DNA barcoding of arbuscular mycorrhizal fungi [Elektronische Ressource] / vorgelegt von Herbert Stockinger

Herbert Stockinger

Sujets

• Biologie

Informations

• Publié par: ludwig-maximilians-universitat_munchen
• Publié le: 01 janvier 2010
• Nombre de lectures: 63
• Langue: Deutsch
• Poids de l'ouvrage: 12 Mo

Extrait

DNA barcoding of arbuscular mycorrhizal fungi












Kumulative Dissertation
zur Erlangung des Doktorgrades der Naturwissenschaften
an der Fakultät für Biologie der Ludwig-Maximilians-Universität München


vorgelegt von
Herbert Stockinger






München, Januar 2010


Ehrenwörtliche Versicherung
Ich versichere hiermit ehrenwörtlich, dass ich die vorliegende Dissertation von mir selbständig und
ohne unerlaubte Hilfe angefertigt ist.


München, am _________________ ___________________________



Erklärung
Hiermit erkläre ich,
dass die Dissertation nicht ganz oder in wesentlichen Teilen einer anderen
Prüfungskommission vorgelegt worden ist.
dass ich mich anderweitig einer Doktorprüfung ohne Erfolg nicht unterzogen habe.



München, am _____________ ____________________________


















Erstgutacher: PD Dr. Arthur Schüßler
Zweitgutachter: Prof. Dr. Martin Parniske
Tag der mündlichen Prüfung: 22 April 2010



Für meine Eltern

Table of contents
Table of contents

List of abbreviations (SI units not included)......................................................................................4
1 Abstract.............................................................................................................................................7
2 Zusammenfassung ...........................................................................................................................8
3 Introduction....................................................................................................................................10
3.1 Arbuscular mycorrhizal fungi (AMF) ............................................................................................... 10
3.1.1 Effects of AMF on plants ............................................................................................................................... 10
3.1.2 Plant nutrition and water relations effected by AMF...................................................................................... 11
3.1.3 AMF spore characteristics and morphology of root colonization................................................................... 13
3.1.4 AMF species communities in the field ........................................................................................................... 14
3.1.4.1 AMF-plant preferences........................................................................................................................... 15
3.1.5 Species concepts for AMF.............................................................................................................................. 15
3.1.6 Taxonomy and phylogeny of AMF................................................................................................................. 16
3.2 DNA barcodes and molecular species identification ........................................................................ 18
3.2.1 Official DNA barcodes................................................................................................................................... 18
3.2.2 Molecular identification of fungi using COX1 ............................................................................................... 19
3.2.3 Molecular identification of fungi using rDNA sequences .............................................................................. 19
3.2.3.1 Primer used for PCR amplification of AMF........................................................................................... 20
3.3 Aim of this study.................................................................................................................................. 21
4 Molecular phylogeny and new taxa in the Archaeosporales (Glomeromycota): Ambispora
fennica gen. sp. nov., Ambisporaceae fam. nov., and emendation of Archaeospora and
Archaeosporaceae. ...........................................................................................................................23
5 DNA-based species level detection of Glomeromycota: one PCR primer set for all arbuscular
mycorrhizal fungi..............................................................................................................................43
6 'Glomus intraradices DAOM197198', a model fungus in arbuscular mycorrhiza research, is
not Glomus intraradices ..................................................................................................................57
7 DNA barcoding of arbuscular mycorrhizal fungi.........................................................................71
7.1 Abstract................................................................................................................................................ 72
7.2 Introduction......................................................................................................................................... 72
7.2.1 Identification of AM fungal species from the field ........................................................................................ 73
7.2.2 DNA barcoding for species definition and identification ............................................................................... 73
7.2.3 DNA barcode(s) for fungi .............................................................................................................................. 74
1 Table of contents
7.2.4 COX1 is not suited as general fungal barcode................................................................................................ 74
7.2.5 Defining a DNA barcoding region for AMF .................................................................................................. 75
7.3 Material & Methods............................................................................................................................ 76
7.3.1 Taxa and public sequences used for analyses ................................................................................................. 76
7.3.2 DNA extraction, PCR amplification, cloning and sequencing ....................................................................... 79
7.3.3 Phylogenetic and sequence divergence analyses............................................................................................ 79
7.4 Results .................................................................................................................................................. 81
7.4.1 Intraspecific rDNA sequence variation .......................................................................................................... 81
7.4.2 Barcode gap analyses ..................................................................................................................................... 81
7.4.3 Phylogenetic analyses of the core dataset ...................................................................................................... 84
7.4.4 Phylogenetic analyses of the extended dataset............................................................................................... 87
7.4.4.1 Analyses of Ambisporaceae.................................................................................................................... 87
7.4.4.2 Analyses of Diversisporaceae ................................................................................................................ 87
7.4.4.3 Analyses of Glomus Group Aa ('Gl. mosseae group')............................................................................. 88
7.5 Discussion............................................................................................................................................. 93
7.5.1 Intraspecific rDNA variation.......................................................................................................................... 93
7.5.2 Barcode gap analyses ..................................................................................................................................... 94
7.5.3 Phylogenetic analyses .................................................................................................................................... 94
7.5.4 The ITS region ............................................................................................................................................... 95
7.5.5 The LSU region.............................................................................................................................................. 96
7.5.6 Database sequences........................................................................................................................................ 96
7.5.7 DNA fragments for 454 GS-FLX Titanium pyrosequencing technology....................................................... 97
7.5.8 Conclusion...................................................................................................................................................... 97
7.6 Acknowledgements...........................................................................................