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Volumn 91, Issue , 2015, Pages 232-247

Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by geographic features

Author keywords

16S rDNA; 16S rRNA gene sequencing; Bacterial community structure; Microbial biogeography; Soil microbiota; Soil organic matter

Indexed keywords

BACTERIA; BIOGEOCHEMISTRY; BIOLOGICAL MATERIALS; ECOLOGY; GENES; LAND USE; MICROORGANISMS; ORGANIC COMPOUNDS; RNA; SOCIAL SCIENCES; WINE;

EID: 84942510839     PISSN: 00380717     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.soilbio.2015.09.002     Document Type: Article
Times cited : (134)

References (85)
  • 2
    • 0002154022 scopus 로고    scopus 로고
    • A new method for non-parametric multivariate analysis of variance
    • Anderson M.J. A new method for non-parametric multivariate analysis of variance. Austral Ecology 2001, 26:32-46.
    • (2001) Austral Ecology , vol.26 , pp. 32-46
    • Anderson, M.J.1
  • 6
    • 84860483735 scopus 로고    scopus 로고
    • Next-generation sequencing reveals significant bacterial diversity of botrytized wine
    • Bokulich N.A., Joseph C.M., Allen G., Benson A.K., Mills D.A. Next-generation sequencing reveals significant bacterial diversity of botrytized wine. PLOS ONE 2012, 7:e36357.
    • (2012) PLOS ONE , vol.7 , pp. e36357
    • Bokulich, N.A.1    Joseph, C.M.2    Allen, G.3    Benson, A.K.4    Mills, D.A.5
  • 9
    • 0034898780 scopus 로고    scopus 로고
    • The structure of microbial communities in soil and the lasting impact of cultivation
    • Buckley D.H., Schmidt T.M. The structure of microbial communities in soil and the lasting impact of cultivation. Microbial Ecology 2001, 42:11-21.
    • (2001) Microbial Ecology , vol.42 , pp. 11-21
    • Buckley, D.H.1    Schmidt, T.M.2
  • 14
    • 33746452202 scopus 로고    scopus 로고
    • Effects of land use on soil respiration: conversion of oak woodlands to vineyards
    • Carlisle E.A., Steenwerth K.L., Smart D.R. Effects of land use on soil respiration: conversion of oak woodlands to vineyards. Journal of Environmental Quality 2006, 35:1396-1404.
    • (2006) Journal of Environmental Quality , vol.35 , pp. 1396-1404
    • Carlisle, E.A.1    Steenwerth, K.L.2    Smart, D.R.3
  • 15
    • 0001463548 scopus 로고
    • Nonparametric estimation of the number of classes in a population
    • Chao A. Nonparametric estimation of the number of classes in a population. Scandinavian Journal of Statistics 1984, 11:265-270.
    • (1984) Scandinavian Journal of Statistics , vol.11 , pp. 265-270
    • Chao, A.1
  • 16
    • 0027806622 scopus 로고
    • A method of linking multivariate community structure to environmental variables
    • Clarke K.R., Ainsworth M. A method of linking multivariate community structure to environmental variables. Marine Ecology Progress Series 1993, 92:205-219.
    • (1993) Marine Ecology Progress Series , vol.92 , pp. 205-219
    • Clarke, K.R.1    Ainsworth, M.2
  • 17
    • 77949264819 scopus 로고    scopus 로고
    • Plant growth-promoting bacteria in the rhizo- and endosphere of plants: their role, colonization, mechanisms involved and prospects for utilization
    • Compant S., Clement C., Sessitsch A. Plant growth-promoting bacteria in the rhizo- and endosphere of plants: their role, colonization, mechanisms involved and prospects for utilization. Soil Biology & Biochemistry 2010, 42:669-678.
    • (2010) Soil Biology & Biochemistry , vol.42 , pp. 669-678
    • Compant, S.1    Clement, C.2    Sessitsch, A.3
  • 18
    • 79960602562 scopus 로고    scopus 로고
    • Endophytes of grapevine flowers, berries, and seeds: identification of cultivable bacteria, comparison with other plant parts, and visualization of niches of colonization
    • Compant S., Mitter B., Colli-Mull J.G., Gangl H., Sessitsch A. Endophytes of grapevine flowers, berries, and seeds: identification of cultivable bacteria, comparison with other plant parts, and visualization of niches of colonization. Microbial Ecology 2011, 62:188-197.
    • (2011) Microbial Ecology , vol.62 , pp. 188-197
    • Compant, S.1    Mitter, B.2    Colli-Mull, J.G.3    Gangl, H.4    Sessitsch, A.5
  • 19
    • 84862644837 scopus 로고    scopus 로고
    • The 125th anniversary of the first postulation of the soil origin of endophytic bacteria - a tribute to M.L.V. Galippe
    • Compant S., Sessitsch A., Mathieu F. The 125th anniversary of the first postulation of the soil origin of endophytic bacteria - a tribute to M.L.V. Galippe. Plant and Soil 2012, 356:299-301.
    • (2012) Plant and Soil , vol.356 , pp. 299-301
    • Compant, S.1    Sessitsch, A.2    Mathieu, F.3
  • 21
    • 0030843524 scopus 로고    scopus 로고
    • Soil development along an elevational transect in the western Sierra Nevada, California
    • Dahlgren R.A., Boettinger J.L., Huntington G.L., Amundson R.G. Soil development along an elevational transect in the western Sierra Nevada, California. Geoderma 1997, 78:207-236.
    • (1997) Geoderma , vol.78 , pp. 207-236
    • Dahlgren, R.A.1    Boettinger, J.L.2    Huntington, G.L.3    Amundson, R.G.4
  • 22
    • 33644845577 scopus 로고    scopus 로고
    • 'Everything is everywhere, but, the environment selects'; what did Baas Becking and Beijerinck really say?
    • De Wit R., Bouvier T. 'Everything is everywhere, but, the environment selects'; what did Baas Becking and Beijerinck really say?. Environmental Microbiology 2006, 8:755-758.
    • (2006) Environmental Microbiology , vol.8 , pp. 755-758
    • De Wit, R.1    Bouvier, T.2
  • 25
    • 13844257500 scopus 로고    scopus 로고
    • Soil water content and organic carbon availability are major determinants of soil microbial community composition
    • Drenovsky R.E., Vo D., Graham K.J., Scow K.M. Soil water content and organic carbon availability are major determinants of soil microbial community composition. Microbial Ecology 2004, 48:424-430.
    • (2004) Microbial Ecology , vol.48 , pp. 424-430
    • Drenovsky, R.E.1    Vo, D.2    Graham, K.J.3    Scow, K.M.4
  • 26
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar R.C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26:2460-2461.
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 27
    • 0026499429 scopus 로고
    • Conservation evaluation and phylogenetic diversity
    • Faith D.P. Conservation evaluation and phylogenetic diversity. Biological Conservation 1992, 61:1-10.
    • (1992) Biological Conservation , vol.61 , pp. 1-10
    • Faith, D.P.1
  • 28
    • 66149139900 scopus 로고    scopus 로고
    • Microbial biogeography: patterns in microbial diversity across space and time
    • American Society for Microbiology, Washington, DC, USA, K. Zengler (Ed.)
    • Fierer N. Microbial biogeography: patterns in microbial diversity across space and time. Accessing Uncultivated Microorganisms: From the Environment to Organisms and Genomes and Back 2008, 95-115. American Society for Microbiology, Washington, DC, USA. K. Zengler (Ed.).
    • (2008) Accessing Uncultivated Microorganisms: From the Environment to Organisms and Genomes and Back , pp. 95-115
    • Fierer, N.1
  • 29
    • 33947236971 scopus 로고    scopus 로고
    • Toward an ecological classification of soil bacteria
    • Fierer N., Bradford M.A., Jackson R.B. Toward an ecological classification of soil bacteria. Ecology 2007, 88:1354-1364.
    • (2007) Ecology , vol.88 , pp. 1354-1364
    • Fierer, N.1    Bradford, M.A.2    Jackson, R.B.3
  • 31
    • 84859911168 scopus 로고    scopus 로고
    • Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients
    • Fierer N., Lauber C.L., Ramirez K.S., Zaneveld J., Bradford M.A., Knight R. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. The ISME Journal 2012, 6:1007-1017.
    • (2012) The ISME Journal , vol.6 , pp. 1007-1017
    • Fierer, N.1    Lauber, C.L.2    Ramirez, K.S.3    Zaneveld, J.4    Bradford, M.A.5    Knight, R.6
  • 35
    • 4744340843 scopus 로고    scopus 로고
    • Microbial diversity in soil: selection of microbial populations by plant and soil type and implications for disease suppressiveness
    • Garbeva P., van Veen J.A., van Elsas J.D. Microbial diversity in soil: selection of microbial populations by plant and soil type and implications for disease suppressiveness. Annual Review of Phytopathology 2004, 42:243-270.
    • (2004) Annual Review of Phytopathology , vol.42 , pp. 243-270
    • Garbeva, P.1    van Veen, J.A.2    van Elsas, J.D.3
  • 37
    • 52949148223 scopus 로고    scopus 로고
    • Molecular C dynamics downstream: the biochemical decomposition sequence and its impact on soil organic matter structure and function
    • Grandy A.S., Neff J.C. Molecular C dynamics downstream: the biochemical decomposition sequence and its impact on soil organic matter structure and function. Science of The Total Environment 2008, 404:297-307.
    • (2008) Science of The Total Environment , vol.404 , pp. 297-307
    • Grandy, A.S.1    Neff, J.C.2
  • 39
    • 53049086655 scopus 로고    scopus 로고
    • Properties of bacterial endophytes and their proposed role in plant growth
    • Hardoim P.R., van Overbeek L.S., van Elsas J.D. Properties of bacterial endophytes and their proposed role in plant growth. Trends in Microbiology 2008, 16:463-471.
    • (2008) Trends in Microbiology , vol.16 , pp. 463-471
    • Hardoim, P.R.1    van Overbeek, L.S.2    van Elsas, J.D.3
  • 41
    • 33845724686 scopus 로고    scopus 로고
    • Is microbial community composition in boreal forest soils determined by pH, C-to-N ratio, the trees, or all three?
    • Hogberg M.N., Hogberg P., Myrold D.D. Is microbial community composition in boreal forest soils determined by pH, C-to-N ratio, the trees, or all three?. Oecologia 2007, 150:590-601.
    • (2007) Oecologia , vol.150 , pp. 590-601
    • Hogberg, M.N.1    Hogberg, P.2    Myrold, D.D.3
  • 42
    • 84930904301 scopus 로고    scopus 로고
    • Using GRASS and R for landscape regionalization through PAM cluster analysis
    • Hollander A.D. Using GRASS and R for landscape regionalization through PAM cluster analysis. OSGeo Journal 2012, 10:26-31.
    • (2012) OSGeo Journal , vol.10 , pp. 26-31
    • Hollander, A.D.1
  • 44
    • 33646095202 scopus 로고    scopus 로고
    • Experimental evaluation of methods to quantify dissolved organic nitrogen (DON) and dissolved organic carbon (DOC) in soil
    • Jones D.L., Willett V.B. Experimental evaluation of methods to quantify dissolved organic nitrogen (DON) and dissolved organic carbon (DOC) in soil. Soil Biology & Biochemistry 2006, 38:991-999.
    • (2006) Soil Biology & Biochemistry , vol.38 , pp. 991-999
    • Jones, D.L.1    Willett, V.B.2
  • 46
    • 0001990469 scopus 로고
    • Re-examination of the determination of ammonium as the indophenol blue complex using salicylate
    • Kempers A.J., Kok C.J. Re-examination of the determination of ammonium as the indophenol blue complex using salicylate. Analytica Chimica Acta 1989, 221:147-155.
    • (1989) Analytica Chimica Acta , vol.221 , pp. 147-155
    • Kempers, A.J.1    Kok, C.J.2
  • 47
    • 0036159340 scopus 로고    scopus 로고
    • The macromolecular organic composition of plant and microbial residues as inputs to soil organic matter
    • Kögel-Knabner I. The macromolecular organic composition of plant and microbial residues as inputs to soil organic matter. Soil Biology & Biochemistry 2002, 34:139-162.
    • (2002) Soil Biology & Biochemistry , vol.34 , pp. 139-162
    • Kögel-Knabner, I.1
  • 48
    • 58149524856 scopus 로고    scopus 로고
    • Comments on the paper by Kemmitt et al. (2008) 'Mineralization of native soil organic matter is not regulated by the size, activity or composition of the soil microbial biomass - a new perspective' [Soil Biology & Biochemistry 40, 61-73]: The biology of the Regulatory Gate
    • Kuzyakov Y., Blagodatskaya E., Blagodatsky S. Comments on the paper by Kemmitt et al. (2008) 'Mineralization of native soil organic matter is not regulated by the size, activity or composition of the soil microbial biomass - a new perspective' [Soil Biology & Biochemistry 40, 61-73]: The biology of the Regulatory Gate. Soil Biology & Biochemistry 2009, 41:435-439.
    • (2009) Soil Biology & Biochemistry , vol.41 , pp. 435-439
    • Kuzyakov, Y.1    Blagodatskaya, E.2    Blagodatsky, S.3
  • 49
    • 0004415067 scopus 로고
    • United States Department of Agriculture, Soil Conservation Service, in cooperation with University of California Agricultural Experiment Station
    • Lambert G., Kashiwagi J.H. Soil Survey of Napa County, California 1978, United States Department of Agriculture, Soil Conservation Service, in cooperation with University of California Agricultural Experiment Station.
    • (1978) Soil Survey of Napa County, California
    • Lambert, G.1    Kashiwagi, J.H.2
  • 50
    • 67651247607 scopus 로고    scopus 로고
    • Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale
    • Lauber C.L., Hamady M., Knight R., Fierer N. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Applied and Environmental Microbiology 2009, 75:5111-5120.
    • (2009) Applied and Environmental Microbiology , vol.75 , pp. 5111-5120
    • Lauber, C.L.1    Hamady, M.2    Knight, R.3    Fierer, N.4
  • 52
    • 80053417123 scopus 로고    scopus 로고
    • Grapevine microbiomics: bacterial diversity on grape leaves and berries revealed by high-throughput sequence analysis of 16S rRNA amplicons
    • Leveau J.H.J., Tech J.J. Grapevine microbiomics: bacterial diversity on grape leaves and berries revealed by high-throughput sequence analysis of 16S rRNA amplicons. Acta Horticulturae 2011, 905:31-42.
    • (2011) Acta Horticulturae , vol.905 , pp. 31-42
    • Leveau, J.H.J.1    Tech, J.J.2
  • 53
    • 84891895219 scopus 로고    scopus 로고
    • High throughput sequencing analysis of biogeographical distribution of bacterial communities in the black soils of northeast China
    • Liu J., Sui Y., Yu Z., Shi Y., Chu H., Jin J., Liu X., Wang G. High throughput sequencing analysis of biogeographical distribution of bacterial communities in the black soils of northeast China. Soil Biology & Biochemistry 2014, 70:113-122.
    • (2014) Soil Biology & Biochemistry , vol.70 , pp. 113-122
    • Liu, J.1    Sui, Y.2    Yu, Z.3    Shi, Y.4    Chu, H.5    Jin, J.6    Liu, X.7    Wang, G.8
  • 55
    • 80052638464 scopus 로고    scopus 로고
    • Soil-specific limitations for acccess and analysis of soil microbial communities by metagenomics
    • Lombard N., Prestat E., van Elsas J.D., Simonet P. Soil-specific limitations for acccess and analysis of soil microbial communities by metagenomics. FEMS Microbiology Ecology 2011, 78:31-49.
    • (2011) FEMS Microbiology Ecology , vol.78 , pp. 31-49
    • Lombard, N.1    Prestat, E.2    van Elsas, J.D.3    Simonet, P.4
  • 56
    • 29144464937 scopus 로고    scopus 로고
    • UniFrac: a new phylogenetic method for comparing microbial communities
    • Lozupone C., Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology 2005, 71:8228-8235.
    • (2005) Applied and Environmental Microbiology , vol.71 , pp. 8228-8235
    • Lozupone, C.1    Knight, R.2
  • 57
    • 17844366280 scopus 로고    scopus 로고
    • Identifying microorganisms responsible for ecologically significant biogeochemical processes
    • Madsen E.L. Identifying microorganisms responsible for ecologically significant biogeochemical processes. Nature Reviews Microbiology 2005, 3:439-446.
    • (2005) Nature Reviews Microbiology , vol.3 , pp. 439-446
    • Madsen, E.L.1
  • 58
    • 84883440328 scopus 로고    scopus 로고
    • Characterization of epiphytic bacterial communities from grapes, leaves, bark and soil of grapevine plants grown, and their relations
    • Martins G., Lauga B., Miot-Sertier C., Mercier A., Lonvaud A., Soulas M.-L., Soulas G., Masneuf-Pomarède I. Characterization of epiphytic bacterial communities from grapes, leaves, bark and soil of grapevine plants grown, and their relations. PLOS ONE 2013, 8:e73013.
    • (2013) PLOS ONE , vol.8 , pp. e73013
    • Martins, G.1    Lauga, B.2    Miot-Sertier, C.3    Mercier, A.4    Lonvaud, A.5    Soulas, M.-L.6    Soulas, G.7    Masneuf-Pomarède, I.8
  • 63
    • 0023519385 scopus 로고
    • An evaluation of the relative robustness of techniques for ecological ordination
    • Minchin P.R. An evaluation of the relative robustness of techniques for ecological ordination. Vegetatio 1987, 69:89-107.
    • (1987) Vegetatio , vol.69 , pp. 89-107
    • Minchin, P.R.1
  • 64
    • 0035709008 scopus 로고    scopus 로고
    • A rapid, simple spectrophotometric method for simultaneous detection of nitrate and nitrite
    • Miranda K.M., Espey M.G., Wink D.A. A rapid, simple spectrophotometric method for simultaneous detection of nitrate and nitrite. Nitric Oxide 2001, 5:62-71.
    • (2001) Nitric Oxide , vol.5 , pp. 62-71
    • Miranda, K.M.1    Espey, M.G.2    Wink, D.A.3
  • 65
    • 84879257619 scopus 로고    scopus 로고
    • Advances in elucidating beneficial interactions between plants, soil, and bacteria
    • Elsevier Academic Press, Inc., San Diego, CA, USA
    • Mitter B., Brader G., Afzal M., Compant S., Naveed M., Trognitz F., Sessitsch A. Advances in elucidating beneficial interactions between plants, soil, and bacteria. Advances in Agronomy 2013, vol. 121:381-445. Elsevier Academic Press, Inc., San Diego, CA, USA.
    • (2013) Advances in Agronomy , vol.121 , pp. 381-445
    • Mitter, B.1    Brader, G.2    Afzal, M.3    Compant, S.4    Naveed, M.5    Trognitz, F.6    Sessitsch, A.7
  • 68
    • 0000366797 scopus 로고
    • Elemental organic analysis. Part 1. Historical developments
    • Pella E. Elemental organic analysis. Part 1. Historical developments. American Laboratory 1990, 22(2):116-125.
    • (1990) American Laboratory , vol.22 , Issue.2 , pp. 116-125
    • Pella, E.1
  • 69
    • 0000366798 scopus 로고
    • Elemental organic analysis. Part 2. State of the art
    • Pella E. Elemental organic analysis. Part 2. State of the art. American Laboratory 1990, 22(12):28-32.
    • (1990) American Laboratory , vol.22 , Issue.12 , pp. 28-32
    • Pella, E.1
  • 70
    • 84869882501 scopus 로고    scopus 로고
    • Physical, chemical, and biochemical mechanisms of soil organic matter stabilization under conservation tillage systems: a central role for microbes and microbial by-products in C sequestration
    • Plaza C., Courtier-Murias D., Fernández J.M., Polo A., Simpson A.J. Physical, chemical, and biochemical mechanisms of soil organic matter stabilization under conservation tillage systems: a central role for microbes and microbial by-products in C sequestration. Soil Biology & Biochemistry 2013, 57:124-134.
    • (2013) Soil Biology & Biochemistry , vol.57 , pp. 124-134
    • Plaza, C.1    Courtier-Murias, D.2    Fernández, J.M.3    Polo, A.4    Simpson, A.J.5
  • 71
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2 - approximately maximum-likelihood trees for large alignments
    • Price M.N., Dehal P.S., Arkin A.P. FastTree 2 - approximately maximum-likelihood trees for large alignments. PLOS ONE 2010, 5:e9490.
    • (2010) PLOS ONE , vol.5 , pp. e9490
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 72
    • 84942519322 scopus 로고    scopus 로고
    • U.S. Department of Agriculture, Natural Resources Conservation Service, National Geospatial Management Center, Fort Worth, Texas
    • PRISM Climate Group, Oregon State University 1981-2010 Annual Average Raster Precip and Temp 2012, U.S. Department of Agriculture, Natural Resources Conservation Service, National Geospatial Management Center, Fort Worth, Texas. http://datagateway.nrcs.usda.gov/.
    • (2012) 1981-2010 Annual Average Raster Precip and Temp
  • 77
    • 84856976594 scopus 로고    scopus 로고
    • USDA NRCS National Geospatial Management Center, Fort Worth, Texas
    • Soil Survey Staff, Natural Resources Conservation Service (NRCS), United States Department of Agriculture (USDA) Soil Survey Geographic Database (SSURGO) 2010-2013, USDA NRCS National Geospatial Management Center, Fort Worth, Texas. http://datagateway.nrcs.usda.gov/.
    • (2010) Soil Survey Geographic Database (SSURGO)
  • 82
    • 34548293679 scopus 로고    scopus 로고
    • Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • Wang Q., Garrity G.M., Tiedje J.M., Cole J.R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology 2007, 73:5261-5267.
    • (2007) Applied and Environmental Microbiology , vol.73 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 83
    • 0001341936 scopus 로고
    • Ammonium production in soil under waterlogged conditions as index of nitrogen availability
    • Waring S.A., Bremner J.M. Ammonium production in soil under waterlogged conditions as index of nitrogen availability. Nature 1964, 201:951-952.
    • (1964) Nature , vol.201 , pp. 951-952
    • Waring, S.A.1    Bremner, J.M.2


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