南海北部水层间及沉积表层细菌群落的比较分析
|
摘要
细菌群落在海洋生物地球化学过程中起着至关重要的作用。分析判别地理距离和环境条件等因素对细菌群落的影响,有助于理解环境变化如何驱动微生物多样性和功能的机制。通过细菌16SrDNA高通量测序的方法,对南海北部水层及沉积表层细菌群落多样性及空间分布进行比较分析,并检验环境因素、地理限制及海底深度等因素对微生物群落的影响。结果表明,约95%的细菌16SrDNA序列归属于γ-变形菌纲、厚壁菌门、蓝细菌门、α-变形菌纲等优势类群。沉积样本中的优势细菌类群主要与粒度、氮(N)等环境参数相关,而水体样本的优势细菌类群与取样深度密切相关。相关性检验结果显示,沉积样本的α-多样性指数与C有着显著的相关关系,而水体样本的α-多样性指数和β-多样性矩阵则显示与取样深度的显著相关;此外,地理距离和海底深度对β-多样性的影响并不显著,这可能与取样空间尺度有关。
Bacterial communities play a vital role in marine biogeochemical processes.Revealing the effects of geographical distance and environmental conditions on bacterial communities is important for better understanding how environmental changes can drive microbial diversity and maintain their functions.In this study,the diversity and spatial distribution of bacterial communities in water and surface sediments of northern South China Sea were analyzed through high-throughput sequencing of bacteria 16 SrDNA,and the effects of environmental factors,geographical restrictions and seabed depth on microbial communities were examined.The results showed that about 95%of bacterial 16 SrDNA sequences belonged to the dominant phyla/classes Gamma-proteobacteria,Firmicutes,Cyanobacteria,Alpha-proteobacteria,etc.The dominant bacterial groups in sedimentary samples were mainly related to the environmental parameters such as grain size and N,while the dominant bacterial groups of water samples were closely related to sampling depth.The results of correlation test showed thatα-diversity indexes of sedimentary samples had significant correlations with C,while bothα-diversity indexes andβ-diversity distance matrix of water samples showed significant correlations with sampling depth.In addition,geographical distance and depth of the seabed were not detected to have a significant effect onβ-diversity,which may be due to the insufficient space scale of sampling.
Bacterial communities play a vital role in marine biogeochemical processes.Revealing the effects of geographical distance and environmental conditions on bacterial communities is important for better understanding how environmental changes can drive microbial diversity and maintain their functions.In this study,the diversity and spatial distribution of bacterial communities in water and surface sediments of northern South China Sea were analyzed through high-throughput sequencing of bacteria 16 SrDNA,and the effects of environmental factors,geographical restrictions and seabed depth on microbial communities were examined.The results showed that about 95%of bacterial 16 SrDNA sequences belonged to the dominant phyla/classes Gamma-proteobacteria,Firmicutes,Cyanobacteria,Alpha-proteobacteria,etc.The dominant bacterial groups in sedimentary samples were mainly related to the environmental parameters such as grain size and N,while the dominant bacterial groups of water samples were closely related to sampling depth.The results of correlation test showed thatα-diversity indexes of sedimentary samples had significant correlations with C,while bothα-diversity indexes andβ-diversity distance matrix of water samples showed significant correlations with sampling depth.In addition,geographical distance and depth of the seabed were not detected to have a significant effect onβ-diversity,which may be due to the insufficient space scale of sampling.
引文
[1] SOGIN M L,MORRISON H G,HUBER J A,et al.Microbial diversity in the deep sea and the underexplored"rare biosphere"[J].Proceedings of the National Academy of Sciences of the United States of America,2006,103(32):12115-12120.
[2] FALKOWSKI P G,FENCHEL T,DELONG E F.The microbial engines that drive earth's biogeochemical cycle[J].Science,2008,320:1034-1039.
[3] WU C H,SERCU B,DE WERFHORST L C,et al.Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators[J].PLoS One,2010,5(6):e11285.
[4] ZHANG R,LAU S C K,KI J S,et al.Response of bacterioplankton community structures to hydrological conditions and anthropogenic pollution in contrasting subtropical environments[J].FEMS Microbiology Ecology,2009,69(3):449-460.
[5] MARTINY J B,BOHANNAN B J,BROWN J H,et al.Microbial biogeography:putting microorganisms on the map[J].Nature Reviews Microbiology,2006,4(2):102-112.
[6] MARTINY J B,EISEN J A,PENN K,et al.Drivers of bacterial beta-diversity depend on spatial scale[J].Proceedings of the National Academy of Sciences of the United States of America,2011,108(19):7850-7854.
[7] DER GAST C.Microbial biogeography and what Baas Becking should have said[J].Microbiology Today,2013,40(3):109-111.
[8] PAERL H W,DYBLE J,MOISANDER P H,et al.Microbial indicators of aquatic ecosystem change:current applications to eutrophication studies[J].FEMS Microbiology Ecology,2003,46(3):233-246.
[9] FODELIANAKIS S,MOUSTAKAS A,PAPAGEORGIOU N,et al.Modified niche optima and breadths explain the historical contingency of bacterial community responses to eutrophication in coastal sediments[J].Molecular Ecology,2017,26(7):2006-2018.
[10] WANG K,YE X,ZHANG H,et al.Regional variations in the diversity and predicted metabolic potential of benthic prokaryotes in coastal northern Zhejiang,East China Sea[J].Scientific Reports,2016(6):38709.
[11] HU J,KAWAMURA H,HONG H,et al.A review on the currents in the South China Sea:seasonal circulation,South China Sea warm current and Kuroshio intrusion[J].Journal of Oceanography,2000,56(6):607-624.
[12] YIN K,QIAN P,WU M C S,et al.Shift from P to N limitation of phytoplankton growth across the Pearl River estuarine plume during summer[J].Marine Ecology Progress Series,2001,221:17-28.
[13] LI J,LI N,LI F,et al.Spatial diversity of bacterioplankton communities in surface water of northern South China Sea[J].PLoS One,2014,9(11):e113014.
[14] National Center of Ocean Standards and Metrology.Specifications for Oceanographic Survey:part 4 Survey of chemical parameters in sea water:GB 12763.4—2007[S].Beijing:Standards Press of China,2007.国家海洋标准计量中心.海洋调查规范:第4部分海水化学要素调查:GB 12763.4—2007[S].北京:中国标准化出版社,2007.
[15] National Center of Ocean Standards and Metrology.Specifictions for oceanographic survey:part 5 Survey of acoustical and optial parameters in the sea:GB/T12763.5—2007[S].Beijing:Standards Press of China,2007.国家海洋标准计量中心.海洋调查规范:第5部分海洋声、光要素调查:GB/T 12763.5—2007[S].北京:中国标准化出版社,2007.
[16] CAPORASO J G,KUCZYNSKI J,STOMBAUGH J,et al.QIIME allows analysis of high-throughput community sequencing data[J].Nature Methods,2010,7(5):335-336.
[17] EDGAR R C,HAAS B J,CLEMENTE J C,et al.UCHIME improves sensitivity and speed of chimera detection[J].Bioinformatics,2011,27(16):2194-2200.
[18] EDGAR R C.Search and clustering orders of magnitude faster than BLAST[J].Bioinformatics,2010,26(19):2460-2461.
[19] CAPORASO J G,BITTINGER K,BUSHMAN F D,et al.PyNAST:a flexible tool for aligning sequences to a template alignment[J].Bioinformatics,2010,26(2):266-267.
[20] PRICE M N,DEHAL P S,ARKIN A P.FastTree 2-approximately maximum-likelihood trees for large alignments[J].Plos One,2010,5(3):e9490.
[21] DESANTIS T Z,HUGENHOLTZ P,LARSEN N,et al.Greengenes,a chimera-checked 16SrRNA gene database and workbench compatible with ARB[J].Applied and Environmental Microbiology,2006,72(7):5069-5072.
[22] BOKULICH N A,SUBRAMANIAN S,FAITH J J,et al.Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing[J].Nature Methods,2013,10(1):57-59.
[23] R Development Core Team.R:A language and environment for statistical computing[M].Vienna:R Foundation for Statistical Computing,2008.
[24] SEGATA N,IZARD J,WALDRON L,et al.Metagenomic biomarker discovery and explanation[J].Genome Biology,2011,12(6):18.
[25] LEGENDRE P,LEGENDRE L F.Numerical ecology[M].Amsterdam:Elsevier,2012.
[26] MUYZER G,STAMS A J M.The ecology and biotechnology of sulphate-reducing bacteria[J].Nature Reviews Microbiology,2008,6(6):441-454.
[27] KUEVER J.The family Desulfobacteraceae[M]∥ROSENBERG E,DELONG E F,LORY S,et al.The Prokaryotes:Deltaproteobacteria and Epsilonproteobacteria.Berlin:Springer Berlin Heidelberg,2014:45-73.
[28] KUEVER J.The family Desulfobulbaceae[M]∥ROSENBERG E,DELONG E F,LORY S,et al.The Prokaryotes:Deltaproteobacteria and Epsilonproteobacteria.Berlin:Springer Berlin Heidelberg,2014:75-86.
[29] LCKER S,DAIMS H.The family Nitrospinaceae[M]∥ROSENBERG E,DELONG E F,LORY S,et al.The Prokaryotes:Deltaproteobacteria and Epsilonproteobacteria.Berlin:Springer Berlin Heidelberg,2014:231-237.
[30] GARRITY G M,HOLT J G,SPIECK E,et al.Phylum BVIII.Nitrospirae phy.Nov[M]∥BOONE D R,CASTENHOLZ R W,GARRITY G M.Bergey’s Manual? of Systematic Bacteriology:Volume One-the archaea and the deeply branching and phototrophic bacteria.New York:Springer,2001:451-464.
[31] BALDANI J I,VIDEIRA S S,DOS SANTOS TEIXEIRA K R,et al.The family Rhodospirillaceae[M]∥ROSENBERG E,DELONG E F,LORY S,et al.The Prokaryotes:Alphaproteobacteria and Betaproteobacteria.Berlin:Springer Berlin Heidelberg,2014:533-618.
[32] DONG Z,WANG K,CHEN X,et al.Temporal dynamics of bacterioplankton communities in response to excessive nitrate loading in oligotrophic coastal water[J].Marine Pollution Bulletin,2016,114(2):656-663.
[33] BALDI F,MARCHETTO D,PINI F,et al.Biochemical and microbial features of shallow marine sediments along the Terra Nova Bay(Ross Sea,Antarctica)[J].Continental Shelf Research,2010,30(15):1614-1625.
[34] CHEN X X,WANG K,GUO A N,et al.Excess phosphate loading shifts bacterioplankton community composition in oligotrophic coastal water microcosms over time[J].Journal of Experimental Marine Biology and Ecology,2016,483:139-146.
[35] SONG H,LI Z,DU B,et al.Bacterial communities in sediments of the shallow Lake Dongping in China[J].Journal of Applied Microbiology,2012,112(1):79-89.
[36] WILLIAMS T J,WILKINS D,LONG E,et al.The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics[J].Environmental Microbiology,2013,15(5):1302-1317.
[37] MANDIC-MULEC I,STEFANIC P,VAN ELSAS J D.Ecology of Bacillaceae[J].Microbiology Spectrum,2015,3(2):TBS-0017-2013.
[38] HOLLEY R A.Brochothrix[M]∥TORTORELLO M L.Encyclopedia of Food Microbiology(Second Edition).Oxford:Academic Press,2014:331-334.
[39] WANG H,WANG B,DONG W W,et al.Co-acclimation of bacterial communities under stresses of hydrocarbons with different structures[J].Scientific Reports,2016(6):34588.
[40] LIU J W,FU B,YANG H,et al.Phylogenetic shifts of bacterioplankton community composition along the Pearl Estuary:the potential impact of hypoxia and nutrients[J].Frontiers in Microbiology,2015(6):64.
[41] DUNGAN J L,PERRY J N,DALE M R T,et al.A balanced view of scale in spatial statistical analysis[J].Ecography,2002,25(5):626-640.
[2] FALKOWSKI P G,FENCHEL T,DELONG E F.The microbial engines that drive earth's biogeochemical cycle[J].Science,2008,320:1034-1039.
[3] WU C H,SERCU B,DE WERFHORST L C,et al.Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators[J].PLoS One,2010,5(6):e11285.
[4] ZHANG R,LAU S C K,KI J S,et al.Response of bacterioplankton community structures to hydrological conditions and anthropogenic pollution in contrasting subtropical environments[J].FEMS Microbiology Ecology,2009,69(3):449-460.
[5] MARTINY J B,BOHANNAN B J,BROWN J H,et al.Microbial biogeography:putting microorganisms on the map[J].Nature Reviews Microbiology,2006,4(2):102-112.
[6] MARTINY J B,EISEN J A,PENN K,et al.Drivers of bacterial beta-diversity depend on spatial scale[J].Proceedings of the National Academy of Sciences of the United States of America,2011,108(19):7850-7854.
[7] DER GAST C.Microbial biogeography and what Baas Becking should have said[J].Microbiology Today,2013,40(3):109-111.
[8] PAERL H W,DYBLE J,MOISANDER P H,et al.Microbial indicators of aquatic ecosystem change:current applications to eutrophication studies[J].FEMS Microbiology Ecology,2003,46(3):233-246.
[9] FODELIANAKIS S,MOUSTAKAS A,PAPAGEORGIOU N,et al.Modified niche optima and breadths explain the historical contingency of bacterial community responses to eutrophication in coastal sediments[J].Molecular Ecology,2017,26(7):2006-2018.
[10] WANG K,YE X,ZHANG H,et al.Regional variations in the diversity and predicted metabolic potential of benthic prokaryotes in coastal northern Zhejiang,East China Sea[J].Scientific Reports,2016(6):38709.
[11] HU J,KAWAMURA H,HONG H,et al.A review on the currents in the South China Sea:seasonal circulation,South China Sea warm current and Kuroshio intrusion[J].Journal of Oceanography,2000,56(6):607-624.
[12] YIN K,QIAN P,WU M C S,et al.Shift from P to N limitation of phytoplankton growth across the Pearl River estuarine plume during summer[J].Marine Ecology Progress Series,2001,221:17-28.
[13] LI J,LI N,LI F,et al.Spatial diversity of bacterioplankton communities in surface water of northern South China Sea[J].PLoS One,2014,9(11):e113014.
[14] National Center of Ocean Standards and Metrology.Specifications for Oceanographic Survey:part 4 Survey of chemical parameters in sea water:GB 12763.4—2007[S].Beijing:Standards Press of China,2007.国家海洋标准计量中心.海洋调查规范:第4部分海水化学要素调查:GB 12763.4—2007[S].北京:中国标准化出版社,2007.
[15] National Center of Ocean Standards and Metrology.Specifictions for oceanographic survey:part 5 Survey of acoustical and optial parameters in the sea:GB/T12763.5—2007[S].Beijing:Standards Press of China,2007.国家海洋标准计量中心.海洋调查规范:第5部分海洋声、光要素调查:GB/T 12763.5—2007[S].北京:中国标准化出版社,2007.
[16] CAPORASO J G,KUCZYNSKI J,STOMBAUGH J,et al.QIIME allows analysis of high-throughput community sequencing data[J].Nature Methods,2010,7(5):335-336.
[17] EDGAR R C,HAAS B J,CLEMENTE J C,et al.UCHIME improves sensitivity and speed of chimera detection[J].Bioinformatics,2011,27(16):2194-2200.
[18] EDGAR R C.Search and clustering orders of magnitude faster than BLAST[J].Bioinformatics,2010,26(19):2460-2461.
[19] CAPORASO J G,BITTINGER K,BUSHMAN F D,et al.PyNAST:a flexible tool for aligning sequences to a template alignment[J].Bioinformatics,2010,26(2):266-267.
[20] PRICE M N,DEHAL P S,ARKIN A P.FastTree 2-approximately maximum-likelihood trees for large alignments[J].Plos One,2010,5(3):e9490.
[21] DESANTIS T Z,HUGENHOLTZ P,LARSEN N,et al.Greengenes,a chimera-checked 16SrRNA gene database and workbench compatible with ARB[J].Applied and Environmental Microbiology,2006,72(7):5069-5072.
[22] BOKULICH N A,SUBRAMANIAN S,FAITH J J,et al.Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing[J].Nature Methods,2013,10(1):57-59.
[23] R Development Core Team.R:A language and environment for statistical computing[M].Vienna:R Foundation for Statistical Computing,2008.
[24] SEGATA N,IZARD J,WALDRON L,et al.Metagenomic biomarker discovery and explanation[J].Genome Biology,2011,12(6):18.
[25] LEGENDRE P,LEGENDRE L F.Numerical ecology[M].Amsterdam:Elsevier,2012.
[26] MUYZER G,STAMS A J M.The ecology and biotechnology of sulphate-reducing bacteria[J].Nature Reviews Microbiology,2008,6(6):441-454.
[27] KUEVER J.The family Desulfobacteraceae[M]∥ROSENBERG E,DELONG E F,LORY S,et al.The Prokaryotes:Deltaproteobacteria and Epsilonproteobacteria.Berlin:Springer Berlin Heidelberg,2014:45-73.
[28] KUEVER J.The family Desulfobulbaceae[M]∥ROSENBERG E,DELONG E F,LORY S,et al.The Prokaryotes:Deltaproteobacteria and Epsilonproteobacteria.Berlin:Springer Berlin Heidelberg,2014:75-86.
[29] LCKER S,DAIMS H.The family Nitrospinaceae[M]∥ROSENBERG E,DELONG E F,LORY S,et al.The Prokaryotes:Deltaproteobacteria and Epsilonproteobacteria.Berlin:Springer Berlin Heidelberg,2014:231-237.
[30] GARRITY G M,HOLT J G,SPIECK E,et al.Phylum BVIII.Nitrospirae phy.Nov[M]∥BOONE D R,CASTENHOLZ R W,GARRITY G M.Bergey’s Manual? of Systematic Bacteriology:Volume One-the archaea and the deeply branching and phototrophic bacteria.New York:Springer,2001:451-464.
[31] BALDANI J I,VIDEIRA S S,DOS SANTOS TEIXEIRA K R,et al.The family Rhodospirillaceae[M]∥ROSENBERG E,DELONG E F,LORY S,et al.The Prokaryotes:Alphaproteobacteria and Betaproteobacteria.Berlin:Springer Berlin Heidelberg,2014:533-618.
[32] DONG Z,WANG K,CHEN X,et al.Temporal dynamics of bacterioplankton communities in response to excessive nitrate loading in oligotrophic coastal water[J].Marine Pollution Bulletin,2016,114(2):656-663.
[33] BALDI F,MARCHETTO D,PINI F,et al.Biochemical and microbial features of shallow marine sediments along the Terra Nova Bay(Ross Sea,Antarctica)[J].Continental Shelf Research,2010,30(15):1614-1625.
[34] CHEN X X,WANG K,GUO A N,et al.Excess phosphate loading shifts bacterioplankton community composition in oligotrophic coastal water microcosms over time[J].Journal of Experimental Marine Biology and Ecology,2016,483:139-146.
[35] SONG H,LI Z,DU B,et al.Bacterial communities in sediments of the shallow Lake Dongping in China[J].Journal of Applied Microbiology,2012,112(1):79-89.
[36] WILLIAMS T J,WILKINS D,LONG E,et al.The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics[J].Environmental Microbiology,2013,15(5):1302-1317.
[37] MANDIC-MULEC I,STEFANIC P,VAN ELSAS J D.Ecology of Bacillaceae[J].Microbiology Spectrum,2015,3(2):TBS-0017-2013.
[38] HOLLEY R A.Brochothrix[M]∥TORTORELLO M L.Encyclopedia of Food Microbiology(Second Edition).Oxford:Academic Press,2014:331-334.
[39] WANG H,WANG B,DONG W W,et al.Co-acclimation of bacterial communities under stresses of hydrocarbons with different structures[J].Scientific Reports,2016(6):34588.
[40] LIU J W,FU B,YANG H,et al.Phylogenetic shifts of bacterioplankton community composition along the Pearl Estuary:the potential impact of hypoxia and nutrients[J].Frontiers in Microbiology,2015(6):64.
[41] DUNGAN J L,PERRY J N,DALE M R T,et al.A balanced view of scale in spatial statistical analysis[J].Ecography,2002,25(5):626-640.