21st Century Guidebook to Fungi with CD

706 Pages·2011·57.03 MB·English

by  David Moore

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21st Century
to
Guidebook Fungi
Fungihavetheirownuniquecellbiologyandlifecycle,butalso DAVID MOORE isaretiredReaderinGeneticsandHonorary
playcriticalrolesinwiderbiologicalsystems.Thistextbook ReaderintheFacultyofLifeSciencesattheUniversityof
providesanall-roundviewoffungalbiology,ranginginscope Manchester.HeisapastPresidentoftheBritishMycologicalSociety
fromtheevolutionaryoriginsoffungiandothereukaryotesmore andwasExecutiveEditoroftheinternationalscientificjournal
thanabillionyearsago,totheimpactfungihaveonourcurrent, MycologicalResearchfortenyears.Inrecentyearshehascreated
everydaylives.Bringingmycologyteachingrightuptodate,this theeducationalwebsitewww.fungi4schools.orgwhichprovides
integrativeapproachgivesstudentsabroaderunderstandingof resourcesforUKschools,sponsoredbytheBritishMycological
fungalbiologythantraditionaltextbooksandprovidesthetools Society.
toincorporatefungiintowiderbiologyteaching.
(cid:1) Uniquesystemsbiologyapproachemphasisesinteractions GEOFFREY D. ROBSON isSeniorLecturerintheFacultyofLife
betweenfungiandotherorganismstoillustratethecriticalroles SciencesattheUniversityofManchester.Heteachesundergraduate
thatfungiplayineveryecosystemandfoodweb courseson‘Microbes,ManandtheEnvironment’,‘FungalEcology
(cid:1) Highlightstheimportanceoffungiin‘new’biology,including andBiotechnology’and‘MicrobialBiotechnology’andis
genomicsandbioinformatics,withexamplesofcomputational ProgrammeDirectorfortheEnterpriseBiotechnologyCourse.He
modelling hasservedasGeneralSecretaryoftheBritishMycologicalSociety
(cid:1) Over20resourceboxesspreadthroughoutthetextpointthe andiscurrentlyPresident-Elect.
readertowardsexternalresourcesthatprovidefurther
information ANTHONY P.J. TRINCI wasBarkerProfessorofCryptogamic
(cid:1) CompanionCDfeaturesahyperlinkedversionofthebook,the BotanyandDeanoftheSchoolofBiologicalSciences,andisnow
fullyintegratedWorldofCyberfungiwebsiteandtheNeighbour- EmeritusProfessorattheUniversityofManchester.Histeachingat
Sensinginteractivefungalgrowthsimulatorprogram Manchesterincludedundergraduatecoursesinmicrobiology,
mycologyandbiotechnology,andpostgraduate-levelunitsin
microbialbiotechnology.HeisapastPresidentofboththeSociety
forGeneralMicrobiologyandtheBritishMycologicalSociety.
Psathyrellamultipedata(crowdedbrittlestem)photographedbyDavidMooreatHarlowCarrGardens.‘Athousand
mushroomscrowdtoakeyhole...Theyliftfrailheadsingravityandgoodfaith...Theyarebeggingus,yousee,
intheirwordlessway...Todosomething,tospeakontheirbehalf...Oratleastnottoclosethedooragain.’
(LinesfromDerekMahon’spoem‘AdisusedshedinCountyWexford’In:CollectedPoems,GalleryPress,1999.)
21st Century
Guidebook
Fungi
to
David Moore
Geoffrey D. Robson
Anthony P. J. Trinci
Facultyof LifeSciences
The University of Manchester
CAMBRIDGEUNIVERSITYPRESS
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Firstpublished2011
PrintedintheUnitedKingdomattheUniversityPress,Cambridge
AcataloguerecordforthispublicationisavailablefromtheBritish
Library
LibraryofCongressCataloging-in-PublicationData
Moore,D.(David),1942–
21stcenturyguidebooktofungi/DavidMoore,GeoffRobson,
TonyTrinci.
p. cm.
ISBN978-1-107-00676-8(Hardback)–ISBN978-0-521-18695-7
(pbk.) 1. Fungi. 2. Fungalmolecularbiology. I. Robson,G.D.
(GeoffreyD.) II. Trinci,A.P.J. III. Title. IV. Title:Twentyfirst
centuryguidebooktofungi.
QK603.M6162011
579.5–dc22 2010040920
ISBN978-1-107-00676-8Hardback
ISBN978-0-521-18695-7Paperback
CambridgeUniversityPresshasnoresponsibilityforthepersistenceor
accuracyofURLsforexternalorthird-partyinternetwebsitesreferredto
inthispublication,anddoesnotguaranteethatanycontentonsuch
websitesis,orwillremain,accurateorappropriate.
CONTENTS
Preface pageix 3.11 Ecosystemmycology 77
3.12 Referencesandfurtherreading 79
Part I Natureand originsof fungi 1
1 21stcenturyfungalcommunities 3 Part II Fungalcellbiology 83
1.1 Whatandwherearefungi? 4 4 Hyphalcellbiologyandgrowthonsolid
1.2 Soil,theessentialterrestrialhabitat 5 substrates 85
1.3 Howmuchsoilisthereandwhereisit? 5 4.1 Mycelium:thehyphalmodeofgrowth 86
1.4 Thenatureofsoilandwhomadeit 5 4.2 Sporegerminationanddormancy 86
1.5 Soilbiotaareextremelyvariedandnumerous 7 4.3 Thefungallifestyle:colonyformation 86
1.6 Microbialdiversityinsoil 7 4.4 Myceliumgrowthkinetics 88
1.7 Microbialdiversityingeneral 8 4.5 Colonygrowthtomaturity 91
1.8 Geomycology 9 4.6 Morphologicaldifferentiationoffungalcolonies 92
1.9 Theoriginsofagricultureandourdependence 4.7 Duplicationcycleinmoulds 92
onfungi 10 4.8 Regulationofnuclearmigration 93
1.10 Referencesandfurtherreading 15 4.9 Growthkinetics 94
4.10 Autotropicreactions 96
2 Evolutionaryorigins 18 4.11 Hyphalbranching 97
2.1 Life,theuniverseandeverything 19 4.12 Septation 99
2.2 PlanetEarth:yourhabitat 21 4.13 Ecologicaladvantageofmycelialgrowthin
2.3 TheGoldilocksplanet 21 colonisingsolidsubstrates 100
2.4 Thetreeoflifehasthreedomains 23 4.14 Referencesandfurtherreading 101
2.5 TheKingdomFungi 29
2.6 Theopisthokonts 30 5 Fungalcellbiology 104
2.7 Fossilfungi 31 5.1 Mechanismsofmycelialgrowth 105
2.8 Thefungalphylogeny 35 5.2 Thefungusasamodeleukaryote 105
2.9 Referencesandfurtherreading 38 5.3 Theessentialsofcellstructure 107
5.4 Subcellularcomponentsofeukaryoticcells:
3 Naturalclassificationoffungi 41 thenucleus 108
3.1 ThemembersoftheKingdomFungi 42 5.5 Thenucleolusandnuclearimportandexport 112
3.2 Thechytrids 42 5.6 Nucleargenetics 114
3.3 Morechytrids:theNeocallimastigomycota 45 5.7 Mitoticnucleardivision 115
3.4 Blastocladiomycota 46 5.8 Meioticnucleardivision 117
3.5 Glomeromycota 50 5.9 TranslationofmRNAandproteinsorting 118
3.6 ThetraditionalZygomycota 52 5.10 Theendomembranesystems 121
3.7 Ascomycota 55 5.11 Cytoskeletalsystems 125
3.8 Basidiomycota 61 5.12 Molecularmotors 127
3.9 Thespeciesconceptinfungi 71 5.13 Plasmamembraneandsignallingpathways 133
3.10 Theuntruefungi 75 5.14 Fungalcellwall 136
vi Contents
5.15 Cellbiologyofthehyphalapex 137 9.4 Aspergillusconidiophores 220
5.16 Hyphalfusionsandmycelialinterconnections 142 9.5 ConidiationinNeurosporacrassa 223
5.17 Cytokinesisandseptation 144 9.6 Conidiomata 223
5.18 Yeast–mycelialdimorphism 150 9.7 Linearstructures:strands,cords,rhizomorphs
5.19 Referencesandfurtherreading 151 andstipes 225
9.8 Globosestructures:sclerotia,stromata,
6 Structureandsynthesisoffungalcellwalls 156 ascomataandbasidiomata 227
6.1 Thefungalwallasaworkingorganelle 157 9.9 Referencesandfurtherreading 231
6.2 Fundamentalsofwallstructureandfunction 157
6.3 Fundamentalsofwallarchitecture 160 Part IV Biochemistry and developmentalbiology
6.4 Thechitincomponent 160 offungi 235
6.5 Theglucancomponent 162 10 Fungiinecosystems 237
6.6 Theglycoproteincomponent 163 10.1 Contributionsoffungitoecosystems 238
6.7 Wallsynthesisandremodelling 165 10.2 Breakdownofpolysaccharide:cellulose 239
6.8 Onthefarside 168 10.3 Breakdownofpolysaccharide:hemicellulose 240
6.9 Thefungalwallasaclinicaltarget 171 10.4 Breakdownofpolysaccharide:pectins 241
6.10 Referencesandfurtherreading 172 10.5 Breakdownofpolysaccharide:chitin 241
10.6 Breakdownofpolysaccharide:starchand
Part III Fungal genetics anddiversity 177 glycogen 241
7 Fromthehaploidtothefunctionaldiploid: 10.7 Lignindegradation 242
homokaryons,heterokaryons,dikaryons 10.8 Digestionofprotein 246
andcompatibility 179 10.9 Lipasesandesterases 247
7.1 Compatibilityandtheindividualisticmycelium 180 10.10 Phosphatasesandsulfatases 247
7.2 Formationofheterokaryons 181 10.11 Theflowofnutrients:transportand
7.3 Breakdownofaheterokaryon 183 translocation 247
7.4 Thedikaryon 183 10.12 Primary(intermediary)metabolism 251
7.5 Vegetativecompatibility 185 10.13 Secondarymetabolites,includingcommercial
7.6 Biologyofincompatibilitysystems 188 productslikestatinsandstrobilurins 257
7.7 Genesegregationduringthemitoticdivisioncycle 189 10.14 Referencesandfurtherreading 264
7.8 Parasexualcycle 194
7.9 Cytoplasmicsegregations:mitochondria, 11 Exploitingfungiforfood 266
plasmids,virusesandprions 194 11.1 Fungiasfood 267
7.10 Referencesandfurtherreading 197 11.2 Fungiinfoodwebs 267
11.3 Wildharvests:commercialmushroompicking 272
8 Sexualreproduction:thebasisofdiversityand 11.4 Cellsandmyceliumashumanfood 274
taxonomy 198 11.5 Fermentedfoods 274
8.1 Theprocessofsexualreproduction 199 11.6 Industrialcultivationmethods 275
8.2 Matinginbuddingyeast 200 11.7 Gardeninginsectsandfungi 279
8.3 Matingtypeswitchinginbuddingyeast 201 11.8 Developmentofafungalfruitbody 280
8.4 MatingtypesofNeurospora 203 11.9 Referencesandfurtherreading 280
8.5 MatingtypesinBasidiomycota 205
8.6 Biologyofmatingtypefactors 210 12 Developmentandmorphogenesis 282
8.7 Referencesandfurtherreading 211 12.1 Developmentandmorphogenesis 283
12.2 Theformalterminologyofdevelopmental
9 Continuingthediversitytheme:cellandtissue biology 283
differentiation 213 12.3 Theobservationalandexperimentalbasisof
9.1 Whatisdiversity? 214 fungaldevelopmentalbiology 285
9.2 Mycelialdifferentiation 214 12.4 Tenwaystomakeamushroom 286
9.3 Makingspores 216 12.5 Competenceandregionalpatterning 289
Contents vii
12.6 TheCoprinopsisfruitbody:makinghymenia 291 14 Fungiaspathogensofplants 367
12.7 CoprinopsisandVolvariellamakinggills(not 14.1 Fungaldiseasesandlossofworldagricultural
forgettinghowpolyporesmaketubes) 295 production 368
12.8 TheCoprinopsisfruitbody:makingstems 301 14.2 Afewexamplesofheadlinecropdiseases 370
12.9 Coordinationofcellinflationthroughoutthe 14.3 ThericeblastfungusMagnaporthegrisea
maturingfruitbody 304 (Ascomycota) 370
12.10 Mushroommechanics 305 14.4 Armillaria(Basidiomycota) 370
12.11 Metabolicregulationinrelationto 14.5 Pathogensthatproducehaustoria
morphogenesis 305 (AscomycotaandBasidiomycota) 371
12.12 Developmentalcommitment 308 14.6 Cercospora(Ascomycota) 372
12.13 Comparisonswithothertissuesandother 14.7 Ophiostoma(Ceratocystis)novo-ulmi(Dutch
organisms 310 elmdiseaseorDED)(Ascomycota) 372
12.14 Classicgeneticapproachestostudydevelopment 14.8 Blackstemrust(Pucciniagraminisf.sp.tritici)
andtheimpactofgenomicdatamining 311 threatensglobalwheatharvest 373
12.15 Degeneration,senescenceanddeath 315 14.9 Plantdiseasebasics:thediseasetriangle 374
12.16 Basicprinciplesoffungaldevelopmentalbiology 316 14.10 Necrotrophicandbiotrophicpathogensofplants 376
12.17 Referencesandfurtherreading 316 14.11 Theeffectsofpathogensontheirhosts 376
14.12 Howpathogensattackplants 379
Part V Fungi assaprotrophs,symbionts and 14.13 Hostpenetrationthroughstomatalopenings 379
pathogens 323 14.14 Directpenetrationofthehostcellwall 382
13 Ecosystemmycology:saprotrophs,and 14.15 Enzymaticpenetrationofthehost 382
mutualismsbetweenplantsandfungi 325 14.16 Preformedandinduceddefencemechanisms
13.1 Ecosystemmycology 326 inplants 385
13.2 Fungiasrecyclersandsaprotrophs 326 14.17 Geneticvariationinpathogensandtheir
13.3 Maketheearthmove 328 hosts:co-evolutionofdiseasesystems 387
13.4 Fungaltoxins:foodcontaminationand 14.18 Referencesandfurtherreading 389
deterioration(includingmentionofstatins
andstrobilurins) 328 15 Fungiassymbiontsandpredatorsofanimals 392
13.5 Decayofstructuraltimberindwellings 331 15.1 Fungalco-operativeventures 393
13.6 Usingfungitoremediatetoxicand 15.2 Antagriculture 393
recalcitrantwastes 334 15.3 TermitegardenersofAfrica 398
13.7 Releaseofchlorohydrocarbonsintothe 15.4 Agricultureinbeetles 399
atmospherebywood-decayfungi 336 15.5 Anaerobicfungiandtheriseoftheruminants 400
13.8 Introductiontomycorrhizas 336 15.6 Nematode-trappingfungi 405
13.9 Typesofmycorrhiza 337 15.7 Referencesandfurtherreading 408
13.10 Arbuscular(AM)endomycorrhizas 338
13.11 Ericoidendomycorrhizas 341 16 Fungiaspathogensofanimals,including
13.12 Arbutoidendomycorrhizas 343 humans 411
13.13 Monotropoidendomycorrhizas 343 16.1 Pathogensofinsects 412
13.14 Orchidaceousendomycorrhizas 344 16.2 Microsporidia 412
13.15 Ectomycorrhizas 346 16.3 Trichomycetes 414
13.16 Ectendomycorrhizas 351 16.4 Laboulbeniales 416
13.17 Theeffectsofmycorrhizasandtheir 16.5 Entomogenousfungi 417
commercialapplicationsandtheimpactof 16.6 Biologicalcontrolofarthropodpests 421
environmentalandclimatechanges 351 16.7 Cutaneouschytridiomycosis:anemerging
13.18 Introductiontolichens 356 infectiousdiseaseofamphibians 422
13.19 Introductiontoendophytes 360 16.8 Aspergillosisdiseaseofcoral 424
13.20 Epiphytes 361 16.9 Mycoses:thefungusdiseasesofhumans 424
13.21 Referencesandfurtherreading 361 16.10 Clinicalgroupingsforhumanfungalinfections 426
viii Contents
16.11 Fungiwithinthehomeandtheireffectson 18 Molecularbiotechnology 511
health:allergensandtoxins 432 18.1 Antifungalagentsthattargetthemembrane 512
16.12 Comparisonofanimalandplantpathogens 18.2 Antifungalagentsthattargetthewall 521
andtheessentialsofepidemiology 436 18.3 Clinicalcontrolofsystemicmycosesatthe
16.13 Mycoparasiticandfungicolousfungi 439 startofthe21stcentury:azoles,polyenesand
16.14 Referencesandfurtherreading 444 combinatorialtherapy 522
18.4 Agriculturalmycocidesatthestartofthe
Part VI Fungal biotechnology andbioinformatics 449 twenty-firstcentury:strobilurins 526
17 Wholeorganismbiotechnology 451 18.5 Understandingfungalgeneticstructure 529
17.1 Fungalfermentationsinsubmergedliquid 18.6 Sequencingfungalgenomes 531
cultures 452 18.7 Annotatingthegenome 535
17.2 Culturingfungi 452 18.8 Fungalgenomesandtheircomparison 540
17.3 Oxygendemandandsupply 456 18.9 Manipulatinggenomes:targetedgene
17.4 Fermenterengineering 458 disruption,transformationandvectors 547
17.5 Fungalgrowthinliquidcultures 460 18.10 Fungiascellfactoriesproducingheterologous
17.6 Fermentergrowthkinetics 462 proteins 552
17.7 Growthyield 464 18.11 Recombinantproteinproductionbyfilamentous
17.8 Stationaryphase 465 fungi 554
17.9 Growthaspellets 466 18.12 Bioinformaticsinmycology:manipulating
17.10 Beyondthebatchculture 469 verylargedatasets 557
17.11 Chemostatsandturbidostats 470 18.13 Genomicdataminingsupportsthenotionthat
17.12 Usesofsubmergedfermentations 473 therearedifferentdevelopmentalcontrol
17.13 Alcoholicfermentations 474 mechanismsinfungi,animalsandplants 560
17.14 Citricacidbiotechnology 477 18.14 Effectsofclimatechangeonfungirevealed
17.15 Penicillinandotherpharmaceuticals 478 byanalysisoflargesurveydatasets 562
17.16 Enzymesforfabricconditioningand 18.15 Cyberfungi:mathematicalmodellingand
processing,andfoodprocessing 483 computersimulationofhyphalgrowth 563
17.17 Steroidsanduseoffungitomakechemical 18.16 Referencesandfurtherreading 567
transformations 486
17.18 TheQuorn™fermentationandevolutionin Part VII Appendices 573
fermenters 487 Appendix1Outlineclassificationoffungi 575
17.19 Productionofsporesandotherinocula 492
17.20 Naturaldigestivefermentationsin Appendix2Mycelialandhyphaldifferentiation 589
herbivores 493
17.21 Solidstatefermentations 494 Index 605
17.22 Digestionoflignocellulosicresidues 497
17.23 Bread:theothersideofthealcoholic Platesections:Section1betweenpages148and149
fermentationequation 499 Section2betweenpages340and341
17.24 Cheeseandsalamimanufacture 501
17.25 Soysauce,tempehandotherfoodproducts 504
17.26 Referencesandfurtherreading 506