Molecular Identification of Fungi (eBook)

Chapter 1: Fungal Pathogens of Plants in the Homogocene 21
Introduction 21
Native Ranges of Fungi 24
Pathogen Release 26
Inferring Native Ranges of Fungi from Pathogen Release 29
Genetic Criteria for Native Range 31
Inferring Native Ranges of Pathogenic Fungi from Resistance 32
First Encounters Between Evolutionarily Naive Plants and Novel Pathogens 35
A ``Tens Rule´´ for Novel Pathogens 40
Transformers 42
Deliberate Introductions of Fungi 43
Inadvertent Co-Introductions of Fungi in Plants 43
Fungi as Facilitators of Plant Invasions 44
Conclusions 45
References 46
Chapter 2: Molecular Techniques for Classification and Diagnosis of Plant Pathogenic Oomycota 53
Introduction 54
Upheaval of Oomycete Taxonomy in the Molecular Era 55
Molecular Tools for Reclassification and Identification of Oomycota 57
Molecular Approaches for Tracing Occurrence of Oomycetes in Plants and Habitats 60
Concluding Remarks 63
References 63
Chapter 3: Plasmodiophorids: The Challenge to Understand Soil-Borne, Obligate Biotrophs with a Multiphasic Life Cycle 69
Introduction 70
What are Plasmodiophorids? 70
The Plasmodiophorids in the Tree of Life 74
Phylogenetic Relationships Within the Plasmodiophoridsplasmodiophorids 75
Economic Importance of Plasmodiophorids 77
Experimental Strategies to Detect and Monitor Plasmodiophorids 78
Direct Observations, Bioassays, and Bait Tests 78
Molecular Approaches 79
Antibody-Based Methods 80
Nucleic Acid-Based Methods 81
Plasmodiophorid Genomicsgenomics 86
How Common are Plasmodiophorids? 89
Conclusions and Future Research 90
References 91
Chapter 4: Applications of Molecular Markers and DNA Sequences in Identifying Fungal Pathogens of Cool Season Grain Legumes 97
Introduction 98
Sclerotinia Stem Rot of Chickpea 98
DNA Isolation and ITS Sequence Analysis 100
Detection of Group I IntronsGroup I Introns 100
Powdery Mildew of Lentil 102
Sample Collection and DNA Sequencing 104
Sequence Analysis 105
Species Confirmation 105
Conclusions 107
References 107
Chapter 5: Quantitative Detection of Fungi by Molecular Methods: A Case Study on Fusarium 110
Introduction 110
Quantification Strategies 112
Competitive PCRPCR 112
Real-Time PCR 113
Species SpecificPCRSpecies specific Quantification 113
Group SpecificPCRGroup specific Quantification Based on the Detection of Toxin Biosynthesis Genes 115
DNA-ArraysDNA-arrays 117
Conclusion 118
References 120
Chapter 6: DNA-Based Tools for the Detection of Fusarium spp. Pathogenic on Maize 123
Introduction 123
Major Fusarium Toxins in Maize 124
Fumonisins 124
Trichothecenes 125
Epidemiology and Etiology of Maize Pink and Red Ear Rot 126
Pink Ear Rot 126
Red Ear Rot 127
General Species Concepts and Species Borders Within the Genus Fusarium 129
Section LiseolaSection Liseola 130
Section Discolor 131
DNA Sequence-Based Diagnosis of Fusarium spp. Pathogenic On Maize: Species Assignment 132
Species-Diagnostic Primers for the Causal Agents of Pink Ear Rot 132
Species-Diagnostic Primers for the Causal Agents of Red Ear Rot 133
DNA Sequence-Based Diagnosis of Fusarium spp. Pathogenic on Maize: Toxigenicity 135
Fumonisin-Producing Fusarium spp 135
Trichothecene-Producing Fusarium spp 137
Conclusion and Future Lines of Research 138
References 138
Chapter 7: Molecular Detection and Identification of Fusarium oxysporum 146
Introduction 146
Earlier Efforts for Identification of Pathogenic Fusarium oxysporum 148
Identification Using Anonymous Markers 148
Restriction Fragment Length Polymorphism 148
Random Amplified Polymorphic DNA 151
Amplified Fragment Length Polymorphism 152
Simple Sequence Repeats 152
Identification Using Sequence-Specific Markers 153
ITS and IGS 153
Transposons 154
Other Genes 155
Multiplex PCR 156
Limitations of PCR-Based Techniques 156
Recent Techniques for Identification of Fusarium oxysporum 157
Real-Time PCR 157
Microarrays 159
Gene/Genome SequencingGenome Sequencing 160
DNA Barcoding 160
Emerging Technologies for Pathogen Identification 162
Next-Generation SequencingNext-Generation Sequencing 162
Single-Nucleotide Polymorphisms 162
MetagenomicsMetagenomics 163
Potential Limitations of Molecular Identification Techniques 163
Conclusions and Future Prospects 164
References 165
Chapter 8: Molecular Chemotyping of Fusarium graminearum, F. culmorum, and F. cerealis Isolates From Finland and Russia 173
Introduction 173
Materials and Methods 177
Fusarium Isolates 177
DNA ExtractionDNA extraction and PCR ChemotypingPCR chemotyping 179
Multilocus GenotypingMultilocus genotyping 181
Mycotoxin Analyses 182
PathogenicityPathogenicity Analysis 182
Results 183
Molecular Chemotype Determination with Tri7 and Tri13 Primer Pairs 183
Multilocus Genotyping 184
DON and ZEN Production 184
Pathogenicity of Isolates 185
Discussion 186
References 188
Chapter 9: Molecular Characterization and Diagnosis of Macrophomina phaseolinaMacrophomina phaseolinabiochemical and serologica 192
Introduction 193
Classification and Nomenclature 193
Identification and Characterization 194
Morphological and Cultural Characteristics 194
Biochemical and Serological Characterization 195
Molecular Methods for Characterization of M. phaseolina 195
Molecular ToolsMolecular toolsrestriction fragment length polymorphism Used for Characterization of M. phaseolina 196
Restriction Fragment Length Polymorphism 196
PCR-Fingerprinting Techniques 197
Diagnostic ToolsDiagnostic Tools Developed for Identification and Detection 197
PCR-Based Identification 199
Hybridization ProbesHybridization probesReal -time PCR technologyTaqMan 200
Recent Developments in the Diagnostics of M. phaseolina 200
Future Prospects 201
Conclusion 201
References 202
Chapter 10: Molecular Diagnosis of Ochratoxigenic Fungi 207
Introduction 207
Molecular Markers for the Detection of Ochratoxigenic Fungi 209
PCR-Detection and Quantification of Ochratoxigenic Species with Sequences Not Associated to Mycotoxin Biosynthesis 210
PCR-Based Detection and Quantification of Ochratoxigenic Species with Biosynthetic Pathway Genes 218
Conclusions 220
References 221
Chapter 11: Molecular Barcoding of Microscopic Fungi with Emphasis on the Mucoralean Genera Mucor and Rhizopus 225
Introduction and Background 225
Methodical Section 228
Isolation, Cultivation and Maintenance of Strains 228
Morphological Identification 228
Extraction of Genomic DNA and PCR Amplification 229
The Fungal Subphylum Mucoromycotina 233
Reconstruction of Multigene Phylogenetic Trees 233
Analysis of the Internal Transcribed Spacer Regions 1 and 2 Including 5.8S rDNA 236
Random Amplified DNA Polymorphisms 240
Sequence Similarity Matrices for Rhizopus and Mucor sp. 240
Results and Discussion 240
Diversity and Coarse Scale Identification of Fungal Species Isolated From Saudi Arabian Soil and Fruits 240
Diversity and Morphological Identification of the Mucoralean Genera Rhizopus and Mucor 247
Phylogenetic Relevance of Morphological Markers 249
Fine Scale Identification of RhizopusRhizopus Isolates Based on Combined Morphological and Molecular Characters 249
Synergistic Application of DNA-Polymorphism and DNA-Sequence Generating Tools 249
Evaluation of Potential Barcoding Methods and the Impact of Extended Species Recognition 252
The Pressing Need for Reliable Species Identification 253
Conclusions 253
Authors´ Contributions and Competing Interests 255
References 255
Chapter 12: Advances in Detection and Identification of Wood Rotting Fungi in Timber and Standing Trees 263
Introduction 263
Problems and Risks Related to Wood Rotting Fungi 264
Indoor Wood Rotting Fungi 264
Wood Rotting FungiWood rotting fungi and Tree StabilityTree stability 265
Rot Diseases and TimberTimber Production 266
Root and Butt Rot Diseases and Fruit Tree Plantations 267
Traditional Techniques of Identification of Wood Rotting FungiWood rotting fungi 268
Analysis of Fruit BodiesFruit bodies and Mycelial Strands 268
Analysis of Pure Fungal Cultures 268
Biochemical Techniques 269
Protein-Based Techniques 269
Immunological Techniques 269
DNA-Based Techniques 270
DNA Extraction from Wood 270
RAPD-PCR 271
PCR-RFLP 272
T-RFLP 273
Taxon-Specific Priming PCR 273
Real-Time PCR 278
DNA SequencingPolymerase Chain ReactionDNA sequencing 278
Conclusion and Perspectives 281
References 281
Chapter 13: Molecular Diversity and Identification of Endophytic Fungi 289
Introduction 289
Molecular Fingerprinting for Endophytic Fungal Population 291
RAPD and RFLP Techniques 291
SSR and AFLP Techniques 292
DGGE Technique 293
Molecular Sequencing for Endophytic Fungal Community 294
Identification of Endophytic Fungi 295
Identification of Nonsporulating Endophytic Funginon-sporulating endophytic fungi 296
Identification of White Morphotype Strains 297
Detection and Identification of Endophytic Fungi Within Plant Tissues 297
Conclusions 301
References 302
Chapter 14: Molecular Identification of Anaerobic Rumen Fungi 309
Introduction 309
Historical Background and the Discovery of Rumen Fungi 310
Traditional and Current Systematics 312
Phylogeny 313
Predicted Impact of Molecular Markers on Future Identification and Phylogeny 315
Molecular Identification and DNA Barcoding 320
Conclusion and Future Line of Research 322
References 323
Chapter 15: New Approaches in Fungal DNA Preparation from Whole Blood and Subsequent Pathogen Detection Via Multiplex PCR 327
Introduction: Fungi as Sepsis Causative PathogensSepsisCausative Pathogen 327
Sepsis Diagnostics: An Overview of Current Methods 329
Fate of Antimycosis 332
Pathogen Detection by Nucleic Acids Amplification Techniques (NAT) 333
Conclusion and Future Line of Research 337
References 338
Chapter 16: Classification of Yeasts of the Genus Malassezia by Sequencing of the ITS and D1/D2 Regions of DNA 346
Introduction 346
Description of the Article 347
Clinical Relevance of the Genus Malassezia 347
The Diagnosis of the Genus Malassezia 350
Current State of the Classification of Malassezia spp. 350
Conclusions and Future Line of Investigation 357
References 361
Chapter 17: DNA-Based Detection of Human Pathogenic Fungi: Dermatophytes, Opportunists, and Causative Agents of Deep Mycoses 365
Introduction 366
DNA Manipulations 370
Panfungal Assays 372
Aspergillus spp. 375
Laboratory Diagnosis 375
Molecular Detection 376
Laboratory Diagnosis 381
Molecular Detection 382
Candida spp. 382
Laboratory Diagnosis 385
Molecular Detection 386
Coccidioides spp. 390
Laboratory Diagnosis 391
Molecular Detection 392
Laboratory Diagnosis 393
Molecular Detection 394
Dematiaceous Fungi 396
Laboratory Diagnosis 396
Molecular Detection 396
Fusarium spp. 397
Laboratory Diagnosis 397
Molecular Detection 398
Laboratory Diagnosis 399
Molecular Detection 399
Trichosporon spp. 400
Laboratory Diagnosis 400
Molecular Detection 401
Zygomycetes 401
Laboratory Diagnosis 402
Molecular Detection 402
Dermatophytes 403
Laboratory Diagnosisdermatophyteslaboratory diagnosis 404
Molecular Detectiondermatophytesmolecular detection 404
Conclusion and Perspectives 405
References 407
Chapter 18: Applications of Loop-Mediated Isothermal Amplificaton Methods (LAMP) for Identification and Diagnosis of Mycotic Di 424
Introduction 425
The Principle of LAMP Method 427
About LAMP Method (http://loopamp.eiken.co.jp/e/lamp/index.html) 427
Primers 427
Basic Principle 428
Cautions 428
Applications of LAMP Method for Identifications of P. brasiliensisParacoccidioides brasiliensis and or/Diagnosis for Paracocci 428
Backgrounds for P. brasiliensis 428
LAMP Method for Identifications of P. brasiliensis 431
P. brasiliensis Isolates and Reference Species 431
Extraction of DNA 431
Detection of gp43 by PCR 434
LAMP Method for gp43 434
Results 435
Comments and Opinions 437
LAMP Method for Identifications of O. gallopava 438
Conclusion and Future Line of Research 441
References 442
Chapter 19: Identification of the Genus Absidia (Mucorales, Zygomycetes): A Comprehensive Taxonomic Revision 445
The Genus Absidia: Current State of the Art - A Brief Survey 445
The Traditional Genus Absidia: Morphological AspectsAbsidiamorphological aspects 446
The Impact of Molecular Data: The Genus Absidia sensu latoAbsidiasensu lato is Distinguished in at Least Three Nonrelated Gene 448
The Genus Absidia Tiegh. sensu strictoAbsidiasensu stricto Deserves a Separate Family, the AbsidiaceaeAbsidiaceae v. Arx 450
The Genus LichtheimiaLichtheimia (Cohn) Vuill. and Its Family LichtheimiaceaeLichtheimiaceae K. Hoffm., G. Walther and K. Voig 451
The Genus LentamycesLentamyces and a Required Excursus to SiepmanniaSiepmannia: Species Boundaries 452
Morphological and Molecular Differentiation of Affected Species Belonging to Absidia sensu lato 455
Synoptic keyAbsidiasynoptic key to Genera and Species 455
The Genus LichtheimiaLichtheimia (Vuill. 1903 Lichtheimiaceae K. Hoffm., G. Walther &
The Genus AbsidiaAbsidia (Tiegh. 1876 Absidiaceae Arx 1982)
The Genus LentamycesLentamyces (K. Hoffm. and K. Voigt 2008) 458
Some Remarks to Uncertain Species 458
Molecular KeyAbsidiamolecular key to the Genera 458
Combining Morphological and Molecular Characters: An Example 460
Methodological Section 460
Media for Cultivation 460
Methods for Strain Maintenance, Cultivation, and Sequence Analyses 460
PCR-RFLP and Sequence Analysis 463
References 463
Chapter 20: Molecular Characters of Zygomycetous Fungi 467
Introduction 468
MolecularCHARACTERMOLECULARPHYLOGENYMOLECULAR Characters for Classifying Zygomycetous FungiZYGOMYCETOUS FUNGI 472
AmoebidialesMesomycetozoea and EccrinalesMesomycetozoeaEccrinales 473
BasidiobolalesZygomycotaBasidiobolales 474
GeosiphonalesGlomeromycotaGeosiphonales 474
MortierellalesZygomycotaMortierellalesMortierellomycotina ined.Mortierellales 475
MucoralesMucorales 475
AbsidiaAbsidia 476
ActinomucorActinomucor 477
CunninghamellaCunninghamella 477
PilairaPilaira 477
RhizomucorRhizomucor 478
RhizopusMucoralesRhizopus 479
MolecularPHYLOGENYMOLECULAR Characters in Industrial Zygomycetous FungiZYGOMYCETOUS FUNGI 480
GlucoamylaseGlucoamylase 480
PolygalacturonasePolygalacturonase 480
Fumaric Acidsacidsfumaric acids 481
Polyunsaturatedfatty acidspolyunsaturated Fatty Acidsacidsfatty acidsacids 481
MolecularPHYLOGENYMOLECULAR CharacterCHARACTERMOLECULARs in Medical Zygomycetous FungiZYGOMYCETOUS FUNGI 482
SSUrDNASSU/LSUrDNALSU rDNADNArDNA 483
ITSrDNAITS rDNADNArDNA 484
CytochromegeneCytochrome b Gene 484
Whole-Genomegenotypingwhole-genomefingerprintingwhole-genome Fingerprintingfingerprinting and Genotypinggenotyping 485
Carbon Assimilation ProfilesCarbon assimilation profiles 485
GenomePROJECTSGENOME ProjectsPROJECTS for Zygomycetous FungiZYGOMYCETOUS FUNGI 486
Prospect 487
References 488
: Index 495