入侵植物小蓬草的细菌群落组成和多样性研究
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摘要
生物入侵现象严重危害生态系统的健康,其中外来植物入侵是生物入侵中的重要组成,会对农业、林业、畜牧业产生直接的经济危害。选取生长状况良好的菊科外来入侵植物小蓬草(Conyza canadensis L.,Asteraceae)植株,利用16S rRNA基因的高通量测序技术和后续分析,探索小蓬草生境中的土壤及其根和叶的细菌群落组成和多样性,并分析表面消毒、冷冻干燥保存和不同研磨方法等处理方式对研究结果的影响。结果表明:小蓬草根样本细菌群落中OTU的数目最多,其次是土壤,小蓬草叶样本的细菌群落中OTU的数目最低;小蓬草细菌群落Alpha多样性在土壤样本中最高,其次是小蓬草根,小蓬草叶的细菌群落Alpha多样性最低;在门的水平,在土壤和小蓬草叶、根的细菌群落均以变形菌门和放线菌门丰度最高,此外在小蓬草根和叶的细菌群落丰度较高的还有厚壁菌门,在土壤细菌群落丰度较高的则是拟杆菌门;小蓬草根和叶细菌群落的优势属包括假单胞菌属(Pseudomonas)、芽孢杆菌属(Bacillus)、甲基杆菌属(Methylobacterium)、鞘氨醇单胞菌属(Sphingomonas)、根瘤菌属(Rhizobium)和无色杆菌属(Achromobacter)等,这些优势属可能包含植物益生菌,并对小蓬草适应不良环境提供一定的帮助;是否进行表面消毒处理的小蓬草叶和根样本的细菌群落组成和多样性有明显的差异,表明小蓬草的根表和根内以及叶表和叶内的细菌群落存在明显的差异;机器研磨、冷冻干燥保存处理的小蓬草样本与人工研磨并及时处理的小蓬草样本相比,其细菌群落组成并没有明显的差异,表明这些处理方式对植物微生物组的研究结果不会产生明显的影响。该研究结果可为微生物在植物入侵机制中所起的作用提供数据支持。
Biological invasion seriously endangers ecosystem health.Invasive plants are the most important part of biological invasion which can cause economic harm to agriculture,forestry and animal husbandry.We select well-growing plants of the invasive species Conyza canadensis L.(Asteraceae) and use high-throughput sequencing analysis of 16 S rRNA gene to explore the composition and diversity of bacterial communities of the soil,roots and leaves associated with C.canadensis.The data may support the important role of microorganisms in plant invasion mechanisms.The effects of surface sterilization,freeze-drying preservation and mechanically grinding on the study results are also analyzed.The results show that the number of OTUs in the root bacterial communities of C.canadensis is the highest,followed by soil,and the lowest in leaf bacterial communities.The Alpha diversity of bacterial communities decreases significantly from the soil to root and leaf samples.Proteobacteria and Actinomycetes are the highest abundant phyla in the bacterial communities of soil,leaf and root samples.In addition,Firmicutes is one of the most abundant phyla in leaf and root bacterial communities and Bacteroidetes is one of the most abundant in soil bacterial communities.The dominant genera of the C.canadensis root and leaf microbiota are Pseudomonas,Bacillus,Methylobacterium,Sphingomonas,Rhizobium and Achromobacter.These genera include plant probiotics according to previous studies and may be helpful for C.canadensis to adapt to adverse environment.There are significant differences in the composition and diversity of bacterial communities from leaf/root samples applied with or without surface sterilization treatment,demonstrating leaf/root microbiota are significantly different on surface and in endosphere.No significant differences are observed between samples grounded by a machine and preserved after freeze-dying and those grounded by hand and processed immediately,indicating that mechanically grinding and freeze-drying preservation of plant samples will not have effect on the results of plant microbiome studies.
Biological invasion seriously endangers ecosystem health.Invasive plants are the most important part of biological invasion which can cause economic harm to agriculture,forestry and animal husbandry.We select well-growing plants of the invasive species Conyza canadensis L.(Asteraceae) and use high-throughput sequencing analysis of 16 S rRNA gene to explore the composition and diversity of bacterial communities of the soil,roots and leaves associated with C.canadensis.The data may support the important role of microorganisms in plant invasion mechanisms.The effects of surface sterilization,freeze-drying preservation and mechanically grinding on the study results are also analyzed.The results show that the number of OTUs in the root bacterial communities of C.canadensis is the highest,followed by soil,and the lowest in leaf bacterial communities.The Alpha diversity of bacterial communities decreases significantly from the soil to root and leaf samples.Proteobacteria and Actinomycetes are the highest abundant phyla in the bacterial communities of soil,leaf and root samples.In addition,Firmicutes is one of the most abundant phyla in leaf and root bacterial communities and Bacteroidetes is one of the most abundant in soil bacterial communities.The dominant genera of the C.canadensis root and leaf microbiota are Pseudomonas,Bacillus,Methylobacterium,Sphingomonas,Rhizobium and Achromobacter.These genera include plant probiotics according to previous studies and may be helpful for C.canadensis to adapt to adverse environment.There are significant differences in the composition and diversity of bacterial communities from leaf/root samples applied with or without surface sterilization treatment,demonstrating leaf/root microbiota are significantly different on surface and in endosphere.No significant differences are observed between samples grounded by a machine and preserved after freeze-dying and those grounded by hand and processed immediately,indicating that mechanically grinding and freeze-drying preservation of plant samples will not have effect on the results of plant microbiome studies.
引文
[1] 易小燕.外来入侵植物的扩散路径与入侵风险管理研究[D].南京:南京农业大学,2008.
[2] 柏成寿.外来入侵物种管理与生物多样性保护[J].环境保护,2002(8):21-23.
[3] 田忠赛,程丹丹,徐琳,等.欧洲千里光在中国入侵状况的初步调查[J]安全与环境工程,2018,25(02):8-14.
[4] Rout M E,Chrzanowski T H.The invasive Sorghum halepense harbors endophytic N2-fixing bacteria and alters soil biogeochemistry[J].Plant & Soil,2009,315(1/2):163-172.
[5] Aschehoug E T,Callaway R M,Newcombe G,et al.Fungal endophyte increases the allelopathic effects of an invasive forb[J].Oecologia,2014,175(1):285-291.
[6] Müller D B,Vogel C,Bai Y,et al.The plant microbiota:Systems-level insights and perspectives[J].Annual Review of Genetics,2016,50(1):211-234.
[7] 吴晓青,周方园,张新建.微生物组学对植物病害微生物防治研究的启示[J].微生物学报,2017,57(6):867-875.
[8] Rout M E,Southworth D.The root microbiome influences scales from molecules to ecosystems:The unseen majority[J].American Journal of Botany,2013,100(9):1689-1691.
[9] Lareen A,Burton F,Sch?Fer P.Plant root-microbe communication in shaping root microbiomes[J].Plant Molecular Biology,2016,90(6):575-587.
[10]Vorholt J A.Microbial life in the phyllosphere[J].Nature Reviews Microbiology,2012,10(12):828-840.
[11]Lindow S E,Leveau J H.Phyllosphere microbiology[J].Current Opinion in Biotechnology,2002,13(3):238-243.
[12]Farré-Armengol G,Filella I,Llusia J,et al.Bidirectional interaction between phyllospheric microbiotas and plant volatile emissions[J].Trends in Plant Science,2016,21(10):854-860.
[13]Vacher C,Hampe A,Porté A J,et al.The phyllosphere:Microbialjungle at the plant–climate interface[J].Annual Review of Ecology Evolution & Systematics,2017,47(1):1-13.
[14]王志伟,纪燕玲,陈永敢.植物内生菌研究及其科学意义[J].微生物学通报,2015,42(2):349-363.
[15]Rodriguez R J,White J,Arnold A E,et al.Fungal endophytes:Diversity and functional roles[J].New Phytologist,2009,182(2):314-330.
[16]Hodgson S,Cates D C,Hodgson J,et al.Vertical transmission of fungal endophytes is widespread in forbs[J].Ecology & Evolution,2014,4(8):1199-1208.
[17]Lugtenberg B,Kamilova F.Plant-growth-promoting rhizobacteria[J].Annual Review of Microbiology,2009(1):541-556.
[18]Bhattacharyya P N,Jha D K.Plant growth-promoting rhizobacteria (PGPR):Emergence in agriculture[J].World Journal of Microbiology & Biotechnology,2012,28(4):1327-1350.
[19]Schulz B,Wanke U,Draeger S,et al.Endophytes from herbaceous plants and shrubs:Effectiveness of surface sterilization methods[J].Mycological Research,1993,97(12):1447-1450.
[20]陈泽斌,夏振远,雷丽萍,等.烟草可培养内生细菌的分离及多样性分析[J].微生物学通报,2011,38(9):1347-1354.
[21]Gottel N R,Castro H F,Kerley M,et al.Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types[J].Applied & Environmental Microbiology,2011,77(17):5934-5944.
[22]Edwards J,Johnson C,Santos-Medellín C,et al.Structure,variation,and assembly of the root-associated microbiomes of rice[J].Proceedings of the National Academy of Sciences of the United States of America,2015,112(8):E911-E920.
[23]Richter-Heitmann T,Eickhorst T,Knauth S,et al.Evaluation of strategies to separate root-associated microbial communities:A crucial choice in rhizobiome research[J].Frontiers in Microbiology,2016,7(148):1-13.
[24]宫璐,李俊生,柳晓燕,等.我国部分国家级自然保护区外来入侵物种的分布概况[J].生态科学,2017,36(4):210-216.
[25]Guyonnet J P,Vautrin F,Meiffren G,et al.The effects of plant nutritional strategy on soil microbial denitrification activity through rhizosphere primary metabolites[J].FEMS Microbiology Ecology,2017,93(4):1-11.
[26]Isroi,Ishola M M,Millati R,et al.Structural changes of oil palm empty fruit bunch (OPEFB) after fungal and phosphoric acid pretreatment[J].Molecules,2012,17(12):14995-15002.
[27]Bodenhausen N,Horton M W,Bergelson J.Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana[J].Plos One,2013,8(2):1-9.
[28]Beckers B,Beeck M,Thijs S,et al.Performance of 16S rDNA primer pairs in the study of rhizosphere and endosphere bacterial microbiomes in metabarcoding studies[J].Frontiers in Microbiology,2016,7:1-15.
[29]Devin C D,Damaris D,Citlali F G,et al.Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species[J].New Phytologist,2016,209(2):798-811.
[30]Bai Y,Müller D B,Srinivas G,et al.Functional overlap of the Arabidopsis leaf and root microbiota[J].Nature,2015,528(7582):364-369.
[31]Ruizpérez C A,Restrepo S,Zambrano M.Microbial and functional diversity within the phyllosphere of Espeletia sp.in an Andean High Mountain ecosystem[J].Applied & Environmental Microbiology,2016,82(6):1807-1817.
[32]Bulgarelli D,Schlaeppi K,Spaepen S.Structure and functions of the bacterial microbiota of plants[J].Annual Review of Plant Biology,2012,64(1):807-838.
[33]台喜生,冯佳丽,李梅,等.鞘氨醇单胞菌在生物降解方面的研究进展[J].湖南农业科学,2011(7):21-25.
[34]胡杰,何晓红,李大平,等.鞘氨醇单胞菌研究进展[J].应用与环境生物学报,2007,13(3):431-437.
[35]Innerebner G.Identification of indigenous phyllosphere isolates of the genus Sphingomonas as plant-protective bacteria[J].American Journal of Roentgenology Radium Therapy & Nuclear Medicine,2011,107(1):1-13.
[36]Tokala R K,Strap J L,Jung C M,et al.Novel plant-microbe rhizosphere interaction involving Streptomyces lydicus WYEC108 and the pea plant (Pisum sativum)[J].Applied & Environmental Microbiology,2002,68(5):2161-2171.
[37]罗菲.东乡野生稻可培养内生与根际微生物多样性及其植物促生活性[D].南昌:江西师范大学,2011.
[38]Cipriano M,Lupatini M,Lopessantos L,et al.Lettuce and rhizosphere microbiome responses to growth promoting Pseudomonas species under field conditions[J].Fems Microbiology Ecology,2016,92(12):1-13.
[39]林丽,陈泽斌,何群香,等.烟草不同部位内生细菌的多样性[J].江苏农业科学,2017,45(22):274-278.
[2] 柏成寿.外来入侵物种管理与生物多样性保护[J].环境保护,2002(8):21-23.
[3] 田忠赛,程丹丹,徐琳,等.欧洲千里光在中国入侵状况的初步调查[J]安全与环境工程,2018,25(02):8-14.
[4] Rout M E,Chrzanowski T H.The invasive Sorghum halepense harbors endophytic N2-fixing bacteria and alters soil biogeochemistry[J].Plant & Soil,2009,315(1/2):163-172.
[5] Aschehoug E T,Callaway R M,Newcombe G,et al.Fungal endophyte increases the allelopathic effects of an invasive forb[J].Oecologia,2014,175(1):285-291.
[6] Müller D B,Vogel C,Bai Y,et al.The plant microbiota:Systems-level insights and perspectives[J].Annual Review of Genetics,2016,50(1):211-234.
[7] 吴晓青,周方园,张新建.微生物组学对植物病害微生物防治研究的启示[J].微生物学报,2017,57(6):867-875.
[8] Rout M E,Southworth D.The root microbiome influences scales from molecules to ecosystems:The unseen majority[J].American Journal of Botany,2013,100(9):1689-1691.
[9] Lareen A,Burton F,Sch?Fer P.Plant root-microbe communication in shaping root microbiomes[J].Plant Molecular Biology,2016,90(6):575-587.
[10]Vorholt J A.Microbial life in the phyllosphere[J].Nature Reviews Microbiology,2012,10(12):828-840.
[11]Lindow S E,Leveau J H.Phyllosphere microbiology[J].Current Opinion in Biotechnology,2002,13(3):238-243.
[12]Farré-Armengol G,Filella I,Llusia J,et al.Bidirectional interaction between phyllospheric microbiotas and plant volatile emissions[J].Trends in Plant Science,2016,21(10):854-860.
[13]Vacher C,Hampe A,Porté A J,et al.The phyllosphere:Microbialjungle at the plant–climate interface[J].Annual Review of Ecology Evolution & Systematics,2017,47(1):1-13.
[14]王志伟,纪燕玲,陈永敢.植物内生菌研究及其科学意义[J].微生物学通报,2015,42(2):349-363.
[15]Rodriguez R J,White J,Arnold A E,et al.Fungal endophytes:Diversity and functional roles[J].New Phytologist,2009,182(2):314-330.
[16]Hodgson S,Cates D C,Hodgson J,et al.Vertical transmission of fungal endophytes is widespread in forbs[J].Ecology & Evolution,2014,4(8):1199-1208.
[17]Lugtenberg B,Kamilova F.Plant-growth-promoting rhizobacteria[J].Annual Review of Microbiology,2009(1):541-556.
[18]Bhattacharyya P N,Jha D K.Plant growth-promoting rhizobacteria (PGPR):Emergence in agriculture[J].World Journal of Microbiology & Biotechnology,2012,28(4):1327-1350.
[19]Schulz B,Wanke U,Draeger S,et al.Endophytes from herbaceous plants and shrubs:Effectiveness of surface sterilization methods[J].Mycological Research,1993,97(12):1447-1450.
[20]陈泽斌,夏振远,雷丽萍,等.烟草可培养内生细菌的分离及多样性分析[J].微生物学通报,2011,38(9):1347-1354.
[21]Gottel N R,Castro H F,Kerley M,et al.Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types[J].Applied & Environmental Microbiology,2011,77(17):5934-5944.
[22]Edwards J,Johnson C,Santos-Medellín C,et al.Structure,variation,and assembly of the root-associated microbiomes of rice[J].Proceedings of the National Academy of Sciences of the United States of America,2015,112(8):E911-E920.
[23]Richter-Heitmann T,Eickhorst T,Knauth S,et al.Evaluation of strategies to separate root-associated microbial communities:A crucial choice in rhizobiome research[J].Frontiers in Microbiology,2016,7(148):1-13.
[24]宫璐,李俊生,柳晓燕,等.我国部分国家级自然保护区外来入侵物种的分布概况[J].生态科学,2017,36(4):210-216.
[25]Guyonnet J P,Vautrin F,Meiffren G,et al.The effects of plant nutritional strategy on soil microbial denitrification activity through rhizosphere primary metabolites[J].FEMS Microbiology Ecology,2017,93(4):1-11.
[26]Isroi,Ishola M M,Millati R,et al.Structural changes of oil palm empty fruit bunch (OPEFB) after fungal and phosphoric acid pretreatment[J].Molecules,2012,17(12):14995-15002.
[27]Bodenhausen N,Horton M W,Bergelson J.Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana[J].Plos One,2013,8(2):1-9.
[28]Beckers B,Beeck M,Thijs S,et al.Performance of 16S rDNA primer pairs in the study of rhizosphere and endosphere bacterial microbiomes in metabarcoding studies[J].Frontiers in Microbiology,2016,7:1-15.
[29]Devin C D,Damaris D,Citlali F G,et al.Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species[J].New Phytologist,2016,209(2):798-811.
[30]Bai Y,Müller D B,Srinivas G,et al.Functional overlap of the Arabidopsis leaf and root microbiota[J].Nature,2015,528(7582):364-369.
[31]Ruizpérez C A,Restrepo S,Zambrano M.Microbial and functional diversity within the phyllosphere of Espeletia sp.in an Andean High Mountain ecosystem[J].Applied & Environmental Microbiology,2016,82(6):1807-1817.
[32]Bulgarelli D,Schlaeppi K,Spaepen S.Structure and functions of the bacterial microbiota of plants[J].Annual Review of Plant Biology,2012,64(1):807-838.
[33]台喜生,冯佳丽,李梅,等.鞘氨醇单胞菌在生物降解方面的研究进展[J].湖南农业科学,2011(7):21-25.
[34]胡杰,何晓红,李大平,等.鞘氨醇单胞菌研究进展[J].应用与环境生物学报,2007,13(3):431-437.
[35]Innerebner G.Identification of indigenous phyllosphere isolates of the genus Sphingomonas as plant-protective bacteria[J].American Journal of Roentgenology Radium Therapy & Nuclear Medicine,2011,107(1):1-13.
[36]Tokala R K,Strap J L,Jung C M,et al.Novel plant-microbe rhizosphere interaction involving Streptomyces lydicus WYEC108 and the pea plant (Pisum sativum)[J].Applied & Environmental Microbiology,2002,68(5):2161-2171.
[37]罗菲.东乡野生稻可培养内生与根际微生物多样性及其植物促生活性[D].南昌:江西师范大学,2011.
[38]Cipriano M,Lupatini M,Lopessantos L,et al.Lettuce and rhizosphere microbiome responses to growth promoting Pseudomonas species under field conditions[J].Fems Microbiology Ecology,2016,92(12):1-13.
[39]林丽,陈泽斌,何群香,等.烟草不同部位内生细菌的多样性[J].江苏农业科学,2017,45(22):274-278.