基于高通量测序的南泥湾湿地土壤细菌多样性分析
|
摘要
为研究南泥湾湿地细菌群落类群结构,本研究利用Illumina高通量测序技术,对土壤样品中细菌的16S rRNA基因进行测序分析。各样地共检测到细菌类群27门、106纲、163目、306科、534属,主要的优势菌门为变形菌门(Proteobacteria)、放线菌门(Actinobacteria)、厚壁菌门(Firmicutes)、绿弯菌门(Chloroflexi)和酸杆菌门(Acidobacteria),主要的优势菌纲为α-变形菌纲(Alphaproteobacteria)、β-变形菌纲(Betaproteobacteria)和γ-变形菌纲(Gammaproteobacteria)。不同退化湿地土壤细菌的数量和种类各不相同。随着退化程度加深,土壤细菌群落多样性降低,南泥湾湿地土壤细菌菌种多样性在不同退化阶段的差异较大。通过典型对应分析发现,土壤p H值、有机质和全钾对南泥湾湿地土壤细菌分布影响较大。人为开垦活动会降低土壤微生物多样性,退耕还湿措施对湿地微生物群落结构有影响。
In order to study the taxonomic structure of bacterial community in Nanniwan wetland,we sequenced the 16 S rRNA gene of bacteria in soil samples by using Illumina high-throughput sequencing technique. In all sites,27 phyla,106 classes,163 orders,306 families and 534 genera of bacterial groups were detected. The main dominant phyla were Proteobacteria,Actinobacteria,Firmicutes,Chloroflexi and Acidobacteria; the main dominant classes were Alphaproteobacteria,Betaproteobacteria and Gammaproteobacteria. The number and types of soil bacteria in different degraded wetlands were different. With the deepening of degradation,the diversity of soil bacterial communities decreased. The diversity of bacterial species in Nanniwan wetland was significantly different at different degradation stages. It was found through canonical correspondence analysis that soil pH,organic matter and total potassium influenced the distribution of soil bacteria in Nanniwan wetland. Artificial reclamation activities would reduce soil microbial diversity. The measures of returning farmland to wet had an impact on the microbial community structure in wetlands.
In order to study the taxonomic structure of bacterial community in Nanniwan wetland,we sequenced the 16 S rRNA gene of bacteria in soil samples by using Illumina high-throughput sequencing technique. In all sites,27 phyla,106 classes,163 orders,306 families and 534 genera of bacterial groups were detected. The main dominant phyla were Proteobacteria,Actinobacteria,Firmicutes,Chloroflexi and Acidobacteria; the main dominant classes were Alphaproteobacteria,Betaproteobacteria and Gammaproteobacteria. The number and types of soil bacteria in different degraded wetlands were different. With the deepening of degradation,the diversity of soil bacterial communities decreased. The diversity of bacterial species in Nanniwan wetland was significantly different at different degradation stages. It was found through canonical correspondence analysis that soil pH,organic matter and total potassium influenced the distribution of soil bacteria in Nanniwan wetland. Artificial reclamation activities would reduce soil microbial diversity. The measures of returning farmland to wet had an impact on the microbial community structure in wetlands.
引文
[1]刘银银,李峰,孙庆业,等.湿地生态系统土壤微生物研究进展[J].应用与环境生物学报,2013,19(3):547-552.
[2]纳小凡,郑国琦,彭励,等.不同种植年限宁夏枸杞根际微生物多样性变化[J].土壤学报,2016,53(1):241-252.
[3]薛菁芳,高艳梅,汪景宽,等.土壤微生物量碳氮作为土壤肥力指标的探讨[J].土壤通报,2007,38(2):247-250.
[4]Roesch L F W,Fulthorpe R R,Riva A,et al. Pyrosequencing enumerates and contrasts soil microbial diversity[J]. The ISME Journal,2007(1):283-284.
[5]Alvarez L,Aliashkevich A,Pedro M A,et al. Bacterial secretion of D-arginine controls environmental microbial biodiversity[J]. The ISME Journal,2018,12(2):438-450.
[6]邵颖,刘长海.土壤微生物与植被、温度及水分关系的研究进展[J].延安大学学报(自然科学版),2017,36(4):43-48.
[7]赵桂玲,刘长海,王文强,等.南泥湾湿地生态变迁研究[J].湿地科学与管理,2015(1):65-67.
[8]Sims A,Zhang Y,Gajaraj S,et al. Toward the development of microbial indicators for wetland assessment[J]. Water Research,2013,47:1711
[9]鲍士旦.土壤农化分析[M].北京:中国农业出版社,2005.
[10]Gans J,Wolinsky M,Dunbar J. Computational improvements reveal great bacterial diversity and high metal toxicity in soil[J]. Science,2005,309(5739):1387-1390.
[11]Harris J A. Measurements of the soil microbial community for estimating the success of restoration[J]. European Journal of Soil Science,2003,54:801-808.
[12]马维伟,李广,石万里,等.甘肃尕海湿地退化过程中植物生物量及物种多样性变化动态[J].草地学报,2016,24(5):960-966.
[13]任国华,邓斌,后源.黄河源区沼泽湿地退化过程中植物群落特征的变化[J].草业科学,2015,32(8):1222-1229.
[14]Mendes L W,Kuramae E E,Navarrete A A,et al. Taxonomical and functional microbial community selection in soybean rhizosphere[J]. The ISME Journal,2014,8(8):1577-1587.
[15]Liu J J,Su Y Y,Yu Z H,et al. Soil carbon content drives the biogeographical distribution of fungal communities in the black soil zone of northeast China[J]. Soil Biology and Biochemistry,2015,83:29-39.
[16]戴雅婷,闰志坚,解继红,等.基于高通量测序的两种植被恢复类型根际土壤细菌多样性研究[J].土壤学报,2017,54(3):735-748.
[17]牛世全,龙洋,李海云,等.应用Illumina Mi Seq高通量测序技术分析河西走廊地区盐碱土壤微生物多样性[J].微生物学通报,2017,44(9):2067-2078.
[18]Griffiths R I,Thomson B C,James P,et al. The bacterial biogeography of British soils[J]. Environmental Microbiology,2011,13(6):1642-1654.
[19]Feng Y,Grogan P,Caporaso J G,et al. pH is a good predictor of the distribution of anoxygenic purple phototrophic bacteria in Arctic soils[J].Soil Biology and Biochemistry,2014,74:193-200.
[20]黄进勇,李春霞.土壤微生物多样性的主要影响因子及其效应[J].河南科技大学学报(农学版),2004,24(4):10-13.
[21]Latour X,Corberand T,Laguerre G,et al. The composition of fluorescent pseudomonad populations associated with roots is influenced by plant and soil types[J]. Appl Environ Microbial,1996,62(7):2449-2456.
[22]Su J Q,Ding L J,Xue K,et al. Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil[J]. Molecular Ecology,2015,24(1):136-150.
[23]Zhang Y T,Shen H,He X H,et al. Fertilization shapes bacterial community structure by alteration of soil pH[J]. Frontiers in Microbiology,2017,8:1325. dio:10. 3389/fmicb. 2017. 01325.
[24]陈谦,张新雄,赵海,等.生物有机肥中几种功能微生物的研究及应用概况[J].应用与环境生物学报,2010,16(2):294-300.
[25]Marschner P,Yang C H,Lieberei R,et al. Soil and plant specific effects on bacterial community composition in the rhizosphere[J]. Soil Biology and Biochemistry,2001,33(11):1437-1445.
[26]Heijedn M G A,Bardgett R D,Straalen N M. The unseen majority:soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems[J]. Ecology Letters,2008,11(3):296-310.
[27]杨刚,谢永宏,陈心胜,等.洞庭湖区退田还湖后不同恢复模式下土壤酶活性的变化[J].应用生态学报,2009,20(9):2187-2192.
[28]曾全超,李鑫,董扬红,等.陕北黄土高原土壤性质及其生态化学计量的纬度变化特征[J].自然资源学报,2015,30(5):870-879.
[29]刘洋,黄懿梅,曾全超.黄土高原不同植被类型下土壤细菌群落特征研究[J].环境科学,2016,37(10):3931-3938.
[2]纳小凡,郑国琦,彭励,等.不同种植年限宁夏枸杞根际微生物多样性变化[J].土壤学报,2016,53(1):241-252.
[3]薛菁芳,高艳梅,汪景宽,等.土壤微生物量碳氮作为土壤肥力指标的探讨[J].土壤通报,2007,38(2):247-250.
[4]Roesch L F W,Fulthorpe R R,Riva A,et al. Pyrosequencing enumerates and contrasts soil microbial diversity[J]. The ISME Journal,2007(1):283-284.
[5]Alvarez L,Aliashkevich A,Pedro M A,et al. Bacterial secretion of D-arginine controls environmental microbial biodiversity[J]. The ISME Journal,2018,12(2):438-450.
[6]邵颖,刘长海.土壤微生物与植被、温度及水分关系的研究进展[J].延安大学学报(自然科学版),2017,36(4):43-48.
[7]赵桂玲,刘长海,王文强,等.南泥湾湿地生态变迁研究[J].湿地科学与管理,2015(1):65-67.
[8]Sims A,Zhang Y,Gajaraj S,et al. Toward the development of microbial indicators for wetland assessment[J]. Water Research,2013,47:1711
[9]鲍士旦.土壤农化分析[M].北京:中国农业出版社,2005.
[10]Gans J,Wolinsky M,Dunbar J. Computational improvements reveal great bacterial diversity and high metal toxicity in soil[J]. Science,2005,309(5739):1387-1390.
[11]Harris J A. Measurements of the soil microbial community for estimating the success of restoration[J]. European Journal of Soil Science,2003,54:801-808.
[12]马维伟,李广,石万里,等.甘肃尕海湿地退化过程中植物生物量及物种多样性变化动态[J].草地学报,2016,24(5):960-966.
[13]任国华,邓斌,后源.黄河源区沼泽湿地退化过程中植物群落特征的变化[J].草业科学,2015,32(8):1222-1229.
[14]Mendes L W,Kuramae E E,Navarrete A A,et al. Taxonomical and functional microbial community selection in soybean rhizosphere[J]. The ISME Journal,2014,8(8):1577-1587.
[15]Liu J J,Su Y Y,Yu Z H,et al. Soil carbon content drives the biogeographical distribution of fungal communities in the black soil zone of northeast China[J]. Soil Biology and Biochemistry,2015,83:29-39.
[16]戴雅婷,闰志坚,解继红,等.基于高通量测序的两种植被恢复类型根际土壤细菌多样性研究[J].土壤学报,2017,54(3):735-748.
[17]牛世全,龙洋,李海云,等.应用Illumina Mi Seq高通量测序技术分析河西走廊地区盐碱土壤微生物多样性[J].微生物学通报,2017,44(9):2067-2078.
[18]Griffiths R I,Thomson B C,James P,et al. The bacterial biogeography of British soils[J]. Environmental Microbiology,2011,13(6):1642-1654.
[19]Feng Y,Grogan P,Caporaso J G,et al. pH is a good predictor of the distribution of anoxygenic purple phototrophic bacteria in Arctic soils[J].Soil Biology and Biochemistry,2014,74:193-200.
[20]黄进勇,李春霞.土壤微生物多样性的主要影响因子及其效应[J].河南科技大学学报(农学版),2004,24(4):10-13.
[21]Latour X,Corberand T,Laguerre G,et al. The composition of fluorescent pseudomonad populations associated with roots is influenced by plant and soil types[J]. Appl Environ Microbial,1996,62(7):2449-2456.
[22]Su J Q,Ding L J,Xue K,et al. Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil[J]. Molecular Ecology,2015,24(1):136-150.
[23]Zhang Y T,Shen H,He X H,et al. Fertilization shapes bacterial community structure by alteration of soil pH[J]. Frontiers in Microbiology,2017,8:1325. dio:10. 3389/fmicb. 2017. 01325.
[24]陈谦,张新雄,赵海,等.生物有机肥中几种功能微生物的研究及应用概况[J].应用与环境生物学报,2010,16(2):294-300.
[25]Marschner P,Yang C H,Lieberei R,et al. Soil and plant specific effects on bacterial community composition in the rhizosphere[J]. Soil Biology and Biochemistry,2001,33(11):1437-1445.
[26]Heijedn M G A,Bardgett R D,Straalen N M. The unseen majority:soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems[J]. Ecology Letters,2008,11(3):296-310.
[27]杨刚,谢永宏,陈心胜,等.洞庭湖区退田还湖后不同恢复模式下土壤酶活性的变化[J].应用生态学报,2009,20(9):2187-2192.
[28]曾全超,李鑫,董扬红,等.陕北黄土高原土壤性质及其生态化学计量的纬度变化特征[J].自然资源学报,2015,30(5):870-879.
[29]刘洋,黄懿梅,曾全超.黄土高原不同植被类型下土壤细菌群落特征研究[J].环境科学,2016,37(10):3931-3938.