芒草种植对土壤细菌群落结构和功能的影响
|
摘要
芒草作为第二代能源植物的代表,其生长过程中根际土壤细菌群落的结构与功能尚不清楚.本研究以种植5年的芒草(湘杂芒1号)为研究对象,选取裸地作为对照,采用16S rRNA基因Miseq测序技术研究其细菌群落组成,同时采用PICRUSt功能预测分析其功能.结果表明:芒草根际细菌由变形菌门、酸杆菌门、放线菌门、绿弯菌门、拟杆菌门和芽单胞菌门等23个门、231个属的细菌组成,表现出群落组成的丰富性.细菌群落分析表明,种植湘杂芒1号改变了根际细菌群落结构,其细菌群落多样性低于裸地对照.PICRUSt功能预测分析表明,湘杂芒1号根际细菌主要涉及氨基酸运输和代谢、细胞壁/细胞膜/膜结构的生物合成、信号转导机制等24个基因功能家族,表现出功能上的丰富性,并有22个基因功能家族预测基因相对丰度高于裸地,表明种植湘杂芒1号提高了根际细菌功能.对氮、磷循环相关基因进行分析表明,种植湘杂芒1号改变了土壤氮、磷代谢能力.
Miscanthus is a promising candidate species of second-generation energy crops. To our knowledge, the composition and function of Miscanthus rhizosphere bacterial communities has not yet been reported. In this study, rhizosphere soil samples were collected from Miscanthus(Xiangzamang No. 1) which was grown in Nanyang City for five years and bareground(as the control) to analyze the bacterial community structure and diversity using 16 S rRNA gene sequencing on the Illumina MiSeq platform. PICRUSt was used to determine the metabolic and functional abilities of soil bacterial communities. Phylogenetic analysis based on 16S rRNA gene sequences showed that sol bacteria could be divided into 23 phyla and 231 genera, with high richness of the community composition. The dominant phyla were Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Bacteroidetes and Gemmatimonadetes. The bacterial community diversity in the rhizosphere samples of Xiangzamang No. 1 was lower than that in unplanted samples. Rhizosphere bacterial communities were affected by Miscanthus crops. Based on the PICRUSt analysis of bacterial community functions, our results revealed a wide genetic diversity of organisms involved in various essential processes,such as amino acid transport and metabolism, cell wall/membrane/envelope biogenesis, signal transduction mechanisms. Based on the 16S rRNA gene copy number of the detected phylotypes, 22 bacterial metabolic function in the rhizosphere samples of Miscanthus was higher than that in bareground. Results from N-and P-cycling gene analysis showed that Miscanthus planting altered the N-and P-cycling metabolic capacities of soil bacteria.
Miscanthus is a promising candidate species of second-generation energy crops. To our knowledge, the composition and function of Miscanthus rhizosphere bacterial communities has not yet been reported. In this study, rhizosphere soil samples were collected from Miscanthus(Xiangzamang No. 1) which was grown in Nanyang City for five years and bareground(as the control) to analyze the bacterial community structure and diversity using 16 S rRNA gene sequencing on the Illumina MiSeq platform. PICRUSt was used to determine the metabolic and functional abilities of soil bacterial communities. Phylogenetic analysis based on 16S rRNA gene sequences showed that sol bacteria could be divided into 23 phyla and 231 genera, with high richness of the community composition. The dominant phyla were Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Bacteroidetes and Gemmatimonadetes. The bacterial community diversity in the rhizosphere samples of Xiangzamang No. 1 was lower than that in unplanted samples. Rhizosphere bacterial communities were affected by Miscanthus crops. Based on the PICRUSt analysis of bacterial community functions, our results revealed a wide genetic diversity of organisms involved in various essential processes,such as amino acid transport and metabolism, cell wall/membrane/envelope biogenesis, signal transduction mechanisms. Based on the 16S rRNA gene copy number of the detected phylotypes, 22 bacterial metabolic function in the rhizosphere samples of Miscanthus was higher than that in bareground. Results from N-and P-cycling gene analysis showed that Miscanthus planting altered the N-and P-cycling metabolic capacities of soil bacteria.
引文
[1] Lewandowski I,Clifton-Brown JC,Scurlock JMO,et al.Miscanthus:European experience with a novel energy crop.Biomass and Bioenergy,2000,19:209-227
[2] Heaton EA,Dohleman FG,Long SP.Meeting US biofuel goals with less land:The potential of Miscanthus.Global Change Biology,2008,14:2000-2014
[3] Yi Z-L (易自力).Exploitation and utilization of Miscanthus as energy plant.Journal of Hunan Agricultural University (Natural Sciences) (湖南农业大学学报:自然科学版),2012,38(5):455-463 (in Chinese)
[4] Yu Y-C (于延冲),Yi Z-L (易自力),Zhou G-K (周功克).Research progress and comprehensive utilization of Miscanthus.Chinese Bulletin of Life Sciences (生命科学),2014,26(5):474-480 (in Chinese)
[5] Wu D-M (吴道铭),Chen X-Y (陈晓阳),Zeng S-C (曾曙才).Heavy metal tolerance of Miscanthus plants and their phytoremediation potential in abandoned mine land.Chinese Journal of Applied Ecology (应用生态学报),2017,28(4):1397-1406 (in Chinese)
[6] Chauhan H,Bagyaraj DJ,Selvakumar G,et al.Novel plant growth promoting rhizobacteria:Prospects and potential.Applied Soil Ecology,2015,95:38-53
[7] Finkel OM,Castrillo G,Herrera Paredes S,et al.Understanding and exploiting plant beneficial microbes.Current Opinion in Plant Biology,2017,38:155-163
[8] Liu C (刘驰),Li J-B (李家宝),Rui J-P (芮俊鹏),et al.The applications of the 16S rRNA gene in microbial ecology:Current situation and problems.Acta Ecologica Sinica (生态学报),2015,35(9):2769-2788 (in Chinese)
[9] Li D-F,Voigt TB,Kent AD.Plant and soil effects on bacterial communities associated with Miscanthus × giganteus rhizosphere and rhizomes.GCB Bioenergy,2016,8:183-193
[10] van Dijk EL,Auger H,Jaszczyszyn Y,et al.Ten years of next-generation sequencing technology.Trends in Genetics,2014,30:418-426
[11] Pham HN,Pham PA,Nguyen TTH,et al.Influence of metal contamination in soil on metabolic profiles of Miscanthus × giganteus belowground parts and associated bacterial communities.Applied Soil Ecology,2018,125:240-249
[12] Zhang B,Penton CR,Xue C,et al.Soil depth and crop determinants of bacterial communities under ten biofuel cropping systems.Soil Biology and Biochemistry,2017,112:140-152
[13] Bourgeois E,Dequiedt S,Lelièvre M,et al.Miscanthus bioenergy crop stimulates nutrient-cycler bacteria and fungi in wastewater-contaminated agricultural soil.Environmental Chemistry Letters,2015,13:503-511
[14] Zheng Y (郑远),Li Y-Y (李玉英),Ding C-Y (丁传雨),et al.Effects of bioenergy cropping on rhizosphere bacteria networks structure in Cd contaminated soil.Acta Scientiae Circumstantiae (环境科学学报),2016,36(7):2605-2612 (in Chinese)
[15] Ding C-Y (丁传雨),Zheng Y (郑远),Ren X-M (任学敏),et al.Changes in bacterial community composition during the remediation of Cd-contaminated soils of bioenergy crops.Acta Scientiae Circumstantiae (环境科学学报),2016,36(8):3009-3016 (in Chinese)
[16] Langille MGI,Zaneveld J,Caporaso JG,et al.Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.Nature Biotechnology,2013,31:814-821
[17] Pii Y,Borruso L,Brusetti L,et al.The interaction between iron nutrition,plant species and soil type shapes the rhizosphere microbiome.Plant Physiology and Biochemistry,2016,99:39-48
[18] Yuan Z,Druzhinina IS,Labbé J,et al.Specialized microbiome of a halophyte and its tole in helping non-Host plants to withstand salinity.Scientific Reports,2016,6:32467
[19] Luo J,Tao Q,Wu K,et al.Structural and functional variability in root-associated bacterial microbiomes of Cd/Zn hyperaccumulator Sedum alfredii.Applied Microbiology and Biotechnology,2017,101:7961-7976
[20] Jiang L,Song M,Yang L,et al.Exploring the influence of environmental factors on bacterial communities within the rhizosphere of the Cu-tolerant plant,Elsholtzia splendens.Scientific Reports,2016,6:36302,doi:10.1038/srep36302
[21] Yi Z-X (易镇邪),Wang Y (王禹),Lin C (林聪),et al.Effects of harvesting stage on biomass and content of N,P and K of hybrid varieties in Miscanthus.Acta Agriculturae Boreali-Sinica (华北农学报),2013,28(3):116-120 (in Chinese)
[22] Bao S-D (鲍士旦).Soil and Agricultural Chemisty Analysis.Beijing:China Agricultural Science and Technology Press,2000 (in Chinese)
[23] Chen ZJ,Zheng Y,Ding CY,et al.Integrated meta-genomics and molecular ecological network analysis of bacterial community composition during the phytoremediation of cadmium-contaminated soils by bioenergy crops.Ecotoxicology and Environmental Safety,2017,145:111-118
[24] Caporaso JG,Kuczynski J,Stombaugh J,et al.QIIME allows analysis of high-throughput community sequencing data.Nature Methods,2010,7:335-336
[25] Schloss PD,Westcott SL,Ryabin T,et al.Introducing mothur:Open-source,platform-independent,community-supported software for describing and comparing microbial communities.Applied and Environmental Microbiology,2009,75:7537-7541
[26] YIin X-W (阴星望),Tian W (田伟),Ding Y (丁一),et al.Composition and predictive functional analysis of bacterial communities in surface sediments of the Danjiangkou Reservoir.Journal of Lake Sciences (湖泊科学),2018,30(4):1052-1063 (in Chinese)
[27] Deng W,Wang Y,Liu Z,et al.HemI:A toolkit for illustrating heatmaps.PLoS One,2014,9(11):e111988
[28] Parks DH,Tyson GW,Hugenholtz P,et al.STAMP:Statistical analysis of taxonomic and functional profiles.Bioinformatics,2014,30:3123-3124
[29] LeBrun E,Kang S.A comparison of computationally predicted functional metagenomes and microarray analysis for microbial P cycle genes in a unique basalt-soil forest.F1000Research,2018,7:179
[30] Zhang F (张菲),Tian W (田伟),Sun F (孙峰),et al.Community structure and predictive functional analysis of surface water bacterioplankton in the Danjiangkou Reservoir.Environmental Science (环境科学),2019,40(3):243-251 (in Chinese)
[31] Yang X-Q (杨雪琴),Lian Y-L (连英丽),Yan Q-Y (颜庆云),et al.Microbially-driven nitrogen cycling in coastal ecosystems.Acta Microbiologica Sinica (微生物学报),2018,58(4):633-648 (in Chinese)
[32] Falkowski PG,Fenchel T,Delong EF.The microbial engines that drive earth’s biogeochemical cycles.Science,2008,320:1034-1039
[33] Pii Y,Mimmo T,Tomasi N,et al.Microbial interactions in the rhizosphere:Beneficial influences of plant growth-promoting rhizobacteria on nutrient acquisition process.A review.Biology and Fertility of Soils,2015,51:403-415
[34] Luo D (罗达),Shi Z-M (史作民),Li D-S (李东胜).Short-term effects of litter treatment on soil C and N transformation and microbial community structure in Erythrophleum fordii plantation.Chinese Journal of Applied Ecology (应用生态学报),2018,29(7):2259-2268 (in Chinese)
[35] Ye W (叶雯),Li Y-C (李永春),Yu W-W (喻卫武),et al.Microbial biodiversity in rhizospheric soil of Torreya grandis ‘Merrillii’ relative to cultivation history.Chinese Journal of Applied Ecology (应用生态学报),2018,29(11):3783-3792 (in Chinese)
[36] Bais HP,Weir TL,Perry LG,et al.The role of root exu-dates in rhizosphere interactions with plants and other organisms.Annual Review of Plant Biology,2006,57:233-266
[37] Sánchez-Caňizares C,Jorrín B,Poole PS,et al.Understanding the holobiont:The interdependence of plants and their microbiome.Current Opinion in Microbiology,2017,38:188-196
[38] Mendes LW,Kuramae EE,Navarrete AA,et al.Taxonomical and functional microbial community selection in soybean rhizosphere.The ISME Journal,2014,8:1577-1587
[2] Heaton EA,Dohleman FG,Long SP.Meeting US biofuel goals with less land:The potential of Miscanthus.Global Change Biology,2008,14:2000-2014
[3] Yi Z-L (易自力).Exploitation and utilization of Miscanthus as energy plant.Journal of Hunan Agricultural University (Natural Sciences) (湖南农业大学学报:自然科学版),2012,38(5):455-463 (in Chinese)
[4] Yu Y-C (于延冲),Yi Z-L (易自力),Zhou G-K (周功克).Research progress and comprehensive utilization of Miscanthus.Chinese Bulletin of Life Sciences (生命科学),2014,26(5):474-480 (in Chinese)
[5] Wu D-M (吴道铭),Chen X-Y (陈晓阳),Zeng S-C (曾曙才).Heavy metal tolerance of Miscanthus plants and their phytoremediation potential in abandoned mine land.Chinese Journal of Applied Ecology (应用生态学报),2017,28(4):1397-1406 (in Chinese)
[6] Chauhan H,Bagyaraj DJ,Selvakumar G,et al.Novel plant growth promoting rhizobacteria:Prospects and potential.Applied Soil Ecology,2015,95:38-53
[7] Finkel OM,Castrillo G,Herrera Paredes S,et al.Understanding and exploiting plant beneficial microbes.Current Opinion in Plant Biology,2017,38:155-163
[8] Liu C (刘驰),Li J-B (李家宝),Rui J-P (芮俊鹏),et al.The applications of the 16S rRNA gene in microbial ecology:Current situation and problems.Acta Ecologica Sinica (生态学报),2015,35(9):2769-2788 (in Chinese)
[9] Li D-F,Voigt TB,Kent AD.Plant and soil effects on bacterial communities associated with Miscanthus × giganteus rhizosphere and rhizomes.GCB Bioenergy,2016,8:183-193
[10] van Dijk EL,Auger H,Jaszczyszyn Y,et al.Ten years of next-generation sequencing technology.Trends in Genetics,2014,30:418-426
[11] Pham HN,Pham PA,Nguyen TTH,et al.Influence of metal contamination in soil on metabolic profiles of Miscanthus × giganteus belowground parts and associated bacterial communities.Applied Soil Ecology,2018,125:240-249
[12] Zhang B,Penton CR,Xue C,et al.Soil depth and crop determinants of bacterial communities under ten biofuel cropping systems.Soil Biology and Biochemistry,2017,112:140-152
[13] Bourgeois E,Dequiedt S,Lelièvre M,et al.Miscanthus bioenergy crop stimulates nutrient-cycler bacteria and fungi in wastewater-contaminated agricultural soil.Environmental Chemistry Letters,2015,13:503-511
[14] Zheng Y (郑远),Li Y-Y (李玉英),Ding C-Y (丁传雨),et al.Effects of bioenergy cropping on rhizosphere bacteria networks structure in Cd contaminated soil.Acta Scientiae Circumstantiae (环境科学学报),2016,36(7):2605-2612 (in Chinese)
[15] Ding C-Y (丁传雨),Zheng Y (郑远),Ren X-M (任学敏),et al.Changes in bacterial community composition during the remediation of Cd-contaminated soils of bioenergy crops.Acta Scientiae Circumstantiae (环境科学学报),2016,36(8):3009-3016 (in Chinese)
[16] Langille MGI,Zaneveld J,Caporaso JG,et al.Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.Nature Biotechnology,2013,31:814-821
[17] Pii Y,Borruso L,Brusetti L,et al.The interaction between iron nutrition,plant species and soil type shapes the rhizosphere microbiome.Plant Physiology and Biochemistry,2016,99:39-48
[18] Yuan Z,Druzhinina IS,Labbé J,et al.Specialized microbiome of a halophyte and its tole in helping non-Host plants to withstand salinity.Scientific Reports,2016,6:32467
[19] Luo J,Tao Q,Wu K,et al.Structural and functional variability in root-associated bacterial microbiomes of Cd/Zn hyperaccumulator Sedum alfredii.Applied Microbiology and Biotechnology,2017,101:7961-7976
[20] Jiang L,Song M,Yang L,et al.Exploring the influence of environmental factors on bacterial communities within the rhizosphere of the Cu-tolerant plant,Elsholtzia splendens.Scientific Reports,2016,6:36302,doi:10.1038/srep36302
[21] Yi Z-X (易镇邪),Wang Y (王禹),Lin C (林聪),et al.Effects of harvesting stage on biomass and content of N,P and K of hybrid varieties in Miscanthus.Acta Agriculturae Boreali-Sinica (华北农学报),2013,28(3):116-120 (in Chinese)
[22] Bao S-D (鲍士旦).Soil and Agricultural Chemisty Analysis.Beijing:China Agricultural Science and Technology Press,2000 (in Chinese)
[23] Chen ZJ,Zheng Y,Ding CY,et al.Integrated meta-genomics and molecular ecological network analysis of bacterial community composition during the phytoremediation of cadmium-contaminated soils by bioenergy crops.Ecotoxicology and Environmental Safety,2017,145:111-118
[24] Caporaso JG,Kuczynski J,Stombaugh J,et al.QIIME allows analysis of high-throughput community sequencing data.Nature Methods,2010,7:335-336
[25] Schloss PD,Westcott SL,Ryabin T,et al.Introducing mothur:Open-source,platform-independent,community-supported software for describing and comparing microbial communities.Applied and Environmental Microbiology,2009,75:7537-7541
[26] YIin X-W (阴星望),Tian W (田伟),Ding Y (丁一),et al.Composition and predictive functional analysis of bacterial communities in surface sediments of the Danjiangkou Reservoir.Journal of Lake Sciences (湖泊科学),2018,30(4):1052-1063 (in Chinese)
[27] Deng W,Wang Y,Liu Z,et al.HemI:A toolkit for illustrating heatmaps.PLoS One,2014,9(11):e111988
[28] Parks DH,Tyson GW,Hugenholtz P,et al.STAMP:Statistical analysis of taxonomic and functional profiles.Bioinformatics,2014,30:3123-3124
[29] LeBrun E,Kang S.A comparison of computationally predicted functional metagenomes and microarray analysis for microbial P cycle genes in a unique basalt-soil forest.F1000Research,2018,7:179
[30] Zhang F (张菲),Tian W (田伟),Sun F (孙峰),et al.Community structure and predictive functional analysis of surface water bacterioplankton in the Danjiangkou Reservoir.Environmental Science (环境科学),2019,40(3):243-251 (in Chinese)
[31] Yang X-Q (杨雪琴),Lian Y-L (连英丽),Yan Q-Y (颜庆云),et al.Microbially-driven nitrogen cycling in coastal ecosystems.Acta Microbiologica Sinica (微生物学报),2018,58(4):633-648 (in Chinese)
[32] Falkowski PG,Fenchel T,Delong EF.The microbial engines that drive earth’s biogeochemical cycles.Science,2008,320:1034-1039
[33] Pii Y,Mimmo T,Tomasi N,et al.Microbial interactions in the rhizosphere:Beneficial influences of plant growth-promoting rhizobacteria on nutrient acquisition process.A review.Biology and Fertility of Soils,2015,51:403-415
[34] Luo D (罗达),Shi Z-M (史作民),Li D-S (李东胜).Short-term effects of litter treatment on soil C and N transformation and microbial community structure in Erythrophleum fordii plantation.Chinese Journal of Applied Ecology (应用生态学报),2018,29(7):2259-2268 (in Chinese)
[35] Ye W (叶雯),Li Y-C (李永春),Yu W-W (喻卫武),et al.Microbial biodiversity in rhizospheric soil of Torreya grandis ‘Merrillii’ relative to cultivation history.Chinese Journal of Applied Ecology (应用生态学报),2018,29(11):3783-3792 (in Chinese)
[36] Bais HP,Weir TL,Perry LG,et al.The role of root exu-dates in rhizosphere interactions with plants and other organisms.Annual Review of Plant Biology,2006,57:233-266
[37] Sánchez-Caňizares C,Jorrín B,Poole PS,et al.Understanding the holobiont:The interdependence of plants and their microbiome.Current Opinion in Microbiology,2017,38:188-196
[38] Mendes LW,Kuramae EE,Navarrete AA,et al.Taxonomical and functional microbial community selection in soybean rhizosphere.The ISME Journal,2014,8:1577-1587