贵州茂兰喀斯特森林不同小生境下土壤细菌群落特征
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摘要
以贵州茂兰喀斯特森林小生境土壤(石洞、石缝、石沟、石槽、土面)为研究对象,利用高通量测序技术对其土壤细菌16S rRNA V3～V4可变区进行高通量测序,分析土壤细菌α多样性、物种组成及丰度差异情况,并应用数量生态学方法分析土壤理化因子对细菌群落结构的影响.结果表明:5类小生境土壤共检测到27个门64个纲128个目242个科367个属704个种;主要优势菌门为变形菌门、放线菌门、酸杆菌门、绿弯菌门、硝化螺旋菌门;石洞表层(0～10 cm)、石洞下层(10～20 cm)、石缝及石槽等生境主要的优势菌门是放线菌门,土面表层(0～10 cm)、土面下层(10～20 cm)的是酸杆菌门,石沟表层(0～10 cm)、石沟下层(10～20cm)的是变形菌门.石缝细菌Simpson多样性最高,土面下层(10～20 cm)最低. LEfSe分析表明,土面表层(0～10 cm)、土面下层(10～20 cm)、石洞下层(10～20 cm)以及石槽不同分类水平上的差异指示种数量高于石缝、石沟表层(0～10 cm)以及石沟下层(10～20 cm).例如,在门水平上,石洞下层(10～20 cm)差异指示种为放线菌门与绿弯菌门,石沟表层(0～10 cm)为变形菌门与Tectomicrobia门,土面表层(0～10 cm)为酸杆菌门、疣微菌门及Latescibacteria门,土面下层(10～20 cm)为硝化螺旋菌门,石槽、石缝以及石沟下层(10～20 cm)无差异指示种;但从门至属,石洞表层(0～10 cm)都无差异指示种.冗余分析(RDA)及集成推进树(ABT)分析表明,土壤有机质、pH及总磷较大程度上解释了细菌门类水平分布对土壤基本理化因子变化的响应机制.
We analyzed the diversity,community composition and relative abundance of soil bacteria communities in five different types of microhabitats( included stone caverns,stone crevices,stone gullies,stone grooves,top-soils) in Maolan karst forest,Guizhou Province,China. Bacterial16 S rRNA V3-V4 variable regions were analyzed by high-throughput sequencing technique. We examined the effects of soil physicochemical factors on bacterial community structure. The results showed that 27 phyla,64 classes,128 orders,242 families,367 genera,and 704 species were detected in the soils from five types of microhabitats. Proteobacteria,Actinomycetes,Acidobacteria,Chlorofleixi and Nitrospirae were the dominant bacterial phyla. Actinomycetes was the dominant phyla in the microhabitats of top-stone cavern( 0-10 cm),sub-stone cavern( 10-20 cm),stone crevice,and stone groove. Acidobacteria was the dominant phyla in the top-soil( 0-10 cm) and the sub-soil( 10-20 cm). Proteobacteria was the dominant phyla in the top-stone gully( 0-10 cm)and the sub-stone gully( 10-20 cm). The highest soil bacterial Simpson index was found in stone crevice microhabitat,while the lowest was found in sub-soil( 10-20 cm) microhabitat. Results from the LEfSe analysis showed that the number of distinct indicator species at the different levels of taxonomy was higher in the top-soil( 0-10 cm),sub-soil( 10-20 cm),sub-stone cavern( 10-20cm),and the stone groove than in the stone crevice,the top-stone gully( 0-10 cm) and sub-stone gully( 10-20 cm). The indicator phyla were Actinobacteria and Chlorofleixi in the sub-stone cavern( 10-20 cm). The top-stone gully( 0-10 cm) were characterized by the phyla of Proteobacteria and Tectomicrobia. The top-soil( 0-10 cm) was featured by Acidobacteria,Verrucomicrobia and Latescibacteria. The sub-soil( 10-20 cm) was dominated by Nitrospirae. There were no indicator species in stone groove,stone crevice,and sub-stone gully( 10-20 cm). There was no indicator species in phylum to genus in top-stone cavern( 0-10 cm). RDA and ABT analysis showed that soil organic matter,pH,and available phosphorus explained a large part of the variation regarding the responses of bacterial community to the changes in basic physicochemical factors in the soil.
We analyzed the diversity,community composition and relative abundance of soil bacteria communities in five different types of microhabitats( included stone caverns,stone crevices,stone gullies,stone grooves,top-soils) in Maolan karst forest,Guizhou Province,China. Bacterial16 S rRNA V3-V4 variable regions were analyzed by high-throughput sequencing technique. We examined the effects of soil physicochemical factors on bacterial community structure. The results showed that 27 phyla,64 classes,128 orders,242 families,367 genera,and 704 species were detected in the soils from five types of microhabitats. Proteobacteria,Actinomycetes,Acidobacteria,Chlorofleixi and Nitrospirae were the dominant bacterial phyla. Actinomycetes was the dominant phyla in the microhabitats of top-stone cavern( 0-10 cm),sub-stone cavern( 10-20 cm),stone crevice,and stone groove. Acidobacteria was the dominant phyla in the top-soil( 0-10 cm) and the sub-soil( 10-20 cm). Proteobacteria was the dominant phyla in the top-stone gully( 0-10 cm)and the sub-stone gully( 10-20 cm). The highest soil bacterial Simpson index was found in stone crevice microhabitat,while the lowest was found in sub-soil( 10-20 cm) microhabitat. Results from the LEfSe analysis showed that the number of distinct indicator species at the different levels of taxonomy was higher in the top-soil( 0-10 cm),sub-soil( 10-20 cm),sub-stone cavern( 10-20cm),and the stone groove than in the stone crevice,the top-stone gully( 0-10 cm) and sub-stone gully( 10-20 cm). The indicator phyla were Actinobacteria and Chlorofleixi in the sub-stone cavern( 10-20 cm). The top-stone gully( 0-10 cm) were characterized by the phyla of Proteobacteria and Tectomicrobia. The top-soil( 0-10 cm) was featured by Acidobacteria,Verrucomicrobia and Latescibacteria. The sub-soil( 10-20 cm) was dominated by Nitrospirae. There were no indicator species in stone groove,stone crevice,and sub-stone gully( 10-20 cm). There was no indicator species in phylum to genus in top-stone cavern( 0-10 cm). RDA and ABT analysis showed that soil organic matter,pH,and available phosphorus explained a large part of the variation regarding the responses of bacterial community to the changes in basic physicochemical factors in the soil.
引文
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[12]Gu M-Y(顾美英),Tang G-M(唐光木),Liu H-L(刘洪亮),et al.Effects of cotton stalk biochar on microbial community structure and function of continuous cropping cotton rhizosphere soil in Xinjiang,China.Chinese Journal of Applied Ecology(应用生态学报),2016,27(1):173-181(in Chinese)
[13]Song Z(宋振),Ji Q-F(纪巧凤),Fu W-D(付卫东),et al.Effects of flaveria bidentis invasion on the diversity of functional bacteria in rhizosphere soil.Chinese Journal of Applied Ecology(应用生态学报),2016,27(8):2636-2644(in Chinese)
[14]Lian B(连宾).Microbial roles in the genesis of soil from carbonate rock weathering.Bulletin of Mineralogy,Petrology and Geochemistry(矿物岩石地球化学通报),2010,29(1):52-56(in Chinese)
[15]Zhu Y-G(朱永官),Duan G-L(段桂兰),Chen B-D(陈保冬),et al.Mineral weathering and cycle of elements on soil-microorganism-plant system.Scientia Sinica Terrae(中国科学:地球科学),2014,44(6):1107-1116(in Chinese)
[16]Li S(李莎),Li F-C(李福春),Cheng L-J(程良娟).Recent development in bio-weathering research.Mineral Resourcesand Geology(矿产与地质),2006,20(6):577-582(in Chinese)
[17]Long J(龙健),Li J(李娟),Jiang X-R(江新荣),et al.Soil microbial activities in Maolan karst forest,Guizhou Province.Acta Pedologica Sinica(土壤学报),2004,41(4):597-602(in Chinese)
[18]Zhang Z,Hu B,Hu G.Spatial heterogeneity of soil chemical properties in a subtropical karst forest,southwest China.The Scientific World Journal,2014,2014:473651
[19]Yu P(玉屏),Lan H-B(兰洪波),Ran J-C(冉景丞),et al.Status and conservation countermeasures of biodiversity in Maolan National Reserve.Modern Agricultural Sciences and Technology(现代农业科技),2011(15):233-234(in Chinese)
[20]Bao S-D(鲍士旦).Soil and Agricultural Chemistry Analysis.3rd Ed.Beijing:China Agriculture Press,2000(in Chinese)
[21]Du C(杜璨),Xu C-Y(许晨阳),Wang Q(王强),et al.Patterns of bacterial community through soil depth profiles and its influencing factors under Betula albosinensis Burkill in the Xinjiashan forest region of Qinling Mountains.Environmental Science(环境科学),2017,38(7):3010-3019(in Chinese)
[22]Romaniuk R,GiuffréL,Costantini A,et al.Assessment of soil microbial diversity measurements as indicators of soil functioning in organic and conventional horticulture systems.Ecological Indicators,2011,11:1345-1353
[23]Jin Z-J(靳振江),Tang H-F(汤华峰),Li M(李敏),et al.Microbial community abundance and diversity in typical karst ecosystem to indicate soil carbon cycle.Environmental Science(环境科学),2014,35(11):4284-4290(in Chinese)
[24]Delgado-Baquerizo M,Oliverio AM,Brewer TE,et al.A global atlas of the dominant bacteria found in soil.Science,2018,359:320-325
[25]Jing Z-B(井赵斌),Cheng J-M(程积民),Zhang B-Q(张宝泉),et al.Eukaryote diversity of typical grassland soil based on 454 pyrosequencing.Pratacultural Science(草业科学),2013,30(11):1690-1697(in Chinese)
[26]Lynd LR,Weimer PJ,van Zyl WH,et al.Microbial cellulose utilization:Fundamentals and biotechnology.Microbiology&Molecular Biology Reviews,2002,66:506-577
[27]Pankratov TA,Ivanova AO,Dedysh SN,et al.Bacterial populations and environmental factors controlling cellulose degradation in an acidic Sphagnum peat.Environmental Microbiology,2011,13:1800-1814
[28]Guo W(郭魏),Qi X-B(齐学斌),Li P(李平),et al.Impact of reclaimed water irrigation and nitrogen fertilization on soil bacterial community structure.Acta Scientiae Circumstantiae(环境科学学报),2017,37(1):280-287(in Chinese)
[29]Chen M-L(陈孟立),Zeng Q-C(曾全超),Huang Y-M(黄懿梅),et al.Effects of the program of converting farmland into forest or grassland on soil bacterial community structure in loess hilly region.Environmental Science(环境科学),2018,39(4):1824-1332(in Chinese)
[30]Zhang T,Shao MF,Ye L.454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants.ISME Journal,2012,6:1137-1147
[31]Liu Y(刘洋),Huang Y-M(黄懿梅),Zeng Q-C(曾全超).Soil bacterial communities under different vegetation types in the loess plateau.Environmental Science(环境科学),2016,37(10):3931-3938(in Chinese)
[32]Warscheid T,Braams J.Biodeterioration of stone:Areview.International Biodeterioration&Biodegradation,2000,46:343-368
[33]Chu Y(褚玥),Cao C-L(曹成亮),Lian B(连宾).Effect on calcium carbonate morphology by a strain of rockactinomycete.Acta Microbiologica Sinica(微生物学报),2016,56(7):1123-1131(in Chinese)
[34]Dion P.Extreme views on prokaryote evolution//Dion P,Nautiyal CS,eds.Microbiology of Extreme Soils.Berlin:Springer,2008:45-70
[35]Pol A,Heijmans K,Harhangi HR,et al.Methanotrophy below p H 1 by a new verrucomicrobia species.Nature,2007,450:874-878
[36]Islam T,Jensen S,Reigstad LJ,et al.Methane oxidation at 55℃and p H 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum.Proceedings of the National Academy of Sciences of the United States of America,2008,105:300-304
[37]Cleveland CC,Townsend AR,Schmidt SK.Phosphorus limitation of microbial processes in moist tropical forests:Evidence from short-term laboratory incubations and field studies.Ecosystems,2002,5:680-691
[2]Sengupta A,Dick WA.Bacterial community diversity in soil under two tillage practices as determined by pyrosequencing.Microbial Ecology,2015,70:853-859
[3]Philippot L,Andersson SGE,Battin TJ,et al.The ecological coherence of high bacterial taxonomic ranks.Nature Reviews Microbiology,2010,8:523-529
[4]Zhou Q-W(周秋文),Luo Y-X(罗雅雪),Zhang S-Q(张思琪),et al.Progresses in research on the spatial estimation of soil erodibility factors in Karst area.Journal of Guizhou Normal University(Natural Science)(贵州师范大学学报:自然科学版),2017,35(6):16-21(in Chinese)
[5]Liao H-K(廖洪凯),Li J(李娟),Long J(龙健),et al.Soil characteristics of different microhabitats of Chinese prickly ash in karst mountain areas of Guizhou Province.Journal of Agro-Environment Science(农业环境科学学报),2013,32(12):2429-2435(in Chinese)
[6]Long J(龙健),Deng Q-Q(邓启琼),Jiang X-R(江新荣),et al.Effects of landuse desertification region types on restoration of soil quality on karst rocky in Guizhou Province.Acta Ecologica Sinica(生态学报),2005,25(12):3188-3195(in Chinese)
[7]Liao H-K(廖洪凯),Long J(龙健),Li J(李娟),et al.Preliminary study on spatial heterogeneity of soil mineral composition and organic carbon content at different micro-habitats that under different vegetation types in karst region.Carsolgica Sinica(中国岩溶),2010,29(4):434-439(in Chinese)
[8]Liao H-K(廖洪凯),Li J(李娟),Long J(龙健).Effect of vegetation type and micro-habitat on soil active organic carbon and basal respiration in karst dry and hot valley region of Guizhou Province,China.Chinese Journal of Soil Science(土壤通报),2013,44(3):580-586(in Chinese)
[9]Liao H-K(廖洪凯),Long J(龙健),Li J(李娟),et al.Distribution characteristics of soil carbon and nitrogen under different vegetation types in microhabitats of karst dry-hot valley region of South Western China.Soils(土壤),2012,44(3):421-428(in Chinese)
[10]Liu F(刘方),Wang S-J(王世杰),Luo H-B(罗海波),et al.Micro-habitats in karst forest ecosystem and variability of soils.Acta Pedologica Sinica(土壤学报),2008,45(6):1055-1062(in Chinese)
[11]Yu J(喻江),Yu Z-H(于镇华),IKENAGA Makoto,et al.Effects of manure application on the diversity of corn root endophytic bacterial communities at seedling stage in eroded Mollisols.Chinese Journal of Applied Ecology(应用生态学报),2016,27(8):2663-2669(in Chinese)
[12]Gu M-Y(顾美英),Tang G-M(唐光木),Liu H-L(刘洪亮),et al.Effects of cotton stalk biochar on microbial community structure and function of continuous cropping cotton rhizosphere soil in Xinjiang,China.Chinese Journal of Applied Ecology(应用生态学报),2016,27(1):173-181(in Chinese)
[13]Song Z(宋振),Ji Q-F(纪巧凤),Fu W-D(付卫东),et al.Effects of flaveria bidentis invasion on the diversity of functional bacteria in rhizosphere soil.Chinese Journal of Applied Ecology(应用生态学报),2016,27(8):2636-2644(in Chinese)
[14]Lian B(连宾).Microbial roles in the genesis of soil from carbonate rock weathering.Bulletin of Mineralogy,Petrology and Geochemistry(矿物岩石地球化学通报),2010,29(1):52-56(in Chinese)
[15]Zhu Y-G(朱永官),Duan G-L(段桂兰),Chen B-D(陈保冬),et al.Mineral weathering and cycle of elements on soil-microorganism-plant system.Scientia Sinica Terrae(中国科学:地球科学),2014,44(6):1107-1116(in Chinese)
[16]Li S(李莎),Li F-C(李福春),Cheng L-J(程良娟).Recent development in bio-weathering research.Mineral Resourcesand Geology(矿产与地质),2006,20(6):577-582(in Chinese)
[17]Long J(龙健),Li J(李娟),Jiang X-R(江新荣),et al.Soil microbial activities in Maolan karst forest,Guizhou Province.Acta Pedologica Sinica(土壤学报),2004,41(4):597-602(in Chinese)
[18]Zhang Z,Hu B,Hu G.Spatial heterogeneity of soil chemical properties in a subtropical karst forest,southwest China.The Scientific World Journal,2014,2014:473651
[19]Yu P(玉屏),Lan H-B(兰洪波),Ran J-C(冉景丞),et al.Status and conservation countermeasures of biodiversity in Maolan National Reserve.Modern Agricultural Sciences and Technology(现代农业科技),2011(15):233-234(in Chinese)
[20]Bao S-D(鲍士旦).Soil and Agricultural Chemistry Analysis.3rd Ed.Beijing:China Agriculture Press,2000(in Chinese)
[21]Du C(杜璨),Xu C-Y(许晨阳),Wang Q(王强),et al.Patterns of bacterial community through soil depth profiles and its influencing factors under Betula albosinensis Burkill in the Xinjiashan forest region of Qinling Mountains.Environmental Science(环境科学),2017,38(7):3010-3019(in Chinese)
[22]Romaniuk R,GiuffréL,Costantini A,et al.Assessment of soil microbial diversity measurements as indicators of soil functioning in organic and conventional horticulture systems.Ecological Indicators,2011,11:1345-1353
[23]Jin Z-J(靳振江),Tang H-F(汤华峰),Li M(李敏),et al.Microbial community abundance and diversity in typical karst ecosystem to indicate soil carbon cycle.Environmental Science(环境科学),2014,35(11):4284-4290(in Chinese)
[24]Delgado-Baquerizo M,Oliverio AM,Brewer TE,et al.A global atlas of the dominant bacteria found in soil.Science,2018,359:320-325
[25]Jing Z-B(井赵斌),Cheng J-M(程积民),Zhang B-Q(张宝泉),et al.Eukaryote diversity of typical grassland soil based on 454 pyrosequencing.Pratacultural Science(草业科学),2013,30(11):1690-1697(in Chinese)
[26]Lynd LR,Weimer PJ,van Zyl WH,et al.Microbial cellulose utilization:Fundamentals and biotechnology.Microbiology&Molecular Biology Reviews,2002,66:506-577
[27]Pankratov TA,Ivanova AO,Dedysh SN,et al.Bacterial populations and environmental factors controlling cellulose degradation in an acidic Sphagnum peat.Environmental Microbiology,2011,13:1800-1814
[28]Guo W(郭魏),Qi X-B(齐学斌),Li P(李平),et al.Impact of reclaimed water irrigation and nitrogen fertilization on soil bacterial community structure.Acta Scientiae Circumstantiae(环境科学学报),2017,37(1):280-287(in Chinese)
[29]Chen M-L(陈孟立),Zeng Q-C(曾全超),Huang Y-M(黄懿梅),et al.Effects of the program of converting farmland into forest or grassland on soil bacterial community structure in loess hilly region.Environmental Science(环境科学),2018,39(4):1824-1332(in Chinese)
[30]Zhang T,Shao MF,Ye L.454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants.ISME Journal,2012,6:1137-1147
[31]Liu Y(刘洋),Huang Y-M(黄懿梅),Zeng Q-C(曾全超).Soil bacterial communities under different vegetation types in the loess plateau.Environmental Science(环境科学),2016,37(10):3931-3938(in Chinese)
[32]Warscheid T,Braams J.Biodeterioration of stone:Areview.International Biodeterioration&Biodegradation,2000,46:343-368
[33]Chu Y(褚玥),Cao C-L(曹成亮),Lian B(连宾).Effect on calcium carbonate morphology by a strain of rockactinomycete.Acta Microbiologica Sinica(微生物学报),2016,56(7):1123-1131(in Chinese)
[34]Dion P.Extreme views on prokaryote evolution//Dion P,Nautiyal CS,eds.Microbiology of Extreme Soils.Berlin:Springer,2008:45-70
[35]Pol A,Heijmans K,Harhangi HR,et al.Methanotrophy below p H 1 by a new verrucomicrobia species.Nature,2007,450:874-878
[36]Islam T,Jensen S,Reigstad LJ,et al.Methane oxidation at 55℃and p H 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum.Proceedings of the National Academy of Sciences of the United States of America,2008,105:300-304
[37]Cleveland CC,Townsend AR,Schmidt SK.Phosphorus limitation of microbial processes in moist tropical forests:Evidence from short-term laboratory incubations and field studies.Ecosystems,2002,5:680-691
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