五大连池火山喷发沉积物古菌多样性及系统发育分析
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摘要
为揭示古菌在五大连池火山区的生态格局,运用Illumina Miseq高通量测序技术与系统发育分析法,解析五大连池火山喷发沉积物中古菌的群落组成和分布规律.研究发现,五大连池火山区沉积泥中的古菌类群主要包含奇古菌门(Thaumarchaeota)、广古菌门(Euryarchaeota)和泉古菌门(Crenarchaeota),其中奇古菌门丰度最高,主要包括SAGMCG-1与Thaumarchaeota Incertae Sedis两大类群;广古菌门主要包括甲烷微菌纲(Methanomicrobia)、甲烷杆菌纲(Methanobacteria)、盐杆菌纲(Halobacteria)、热原体纲(Thermoplasmata)和甲烷球菌纲(Methanococci),其中甲烷微菌纲是优势种群,下分7目13科23属,多样性丰富;泉古菌门主要为热变形菌纲(Thermoprotei)与Soil Crenarchaeotic Group(SCG).从古菌进化角度,泉古菌门与奇古菌门进化关系较近,二者与广古菌门距离较远.从沉积环境角度,火烧山与药泉山、焦得布山与龙门山沉积泥带古菌种群结构具有一定的相似性,其余泥带间均存在不同程度的差异性.因此,五大连池火山沉积环境中含有丰富的古菌资源,存在大量潜在新种,古菌多样性异于报道较多的陆地及海底沉积环境;结果可为今后挖掘功能性种质资源及探讨古菌群落在火山环境中的生态规律奠定科学基础.
This study was done to improve our understanding of the ecology of archaea in the Wudalianchi volcanic region of China. High-throughput sequencing with the Illumina MiSeq system and phylogenetic analysis were used to analyze the community composition and distribution of the archaea occurring in the volcanic sediments of the Wudalianchi region. Three categories of archaea, including Thaumarchaeota, Euryarchaeota, and Crenarchaeota, were found and further analyzed. Among these, the abundance of Thaumarchaeota was the highest, and mainly included SAGMCG-1 and Thaumarchaeota Incertae Sedis. Within the Euryarchaeota, the Methanomicrobia, Methanobacteria, Halobacteria, Thermoplasmata, and Methanococci were abundant. Methanomicrobia was the predominant class of Euryarchaeota, and the members of this group found were divided into 7 orders, 13 families, and 23 genera, all of which were rich in biodiversity. Thermoprotei and SCG were the main classes found that belonged to Crenarchaeota. Additionally, in the evolutionary tree produced Crenarchaeota was phylogenetically closer to Thaumarchaeota, which was in turn far away from Euryarchaeota. There was some similarity between the archaea communities of Huoshao volcano and Yaoquan volcano, and also between those of Jiaodebu volcano and Longmen volcano, whereas all the other communities examined differed in their archaea community composition to different degrees among different sedimentary environments. These results indicated that microbial resources are abundant in the volcanic sedimentary environments of the Wudalianchi region, and there should be a plenty of new, unknown taxa there. This makes the archaea of Wudalianchi significantly different from those reported in other terrestrial and marine sedimentary environments. This study's results will provide the scientific foundation for the future mining of functional microbial resources and exploration of the ecological regularity of the archaea communities in volcanic environments.
This study was done to improve our understanding of the ecology of archaea in the Wudalianchi volcanic region of China. High-throughput sequencing with the Illumina MiSeq system and phylogenetic analysis were used to analyze the community composition and distribution of the archaea occurring in the volcanic sediments of the Wudalianchi region. Three categories of archaea, including Thaumarchaeota, Euryarchaeota, and Crenarchaeota, were found and further analyzed. Among these, the abundance of Thaumarchaeota was the highest, and mainly included SAGMCG-1 and Thaumarchaeota Incertae Sedis. Within the Euryarchaeota, the Methanomicrobia, Methanobacteria, Halobacteria, Thermoplasmata, and Methanococci were abundant. Methanomicrobia was the predominant class of Euryarchaeota, and the members of this group found were divided into 7 orders, 13 families, and 23 genera, all of which were rich in biodiversity. Thermoprotei and SCG were the main classes found that belonged to Crenarchaeota. Additionally, in the evolutionary tree produced Crenarchaeota was phylogenetically closer to Thaumarchaeota, which was in turn far away from Euryarchaeota. There was some similarity between the archaea communities of Huoshao volcano and Yaoquan volcano, and also between those of Jiaodebu volcano and Longmen volcano, whereas all the other communities examined differed in their archaea community composition to different degrees among different sedimentary environments. These results indicated that microbial resources are abundant in the volcanic sedimentary environments of the Wudalianchi region, and there should be a plenty of new, unknown taxa there. This makes the archaea of Wudalianchi significantly different from those reported in other terrestrial and marine sedimentary environments. This study's results will provide the scientific foundation for the future mining of functional microbial resources and exploration of the ecological regularity of the archaea communities in volcanic environments.
引文
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12 Xiang X,Wang RC,Wang HM,Gong LF,Man BY,Xu Y.Distribution of bathyarchaeota communities across different terrestrial settings and their potential ecological functions[J].Sci Rep,2017,7:45028
13 Fillol M,Sànchez-MelsióA,Gich F,Bor rego CM.Diversit y of miscellaneous crenarchaeotic group archaea in freshwater karstic lakes and their segregation between planktonic and sediment habitats[J].FEMS Microbiol Ecol,2015,91(4):1-16
14 Zhang Y,Dong SK,Gao QZ,Liu SL,Zhou HK,Ganjurjavc H,Wang XX.Climate change and human activities altered the diversity and composition of soil microbial community in alpine grasslands ofthe Qinghai-Tibetan Plateau[J].Sci Total Environ,2016,562:353-363
15 De Long EF.Archaea in coastal marine environments[J].PNAS,1992,89:5685-5689
16 Takai K,Moser DP,Deflaun M,Onstott TC,Fredrickson JK.Archaeal diversity in waters from deep south African gold mines[J].Appl Environ Microbiol,2001,67(12):5750-5760
17 Ivanova I,Atanassov I,Lyutskanova D,Disheva MS,Dimitrova D,Tomova I,Derekova A,Radeva G,Buchvarova V,Kambourova M.High archaea diversity in Varvara hot spring,Bulgaria[J].J Basic Microbiol,2011,51:163-172
18 Solden L,Lloyd K,Wrighton K.The bright side of microbial dark matter:lessons learned from the uncultivated majority[J].Curr Opin Microbiol,2016,31:217-226
19张丹丹,蔡征文,姚谦豪,张光亚.嗜冷嗜盐菌Halor ubr u m la c u sprof u n di中蛋白质稳定性机制的探讨[J].计算机与应用化学,2016,6(10):43-48[Zhang DD,Cai ZW,Yao QH,Zhang GY.The molecular basis of proteins stability from Halorubrum lacusprofundi[J].Comput Appl Chem,2016,6(10):43-48]
20 Stein LY,Jones G,Alexander B,Elmund K,Wright-Jones C,Nealson KH.Intriguing microbial diversity associated with metal rich particles from a freshwater reservoir[J].FEMS Microbiol Ecol,2002,42(3):431-440
21 Hultman J,Waldrop MP,Mackelprang R,David MM,McFarland J,Bla zew icz SJ,Ha rde n J,Tu ret sk y M R,McG u i re A D,Sha h M B,VerBerk moes NC,Lee LH,Mav rom matis K,Jansson J K.Multiomics of permafrost,active layer and thermokarst bog soil microbiomes[J].Nature,2015,521:208-216
22 Caporaso JG,Kuczynski J,Stombaugh J,Bittinger K,Bushman F D,C o s t el lo E K,Fie r e r N,Pe?a AG,G o o d r ich J K,G o r d o n JI,Huttley GA,Kelley ST,Knights D,Koenig JE,Ley RE,Lozupone CA,McDonald D,Muegge BD,Pir r ung M,Reeder J,Sevinsk y JR,Turnbaugh PJ,Walters WA,Widmann J,Yatsunenko T,Zaneveld J,Knight R.QIIME allows analysis of high-throughput community sequencing data[J].Nat Methods,2010,7(5):335-336
23 Edgar RC.Search and clustering orders of magnitude faster than BLAST[J].Bioinformatics,2010,26(19):2460-2461
24 Hanbo C,Paul CB.VennDiagram:a package for the generation of highly-customizable Venn and Euler diagrams in R[J].BMCBioinformatics,2011,12(1):35
25张丽梅,贺纪正.一个新的古菌类群--奇古菌门(Thaumarchaeota)[J].微生物学报,2012:52(4):516-524[Zhang LM,He JZ.A novel archaeal phylum:Thaumarchaeota-A review[J].Acta Microbiol Sin,2012,52(4):516-524]
26 Yatsunenko T,Rey FE,Manar y MJ,Trehan I,Dominguez-Bello MG,Contreras M,Magris M,Hidalgo G,Baldassano RN,Anokhin A P,He a t h AC,Wa r n e r B,Re e d e r J,Ku cz y n s k i J,C a p o r a s o JG,Loz upone CA,Lauber C,Clemente JC,K nights D,K night R,Gordon JI.Human gut microbiome viewed across age and geography[J].Nature,2012,6(14):222-227
27 Jiang XT,Peng X,Deng GH,Sheng HF,Wang Y,Zhou HW,Yee Tam NF.Illumina sequencing of 16S rRNA tag revealed spatial variations of bacterial communities in a mangrove wetland[J].Microbial Ecol,2013,66:96-104
28刘青,谢运标,陈逍遥,周梅先.东太平洋海隆深海热液区沉积物古菌多样性分析[J].应用海洋学学报,2014,33(4):516-524[Liu Q,Xie YB,Chen XY,Zhou MX.Archaeal diversity in deep-sea hydrothermal sediments from the East Pacific rise[J].J Appl Oceanogr,2014,33(4):516-524]
29覃千山,承磊,张辉,胡国全.新疆泥火山微生物群落[J].中国沼气,2015,33(3):3-9[Qin QS,Cheng L,Zhang H,Hu GQ.Microbial community of mud volcanoes in Xinjiang Province[J].China Biogas,2015,33(3):3-9]
30杨玉峰,雷怀彦,史春潇.南海北部天然气水合物潜在区973-3岩心古菌多样性[J].石油与天然气地质,2016,37(3):415-421[Yang YF,Lei HY,Shi CX.Archaeal diversity analyses of core 973-3 from potential gas hydrate area in northern South China Sea[J].Oil Gas Geol,2016,37(3):415-421]
31范习贝,梁前勇,牛明杨,余甜甜,王寅炤,王风平.中国南海北部陆坡沉积物古菌多样性及丰度分析[J].微生物学通报,2017,44(7):1589-1601[Fan XB,Liang QY,Niu MY,Yu TT,Wang YZ,Wang FP.The diversity and richness of archaea in the northern continental slope of South China Sea[J].Microbiology,2017,44(7):1589-1601]
2 Seitz KW,Lazar CS,Hinrichs KU,Teske AP,Baker BJ.Genomic reconstruction of a novel,deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction[J].ISME J,2016,10(7):1696-1705
3 Vanwonterghem I,Evans PN,Parks DH,Jensen PD,Woodcroft BJ,Hugenholtz P,Tyson GW.Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota[J].Nat Microbiol,2016,1:16-17
4 Fillol M,Auguet JC,Casamayor EO,Borrego CM.Insights in the ecology and evolutionary history of the Miscellaneous Crenarchaeotic Group lineage[J].ISME J,2016,10(3):665-677
5 Za remba N K,Caceres EF,Saw J H,B?ckst r?m D,Ju zokaite L,Vancaester E,Seitz KW,Anantharaman K,Starnawski P,Kjeldsen KU,Stott MB,Nunoura T,Banfield JF,Schramm A,Baker BJ,Spang A,Ettema TJ.Asgard archaea illuminate the origin of eukaryotic cellular complexity[J].Nature,2017,541(7637):353-358
6 He Y,Li M,Perumal V,Feng X,Fang J,Xie J,Sievert SM,Wang F.Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments[J].Nat Microbiol,2016,1(6):16-35
7石国强,彭剑峰,宋永会,袁林江,姜诗慧.浑河底泥产甲烷古菌多样性空间分布特征[J].环境科学学报,2016,36(5):1766-1773[Shi GQ,Peng JF,Song YH,Yuan LJ,Jiang SH.Spatial distribution of methanogenic archaea diversity in the sediments of Hun River[J].Acta Sci Circum,2016,36(5):1766-1773]
8 Li ZX,Jin WB,Liang ZY,Yue YY,LüJH.Abundance and diversity of ammonia-oxidizing archaea in response to various habitats in Pearl River Delta of China,a subtropical maritime zone[J].J Environ Sci,2013,25(6):1195-1205
9 Naj ja r i A,Elsha he d MS,Che r if A,You ssef N H.Pat t e r n s a nd determinants of halophilic archaea(Class Halobacteria)diversity in Tunisian Endorheic Salt Lakes[J].Appl Environ Microbiol,2015,81:4432-4441
10 Baricz A,Cristea A,Muntean V,Teodosiu G,Andrei AS,Molnár L,Alexe M,Tican ER,Banciu HL.Culturable diversity of aerobic haloph ilic a rchaea(Fam.Halobacter iaceae)f rom hy persali ne,meromictic Transylvanian lakes[J].Extremophiles,2015,19:525-537
11 Lazar CS,Baker BJ,Seitz K,Hyde AS,Dick GJ,Hinrichs KU,Teske AP.Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments[J].Environ Microbiol,2016,18(4):1200-1211
12 Xiang X,Wang RC,Wang HM,Gong LF,Man BY,Xu Y.Distribution of bathyarchaeota communities across different terrestrial settings and their potential ecological functions[J].Sci Rep,2017,7:45028
13 Fillol M,Sànchez-MelsióA,Gich F,Bor rego CM.Diversit y of miscellaneous crenarchaeotic group archaea in freshwater karstic lakes and their segregation between planktonic and sediment habitats[J].FEMS Microbiol Ecol,2015,91(4):1-16
14 Zhang Y,Dong SK,Gao QZ,Liu SL,Zhou HK,Ganjurjavc H,Wang XX.Climate change and human activities altered the diversity and composition of soil microbial community in alpine grasslands ofthe Qinghai-Tibetan Plateau[J].Sci Total Environ,2016,562:353-363
15 De Long EF.Archaea in coastal marine environments[J].PNAS,1992,89:5685-5689
16 Takai K,Moser DP,Deflaun M,Onstott TC,Fredrickson JK.Archaeal diversity in waters from deep south African gold mines[J].Appl Environ Microbiol,2001,67(12):5750-5760
17 Ivanova I,Atanassov I,Lyutskanova D,Disheva MS,Dimitrova D,Tomova I,Derekova A,Radeva G,Buchvarova V,Kambourova M.High archaea diversity in Varvara hot spring,Bulgaria[J].J Basic Microbiol,2011,51:163-172
18 Solden L,Lloyd K,Wrighton K.The bright side of microbial dark matter:lessons learned from the uncultivated majority[J].Curr Opin Microbiol,2016,31:217-226
19张丹丹,蔡征文,姚谦豪,张光亚.嗜冷嗜盐菌Halor ubr u m la c u sprof u n di中蛋白质稳定性机制的探讨[J].计算机与应用化学,2016,6(10):43-48[Zhang DD,Cai ZW,Yao QH,Zhang GY.The molecular basis of proteins stability from Halorubrum lacusprofundi[J].Comput Appl Chem,2016,6(10):43-48]
20 Stein LY,Jones G,Alexander B,Elmund K,Wright-Jones C,Nealson KH.Intriguing microbial diversity associated with metal rich particles from a freshwater reservoir[J].FEMS Microbiol Ecol,2002,42(3):431-440
21 Hultman J,Waldrop MP,Mackelprang R,David MM,McFarland J,Bla zew icz SJ,Ha rde n J,Tu ret sk y M R,McG u i re A D,Sha h M B,VerBerk moes NC,Lee LH,Mav rom matis K,Jansson J K.Multiomics of permafrost,active layer and thermokarst bog soil microbiomes[J].Nature,2015,521:208-216
22 Caporaso JG,Kuczynski J,Stombaugh J,Bittinger K,Bushman F D,C o s t el lo E K,Fie r e r N,Pe?a AG,G o o d r ich J K,G o r d o n JI,Huttley GA,Kelley ST,Knights D,Koenig JE,Ley RE,Lozupone CA,McDonald D,Muegge BD,Pir r ung M,Reeder J,Sevinsk y JR,Turnbaugh PJ,Walters WA,Widmann J,Yatsunenko T,Zaneveld J,Knight R.QIIME allows analysis of high-throughput community sequencing data[J].Nat Methods,2010,7(5):335-336
23 Edgar RC.Search and clustering orders of magnitude faster than BLAST[J].Bioinformatics,2010,26(19):2460-2461
24 Hanbo C,Paul CB.VennDiagram:a package for the generation of highly-customizable Venn and Euler diagrams in R[J].BMCBioinformatics,2011,12(1):35
25张丽梅,贺纪正.一个新的古菌类群--奇古菌门(Thaumarchaeota)[J].微生物学报,2012:52(4):516-524[Zhang LM,He JZ.A novel archaeal phylum:Thaumarchaeota-A review[J].Acta Microbiol Sin,2012,52(4):516-524]
26 Yatsunenko T,Rey FE,Manar y MJ,Trehan I,Dominguez-Bello MG,Contreras M,Magris M,Hidalgo G,Baldassano RN,Anokhin A P,He a t h AC,Wa r n e r B,Re e d e r J,Ku cz y n s k i J,C a p o r a s o JG,Loz upone CA,Lauber C,Clemente JC,K nights D,K night R,Gordon JI.Human gut microbiome viewed across age and geography[J].Nature,2012,6(14):222-227
27 Jiang XT,Peng X,Deng GH,Sheng HF,Wang Y,Zhou HW,Yee Tam NF.Illumina sequencing of 16S rRNA tag revealed spatial variations of bacterial communities in a mangrove wetland[J].Microbial Ecol,2013,66:96-104
28刘青,谢运标,陈逍遥,周梅先.东太平洋海隆深海热液区沉积物古菌多样性分析[J].应用海洋学学报,2014,33(4):516-524[Liu Q,Xie YB,Chen XY,Zhou MX.Archaeal diversity in deep-sea hydrothermal sediments from the East Pacific rise[J].J Appl Oceanogr,2014,33(4):516-524]
29覃千山,承磊,张辉,胡国全.新疆泥火山微生物群落[J].中国沼气,2015,33(3):3-9[Qin QS,Cheng L,Zhang H,Hu GQ.Microbial community of mud volcanoes in Xinjiang Province[J].China Biogas,2015,33(3):3-9]
30杨玉峰,雷怀彦,史春潇.南海北部天然气水合物潜在区973-3岩心古菌多样性[J].石油与天然气地质,2016,37(3):415-421[Yang YF,Lei HY,Shi CX.Archaeal diversity analyses of core 973-3 from potential gas hydrate area in northern South China Sea[J].Oil Gas Geol,2016,37(3):415-421]
31范习贝,梁前勇,牛明杨,余甜甜,王寅炤,王风平.中国南海北部陆坡沉积物古菌多样性及丰度分析[J].微生物学通报,2017,44(7):1589-1601[Fan XB,Liang QY,Niu MY,Yu TT,Wang YZ,Wang FP.The diversity and richness of archaea in the northern continental slope of South China Sea[J].Microbiology,2017,44(7):1589-1601]