青藏高原小柴旦盐湖微生物群落结构及多样性
|
摘要
通过探究小柴旦盐湖微生物群落结构与多样性,为盐湖微生物资源的开发利用和生态保护提供重要的理论参考依据。利用Illumina Mi Seq测序平台对小柴旦盐湖细菌和古菌的16S rRNA基因(V3~V5区)进行高通量测序,获得细菌和古菌的物种注释OTU(Operational Taxonomic Units)数目分别为870和410,其中分类地位明确的细菌有18门、24纲、135属,古菌2门、4纲、22属。细菌优势类群依次是厚壁菌门(Firmicutes,34.05%)、变形菌门(Proteobacteria,32.91%)、拟杆菌门(Bacteroidetes,18.01%)和蓝细菌门(Cyanobacteria,8.46%);优势种群依次是芽孢杆菌属(Bacillus,21.53%)、Chloroplast-norank(6.65%)和海杆菌属(Marinobacter,4.05%)。古菌的优势类群和优势种群主要是未确定分类地位的沃斯古菌门(Woesearchaeota DHVEG-6,80.84%),相关的系统分类学尚需深入研究。小柴旦盐湖微生物的种群结构复杂、类群丰富,细菌Shannon多样性指数(4.77±0.45)显著高于古菌(2.79±0.45),且存在大量的新种资源。
Unique halophilic bacteria and archaea with rich species genetic diversity inhabit Xiaochaidan Salt Lake and play a critical role in material circulation,energy flow and ecosystem succession of the salt lake ecosystem. Xiaochaidan Salt Lake is located in the Qinghai-Tibetan Plateau of China and is a representative extreme hypersaline ecosystem,yet its microbial diversity has remained unknown. In this study,we investigated the microbial community structure and diversity in the water and sediment of Xiaochaidan Salt Lake via high-throughput sequencing of the V3-V5 regions from 16 S rRNA gene of archaea and of bacteria based on an Illumina platform. The objective was to provide a theoretical reference to support environmental protection and microbial resource utilization of the lake.In July 2015,mixed samples of water and sediment were collected from four sampling sites in Xiaochaidan Salt Lake( X1,X2,X3 and X4). The sample sites were spaced at 100 m intervals and samples were collected at depths of 10,20,30 and 40 cm. Ion chromatographic analysis was used to determine total dissolved salt( TDS,108. 82-113. 84 g/L),total organic carbon( TOC,3. 12-4. 28 g/L),total nitrogen( TN,0. 12-0. 32 g/L)and pH( 7. 8-8. 2). Based on hydrochemical characteristics,Xiaochaidan Salt Lake was characterized as a magnesium sulfate-subtype brine lake. A total of 147,410 sequences were obtained for bacteria and 118,216 sequences for archaea. A high diversity of OTUs( operational taxonomic units) were detected for bacteria( 870) and archaea( 410) : 18 phyla,24 classes and 135 genera of bacteria and 2 phyla,4 classes and 22 genera of archaea.Firmicutes( 34. 05%) was the dominant bacterial phyla,followed by Proteobacteria( 32. 91%),Bacteroidetes( 18. 01%),Cyanobacteria( 8. 46%),Actinobacteria( 2. 39%) and Chloroflexi( 1. 09%). The dominant bacterial genus was Bacillus( 21. 53%),followed by Chloroplast-norank( 6. 65%),Marinobacter( 4. 05%),Oceanobacillus( 3. 82%),Lactococcus( 3. 65%) and Pseudomonas( 3. 46%). The dominant taxa of archaea was unclassified Woesearchaeota DHVEG-6( 80. 84%) with no clear taxonomic classification. The microbial community in Xiaochaidan Salt Lake is abundant and complex,with high species richness. The Shannon diversity( 4. 77 ±0. 45),Ace and the Chao1 indices of the bacterial community were much higher than the indices of the archaeal community( Shannon diversity index,2. 79 ± 0. 45). Many new species remain unknown in Xiaochaidan Salt Lake,particularly in the Woesearchaeota phylum,and need further study. This research,based on high-throughput sequencing,comprehensively explored and characterized the microbial resources in Xiaochaidan Salt Lake and the findings will support further exploitation of the microbial resource.
Unique halophilic bacteria and archaea with rich species genetic diversity inhabit Xiaochaidan Salt Lake and play a critical role in material circulation,energy flow and ecosystem succession of the salt lake ecosystem. Xiaochaidan Salt Lake is located in the Qinghai-Tibetan Plateau of China and is a representative extreme hypersaline ecosystem,yet its microbial diversity has remained unknown. In this study,we investigated the microbial community structure and diversity in the water and sediment of Xiaochaidan Salt Lake via high-throughput sequencing of the V3-V5 regions from 16 S rRNA gene of archaea and of bacteria based on an Illumina platform. The objective was to provide a theoretical reference to support environmental protection and microbial resource utilization of the lake.In July 2015,mixed samples of water and sediment were collected from four sampling sites in Xiaochaidan Salt Lake( X1,X2,X3 and X4). The sample sites were spaced at 100 m intervals and samples were collected at depths of 10,20,30 and 40 cm. Ion chromatographic analysis was used to determine total dissolved salt( TDS,108. 82-113. 84 g/L),total organic carbon( TOC,3. 12-4. 28 g/L),total nitrogen( TN,0. 12-0. 32 g/L)and pH( 7. 8-8. 2). Based on hydrochemical characteristics,Xiaochaidan Salt Lake was characterized as a magnesium sulfate-subtype brine lake. A total of 147,410 sequences were obtained for bacteria and 118,216 sequences for archaea. A high diversity of OTUs( operational taxonomic units) were detected for bacteria( 870) and archaea( 410) : 18 phyla,24 classes and 135 genera of bacteria and 2 phyla,4 classes and 22 genera of archaea.Firmicutes( 34. 05%) was the dominant bacterial phyla,followed by Proteobacteria( 32. 91%),Bacteroidetes( 18. 01%),Cyanobacteria( 8. 46%),Actinobacteria( 2. 39%) and Chloroflexi( 1. 09%). The dominant bacterial genus was Bacillus( 21. 53%),followed by Chloroplast-norank( 6. 65%),Marinobacter( 4. 05%),Oceanobacillus( 3. 82%),Lactococcus( 3. 65%) and Pseudomonas( 3. 46%). The dominant taxa of archaea was unclassified Woesearchaeota DHVEG-6( 80. 84%) with no clear taxonomic classification. The microbial community in Xiaochaidan Salt Lake is abundant and complex,with high species richness. The Shannon diversity( 4. 77 ±0. 45),Ace and the Chao1 indices of the bacterial community were much higher than the indices of the archaeal community( Shannon diversity index,2. 79 ± 0. 45). Many new species remain unknown in Xiaochaidan Salt Lake,particularly in the Woesearchaeota phylum,and need further study. This research,based on high-throughput sequencing,comprehensively explored and characterized the microbial resources in Xiaochaidan Salt Lake and the findings will support further exploitation of the microbial resource.
引文
杜尧,马腾,肖骢,等,2016.小柴旦盐湖相淤泥水化学特征分析[J].干旱区研究,(1):94-100.
何聪聪,2015.环境因子对嗜盐古菌及其噬菌体SNJ1相互作用关系的影响[D].武汉:武汉轻工大学.
黄媛,方序,褚文珂,2015.杭州西溪湿地沉积物细菌的群落结构和多样性[J].海洋与湖沼,46(5):1202-1208.
李国强,薛林贵,莫天录,等,2015.湖泊沉积物微生物多样性研究方法的新进展[J].兰州交通大学学报,(6):12-16.
李红晓,张殿朋,郝雅荞,2016.青海固沙草根际微生态体系中微生物多样性分析[J].沈阳师范大学学报,34(2):227-233.
李坤珺,龙健,2015.山西运城盐湖嗜盐细菌的系统发育与种群多样性[J].贵州农业科学,(11):95-101.
李璐,郝春博,王丽华,等,2015.巴丹吉林沙漠盐湖微生物多样性[J].微生物学报,(4):412-424.
李明,郭嘉,石正国,等,2013a.春季青藏高原东北部湖泊细菌种类组成[J].应用与环境生物学报,(5):750-758.
李明,郭嘉,刘玉杰,等,2013b.青藏高原湖泊细菌种群结构的研究综述[J].地球环境学报,(2):1287-1300.
刘文,杨渐,吴耿,等,2016.青藏高原北部湖泊沉积物中基于不同碳源可培养细菌多样性[J].盐湖研究,(2):92-101.
时玉,孙怀博,刘勇勤,等,2014.青藏高原淡水湖普莫雍错和盐水湖阿翁错湖底沉积物中细菌群落的垂直分布[J].微生物学通报,(11):2379-2387.
王璐,2014.不同盐湖、盐田之间嗜盐古菌多样性比较[D].徐州:江苏师范大学.
王鑫,2014.青藏高原不同海拔咸水湖微生物多样性及适应性特征[D].兰州:兰州交通大学.
魏有霞,李宁,马国良,等,2007.青海茶卡盐湖抗生素产生菌的活性筛选及生物学特性的初步研究[J].青海大学学报(自然科学版),(2):13-17.
杨渐,2015.青藏高原湖泊微生物群落演替及其环境指示意义[D].北京:中国地质大学.
杨素萍,林志华,崔小华,等,2008.不产氧光合细菌的分类学进展[J].微生物学报,(11):1562-1566.
张红光,2013.青藏高原不同海拔湖水中微生物多样性和蓝藻适应性比较研究[D].兰州:兰州交通大学.
张现辉,孔凡晶,2010.西藏扎布耶盐湖细菌多样性的免培养技术分析[J].微生物学报,(3):334-341.
赵婉雨,杨渐,董海良,等,2013.柴达木盆地达布逊盐湖微生物多样性研究[J].地球与环境,(4):398-405.
郑绵平,刘喜方,2010.青藏高原盐湖水化学及其矿物组合特征[J].地质学报,(11):1585-1600.
中国科学院青海盐湖研究所分析室,1988.卤水和盐的分析方法(第2版)[M].北京:科学出版社.
周延,王芳,王琳,2013.盐湖开发对柴达木盆地盐湖湖水细菌的多样性影响[J].化工进展,(S1):234-239.
朱德锐,刘建,韩睿,等,2012.青海湖嗜盐微生物系统发育与种群多样性[J].生物多样性,20(4):495-504
朱莉,杨红梅,王芸,2012.新疆顿巴斯他乌盐湖沉积物免培养古菌多样性[J].微生物学报,(6):769-775.
Abdallah M B,Karray F,Mhiri N,et al,2016.Prokaryotic diversity in a Tunisian hypersaline lake,Chott El Jerid[J].Extremophiles,20(2):125-38.
Aguirre-Garrido J F,Ramírez-Saad H C,Toro N,et al,2016.Bacterial Diversity in the Soda Saline Crater Lake from Isabel Island,Mexico[J].Microbial Ecology,71(1):68-77.
Casamayor E O,Triadó-Margarit X,Casta1eda C,2013.Microbial biodiversity in saline shallow lakes of the Monegros Desert,Spain[J].FEMS Microbiology Ecology,85:503-518.
Castelle C J,Wrighton K C,Thomas B C,et al,2015.Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling[J].Current Biology,25:690-701.
Dinesh K,Meenu S,Kishan G R,2015.Halophiles:Biodiversity and Sustainable Exploitation[M].Volume 6,Springer.
Durbin A M,Teske A P,2012.Archaea in organic-lean and organic-rich marine subsurface sediments:an environmental gradient reflected in distinct phylogenetic lineages[J].Frontiers in Microbiology,168(3):1-26.
Eme L,Doolittle W F,2015.Microbial diversity:a bonanza of phyla[J].Current Biology,25(6):227-230.
Hamedi J,Mohammadipanah F,Ventosa A,2013.Systematic and biotechnological aspects of halophilic and halotolerant actinomycetes[J].Extremophiles,17(1):1-13.
Langille M G,Zaneveld J,Caporaso J G,et al,2013.Predictive functional profiling of microbial communities using 16SrRNA marker gene sequences[J].Nature Biotechnology,31(9):814-821.
Librado P,Rozas J,2009.DNAsp v5:a software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,25:1451-1452.
Liu Y,Yao T,Jiao N,et al,2013.Salinity impact on bacterial community composition in five high-altitude lakes from the Tibetan plateau,Western China[J].Geomicrobiology Journal,30(5):462-469.
Markowitz V M,Chen I M,Palaniappan K,et al,2014.IMG 4version of the integrated microbial genomes comparative analysis system[J].Nucleic Acids Res,42:560-567.
Oren A,2002.Diversity of halophilic microorganisms:environments,phylogeny,physiology,and applications[J].Journal of Industrial Microbiology and Biotechnology,28(1):56-63.
Ortiz-Alvarez R,Casamayor E O,2016.High occurrence of Pacearchaeota and Woesearchaeota(Archaea superphylum DPANN)in the surface waters of oligotrophic high-altitude lakes[J].Environmental Microbiology Reports,8(2):210-217.
Schloss P D,Gevers D,Westcott S L,2011.Reducing the Effects of PCR Amplification and Sequencing Artifacts on16S rRNA-Based Studies[J].Plos One,6(12):e27310.
Sorokin D Y,Berben T,Melton E D,et al,2014.Microbial diversity and biogeochemical cycling in soda lakes[J].Extremophiles Life Under Extreme Conditions,18(5):791-809.
Sun Y J,Lai Z P,Long H,et al,2010.Quartz OSL dating of archaeological sites in Xiao Qaidam Lake of the NE Qinghai-Ti-betan Plateau and its implications for palaeoenrionmental changes[J].Quaternary Geochronology,5:360-364.
Ventosa A,Fernández A B,León M J,2014.The Santa Pola saltern as a model for studying the microbiota of hypersaline environments[J].Extremophiles,18(5):811-824.
Yang S,Wen X,Jin H,et al,2012.Pyrosequencing investigation into the bacterial community in permafrostsoils along the China-Russia crude oil pipeline[J].Plos One,7(12):e52730.
Yuan S,Xie Y H,Zhang H X,et al,2014.The Application of PCR-DGGE Technique in Sheep Intestinal Microbial Diversity Research[J].Advanced Materials Research,884/885:540-543.
何聪聪,2015.环境因子对嗜盐古菌及其噬菌体SNJ1相互作用关系的影响[D].武汉:武汉轻工大学.
黄媛,方序,褚文珂,2015.杭州西溪湿地沉积物细菌的群落结构和多样性[J].海洋与湖沼,46(5):1202-1208.
李国强,薛林贵,莫天录,等,2015.湖泊沉积物微生物多样性研究方法的新进展[J].兰州交通大学学报,(6):12-16.
李红晓,张殿朋,郝雅荞,2016.青海固沙草根际微生态体系中微生物多样性分析[J].沈阳师范大学学报,34(2):227-233.
李坤珺,龙健,2015.山西运城盐湖嗜盐细菌的系统发育与种群多样性[J].贵州农业科学,(11):95-101.
李璐,郝春博,王丽华,等,2015.巴丹吉林沙漠盐湖微生物多样性[J].微生物学报,(4):412-424.
李明,郭嘉,石正国,等,2013a.春季青藏高原东北部湖泊细菌种类组成[J].应用与环境生物学报,(5):750-758.
李明,郭嘉,刘玉杰,等,2013b.青藏高原湖泊细菌种群结构的研究综述[J].地球环境学报,(2):1287-1300.
刘文,杨渐,吴耿,等,2016.青藏高原北部湖泊沉积物中基于不同碳源可培养细菌多样性[J].盐湖研究,(2):92-101.
时玉,孙怀博,刘勇勤,等,2014.青藏高原淡水湖普莫雍错和盐水湖阿翁错湖底沉积物中细菌群落的垂直分布[J].微生物学通报,(11):2379-2387.
王璐,2014.不同盐湖、盐田之间嗜盐古菌多样性比较[D].徐州:江苏师范大学.
王鑫,2014.青藏高原不同海拔咸水湖微生物多样性及适应性特征[D].兰州:兰州交通大学.
魏有霞,李宁,马国良,等,2007.青海茶卡盐湖抗生素产生菌的活性筛选及生物学特性的初步研究[J].青海大学学报(自然科学版),(2):13-17.
杨渐,2015.青藏高原湖泊微生物群落演替及其环境指示意义[D].北京:中国地质大学.
杨素萍,林志华,崔小华,等,2008.不产氧光合细菌的分类学进展[J].微生物学报,(11):1562-1566.
张红光,2013.青藏高原不同海拔湖水中微生物多样性和蓝藻适应性比较研究[D].兰州:兰州交通大学.
张现辉,孔凡晶,2010.西藏扎布耶盐湖细菌多样性的免培养技术分析[J].微生物学报,(3):334-341.
赵婉雨,杨渐,董海良,等,2013.柴达木盆地达布逊盐湖微生物多样性研究[J].地球与环境,(4):398-405.
郑绵平,刘喜方,2010.青藏高原盐湖水化学及其矿物组合特征[J].地质学报,(11):1585-1600.
中国科学院青海盐湖研究所分析室,1988.卤水和盐的分析方法(第2版)[M].北京:科学出版社.
周延,王芳,王琳,2013.盐湖开发对柴达木盆地盐湖湖水细菌的多样性影响[J].化工进展,(S1):234-239.
朱德锐,刘建,韩睿,等,2012.青海湖嗜盐微生物系统发育与种群多样性[J].生物多样性,20(4):495-504
朱莉,杨红梅,王芸,2012.新疆顿巴斯他乌盐湖沉积物免培养古菌多样性[J].微生物学报,(6):769-775.
Abdallah M B,Karray F,Mhiri N,et al,2016.Prokaryotic diversity in a Tunisian hypersaline lake,Chott El Jerid[J].Extremophiles,20(2):125-38.
Aguirre-Garrido J F,Ramírez-Saad H C,Toro N,et al,2016.Bacterial Diversity in the Soda Saline Crater Lake from Isabel Island,Mexico[J].Microbial Ecology,71(1):68-77.
Casamayor E O,Triadó-Margarit X,Casta1eda C,2013.Microbial biodiversity in saline shallow lakes of the Monegros Desert,Spain[J].FEMS Microbiology Ecology,85:503-518.
Castelle C J,Wrighton K C,Thomas B C,et al,2015.Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling[J].Current Biology,25:690-701.
Dinesh K,Meenu S,Kishan G R,2015.Halophiles:Biodiversity and Sustainable Exploitation[M].Volume 6,Springer.
Durbin A M,Teske A P,2012.Archaea in organic-lean and organic-rich marine subsurface sediments:an environmental gradient reflected in distinct phylogenetic lineages[J].Frontiers in Microbiology,168(3):1-26.
Eme L,Doolittle W F,2015.Microbial diversity:a bonanza of phyla[J].Current Biology,25(6):227-230.
Hamedi J,Mohammadipanah F,Ventosa A,2013.Systematic and biotechnological aspects of halophilic and halotolerant actinomycetes[J].Extremophiles,17(1):1-13.
Langille M G,Zaneveld J,Caporaso J G,et al,2013.Predictive functional profiling of microbial communities using 16SrRNA marker gene sequences[J].Nature Biotechnology,31(9):814-821.
Librado P,Rozas J,2009.DNAsp v5:a software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,25:1451-1452.
Liu Y,Yao T,Jiao N,et al,2013.Salinity impact on bacterial community composition in five high-altitude lakes from the Tibetan plateau,Western China[J].Geomicrobiology Journal,30(5):462-469.
Markowitz V M,Chen I M,Palaniappan K,et al,2014.IMG 4version of the integrated microbial genomes comparative analysis system[J].Nucleic Acids Res,42:560-567.
Oren A,2002.Diversity of halophilic microorganisms:environments,phylogeny,physiology,and applications[J].Journal of Industrial Microbiology and Biotechnology,28(1):56-63.
Ortiz-Alvarez R,Casamayor E O,2016.High occurrence of Pacearchaeota and Woesearchaeota(Archaea superphylum DPANN)in the surface waters of oligotrophic high-altitude lakes[J].Environmental Microbiology Reports,8(2):210-217.
Schloss P D,Gevers D,Westcott S L,2011.Reducing the Effects of PCR Amplification and Sequencing Artifacts on16S rRNA-Based Studies[J].Plos One,6(12):e27310.
Sorokin D Y,Berben T,Melton E D,et al,2014.Microbial diversity and biogeochemical cycling in soda lakes[J].Extremophiles Life Under Extreme Conditions,18(5):791-809.
Sun Y J,Lai Z P,Long H,et al,2010.Quartz OSL dating of archaeological sites in Xiao Qaidam Lake of the NE Qinghai-Ti-betan Plateau and its implications for palaeoenrionmental changes[J].Quaternary Geochronology,5:360-364.
Ventosa A,Fernández A B,León M J,2014.The Santa Pola saltern as a model for studying the microbiota of hypersaline environments[J].Extremophiles,18(5):811-824.
Yang S,Wen X,Jin H,et al,2012.Pyrosequencing investigation into the bacterial community in permafrostsoils along the China-Russia crude oil pipeline[J].Plos One,7(12):e52730.
Yuan S,Xie Y H,Zhang H X,et al,2014.The Application of PCR-DGGE Technique in Sheep Intestinal Microbial Diversity Research[J].Advanced Materials Research,884/885:540-543.