soybean and oilseed rape rhizosphere soil collected from the field by 16 S rRNA(for identification of prokaryotes) and the internal transcribed spacer(ITS)(for identification of fungi) sequencing. The results showed that both soybean and oilseed rape rhizosphere soils had Proteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, Ascomycota, Zygomycota, Basidiomycota and Chytridiomycota. Many microbial genera(e.g., Flavobacterium, Sphingomonas, Bacillus, Streptomyces, Pseudomonas, Trichoderma and Coniothyrium) with activities of biological control and plant growth promotion were more abundant in soybean rhizosphere soil than in the oilseed rape rhizosphere soil. The abundance of plant pathogenic bacteria and fungi was higher in the oilseed rape rhizosphere soil than in the soybean rhizosphere soil. Moreover, the soybean rhizosphere soil was enriched with Rhizobium, Bradyrhizobium(both for nitrogen fixation), and arbuscular mycorrhizal fungus(Glomus). These results indicated that soybean rhizosphere soil could promote the growth and proliferation of beneficial microorga-nisms, but inhibit that of plant pathogens. Our results provide evidence for explanation of the effectiveness of soybean-oilseed rape rotation to control clubroot of oilseed rape and provide potential bio-control resources for clubroot prevention.
Clubroot, caused by the soil-borne obligate pathogen Plasmodiophora brassicae, is one of the most severe disease in cruciferous crops. Previous studies showed that when oilseed rape was planted after soybean(namely soybean-oilseed rotation), the incidence and severity of clubroot of oilseed rape could be significantly reduced, compared with that with oilseed rape-oilseed rape conti-nuous cropping. Therefore, the soybean-oilseed rape rotation is a good way to suppress clubroot of oilseed rape. In this study, we compared the rhizosphere microbiome of soybean and oilseed rape rhizosphere soil collected from the field by 16 S rRNA(for identification of prokaryotes) and the internal transcribed spacer(ITS)(for identification of fungi) sequencing. The results showed that both soybean and oilseed rape rhizosphere soils had Proteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, Ascomycota, Zygomycota, Basidiomycota and Chytridiomycota. Many microbial genera(e.g., Flavobacterium, Sphingomonas, Bacillus, Streptomyces, Pseudomonas, Trichoderma and Coniothyrium) with activities of biological control and plant growth promotion were more abundant in soybean rhizosphere soil than in the oilseed rape rhizosphere soil. The abundance of plant pathogenic bacteria and fungi was higher in the oilseed rape rhizosphere soil than in the soybean rhizosphere soil. Moreover, the soybean rhizosphere soil was enriched with Rhizobium, Bradyrhizobium(both for nitrogen fixation), and arbuscular mycorrhizal fungus(Glomus). These results indicated that soybean rhizosphere soil could promote the growth and proliferation of beneficial microorga-nisms, but inhibit that of plant pathogens. Our results provide evidence for explanation of the effectiveness of soybean-oilseed rape rotation to control clubroot of oilseed rape and provide potential bio-control resources for clubroot prevention.
引文
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[3] Zhou Q (周泉),Wang L-C (王龙昌),Xing Y (邢毅),et al.Effects of intercropping Chinese milk vetch on functional characteristics of soil microbial community in rape rhizosphere.Chinese Journal of Applied Ecology (应用生态学报),2018,29(3):909-914 (in Chinese)
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[11] Sun L-B (孙连波).Selection and Identification of Chitinophaga eiseniae of Antagonist Alternaria alternate and Initial Analysis of Its Antipathogenic Activity.Master Thesis.Nanjing:Nanjing Agricultural University,2012 (in Chinese)
[12] Tagele SB,Kim SW,Lee HG,et al.Effectiveness of multi-trait Burkholderia contaminans KNU17BI1 in growth promotion and management of banded leaf and sheath blight in maize seedling.Microbiological Research,2018,214:8-18
[13] Arau? jo WL,Marcon J,Maccheroni W,et al.Diversity of endophytic bacterial populations and their interaction with Xylella fastidiosa in citrus plants.Applied and Environmental Microbiology,2002,68:4906-4914
[14] Príncipe A,Fernandez M,Torasso M,et al.Effectiveness of tailocins produced by Pseudomonas fluorescens SF4c in controlling the bacterial-spot disease in tomatoes caused by Xanthomonas vesicatoria.Microbiological Research,2018,212/213:94-102
[15] Dye DW,Kemp WJ.A taxonomic study of plant pathogenic Corynebacterium species.New Zealand Journal of Agricultural Research,1977,20:563-582
[16] Rodríguez MA,Cabrera G,Gozzo FC,et al.Clonostachys rosea BAFC3874 as a Sclerotinia sclerotiorum antagonist:Mechanisms involved and potential as a biocontrol agent.Journal of Applied Microbiology,2011,110:1177-1186
[17] Cheah LH,Veerakone S,Kent G.Biological control of clubroot on cauliflower with Trichoderma and Streptomyces spp.New Zealand Plant Protection,2000,53:18-21
[18] Park JH,Choi GJ,Jang KS,et al.Antifungal activity against plant pathogenic fungi of chaetoviridins isolated from Chaetomium globosum.FEMS Microbiology Letters,2005,252:309-313
[19] Liang X-L (梁雪亮).Postharvest Biological Control Green Mold of Citrus Fruits by Candida sp.Master Thesis.Wuhan:Huazhong Agricultural University,2004 (in Chinese)
[20] Yang XX,Cui H,Cheng JS,et al.A HOPS protein,CmVps39,is required for vacuolar morphology,auto-phagy,growth,conidiogenesis and mycoparasitistic functions of Coniothyrium minitans.Environmental Microbiology,2016,18:3785-3797
[21] Liu J,Deng JC,Yang CQ,et al.Fungal diversity in field mold-damaged soybean fruits and pathogenicity identification based on high-throughput rDNA sequencing.Frontiers in Microbiology,2017,8:779,doi:10.3389/fmicb.2017.00779
[22] Wang C,Yang Q,Wang W,et al.A transposon-directed epigenetic change in ZmCCT underlies quantitative resistance to Gibberella stalk rot in maize.New Phytologist,2017,215:1503-1515
[23] Liu FL,Tang GT,Zheng XJ,et al.Molecular and phenotypic characterization of Colletotrichum species asso-ciated with anthracnose disease in peppers from Sichuan Province,China.Scientific Reports,2016,6:32761,doi:10.1038/srep32761
[24] Pedro WC,Johannes ZG,Marizeth G,et al.Species of Cercospora associated with grey leaf spot of maize.Stu-dies in Mycology,2006,55:189-197
[25] Lebeis SL,Rott M,Dangl JL,et al.Culturing a plant microbiome community at the cross-Rhodes.New Phyto-logist,2012,196:341-344
[26] Trinh CS,Jeong CY,Lee WJ,et al.Paenibacillus pabuli strain P7S promotes plant growth and induces anthocyanin accumulation in Arabidopsis thaliana.Plant Physio-logy and Biochemistry,2018,129:264-272
[27] Brooks DS,Gonzalez CF,Appel DN,et al.Evaluation of endophytic bacteria as potential biological-control agents for oak wilt.Biological Control,1994,4:373-381
[28] Chen C,Bauske EM,Musson G,et al.Biological control of Fusarium wilt on cotton by use of endophytic bacteria.Biological Control,1995,5:83-91
[29] Zhao Y (赵莹).Interaction among Host,Plasmodiophora brassicae and Microbiome of Brassica napu.PhD Thesis.Wuhan:Huazhong Agricultural University,2016 (in Chinese)
[30] Dong Y (董艳),Dong K (董坤),Yang Z-X (杨智仙),et al.Rhizosphere microbial impacts of alleviating faba bean Fusarium wilt with inoculating AM fungi.Chinese Journal of Applied Ecology (应用生态学报),2016,27(12):4029-4038 (in Chinese)
[2] Yang P-W (杨佩文),Li J-R (李家瑞),Yang Q-Z (杨勤忠),et al.Research progress in clubroot of crucifer.Plant Protection (植物保护),2002,28(5):43-45 (in Chinese)
[3] Zhou Q (周泉),Wang L-C (王龙昌),Xing Y (邢毅),et al.Effects of intercropping Chinese milk vetch on functional characteristics of soil microbial community in rape rhizosphere.Chinese Journal of Applied Ecology (应用生态学报),2018,29(3):909-914 (in Chinese)
[4] Tang L (唐林).Characterization of the Efficacy and Mechanisms of Soybean as A Bait Plant to Control Plasmodiophora brassicae.Master Thesis.Wuhan:Huazhong Agricultural University,2016 (in Chinese)
[5] Hahm S,Kim J,Han K,et al.Biocontrol efficacy of endophytic bacteria Flavobacterium hercynim EPB-C313 for control of Chinese cabbage clubroot.Research in Plant Disease,2012,18:210-216
[6] Adhikari TB,Joseph CM,Yang G,et al.Evaluation of bacteria isolated from rice for plant growth promotion and biological control of seedling disease of rice.Canadian Journal of Microbiology,2001,47:916-924
[7] Luo Y,Cheng Y,Yi J,et al.Complete genome sequence of industrial biocontrol strain Paenibacillus polymyxa HY96-2 and further analysis of its biocontrol mechanism.Frontiers in Microbiology,2018,9:1250,doi:10.3389/fmicb.2018.01520
[8] Peng G,McGregor L,Lahlali R,et al.Potential biolo-gical control of clubroot on canola and crucifer vegetable crops.Plant Pathology,2011,60:566-574
[9] Vurukonda,Davide G,Emilio S.Plant growth promoting and biocontrol activity of Streptomyces spp.as endophytes.International Journal of Molecular Sciences,2018,19:952,doi:10.3390/ijms19040952
[10] Adhikari TB,Joseph CM,Yang G,et al.Evaluation of bacteria isolated from rice for plant growth promotion and biological control of seedling disease of rice.Canadian Journal of Microbiology,2001,47:916-924
[11] Sun L-B (孙连波).Selection and Identification of Chitinophaga eiseniae of Antagonist Alternaria alternate and Initial Analysis of Its Antipathogenic Activity.Master Thesis.Nanjing:Nanjing Agricultural University,2012 (in Chinese)
[12] Tagele SB,Kim SW,Lee HG,et al.Effectiveness of multi-trait Burkholderia contaminans KNU17BI1 in growth promotion and management of banded leaf and sheath blight in maize seedling.Microbiological Research,2018,214:8-18
[13] Arau? jo WL,Marcon J,Maccheroni W,et al.Diversity of endophytic bacterial populations and their interaction with Xylella fastidiosa in citrus plants.Applied and Environmental Microbiology,2002,68:4906-4914
[14] Príncipe A,Fernandez M,Torasso M,et al.Effectiveness of tailocins produced by Pseudomonas fluorescens SF4c in controlling the bacterial-spot disease in tomatoes caused by Xanthomonas vesicatoria.Microbiological Research,2018,212/213:94-102
[15] Dye DW,Kemp WJ.A taxonomic study of plant pathogenic Corynebacterium species.New Zealand Journal of Agricultural Research,1977,20:563-582
[16] Rodríguez MA,Cabrera G,Gozzo FC,et al.Clonostachys rosea BAFC3874 as a Sclerotinia sclerotiorum antagonist:Mechanisms involved and potential as a biocontrol agent.Journal of Applied Microbiology,2011,110:1177-1186
[17] Cheah LH,Veerakone S,Kent G.Biological control of clubroot on cauliflower with Trichoderma and Streptomyces spp.New Zealand Plant Protection,2000,53:18-21
[18] Park JH,Choi GJ,Jang KS,et al.Antifungal activity against plant pathogenic fungi of chaetoviridins isolated from Chaetomium globosum.FEMS Microbiology Letters,2005,252:309-313
[19] Liang X-L (梁雪亮).Postharvest Biological Control Green Mold of Citrus Fruits by Candida sp.Master Thesis.Wuhan:Huazhong Agricultural University,2004 (in Chinese)
[20] Yang XX,Cui H,Cheng JS,et al.A HOPS protein,CmVps39,is required for vacuolar morphology,auto-phagy,growth,conidiogenesis and mycoparasitistic functions of Coniothyrium minitans.Environmental Microbiology,2016,18:3785-3797
[21] Liu J,Deng JC,Yang CQ,et al.Fungal diversity in field mold-damaged soybean fruits and pathogenicity identification based on high-throughput rDNA sequencing.Frontiers in Microbiology,2017,8:779,doi:10.3389/fmicb.2017.00779
[22] Wang C,Yang Q,Wang W,et al.A transposon-directed epigenetic change in ZmCCT underlies quantitative resistance to Gibberella stalk rot in maize.New Phytologist,2017,215:1503-1515
[23] Liu FL,Tang GT,Zheng XJ,et al.Molecular and phenotypic characterization of Colletotrichum species asso-ciated with anthracnose disease in peppers from Sichuan Province,China.Scientific Reports,2016,6:32761,doi:10.1038/srep32761
[24] Pedro WC,Johannes ZG,Marizeth G,et al.Species of Cercospora associated with grey leaf spot of maize.Stu-dies in Mycology,2006,55:189-197
[25] Lebeis SL,Rott M,Dangl JL,et al.Culturing a plant microbiome community at the cross-Rhodes.New Phyto-logist,2012,196:341-344
[26] Trinh CS,Jeong CY,Lee WJ,et al.Paenibacillus pabuli strain P7S promotes plant growth and induces anthocyanin accumulation in Arabidopsis thaliana.Plant Physio-logy and Biochemistry,2018,129:264-272
[27] Brooks DS,Gonzalez CF,Appel DN,et al.Evaluation of endophytic bacteria as potential biological-control agents for oak wilt.Biological Control,1994,4:373-381
[28] Chen C,Bauske EM,Musson G,et al.Biological control of Fusarium wilt on cotton by use of endophytic bacteria.Biological Control,1995,5:83-91
[29] Zhao Y (赵莹).Interaction among Host,Plasmodiophora brassicae and Microbiome of Brassica napu.PhD Thesis.Wuhan:Huazhong Agricultural University,2016 (in Chinese)
[30] Dong Y (董艳),Dong K (董坤),Yang Z-X (杨智仙),et al.Rhizosphere microbial impacts of alleviating faba bean Fusarium wilt with inoculating AM fungi.Chinese Journal of Applied Ecology (应用生态学报),2016,27(12):4029-4038 (in Chinese)