Elevational patterns of abundant and rare bacterial diversity and composition in mountain streams in the southeast of the Tibetan Plateau
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摘要
Elevational gradients are powerful ‘natural laboratory' for testing the responses of microbes to geophysical influences. Microbial communities are normally composed of a few abundant and many rare taxa. Abundant and rare taxa play different ecological roles in kinds of environments, but how their diversity and composition patterns response to elevation gradients is still poorly elucidated. In this study, we investigated the elevational patterns of abundant and rare bacterial diversity and composition in a mountain stream from 712 to 3435 m at Gangrigabu Mountain on the Tibetan Plateau, China. Our results revealed abundant and rare bacteria had similar decreasing elevation trend of alpha diversity, and both of them showed a significant elevational distance-decay relationship. However, the turnover rate of the elevational distance-decay of rare bacteria was higher than that of abundant bacteria. The species-abundance distribution patterns of rare taxonomic composition were associated with the elevational gradient, while most of abundant bacterial clades did not display any relationships with elevation.Our results suggested that rare bacteria were more sensitive to changes in elevation gradient.
Elevational gradients are powerful ‘natural laboratory' for testing the responses of microbes to geophysical influences. Microbial communities are normally composed of a few abundant and many rare taxa. Abundant and rare taxa play different ecological roles in kinds of environments, but how their diversity and composition patterns response to elevation gradients is still poorly elucidated. In this study, we investigated the elevational patterns of abundant and rare bacterial diversity and composition in a mountain stream from 712 to 3435 m at Gangrigabu Mountain on the Tibetan Plateau, China. Our results revealed abundant and rare bacteria had similar decreasing elevation trend of alpha diversity, and both of them showed a significant elevational distance-decay relationship. However, the turnover rate of the elevational distance-decay of rare bacteria was higher than that of abundant bacteria. The species-abundance distribution patterns of rare taxonomic composition were associated with the elevational gradient, while most of abundant bacterial clades did not display any relationships with elevation.Our results suggested that rare bacteria were more sensitive to changes in elevation gradient.
Elevational gradients are powerful ‘natural laboratory' for testing the responses of microbes to geophysical influences. Microbial communities are normally composed of a few abundant and many rare taxa. Abundant and rare taxa play different ecological roles in kinds of environments, but how their diversity and composition patterns response to elevation gradients is still poorly elucidated. In this study, we investigated the elevational patterns of abundant and rare bacterial diversity and composition in a mountain stream from 712 to 3435 m at Gangrigabu Mountain on the Tibetan Plateau, China. Our results revealed abundant and rare bacteria had similar decreasing elevation trend of alpha diversity, and both of them showed a significant elevational distance-decay relationship. However, the turnover rate of the elevational distance-decay of rare bacteria was higher than that of abundant bacteria. The species-abundance distribution patterns of rare taxonomic composition were associated with the elevational gradient, while most of abundant bacterial clades did not display any relationships with elevation.Our results suggested that rare bacteria were more sensitive to changes in elevation gradient.
引文
Antwis R E,Griffiths S M,Harrison X A,Aranega-Bou P,Arce A,Bettridge A S,Brailsford F L,de Menezes A,Devaynes A,Forbes K M,Fry E L,Goodhead I,Haskell E,Heys C,James C,Johnston S R,Lewis G R,Lewis Z,Macey M C,McCarthy A,McDonald J E,Mejia-Florez N L,O'Brien D,Orland C,Pautasso M,Reid W D K,Robinson H A,Wilson K,Sutherland W J.2017.Fifty important research questions in microbial ecology.FEMS Microbiol Ecol,93:1-10
Bryant J A,Lamanna C,Morlon H,Kerkhoff A J,Enquist B J,Green J L.2008.Microbes on mountainsides:Contrasting elevational patterns of bacterial and plant diversity.Proc Natl Acad Sci USA,105:11505-11511
Caporaso J G,Kuczynski J,Stombaugh J,Bittinger K,Bushman F D,Costello E K,Fierer N,Pe?a A G,Goodrich J K,Gordon J I,Huttley GA,Kelley S T,Knights D,Koenig J E,Ley R E,Lozupone C A,McDonald D,Muegge B D,Pirrung M,Reeder J,Sevinsky J R,Turnbaugh P J,Walters W A,Widmann J,Yatsunenko T,Zaneveld J,Knight R.2010.QIIME allows analysis of high-throughput community sequencing data.Nat Methods,7:335-336
Caporaso J G,Lauber C L,Walters W A,Berg-Lyons D,Huntley J,Fierer N,Owens S M,Betley J,Fraser L,Bauer M,Gormley N,Gilbert J A,Smith G,Knight R.2012.Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms.ISME J,6:1621-1624
Chao A.1984.Nonparametric estimation of the number of classes in a population.Scand J Stat,11:265-270
Chu H,Sun H,Tripathi B M,Adams J M,Huang R,Zhang Y,Shi Y.2016.Bacterial community dissimilarity between the surface and subsurface soils equals horizontal differences over several kilometers in the western Tibetan Plateau.Environ Microbiol,18:1523-1533
DeSantis T Z,Hugenholtz P,Larsen N,Rojas M,Brodie E L,Keller K,Huber T,Dalevi D,Hu P,Andersen G L.2006.Greengenes,a chimerachecked 16S rRNA gene database and workbench compatible with ARB.Appl Environ Microbiol,72:5069-5072
Dray S,Blanchet G,Borcard D,Guenard G,Jombart T,Legendre P,Wagner H.2017.adespatial:Multivariate multiscale spatial analysis.Rpackage version 00-8 Retrieved from https://CRAN R-project org/package=adespatial
Edgar R C.2010.Search and clustering orders of magnitude faster than BLAST.Bioinformatics,26:2460-2461
Faith D P.1992.Conservation evaluation and phylogenetic diversity.Biol Conservation,61:1-10
Galand P E,Casamayor E O,Kirchman D L,Lovejoy C.2009.Ecology of the rare microbial biosphere of the Arctic Ocean.Proc Natl Acad Sci USA,106:22427-22432
Gibbons S M,Caporaso J G,Pirrung M,Field D,Knight R,Gilbert J A.2013.Evidence for a persistent microbial seed bank throughout the global ocean.Proc Natl Acad Sci USA,110:4651-4655
Gobet A,Quince C,Ramette A.2010.Multivariate Cutoff Level Analysis(MultiCoLA)of large community data sets.Nucleic Acids Res,38:e155
Greenberg Arnold E,Clesceri Lenore S.1992.Standard Methods for the Examination of Water and Wastewater.USA:American Public Health Association
Hayden C J,Beman J M.2016.Microbial diversity and community structure along a lake elevation gradient in Yosemite National Park,California,USA.Environ Microbiol,18:1782-1791
Jones S E,Lennon J T.2010.Dormancy contributes to the maintenance of microbial diversity.Proc Natl Acad Sci USA,107:5881-5886
Kembel S W,Cowan P D,Helmus M R,Cornwell W K,Morlon H,Ackerly D D,Blomberg S P,Webb C O.2010.Picante:R tools for integrating phylogenies and ecology.Bioinformatics,26:1463-1464
Lear G,Washington V,Neale M,Case B,Buckley H,Lewis G.2013.The biogeography of stream bacteria.Glob Ecol Biogeogr,22:544-554
Legendre P,De Cáceres M.2013.Beta diversity as the variance of community data:Dissimilarity coefficients and partitioning.Ecol Lett,16:951-963
Li H,Zeng J,Ren L,Wang J,Xing P,Wu Q L.2017.Contrasting patterns of diversity of abundant and rare bacterioplankton in freshwater lakes along an elevation gradient.Limnol Oceanogr,62:1570-1585
Liao J,Cao X,Wang J,Zhao L,Sun J,Jiang D,Huang Y.2017.Similar community assembly mechanisms underlie similar biogeography of rare and abundant bacteria in lakes on Yungui Plateau,China.Limnol Oceanogr,62:723-735
Liu L,Yang J,Yu Z,Wilkinson D M.2015.The biogeography of abundant and rare bacterioplankton in the lakes and reservoirs of China.ISME J,9:2068-2077
Liu Y,Priscu J C,Yao T,Vick-Majors T J,Michaud A B,Jiao N,Hou J,Tian L,Hu A,Chen Z Q.2014.A comparison of pelagic,littoral,and riverine bacterial assemblages in Lake Bangongco,Tibetan Plateau.FEMS Microbiol Ecol,89:211-221
Logares R,Audic S,Bass D,Bittner L,Boutte C,Christen R,Claverie J M,Decelle J,Dolan J R,Dunthorn M,Edvardsen B,Gobet A,Kooistra WH C F,MahéF,Not F,Ogata H,Pawlowski J,Pernice M C,Romac S,Shalchian-Tabrizi K,Simon N,Stoeck T,Santini S,Siano R,Wincker P,Zingone A,Richards T A,de Vargas C,Massana R.2014.Patterns of rare and abundant marine microbial eukaryotes.Curr Biol,24:813-821
Logares R,Lindstr?m E S,Langenheder S,Logue J B,Paterson H,Laybourn-Parry J,Rengefors K,Tranvik L,Bertilsson S.2013.Biogeography of bacterial communities exposed to progressive long-term environmental change.ISME J,7:937-948
Mago?T,Salzberg S L.2011.FLASH:Fast length adjustment of short reads to improve genome assemblies.Bioinformatics,27:2957-2963
Mason C H,Perreault Jr W D.1991.Collinearity,power,and interpretation of multiple regression analysis.J Marketing Res,28:268-280
McArdle B H,Anderson M J.2001.Fitting multivariate models to community data:A comment on distance-based redundancy analysis.Ecology,82:290-297
Pedrós-AlióC.2006.Marine microbial diversity:Can it be determined?Trends MicroBiol,14:257-263
Pedrós-AlióC.2012.The rare bacterial biosphere.Annu Rev Mar Sci,4:449-466
Shen C,Ni Y,Liang W,Wang J,Chu H.2015.Distinct soil bacterial communities along a small-scale elevational gradient in alpine tundra.Front Microbiol,6:582
Sogin M L,Morrison H G,Huber J A,Mark Welch D,Huse S M,Neal P R,Arrieta J M,Herndl G J.2006.Microbial diversity in the deep sea and the underexplored“rare biosphere”.Proc Natl Acad Sci USA,103:12115-12120
Sutherland W J,Freckleton R P,Godfray H C J,Beissinger S R,Benton T,Cameron D D,Carmel Y,Coomes D A,Coulson T,Emmerson M C.2013.Identification of 100 fundamental ecological questions.J Ecol,101:58-67
R Core Team.2014.R:A language and environment for statistical computing.Vienna,Austria:R Foundation for Statistical Computing,2013
Wang J,Meier S,Soininen J,Casamayor E O,Pan F,Tang X,Yang X,Zhang Y,Wu Q,Zhou J,Shen J.2017.Regional and global elevational patterns of microbial species richness and evenness.Ecography,40:393-402
Wang J,Soininen J,He J,Shen J.2012.Phylogenetic clustering increases with elevation for microbes.Environ Microbiol Rep,4:217-226
Wang J,Soininen J,Zhang Y,Wang B,Yang X,Shen J.2011.Contrasting patterns in elevational diversity between microorganisms and macroorganisms.J Biogeogr,38:595-603
Wilhelm L,Singer G A,Fasching C,Battin T J,Besemer K.2013.Microbial biodiversity in glacier-fed streams.ISME J,7:1651-1660
Xiong J,Chen H,Hu C,Ye X,Kong D,Zhang D.2015.Evidence of bacterioplankton community adaptation in response to long-term mariculture disturbance.Sci Rep,5:15274
Xiong J,Xiong S,Qian P,Zhang D,Liu L,Fei Y.2016.Thermal discharge-created increasing temperatures alter the bacterioplankton composition and functional redundancy.AMB Expr,6:68
Yang J,Jiang H,Wu G,Liu W,Zhang G.2016.Distinct factors shape aquatic and sedimentary microbial community structures in the lakes of western china.Front Microbiol,7:1782
Zeng J,Zhao D,Li H,Huang R,Wang J,Wu Q L.2016.A monotonically declining elevational pattern of bacterial diversity in freshwater lake sediments.Environ Microbiol,18:5175-5186
Bryant J A,Lamanna C,Morlon H,Kerkhoff A J,Enquist B J,Green J L.2008.Microbes on mountainsides:Contrasting elevational patterns of bacterial and plant diversity.Proc Natl Acad Sci USA,105:11505-11511
Caporaso J G,Kuczynski J,Stombaugh J,Bittinger K,Bushman F D,Costello E K,Fierer N,Pe?a A G,Goodrich J K,Gordon J I,Huttley GA,Kelley S T,Knights D,Koenig J E,Ley R E,Lozupone C A,McDonald D,Muegge B D,Pirrung M,Reeder J,Sevinsky J R,Turnbaugh P J,Walters W A,Widmann J,Yatsunenko T,Zaneveld J,Knight R.2010.QIIME allows analysis of high-throughput community sequencing data.Nat Methods,7:335-336
Caporaso J G,Lauber C L,Walters W A,Berg-Lyons D,Huntley J,Fierer N,Owens S M,Betley J,Fraser L,Bauer M,Gormley N,Gilbert J A,Smith G,Knight R.2012.Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms.ISME J,6:1621-1624
Chao A.1984.Nonparametric estimation of the number of classes in a population.Scand J Stat,11:265-270
Chu H,Sun H,Tripathi B M,Adams J M,Huang R,Zhang Y,Shi Y.2016.Bacterial community dissimilarity between the surface and subsurface soils equals horizontal differences over several kilometers in the western Tibetan Plateau.Environ Microbiol,18:1523-1533
DeSantis T Z,Hugenholtz P,Larsen N,Rojas M,Brodie E L,Keller K,Huber T,Dalevi D,Hu P,Andersen G L.2006.Greengenes,a chimerachecked 16S rRNA gene database and workbench compatible with ARB.Appl Environ Microbiol,72:5069-5072
Dray S,Blanchet G,Borcard D,Guenard G,Jombart T,Legendre P,Wagner H.2017.adespatial:Multivariate multiscale spatial analysis.Rpackage version 00-8 Retrieved from https://CRAN R-project org/package=adespatial
Edgar R C.2010.Search and clustering orders of magnitude faster than BLAST.Bioinformatics,26:2460-2461
Faith D P.1992.Conservation evaluation and phylogenetic diversity.Biol Conservation,61:1-10
Galand P E,Casamayor E O,Kirchman D L,Lovejoy C.2009.Ecology of the rare microbial biosphere of the Arctic Ocean.Proc Natl Acad Sci USA,106:22427-22432
Gibbons S M,Caporaso J G,Pirrung M,Field D,Knight R,Gilbert J A.2013.Evidence for a persistent microbial seed bank throughout the global ocean.Proc Natl Acad Sci USA,110:4651-4655
Gobet A,Quince C,Ramette A.2010.Multivariate Cutoff Level Analysis(MultiCoLA)of large community data sets.Nucleic Acids Res,38:e155
Greenberg Arnold E,Clesceri Lenore S.1992.Standard Methods for the Examination of Water and Wastewater.USA:American Public Health Association
Hayden C J,Beman J M.2016.Microbial diversity and community structure along a lake elevation gradient in Yosemite National Park,California,USA.Environ Microbiol,18:1782-1791
Jones S E,Lennon J T.2010.Dormancy contributes to the maintenance of microbial diversity.Proc Natl Acad Sci USA,107:5881-5886
Kembel S W,Cowan P D,Helmus M R,Cornwell W K,Morlon H,Ackerly D D,Blomberg S P,Webb C O.2010.Picante:R tools for integrating phylogenies and ecology.Bioinformatics,26:1463-1464
Lear G,Washington V,Neale M,Case B,Buckley H,Lewis G.2013.The biogeography of stream bacteria.Glob Ecol Biogeogr,22:544-554
Legendre P,De Cáceres M.2013.Beta diversity as the variance of community data:Dissimilarity coefficients and partitioning.Ecol Lett,16:951-963
Li H,Zeng J,Ren L,Wang J,Xing P,Wu Q L.2017.Contrasting patterns of diversity of abundant and rare bacterioplankton in freshwater lakes along an elevation gradient.Limnol Oceanogr,62:1570-1585
Liao J,Cao X,Wang J,Zhao L,Sun J,Jiang D,Huang Y.2017.Similar community assembly mechanisms underlie similar biogeography of rare and abundant bacteria in lakes on Yungui Plateau,China.Limnol Oceanogr,62:723-735
Liu L,Yang J,Yu Z,Wilkinson D M.2015.The biogeography of abundant and rare bacterioplankton in the lakes and reservoirs of China.ISME J,9:2068-2077
Liu Y,Priscu J C,Yao T,Vick-Majors T J,Michaud A B,Jiao N,Hou J,Tian L,Hu A,Chen Z Q.2014.A comparison of pelagic,littoral,and riverine bacterial assemblages in Lake Bangongco,Tibetan Plateau.FEMS Microbiol Ecol,89:211-221
Logares R,Audic S,Bass D,Bittner L,Boutte C,Christen R,Claverie J M,Decelle J,Dolan J R,Dunthorn M,Edvardsen B,Gobet A,Kooistra WH C F,MahéF,Not F,Ogata H,Pawlowski J,Pernice M C,Romac S,Shalchian-Tabrizi K,Simon N,Stoeck T,Santini S,Siano R,Wincker P,Zingone A,Richards T A,de Vargas C,Massana R.2014.Patterns of rare and abundant marine microbial eukaryotes.Curr Biol,24:813-821
Logares R,Lindstr?m E S,Langenheder S,Logue J B,Paterson H,Laybourn-Parry J,Rengefors K,Tranvik L,Bertilsson S.2013.Biogeography of bacterial communities exposed to progressive long-term environmental change.ISME J,7:937-948
Mago?T,Salzberg S L.2011.FLASH:Fast length adjustment of short reads to improve genome assemblies.Bioinformatics,27:2957-2963
Mason C H,Perreault Jr W D.1991.Collinearity,power,and interpretation of multiple regression analysis.J Marketing Res,28:268-280
McArdle B H,Anderson M J.2001.Fitting multivariate models to community data:A comment on distance-based redundancy analysis.Ecology,82:290-297
Pedrós-AlióC.2006.Marine microbial diversity:Can it be determined?Trends MicroBiol,14:257-263
Pedrós-AlióC.2012.The rare bacterial biosphere.Annu Rev Mar Sci,4:449-466
Shen C,Ni Y,Liang W,Wang J,Chu H.2015.Distinct soil bacterial communities along a small-scale elevational gradient in alpine tundra.Front Microbiol,6:582
Sogin M L,Morrison H G,Huber J A,Mark Welch D,Huse S M,Neal P R,Arrieta J M,Herndl G J.2006.Microbial diversity in the deep sea and the underexplored“rare biosphere”.Proc Natl Acad Sci USA,103:12115-12120
Sutherland W J,Freckleton R P,Godfray H C J,Beissinger S R,Benton T,Cameron D D,Carmel Y,Coomes D A,Coulson T,Emmerson M C.2013.Identification of 100 fundamental ecological questions.J Ecol,101:58-67
R Core Team.2014.R:A language and environment for statistical computing.Vienna,Austria:R Foundation for Statistical Computing,2013
Wang J,Meier S,Soininen J,Casamayor E O,Pan F,Tang X,Yang X,Zhang Y,Wu Q,Zhou J,Shen J.2017.Regional and global elevational patterns of microbial species richness and evenness.Ecography,40:393-402
Wang J,Soininen J,He J,Shen J.2012.Phylogenetic clustering increases with elevation for microbes.Environ Microbiol Rep,4:217-226
Wang J,Soininen J,Zhang Y,Wang B,Yang X,Shen J.2011.Contrasting patterns in elevational diversity between microorganisms and macroorganisms.J Biogeogr,38:595-603
Wilhelm L,Singer G A,Fasching C,Battin T J,Besemer K.2013.Microbial biodiversity in glacier-fed streams.ISME J,7:1651-1660
Xiong J,Chen H,Hu C,Ye X,Kong D,Zhang D.2015.Evidence of bacterioplankton community adaptation in response to long-term mariculture disturbance.Sci Rep,5:15274
Xiong J,Xiong S,Qian P,Zhang D,Liu L,Fei Y.2016.Thermal discharge-created increasing temperatures alter the bacterioplankton composition and functional redundancy.AMB Expr,6:68
Yang J,Jiang H,Wu G,Liu W,Zhang G.2016.Distinct factors shape aquatic and sedimentary microbial community structures in the lakes of western china.Front Microbiol,7:1782
Zeng J,Zhao D,Li H,Huang R,Wang J,Wu Q L.2016.A monotonically declining elevational pattern of bacterial diversity in freshwater lake sediments.Environ Microbiol,18:5175-5186