Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes
Liebe S, Wibberg D, Winkler A, Pühler A, Schlüter A, Varrelmann M (2016)
FEMS Microbiology Ecology 92(2): fiw004.
Zeitschriftenaufsatz
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Autor*in
Liebe, Sebastian;
Wibberg, DanielUniBi;
Winkler, AnikaUniBi;
Pühler, AlfredUniBi 
;
Schlüter, AndreasUniBi ;
Varrelmann, Mark
;
Schlüter, AndreasUniBi ;
Varrelmann, MarkEinrichtung
Abstract / Bemerkung
Post-harvest colonization of sugar beets accompanied by rot development is a serious problem due to sugar losses and negative impact on processing quality. Studies on the microbial community associated with rot development and factors shaping their structure are missing. Therefore, high-throughput sequencing was applied to describe the influence of environment, plant genotype and storage temperature (8 degrees C and 20 degrees C) on three different communities in stored sugar beets, namely fungi (internal transcribed spacers 1 and 2), Fusarium spp. (elongation factor-1 alpha gene fragment) and oomycetes (internal transcribed spacers 1). The composition of the fungal community changed during storage mostly influenced by the storage temperature followed by a weak environmental effect. Botrytis cinerea was the prevalent species at 8 degrees C whereas members of the fungal genera Fusarium and Penicillium became dominant at 20 degrees C. This shift was independent of the plant genotype. Species richness within the genus Fusarium also increased during storage at both temperatures whereas the oomycetes community did not change. Moreover, oomycetes species were absent after storage at 20 degrees C. The results of the present study clearly show that rot development during sugar beet storage is associated with pathogens well known as causal agents of post-harvest diseases in many other crops.
Stichworte
bioinformatic analysis pipeline;
Botrytis cinerea;
genotype;
post-harvest disease;
environment;
storage temperature
Erscheinungsjahr
2016
Zeitschriftentitel
FEMS Microbiology Ecology
Band
92
Ausgabe
2
Art.-Nr.
fiw004
ISSN
0168-6496
eISSN
1574-6941
Page URI
https://pub.uni-bielefeld.de/record/2902126
Zitieren
Liebe S, Wibberg D, Winkler A, Pühler A, Schlüter A, Varrelmann M. Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes. FEMS Microbiology Ecology. 2016;92(2): fiw004.
Liebe, S., Wibberg, D., Winkler, A., Pühler, A., Schlüter, A., & Varrelmann, M. (2016). Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes. FEMS Microbiology Ecology, 92(2), fiw004. doi:10.1093/femsec/fiw004
Liebe, Sebastian, Wibberg, Daniel, Winkler, Anika, Pühler, Alfred, Schlüter, Andreas, and Varrelmann, Mark. 2016. “Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes”. FEMS Microbiology Ecology 92 (2): fiw004.
Liebe, S., Wibberg, D., Winkler, A., Pühler, A., Schlüter, A., and Varrelmann, M. (2016). Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes. FEMS Microbiology Ecology 92:fiw004.
Liebe, S., et al., 2016. Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes. FEMS Microbiology Ecology, 92(2): fiw004.
S. Liebe, et al., “Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes”, FEMS Microbiology Ecology, vol. 92, 2016, : fiw004.
Liebe, S., Wibberg, D., Winkler, A., Pühler, A., Schlüter, A., Varrelmann, M.: Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes. FEMS Microbiology Ecology. 92, : fiw004 (2016).
Liebe, Sebastian, Wibberg, Daniel, Winkler, Anika, Pühler, Alfred, Schlüter, Andreas, and Varrelmann, Mark. “Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes”. FEMS Microbiology Ecology 92.2 (2016): fiw004.
Daten bereitgestellt von European Bioinformatics Institute (EBI)
6 Zitationen in Europe PMC
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Menzel W, Jelkmann W, Maiss E., J. Virol. Methods 99(1-2), 2002
PMID: 11684306
Utilizing ITS1 and ITS2 to study environmental fungal diversity using pyrosequencing.
Monard C, Gantner S, Stenlid J., FEMS Microbiol. Ecol. 84(1), 2012
PMID: 23176677
Monard C, Gantner S, Stenlid J., FEMS Microbiol. Ecol. 84(1), 2012
PMID: 23176677
Influence of soil type, cultivar and Verticillium dahliae on the structure of the root and rhizosphere soil fungal microbiome of strawberry.
Nallanchakravarthula S, Mahmood S, Alstrom S, Finlay RD., PLoS ONE 9(10), 2014
PMID: 25347069
Nallanchakravarthula S, Mahmood S, Alstrom S, Finlay RD., PLoS ONE 9(10), 2014
PMID: 25347069
Intraspecific ITS variability in the kingdom fungi as expressed in the international sequence databases and its implications for molecular species identification.
Nilsson RH, Kristiansson E, Ryberg M, Hallenberg N, Larsson KH., Evol. Bioinform. Online 4(), 2008
PMID: 19204817
Nilsson RH, Kristiansson E, Ryberg M, Hallenberg N, Larsson KH., Evol. Bioinform. Online 4(), 2008
PMID: 19204817
Unravelling soil fungal communities from different Mediterranean land-use backgrounds.
Orgiazzi A, Lumini E, Nilsson RH, Girlanda M, Vizzini A, Bonfante P, Bianciotto V., PLoS ONE 7(4), 2012
PMID: 22536336
Orgiazzi A, Lumini E, Nilsson RH, Girlanda M, Vizzini A, Bonfante P, Bianciotto V., PLoS ONE 7(4), 2012
PMID: 22536336
Effects of host plant environment and Ustilago maydis infection on the fungal endophyte community of maize (Zea mays).
Pan JJ, Baumgarten AM, May G., New Phytol. 178(1), 2008
PMID: 18194146
Pan JJ, Baumgarten AM, May G., New Phytol. 178(1), 2008
PMID: 18194146
Characterization of Fusarium spp. responsible for causing dry rot of potato in Great Britain
AUTHOR UNKNOWN, Plant Pathol. 57(2), 2008
PMID: IND44032800
AUTHOR UNKNOWN, Plant Pathol. 57(2), 2008
PMID: IND44032800
Characterization and detection of several filamentous viruses of cherry: adaptation of an alternative cloning method (DOP-PCR), and modification of an RNA extraction protocol.
Rott ME, Jelkmann W., Eur. J. Plant Pathol. 107(4), 2001
PMID: IND23229335
Rott ME, Jelkmann W., Eur. J. Plant Pathol. 107(4), 2001
PMID: IND23229335
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi.
Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W; Fungal Barcoding Consortium; Fungal Barcoding Consortium Author List, Bolchacova E, Voigt K, Crous PW, Miller AN, Wingfield MJ, Aime MC, An KD, Bai FY, Barreto RW, Begerow D, Bergeron MJ, Blackwell M, Boekhout T, Bogale M, Boonyuen N, Burgaz AR, Buyck B, Cai L, Cai Q, Cardinali G, Chaverri P, Coppins BJ, Crespo A, Cubas P, Cummings C, Damm U, de Beer ZW, de Hoog GS, Del-Prado R, Dentinger B, Dieguez-Uribeondo J, Divakar PK, Douglas B, Duenas M, Duong TA, Eberhardt U, Edwards JE, Elshahed MS, Fliegerova K, Furtado M, Garcia MA, Ge ZW, Griffith GW, Griffiths K, Groenewald JZ, Groenewald M, Grube M, Gryzenhout M, Guo LD, Hagen F, Hambleton S, Hamelin RC, Hansen K, Harrold P, Heller G, Herrera C, Hirayama K, Hirooka Y, Ho HM, Hoffmann K, Hofstetter V, Hognabba F, Hollingsworth PM, Hong SB, Hosaka K, Houbraken J, Hughes K, Huhtinen S, Hyde KD, James T, Johnson EM, Johnson JE, Johnston PR, Jones EB, Kelly LJ, Kirk PM, Knapp DG, Koljalg U, Kovacs GM, Kurtzman CP, Landvik S, Leavitt SD, Liggenstoffer AS, Liimatainen K, Lombard L, Luangsa-Ard JJ, Lumbsch HT, Maganti H, Maharachchikumbura SS, Martin MP, May TW, McTaggart AR, Methven AS, Meyer W, Moncalvo JM, Mongkolsamrit S, Nagy LG, Nilsson RH, Niskanen T, Nyilasi I, Okada G, Okane I, Olariaga I, Otte J, Papp T, Park D, Petkovits T, Pino-Bodas R, Quaedvlieg W, Raja HA, Redecker D, Rintoul TL, Ruibal C, Sarmiento-Ramirez JM, Schmitt I, Schußler A, Shearer C, Sotome K, Stefani FO, Stenroos S, Stielow B, Stockinger H, Suetrong S, Suh SO, Sung GH, Suzuki M, Tanaka K, Tedersoo L, Telleria MT, Tretter E, Untereiner WA, Urbina H, Vagvolgyi C, Vialle A, Vu TD, Walther G, Wang QM, Wang Y, Weir BS, Weiß M, White MM, Xu J, Yahr R, Yang ZL, Yurkov A, Zamora JC, Zhang N, Zhuang WY, Schindel D., Proc. Natl. Acad. Sci. U.S.A. 109(16), 2012
PMID: 22454494
Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W; Fungal Barcoding Consortium; Fungal Barcoding Consortium Author List, Bolchacova E, Voigt K, Crous PW, Miller AN, Wingfield MJ, Aime MC, An KD, Bai FY, Barreto RW, Begerow D, Bergeron MJ, Blackwell M, Boekhout T, Bogale M, Boonyuen N, Burgaz AR, Buyck B, Cai L, Cai Q, Cardinali G, Chaverri P, Coppins BJ, Crespo A, Cubas P, Cummings C, Damm U, de Beer ZW, de Hoog GS, Del-Prado R, Dentinger B, Dieguez-Uribeondo J, Divakar PK, Douglas B, Duenas M, Duong TA, Eberhardt U, Edwards JE, Elshahed MS, Fliegerova K, Furtado M, Garcia MA, Ge ZW, Griffith GW, Griffiths K, Groenewald JZ, Groenewald M, Grube M, Gryzenhout M, Guo LD, Hagen F, Hambleton S, Hamelin RC, Hansen K, Harrold P, Heller G, Herrera C, Hirayama K, Hirooka Y, Ho HM, Hoffmann K, Hofstetter V, Hognabba F, Hollingsworth PM, Hong SB, Hosaka K, Houbraken J, Hughes K, Huhtinen S, Hyde KD, James T, Johnson EM, Johnson JE, Johnston PR, Jones EB, Kelly LJ, Kirk PM, Knapp DG, Koljalg U, Kovacs GM, Kurtzman CP, Landvik S, Leavitt SD, Liggenstoffer AS, Liimatainen K, Lombard L, Luangsa-Ard JJ, Lumbsch HT, Maganti H, Maharachchikumbura SS, Martin MP, May TW, McTaggart AR, Methven AS, Meyer W, Moncalvo JM, Mongkolsamrit S, Nagy LG, Nilsson RH, Niskanen T, Nyilasi I, Okada G, Okane I, Olariaga I, Otte J, Papp T, Park D, Petkovits T, Pino-Bodas R, Quaedvlieg W, Raja HA, Redecker D, Rintoul TL, Ruibal C, Sarmiento-Ramirez JM, Schmitt I, Schußler A, Shearer C, Sotome K, Stefani FO, Stenroos S, Stielow B, Stockinger H, Suetrong S, Suh SO, Sung GH, Suzuki M, Tanaka K, Tedersoo L, Telleria MT, Tretter E, Untereiner WA, Urbina H, Vagvolgyi C, Vialle A, Vu TD, Walther G, Wang QM, Wang Y, Weir BS, Weiß M, White MM, Xu J, Yahr R, Yang ZL, Yurkov A, Zamora JC, Zhang N, Zhuang WY, Schindel D., Proc. Natl. Acad. Sci. U.S.A. 109(16), 2012
PMID: 22454494
Impact of agricultural practices on the Zea mays L. endophytic community.
Seghers D, Wittebolle L, Top EM, Verstraete W, Siciliano SD., Appl. Environ. Microbiol. 70(3), 2004
PMID: 15006768
Seghers D, Wittebolle L, Top EM, Verstraete W, Siciliano SD., Appl. Environ. Microbiol. 70(3), 2004
PMID: 15006768
Isolation, quantity distribution and characterization of endophytic microorganisms within sugar beet
Shi, Afr J Biotechnol 8(), 2009
Shi, Afr J Biotechnol 8(), 2009
Illumina-based analysis of endophytic bacterial diversity and space-time dynamics in sugar beet on the north slope of Tianshan mountain.
Shi Y, Yang H, Zhang T, Sun J, Lou K., Appl. Microbiol. Biotechnol. 98(14), 2014
PMID: 24752839
Shi Y, Yang H, Zhang T, Sun J, Lou K., Appl. Microbiol. Biotechnol. 98(14), 2014
PMID: 24752839
Bacteria and Yeast Associated with Sugar Beet Root Rot at Harvest in the Intermountain West
Strausbaugh CA, Gillen AM., Plant Dis. 92(3), 2008
PMID: IND44045224
Strausbaugh CA, Gillen AM., Plant Dis. 92(3), 2008
PMID: IND44045224
Sugar beet root rot at harvest in the US Intermountain West
Strausbaugh, Can J Plant Sci 31(), 2009
Strausbaugh, Can J Plant Sci 31(), 2009
Exopolysaccharide-producing bacteria from sugar beets.
Tallgren AH, Airaksinen U, von Weissenberg R , Ojamo H, Kuusisto J, Leisola M., Appl. Environ. Microbiol. 65(2), 1999
PMID: 9925632
Tallgren AH, Airaksinen U, von Weissenberg R , Ojamo H, Kuusisto J, Leisola M., Appl. Environ. Microbiol. 65(2), 1999
PMID: 9925632
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.
Wang Q, Garrity GM, Tiedje JM, Cole JR., Appl. Environ. Microbiol. 73(16), 2007
PMID: 17586664
Wang Q, Garrity GM, Tiedje JM, Cole JR., Appl. Environ. Microbiol. 73(16), 2007
PMID: 17586664
Statistical methods for detecting differentially abundant features in clinical metagenomic samples.
White JR, Nagarajan N, Pop M., PLoS Comput. Biol. 5(4), 2009
PMID: 19360128
White JR, Nagarajan N, Pop M., PLoS Comput. Biol. 5(4), 2009
PMID: 19360128
Linking fungal communities in roots, rhizosphere, and soil to the health status of Pisum sativum.
Xu L, Ravnskov S, Larsen J, Nicolaisen M., FEMS Microbiol. Ecol. 82(3), 2012
PMID: 22775574
Xu L, Ravnskov S, Larsen J, Nicolaisen M., FEMS Microbiol. Ecol. 82(3), 2012
PMID: 22775574
Soil fungal community structure along a soil health gradient in pea fields examined using deep amplicon sequencing
Xu L, Ravnskov S, Larsen J, Nilsson RH, Nicolaisen M., Soil Biol. Biochem. 46(), 2012
PMID: IND44711645
Xu L, Ravnskov S, Larsen J, Nilsson RH, Nicolaisen M., Soil Biol. Biochem. 46(), 2012
PMID: IND44711645
A novel Asian clade within the Fusarium graminearum species complex includes a newly discovered cereal head blight pathogen from the Russian Far East.
Yli-Mattila T, Gagkaeva T, Ward TJ, Aoki T, Kistler HC, O'Donnell K., Mycologia 101(6), 2009
PMID: 19927749
Yli-Mattila T, Gagkaeva T, Ward TJ, Aoki T, Kistler HC, O'Donnell K., Mycologia 101(6), 2009
PMID: 19927749
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
Differences between the rhizosphere microbiome of Beta vulgaris ssp. maritima-ancestor of all beet crops-and modern sugar beets.
Zachow C, Muller H, Tilcher R, Berg G., Front Microbiol 5(), 2014
PMID: 25206350
Zachow C, Muller H, Tilcher R, Berg G., Front Microbiol 5(), 2014
PMID: 25206350
Reproducibility and quantitation of amplicon sequencing-based detection.
Zhou J, Wu L, Deng Y, Zhi X, Jiang YH, Tu Q, Xie J, Van Nostrand JD, He Z, Yang Y., ISME J 5(8), 2011
PMID: 21346791
Zhou J, Wu L, Deng Y, Zhi X, Jiang YH, Tu Q, Xie J, Van Nostrand JD, He Z, Yang Y., ISME J 5(8), 2011
PMID: 21346791
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