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INDEX

Absidia corymbifera, 431Acaulospora spp., 52, 340, 441Acaulosporaceae, 52, 340acervulae, 198, 223acetyl-coenzyme A (acetyl-CoA), 47, 252,

477acetylenes, 264achlorophyllous orchidsobligate mycoheterotrophs, 346

Achlya bisexualis, 138, 199growth mechanism, 160pheromones, 77

Achlya spp., 31, 75, 85acostromata, 60Acrasiales, 77Acrasiomycota, 77Acrasis spp., 77Acremonium spp., 442Acromyrmex spp., 396actin, 126actin-binding proteins (ABPs), 126actin filaments, 126actin gene mutations, 126actin-associated myosins, 127–33actins, 25activator-inhibitor model, 293active transport across a membrane, 249plasma membrane, 133

actomyosin ringassembly during cell division, 145

adhesins, 168–70affluent dietland required per person, 5

aflatoxicosis, 330, 435–6aflatoxins, 56, 262, 330, 435–6African histoplasmosis, 428AFTOL study, 35, 45, 50, 51, 55, 56, 61Agaricaceae, 66Agaricales, 63–5, 66, 394Agaricomycetes, 66Agaricomycetidae, 63, 66Agaricomycotina, 62, 63–71Agaricus bisporus, 71, 117, 195, 200, 245,

247, 252, 254, 263, 311brown spot disease, 443commercial cultivation technique, 276–8dry bubble disease, 443genome, 546hymenia development, 295

La France disease, 196mycoparasite problems, 443–4wet bubble disease, 443white mould disease, 443

Agaricus bitorquis, 195Agaricus brunnescens, 195Agaricus spp.

use of protein, 246agaritine, 263Agaromycotina

AFTOL classification, 66–9agglutinins, 168agonomycetes, 198agricultural myocides, 529agricultural soil

area on the Earth, 5agricultural waste

breakdown by fungi, 238cultivation of Pleurotus spp., 278lignocellulose biodegradation, 497–9remediation by fungi, 334–6

agricultureaffluent diet requirement, 5agricultural fungi, 15amount of land used to supply food, 5human dependence on fungi, 15losses to fungal diseases, 4losses to pests and diseases, 368–70mycorrhizal fungi in crop plants, 4origins of, 10–15role of fungi in herbivore digestion, 4ruminants and anaerobic chytrids, 400–5strobilurin fungicides, 4subsistence diet requirement, 5

Agrobacterium tumefaciens-mediatedtransformation (AMT), 389, 551

agroclavine, 54AIDS patients

candidiasis, 429cryptococcosis, 428opportunistic fungal infections, 429susceptibility to fungal infections, 429See also immunocompromised patients

Ajellomyces capsulatus, 428Albugo candida, 379Albugo spp., 31, 75alcohol, 4alcohol production

fermentation research, 105–6

alcoholic fermentations, 474–7Aleuria spp., 60, 228alkaloids produced by endophytes, 360allergic aspergillosis, 430allergic reactions, 433Allomyces macrogynus, 48, 199Allomyces spp., 47–8Allotropa spp., 343a-amanitin, 264a-tubulin, 25Alternaria brassicicola, 383aluminium in soil minerals, 6Amanita muscaria, 78, 263, 338,

347, 354toxins, 328–30

Amanita pantherina, 329Amanita phalloides, 264Amanita spp., 78, 347accumulation of metal ion, 327amatoxins, 433–4mycorrhizal fungi, 337, 338phallotoxin, 433–4poisoning, 433–4toxins, 264

Amanita virosa, 62amatoxins, 433–4amberfungal fossils, 32–3

ambrosia beetles, 62and fungi, 399–400

Ambrosiella spp., 399, 400American Type Culture Collection (ATCC),

562Amoebidiales, 29, 52, 77Amoebidium parasiticum, 415amorphous cellulose, 239amphibianscutaneous chytridiomycosis, 43, 422–4

amphipathic structure of hydrophobins,170

amphotericin B, 431, 515–16amphotericin B liposomes (AmBisomes),

517amylases, 241, 242amyloglucosidases, 241amylopectins, 241amylose, 241anaerobic chytrids, 29, 45–6and ruminants, 400–5

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anaerobic early eukaryotes, 23Anaeromyces spp., 401analogous organs, 63anamorph (asexual stage), 42anamorphic fungi, 198–9anastomosis. See hyphal fusionang-kak, 274, 506anidulafungin, 521animal pathogenscomparison with plant pathogens, 436–9

Anisolpidiales, 75Anisolpidium spp., 75ant agriculturecoral fungus agriculture, 396demand for leaf material, 395–6Escovopsis fungal parasite, 397gardening ants, 393–8generalised higher agriculture, 396leaf-cutter agriculture, 396lower agriculture, 396molecular phylogenies of attine ants,

396–7obligate symbiosis with the fungus, 396symbiotic Streptomyces, 397–8yeast agriculture, 396

antheridiol, 199antibiotic resistance, 108antibiotics, 4, 55, 473, 512antibiotics production, 353antifeedants, 328antifungal agentsazoles, 517–21cell wall as a target, 171–2fungal cell wall as target, 157polyenes, 514–17protective agents, 512systemic agents, 512–13targeting the cell wall, 521–2targeting the membrane, 512–21types of, 512

antigens, 437antiporters, 249antitumour agents, 473Antrodia vaillantii, 332Antrodia xantha, 332ants and fungi, 279Aphelenchoides composticola, 270apical growth of the hypha, 100Apodachlyella spp., 75apoptosis, 185, 315–16, 465apothecia, 59, 228apple blotch, 370appressorium, 379Apterostigma spp., 396aquatic fungi, 78arabanases, 241arabans, 240Arabidopsis thaliana, 376arachidonic acid biotechnology, 482–3arbuscular endomycorrhizas, 337, 338–42arbuscular mycorrhizal fungi, 32, 50–2, 78,

171, 441arbuscules, 51, 338

arbutoid endomycorrhizas, 337, 343Arbutus spp., 343Archaea, 24Archaeospora spp., 340Archaeosporales, 340archiascomycetes, 56Arctostaphylos spp., 343Armillaria bulbosa, 195Armillaria gallica, 71Armillaria mellea, 227, 246, 251, 335, 344,

346Armillaria spp., 117, 195, 246, 370–2, 444

genomes, 547Armillariella spp., 444aromatic hydrocarbon pesticides, 334Arthoniomycetes, 60, 61Arthrinium sphaerosperma, 522Arthrobotrys oligospora, 406, 439arthropod endosymbiont fungi, 53arthropod pathogens

Laboulbeniales, 416–17arthropod pests

biological control, 421–2chemical pesticides, 421integrated pest management (IPM), 422microbial control agents, 422use of transgenic plants, 422

arthrospores, 208Artiodactyla, 403

and anaerobic chytrids, 400–5aryl alcohol oxidase, 245asci, 55, 228

Pezizomycotina, 60–1Ascobolus heterothallicus, 186Ascobolus stercorarius, 186ascochlorins, 263ascolichens, 358ascoma morphologies

Pezizomycotina, 59–60ascomata, 228Ascomycetes, 23, 29, 55Ascomycota, 29, 30, 35, 55–61, 78, 346,

351, 438, 442asexual fungi, 56endophytes, 360important species, 55–6lichens, 79meiosis, 118morphology, 55septal pores, 99Woronin bodies, 99

Ascomycotina, 50ascospores, 55, 228ascostromata, 59Asellaria ligiae, 415Asellariales, 52, 53, 415asexual fungi, 180Ashbya gossypii

asynchronous nuclear division, 147aspartic proteinases, 247aspergillosis, 429–30, 430–1, 524aspergillosis disease of coral, 424Aspergillus awamori, 502

Aspergillus flavus, 189Aspergillus fumigatus, 262chitin synthase genes, 160genome, 544

Aspergillus giganteus, 484Aspergillus lentulus, 431Aspergillus nidulans, 42, 126, 127, 460,

467–8conidiophores, 220–3duplication cycle, 92–3genome, 544het genes, 186heterokaryon formation, 186mitosis, 116, 117mitotic gene segregation, 189, 192–4mutations, 116negative autotropism, 96nuclear migration, 132nutritional selection for diploid strains,189, 192–4

parasynchronous nuclear division, 148Aspergillus niger, 92, 189, 468, 474, 477Aspergillus oryzae, 189, 474, 484, 505, 506Aspergillus sojae, 505Aspergillus spp., 56, 60, 228, 262, 274aflatoxins, 330, 435–6aspergillosis, 429–30, 430–1in the home, 432proteinases, 246

Aspergillus sydowiiinfection of sea fans, 424

Aspergillus terreus, 55, 262, 431, 473Assembling the Fungal Tree of Life project.

See AFTOL studyAsterodon ferruginosus, 301Asterostroma spp., 332asthmatic reactionsallergic aspergillosis, 430

astral microtubules, 118, 146asynchronous division of nuclei, 146–8Atheliales, 66athlete’s foot, 425atmospheric pollutionchlorohydrocarbon release by wood-decay fungi, 336

sensitivity of lichens to, 358sources of chloromethane, 336

ATP, 121, 122ATP synthesisprimary metabolism, 251, 253

ATPase genesphylogenetic studies, 24–5

Atta spp., 396attine antsmolecular phylogenies, 396–7

Aureobasidium spp., 60Auricularia polytricha (wood ear fungus)

trade, 273Auriculariales, 67aurora australis, 22aurora borealis, 22autotropism, 96–7mycelium growth, 87–8

606 Index






auxotrophs, 181avirulence gene, 437avoidance mechanism in hyphae, 96azoles, 514, 517–21

Bacillus thuringiensis, 422bacteria, 326and soil health, 7numbers in soil, 7oldest known fossils, 23

bacterial artificial chromosome (BAC), 532bakanae disease of rice, 379baker’s yeast, 55, 105bark beetles, 373, 399barley (Hordeum), 11barley powdery mildew (Blumeria graminis

hordei), 371, 389barrage formationvegetative incompatibility response, 188

basidia, 228, 291, 293Basidiobolus ranarum, 55Basidiobolus spp., 55basidiolichens, 358basidiomata, 228–31Basidiomycetes, 23, 29, 61, 62basidiomycetous yeasts, 63Basidiomycota, 29, 35, 59, 61–71, 78, 338,

344, 346basidiospores, 62commercially farmed fungi, 71dolipore septum, 99ectomycorrhizas, 78largest and longest-lived fungi, 71lichens, 79mating types, 205–10meiosis, 118mutualistic associations with insects, 62number of species, 61phylogeny, 62–9

Basidiomycotina, 50basidiospores, 62, 228, 292, 380Batrachochytrium dendrobatidis, 43, 401,

422–4Beadle, George, 106bean (Phaseolus vulgaris), 62Beauveria bassiana, 419beech (Fagus), 346beer-making, 475–6beet leaf spot, 370beetlesagriculture in beetles, 399–400ambrosia beetles and fungi, 399–400

benomyl, 334, 522b-glucanfungal cell wall, 137

b1,3-glucan, 158, 163b1,3-glucan synthase inhibitors, 172b1,3-glucan synthases, 163b-tubulin, 25biflagellate zoospores, 75big bang theory, 19–21bilberry (Vaccinium), 78biodiversity

definition, 213biofilms, 28–9, 170biogeochemical transformations

role of fungi, 9–10bioinformatics, 531

analysis of large survey data sets, 563definition, 557effects of climate change on fungi, 563genomic data mining, 562genomics research data, 557mathematical modelling of hyphalgrowth, 566

non-genomic data, 557biolistic transformation, 551biological control, 63

arthropod pests, 421–2fungal pathogens of insects, 412mycoherbicide production, 492–3mycopesticide production, 492–3nematode-trapping fungi, 407Trichoderma spp., 444

biological speciescompatibility systems, 189

biological species concept, 71–4biology of incompatibility systems, 188–90bioluminescence in fungi, 246biopulping, 245bioremediation with fungi, 9–10, 238biotechnology

use of fungal enzymes, 4See also whole organism biotechnology

biotrophic fungi, 238, 327, 337, 338, 376–8bioweathering, 9bipolar heterothallism, 199

Neurospora spp., 203birch (Betula), 346, 347, 354bird mycosis

aspergillosis, 429bird’s-nest fungi, 228birds of prey

indirect dependence on fungi, 271–2bivalents formed during meiosis, 118black stem rust of wheat (Puccinia graminis

tritici), 373–4Blastocladiales, 29, 45, 46Blastocladiella spp., 47, 48–9Blastocladiomycota, 29, 45, 46–50

alternation of generations, 47free cell formation of zoospores, 48–50hormone production, 47–8life history, 47spore formation process, 48–50sportic meiosis, 47

Blastomyces dermatitidis, 150, 167, 428adhesin which potentiates infection, 170

blastomycosis, 170, 428Blobel, Gunter, 119blue–green algae, 254, 357Blumeria fischeri, 389Blumeria graminis, 371, 389Blumeria spp., 382–3Boletales, 64, 66Boletus edulis, 71, 344

Boletus elegans, 78, 338, 347Boletus parasiticus, 442Boletus spp., 78, 344, 347, 353mycorrhizal fungi, 337, 338

Bombardia spp., 60bootlace fungus. See Armillaria spp.Bordeaux mixture, 512Botrytis cinerea, 183, 382, 383–4, 385, 493Botrytis elliptica, 384Botrytis fabae, 384Botrytis spp., 384bovine spongiform encephalopathy (BSE),

196Bovril, 274Brachiola spp., 413bracket fungi, 228, 229bread, 4bread-making, 499–501brefeldin, 264brefeldin A, 162Bremia spp., 31brewer’s yeast, 55, 105Bridgeoporus nobilissimus, 71British Mycological Society, 562bromatia, 394bronchopulmonary aspergillosis, 430brown-rot fungi, 78, 238, 240Brundrett, Mark, 337Buchner, Eduard, 106budding yeast, 105, 116building structurescellar rot fungus, 332decay of structural timber, 331–3dry rot, 331–3wet rot, 332

bulk flow of nutrients, 248Buller’s drop, 229, 231buna shimeji (Hypsizygus marmoreus), 277buthiobate, 518button mushroom. See Agaricus bisporus

C3 and C4 photosynthetic pathways, 404Caecomyces spp., 401, 403cage fungi, 66calcium gradient in the hyphal tip, 141–2Calluna (ling)mycorrhizas, 337, 341

Calvatia gigantea, 71Camembert cheese, 264campesterol, 512cancer therapy patients.

See immunocompromised patientsCandida albicans, 59, 198, 425–6, 522, 525candidiasis, 429chitin synthase genes, 161phenotype switching, 429yeast–mycelial dimorphism, 150–1

Candida glabrata, 429Candida spp., 55chlamydospores, 214genomes, 545

candidiasis, 522Cantharellales, 66–9

Index 607






Cantharellus cibarius, 71, 272, 273, 337Cantharellus spp., 66carbendazim, 522carbohydrate catabolism, 251–2carbonationchemical weathering process, 6

carotenes, 260carotenoid pigmenation, 168carotenoids, 258, 260caspofungin, 521catastrophe (microtubule switch), 126celldiscovery of, 107

cell and tissue differentiationascomata, 228basidiomata, 228–31conidiation in Neurospora crassa, 223conidiomata, 223–5conidiophores of Aspergillus nidulans,

220–3diversity in relation to fungi, 214globose structures, 227–30linear structures, 225–7mycelial differentiation, 214–16rhizomorphs, 226–7rhythmic growth, 214–16sclerotia, 227–8spore formation, 216–20strand and cord formation, 225–7

cell cycle, 115–16budding yeast cell cycle, 150checkpoints, 149control and coordination of events,

148–50control of nuclear division, 148genetic studies on yeasts, 149–50phases, 149research, 107

cell deathvegetative incompatibility, 185

cell divisionfungi, animals and plants compared,

145–6cell inflationcoordination in the fruit body, 304–5

cell membrane, 107, 123–4cholesterol, 29ergosterol, 29structure, 123transport channels, 123

cell organelles, 107cell polarity, 148cell structureeukaryotes, 107–8prokaryotes, 107–8

cell targeting system, 48cell theory, 107cell-anchor receptors, 349cellar rot fungus, 332cellobiase, 240cellobiose oxidoreductases, 240cellular element term, 225cellulases, 240, 384

cellulose, 238in cell walls, 29

cellulose breakdown, 238, 239–40cellulosomes, 240Centraalbureau voor Schimmelcultures

(CBS), 562central vacuole, 124centrosomes, 116cep. See Boletus eduliscephalosporins, 264–3Cephalosporium acremonium, 474Ceratocystis fagacearum, 148Ceratocystis novo-ulmi. See Dutch elm

diseaseCeratocystis spp., 400Cercospora beticola, 372Cercospora spp.

leaf spot diseases, 372Ceriporiopsis subvermispora, 245Chain, Ernst, 478, 480chanterelles, 71, 272, 273, 337chaperonins, 119, 120checkpoints in the cell cycle, 116, 149cheese, 4, 56

blue cheeses, 275mould ripening, 275, 495, 503production, 501–5role of fungi in production, 274–5

chemical attractants, 47–8chemical pesticides

advantages and disadvantages, 421chemical safety information, 513chemical transformations

use of fungi, 486–7chemical weathering, 6

carbonation, 6hydration, 6hydroloysis, 6oxidation and reduction, 6

chemo-organoheterotrophism, 326chemostat cultures, 470–3chemotropic hyphae

Oomycota, 75Chernobyl incident, 327chestnut blight, 370chiasmata formed during meiosis, 118Chicxulub meteor impact

effects on fungi, 37–8chimeras, 290chitin, 158, 160

breakdown by fungi, 241fungal cell wall, 136–7in cell walls, 29measurement in soil, 7

chitin synthasefunctions in the cell wall, 160–2genes, 160–1inhibitors, 171–2

chitin synthesis inhibitors, 521–2chitinase, 241, 439chitosomes, 140, 161–2chlamydospores, 198, 214chloramphenicol, 195

chlorinated biphenyl pesticides, 334chloroaromatics, 245, 336Chlorociboria aeruginascens, 333chlorohydrocarbon release by wood-decay

fungi, 336chloromethane, 245sources of atmospheric pollution, 336

chloroplasts, 108, 121–2endosymbiont theory, 23, 121–2protein transport, 121

Choanozoa, 30, 77chocolate production, 495cholesterol, 133, 259, 512in cell membranes, 29

cholesterol levelsuse of statins to control, 4

chromatids, 109–12, 116chromatin structure, 109–12Chromocrea spinulosa, 202chromosome non-disjunction, 194Chrysanthemoides monilifera, 63Chrysosporium parvum, 442Chytridiales, 42, 45chytridiomycosisamphibians, 43, 422–4

Chytridiomycota, 29, 30, 35, 42–5classification as true fungi, 43–5habitats, 42important species, 42–3phylogeny, 43–5reproduction, 42–4roles in food-web dynamics, 43water moulds, 75

chytrids, 30, 42–5, 45–6ruminants and anaerobic chytrids, 400–5

Chytriomyces spp., 43ciliaendosymbiont theory, 23, 121

circadian rhythmsclock genes and proteins, 215–16feedback loops, 215mycelial growth, 214–16oscillators, 215, 216

citric acid biotechnology, 468, 477–8citrinin, 262cladedefinition, 28

cladisticsdefinition, 27–8

Cladobotryum dendroides, 444Cladonia spp., 60Cladosporium fulvum, 387Cladosporium spp., 432, 440clamp connections, 142, 184, 185classificationdefinition, 27

classification of fungi. See naturalclassification of fungi

clathrin coated pits, 123Claviceps purpurea, 259, 263, 434clay minerals, 6claysfungal–clay interactions, 9

608 Index






cleavage plane in cell division, 146cleavage polyadenylation specificity factor

(CPSF), 111cleistothecia, 59, 228climateeffects on soil formation, 6

climate changeeffects on fungi, 563impacts on mycorrhizas, 354–5

Clitocybe nebularismycelial network, 267

Clitocybe spp., 263, 353clock genes and proteins, 215–16closed mitosis in fungi, 115clotrimazole, 518clouded agaric, clouded funnel (Clitocybe

nebularis), 267Coccidioides immitis, 428Coccidioides posadasii, 161, 167, 428Coccidioides spp., 60coccidioidomycosis, 428, 522Cochliobolus carbonum, 378Cochliobolus heterostrophus, 203Coelomomyces spp., 47, 418, 419coelomycetes, 198co-evolution of plant–pathogen disease

systems, 387–9coffee production, 495–6collembola (springtails), 331grazing on fungi, 267–70

Colletotrichum graminicola, 161Collybia tuberosa, 246colonisation of solid substrata, 99colony formation, 86–8commercial applicationsmycorrhizas, 355–6

commercial exploitation of wildmushrooms, 272–4

commercial mushroom production, 71,275–9

mycoparasite problems, 443–4common ancestor of a group, 28comparative genomics, 547compatibility and the individualistic

mycelium, 180–1compatibility test, 185competitive interactions among fungi, 439–

44computer simulation of hyphal growth, 566concentration gradientsplasma membrane, 248

conidia, 53, 55conidia production, 198conidiation in Neurospora crassa, 223conidiomata, 223–5conidiophores, 53, 217–19Aspergillus nidulans

Coniferophyta, 343coniferyl alcohol, 242Coniophora puteana, 78Coniothyrium minitans, 493Coniphora puteana, 332

consensus model of hyphal tip extension,139–40

conservationimportance of records about fungi, 563

conservation patterns in genes, 24convergent evolution, 24, 227COPI coat protein complex, 122, 124COPII vesicle coat proteins, 122, 124copolymers, 240Coprinellus pellucidus, 290Coprinopsis bisporus, 200Coprinopsis cinerea, 117, 180, 189, 195,

210, 227, 252, 255, 311, 312, 444, 454developmental commitment, 308–10genome, 546metabolic regulation, 305–8tetrapolar heterothallism, 206–10

Coprinopsis congregatus, 208Coprinopsis fruit body

coordination of cell inflation in the fruitbody, 304–5

hymenia development, 291–5making gills, 295–301mushroom mechanics, 305stem development, 301–4

Coprinopsis patouillardii, 208Coprinopsis radiatus, 208Coprinopsis spp., 170, 185

use of protein, 246Coprinus cinereus, 117Copromyxa spp., 77coral disease

aspergillosis, 424coral fungus

ant agriculture, 396Corallorhiza spp., 346Cordyceps canadensis, 443Cordyceps capitata, 443Cordyceps militaris, 442, 443Cordyceps spp., 60, 442, 443Corticiaceae, 66Corticiales, 67cortisone, 486cosmid, 532coumaryl alcohol, 242Craterellus spp., 66Cretaceous–Tertiary (K–T) extinction event

effects on fungi, 37–8crown rust of wild oats, 389croziers, 142Cryphonectria parasitica, 186, 205Cryphonectria spp., 55Crypticola spp., 75cryptococcal meningitis, 62, 69cryptococcosis, 428, 546Cryptococcus neoformans, 327, 428

genome, 546phenotype switching, 429

Cryptococcus spp., 62, 69Cryptosporidium, 414crystalline cellulose, 239Cudonia spp., 60Cunninghamella bertholletiae, 55

Cunninghamella echinulata, 55Cunninghamella elegans, 55Cunninghamella spp., 55Currie, James, 477cushion bracket, 336cutaneous chytridiomycosisamphibians, 43, 422–4

cyanobacteria, 52, 340, 357cyber fungimodelling and computer simulation, 566Neighbour-Sensing model of hyphalgrowth, 566

cyclic AMP (cAMP), 134cyclin-dependent kinases, 56, 150cyclins, 150cyclopentanes, 264cyclosporine, 4, 473Cyllamyces spp., 401Cymbidium spp., 344Cyphomyrmex spp., 396cysteine proteinases, 247cystesia, 295cystidia, 228, 291, 292, 293Cystofilobasidiales, 66cytochromes, 25cytokinesiscomparison with septation, 145–6

cytoplasm, 107cytoplasmic segregation, 194–7mitochondria, 194–6plasmids, 195–6prion proteins, 196virus-like particles, 196

cytoskeletal systems, 125–7

Dacrymycetales, 66Dacrymycetes, 66Dactylellina spp., 406damping-off in seedlings, 327dandruff, 62Darwin, Charles, 7data mining, 314–15, 562databases of information about fungi, 562deep divergences, 28deep time, 26, 28Dendryphiella spp., 254dermatomycosis, 426–7‘Destroying Angel’ (Amanita virosa), 62Deuteromycetes, 23, 29, 56, 198Deuteromycota, 56, 198Deuteromycotina, 56, 198developmental biology of fungi, 282–316activator–inhibitor model, 293apoptosis, 315–16basic principles, 316bulbangiocarpic development, 287comparison with other tissues andorganisms, 310–11

comparison with plants and animals,283–5

competence, 289–90coordination of cell inflation in the fruitbody, 304–5

Index 609






developmental biology of fungi (cont.)Coprinopsis cinerea, 289Coprinopsis fruit body, 291–5, 295–301,

301–4, 304–5definition of development, 284definition of morphogenesis, 285degeneration, senescence and death,

315–16development and morphogenesis, 283development of a mushroom, 284developmental commitment, 308–10developmental variants, 311–12, 312–13differential growth, 283distinctive characteristics of fungi, 283–5endocarpic development, 288environmental influences, 290formal terminology of developmental

biology, 283–5formation of multicellular structures, 283fruit body chimeras, 290fungal wall remodelling, 283fuzzy logic approach, 313–14genetic approaches, 311–15genomic data mining, 314–15geometric proportions of the stem, 286gymnocarpic development, 286gymnovelangiocarpic development, 287hymenia development, 291–5hyphal analysis, 301–4hyphal tuft (hyphal knot), 283making gills, 295–301making stems, 301–4metabolic regulation and morphogenesis,

305–8modular nature of fungi, 283morphogenetic field model, 293morphogenetic polarities, 291mushroom mechanics, 305observational and experimental basis,

285–6pattern formation, 283, 284patterning genes, 314pilangiocarpic development, 287placement of hyphal branches, 285polypore growth patterns, 300–1pore formation in polypores, 301primordia, 283programmed cell death, 315–16regional patterning (regional

specification), 283, 290–1renewed fruiting, 315stipitangiocarpic development, 288terminology, 283tolerance of imprecision, 312–13tube formation in polypores, 301typical mushroom structure, 285–6velangiocarpic development, 289

developmental variants, 311–12, 312–13Devonian Rhynie chert, 31, 403, 442Diaporthe spp., 60Dicranophora spp., 440Dictylenchus myceliophagus, 270dictyosomes, 122, 124

Dictyosteliales, 77Dictyostelium spp., 77Didymium spp., 77dieldrin, 334diffusion of nutrients

facilitated diffusion, 133, 248–9simple diffusion, 248

Dikarya, 29, 35dikaryon, 207

definition, 180functional diploidy, 183–5maintaining the dikaryon state, 184–5

Dimargaris spp., 440, 442Dimargaritales, 52dimorphism

yeast and mycelial growth forms, 150–1diploid state in fungi, 117

dikaryon, 183–5diploid strains

nutritional selection for, 189dipteran fly larvae (maggots), 270–1Dipterocarpaceae, 346disease triangle, 374–6Dispira spp., 440diterpenes, 259Diversispora spp., 340diversity

ascomata, 228basidiomata, 228–31biodiversity in fungi, 213complexity of the concept, 7conidiation in Neurospora crassa, 223conidiomata, 223–5conidiophores of Aspergillus nidulans,220–3

definition, 214ecosystem level aspects, 7globose structures, 227–30in relation to fungi, 214linear structures, 225–7mycelial differentiation, 214–16production and dispersal of spores, 214rhizomorphs, 226–7rhythmic growth, 214–16sclerotia, 227–8spore formation, 216–20stipes of fruiting bodies, 227strand and cord formation, 225–7

DNA, 107chromatin structure, 109extrachromosomal, 108introns in fungal DNA, 114molecular processes in the nucleus, 109plasmids, 108prokaryotes, 107replication before meiosis I, 117

DNA microarrays, 559DNA probes

soil microbes, 8dolipore septum, 99Domain Archaea, 24, 26–8Domain Eubacteria, 24, 26–8Domain Eukaryota, 24, 26–8

domains of the tree of life, 23–9Donkioporia expansa, 332dormancy in spores, 86Dothidea, 60Dothideomycetes, 60, 61, 438Dothidia spp., 60double-stranded RNA (dsRNA) virus, 196Douglas fir, 347Drechslerella spp., 406Drosophila (fruit fly), 206Drosophila funebris, 270Drosophila melanogaster, 115drug discovery approach (Ehrlich), 512drug targets, 107dry-rot fungus, 226, 331–3Ducellieria spp., 75Duddingtonia flagrans, 407duplication cycle in fungi, 92–3Dutch elm disease (Ophiostoma novo-ulmi),

370, 372–3role of elm bark beetles, 373, 399

dynactin, 116, 117, 129dynein, 117, 129microtubule-associated dynein, 127–33molecular motors, 127–33

dynein motors, 116, 127

early-stage fungi, 354Earthaxial tilt, 22, 23development of life on, 23–9effects of the solar wind, 22–3formation of, 21greening of the Earth, 28–9magnetic field (magnetosphere), 22–3molten iron core, 21, 22ozone layer, 22–3rate of rotation, 22seasons, 22, 23temperature range for liquid water, 21–2Theia–Earth impact, 22, 23

Earth–Moon binary system, 22, 23earthwormsDarwin’s experiments on, 7numbers in soil, 7

Eccrinales, 52, 77echinocandins, 172, 521–2ecological species concept, 74ecosystem diversity, 7ecosystem functions of fungi, 237–64bioluminescence in fungi, 246bioremediation, 238biotrophs, 238breakdown of agricultural wastes, 238breakdown of cellulose, 239–40breakdown of chitin, 241breakdown of glycogen, 242–3breakdown of hemicellulose, 241breakdown of pectins, 241breakdown of polysaccharides, 239–42breakdown of starch, 241–2breakdown of toxic wastes, 238external digestion in fungi, 237

610 Index






flow of nutrients, 247–51fungal nutritional modes, 238lignin degradation, 242–6necrotrophs, 238primary (intermediary) metabolism,

251–6production of esterases, 247production of extracellular enzymes, 239production of lipases, 247production of phosphatases, 247production of sulfatases, 247protein digestion, 246–7range of contributions, 238–9release of greenhouse gases, 245–6saprotrophs, 238secondary metabolites, 257transport and translocation of nutrients,

247–51wood-decay fungi, 238

ecosystem mycology, 77–9, 325–61aquatic fungi, 78chemo-organoheterotrophism, 326chlorohydrocarbon release by wood-

decay fungi, 336decay of structural timber, 331–3degradation of man-made polymers,

333–4ecosystem roles of fungi, 325–6effects of land management practices,

326endophytes, 79, 360–1environmental issues, 326epiphytes, 79, 361food contamination and deterioration,

328–31fungal contribution to soil structure, 326fungi as food for other organisms, 326fungi as predators, 326fungi as prey, 326fungi as recyclers, 326–8habitat creation by fungi, 326inorganic transformations, 327lichens, 79, 356–60mutualism, 325mycorrhizas, 78–9, 336–56nitrogen sources in plant litter, 327nutrient availability, 327parasitic fungi, 326pathogenic fungi, 326physical power of growing fungi, 328–30recalcitrant waste remediation, 334–6saprotrophic fungi, 326–8toxic waste remediation, 334–6toxins produced by fungi, 328–31waste remediation, 334–6wood-decay fungi, 78, 327

ectendomycorrhizas, 338, 343, 346, 351ectomycorrhizas, 62, 78–9, 338, 346–51cell-anchor receptors, 349mobile signal ligands, 349nutrient exchange, 349–50

ectotrophic mycorrhizas, 337edible mushrooms, 71

edifenphos, 526Ehrlich, Paul

drug discovery approach, 512Elaphomyces muricatus, 443Elaphomyces spp., 442electrochemical proton gradient, 133Electrogella spp., 75electromagnetic radiation

resistance to, 167electrophoresis technique, 115electroporation, 550element cycling, 9elements

creation in stars, 20elm bark beetles, 373, 399Embden–Meyerhof–Parnass (EMP)

pathway, 251emergence of new diseases, 424Emericella spp., 42Encephalitozoon cuniculi, 413Encephalitozoon hellem, 413Encephalitozoon intestinalis, 413endocytosis, 123endo-enzymes, 239endoglucanase, 240Endogonales, 52, 53Endogone spp., 346endomembrane systems, 121–5endomycorrhizas, 51, 78, 337–9Endophyllum spp., 62endophytic fungi, 79, 360–1endoplasmic reticulum (ER), 120, 122, 124,

163endospores, 228endosymbiont theory, 23, 121–2, 195endotrophic mycorrhizas, 337endoxylanases, 240enilconazole, 518enoki (Flammulina velutipes), 277enokitake (Flammulina velutipes), 71Enterocytozoon bieneusi, 413Entner–Doudoroff (ED) pathway, 252entomogenous fungi, 417–21Entomophthora muscae, 55, 421Entomophthora spp., 419Entomophthorales, 52, 53, 417Entomophthoromycotina, 30, 52Entrophospora spp., 52, 340environmental biotechnology

use of fungi, 9–10enzymes secreted by fungi, 239

immobilisation, 239medical uses, 4use in biotechnology, 4

Epacridaceae, 341Epacris spp., 341epidemiology of fungal infections, 430–2,

436–9Epidermophyton spp., 426epigenetic phenomena

phenotype switching, 429epigeous taxa, 66epiphytic fungi, 79, 361

ergobasines, 435ergocristine, 263ergosterol, 133, 259–61in cell membranes, 29measurement in soil, 8target for antifungal agents, 512–21

ergot alkaloids, 263, 473ergotamines, 435ergotism (ergot poisoning), 434–5ergotoxines, 435Erica (heather)mycorrhizas, 337, 341

Ericaceaemycorrhizas, 341–3

Ericales, 343ericoid endomycorrhizas, 78, 337, 341–3ericoid mycorrhizasfacultative symbiosis, 342

Erynia neoaphidis, 418Erysiphe graminis, 327, 371Erysiphe spp., 382erythromycin, 195Erythrorchis spp., 345Escherichia coli genome, 537Escherichia spp., 106esterases, 247ethylenediamine tetra acetic acid (EDTA),

247euagarics clade, 63euascomycetes, 56, 59Eubacteria, 24Eucalyptus spp., 346, 347Eucarya, 24Eukaryota, 24eukaryote cell biologycontribution of fungal research, 105–7

eukaryote/prokaryote distinction, 23eukaryotescell structure, 107–8early anaerobic forms, 23first terrestrial eukaryotes, 37fungus as model eukaryote, 105–7modes of nutrition, 29primitive present-day forms, 23

eukaryotic cellssubcellular components, 109

Euler-Chelpin, Hans von, 106Eumycota, 29EUROSCARF collection, 557Eurotiomycetes, 60, 61, 438Eurychasma spp., 75evolutionary clock, 24evolutionary origins, 18–38big bang theory, 19–21collision during Earth’s development, 21creation of the elements, 20development of life on Earth, 23–9domains of the tree of life, 23–9Earth–Moon binary system, 22, 23Earth’s magnetic field (magnetosphere),22–3

effects of extinction events, 37–8formation of the Earth, 21–3

Index 611






evolutionary origins (cont.)formation of the Moon, 21, 23formation of the oceans, 21fossil fungi, 31–3fungal phylogeny, 35–8Goldilocks orbit of the Earth, 21–2greening of the Earth, 28–9heterokonts, 30–1Kingdom Fungi phylogenetic

classification, 29–30location of the Earth’s orbit, 21–2molecular phylogenetic studies, 33oldest known fossils, 23opisthokonts, 30phylogenetic classification systems, 23–9Theia–Earth impact, 21, 23

evolutionary species concept, 74Exobasidium camelliae, 440Exobasidium spp., 62exocytosis, 123exo-enzymes, 239exoglucanase, 240Exophiala werneckii, 442exospores, 228exportins, 113extinction eventseffects on fungi, 37–8

extracellular matrices, 159extracellular proteinases, 246–7extraradical mycelium, 349extreme environments, 8

fabric manufactureenzymes used in, 483–4, 484–6

facilitated diffusion, 248–9plasma membrane, 133

facultative symbiosisericoid mycorrhizas, 342

FADH2, 252, 253fatsprimary metabolism, 254–5

fatty acid synthesis, 261–3feedback fixation, 222feedback loopscircadian rhythms, 215

fermentation processes. See whole organismbiotechnology

fermentation research, 105–6fermented foods, 274–5fibre hyphae, 225filamentous cell cycle, 216filamentous extension strategy, 86filamentous mould fungi in amber, 32–3filasomes, 141Filobasidiales, 66Filobasidiella neoformans, 69Filobasidiella spp., 62fir (Abies), 346fission yeast, 118flagella, 107endosymbiont theory, 23, 121

flagellin, 107flagellum

loss of, 35Flammulina velutipes, 71flax rust (Melampsora lini), 371, 389Fleming, Alexander, 478, 480Florey, Howard, 478, 480fluconazole, 429, 5185-fluorocytosine, 522fluotrimazole, 518fly agaric. See Amanita muscariaFolsomia candida, 270Fomes annosus, 264Fomes fomentarius, 273food contamination and deterioration,

328–31aflatoxins, 330

food from fungi, 326ang-kak, 274birds of prey, 271–2button mushrooms (Agaricus bisporus),276–8

cells and mycelium as human food, 274cheeses, 274–5Collembola (springtails), 267–70commercial exploitation of wildmushrooms, 272–4

commercial mushroom production,275–9

development of a fungal fruit body, 280fermented foods, 274–5, 504–6fermented meat products, 503–4fermented soy foods, 504–6fungi as food, 267–8fungi in food webs, 267–72gardening insects and fungi, 279–80gourmet fungi, 272–3gourmet mushrooms, 278industrial cultivation of fungi, 275–9larvae (maggots) of dipteran flies, 270–1lichens, 358microarthropod fungivores, 267mites, 270mushroom flies, 270–1mycelial networks at the soil–litterinterface, 267

myco-protein, 274nematodes, 270New Zealand wood ear fungus trade, 273nutritional value, 266oyster mushrooms (Pleurotus spp.), 278paddy straw mushroom (Volvariellavolvacea), 279

Quorn™ myco-protein, 274shiitake (Lentinula edodes), 278–9slugs and snails, 271small mammals, 271–2soy sauce, 274tempeh, 274truffles (Tuber spp.), 279wild harvests, 272–4yeast extracts, 274

food web connected to soil, 7food webs

fungi as food, 267–72

foregut fermentationruminants, 403

forestry wastelignocellulose biodegradation, 497–9

formin-homology (FH) proteins, 145formins, 126fossil fungi, 31–3, 51, 326, 407lichens, 357

fossilsoldest known fossils, 23

Frank, Albert Bernhard, 336free cell formation of zoospores, 48–50Fries, Elias, 71fructose bisphosphatase, 254fruit bodies, 226ascomata, 228basidiomata, 228–31development, 167–8formation, 96–7, 184, 185gills or lamellae, 228–9pores, 228–9

Fugu rubripes (puffer fish), 114Fuligo spp., 77fumigatin, 262functional genomics, 558fungal biodiversityin general, 8–9in soil, 7–8measurement challenges, 7–8number of undescribed fungi, 7–8, 8–9number which cannot be cultivated, 7–8

fungal cell biology, 104–51cell cycle, 115–16cell membrane, 107cell plasma membrane, 123–4cell structure, 107–8cell wall, 136–7central vacuole, 124chloroplasts, 121–2chromatids, 109–12, 116chromatin structure, 109–12closed mitosis, 115contribution of yeast research, 105–7cytokinesis and septation, 144–50cytoplasm, 107cytoskeletal systems, 125–7DNA, 107, 108endomembrane systems, 121–5endoplasmic reticulum (ER), 120, 122,124

extrachromosomal DNA, 108fungus as model eukaryote, 105–7genetic material, 107, 108genome plasticity, 115Golgi apparatus, 120, 122–3, 123–5hyphal extension mechanisms, 105,137–42

hyphal fusion, 142–4intranuclear mitosis, 115karyotypes, 115meiotic nuclear division, 117–18mitochondria, 121–2mitotic nuclear division, 115–17

612 Index






molecular motors, 127–33movement, 127–33mRNA translation, 118–19mycelial growth mechanisms, 105mycelial interconnections, 142–4nature of the fungal cell, 99–100nuclear–cytoplasmic trafficking, 114nuclear genetics, 114–15nuclear migration, 116–17nucleolus, 112–13nucleus, 108–12number of nuclei per cell, 117organelles, 107peroxisomes, 120plasmalemma, 123–4plastids, 121–2ploidy and nuclear number, 117protein destruction, 121protein sorting/targeting mechanism,

119–21protein synthesis in the cytoplasm,

118–19RNA, 107Saccharomyces cerevisiae as model

organism, 105–7septal pores, 99septation and cytokinesis, 144–50signalling pathways, 134–5Spitzenkorper, 125subcellular components of eukaryotic

cells, 109transmembrane proteins, 120transport vesicles, 124yeast–mycelial dimorphism, 150–1

fungal cell wall, 136–7, 156–72active interface, 136adaptation to varying conditions, 157adhesins, 168–70adhesive properties, 158antigenic properties, 158as a clinical target, 171–2as a working organelle, 157b-glucan, 136, 137, 163functions of b1,3-glucan synthases, 163carotenoid pigmenation, 168cell shape, 159cellulose, 29chitin, 29, 136–7, 158, 160dynamic structure, 136extracellular matrices, 159fibrillar polysaccharides, 157functions of chitin synthases, 160–2glomalin, 171glucans, 158, 162–3glycoproteins, 158, 163–5hydrophobic/hydrophilic properties, 158hydrophobins, 170–1hyphal tip extension, 165internal thickenings, 167–8maintenance of cell shape, 157mannans, 158mannoproteins, 137melanin pigmentation, 167

molecules on the outer surface, 168–71outer surface, 168–71pigmentation, 167–8polysaccharides, 158–9protection against physical stress, 157proteins, 158, 163–5scaffold for proteins, 157secondary hyphal walls, 167–8structural components, 136–7structure and function, 157–60studies of model fungal systems, 157surface properties, 158target for antifungal agents, 157taxonomic significance, 158–9turgor pressure, 159two-phase system, 159–60wall architecture, 160wall synthesis and remodelling, 165–8

fungal coloniesmorphological differentiation, 92–5

fungal co-operative ventures, 393Fungal Genetics Stock Center (FGSC), 562Fungal Genome Initiative, 547fungal growth forms

yeast–mycelial dimorphism, 150–1fungal individual

definition, 188fungal individuals

and incompatibility systems, 188–90fungal karyotypes, 115fungal life style

contribution to eukaryote cell biology,105–7

exploitation of substrates, 86exploration and invasion, 85–6heterokaryosis, 180–1

fungal nomenclature, 52fungal origins

fossil evidence, 31–3molecular phylogenetic studies, 33

fungal pathogensstrains of varying pathogenicity, 186

fungal pegs, 344fungal phylogeny, 35–8Fungal Records Database of Britain and

Ireland (FRDBI), 562fungal species

naming, 42naming of sexual and asexual stages, 42numbers of, 42

fungal taxonomyprincipal taxonomic ranks, 28

fungal toxinsaflatoxins, 330Amanita muscaria, 328–30poisoning, 433–6potential as weapons, 331statins, 331strobilurins, 331

fungibeneficial effects, 4contribution to human existence, 4databases of information about, 562

importance of, 4–5mistaken ideas about, 4–5nature of fungi, 4–5pathogens, 5primitive biofilms, 28–9where and what they are, 4–5

Fungi Imperfecti, 23, 29fungi in the homeeffects on health, 432–6

fungicidesstrobilurins, 331

fungicolous fungi, 439–44fungus as model eukaryote, 105–7fungus gardening. See ant agriculture;

termite gardenersfusaric acid, 378Fusarium moniliforme, 259, 379Fusarium oxysporum, 148, 353, 384, 493Fusarium solani, 432Fusarium spp., 55, 327, 378, 442chlamydospores, 214genomes, 545

Fusarium venenatum, 56, 461, 473, 474,487–92

fuzzy logic approach, 313–14

galactanases, 241galactans, 240galectins, 170Galeola spp., 346gall wasps, 361gall-forming insects, 361gallic acid, 263Ganoderma spp.cultivation, 279traditional herbal medicine, 279

gardening insects and fungi, 279–80gasteromycetes, 288Gastrodia elata, 344, 346Gastrodia spp., 344, 346Geastrales, 66Gelasinospora tetrasperma, 116, 208geldanamycin, 525gene ontology, 540gene-for-gene interactions, 387–9general transcription factors, 109–10genesconservation patterns, 24duplications, 24evolutionary clock, 24expression, 109–10rate of mutation, 24rate of mutational change, 24segregation during mitotic division,189–94

genetic approaches to development,314–15

developmental variants, 311–12, 312–13molecular genetics, 312–15

genetic control of mating, 201mating type switching in budding yeast,201–3

genetic material

Index 613






genetic material (cont.)in eukaryotes, 107plasmids, 108

genetic researchcell cycle in yeasts, 149–50yeast breeding experiments, 106

genetic variationco-evolution of plant–pathogen disease

systems, 387–9parasexual cycle, 194

geneticsapplied genetics, 388mapping panels, 529molecular studies of pathogen virulence,

389research, 106–7restriction mapping, 529steps in understanding fungal genetic

structure, 531genome analysisfungal genome plasticity, 115fungal genome size, 114introns in fungal DNA, 114protein-coding genes, 115

genomics, 531, 557annotating the genome, 540comparing genomes, 537comparison of fungal genomes, 547data mining, 314–15, 562functional genomics, 550Fungal Genome Initiative, 547manipulating genomes, 552recombinant vectors, 552reverse genetics, 550sequencing fungal genomes, 535targeted gene disruption, 550transformation of cells, 551

genospecies, 189Geoglossum spp., 60geological time, 28geomycology, 9–10Geosiphon pyriformis, 52, 340Geosiphon spp., 340Geosiphonaceae, 52Geotrichum candidum, 460geranylpyrophosphate, 258germicidal UV (UV-C), 22–3giant puffball (Calvatia gigantea), 71Gibberella fujikuroi, 185, 259, 379gibberellins, 259, 379Gigaspora gigantea, 442Gigaspora spp., 52, 340, 441Gigasporaceae, 52, 338, 340Gilbertella persicaria, 49–50gills or lamellae of the fruit body, 63, 66–9,

228Ginkgo, 343Gliodadium spp., 440Gliomastix spp., 442globose structures, 227–30Gloeophyllales, 67Glomales, 35, 50glomalin, 171

Glomeraceae, 51, 340Glomerales, 51, 340Glomerella cingulata, 202Glomeromycota, 29, 32, 35, 50–2, 78, 337,

338, 340, 441arbuscules, 51difficulty of studying, 50–1endomycorrhizal associations, 51importance to land plants, 51phylogeny, 51–2reproduction, 51vesicular-arbuscular mycorrhizas, 51

glomeromycotan fossils, 31–2Glomus spp., 52, 78, 340, 441glucanases, 439glucans, 158, 162–3glucoamylases, 241gluconeogenesis

primary metabolism, 253–4glucose-stat cultures, 473glucosidases, 242glutamate decarboxylation loop, 253glutamate dehydrogenase, 254glutamine synthetase, 308glutamine synthetase/glutamate synthase

system, 256glutaminyl hydroxybenzene (GHB), 263glycogen degradation, 242–3glycolysis, 251–2, 254glycoproteins

fungal cell wall, 163–5glycosylphosphatidylinositol (GPI) anchors,

135, 164–5glyoxal oxidase, 243, 245Golgi apparatus, 120, 122–3, 123–5Gomphales, 66gomphoid–phalloid fungi, 66gongylidia, 394gourmet fungi, 272–3gourmet mushrooms, 278GPI anchors, 135, 164–5G-protein-coupled receptors, 135G-proteins, 134–5, 206Graphiola spp., 62grasses (Poaceae), 62

C3 and C4 photosynthetic pathways, 404genome analysis, 114

gravitropism, 231grazing animals

and anaerobic fungi, 400–5Great Dying (extinction event)

effects on fungi, 37–8greenhouse gases

chlorohydrocarbon release by wood-decay fungi, 336

chloromethane, 336fungal breakdown products, 245–6

greening of the Earth, 28–9grey mould pathogen, 382, 383–4griseofulvin, 127, 262, 522, 526GTP (guanosine triphosphate), 252, 253GTP hydrolysis, 126Guinness Book of World Records

largest and longest-lived fungi, 71gyrocyanin, 263Gyromitra spp., 60Gyroporus cyanescens, 263

habitat creation by fungi, 326Haeckel, Ernst, 23Haliphthoros spp., 75hallucinogenic toxins, 62hamathecium (hamathecial tissue), 60haploid nature of fungal mycelia, 179haploid nature of true fungi, 180–1haploid state in fungi, 117haploidisation, 194Haptoglossa spp., 75Haptoglossales, 75Harden, Arthur, 106Harpellales, 52, 53, 415Hartig net, 338, 343, 344, 346, 347, 351Hartwell, Lee, 56Hartwell, Leland, 105, 107haustoria produced by plant pathogens,

371–2HC-toxin, 378heather (Erica), 78Heatley, Norman, 480heat-shock proteins, 98Hebeloma mesophaeurn, 442Helminthosporium maydis, 378Helminthosporium victoriae, 378hemiascomycetes, 56hemibiotrophic fungi, 376–8, 382hemicellulases, 384hemicellulose, 238hemicellulose breakdown, 238, 241Hemitomes spp., 343herbal medicineGanoderma spp., 279

herbivore digestionanaerobic chitrids, 45–6role of fungi, 4

herbivore dungbreakdown of, 238

Herpomyces spp., 60het loci, 185–6, 188Heterobasidion annosum, 69Heterodera avenae, 407heterogeneous nuclear ribonucleoproteins

(hnRNPs), 112heterokaryon, 117, 180breakdown, 183–4definition, 180phenotype, 181–3propagation of the state, 183

heterokaryon formation, 181–3positive autotropism, 181vegetative compatibility, 185–8

heterokaryon incompatibility.See vegetative compatibility

heterokaryosisand hyphal anastomosis, 180–1benefits for fungi, 181consequences, 181–3

614 Index






expression of mutations, 181heterokaryotic mycelium, 117heterokontsevolutionary origins, 30–1

Heteropeza pygmaea, 271heteroplasmic mixtures, 195heteroplasmons, 195heterothallic fungi, 180, 199–200Hevea brasiliensis, 261hexatriyene, 264hexokinase, 253hexose monophosphate pathway, 252high mobility group (HMG) proteins, 205hindgut fermentationnon-ruminant herbivores, 403

hispidin, 263histoneschromatin structure, 109

Histoplasma capsulatum, 150, 167, 428, 438Histoplasma spp., 60histoplasmosis, 428, 522history of the fungi, 326HIV patientsCandida albicans infections, 59, 150–1See also immunocompromised patients

HIV-related opportunistic infections, 425–6HMG-CoA reductase inhibitors, 262, 331HMT toxin, 378Hodgkin, Dorothy, 478homeobox, 206homeodomain proteins, 206homeotic (Hox) genes, 206Homo genusemergence in the Pliocene, 404

homobasidiomycetes, 63homokaryon, 183, 207definition, 180

homologous organs, 63homothallic fungi, 180, 199, 200homotypic interactions, 168honey bee (Apis melifera)microsporidian parasite, 414

honey fungus. See Armillaria melleahoof fungus, 273Hooke, Robert, 107horizontal mitochondrial transmission, 195hormone production in fungi, 47–8hormones involved in sexual reproduction,

199host-selective toxins, 384host-specific toxins, 378Hubble Ultra Deep Field (HUDF), 20human dependence on fungi, 15human fungal infectionsaflatoxicosis, 435–6African histoplasmosis, 428allergic reactions, 433aspergillosis, 429–30, 430–1athlete’s foot, 425blastomycosis, 428Candida albicans, 150–1candidiasis, 425–6, 429clinical groupings, 426–32

coccidioidomycosis, 428cryptococcal meningitis, 62cryptococcosis, 428cutaneous mycoses, 426dermatomycosis, 426–7effects of fungi in the home, 432–6epidemiology, 430–2ergotism (ergot poisoning), 434–5fingernails, 426fusariosis, 432histoplasmosis, 428HIV-related opportunistic infections,425–6

infant pulmonary haemorrhage, 432infantile pneumonia, 431ingestion of toxins, 433–6microsporidiosis, 413mycetoma (madura foot), 427mycoses, 424–6North American histoplasmosis, 428onychomycosis, 426opportunistic infections, 5, 54, 55, 59,425–6, 428

opportunistic systemic mycoses, 428–30Piedraia hortae, 426pneumocystis pneumonia (PCP), 431pneumocystosis, 431poisoning from fungal toxins, 433–6resistance in fungal pathogens, 430–1ringworm, 425rose-handler’s disease, 427sick building syndrome, 432sporotrichosis, 427St Anthony’s fire, 434–5subcutaneous mycoses, 426–7superficial mycoses (tineas), 426systemic mycoses, 427–30thrush, 429toenails, 426Trichosporon cutaneum, 426valley fever, 428zygomycosis, 431–2

human geneticsgene assignments to chromosomes, 194

human genome, 114humic substances (humus), 6Hunt, Tim, 56, 105Hyaloraphidium curvatum, 30hybridisation array analysis, 558hydration

chemical weathering process, 6hydrogen peroxide, 384hydrogenosomes, 45, 46, 402hydroloysis

chemical weathering process, 6hydrophobins, 137, 170–1

amphipathic structure, 170hymenia development, 291–5hymenium, 228Hymenochaetaceae, 66Hymenochaetales, 66, 67Hymenochaete corrugata, 227hymenomycetes, 62, 63

commercially farmed fungi, 71Hymenoscyphus ericae, 78, 337Hymenoscyphus spp., 60hypermycoparasite fungi, 443hypersensitive response, 388hyphaequantity in soil, 7

hyphal analysis, 301–4hyphal branching, 97–9and septation, 97–8branch initiation, 97–9pattern of branching, 97

hyphal differentiation, 92–5hyphal extensiondefinition, 88mechanisms, 105

hyphal fusion, 96–7, 117, 142–4and mycelium functioning, 181heterokaryon formation, 181–3heterokaryosis, 180–1non-sexual fusions, 181ping-pong signalling mechanism, 142–3potential hazards, 185pre-contact behaviour, 142role of the Spitzenkorper, 142self-signalling between hyphal tips,142–3

stages in the process, 142vegetative compatibility, 185–8

hyphal growthapical growth process, 100autotropic reactions, 96–7autotropism, 87–8avoidance mechanism, 96branch initiation, 97–9branching, 97–9branching processes, 86–8colonisation of solid substrata, 99computer simulation, 564distinction between growth andextension, 88

duplication cycle, 92–3emergence of germ tubes (hyphal tips),86

germ tube extension, 87germination of spores, 86–7hyphal fusion, 87, 96–7mathematical modelling, 564mode of growth, 86, 88–91, 94–7negative autotropism, 96Neighbour-Sensing model, 564nuclear migration regulation, 93–4nuclear mitosis, 93–4pattern of branching, 97positive autotropism, 96–7rates of growth, 86–8septation, 92–3, 99–100size-detecting mechanism, 93synchronous mitosis, 93types of septa, 99viscoelastic cell wall, 100

hyphal growth kinetics, 88–91mathematical models, 94–7

Index 615






hyphal tip extension, 137–42cell wall, 165consensus model, 139–40hyphoid model, 138–9steady state (soft spot) model, 139tip-high calcium gradient, 141–2turgor pressure, 137–8

hyphal tuft (hyphal knot), 283Hyphochytriomycota, 29, 75, 77Hyphochytrium spp., 77hyphoid model of hyphal tip extension,

138–9hyphomycetes, 198Hypocrea spp., 60Hypocreales, 60hypogeous taxa, 66Hypsizygus tessulatus, 71Hysterangiales, 66hysterothecia, 60

ibotenic acid, 329Iceman (Neolithic traveller)fungal products found with, 273

igneous rocks, 6imazalil, 518imidazoles, 518immune system responseeffects of hydrophobin, 170

immunocompromised patientsaspergillosis, 430–1candidiasis, 425–6cryptococcal meningitis, 62cryptococcosis, 428epidemiology of fungal infections, 430–2fusariosis, 432microsporidiosis, 413opportunistic infections, 5, 54, 55, 59,

150–1opportunistic systemic mycoses,

428–30pneumocystis pneumonia (PCP), 431pneumocystosis, 431zygomycosis, 431–2

imperfect fungi, 194, 198–9importins, 113incompatibility mechanisms, 117incompatibility systemsfungal individuality, 188–90

infant pulmonary haemorrhage, 432infantile pneumonia, 431ink cap mushroom. See Coprinopsis

cinereaInocybe spp., 263Inonotus spp., 245inorganic transformations, 327insects, 326entomogenous fungi, 417–21fungal pathogens, 412gardening insects, 279–80Laboulbeniales pathogens, 416–17mutualistic associations with fungi, 62pathogenic gut fungi (Trichomycetes),

414–16

insertional mutagenesis, 389integrated pest management (IPM), 422intermediary metabolism. See primary

metabolismintermediate filaments (cytoskeleton), 126International Programme on Chemical

Safety, 513interzonal microtubules, 146intracellular proteinases, 246intranuclear mitosis, 115introns in fungal DNA, 114invertebrates

fungal toxins, 330ion channels, 133–4ion pumps, 249ionising radiation

resistance to, 167IQGAP proteins, 145iron core of the Earth, 21, 22iron-binding compounds, 264itraconazole, 518

Jirovec, Otto, 56, 431

K-selected species, 354karyogamy, 117, 118, 198karyopherins, 113ketoconazole, 518Kickxellales, 52Kickxellomycotina, 30, 52, 442killer phenomenon

Kluyveromyces lactis, 196kinesins, 128–9

microtubule-associated kinesins, 127–33molecular motors, 127–33

kinetochores, 116, 118King Oyster (Pleurotus eryngii), 277Kingdom Animalia, 23, 30Kingdom Chromista, 29, 30–1, 75–7, 158,

160Kingdom Fungi, 4–5, 23

anaerobic chytrids, 45–6Ascomycota, 55–61Basidiomycota, 61–71Blastocladiomycota, 46–50Chytridiomycota, 42–5chytrids, 42–5, 45–6common ancestor with animals andplants, 29

distinctions from animals and plants, 29Glomeromycota, 50–2members of the Kingdom, 42monophyletic group, 29–30Neocallimastigomycota, 45–6phylogenetic classification, 29–30phylogeny, 35–8tree of life, 35–8Zygomycota, 52–5

Kingdom Monera, 23Kingdom Plantae, 23Kingdom Protista, 23Kingdom Protozoa, 77Kluyveromyces lactis, 502

killer phenomenon, 196Koch’s postulates, 424Kornberg, Roger D., 107Krebs (TCA) cycle, 252, 477kuru, 196

La France disease, 196Laboulbeniales, 60, 416–17Laboulbeniomycetes, 60Labyrinthula spp., 77Labyrinthulales, 77Labyrinthulomycota, 77Laccaria proxima, 354laccases, 243, 245Lacrymaria spp., 261lactarinic acid, 261Lactarius rufus, 261Lactarius spp., 261Lagena spp., 75Lagenisma spp., 75Lagenismatales, 75land management practiceseffects on fungal populations, 326

larch (Larix), 347, 351mycorrhizal associations, 338

large ribosomal RNA subunit, 33largest fungal structures, 71late stage fungi, 354lateral gene transfer, 24latex, 264Law, Barbara, 478leachingweathering process, 6

leaf and stem blotch of mature plants, 327leaf spot diseases, 223, 372leaf-cutter ants, 62Lecanactis abietina, 60Lecanora spp., 60Lecanoromycetes, 60, 61, 416Lederberg, Joshua, 106Lempholemma spp., 60Lentinula edodes, 71, 195, 254, 277, 311,

312, 444cultivation, 278–9mycorrhizas, 344

Leotia spp., 60Leotiomycetes, 60, 61, 438Leptolegnia spp., 75Leptolegniella spp., 75Leptomitales, 75, 512Leptomitus spp., 75Leucoagaricus gongylophorus, 396Leucoagaricus spp., 396Leucocoprineae, 396Leucocoprinus gongylophorus, 279Leucocoprinus spp., 396lichenised fungi, 55, 59lichens, 79, 170, 171, 325, 356–60as food, 358chemical produced by, 358cyanobacteria associations, 357fossils, 357fungal species involved, 358

616 Index






nature of the symbiotic relationship,357–8

reproduction, 357sensitivity to atmospheric pollution, 358taxonomy, 358thallus morphology, 356tolerence of extreme conditions, 358

Lichinomycetes, 60lignin, 78, 238composition and structure, 242–4resistance to microbial degradation,

242–3lignin breakdown, 238, 242–6, 327chlorohydrocarbon release, 336

lignin peroxidase, 243, 244–5ligninases, 384lignocellulose, 78Lindegren, Carl, 106linear structures, 225–7ling (Calluna), 78lingzhi, 279lipases, 247lipophilic yeasts, 62liquid chromatography, 559litter-trapping rhizomorph networks, 227liver cancer, 330, 436LL-Z1272a (antibiotic), 263Lobaria spp., 60Loma salmonae, 414longest-lived fungi, 71longest-lived mycelium, 71long-term plasmogamy, 231lovastatin, 262, 473luciferase, 246luciferin, 246lycopene, 261lysergic acid amide, 263lysosomal proteolysis, 121

macroconidia, 223Macrotermitinae termites, 398–9macrovesicles, 161–2Madurella grisea, 426Madurella mycetomatis, 426magic bullet concept, 512Magnaporthe grisea, 203, 327, 370, 379, 389genome, 546

Magnaporthe oryzae, 382, 389Magnaporthe spp., 55magnetosphere (Earth’s magnetic field),

22–3maize (Zea mays), 62Malassezia globosa, 62Malassezia spp., 62manganese peroxidase, 243, 245man-made polymersmicrobial degradation, 333–4

mannanases, 240mannans, 158, 240mannitol, 254, 311mannoproteins, 137, 163MAP kinase, 143, 206MAP kinase signalling pathway, 135

maple leaf spot, 370Marasmiellus spp., 32Marasmius spp., 32, 227Marmite, 274Mars, 22mass flow of nutrients, 248mass spectrometry, 559Massospora spp., 417mathematical models

fungal growth, 94–7hyphal growth, 564

mating in budding yeast, 200–1mating proteins, 168mating strategies of Neurospora spp.,

203mating systems, 199–200mating type factors, 62, 185, 186, 199

biology of, 210–11mating type genes, 203–5mating type loci, 203–5mating type pheromones, 199mating types, 199

Basidiomycota, 205–10Neurospora crassa, 186–8Neurospora spp., 203–5switching, 200switching in budding yeast, 201–3tetrapolar heterothallism, 206–10

matsutake, 71, 272, 273Megaselia halterata, 271Megaselia nigra, 271meiocyte, 228meiosis

stage in sexual reproduction, 198meiotic nuclear division, 117–18Melampsora lini, 371melanin, 167, 382mellein, 262membrane transport. See transport of

nutrientsMendel, Gregor, 106Mesomycetozoea, 77, 415messenger RNA. See mRNAmetabolic pathways research, 106, 107metabolic regulation and morphogenesis,

305–8metabolomics, 557metacaspases, 385metal cycling

role of fungi, 10metal ions

accumulation by fungi, 327metalaxyl, 522, 526metal–fungal interactions, 9metalloproteinases, 247metamorphic rocks, 6Metarhizium anisopliae, 167, 419Metarhizium spp., 420methanogenic rumen bacteria, 402methyl p-methoxycinnamate, 2633-methylfuran, 432Mevastatin, 262mevinolin, 473

micafungin, 521Michaelis constant, 464Michaelis–Menten kinetics, 249, 463miconazole, 518microarthropods, 326, 353Collembola, 267–70fungivores, 267numbers in soil, 7

microbial diversitycomplexity of the concept, 7in general, 8–9in soil, 7–8measurement challenges, 7–8number which cannot be cultivated, 7–8

microbial diversity in soilchemical analysis, 8chitin measurement, 7counting numbers, 7ergosterol measurement, 8polymerase chain reaction (PCR), 8RNA and DNA probes, 8

microconidia, 223microfilaments, 126Microglossum spp., 60Microsporidia, 29, 30, 35, 412–14human pathogens, 413phylogeny, 396–7xenoma formation, 413

microsporidial gill disease of salmon(MGDS), 414

microsporidiosis, 413Microsporidium africanum, 413Microsporidium ceylonensis, 413Microsporum spp., 247, 425, 426Microstroma spp., 62microtubule motors, 127microtubule-associated dynein, 127–33microtubule-associated kinesins, 127–33microtubule-associated proteins (MAPs),

127microtubule-binding proteins, 127microtubules, 126–7role in cell cleavage, 145role in cytokinesis, 145–6

microvesicles, 161–2mineral transformationsgeomycology, 9–10

minerals, 5composition of rocks, 6igneous rocks, 6metamorphic rocks, 6primary minerals, 5secondary minerals, 5sedimentary rocks, 6

miso, 506mitesfeeding on fungi, 270numbers in soil, 7

mitochondria, 23, 108, 121–2, 252cytoplasmic segregation, 194–6endosymbiont theory, 23, 121–2protein coding genes, 25

mitochondrial DNA (mtDNA), 195

Index 617






mitochondrial inheritance, 33, 195mitochondrial mosaics, 195mitochondrial phenotypes, 195mitochondrial protein transport, 120mitochondrial ribosomes, 33, 195mitosisclosed, 115intranuclear, 115

mitosporic fungi, 198–9mitotic crossing-over, 194mitotic nuclear division, 115–17, 189–94Mitrula spp., 60mobile signal ligands, 349molecular biologycontribution of yeast research, 105–7

molecular biotechnology, 566agricultural myocides, 529analysis of large survey data sets, 563annotating the genome, 540antifungal agents that target the cell wall,

521–2antifungal agents that target the

membrane, 512–21antifungal resistance, 522–6azoles, 517–21, 523bioinformatics in mycology, 560clinical control of systemic mycoses,

522–6combinatorial therapy, 525–6computer simulation of hyphal growth,

564cyber fungi, 564effects of climate change on fungi, 563functional genomics, 550Fungal Genome Initiative, 547fungal genomes and their comparison,

547fungi as cell factories producing

heterologous proteins, 554genomics, 531, 562improving fungal strains, 554manipulating genomes, 552manipulating very large data sets, 560mathematical modelling of hyphal

growth, 566polyenes, 514–17, 523recombinant protein production by

filamentous fungi, 557reverse genetics, 550sequencing fungal genomes, 535steps in understanding fungal genetic

structure, 531strobilurins, 526–9synthetic biology, 560systems biology approach, 531targeted gene disruption, 550transformation of cells, 551vectors for DNA cloning, 552

molecular machines, 109molecular motors, 127–33molecular phylogenetic approach, 74–5molecular studies of pathogen virulence,

389

Monascus purpureus, 506Monascus spp., 274Monilinia fructigena, 247Monilinia spp., 60Monoblepharidales, 30, 45Monod equation, 463monokaryon, 207

definition, 180monolignols, 242monophyletic group, 28Monotropa spp., 343, 344monotropoid endomycorrhizas, 337, 343–4Monotropsis spp., 343Montropaceae, 337, 343Moon

formation of, 21, 23influences on the Earth, 23stabilizing the Earth, 23tides on the Earth, 23

Morchella deliciosa, 272Morchella elata, 272Morchella esculenta, 56, 272Morchella spp., 60, 272morels. See Morchellamorphogenesis

definition, 285morphogenetic field model, 293morphological species concept, 71Mortierella ramanniana, 442Mortierella spp., 55, 474, 483Mortierella wolfii, 55Mortierellales, 52movement

molecular motors, 127–33mRNA, 107

protein synthesis in the cytoplasm,118–19

synthesis and processing, 109–12translation, 118–19

mucopolysaccharides, 241Mucor hiemalis

negative autotropism, 96Mucor miehei, 274Mucor mucedo, 199Mucor spp., 53–4, 59, 99Mucorales, 52Mucoromycotina, 30, 52, 442multiple uptake systems for nutrients, 249muscaridines, 263muscarines, 263muscimol, 329mushroom flies, 270–1mushroom fossils, 32mushroom poisoning, 264mushrooms, 62, 228, 229

commercial mushroom production,275–9

cultivation, 474solid state fermentation, 495

mutationsexpression in haploid fungi, 180expression in heterokaryotes, 181

mutualism, 325

agriculture in beetles, 399–400ambrosia beetles and fungi, 399–400fungal co-operative ventures, 393gardening ants, 393–8gardening insects, 279–80lichens, 357–8ruminants and anaerobic chytrids, 400–5termite gardeners, 398–9types of fungal relationships, 392–3See also mycorrhizas

mycelial interconnections, 142–4mycelial networks at the soil–litter

interface, 267mycelial senescence caused by plasmids,

195myceliummigratory role of strands, 226point growth, 226translocation routes, 225, 226

mycelium differentiation, 214–16mycelium growthapical growth of the hypha, 100autotropic reactions, 96–7autotropism, 87–8circadian rhythms, 214–16colony formation, 86–8colony growth to maturity, 91–2distinction between growth andextension, 88

ecological advantages on solid substrates,100–1

filamentous extension strategy, 86fungal life style, 86gradients in requirements for growth,91–5

heterogeneous growth under restrictedconditions, 91–2

hyphal branching, 97–9hyphal differentiation, 92–5hyphal fusions, 87hyphal mode of growth, 86, 88–91, 94–7mechanisms, 105mophological differentiation, 92–5phases of growth, 94polarised hyphal growth, 87rates of growth and development, 86–8regulatory mechanisms, 144restricted growth, 91–2septation, 99–100strand and cord formation, 225–7success of the growth habit, 100–1yeast–mycelial dimorphism, 150–1

mycelium growth kinetics, 88–91mathematical models, 94–7

Mycena osmundicola, 344Mycena spp., 246, 261, 344mycetoma (madura foot), 427mycobionts, 356Mycogone perniciosa, 443–4mycoherbicide production, 492–3mycoheterotrophs, 343, 346mycoparasitic fungi, 439–44mycopesticide production, 492–3

618 Index






mycopesticides, 444myco-protein, 56production, 487–92

mycorrhizas, 78–9, 170, 325, 336–56advantages of mycorrhizal associations,

351–4arbuscular endomycorrhizas, 337,

338–42arbuscular mycorrhizas, 78, 441arbutoid endomycorrhizas, 337, 343bi-directional nutrient transfer, 340–1changes in natural communities, 353–4commercial applications, 340, 355–6ectendomycorrhizas, 338, 343, 346, 351ectomycorrhizas, 78–9, 338, 346–51ectotrophic/endotrophic classification,

337endomycorrhizas, 78, 337–9ericoid endomycorrhizas, 78, 337, 341–3impact of climate change, 354–5importance for crop plants, 4inorganic transformations, 327monotropoid endomycorrhizas, 337,

343–4nature of the mutualist association,

336–7networks linking plant communities, 337non-mycorrhizal plant families, 337nutrient transfers, 351–3orchidaceous endomycorrhizas, 78, 337,

344–6redistribution of plant-derived

carbohydrates, 353resistance to pathogen attack, 353strand formation, 226structure of natural communities, 353–4types of mycorrhiza, 337–8use of protein, 246vesicular-arbuscular mycorrhizas, 337water relations, 353‘wood-wide-web’, 338

mycoses, 424–6myosins, 128actin-associated myosins, 127–33molecular motors, 127–33

Myxomycota, 77Myxomycotina, 23Myzocytiopsidales, 75

NAD, 254NADH, 121, 251, 256NADH2, 252NADP, 254NADPH, 121, 251, 256NADPH2, 252, 256NADP-linked glutamate dehydrogenase,

255–6, 308natto, 506natural classification of fungi, 41–79anaerobic chytrids, 45–6anamorph (asexual stage), 42Ascomycota, 55–61Basidiomycota, 61–71

Blastocladiomycota, 46–50Chytridiomycota, 42–5, 45–6definition, 41ecosystem mycology, 77–9Glomeromycota, 50–2members of the Kingdom Fungi, 42naming of fungal species, 42naming of sexual and asexual stages, 42Neocallimastigomycota, 45–6number of species, 42slime moulds, 77species concept in fungi, 71–5teleomorph (sexual stage), 42untrue fungi, 75–7water moulds, 75–7Zygomycota, 52–5

natural group, 28necrosis and ethylene inducing proteins

(NEPs), 384necrotrophic fungi, 238, 327, 376–8, 383Nectria haematococca, 132negative autotropism, 96, 181Neighbour-Sensing model of hyphal

growth, 566nematodes, 326

feeding on fungi, 270numbers in soil, 7

nematode-trapping fungi, 405–8potential biological control, 407types of trapping device, 405

Nematophthora gynophila, 407nematophytes, 31–4Neocallimastigales, 29, 45, 401Neocallimastigomycota, 29, 45–6, 400–5Neocallimastix frontalis, 46, 401, 402Neocallimastix spp., 401Neolecta spp., 56Neolecta vitellina, 56Neolithic traveller (the Iceman)

fungal products found with, 273Neotiella spp., 117net blotch of barley, 370Neurospora crassa, 86, 87, 115, 185, 454,

460asynchronous nuclear division, 147circadian system, 215conidiation, 223genome, 544het genes, 186het loci, 188heterokaryon formation, 186hyphal extension, 88–9, 140incompatibility response, 186–8mating types, 186–8, 199mitochondrial genes, 194mitochondrial phenotypes, 195mutations, 116negative autotropism, 96proteinases, 246

Neurospora spp., 60, 106, 228mating strategies, 203mating types, 203–5

Neurospora tetrasperma, 200

new variant Creutzfeldt–Jakob disease(nvCJD), 196

New Zealand wood ear fungus trade, 273nikkomycins, 171, 521, 526nitrate reductase, 256nitrogenprimary metabolism, 254–7sources in the soil, 238–9

nitrogen-fixing bacteria, 254N-linked oligosaccharides, 163–4Nobel Prize laureates, 119, 512yeast-related research, 105–7

‘noble rot’ of wine grapes, 382nomenclaturedefinition, 27fungi, 52

Nomuraea rileyi, 419non-disjunction of chromosomes, 194non-mycorrhizal plant families, 337non-ruminant herbivoreshindgut fermentation, 403

North American histoplasmosis, 428Norway spruce (Picea abies), 347Nosema apis, 414Nosema bombycis, 412Nosema ocularum, 413Nosema sp., 414Nostoc punctiforme, 52, 340Nothofagus (Southern beech), 346nuclear–cytoplasmic trafficking, 114nuclear division patterns, 146–8nuclear export signal (NES), 113nuclear genetics, 114–15nuclear localisation signal (NLS), 113nuclear migration, 116–17regulation, 93–4

nuclear mitosis, 93–4nuclear number and ploidy, 117nuclear pore complexes (NPC), 113–14, 121nuclear ribosomal DNA (rDNA)phylogenetic studies, 33

nucleolus, 112–13nucleoporins, 113nucleuschromatin structure, 109–12control of nuclear division, 148DNA molecular processes, 109functions, 108–12gene expression, 109–10mRNA synthesis and processing, 109–12nuclear–cytoplasmic trafficking, 108nuclear import and export, 113–14nuclear pore complexes (NPC), 113–14number of nuclei per cell, 117protein transport from the cytoplasm,121

transcription factors, 109–10transporter proteins, 113

nud (nuclear distribution) genes, 117Nurse, Paul, 56, 105, 107nutrient cycling in soils, 6nutrient distribution in soilseffects on fungal growth, 10

Index 619






nutrient transferbi-directional transfer in mycorrhizas,

340–1ectomycorrhizas, 349–50transport and translocation, 247–51

nutristat cultures, 473nutrition modedistinctions between eukaryotes, 29

nutritional selection for diploid strains, 189nystatin, 515

oak (Quercus), 346endophytic fungi, 361gall wasps, 361

2-octen-1-ol, 432odours of fungi, 263, 328oidia, 208oligotrophic growth in fungi, 10O-linked oligosaccharides, 164Oliver, Steve, 105Olpidiopsidales, 75Olpidiopsis spp., 75Olpidium spp., 43Omphalotus olearius, 246Omphalotus spp., 246onychomycosis, 426oogoniol, 199Oomycota, 29, 50, 75–7, 85, 86, 138, 141growth mechanism, 160

Ophiostoma novo-ulmi. See Dutch elmdisease

Ophiostoma spp., 399, 400Ophiostoma stenoceras, 427Ophiostoma ulmi, 150, 202Ophiostomatales, 399ophiostomatoid fungi, 399, 400opisthokonts, 105, 415evolutionary origins, 30

opportunistic infections, 5, 54, 55, 59Candida albicans, 150–1microsporidiosis, 413

opportunistic pathogens, 424Orbilia spp., 60Orbiliaceae, 405Orbiliomycetes, 60Orchidaceae, 78orchidaceous endomycorrhizas, 78, 337,

344–6ptyophagy, 346tolypophagy, 346

organelles, 107organic matter, 5decomposing and stable stages, 6food source for soil organisms, 6

ornithine acetyltransferase, 308ornithine carbamoyltransferase, 308Orpinomyces spp., 46, 401orsellinic acid, 262oscillatorscircadian rhythms, 215, 216

oudemansins, 331oxalate oxidase, 245oxalic acid, 384

oxidation and reductionchemical weathering processes, 6

oxidative burst, 384–5oxidative phosphorylation, 253oxygen in soil minerals, 6oyster mushrooms. See Pleurotus spp.ozone layer, 22–3

Pacispora spp., 340paddy straw mushroom. See Volvariella

volvaceaPaecilomyces varioti, 263Panellus stipticus, 246Papularia sphaerosperma, 522Paracoccidioides brasiliensis, 150, 161, 167Paraglomerales, 340Paraglomus spp., 340paraphyses, 228, 291, 292parasexual cycle, 194parasitic fungi, 326Parasola misera, 290parasynchronous division of nuclei, 146–8parenthesome, 99parisin, 48PAS domain, 215Pasteur, Louis, 56, 105, 106, 500pathogen associated molecular patterns

(PAMPs), 387pathogenic fungi, 5, 326pattern formation, 283Paxillus panuoides, 332peach leaf curl, 56, 370peat formation, 6pectin lyases, 241pectinases, 241, 384pectins, 238

breakdown, 241Pellicularia sasakii, 521peloton, 345Peltigera spp., 60Peltula spp., 60penetration peg, 382penicillin, 55, 264–3, 512

history and production, 478–82Penicillium camemberti, 56, 264, 275, 493,

503Penicillium chrysogenum, 55, 87, 189, 194,

468, 474, 480, 482Penicillium citrinum, 55, 262Penicillium cyclopium, 182Penicillium digitatum, 189Penicillium expansum, 189Penicillium griseofulvum, 262Penicillium nalgiovense, 503Penicillium notatum, 478Penicillium roqueforti, 56, 275, 493, 503Penicillium spp., 60, 432penny bun. See Boletus edulispentachlorophenol (PCP), 245, 334

bioremediation by fungi, 334–6pentose phosphate pathway (PPP), 252, 311peptidases, 247peptide pheromones, 199

perfect fungi, 198Perissodactyla, 403, 404perithecia, 59, 203, 224, 228Permian–Triassic extinction eventeffects on fungi, 37–8

permittistat cultures, 473Peronosporales, 75peroxisomes, 23, 120, 144pestdefinition, 334

pest management on plants, 376–7pesticides, 238, 368bioremediation by fungi, 334–6breakdown by fungi, 245

Peziza spp., 60Pezizomycetes, 60Pezizomycotina, 56, 59–61ascoma morphologies, 59–60ascus types, 60–1phylogeny, 60–1

pH auxostat cultures, 473Phallales, 66phalloidin, 264Phallomycetidae, 66phalloxin, 433–4Phanerochaete chrysosporium, 78, 240,

244–6, 484genome, 546

pharmaceuticals, 473chemical transformation by laccases, 245whole organism biotechnology, 478–83

Phellinus contiguus, 300, 301, 332Phellinus megaloporus, 332Phellinus pomaceus, 336Phellinus spp., 245Phellinus tuberculosus, 336Phellinus weirii, 69phenolics, 238phenotype of sexual reproduction, 199phenotype switching, 429phenylalanine, 263phenylpropanoid alcohols, 242pheromone response element (PRE), 206pheromones, 77, 201, 209–10Phlyctochytrium spp., 43phosphatases, 247phosphate mobilization, 327phosphofructokinase, 253, 254photobionts, 356photosynthesisC3 and C4 pathways, 404

phragmoplast, 146phycobionts, 356Phycomyces blakesleeanus, 55Phycomyces spp., 442Phycomycetes, 23, 29phylogenetic classificationdivergence of Archaea and Eukaryota,26–8

divergence of Eubacteria and Archaea,26–8

Kingdom Fungi, 29–30phylogenetic classification systems, 23–9

620 Index






phylogenetic species concept, 74–5phylogenetic studiesATPase genes, 24–5evolutionary clock, 24molecular studies, 33molecular techniques, 24–6protein sequences, 25–6range of molecules studied, 24–6ribosomal gene cluster, 25small subunit ribosomal RNA (SSU rRNA)

genes, 24suitable genes for study, 24universal ancestor concept, 24

phylogeny of fungi, 35–8Physarales, 77Physarum spp., 77physical power of growing fungi, 328–30physical weathering, 6physiological species concept, 74Physoderma spp., 47phytoalexins, 386, 387phytoanticipins, 386phytodebris, 31–4Phytophthora cactorum, 514Phytophthora infestans, 75, 368, 370, 376,

512, 522Phytophthora megasperma, 75, 387Phytophthora palmivora, 75Phytophthora parasitica, 353Phytophthora spp., 29, 30, 75, 384Piedraia hortae, 426pigmenation of fungal cell walls, 167–8Pilaira spp., 442pileipellis, 291pili, 107Pilobolus spp., 442pine (Pinus), 346, 347, 349, 351, 354mycorrhizal associations, 338

Piptocephalis spp., 440, 442Piptoporus betulinus, 78, 273PIR proteins, 165Piromyces spp., 46, 401, 403Pityopus spp., 343plant diseasedisease triangle, 374–6pathogen–host–environment

relationships, 374–6plant pathogens, 367–89Armillaria spp., 370–2avoiding nutrient or water stress in

plants, 376barley powdery mildew (Blumeria

graminis), 371biological control methods, 377biotrophs, 376–8black stem rust of wheat (Puccinia

graminis tritici), 373–4changing host metabolism, 378–9co-evolution of plant–pathogen disease

systems, 387–9comparison with animal pathogens, 436–9defence mechanisms in plants, 384–5,

385–7

direct penetration of the host cell wall,382

disease triangle, 374–6Dutch elm disease (Ophiostoma novo-ulmi), 372–3

effects of pathogens on hosts, 377–9effects on plant hormones, 378–9enzymatic penetration of the host, 382–5flax rust (Melampsora lini), 371gene-for-gene interactions with plants,387–9

general short-term response in the host,386

genetic variation in pathogens and hosts,387–9

good sanitation to help control, 376headline crop diseases, 370hemibiotrophs, 376–8horizontal resistance, 387host penetration through stomata,379–81

host-selective toxins, 384host-specific toxins, 378hypersensitive response in the host,384–5, 386, 388

induction of programmed cell death,384–5

insertional mutagenesis, 389integrated pest management, 376–7leaf spot diseases (Cercospora spp.), 372losses to world agricultural production,368–70

molecular studies of pathogen virulence,389

necrotrophs, 376–8oxidative burst in the host, 384–5pathogen–host–environmentrelationships, 374–6

pathogens that produce haustoria, 371–2pre-formed and induced defencemechanisms, 385–7

rice blast fungus (Magnaporthe grisea),370

rust fungi, 371–2, 379–81smut fungi, 371–2symptoms of disease in plants, 377–9systemic acquired resistance in plants,386–7

tolerance in plants, 387using disease resistant cultivars, 376vertical resistance, 387

plantsbenefits of mycorrhizal associations, 325dependence on mycorrhizal associations,325

plasma membrane, 133–6active transport processes, 133electrochemical proton gradient, 133facilitated diffusion, 133GPI-anchors, 135ion channels, 133–4ion pumping, 133signalling pathways, 134–5

transport mechanisms, 133–4plasmalemma, 123–4plasmid DNA, 195–6plasmids, 108cytoplasmic segregation, 195–6

Plasmodiophora spp., 77Plasmodiophoromycota, 77plasmogamy, 198, 231Plasmopara spp., 31plasticsmicrobial degradation, 333–4

plastids, 121–2Platypodinae, 399plectenchyma, 224–5Pleistophora sp., 413Pleospora spp., 60Pleuricospora spp., 343Pleurotus ostreatus, 195, 406–7, 444genome, 546

Pleurotus pulmonarius, 311bioremediation of pentachlorophenol(PCP), 334–6

Pleurotus pulmonarius fruit bodyformation of gills, 297–8

Pleurotus spp., 71, 277cultivation, 278remediation of agricultural waste, 278

ploidy and nuclear number, 117plus end tracking proteins (þTIPs), 127Pneumocystis carinii, 30, 56, 431genome, 546

Pneumocystis jirovecii, 30, 56, 431pneumocystis pneumonia (PCP), 30, 56, 431Pneumocystis spp., 30, 55, 56, 438pneumocystosis, 431, 522Podospora anserina, 185, 186, 195, 203clock mutant, 215–16het loci, 188post-fusion incompatibility response, 188prion protein, 196

Podospora spp., 203, 210poisoning from fungal toxins, 433–6poly-A polymerase, 111polyacetylenes, 264polychlorinated biphenyls (PCBs), 245polyenes, 514–17, 523polygalacturonases, 241polyketides, 260, 261–3polymerase chain reaction (PCR), 25, 33soil microbes, 8

Polymyxa spp., 77polyoxins, 171polyoxorims, 521, 526polyphyletic group, 28Polyporaceae, 66Polyporales, 67polyporespore (tube) formation, 301

Polyporus hispidus, 263Polyporus mylittae, 227polysaccharidesbreakdown by fungi, 239–42

Polystictus versicolor, 94

Index 621






Polystictus xanthopus, 301polystyrenemicrobial degradation, 334

polyurethanesmicrobial degradation, 334

Pontisma spp., 75poplar (Populus), 346porcini. See Boletus edulispore space in soil, 6–7posaconazole, 524positive autotropism, 96–7, 181post-fusion incompatibility response, 185,

186, 188potato blight, 75, 368, 522powdery mildews, 327, 382–3, 389pravastatin, 473predatory funginematode-trapping fungi, 405–8

pre-mRNA, 111, 113splicing, 111–12

pre-ribosomal RNAs (pre-rRNAs), 112primary homothallismNeurospora spp., 203

primary metabolism, 251–6acetyl-CoA, 252ATP synthesis, 251, 253basic function, 251catabolism of carbohydrate, 251–2Embden–Meyerhof–Parnass (EMP)

pathway, 251Entner–Doudoroff (ED) pathway, 252excretion of excess nitrogen, 256–7fats, 254–5formation of NADH and NADPH, 251gluconeogenesis, 253–4glutamate decarboxylation loop, 253glutamine synthetase/glutamate synthase

system, 256glycolysis, 251–2, 254hexose monophosphate pathway (HMP),

252Krebs (TCA) cycle, 252mannitol, 254NADP-GDH, 255–6nitrogen, 254–7oxidative phosphorylation, 253pentose phosphate pathway (PPP), 252protein as a carbon source, 256–7proton gradients, 253pyruvate formation, 251–2TCA (tricarboxylic acid) cycle, 252trehalose, 254urea production, 256–7

primary pathwaysdefinition, 251

primordium of a structure, 283prion proteins, 188propagation and transmission, 196

prochloraz, 518profilin, 145programmed cell death, 185, 315–16, 376in cultures, 465–6

prokaryote/eukaryote distinction, 23

prokaryotescell membrane, 107cell structure, 107–8DNA, 107extrachromosomal DNA, 108plasmids, 108

prosenchyma, 225proteasomal proteolysis, 121proteasomes, 246protective antifungal agents, 512protein

as nitrogen and carbon source, 246,256–7, 327

digestion by fungi, 246–7protein-coding genes, 33, 115protein prenylation, 135protein sequences

phylogenetic studies, 25–6protein sorting/targeting mechanism,

119–21proteinaceous hereditary elements.

See prion proteinsproteinases, 246–7, 327

extracellular, 246–7intracellular, 246

proteinschloroplast protein transport, 121destruction, 121fungal cell wall, 163–5mitochondrial protein transport, 120mRNA translation, 118–19proteolysis, 121signal peptides, 119–20synthesis, 107synthesis in the cytoplasm, 118–19targeting peptides, 119–20transmembrane proteins, 120transport into the nucleus, 121

proteome analysis, 559proteomics, 557protobasidia, 292proton gradients, 253Prototaxites spp., 31–4protozoa

numbers in soil, 7pseudoparenchyma, 225pseudorhizas, 227pseudosclerotial plate, 227Pseudosphaerita spp., 75pseudothecia, 60Psilocybe cubensis, 62Psilocybe spp., 263psilocybin, 263Pterospora spp., 343, 344Pterulaceae, 396Puccinia coronata f. sp. avenae, 389Puccinia graminis, 62, 199, 512

genome, 557Puccinia graminis tritici, 373–4Puccinia spp., 62Pucciniales, 62–3Pucciniomycotina, 62–3puffballs, 66, 228, 288

pullulanase, 242PVCmicrobial degradation, 334

pycnidia, 198, 223–4pyrenomycetes, 60pyridines, 518pyrimidine analogues, 518pyrogallol, 263Pyrola spp., 343Pyrolaceae, 343Pyronema spp., 60pyruvate carboxylase, 253pyruvate formationglycolysis, 251–2

pyruvate kinase, 253Pythiales, 75Pythiogeton spp., 75Pythium aphanidermatum, 75Pythium spp., 30, 75, 199, 327, 331, 440Pyxidiophora spp., 60Pyxidiophorales, 60

Quorn™ myco-protein, 56, 274production, 473Quorn™ fermentation, 487–92Quorn™ fungus, 461

r-selected species, 354Raffaelea spp., 399, 400rainfalleffects on soil formation, 6

Raistrick, Harold, 480Ran protein, 113RAS protein activation, 134–5ravuconazole, 524Rayner, Alan, 214reactive oxygen species (ROS), 384recalcitrant wasteremediation by fungi, 334–6

recombinant protein production byfilamentous fungi, 557

recombinant vectors, 552Red Data lists, 563red pepper mites (Pygmephorus spp.), 270regional patterning (regional specification),

283, 290–1reishi, 279remediation of agricultural/industrial

wastes, 278, 334–6renewed fruiting, 315rescue (microtubule switch), 126resistance (R) proteins, 387resistance to antifungal agents, 430–1,

522–6resupinate fruit body, 332reverse genetics, 550, 554Rhipidiales, 75Rhipidium spp., 75Rhizanthella spp., 346Rhizidiomyces spp., 77Rhizoctonia solani, 69, 186, 440, 444Rhizoctonia spp., 78, 91, 327, 337, 344, 345rhizomorphs, 226–7

622 Index






Rhizomucor pusillus, 431Rhizophlyctis spp., 43Rhizophydiales, 45Rhizophydium spp., 43Rhizopus arrhizus, 54, 431Rhizopus nigricans, 54Rhizopus oligosporus, 54, 274Rhizopus oryzae, 54Rhizopus rot, 54Rhizopus sexualis, 199Rhizopus spp., 55, 247Rhizopus stolonifer, 54Rhododendron spp., 341Rhodosporidium sphaerocarpum, 150Rhodosporidium spp., 63Rhodotorula spp., 63Rhynchonectria spp., 60rhythmic growthmycelium, 214–16

ribosomal DNA (rDNA) sequencing, 25ribosomal gene clusterexternally transcribed spacer region

(ETS), 25intergenic spacer regions (IGS), 25internally transcribed spacers (ITS), 25non-transcribed spacer region (NTS), 25phylogenetic studies, 25spacer regions, 25

ribosomal protein factors, 25ribosomal RNA. See rRNAribosome assembly, 112–13ribosomes, 107mitochondrial, 195mRNA translation, 118–19protein synthesis, 118–19

ricebakanae disease, 379

rice blast fungus, 327, 370, 379, 382, 389,545

rice sheath blight, 521Rigidoporus ulmarius, 71ringworm, 425RNA, 107features of the universal ancestor, 24

RNA polymerases, 109RNA probessoil microbes, 8

RNA-processing machines, 111RNP machines, 118ro (ropy) genes, 117rock surfacesfungal growth, 10

rodentstarget of aflatoxins, 330

root rots, 327root–soil interfaceimportance of fungi, 10

rose handler’s disease, 427Royal Botanic Gardens, Kew, 71Rozella spp., 35Rozellopsidales, 75Rozellopsis spp., 75rRNA, 107, 109, 113

transcription and processing, 112–13Ruminantia, 403ruminants

anaerobic chytrids in, 45–6, 400–5digestion, 493–4evolution, 403–4foregut fermentation, 403

Ruminococcus albus, 402Russula bella, 330Russulales, 67, 72rust fungi, , 62–3, 199, 371–2, 373–4

Saccharomyces carlsbergensis, 476Saccharomyces cerevisiae, 55, 56, 105, 116,

117, 127, 475actin gene mutations, 126bread-making, 499–501chitin synthases 161, 162chromosome and genome sequencing,105

fermentation, 105–6genome, 113, 537killer/immunity phenotype, 196mating process, 200–1mating types, 199, 200, 201–3mitochondrial genes, 194model organism for research,105–7

molecular motors, 128Sup35p prion protein, 196virus-like particles, 196

Saccharomyces ellipsoideus, 477Saccharomyces rouxii, 505Saccharomyces spp., 56–8Saccharomycetales, 56Saccharomycotina, 56–9salami, 495, 503–4Salilagenidiales, 75Salmonella spp., 106Salvarsan, 512Saprolegnia ferax, 138, 141

growth mechanism, 160Saprolegnia spp., 31, 75, 85Saprolegniales, 75, 514saprotrophic fungi, 62, 238, 326, 327

decay of structural timber, 331–3dry rot, 331–3inorganic transformations, 327nitrogen sources in plant litter, 327physical power of growing fungi,328–30

range of substrate materials, 327release of chlorohydrocarbons, 336toxins produced by, 328–31waste remediation, 334–6

sap-stain fungi, 333Sarcodes spp., 343, 344satratoxins, 432Scheele, Karl William, 477Schizophyllum commune, 170, 180, 189,

195, 210, 311genome, 546tetrapolar heterothallism, 206–10

Schizosaccharomyces pombe, 56, 93, 105,118, 127, 475

chitin synthase gene, 160mating types, 200molecular motors, 128

Schizosaccharomyces spp., 116Schleiden, Matthias Jakob, 107Schwann, Theodor, 107Sclerocystis spp., 441Scleroderma bovista, 328Scleroderma citrinum, 442Sclerospora spp., 75Sclerosporales, 75sclerotia, 198, 227–8Sclerotinia sclerotiorum, 384, 385, 493Sclerotinia spp., 60Sclerotinia trifoliorum, 202Scolytinae, 399scrapie disease in sheep, 196Scutellospora spp., 52, 340, 441seasons on the Earth, 23Sebacinales, 67seborrhoeic dermatitis, 62secondary homothallismNeurospora tetrasperma, 203

secondary metabolismdefinition, 257

secondary metabolites, 257aflatoxins, 262agaritine, 263Amanita toxins, 264carotenes, 260carotenoids, 258, 260cephalosporins, 264–3cyclopentanes, 264diterpenes, 259ergosterol, 259–61ergot alkaloids, 263fatty acid synthesis, 261–3gibberellins, 259growth inhibition, 91iron-binding compounds, 264latex, 264muscarines and muscaridines, 263nature of secondary metabolism, 257penicillins, 264–3polyacetylenes, 264polyketides, 260, 261–3precursors, 257sesquiterpenes, 259shikimate-chorismate derivatives, 263–1siderophores, 264statins, 263steroids, 258sterols, 259–61strobilurins, 263terpenes, 258–9triterpenes, 259zearalenone, 262

secondary pathwaysdefinition, 251

secretory vesicles, 161–2sedges (Cyperaceae), 62

Index 623






sedimentary rocks, 6selective toxicity concept, 512self/non-self recognition. See vegetative

compatibilityself-fertilisation, 180self-incompatibility, 180self-sterility, 180septation, 92–3, 99–100and branching, 97–8comparison with cytokinesis, 145–6formation of septa, 100multinucleate hyphae, 146–8nature of the fungal cell, 99–100orientation of septa, 100process, 144–5septal band, 147septal form, 144septal pores, 99types of septa, 99

septins, 145Septoria spp., 223, 327Sericomyrmex spp., 396serine proteinases, 247Serpula lacrymans, 78, 226, 250, 331–3sesquiterpenes, 259sex pheromones in fungi, 48sexual behaviourcreation of a dikaryon, 180creation of a monokaryon, 180

sexual reproduction, 198–211anamorphic fungi, 198–9biology of mating type factors, 210–11diversity of behaviours in fungi, 180duration of stages, 199fungi which lack sexual reproduction,

198–9genetic control of mating, 201heterothallic fungi, 180, 199–200homothallic fungi, 180, 199, 200hormones involved, 199hyphal fusion, 142incompatibility systems, 199karyogamy, 198mating in budding yeast, 200–1mating systems, 199–200mating type switching in budding yeast,

201–3mating types, 199mating types in Basidiomycota, 205–10mating types in Neurospora spp., 203–5meiosis, 198mitosporic fungi, 198–9morphology of structures involved, 199phenotype of sexual reproduction, 199plasmogamy, 198process, 199–200spore production, 199stages, 198

Sheehan, John, 478shiitake. See Lentinula edodesshikimate-chorismate derivatives, 263–1shikimic acid pathway, 252shimejitake (Hypsizygus tessulatus), 71

shiroshimeji (Pleurotus ostreatus), 277shmoos, 118Siberian Traps flood basalts, 37sick building syndrome, 432siderophores, 264signal peptides, 119–20signal recognition particle, 120signalling pathways, 134–5

GPI anchors, 135G-proteins, 134–5MAP kinase, 135, 143RAS protein activation, 134–5signal amplification, 135

silicon in soil minerals, 6simvastatin, 473sinapyl alcohol, 242sirenin, 47, 48, 199Sirolpidium spp., 75sitosterol, 512slime moulds, 23, 29, 52slugs and snails

fungi as food, 271small mammals

fungi as food of, 271–2small subunit ribosomal RNA (SSU rRNA)

genesphylogenetic studies, 24, 33

smut fungi, 62, 371–2SNARE proteins, 124, 146snoRNA, 113snoRNP, 113snRNA, 112, 113snRNP, 112soft rots, 238, 384soil

amount of land used to supply food, 5association of fungi with, 5importance as a terrestrial habitat, 5

soil atmosphere, 5, 6–7soil biota

diversity and quantity, 7effects of soil formation on, 6microarthopod fungivores, 267microbial diversity in soil, 7–8organic matter food source, 6

soil components, 5–7clays, 6dynamic matrix, 7elements found in soil minerals, 6gaseous phase, 5humic substances (humus), 6liquid phase, 5minerals, 5–6organic matter, 5, 6pore space, 6–7sand, 6–7soil atmosphere, 5soil solution, 5, 6–7solid phase, 5–6

soil food web, 7soil formation

and rainfall, 6climatic effects, 6

dynamic matrix, 7effects of living organisms, 6organic matter, 6soil tilth, 6temperature effects, 6weathering processes, 6

soil geochemistrygeomycology, 9–10

soil solution, 5, 6–7soil structurecontribution of fungi, 11, 326effects of glomalin, 171

soil tilth, 6soil typesnutrient cycling, 6organic soil, 6

solar wind, 22–3solid substratesadvantages of mycelial growth, 100–1

somatic incompatibility. See vegetativecompatibility

Sordaria brevicollis, 186Sordaria spp., 60, 228Sordariales, 522sordarins, 522Sordariomycetes, 60, 61, 438Sordariomycetidae, 399sorus, 62soy foods, 504–6soy sauce, 274, 495production, 504–6

soya bean (Glycine max), 387spalting, 333species concept in fungi, 71–5biological species concept, 71–4ecological species concept, 74evolutionary species concept, 74molecular phylogenetic approach, 74–5morphological species concept, 71phylogenetic species concept, 74–5physiological species concept, 74

spindle apparatus, 116spindle checkpoint, 116spindle pole body, 115, 116, 145Spinellus spp., 440Spitzenkorper, 125, 139, 141, 142, 161, 162Spizellomycetales, 45spliceosomes, 112splicing of pre-mRNA, 111–12Spongospora spp., 77sporesdispersal, 214dormancy, 86emergence of germ tubes (hyphal tips), 86formation, 216–20germination, 86–7initiation, 92multinucleate, 183production, 199, 214spherical growth stage, 86uninucleate, 183

Sporidiobolus spp., 63Sporobolomyces spp., 63

624 Index






sporodochium, 223sporopollenin, 401Sporothrix schenckii, 167, 427sporotrichosis, 427spruce (Picea), 346, 347, 351, 354squalene, 259Squamanita odorata, 442SR proteins, 112St Anthony’s fire, 434–5Stachybotrys chartarum, 432–3Stachybotrys elegans, 440stachylysin, 432starch breakdown, 241–2statins, 4, 55, 263, 331, 473steady state (soft spot) model of hyphal tip

extention, 139Stemonitales, 77Stemonitis spp., 77Stereaceae, 66steroids, 258derivatives, 473manufacture, 486–7

sterols, 133, 199, 259–61, 512stigmasterol, 512stinkhorns, 66, 228, 288stinking smut, 62stipes of fruiting bodies, 227stramenopiles, 31Streptomycessymbiosis with gardening ants, 397–8

Streptomyces cacaoi var. asoensis, 521Streptomyces coelicolor genome, 536, 537Streptomyces noursei, 515Streptomyces tendae, 521streptomycete bacteria, 85, 86stringy oak rot, 332strobilurins, 4, 263, 331, 526–9Strobilurus ohshimae, 331stromata, 198, 223–4Strongwellsea spp., 418structural timberdry rot, 331–3effects of wood-decay fungi, 331–3

subsistence dietland required per person, 5

succinate dehydrogenase, 252sudden infant death syndrome (SIDS), 431sufu, 506sugar beet leaf disease (Cercospora beticola),

372sulfatases, 247sulfur in the soil, 239superoxide, 384surface tension catapult, 229symbiosis. See mutualism, mycorrhizassymport, 249synchronous division of nuclei, 146–8synchronous mitosishyphal growth, 93

Synchytrium spp., 43synnemata, 223syntaxins, 146synthetic biology, 560

systematicsdefinition, 27

systemic acquired resistance in plants,386–7

systemic antifungal agents, 512–13systemic mycoses

clinical control of, 522–6systems biology approach, 531, 557

tannins, 238Taphrina betulina, 56Taphrina deformans, 56Taphrina spp., 56–7Taphrinomycetes, 438Taphrinomycotina, 30, 56, 431targeting peptides, 119–20Tarsonemus myceliophagus, 270TATA-box binding protein-associated

factor(s) (TAFs), 109, 111Tatum, Edward, 106taxon

definition, 27taxonomic ranks for fungi, 28taxonomy

definition, 27fungal cell wall structure, 158–9fungi, 27

TCA (tricarboxylic acid) cycle, 252, 477tea production, 496teleomorph (sexual stage), 42tempeh, 54, 274, 506temperature

effects on soil formation, 6tendril hyphae, 225termites, 62

and fungi, 279gardening, 279–80, 398–9

Termitomyces spp., 280, 398–9Termitomyces titanicus, 398terpenes

secondary metabolites, 258–9tetrapolar mating system, 205–6

Ustilago maydis, 205–6Thallophyta, 23Thanatephorus cucumeris, 69Theia–Earth impact, 21, 22, 23Thelephorales, 69thigmotropism, 379Thraustochytriales, 77Thraustochytrium spp., 77thrush (fungal infection), 429thyriothecia, 60Tieghemomyces spp., 440Tilletia spp., 62Tilletia tritici, 264tinder bracket fungus, 273toadstools, 228tofu, 506tolypophagy, 346toxic waste

breakdown by fungi, 238remediation by fungi, 334–6

toxicity

access to information about, 513toxins produced by fungi, 331, 433–6Trachipleistophora anthropophthera, 413Trachipleistophora hominis, 413Trachymyrmex spp., 396trama, 292Trametes versicolor, 78transcription factors, 109–10transcription research, 107transcriptome analysis, 559transcriptomics, 557transfer RNA. See tRNAtransformation of cells, 551transgenic plants, 422translational triggering, 222translocase of inner membrane (TIM), 120translocase of outer membrane (TOM), 120transmembrane glycoproteins, 248transmembrane proteins, 120, 162transplant patientsprevention of organ rejection, 4See also immunocompromised patients

transport vesicles, 124transportation of nutrients, 247–51active transport, 249bulk flow, 248effects on water potential, 249–51facilitated diffusion, 248–9ion pumps, 249mass flow, 248simple diffusion, 248solute transport systems, 248transmembrane glycoproteins, 248transporter molecules, 248

Trechisporales, 69Tree of Life Project, 26, 31trehalose, 254Tremella spp., 208Tremellales, 66Tremellomycetes, 66triadimefon, 518triarimol, 518triazbutil, 518triazoles, 518Trichloma spp., 353Trichoderma harzianum, 493Trichoderma pleuroticola, 444Trichoderma pleurotum, 444Trichoderma reesei, 240, 474Trichoderma spp., 270, 440, 442, 444, 493biological control, 444

Trichoderma virens, 484Trichoderma viride, 444Trichoglossum spp., 60Tricholoma fumosum, 338, 349Tricholoma matsutake, 71, 272, 273Tricholoma spp., 78, 338, 347Tricholomataceae, 246, 280, 398Trichomycetes, 53, 414–16Trichophyton rubrum, 425Trichophyton spp., 247, 425, 426Trichosporon cutaneum, 426tricyclazole, 526

Index 625






trisporic acid, 199triterpenes, 259tRNA, 107, 109, 113, 118truffieres (truffle groves), 279truffles, 56, 272, 288, 337, 346cultivation in truffle groves, 279See also Tuber spp.

tryptophan, 263Tuber magnatum, 56, 272Tuber melanosporum, 56, 272Tuber spp., 60See also truffles

Tubeufia spp., 60Tunbridge ware, 333turbidostat cultures, 472–3turgor pressure, 250two-dimensional gel electrophoresis, 559Tylopoda (pseudoruminants), 403Tyrannosorus spp., 60Tyromyces placentus, 332tyrosine, 263

ubiquitin, 121Ulocladium atrum, 493ultraviolet (UV) radiation, 22–3shielding from, 167

unifactorial incompatibility, 199United Kingdom National Culture

Collection, 562universal ancestor concept, 24universal common descent theory, 28untrue fungi, 75–7urea, 311osmotic metabolite, 308, 311production in fungi, 256–7

Urediniomycetes, 62urediospores, 380Uromyces appendiculatus, 62Uromyces fabaehost penetration through stomata, 379–

81Uromyces spp., 62, 379–81Usnea spp., 60Ustilaginomycetes, 62Ustilaginomycotina, 62Ustilago hordei, 389Ustilago maydis, 62, 127, 132, 150genome, 546pheromone signalling, 209tetrapolar mating system, 205–6

Ustilago spp., 62, 371Ustilago violacea, 195

Vaccinium (bilberry)mycorrhizas, 337, 341

vacuoles, 128–9valley fever, 428variotin, 263Vegemite, 274vegetative compatibility, 180, 185–8compatibility test, 185het loci, 185–6, 188

post-fusion incompatibility response,185, 186

vegetative compatibility (v-c) group, 185vegetative compatibility reactions, 441vegetative incompatibility

barrage formation, 188cell death caused by, 185clear zone formation, 188See also vegetative compatibility

Venus, 22veratryl alcohol, 244, 245, 336Verrucalvus spp., 75Vertalac, 422vertical mitochondrial transmission, 195Verticillium dahliae, 185Verticillium fungicola, 443–4Verticillium lecanii, 418, 422Verticillium spp., 60, 330, 442vesicles, 162

in arbuscular mycorrhizas, 338types of, 161–2

vesicular-arbuscular mycorrhizas (VAM),51, 326, 337, 338

vessel hyphae, 225victorin, 378Virtual Library, 562virulence, 437virus-like particles

cytoplasmic segregation, 196Vittaforma corneae, 413Volvariella bombycina, 312Volvariella fruit body

formation of gills, 296–7Volvariella spp.

use of protein, 246Volvariella volvacea, 71, 210, 443

cultivation, 279voriconazole, 431, 524

Walksman, Selman, 480waste remediation by fungi, 334–6water distribution in soils

effects on fungal growth, 10water moulds, 75–7water potential, 249–51water relationships in the fungal cell,

249–51weathering processes, 6

chemical weathering, 6leaching, 6physical weathering, 6

wet-rot fungi, 332wheat

black stem rust (Puccinia graminis tritici),373–4

wheat (Triticum), 11white-rot fungi, 62, 78, 238, 240, 244–6,

336, 345white rust, 379Whitfields ointment, 512Whittaker, R. H., 23whole organism biotechnology, 451–506

alcoholic fermentations, 474–7

ang-kak, 506arachidonic acid, 482–3autolysis in cultures, 465–6batch culture, 452–69beer-making, 475–6bioreactors, 496bread-making, 499–501cheese production, 501–5chemostats, 470–3chocolate production, 495citric acid biotechnology, 468, 477–8coffee production, 495–6culturing fungi, 452–6digestion of lignocellulosic residues,497–9

evolution in fermenters, 487–92fabric manufacture, 483–4, 484–6fed-batch culture, 451–70fermented foods, 504–6fermented meat products, 503–4fermented soy foods, 504–6fermenter engineering, 458–60fermenter growth kinetics, 462–4fermenters, 451–2food processing, 484–6fungal biological control agents, 492–3fungal fermentations in submerged liquidcultures, 452

fungal growth in liquid cultures, 460–3glucose-stats, 473growth as pellets, 466–9growth yield, 464–5mycoherbicides, 492–3mycopesticides, 492–3myco-protein, 487–92natural digestive fermentations inherbivores, 493–4

nutristats, 473open (continuous) systems, 453oxygen demand of the culture, 456–8oxygen supply to the culture, 456–8penicillin history and production, 478–82permittistats, 473pH auxostats, 473pharmaceuticals, 473, 478–83programmed cell death in cultures, 465–6Quorn™ fermentation, 487–92range of uses of submergedfermentations, 473–4

ruminant digestion, 493–4salami production, 503–4solid state fermentations, 494–7soy sauce, 504–6spore and inocula production, 492–3stationary phase, 465–6steroid manufacture, 486–7surface fermentation, 477tea production, 496turbidostat cultures, 472–3use of fungi to make chemicaltransformations, 486–7

wine-making, 476–7Wilcoxina spp., 351

626 Index






wild mushroomscommercial exploitation, 272–4

willow (Salix), 346wine making, 476–7witches’ broom disease of birch, 56Woese, Carl, 24wood ear fungus (Auricularia polytricha)

trade, 273‘wood-wide-web’ectomycorrhizas, 338mycorrhizas, 349

wood-decay fungi, 78, 238, 327, 345chlorohydrocarbon release, 336decay of structural timber, 331–3dry rot, 331–3

woodland mushrooms, 347ectomycorrhizas, 338

World Data Centre for Microorganisms(WDCM), 562

World Federation of Culture Collections,562

world’s largest individual organism, 370

Woronin bodies, 99, 144Wurzelpilze, 336Wurzelsymbiose, 336

Xerocomus parasiticus, 442xylanases, 241xylans, 240Xylaria polymorpha, 78Xylaria spp., 60xylosidase, 240

yeast, 55, 56–9basidiomycetous, 63cell cycle genetic studies, 149–50cell cycle in budding yeast, 150definition, 105epiphytes, 79genome, 537lipophilic, 62number of protein coding genes, 115switching mating types, 200

yeast artificial chromosome (YAC), 532, 552

yeast researchbreeding experiments, 106contribution to eukaryote cell biology,105–7

fermentation, 105–6genetics, 106

yeast–mycelial dimorphism, 150–1

zearalenone, 262zinc finger protein, 221zoonoses, 425Zoopagales, 52Zoopagomycotina, 30, 52, 442zoosporesfree cell formation, 48–50

zygomycetes, 52zygomycosis, 53, 54, 431–2Zygomycota, 29, 30, 35, 50, 52–5, 414meiosis, 118polyphyletic nature, 52

zygosporangium, 52zymogen, 136

Index 627






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