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Cambridge University Press 978-0-521-18695-7 - 21st Century: Guidebook to Fungi David Moore, Geoffrey D. Robson and Anthony P. J. Trinci Index More information

INDEX

Absidia corymbifera, 431 La France disease, 196 alcoholic fermentations, 474–7 Acaulospora spp., 52, 340, 441 mycoparasite problems, 443–4 Aleuria spp., 60, 228 Acaulosporaceae, 52, 340 wet bubble disease, 443 alkaloids produced by endophytes, 360 acervulae, 198, 223 white mould disease, 443 allergic aspergillosis, 430 acetyl-coenzyme A (acetyl-CoA), 47, 252, Agaricus bitorquis, 195 allergic reactions, 433 477 Agaricus brunnescens, 195 Allomyces macrogynus, 48, 199 acetylenes, 264 Agaricus spp. Allomyces spp., 47–8 achlorophyllous orchids use of protein, 246 Allotropa spp., 343 obligate mycoheterotrophs, 346 agaritine, 263 a-amanitin, 264 Achlya bisexualis, 138, 199 Agaromycotina a-tubulin, 25 growth mechanism, 160 AFTOL classification, 66–9 Alternaria brassicicola, 383 pheromones, 77 agglutinins, 168 aluminium in soil minerals, 6 Achlya spp., 31, 75, 85 agonomycetes, 198 Amanita muscaria, 78, 263, 338, acostromata, 60 agricultural myocides, 529 347, 354 Acrasiales, 77 agricultural soil toxins, 328–30 Acrasiomycota, 77 area on the Earth, 5 Amanita pantherina, 329 Acrasis spp., 77 agricultural waste Amanita phalloides, 264 Acremonium spp., 442 breakdown by fungi, 238 Amanita spp., 78, 347 Acromyrmex spp., 396 cultivation of Pleurotus spp., 278 accumulation of metal ion, 327 actin, 126 lignocellulose biodegradation, 497–9 amatoxins, 433–4 actin-binding proteins (ABPs), 126 remediation by fungi, 334–6 mycorrhizal fungi, 337, 338 actin filaments, 126 agriculture phallotoxin, 433–4 actin gene mutations, 126 affluent diet requirement, 5 poisoning, 433–4 actin-associated myosins, 127–33 agricultural fungi, 15 toxins, 264 actins, 25 amount of land used to supply food, 5 Amanita virosa,62 activator-inhibitor model, 293 human dependence on fungi, 15 amatoxins, 433–4 active transport across a membrane, 249 losses to fungal diseases, 4 amber plasma membrane, 133 losses to pests and diseases, 368–70 fungal fossils, 32–3 actomyosin ring mycorrhizal fungi in crop plants, 4 ambrosia beetles, 62 assembly during cell division, 145 origins of, 10–15 and fungi, 399–400 adhesins, 168–70 role of fungi in herbivore digestion, 4 Ambrosiella spp., 399, 400 affluent diet ruminants and anaerobic chytrids, 400–5 American Type Culture Collection (ATCC), land required per person, 5 strobilurin fungicides, 4 562 aflatoxicosis, 330, 435–6 subsistence diet requirement, 5 Amoebidiales, 29, 52, 77 aflatoxins, 56, 262, 330, 435–6 Agrobacterium tumefaciens-mediated Amoebidium parasiticum, 415 African histoplasmosis, 428 transformation (AMT), 389, 551 amorphous cellulose, 239 AFTOL study, 35, 45, 50, 51, 55, 56, 61 agroclavine, 54 amphibians Agaricaceae, 66 AIDS patients cutaneous chytridiomycosis, 43, 422–4 Agaricales, 63–5, 66, 394 candidiasis, 429 amphipathic structure of hydrophobins, Agaricomycetes, 66 cryptococcosis, 428 170 Agaricomycetidae, 63, 66 opportunistic fungal infections, 429 amphotericin B, 431, 515–16 Agaricomycotina, 62, 63–71 susceptibility to fungal infections, 429 amphotericin B liposomes (AmBisomes), Agaricus bisporus, 71, 117, 195, 200, 245, See also immunocompromised patients 517 247, 252, 254, 263, 311 Ajellomyces capsulatus, 428 amylases, 241, 242 brown spot disease, 443 Albugo candida, 379 amyloglucosidases, 241 commercial cultivation technique, 276–8 Albugo spp., 31, 75 amylopectins, 241 dry bubble disease, 443 alcohol, 4 amylose, 241 genome, 546 alcohol production anaerobic chytrids, 29, 45–6 hymenia development, 295 fermentation research, 105–6 and ruminants, 400–5

© in this web service Cambridge University Press www.cambridge.org Cambridge University Press 978-0-521-18695-7 - 21st Century: Guidebook to Fungi David Moore, Geoffrey D. Robson and Anthony P. J. Trinci Index More information

606 Index

anaerobic early eukaryotes, 23 arbutoid endomycorrhizas, 337, 343 Aspergillus ﬂavus, 189 Anaeromyces spp., 401 Arbutus spp., 343 Aspergillus fumigatus, 262 analogous organs, 63 Archaea, 24 chitin synthase genes, 160 anamorph (asexual stage), 42 Archaeospora spp., 340 genome, 544 anamorphic fungi, 198–9 Archaeosporales, 340 Aspergillus giganteus, 484 anastomosis. See hyphal fusion archiascomycetes, 56 Aspergillus lentulus, 431 ang-kak, 274, 506 Arctostaphylos spp., 343 Aspergillus nidulans, 42, 126, 127, 460, anidulafungin, 521 Armillaria bulbosa, 195 467–8 animal pathogens Armillaria gallica,71 conidiophores, 220–3 comparison with plant pathogens, 436–9 Armillaria mellea, 227, 246, 251, 335, 344, duplication cycle, 92–3 Anisolpidiales, 75 346 genome, 544 Anisolpidium spp., 75 Armillaria spp., 117, 195, 246, 370–2, 444 het genes, 186 ant agriculture genomes, 547 heterokaryon formation, 186 coral fungus agriculture, 396 Armillariella spp., 444 mitosis, 116, 117 demand for leaf material, 395–6 aromatic hydrocarbon pesticides, 334 mitotic gene segregation, 189, 192–4 Escovopsis fungal parasite, 397 Arthoniomycetes, 60, 61 mutations, 116 gardening ants, 393–8 Arthrinium sphaerosperma, 522 negative autotropism, 96 generalised higher agriculture, 396 Arthrobotrys oligospora, 406, 439 nuclear migration, 132 leaf-cutter agriculture, 396 arthropod endosymbiont fungi, 53 nutritional selection for diploid strains, lower agriculture, 396 arthropod pathogens 189, 192–4 molecular phylogenies of attine ants, Laboulbeniales, 416–17 parasynchronous nuclear division, 148 396–7 arthropod pests Aspergillus niger, 92, 189, 468, 474, 477 obligate symbiosis with the fungus, 396 biological control, 421–2 Aspergillus oryzae, 189, 474, 484, 505, 506 symbiotic Streptomyces, 397–8 chemical pesticides, 421 Aspergillus sojae, 505 yeast agriculture, 396 integrated pest management (IPM), 422 Aspergillus spp., 56, 60, 228, 262, 274 antheridiol, 199 microbial control agents, 422 aﬂatoxins, 330, 435–6 antibiotic resistance, 108 use of transgenic plants, 422 aspergillosis, 429–30, 430–1 antibiotics, 4, 55, 473, 512 arthrospores, 208 in the home, 432 antibiotics production, 353 Artiodactyla, 403 proteinases, 246 antifeedants, 328 and anaerobic chytrids, 400–5 Aspergillus sydowii antifungal agents aryl alcohol oxidase, 245 infection of sea fans, 424 azoles, 517–21 asci, 55, 228 Aspergillus terreus, 55, 262, 431, 473 cell wall as a target, 171–2 Pezizomycotina, 60–1 Assembling the Fungal Tree of Life project. fungal cell wall as target, 157 Ascobolus heterothallicus, 186 See AFTOL study polyenes, 514–17 Ascobolus stercorarius, 186 Asterodon ferruginosus, 301 protective agents, 512 ascochlorins, 263 Asterostroma spp., 332 systemic agents, 512–13 ascolichens, 358 asthmatic reactions targeting the cell wall, 521–2 ascoma morphologies allergic aspergillosis, 430 targeting the membrane, 512–21 Pezizomycotina, 59–60 astral microtubules, 118, 146 types of, 512 ascomata, 228 asynchronous division of nuclei, 146–8 antigens, 437 Ascomycetes, 23, 29, 55 Atheliales, 66 antiporters, 249 Ascomycota, 29, 30, 35, 55–61, 78, 346, athlete’s foot, 425 antitumour agents, 473 351, 438, 442 atmospheric pollution Antrodia vaillantii, 332 asexual fungi, 56 chlorohydrocarbon release by wood- Antrodia xantha, 332 endophytes, 360 decay fungi, 336 ants and fungi, 279 important species, 55–6 sensitivity of lichens to, 358 Aphelenchoides composticola, 270 lichens, 79 sources of chloromethane, 336 apical growth of the hypha, 100 meiosis, 118 ATP, 121, 122 Apodachlyella spp., 75 morphology, 55 ATP synthesis apoptosis, 185, 315–16, 465 septal pores, 99 primary metabolism, 251, 253 apothecia, 59, 228 Woronin bodies, 99 ATPase genes apple blotch, 370 Ascomycotina, 50 phylogenetic studies, 24–5 appressorium, 379 ascospores, 55, 228 Atta spp., 396 Apterostigma spp., 396 ascostromata, 59 attine ants aquatic fungi, 78 Asellaria ligiae, 415 molecular phylogenies, 396–7 arabanases, 241 Asellariales, 52, 53, 415 Aureobasidium spp., 60 arabans, 240 asexual fungi, 180 Auricularia polytricha (wood ear fungus) Arabidopsis thaliana, 376 Ashbya gossypii trade, 273 arachidonic acid biotechnology, 482–3 asynchronous nuclear division, 147 Auriculariales, 67 arbuscular endomycorrhizas, 337, 338–42 aspartic proteinases, 247 aurora australis, 22 arbuscular mycorrhizal fungi, 32, 50–2, 78, aspergillosis, 429–30, 430–1, 524 aurora borealis, 22 171, 441 aspergillosis disease of coral, 424 autotropism, 96–7 arbuscules, 51, 338 Aspergillus awamori, 502 mycelium growth, 87–8

Index 607

auxotrophs, 181 definition, 213 Boletus elegans, 78, 338, 347 avirulence gene, 437 biofilms, 28–9, 170 Boletus parasiticus, 442 avoidance mechanism in hyphae, 96 biogeochemical transformations Boletus spp., 78, 344, 347, 353 azoles, 514, 517–21 role of fungi, 9–10 mycorrhizal fungi, 337, 338 bioinformatics, 531 Bombardia spp., 60 Bacillus thuringiensis, 422 analysis of large survey data sets, 563 bootlace fungus. See Armillaria spp. bacteria, 326 definition, 557 Bordeaux mixture, 512 and soil health, 7 effects of climate change on fungi, 563 Botrytis cinerea, 183, 382, 383–4, 385, 493 numbers in soil, 7 genomic data mining, 562 Botrytis elliptica, 384 oldest known fossils, 23 genomics research data, 557 Botrytis fabae, 384 bacterial artificial chromosome (BAC), 532 mathematical modelling of hyphal Botrytis spp., 384 bakanae disease of rice, 379 growth, 566 bovine spongiform encephalopathy (BSE), baker’s yeast, 55, 105 non-genomic data, 557 196 bark beetles, 373, 399 biolistic transformation, 551 Bovril, 274 barley (Hordeum), 11 biological control, 63 Brachiola spp., 413 barley powdery mildew (Blumeria graminis arthropod pests, 421–2 bracket fungi, 228, 229 hordei), 371, 389 fungal pathogens of insects, 412 bread, 4 barrage formation mycoherbicide production, 492–3 bread-making, 499–501 vegetative incompatibility response, 188 mycopesticide production, 492–3 brefeldin, 264 basidia, 228, 291, 293 nematode-trapping fungi, 407 brefeldin A, 162 Basidiobolus ranarum,55 Trichoderma spp., 444 Bremia spp., 31 Basidiobolus spp., 55 biological species brewer’s yeast, 55, 105 basidiolichens, 358 compatibility systems, 189 Bridgeoporus nobilissimus,71 basidiomata, 228–31 biological species concept, 71–4 British Mycological Society, 562 Basidiomycetes, 23, 29, 61, 62 biology of incompatibility systems, 188–90 bromatia, 394 basidiomycetous yeasts, 63 bioluminescence in fungi, 246 bronchopulmonary aspergillosis, 430 Basidiomycota, 29, 35, 59, 61–71, 78, 338, biopulping, 245 brown-rot fungi, 78, 238, 240 344, 346 bioremediation with fungi, 9–10, 238 Brundrett, Mark, 337 basidiospores, 62 biotechnology Buchner, Eduard, 106 commercially farmed fungi, 71 use of fungal enzymes, 4 budding yeast, 105, 116 dolipore septum, 99 See also whole organism biotechnology building structures ectomycorrhizas, 78 biotrophic fungi, 238, 327, 337, 338, 376–8 cellar rot fungus, 332 largest and longest-lived fungi, 71 bioweathering, 9 decay of structural timber, 331–3 lichens, 79 bipolar heterothallism, 199 dry rot, 331–3 mating types, 205–10 Neurospora spp., 203 wet rot, 332 meiosis, 118 birch (Betula), 346, 347, 354 bulk flow of nutrients, 248 mutualistic associations with insects, 62 bird mycosis Buller’s drop, 229, 231 number of species, 61 aspergillosis, 429 buna shimeji (Hypsizygus marmoreus), 277 phylogeny, 62–9 bird’s-nest fungi, 228 buthiobate, 518 Basidiomycotina, 50 birds of prey button mushroom. See Agaricus bisporus basidiospores, 62, 228, 292, 380 indirect dependence on fungi, 271–2 Batrachochytrium dendrobatidis, 43, 401, bivalents formed during meiosis, 118 C3 and C4 photosynthetic pathways, 404 422–4 black stem rust of wheat (Puccinia graminis Caecomyces spp., 401, 403 Beadle, George, 106 tritici), 373–4 cage fungi, 66 bean (Phaseolus vulgaris), 62 Blastocladiales, 29, 45, 46 calcium gradient in the hyphal tip, 141–2 Beauveria bassiana, 419 Blastocladiella spp., 47, 48–9 Calluna (ling) beech (Fagus), 346 Blastocladiomycota, 29, 45, 46–50 mycorrhizas, 337, 341 beer-making, 475–6 alternation of generations, 47 Calvatia gigantea,71 beet leaf spot, 370 free cell formation of zoospores, 48–50 Camembert cheese, 264 beetles hormone production, 47–8 campesterol, 512 agriculture in beetles, 399–400 life history, 47 cancer therapy patients. ambrosia beetles and fungi, 399–400 spore formation process, 48–50 See immunocompromised patients benomyl, 334, 522 sportic meiosis, 47 Candida albicans, 59, 198, 425–6, 522, 525 b-glucan Blastomyces dermatitidis, 150, 167, 428 candidiasis, 429 fungal cell wall, 137 adhesin which potentiates infection, 170 chitin synthase genes, 161 b1,3-glucan, 158, 163 blastomycosis, 170, 428 phenotype switching, 429 b1,3-glucan synthase inhibitors, 172 Blobel, Gu¨nter, 119 yeast–mycelial dimorphism, 150–1 b1,3-glucan synthases, 163 blue–green algae, 254, 357 Candida glabrata, 429 b-tubulin, 25 Blumeria fischeri, 389 Candida spp., 55 biflagellate zoospores, 75 Blumeria graminis, 371, 389 chlamydospores, 214 big bang theory, 19–21 Blumeria spp., 382–3 genomes, 545 bilberry (Vaccinium), 78 Boletales, 64, 66 candidiasis, 522 biodiversity Boletus edulis, 71, 344 Cantharellales, 66–9

608 Index

Cantharellus cibarius, 71, 272, 273, 337 cellulose, 238 chlorinated biphenyl pesticides, 334 Cantharellus spp., 66 in cell walls, 29 chloroaromatics, 245, 336 carbendazim, 522 cellulose breakdown, 238, 239–40 Chlorociboria aeruginascens, 333 carbohydrate catabolism, 251–2 cellulosomes, 240 chlorohydrocarbon release by wood-decay carbonation Centraalbureau voor Schimmelcultures fungi, 336 chemical weathering process, 6 (CBS), 562 chloromethane, 245 carotenes, 260 central vacuole, 124 sources of atmospheric pollution, 336 carotenoid pigmenation, 168 centrosomes, 116 chloroplasts, 108, 121–2 carotenoids, 258, 260 cep. See Boletus edulis endosymbiont theory, 23, 121–2 caspofungin, 521 cephalosporins, 264–3 protein transport, 121 catastrophe (microtubule switch), 126 Cephalosporium acremonium, 474 Choanozoa, 30, 77 cell Ceratocystis fagacearum, 148 chocolate production, 495 discovery of, 107 Ceratocystis novo-ulmi. See Dutch elm cholesterol, 133, 259, 512 cell and tissue differentiation disease in cell membranes, 29 ascomata, 228 Ceratocystis spp., 400 cholesterol levels basidiomata, 228–31 Cercospora beticola, 372 use of statins to control, 4 conidiation in Neurospora crassa, 223 Cercospora spp. chromatids, 109–12, 116 conidiomata, 223–5 leaf spot diseases, 372 chromatin structure, 109–12 conidiophores of Aspergillus nidulans, Ceriporiopsis subvermispora, 245 Chromocrea spinulosa, 202 220–3 Chain, Ernst, 478, 480 chromosome non-disjunction, 194 diversity in relation to fungi, 214 chanterelles, 71, 272, 273, 337 Chrysanthemoides monilifera,63 globose structures, 227–30 chaperonins, 119, 120 Chrysosporium parvum, 442 linear structures, 225–7 checkpoints in the cell cycle, 116, 149 Chytridiales, 42, 45 mycelial differentiation, 214–16 cheese, 4, 56 chytridiomycosis rhizomorphs, 226–7 blue cheeses, 275 amphibians, 43, 422–4 rhythmic growth, 214–16 mould ripening, 275, 495, 503 Chytridiomycota, 29, 30, 35, 42–5 sclerotia, 227–8 production, 501–5 classification as true fungi, 43–5 spore formation, 216–20 role of fungi in production, 274–5 habitats, 42 strand and cord formation, 225–7 chemical attractants, 47–8 important species, 42–3 cell cycle, 115–16 chemical pesticides phylogeny, 43–5 budding yeast cell cycle, 150 advantages and disadvantages, 421 reproduction, 42–4 checkpoints, 149 chemical safety information, 513 roles in food-web dynamics, 43 control and coordination of events, chemical transformations water moulds, 75 148–50 use of fungi, 486–7 chytrids, 30, 42–5, 45–6 control of nuclear division, 148 chemical weathering, 6 ruminants and anaerobic chytrids, 400–5 genetic studies on yeasts, 149–50 carbonation, 6 Chytriomyces spp., 43 phases, 149 hydration, 6 cilia research, 107 hydroloysis, 6 endosymbiont theory, 23, 121 cell death oxidation and reduction, 6 circadian rhythms vegetative incompatibility, 185 chemo-organoheterotrophism, 326 clock genes and proteins, 215–16 cell division chemostat cultures, 470–3 feedback loops, 215 fungi, animals and plants compared, chemotropic hyphae mycelial growth, 214–16 145–6 Oomycota, 75 oscillators, 215, 216 cell inflation Chernobyl incident, 327 citric acid biotechnology, 468, 477–8 coordination in the fruit body, 304–5 chestnut blight, 370 citrinin, 262 cell membrane, 107, 123–4 chiasmata formed during meiosis, 118 clade cholesterol, 29 Chicxulub meteor impact definition, 28 ergosterol, 29 effects on fungi, 37–8 cladistics structure, 123 chimeras, 290 definition, 27–8 transport channels, 123 chitin, 158, 160 Cladobotryum dendroides, 444 cell organelles, 107 breakdown by fungi, 241 Cladonia spp., 60 cell polarity, 148 fungal cell wall, 136–7 Cladosporium fulvum, 387 cell structure in cell walls, 29 Cladosporium spp., 432, 440 eukaryotes, 107–8 measurement in soil, 7 clamp connections, 142, 184, 185 prokaryotes, 107–8 chitin synthase classification cell targeting system, 48 functions in the cell wall, 160–2 definition, 27 cell theory, 107 genes, 160–1 classification of fungi. See natural cell-anchor receptors, 349 inhibitors, 171–2 classification of fungi cellar rot fungus, 332 chitin synthesis inhibitors, 521–2 clathrin coated pits, 123 cellobiase, 240 chitinase, 241, 439 Claviceps purpurea, 259, 263, 434 cellobiose oxidoreductases, 240 chitosomes, 140, 161–2 clay minerals, 6 cellular element term, 225 chlamydospores, 198, 214 clays cellulases, 240, 384 chloramphenicol, 195 fungal–clay interactions, 9

Index 609

cleavage plane in cell division, 146 consensus model of hyphal tip extension, Cunninghamella echinulata,55 cleavage polyadenylation specificity factor 139–40 Cunninghamella elegans,55 (CPSF), 111 conservation Cunninghamella spp., 55 cleistothecia, 59, 228 importance of records about fungi, 563 Currie, James, 477 climate conservation patterns in genes, 24 cushion bracket, 336 effects on soil formation, 6 convergent evolution, 24, 227 cutaneous chytridiomycosis climate change COPI coat protein complex, 122, 124 amphibians, 43, 422–4 effects on fungi, 563 COPII vesicle coat proteins, 122, 124 cyanobacteria, 52, 340, 357 impacts on mycorrhizas, 354–5 copolymers, 240 cyber fungi Clitocybe nebularis Coprinellus pellucidus, 290 modelling and computer simulation, 566 mycelial network, 267 Coprinopsis bisporus, 200 Neighbour-Sensing model of hyphal Clitocybe spp., 263, 353 Coprinopsis cinerea, 117, 180, 189, 195, growth, 566 clock genes and proteins, 215–16 210, 227, 252, 255, 311, 312, 444, 454 cyclic AMP (cAMP), 134 closed mitosis in fungi, 115 developmental commitment, 308–10 cyclin-dependent kinases, 56, 150 clotrimazole, 518 genome, 546 cyclins, 150 clouded agaric, clouded funnel (Clitocybe metabolic regulation, 305–8 cyclopentanes, 264 nebularis), 267 tetrapolar heterothallism, 206–10 cyclosporine, 4, 473 Coccidioides immitis, 428 Coprinopsis congregatus, 208 Cyllamyces spp., 401 Coccidioides posadasii, 161, 167, 428 Coprinopsis fruit body Cymbidium spp., 344 Coccidioides spp., 60 coordination of cell inflation in the fruit Cyphomyrmex spp., 396 coccidioidomycosis, 428, 522 body, 304–5 cysteine proteinases, 247 Cochliobolus carbonum, 378 hymenia development, 291–5 cystesia, 295 Cochliobolus heterostrophus, 203, 378 making gills, 295–301 cystidia, 228, 291, 292, 293 Cochliobolus victoriae, 378 mushroom mechanics, 305 Cystofilobasidiales, 66 Coelomomyces spp., 47, 418, 419 stem development, 301–4 cytochromes, 25 coelomycetes, 198 Coprinopsis patouillardii, 208 cytokinesis co-evolution of plant–pathogen disease Coprinopsis radiatus, 208 comparison with septation, 145–6 systems, 387–9 Coprinopsis spp., 170, 185 cytoplasm, 107 coffee production, 495–6 use of protein, 246 cytoplasmic segregation, 194–7 collembola (springtails), 331 Coprinus cinereus, 117 mitochondria, 194–6 grazing on fungi, 267–70 Copromyxa spp., 77 plasmids, 195–6 Colletotrichum graminicola, 161 coral disease prion proteins, 196 Collybia tuberosa, 246 aspergillosis, 424 virus-like particles, 196 colonisation of solid substrata, 99 coral fungus cytoskeletal systems, 125–7 colony formation, 86–8 ant agriculture, 396 commercial applications Corallorhiza spp., 346 Dacrymycetales, 66 mycorrhizas, 355–6 Cordyceps canadensis, 443 Dacrymycetes, 66 commercial exploitation of wild Cordyceps capitata, 443 Dactylellina spp., 406 mushrooms, 272–4 Cordyceps militaris, 442, 443 damping-off in seedlings, 327 commercial mushroom production, 71, Cordyceps spp., 60, 442, 443 dandruff, 62 275–9 Corticiaceae, 66 Darwin, Charles, 7 mycoparasite problems, 443–4 Corticiales, 67 data mining, 314–15, 562 common ancestor of a group, 28 cortisone, 486 databases of information about fungi, 562 comparative genomics, 547 cosmid, 532 deep divergences, 28 compatibility and the individualistic coumaryl alcohol, 242 deep time, 26, 28 mycelium, 180–1 Craterellus spp., 66 Dendryphiella spp., 254 compatibility test, 185 Cretaceous–Tertiary (K–T) extinction event dermatomycosis, 426–7 competitive interactions among fungi, 439– effects on fungi, 37–8 ‘Destroying Angel’ (Amanita virosa), 62 44 crown rust of wild oats, 389 Deuteromycetes, 23, 29, 56, 198 computer simulation of hyphal growth, 566 croziers, 142 Deuteromycota, 56, 198 concentration gradients Cryphonectria parasitica, 186, 205 Deuteromycotina, 56, 198 plasma membrane, 248 Cryphonectria spp., 55 developmental biology of fungi, 282–316 conidia, 53, 55 Crypticola spp., 75 activator–inhibitor model, 293 conidia production, 198 cryptococcal meningitis, 62, 69 apoptosis, 315–16 conidiation in Neurospora crassa, 223 cryptococcosis, 428, 546 basic principles, 316 conidiomata, 223–5 Cryptococcus neoformans, 327, 428 bulbangiocarpic development, 287 conidiophores, 53, 217–19 genome, 546 comparison with other tissues and Aspergillus nidulans phenotype switching, 429 organisms, 310–11 Coniferophyta, 343 Cryptococcus spp., 62, 69 comparison with plants and animals, coniferyl alcohol, 242 Cryptosporidium, 414 283–5 Coniophora puteana,78 crystalline cellulose, 239 competence, 289–90 Coniothyrium minitans, 493 Cudonia spp., 60 coordination of cell inflation in the fruit Coniphora puteana, 332 Cunninghamella bertholletiae,55 body, 304–5

610 Index

developmental biology of fungi (cont.) Dictyosteliales, 77 domains of the tree of life, 23–9 Coprinopsis cinerea, 289 Dictyostelium spp., 77 Donkioporia expansa, 332 Coprinopsis fruit body, 291–5, 295–301, Didymium spp., 77 dormancy in spores, 86 301–4, 304–5 dieldrin, 334 Dothidea, 60 definition of development, 284 diffusion of nutrients Dothideomycetes, 60, 61, 438 definition of morphogenesis, 285 facilitated diffusion, 133, 248–9 Dothidia spp., 60 degeneration, senescence and death, simple diffusion, 248 double-stranded RNA (dsRNA) virus, 196 315–16 Dikarya, 29, 35 Douglas fir, 347 development and morphogenesis, 283 dikaryon, 207 Drechslerella spp., 406 development of a mushroom, 284 definition, 180 Drosophila (fruit fly), 206 developmental commitment, 308–10 functional diploidy, 183–5 Drosophila funebris, 270 developmental variants, 311–12, 312–13 maintaining the dikaryon state, 184–5 Drosophila melanogaster, 115 differential growth, 283 Dimargaris spp., 440, 442 drug discovery approach (Ehrlich), 512 distinctive characteristics of fungi, 283–5 Dimargaritales, 52 drug targets, 107 endocarpic development, 288 dimorphism dry-rot fungus, 226, 331–3 environmental influences, 290 yeast and mycelial growth forms, 150–1 Ducellieria spp., 75 formal terminology of developmental diploid state in fungi, 117 Duddingtonia flagrans, 407 biology, 283–5 dikaryon, 183–5 duplication cycle in fungi, 92–3 formation of multicellular structures, 283 diploid strains Dutch elm disease (Ophiostoma novo-ulmi), fruit body chimeras, 290 nutritional selection for, 189 370, 372–3 fungal wall remodelling, 283 dipteran fly larvae (maggots), 270–1 role of elm bark beetles, 373, 399 fuzzy logic approach, 313–14 Dipterocarpaceae, 346 dynactin, 116, 117, 129 genetic approaches, 311–15 disease triangle, 374–6 dynein, 117, 129 genomic data mining, 314–15 Dispira spp., 440 microtubule-associated dynein, 127–33 geometric proportions of the stem, 286 diterpenes, 259 molecular motors, 127–33 gymnocarpic development, 286 Diversispora spp., 340 dynein motors, 116, 127 gymnovelangiocarpic development, 287 diversity hymenia development, 291–5 ascomata, 228 early-stage fungi, 354 hyphal analysis, 301–4 basidiomata, 228–31 Earth hyphal tuft (hyphal knot), 283 biodiversity in fungi, 213 axial tilt, 22, 23 making gills, 295–301 complexity of the concept, 7 development of life on, 23–9 making stems, 301–4 conidiation in Neurospora crassa, 223 effects of the solar wind, 22–3 metabolic regulation and morphogenesis, conidiomata, 223–5 formation of, 21 305–8 conidiophores of Aspergillus nidulans, greening of the Earth, 28–9 modular nature of fungi, 283 220–3 magnetic field (magnetosphere), 22–3 morphogenetic field model, 293 definition, 214 molten iron core, 21, 22 morphogenetic polarities, 291 ecosystem level aspects, 7 ozone layer, 22–3 mushroom mechanics, 305 globose structures, 227–30 rate of rotation, 22 observational and experimental basis, in relation to fungi, 214 seasons, 22, 23 285–6 linear structures, 225–7 temperature range for liquid water, 21–2 pattern formation, 283, 284 mycelial differentiation, 214–16 Theia–Earth impact, 22, 23 patterning genes, 314 production and dispersal of spores, 214 Earth–Moon binary system, 22, 23 pilangiocarpic development, 287 rhizomorphs, 226–7 earthworms placement of hyphal branches, 285 rhythmic growth, 214–16 Darwin’s experiments on, 7 polypore growth patterns, 300–1 sclerotia, 227–8 numbers in soil, 7 pore formation in polypores, 301 spore formation, 216–20 Eccrinales, 52, 77 primordia, 283 stipes of fruiting bodies, 227 echinocandins, 172, 521–2 programmed cell death, 315–16 strand and cord formation, 225–7 ecological species concept, 74 regional patterning (regional DNA, 107 ecosystem diversity, 7 specification), 283, 290–1 chromatin structure, 109 ecosystem functions of fungi, 237–64 renewed fruiting, 315 extrachromosomal, 108 bioluminescence in fungi, 246 stipitangiocarpic development, 288 introns in fungal DNA, 114 bioremediation, 238 terminology, 283 molecular processes in the nucleus, 109 biotrophs, 238 tolerance of imprecision, 312–13 plasmids, 108 breakdown of agricultural wastes, 238 tube formation in polypores, 301 prokaryotes, 107 breakdown of cellulose, 239–40 typical mushroom structure, 285–6 replication before meiosis I, 117 breakdown of chitin, 241 velangiocarpic development, 289 DNA microarrays, 559 breakdown of glycogen, 242–3 developmental variants, 311–12, 312–13 DNA probes breakdown of hemicellulose, 241 Devonian Rhynie chert, 31, 403, 442 soil microbes, 8 breakdown of pectins, 241 Diaporthe spp., 60 dolipore septum, 99 breakdown of polysaccharides, 239–42 Dicranophora spp., 440 Domain Archaea, 24, 26–8 breakdown of starch, 241–2 Dictylenchus myceliophagus, 270 Domain Eubacteria, 24, 26–8 breakdown of toxic wastes, 238 dictyosomes, 122, 124 Domain Eukaryota, 24, 26–8 external digestion in fungi, 237

Index 611

flow of nutrients, 247–51 edifenphos, 526 ergobasines, 435 fungal nutritional modes, 238 Ehrlich, Paul ergocristine, 263 lignin degradation, 242–6 drug discovery approach, 512 ergosterol, 133, 259–61 necrotrophs, 238 Elaphomyces muricatus, 443 in cell membranes, 29 primary (intermediary) metabolism, Elaphomyces spp., 442 measurement in soil, 8 251–6 electrochemical proton gradient, 133 target for antifungal agents, 512–21 production of esterases, 247 Electrogella spp., 75 ergot alkaloids, 263, 473 production of extracellular enzymes, 239 electromagnetic radiation ergotamines, 435 production of lipases, 247 resistance to, 167 ergotism (ergot poisoning), 434–5 production of phosphatases, 247 electrophoresis technique, 115 ergotoxines, 435 production of sulfatases, 247 electroporation, 550 Erica (heather) protein digestion, 246–7 element cycling, 9 mycorrhizas, 337, 341 range of contributions, 238–9 elements Ericaceae release of greenhouse gases, 245–6 creation in stars, 20 mycorrhizas, 341–3 saprotrophs, 238 elm bark beetles, 373, 399 Ericales, 343 secondary metabolites, 257 Embden–Meyerhof–Parnass (EMP) ericoid endomycorrhizas, 78, 337, 341–3 transport and translocation of nutrients, pathway, 251 ericoid mycorrhizas 247–51 emergence of new diseases, 424 facultative symbiosis, 342 wood-decay fungi, 238 Emericella spp., 42 Erynia neoaphidis, 418 ecosystem mycology, 77–9, 325–61 Encephalitozoon cuniculi, 413 Erysiphe graminis, 327, 371 aquatic fungi, 78 Encephalitozoon hellem, 413 Erysiphe spp., 382 chemo-organoheterotrophism, 326 Encephalitozoon intestinalis, 413 erythromycin, 195 chlorohydrocarbon release by wood- endocytosis, 123 Erythrorchis spp., 345 decay fungi, 336 endo-enzymes, 239 Escherichia coli genome, 537 decay of structural timber, 331–3 endoglucanase, 240 Escherichia spp., 106 degradation of man-made polymers, Endogonales, 52, 53 esterases, 247 333–4 Endogone spp., 346 ethylenediamine tetra acetic acid (EDTA), ecosystem roles of fungi, 325–6 endomembrane systems, 121–5 247 effects of land management practices, endomycorrhizas, 51, 78, 337–9 euagarics clade, 63 326 Endophyllum spp., 62 euascomycetes, 56, 59 endophytes, 79, 360–1 endophytic fungi, 79, 360–1 Eubacteria, 24 environmental issues, 326 endoplasmic reticulum (ER), 120, 122, 124, Eucalyptus spp., 346, 347 epiphytes, 79, 361 163 Eucarya, 24 food contamination and deterioration, endospores, 228 Eukaryota, 24 328–31 endosymbiont theory, 23, 121–2, 195 eukaryote cell biology fungal contribution to soil structure, 326 endotrophic mycorrhizas, 337 contribution of fungal research, 105–7 fungi as food for other organisms, 326 endoxylanases, 240 eukaryote/prokaryote distinction, 23 fungi as predators, 326 enilconazole, 518 eukaryotes fungi as prey, 326 enoki (Flammulina velutipes), 277 cell structure, 107–8 fungi as recyclers, 326–8 enokitake (Flammulina velutipes), 71 early anaerobic forms, 23 habitat creation by fungi, 326 Enterocytozoon bieneusi, 413 first terrestrial eukaryotes, 37 inorganic transformations, 327 Entner–Doudoroff (ED) pathway, 252 fungus as model eukaryote, 105–7 lichens, 79, 356–60 entomogenous fungi, 417–21 modes of nutrition, 29 mutualism, 325 Entomophthora muscae, 55, 421 primitive present-day forms, 23 mycorrhizas, 78–9, 336–56 Entomophthora spp., 419 eukaryotic cells nitrogen sources in plant litter, 327 Entomophthorales, 52, 53, 417 subcellular components, 109 nutrient availability, 327 Entomophthoromycotina, 30, 52 Euler-Chelpin, Hans von, 106 parasitic fungi, 326 Entrophospora spp., 52, 340 Eumycota, 29 pathogenic fungi, 326 environmental biotechnology EUROSCARF collection, 557 physical power of growing fungi, 328–30 use of fungi, 9–10 Eurotiomycetes, 60, 61, 438 recalcitrant waste remediation, 334–6 enzymes secreted by fungi, 239 Eurychasma spp., 75 saprotrophic fungi, 326–8 immobilisation, 239 evolutionary clock, 24 toxic waste remediation, 334–6 medical uses, 4 evolutionary origins, 18–38 toxins produced by fungi, 328–31 use in biotechnology, 4 big bang theory, 19–21 waste remediation, 334–6 Epacridaceae, 341 collision during Earth’s development, 21 wood-decay fungi, 78, 327 Epacris spp., 341 creation of the elements, 20 ectendomycorrhizas, 338, 343, 346, 351 epidemiology of fungal infections, 430–2, development of life on Earth, 23–9 ectomycorrhizas, 62, 78–9, 338, 346–51 436–9 domains of the tree of life, 23–9 cell-anchor receptors, 349 Epidermophyton spp., 426 Earth–Moon binary system, 22, 23 mobile signal ligands, 349 epigenetic phenomena Earth’s magnetic field (magnetosphere), nutrient exchange, 349–50 phenotype switching, 429 22–3 ectotrophic mycorrhizas, 337 epigeous taxa, 66 effects of extinction events, 37–8 edible mushrooms, 71 epiphytic fungi, 79, 361 formation of the Earth, 21–3

612 Index

evolutionary origins (cont.) loss of, 35 foregut fermentation formation of the Moon, 21, 23 Flammulina velutipes,71 ruminants, 403 formation of the oceans, 21 flax rust (Melampsora lini), 371, 389 forestry waste fossil fungi, 31–3 Fleming, Alexander, 478, 480 lignocellulose biodegradation, 497–9 fungal phylogeny, 35–8 Florey, Howard, 478, 480 formin-homology (FH) proteins, 145 Goldilocks orbit of the Earth, 21–2 fluconazole, 429, 518 formins, 126 greening of the Earth, 28–9 5-fluorocytosine, 522 fossil fungi, 31–3, 51, 326, 407 heterokonts, 30–1 fluotrimazole, 518 lichens, 357 Kingdom Fungi phylogenetic fly agaric. See Amanita muscaria fossils classification, 29–30 Folsomia candida, 270 oldest known fossils, 23 location of the Earth’s orbit, 21–2 Fomes annosus, 264 Frank, Albert Bernhard, 336 molecular phylogenetic studies, 33 Fomes fomentarius, 273 free cell formation of zoospores, 48–50 oldest known fossils, 23 food contamination and deterioration, Fries, Elias, 71 opisthokonts, 30 328–31 fructose bisphosphatase, 254 phylogenetic classification systems, 23–9 aflatoxins, 330 fruit bodies, 226 Theia–Earth impact, 21, 23 food from fungi, 326 ascomata, 228 evolutionary species concept, 74 ang-kak, 274 basidiomata, 228–31 Exobasidium camelliae, 440 birds of prey, 271–2 development, 167–8 Exobasidium spp., 62 button mushrooms (Agaricus bisporus), formation, 96–7, 184, 185 exocytosis, 123 276–8 gills or lamellae, 228–9 exo-enzymes, 239 cells and mycelium as human food, 274 pores, 228–9 exoglucanase, 240 cheeses, 274–5 Fugu rubripes (puffer fish), 114 Exophiala werneckii, 442 Collembola (springtails), 267–70 Fuligo spp., 77 exospores, 228 commercial exploitation of wild fumigatin, 262 exportins, 113 mushrooms, 272–4 functional genomics, 558 extinction events commercial mushroom production, fungal biodiversity effects on fungi, 37–8 275–9 in general, 8–9 extracellular matrices, 159 development of a fungal fruit body, 280 in soil, 7–8 extracellular proteinases, 246–7 fermented foods, 274–5, 504–6 measurement challenges, 7–8 extraradical mycelium, 349 fermented meat products, 503–4 number of undescribed fungi, 7–8, 8–9 extreme environments, 8 fermented soy foods, 504–6 number which cannot be cultivated, 7–8 fungi as food, 267–8 fungal cell biology, 104–51 fabric manufacture fungi in food webs, 267–72 cell cycle, 115–16 enzymes used in, 483–4, 484–6 gardening insects and fungi, 279–80 cell membrane, 107 facilitated diffusion, 248–9 gourmet fungi, 272–3 cell plasma membrane, 123–4 plasma membrane, 133 gourmet mushrooms, 278 cell structure, 107–8 facultative symbiosis industrial cultivation of fungi, 275–9 cell wall, 136–7 ericoid mycorrhizas, 342 larvae (maggots) of dipteran flies, 270–1 central vacuole, 124 FADH2, 252, 253 lichens, 358 chloroplasts, 121–2 fats microarthropod fungivores, 267 chromatids, 109–12, 116 primary metabolism, 254–5 mites, 270 chromatin structure, 109–12 fatty acid synthesis, 261–3 mushroom flies, 270–1 closed mitosis, 115 feedback fixation, 222 mycelial networks at the soil–litter contribution of yeast research, 105–7 feedback loops interface, 267 cytokinesis and septation, 144–50 circadian rhythms, 215 myco-protein, 274 cytoplasm, 107 fermentation processes. See whole organism nematodes, 270 cytoskeletal systems, 125–7 biotechnology New Zealand wood ear fungus trade, 273 DNA, 107, 108 fermentation research, 105–6 nutritional value, 266 endomembrane systems, 121–5 fermented foods, 274–5 oyster mushrooms (Pleurotus spp.), 278 endoplasmic reticulum (ER), 120, 122, fibre hyphae, 225 paddy straw mushroom (Volvariella 124 filamentous cell cycle, 216 volvacea), 279 extrachromosomal DNA, 108 filamentous extension strategy, 86 Quorn™ myco-protein, 274 fungus as model eukaryote, 105–7 filamentous mould fungi in amber, 32–3 shiitake (Lentinula edodes), 278–9 genetic material, 107, 108 filasomes, 141 slugs and snails, 271 genome plasticity, 115 Filobasidiales, 66 small mammals, 271–2 Golgi apparatus, 120, 122–3, 123–5 Filobasidiella neoformans,69 soy sauce, 274 hyphal extension mechanisms, 105, Filobasidiella spp., 62 tempeh, 274 137–42 fir (Abies), 346 truffles (Tuber spp.), 279 hyphal fusion, 142–4 fission yeast, 118 wild harvests, 272–4 intranuclear mitosis, 115 flagella, 107 yeast extracts, 274 karyotypes, 115 endosymbiont theory, 23, 121 food web connected to soil, 7 meiotic nuclear division, 117–18 flagellin, 107 food webs mitochondria, 121–2 flagellum fungi as food, 267–72 mitotic nuclear division, 115–17

Index 613

molecular motors, 127–33 molecules on the outer surface, 168–71 importance of, 4–5 movement, 127–33 outer surface, 168–71 mistaken ideas about, 4–5 mRNA translation, 118–19 pigmentation, 167–8 nature of fungi, 4–5 mycelial growth mechanisms, 105 polysaccharides, 158–9 pathogens, 5 mycelial interconnections, 142–4 protection against physical stress, 157 primitive biofilms, 28–9 nature of the fungal cell, 99–100 proteins, 158, 163–5 where and what they are, 4–5 nuclear–cytoplasmic trafficking, 114 scaffold for proteins, 157 Fungi Imperfecti, 23, 29 nuclear genetics, 114–15 secondary hyphal walls, 167–8 fungi in the home nuclear migration, 116–17 structural components, 136–7 effects on health, 432–6 nucleolus, 112–13 structure and function, 157–60 fungicides nucleus, 108–12 studies of model fungal systems, 157 strobilurins, 331 number of nuclei per cell, 117 surface properties, 158 fungicolous fungi, 439–44 organelles, 107 target for antifungal agents, 157 fungus as model eukaryote, 105–7 peroxisomes, 120 taxonomic significance, 158–9 fungus gardening. See ant agriculture; plasmalemma, 123–4 turgor pressure, 159 termite gardeners plastids, 121–2 two-phase system, 159–60 fusaric acid, 378 ploidy and nuclear number, 117 wall architecture, 160 Fusarium moniliforme, 259, 379 protein destruction, 121 wall synthesis and remodelling, 165–8 Fusarium oxysporum, 148, 353, 384, 493 protein sorting/targeting mechanism, fungal colonies Fusarium solani, 432 119–21 morphological differentiation, 92–5 Fusarium spp., 55, 327, 378, 442 protein synthesis in the cytoplasm, fungal co-operative ventures, 393 chlamydospores, 214 118–19 Fungal Genetics Stock Center (FGSC), 562 genomes, 545 RNA, 107 Fungal Genome Initiative, 547 Fusarium venenatum, 56, 461, 473, 474, Saccharomyces cerevisiae as model fungal growth forms 487–92 organism, 105–7 yeast–mycelial dimorphism, 150–1 fuzzy logic approach, 313–14 septal pores, 99 fungal individual septation and cytokinesis, 144–50 definition, 188 galactanases, 241 signalling pathways, 134–5 fungal individuals galactans, 240 Spitzenko¨rper, 125 and incompatibility systems, 188–90 galectins, 170 subcellular components of eukaryotic fungal karyotypes, 115 Galeola spp., 346 cells, 109 fungal life style gall wasps, 361 transmembrane proteins, 120 contribution to eukaryote cell biology, gall-forming insects, 361 transport vesicles, 124 105–7 gallic acid, 263 yeast–mycelial dimorphism, 150–1 exploitation of substrates, 86 Ganoderma spp. fungal cell wall, 136–7, 156–72 exploration and invasion, 85–6 cultivation, 279 active interface, 136 heterokaryosis, 180–1 traditional herbal medicine, 279 adaptation to varying conditions, 157 fungal nomenclature, 52 gardening insects and fungi, 279–80 adhesins, 168–70 fungal origins gasteromycetes, 288 adhesive properties, 158 fossil evidence, 31–3 Gastrodia elata, 344, 346 antigenic properties, 158 molecular phylogenetic studies, 33 Gastrodia spp., 344, 346 as a clinical target, 171–2 fungal pathogens Geastrales, 66 as a working organelle, 157 strains of varying pathogenicity, 186 Gelasinospora tetrasperma, 116, 208 b-glucan, 136, 137, 163 fungal pegs, 344 geldanamycin, 525 functions of b1,3-glucan synthases, 163 fungal phylogeny, 35–8 gene ontology, 540 carotenoid pigmenation, 168 Fungal Records Database of Britain and gene-for-gene interactions, 387–9 cell shape, 159 Ireland (FRDBI), 562 general transcription factors, 109–10 cellulose, 29 fungal species genes chitin, 29, 136–7, 158, 160 naming, 42 conservation patterns, 24 dynamic structure, 136 naming of sexual and asexual stages, 42 duplications, 24 extracellular matrices, 159 numbers of, 42 evolutionary clock, 24 fibrillar polysaccharides, 157 fungal taxonomy expression, 109–10 functions of chitin synthases, 160–2 principal taxonomic ranks, 28 rate of mutation, 24 glomalin, 171 fungal toxins rate of mutational change, 24 glucans, 158, 162–3 aflatoxins, 330 segregation during mitotic division, glycoproteins, 158, 163–5 Amanita muscaria, 328–30 189–94 hydrophobic/hydrophilic properties, 158 poisoning, 433–6 genetic approaches to development, hydrophobins, 170–1 potential as weapons, 331 314–15 hyphal tip extension, 165 statins, 331 developmental variants, 311–12, 312–13 internal thickenings, 167–8 strobilurins, 331 molecular genetics, 312–15 maintenance of cell shape, 157 fungi genetic control of mating, 201 mannans, 158 beneficial effects, 4 mating type switching in budding yeast, mannoproteins, 137 contribution to human existence, 4 201–3 melanin pigmentation, 167 databases of information about, 562 genetic material

614 Index

genetic material (cont.) Glomeraceae, 51, 340 Guinness Book of World Records in eukaryotes, 107 Glomerales, 51, 340 largest and longest-lived fungi, 71 plasmids, 108 Glomerella cingulata, 202 gyrocyanin, 263 genetic research Glomeromycota, 29, 32, 35, 50–2, 78, 337, Gyromitra spp., 60 cell cycle in yeasts, 149–50 338, 340, 441 Gyroporus cyanescens, 263 yeast breeding experiments, 106 arbuscules, 51 genetic variation difficulty of studying, 50–1 habitat creation by fungi, 326 co-evolution of plant–pathogen disease endomycorrhizal associations, 51 Haeckel, Ernst, 23 systems, 387–9 importance to land plants, 51 Haliphthoros spp., 75 parasexual cycle, 194 phylogeny, 51–2 hallucinogenic toxins, 62 genetics reproduction, 51 hamathecium (hamathecial tissue), 60 applied genetics, 388 vesicular-arbuscular mycorrhizas, 51 haploid nature of fungal mycelia, 179 mapping panels, 529 glomeromycotan fossils, 31–2 haploid nature of true fungi, 180–1 molecular studies of pathogen virulence, Glomus spp., 52, 78, 340, 441 haploid state in fungi, 117 389 glucanases, 439 haploidisation, 194 research, 106–7 glucans, 158, 162–3 Haptoglossa spp., 75 restriction mapping, 529 glucoamylases, 241 Haptoglossales, 75 steps in understanding fungal genetic gluconeogenesis Harden, Arthur, 106 structure, 531 primary metabolism, 253–4 Harpellales, 52, 53, 415 genome analysis glucose-stat cultures, 473 Hartig net, 338, 343, 344, 346, 347, 351 fungal genome plasticity, 115 glucosidases, 242 Hartwell, Lee, 56 fungal genome size, 114 glutamate decarboxylation loop, 253 Hartwell, Leland, 105, 107 introns in fungal DNA, 114 glutamate dehydrogenase, 254 haustoria produced by plant pathogens, protein-coding genes, 115 glutamine synthetase, 308 371–2 genomics, 531, 557 glutamine synthetase/glutamate synthase HC-toxin, 378 annotating the genome, 540 system, 256 heather (Erica), 78 comparing genomes, 537 glutaminyl hydroxybenzene (GHB), 263 Heatley, Norman, 480 comparison of fungal genomes, 547 glycogen degradation, 242–3 heat-shock proteins, 98 data mining, 314–15, 562 glycolysis, 251–2, 254 Hebeloma mesophaeurn, 442 functional genomics, 550 glycoproteins Helminthosporium maydis, 378 Fungal Genome Initiative, 547 fungal cell wall, 163–5 hemiascomycetes, 56 manipulating genomes, 552 glycosylphosphatidylinositol (GPI) anchors, hemibiotrophic fungi, 376–8, 382 recombinant vectors, 552 135, 164–5 hemicellulases, 384 reverse genetics, 550 glyoxal oxidase, 243, 245 hemicellulose, 238 sequencing fungal genomes, 535 Golgi apparatus, 120, 122–3, 123–5 hemicellulose breakdown, 238, 241 targeted gene disruption, 550 Gomphales, 66 Hemitomes spp., 343 transformation of cells, 551 gomphoid–phalloid fungi, 66 herbal medicine genospecies, 189 gongylidia, 394 Ganoderma spp., 279 Geoglossum spp., 60 gourmet fungi, 272–3 herbivore digestion geological time, 28 gourmet mushrooms, 278 anaerobic chitrids, 45–6 geomycology, 9–10 GPI anchors, 135, 164–5 role of fungi, 4 Geosiphon pyriformis, 52, 340 G-protein-coupled receptors, 135 herbivore dung Geosiphon spp., 340 G-proteins, 134–5, 206 breakdown of, 238 Geosiphonaceae, 52 Graphiola spp., 62 Herpomyces spp., 60 Geotrichum candidum, 460 grasses (Poaceae), 62 het loci, 185–6, 188 geranylpyrophosphate, 258 C3 and C4 photosynthetic pathways, Heterobasidion annosum,69 germicidal UV (UV-C), 22–3 404 Heterodera avenae, 407 giant puffball (Calvatia gigantea), 71 genome analysis, 114 heterogeneous nuclear ribonucleoproteins Gibberella fujikuroi, 185, 259, 379 gravitropism, 231 (hnRNPs), 112 gibberellins, 259, 379 grazing animals heterokaryon, 117, 180 Gigaspora gigantea, 442 and anaerobic fungi, 400–5 breakdown, 183–4 Gigaspora spp., 52, 340, 441 Great Dying (extinction event) definition, 180 Gigasporaceae, 52, 338, 340 effects on fungi, 37–8 phenotype, 181–3 Gilbertella persicaria, 49–50 greenhouse gases propagation of the state, 183 gills or lamellae of the fruit body, 63, 66–9, chlorohydrocarbon release by wood- heterokaryon formation, 181–3 228 decay fungi, 336 positive autotropism, 181 Ginkgo, 343 chloromethane, 336 vegetative compatibility, 185–8 Gliodadium spp., 440 fungal breakdown products, 245–6 heterokaryon incompatibility. Gliomastix spp., 442 greening of the Earth, 28–9 See vegetative compatibility globose structures, 227–30 grey mould pathogen, 382, 383–4 heterokaryosis Gloeophyllales, 67 griseofulvin, 127, 262, 522, 526 and hyphal anastomosis, 180–1 Glomales, 35, 50 GTP (guanosine triphosphate), 252, 253 benefits for fungi, 181 glomalin, 171 GTP hydrolysis, 126 consequences, 181–3

Index 615

expression of mutations, 181 coccidioidomycosis, 428 commercially farmed fungi, 71 heterokaryotic mycelium, 117 cryptococcal meningitis, 62 Hymenoscyphus ericae, 78, 337 heterokonts cryptococcosis, 428 Hymenoscyphus spp., 60 evolutionary origins, 30–1 cutaneous mycoses, 426 hypermycoparasite fungi, 443 Heteropeza pygmaea, 271 dermatomycosis, 426–7 hypersensitive response, 388 heteroplasmic mixtures, 195 effects of fungi in the home, 432–6 hyphae heteroplasmons, 195 epidemiology, 430–2 quantity in soil, 7 heterothallic fungi, 180, 199–200 ergotism (ergot poisoning), 434–5 hyphal analysis, 301–4 Hevea brasiliensis, 261 fingernails, 426 hyphal branching, 97–9 hexatriyene, 264 fusariosis, 432 and septation, 97–8 hexokinase, 253 histoplasmosis, 428 branch initiation, 97–9 hexose monophosphate pathway, 252 HIV-related opportunistic infections, pattern of branching, 97 high mobility group (HMG) proteins, 205 425–6 hyphal differentiation, 92–5 hindgut fermentation infant pulmonary haemorrhage, 432 hyphal extension non-ruminant herbivores, 403 infantile pneumonia, 431 definition, 88 hispidin, 263 ingestion of toxins, 433–6 mechanisms, 105 histones microsporidiosis, 413 hyphal fusion, 96–7, 117, 142–4 chromatin structure, 109 mycetoma (madura foot), 427 and mycelium functioning, 181 Histoplasma capsulatum, 150, 167, 428, 438 mycoses, 424–6 heterokaryon formation, 181–3 Histoplasma spp., 60 North American histoplasmosis, 428 heterokaryosis, 180–1 histoplasmosis, 428, 522 onychomycosis, 426 non-sexual fusions, 181 history of the fungi, 326 opportunistic infections, 5, 54, 55, 59, ping-pong signalling mechanism, 142–3 HIV patients 425–6, 428 potential hazards, 185 Candida albicans infections, 59, 150–1 opportunistic systemic mycoses, 428–30 pre-contact behaviour, 142 See also immunocompromised patients Piedraia hortae, 426 role of the Spitzenko¨rper, 142 HIV-related opportunistic infections, 425–6 pneumocystis pneumonia (PCP), 431 self-signalling between hyphal tips, HMG-CoA reductase inhibitors, 262, 331 pneumocystosis, 431 142–3 HMT toxin, 378 poisoning from fungal toxins, 433–6 stages in the process, 142 Hodgkin, Dorothy, 478 resistance in fungal pathogens, 430–1 vegetative compatibility, 185–8 homeobox, 206 ringworm, 425 hyphal growth homeodomain proteins, 206 rose-handler’s disease, 427 apical growth process, 100 homeotic (Hox) genes, 206 sick building syndrome, 432 autotropic reactions, 96–7 Homo genus sporotrichosis, 427 autotropism, 87–8 emergence in the Pliocene, 404 St Anthony’s fire, 434–5 avoidance mechanism, 96 homobasidiomycetes, 63 subcutaneous mycoses, 426–7 branch initiation, 97–9 homokaryon, 183, 207 superficial mycoses (tineas), 426 branching, 97–9 definition, 180 systemic mycoses, 427–30 branching processes, 86–8 homologous organs, 63 thrush, 429 colonisation of solid substrata, 99 homothallic fungi, 180, 199, 200 toenails, 426 computer simulation, 564 homotypic interactions, 168 Trichosporon cutaneum, 426 distinction between growth and honey bee (Apis melifera) valley fever, 428 extension, 88 microsporidian parasite, 414 zygomycosis, 431–2 duplication cycle, 92–3 honey fungus. See Armillaria mellea human genetics emergence of germ tubes (hyphal tips), hoof fungus, 273 gene assignments to chromosomes, 194 86 Hooke, Robert, 107 human genome, 114 germ tube extension, 87 horizontal mitochondrial transmission, 195 humic substances (humus), 6 germination of spores, 86–7 hormone production in fungi, 47–8 Hunt, Tim, 56, 105 hyphal fusion, 87, 96–7 hormones involved in sexual reproduction, Hyaloraphidium curvatum,30 mathematical modelling, 564 199 hybridisation array analysis, 558 mode of growth, 86, 88–91, 94–7 host-selective toxins, 384 hydration negative autotropism, 96 host-specific toxins, 378 chemical weathering process, 6 Neighbour-Sensing model, 564 Hubble Ultra Deep Field (HUDF), 20 hydrogen peroxide, 384 nuclear migration regulation, 93–4 human dependence on fungi, 15 hydrogenosomes, 45, 46, 402 nuclear mitosis, 93–4 human fungal infections hydroloysis pattern of branching, 97 aflatoxicosis, 435–6 chemical weathering process, 6 positive autotropism, 96–7 African histoplasmosis, 428 hydrophobins, 137, 170–1 rates of growth, 86–8 allergic reactions, 433 amphipathic structure, 170 septation, 92–3, 99–100 aspergillosis, 429–30, 430–1 hymenia development, 291–5 size-detecting mechanism, 93 athlete’s foot, 425 hymenium, 228 synchronous mitosis, 93 blastomycosis, 428 Hymenochaetaceae, 66 types of septa, 99 Candida albicans, 150–1 Hymenochaetales, 66, 67 viscoelastic cell wall, 100 candidiasis, 425–6, 429 Hymenochaete corrugata, 227 hyphal growth kinetics, 88–91 clinical groupings, 426–32 hymenomycetes, 62, 63 mathematical models, 94–7

616 Index

hyphal tip extension, 137–42 insertional mutagenesis, 389 killer phenomenon, 196 cell wall, 165 integrated pest management (IPM), 422 Koch’s postulates, 424 consensus model, 139–40 intermediary metabolism. See primary Kornberg, Roger D., 107 hyphoid model, 138–9 metabolism Krebs (TCA) cycle, 252, 477 steady state (soft spot) model, 139 intermediate ﬁlaments (cytoskeleton), 126 kuru, 196 tip-high calcium gradient, 141–2 International Programme on Chemical turgor pressure, 137–8 Safety, 513 La France disease, 196 hyphal tuft (hyphal knot), 283 interzonal microtubules, 146 Laboulbeniales, 60, 416–17 Hyphochytriomycota, 29, 75, 77 intracellular proteinases, 246 Laboulbeniomycetes, 60 Hyphochytrium spp., 77 intranuclear mitosis, 115 Labyrinthula spp., 77 hyphoid model of hyphal tip extension, introns in fungal DNA, 114 Labyrinthulales, 77 138–9 invertebrates Labyrinthulomycota, 77 hyphomycetes, 198 fungal toxins, 330 Laccaria proxima, 354 Hypocrea spp., 60 ion channels, 133–4 laccases, 243, 245 Hypocreales, 60 ion pumps, 249 Lacrymaria spp., 261 hypogeous taxa, 66 ionising radiation lactarinic acid, 261 Hypsizygus tessulatus,71 resistance to, 167 Lactarius rufus, 261 Hysterangiales, 66 IQGAP proteins, 145 Lactarius spp., 261 hysterothecia, 60 iron core of the Earth, 21, 22 Lagena spp., 75 iron-binding compounds, 264 Lagenisma spp., 75 ibotenic acid, 329 itraconazole, 518 Lagenismatales, 75 Iceman (Neolithic traveller) land management practices fungal products found with, 273 Jirovec, Otto, 56, 431 effects on fungal populations, 326 igneous rocks, 6 larch (Larix), 347, 351 imazalil, 518 K-selected species, 354 mycorrhizal associations, 338 imidazoles, 518 karyogamy, 117, 118, 198 large ribosomal RNA subunit, 33 immune system response karyopherins, 113 largest fungal structures, 71 effects of hydrophobin, 170 ketoconazole, 518 late stage fungi, 354 immunocompromised patients Kickxellales, 52 lateral gene transfer, 24 aspergillosis, 430–1 Kickxellomycotina, 30, 52, 442 latex, 264 candidiasis, 425–6 killer phenomenon Law, Barbara, 478 cryptococcal meningitis, 62 Kluyveromyces lactis, 196 leaching cryptococcosis, 428 kinesins, 128–9 weathering process, 6 epidemiology of fungal infections, 430–2 microtubule-associated kinesins, 127–33 leaf and stem blotch of mature plants, 327 fusariosis, 432 molecular motors, 127–33 leaf spot diseases, 223, 372 microsporidiosis, 413 kinetochores, 116, 118 leaf-cutter ants, 62 opportunistic infections, 5, 54, 55, 59, King Oyster (Pleurotus eryngii), 277 Lecanactis abietina,60 150–1 Kingdom Animalia, 23, 30 Lecanora spp., 60 opportunistic systemic mycoses, Kingdom Chromista, 29, 30–1, 75–7, 158, Lecanoromycetes, 60, 61, 416 428–30 160 Lederberg, Joshua, 106 pneumocystis pneumonia (PCP), 431 Kingdom Fungi, 4–5, 23 Lempholemma spp., 60 pneumocystosis, 431 anaerobic chytrids, 45–6 Lentinula edodes, 71, 195, 254, 277, 311, zygomycosis, 431–2 Ascomycota, 55–61 312, 444 imperfect fungi, 194, 198–9 Basidiomycota, 61–71 cultivation, 278–9 importins, 113 Blastocladiomycota, 46–50 mycorrhizas, 344 incompatibility mechanisms, 117 Chytridiomycota, 42–5 Leotia spp., 60 incompatibility systems chytrids, 42–5, 45–6 Leotiomycetes, 60, 61, 438 fungal individuality, 188–90 common ancestor with animals and Leptolegnia spp., 75 infant pulmonary haemorrhage, 432 plants, 29 Leptolegniella spp., 75 infantile pneumonia, 431 distinctions from animals and plants, 29 Leptomitales, 75, 512 ink cap mushroom. See Coprinopsis Glomeromycota, 50–2 Leptomitus spp., 75 cinerea members of the Kingdom, 42 Leucoagaricus gongylophorus, 396 Inocybe spp., 263 monophyletic group, 29–30 Leucoagaricus spp., 396 Inonotus spp., 245 Neocallimastigomycota, 45–6 Leucocoprineae, 396 inorganic transformations, 327 phylogenetic classiﬁcation, 29–30 Leucocoprinus gongylophorus, 279 insects, 326 phylogeny, 35–8 Leucocoprinus spp., 396 entomogenous fungi, 417–21 tree of life, 35–8 lichenised fungi, 55, 59 fungal pathogens, 412 Zygomycota, 52–5 lichens, 79, 170, 171, 325, 356–60 gardening insects, 279–80 Kingdom Monera, 23 as food, 358 Laboulbeniales pathogens, 416–17 Kingdom Plantae, 23 chemical produced by, 358 mutualistic associations with fungi, 62 Kingdom Protista, 23 cyanobacteria associations, 357 pathogenic gut fungi (Trichomycetes), Kingdom Protozoa, 77 fossils, 357 414–16 Kluyveromyces lactis, 502 fungal species involved, 358

Index 617

nature of the symbiotic relationship, maple leaf spot, 370 micafungin, 521 357–8 Marasmiellus spp., 32 Michaelis constant, 464 reproduction, 357 Marasmius spp., 32, 227 Michaelis–Menten kinetics, 249, 463 sensitivity to atmospheric pollution, 358 Marmite, 274 miconazole, 518 taxonomy, 358 Mars, 22 microarthropods, 326, 353 thallus morphology, 356 mass flow of nutrients, 248 Collembola, 267–70 tolerence of extreme conditions, 358 mass spectrometry, 559 fungivores, 267 Lichinomycetes, 60 Massospora spp., 417 numbers in soil, 7 lignin, 78, 238 mathematical models microbial diversity composition and structure, 242–4 fungal growth, 94–7 complexity of the concept, 7 resistance to microbial degradation, hyphal growth, 564 in general, 8–9 242–3 mating in budding yeast, 200–1 in soil, 7–8 lignin breakdown, 238, 242–6, 327 mating proteins, 168 measurement challenges, 7–8 chlorohydrocarbon release, 336 mating strategies of Neurospora spp., number which cannot be cultivated, 7–8 lignin peroxidase, 243, 244–5 203 microbial diversity in soil ligninases, 384 mating systems, 199–200 chemical analysis, 8 lignocellulose, 78 mating type factors, 62, 185, 186, 199 chitin measurement, 7 Lindegren, Carl, 106 biology of, 210–11 counting numbers, 7 linear structures, 225–7 mating type genes, 203–5 ergosterol measurement, 8 ling (Calluna), 78 mating type loci, 203–5 polymerase chain reaction (PCR), 8 lingzhi, 279 mating type pheromones, 199 RNA and DNA probes, 8 lipases, 247 mating types, 199 microconidia, 223 lipophilic yeasts, 62 Basidiomycota, 205–10 microfilaments, 126 liquid chromatography, 559 Neurospora crassa, 186–8 Microglossum spp., 60 litter-trapping rhizomorph networks, 227 Neurospora spp., 203–5 Microsporidia, 29, 30, 35, 412–14 liver cancer, 330, 436 switching, 200 human pathogens, 413 LL-Z1272a (antibiotic), 263 switching in budding yeast, 201–3 phylogeny, 396–7 Lobaria spp., 60 tetrapolar heterothallism, 206–10 xenoma formation, 413 Loma salmonae, 414 matsutake, 71, 272, 273 microsporidial gill disease of salmon longest-lived fungi, 71 Megaselia halterata, 271 (MGDS), 414 longest-lived mycelium, 71 Megaselia nigra, 271 microsporidiosis, 413 long-term plasmogamy, 231 meiocyte, 228 Microsporidium africanum, 413 lovastatin, 262, 473 meiosis Microsporidium ceylonensis, 413 luciferase, 246 stage in sexual reproduction, 198 Microsporum spp., 247, 425, 426 luciferin, 246 meiotic nuclear division, 117–18 Microstroma spp., 62 lycopene, 261 Melampsora lini, 371 microtubule motors, 127 lysergic acid amide, 263 melanin, 167, 382 microtubule-associated dynein, 127–33 lysosomal proteolysis, 121 mellein, 262 microtubule-associated kinesins, 127–33 membrane transport. See transport of microtubule-associated proteins (MAPs), macroconidia, 223 nutrients 127 Macrotermitinae termites, 398–9 Mendel, Gregor, 106 microtubule-binding proteins, 127 macrovesicles, 161–2 Mesomycetozoea, 77, 415 microtubules, 126–7 Madurella grisea, 426 messenger RNA. See mRNA role in cell cleavage, 145 Madurella mycetomatis, 426 metabolic pathways research, 106, 107 role in cytokinesis, 145–6 magic bullet concept, 512 metabolic regulation and morphogenesis, microvesicles, 161–2 Magnaporthe grisea, 203, 327, 370, 379, 389 305–8 mineral transformations genome, 546 metabolomics, 557 geomycology, 9–10 Magnaporthe oryzae, 382, 389 metacaspases, 385 minerals, 5 Magnaporthe spp., 55 metal cycling composition of rocks, 6 magnetosphere (Earth’s magnetic field), role of fungi, 10 igneous rocks, 6 22–3 metal ions metamorphic rocks, 6 maize (Zea mays), 62 accumulation by fungi, 327 primary minerals, 5 Malassezia globosa,62 metalaxyl, 522, 526 secondary minerals, 5 Malassezia spp., 62 metal–fungal interactions, 9 sedimentary rocks, 6 manganese peroxidase, 243, 245 metalloproteinases, 247 miso, 506 man-made polymers metamorphic rocks, 6 mites microbial degradation, 333–4 Metarhizium anisopliae, 167, 419 feeding on fungi, 270 mannanases, 240 Metarhizium spp., 420 numbers in soil, 7 mannans, 158, 240 methanogenic rumen bacteria, 402 mitochondria, 23, 108, 121–2, 252 mannitol, 254, 311 methyl p-methoxycinnamate, 263 cytoplasmic segregation, 194–6 mannoproteins, 137, 163 3-methylfuran, 432 endosymbiont theory, 23, 121–2 MAP kinase, 143, 206 Mevastatin, 262 protein coding genes, 25 MAP kinase signalling pathway, 135 mevinolin, 473 mitochondrial DNA (mtDNA), 195

618 Index

mitochondrial inheritance, 33, 195 Monascus purpureus, 506 agriculture in beetles, 399–400 mitochondrial mosaics, 195 Monascus spp., 274 ambrosia beetles and fungi, 399–400 mitochondrial phenotypes, 195 Monilinia fructigena, 247 fungal co-operative ventures, 393 mitochondrial protein transport, 120 Monilinia spp., 60 gardening ants, 393–8 mitochondrial ribosomes, 33, 195 Monoblepharidales, 30, 45 gardening insects, 279–80 mitosis Monod equation, 463 lichens, 357–8 closed, 115 monokaryon, 207 ruminants and anaerobic chytrids, 400–5 intranuclear, 115 definition, 180 termite gardeners, 398–9 mitosporic fungi, 198–9 monolignols, 242 types of fungal relationships, 392–3 mitotic crossing-over, 194 monophyletic group, 28 See also mycorrhizas mitotic nuclear division, 115–17, 189–94 Monotropa spp., 343, 344 mycelial interconnections, 142–4 Mitrula spp., 60 monotropoid endomycorrhizas, 337, 343–4 mycelial networks at the soil–litter mobile signal ligands, 349 Monotropsis spp., 343 interface, 267 molecular biology Montropaceae, 337, 343 mycelial senescence caused by plasmids, contribution of yeast research, 105–7 Moon 195 molecular biotechnology, 566 formation of, 21, 23 mycelium agricultural myocides, 529 influences on the Earth, 23 migratory role of strands, 226 analysis of large survey data sets, 563 stabilizing the Earth, 23 point growth, 226 annotating the genome, 540 tides on the Earth, 23 translocation routes, 225, 226 antifungal agents that target the cell wall, Morchella deliciosa, 272 mycelium differentiation, 214–16 521–2 Morchella elata, 272 mycelium growth antifungal agents that target the Morchella esculenta, 56, 272 apical growth of the hypha, 100 membrane, 512–21 Morchella spp., 60, 272 autotropic reactions, 96–7 antifungal resistance, 522–6 morels. See Morchella autotropism, 87–8 azoles, 517–21, 523 morphogenesis circadian rhythms, 214–16 bioinformatics in mycology, 560 definition, 285 colony formation, 86–8 clinical control of systemic mycoses, morphogenetic field model, 293 colony growth to maturity, 91–2 522–6 morphological species concept, 71 distinction between growth and combinatorial therapy, 525–6 Mortierella ramanniana, 442 extension, 88 computer simulation of hyphal growth, Mortierella spp., 55, 474, 483 ecological advantages on solid substrates, 564 Mortierella wolfii,55 100–1 cyber fungi, 564 Mortierellales, 52 filamentous extension strategy, 86 effects of climate change on fungi, 563 movement fungal life style, 86 functional genomics, 550 molecular motors, 127–33 gradients in requirements for growth, Fungal Genome Initiative, 547 mRNA, 107 91–5 fungal genomes and their comparison, protein synthesis in the cytoplasm, heterogeneous growth under restricted 547 118–19 conditions, 91–2 fungi as cell factories producing synthesis and processing, 109–12 hyphal branching, 97–9 heterologous proteins, 554 translation, 118–19 hyphal differentiation, 92–5 genomics, 531, 562 mucopolysaccharides, 241 hyphal fusions, 87 improving fungal strains, 554 Mucor hiemalis hyphal mode of growth, 86, 88–91, 94–7 manipulating genomes, 552 negative autotropism, 96 mechanisms, 105 manipulating very large data sets, 560 Mucor miehei, 274 mophological differentiation, 92–5 mathematical modelling of hyphal Mucor mucedo, 199 phases of growth, 94 growth, 566 Mucor spp., 53–4, 59, 99 polarised hyphal growth, 87 polyenes, 514–17, 523 Mucorales, 52 rates of growth and development, 86–8 recombinant protein production by Mucoromycotina, 30, 52, 442 regulatory mechanisms, 144 filamentous fungi, 557 multiple uptake systems for nutrients, 249 restricted growth, 91–2 reverse genetics, 550 muscaridines, 263 septation, 99–100 sequencing fungal genomes, 535 muscarines, 263 strand and cord formation, 225–7 steps in understanding fungal genetic muscimol, 329 success of the growth habit, 100–1 structure, 531 mushroom flies, 270–1 yeast–mycelial dimorphism, 150–1 strobilurins, 526–9 mushroom fossils, 32 mycelium growth kinetics, 88–91 synthetic biology, 560 mushroom poisoning, 264 mathematical models, 94–7 systems biology approach, 531 mushrooms, 62, 228, 229 Mycena osmundicola, 344 targeted gene disruption, 550 commercial mushroom production, Mycena spp., 246, 261, 344 transformation of cells, 551 275–9 mycetoma (madura foot), 427 vectors for DNA cloning, 552 cultivation, 474 mycobionts, 356 molecular machines, 109 solid state fermentation, 495 Mycogone perniciosa, 443–4 molecular motors, 127–33 mutations mycoherbicide production, 492–3 molecular phylogenetic approach, 74–5 expression in haploid fungi, 180 mycoheterotrophs, 343, 346 molecular studies of pathogen virulence, expression in heterokaryotes, 181 mycoparasitic fungi, 439–44 389 mutualism, 325 mycopesticide production, 492–3

Index 619

mycopesticides, 444 Blastocladiomycota, 46–50 new variant Creutzfeldt–Jakob disease myco-protein, 56 Chytridiomycota, 42–5, 45–6 (nvCJD), 196 production, 487–92 definition, 41 New Zealand wood ear fungus trade, 273 mycorrhizas, 78–9, 170, 325, 336–56 ecosystem mycology, 77–9 nikkomycins, 171, 521, 526 advantages of mycorrhizal associations, Glomeromycota, 50–2 nitrate reductase, 256 351–4 members of the Kingdom Fungi, 42 nitrogen arbuscular endomycorrhizas, 337, naming of fungal species, 42 primary metabolism, 254–7 338–42 naming of sexual and asexual stages, 42 sources in the soil, 238–9 arbuscular mycorrhizas, 78, 441 Neocallimastigomycota, 45–6 nitrogen-fixing bacteria, 254 arbutoid endomycorrhizas, 337, 343 number of species, 42 N-linked oligosaccharides, 163–4 bi-directional nutrient transfer, 340–1 slime moulds, 77 Nobel Prize laureates, 119, 512 changes in natural communities, 353–4 species concept in fungi, 71–5 yeast-related research, 105–7 commercial applications, 340, 355–6 teleomorph (sexual stage), 42 ‘noble rot’ of wine grapes, 382 ectendomycorrhizas, 338, 343, 346, 351 untrue fungi, 75–7 nomenclature ectomycorrhizas, 78–9, 338, 346–51 water moulds, 75–7 definition, 27 ectotrophic/endotrophic classification, Zygomycota, 52–5 fungi, 52 337 natural group, 28 Nomuraea rileyi, 419 endomycorrhizas, 78, 337–9 necrosis and ethylene inducing proteins non-disjunction of chromosomes, 194 ericoid endomycorrhizas, 78, 337, 341–3 (NEPs), 384 non-mycorrhizal plant families, 337 impact of climate change, 354–5 necrotrophic fungi, 238, 327, 376–8, 383 non-ruminant herbivores importance for crop plants, 4 Nectria haematococca, 132 hindgut fermentation, 403 inorganic transformations, 327 negative autotropism, 96, 181 North American histoplasmosis, 428 monotropoid endomycorrhizas, 337, Neighbour-Sensing model of hyphal Norway spruce (Picea abies), 347 343–4 growth, 566 Nosema apis, 414 nature of the mutualist association, nematodes, 326 Nosema bombycis, 412 336–7 feeding on fungi, 270 Nosema ocularum, 413 networks linking plant communities, 337 numbers in soil, 7 Nosema sp., 414 non-mycorrhizal plant families, 337 nematode-trapping fungi, 405–8 Nostoc punctiforme, 52, 340 nutrient transfers, 351–3 potential biological control, 407 Nothofagus (Southern beech), 346 orchidaceous endomycorrhizas, 78, 337, types of trapping device, 405 nuclear–cytoplasmic trafficking, 114 344–6 Nematophthora gynophila, 407 nuclear division patterns, 146–8 redistribution of plant-derived nematophytes, 31–4 nuclear export signal (NES), 113 carbohydrates, 353 Neocallimastigales, 29, 45, 401 nuclear genetics, 114–15 resistance to pathogen attack, 353 Neocallimastigomycota, 29, 45–6, 400–5 nuclear localisation signal (NLS), 113 strand formation, 226 Neocallimastix frontalis, 46, 401, 402 nuclear migration, 116–17 structure of natural communities, 353–4 Neocallimastix spp., 401 regulation, 93–4 types of mycorrhiza, 337–8 Neolecta spp., 56 nuclear mitosis, 93–4 use of protein, 246 Neolecta vitellina,56 nuclear number and ploidy, 117 vesicular-arbuscular mycorrhizas, 337 Neolithic traveller (the Iceman) nuclear pore complexes (NPC), 113–14, 121 water relations, 353 fungal products found with, 273 nuclear ribosomal DNA (rDNA) ‘wood-wide-web’, 338 Neotiella spp., 117 phylogenetic studies, 33 mycoses, 424–6 net blotch of barley, 370 nucleolus, 112–13 myosins, 128 Neurospora crassa, 86, 87, 115, 185, 454, nucleoporins, 113 actin-associated myosins, 127–33 460 nucleus molecular motors, 127–33 asynchronous nuclear division, 147 chromatin structure, 109–12 Myxomycota, 77 circadian system, 215 control of nuclear division, 148 Myxomycotina, 23 conidiation, 223 DNA molecular processes, 109 Myzocytiopsidales, 75 genome, 544 functions, 108–12 het genes, 186 gene expression, 109–10 NAD, 254 het loci, 188 mRNA synthesis and processing, 109–12 NADH, 121, 251, 256 heterokaryon formation, 186 nuclear–cytoplasmic trafficking, 108 NADH2, 252 hyphal extension, 88–9, 140 nuclear import and export, 113–14 NADP, 254 incompatibility response, 186–8 nuclear pore complexes (NPC), 113–14 NADPH, 121, 251, 256 mating types, 186–8, 199 number of nuclei per cell, 117 NADPH2, 252, 256 mitochondrial genes, 194 protein transport from the cytoplasm, NADP-linked glutamate dehydrogenase, mitochondrial phenotypes, 195 121 255–6, 308 mutations, 116 transcription factors, 109–10 natto, 506 negative autotropism, 96 transporter proteins, 113 natural classification of fungi, 41–79 proteinases, 246 nud (nuclear distribution) genes, 117 anaerobic chytrids, 45–6 Neurospora spp., 60, 106, 228 Nurse, Paul, 56, 105, 107 anamorph (asexual stage), 42 mating strategies, 203 nutrient cycling in soils, 6 Ascomycota, 55–61 mating types, 203–5 nutrient distribution in soils Basidiomycota, 61–71 Neurospora tetrasperma, 200 effects on fungal growth, 10

620 Index

nutrient transfer oxidation and reduction perfect fungi, 198 bi-directional transfer in mycorrhizas, chemical weathering processes, 6 Perissodactyla, 403, 404 340–1 oxidative burst, 384–5 perithecia, 59, 203, 224, 228 ectomycorrhizas, 349–50 oxidative phosphorylation, 253 Permian–Triassic extinction event transport and translocation, 247–51 oxygen in soil minerals, 6 effects on fungi, 37–8 nutristat cultures, 473 oyster mushrooms. See Pleurotus spp. permittistat cultures, 473 nutrition mode ozone layer, 22–3 Peronosporales, 75 distinctions between eukaryotes, 29 peroxisomes, 23, 120, 144 nutritional selection for diploid strains, 189 Pacispora spp., 340 pest nystatin, 515 paddy straw mushroom. See Volvariella definition, 334 volvacea pest management on plants, 376–7 oak (Quercus), 346 Paecilomyces varioti, 263 pesticides, 238, 368 endophytic fungi, 361 Panellus stipticus, 246 bioremediation by fungi, 334–6 gall wasps, 361 Papularia sphaerosperma, 522 breakdown by fungi, 245 2-octen-1-ol, 432 Paracoccidioides brasiliensis, 150, 161, 167 Peziza spp., 60 odours of fungi, 263, 328 Paraglomerales, 340 Pezizomycetes, 60 oidia, 208 Paraglomus spp., 340 Pezizomycotina, 56, 59–61 oligotrophic growth in fungi, 10 paraphyses, 228, 291, 292 ascoma morphologies, 59–60 O-linked oligosaccharides, 164 parasexual cycle, 194 ascus types, 60–1 Oliver, Steve, 105 parasitic fungi, 326 phylogeny, 60–1 Olpidiopsidales, 75 Parasola misera, 290 pH auxostat cultures, 473 Olpidiopsis spp., 75 parasynchronous division of nuclei, 146–8 Phallales, 66 Olpidium spp., 43 parenthesome, 99 phalloidin, 264 Omphalotus olearius, 246 parisin, 48 Phallomycetidae, 66 Omphalotus spp., 246 PAS domain, 215 phalloxin, 433–4 onychomycosis, 426 Pasteur, Louis, 56, 105, 106, 500 Phanerochaete chrysosporium, 78, 240, oogoniol, 199 pathogen associated molecular patterns 244–6, 484 Oomycota, 29, 50, 75–7, 85, 86, 138, 141 (PAMPs), 387 genome, 546 growth mechanism, 160 pathogenic fungi, 5, 326 pharmaceuticals, 473 Ophiostoma novo-ulmi. See Dutch elm pattern formation, 283 chemical transformation by laccases, 245 disease Paxillus panuoides, 332 whole organism biotechnology, 478–83 Ophiostoma spp., 399, 400 peach leaf curl, 56, 370 Phellinus contiguus, 300, 301, 332 Ophiostoma stenoceras, 427 peat formation, 6 Phellinus megaloporus, 332 Ophiostoma ulmi, 150, 202 pectin lyases, 241 Phellinus pomaceus, 336 Ophiostomatales, 399 pectinases, 241, 384 Phellinus spp., 245 ophiostomatoid fungi, 399, 400 pectins, 238 Phellinus tuberculosus, 336 opisthokonts, 105, 415 breakdown, 241 Phellinus weirii,69 evolutionary origins, 30 Pellicularia sasakii, 521 phenolics, 238 opportunistic infections, 5, 54, 55, 59 peloton, 345 phenotype of sexual reproduction, 199 Candida albicans, 150–1 Peltigera spp., 60 phenotype switching, 429 microsporidiosis, 413 Peltula spp., 60 phenylalanine, 263 opportunistic pathogens, 424 penetration peg, 382 phenylpropanoid alcohols, 242 Orbilia spp., 60 penicillin, 55, 264–3, 512 pheromone response element (PRE), 206 Orbiliaceae, 405 history and production, 478–82 pheromones, 77, 201, 209–10 Orbiliomycetes, 60 Penicillium camemberti, 56, 264, 275, 493, Phlyctochytrium spp., 43 Orchidaceae, 78 503 phosphatases, 247 orchidaceous endomycorrhizas, 78, 337, Penicillium chrysogenum, 55, 87, 189, 194, phosphate mobilization, 327 344–6 468, 474, 480, 482 phosphofructokinase, 253, 254 ptyophagy, 346 Penicillium citrinum, 55, 262 photobionts, 356 tolypophagy, 346 Penicillium cyclopium, 182 photosynthesis organelles, 107 Penicillium digitatum, 189 C3 and C4 pathways, 404 organic matter, 5 Penicillium expansum, 189 phragmoplast, 146 decomposing and stable stages, 6 Penicillium griseofulvum, 262 phycobionts, 356 food source for soil organisms, 6 Penicillium nalgiovense, 503 Phycomyces blakesleeanus,55 ornithine acetyltransferase, 308 Penicillium notatum, 478 Phycomyces spp., 442 ornithine carbamoyltransferase, 308 Penicillium roqueforti, 56, 275, 493, 503 Phycomycetes, 23, 29 Orpinomyces spp., 46, 401 Penicillium spp., 60, 432 phylogenetic classification orsellinic acid, 262 penny bun. See Boletus edulis divergence of Archaea and Eukaryota, oscillators pentachlorophenol (PCP), 245, 334 26–8 circadian rhythms, 215, 216 bioremediation by fungi, 334–6 divergence of Eubacteria and Archaea, oudemansins, 331 pentose phosphate pathway (PPP), 252, 311 26–8 oxalate oxidase, 245 peptidases, 247 Kingdom Fungi, 29–30 oxalic acid, 384 peptide pheromones, 199 phylogenetic classification systems, 23–9

Index 621

phylogenetic species concept, 74–5 direct penetration of the host cell wall, transport mechanisms, 133–4 phylogenetic studies 382 plasmalemma, 123–4 ATPase genes, 24–5 disease triangle, 374–6 plasmid DNA, 195–6 evolutionary clock, 24 Dutch elm disease (Ophiostoma novo- plasmids, 108 molecular studies, 33 ulmi), 372–3 cytoplasmic segregation, 195–6 molecular techniques, 24–6 effects of pathogens on hosts, 377–9 Plasmodiophora spp., 77 protein sequences, 25–6 effects on plant hormones, 378–9 Plasmodiophoromycota, 77 range of molecules studied, 24–6 enzymatic penetration of the host, 382–5 plasmogamy, 198, 231 ribosomal gene cluster, 25 flax rust (Melampsora lini), 371 Plasmopara spp., 31 small subunit ribosomal RNA (SSU rRNA) gene-for-gene interactions with plants, plastics genes, 24 387–9 microbial degradation, 333–4 suitable genes for study, 24 general short-term response in the host, plastids, 121–2 universal ancestor concept, 24 386 Platypodinae, 399 phylogeny of fungi, 35–8 genetic variation in pathogens and hosts, plectenchyma, 224–5 Physarales, 77 387–9 Pleistophora sp., 413 Physarum spp., 77 good sanitation to help control, 376 Pleospora spp., 60 physical power of growing fungi, 328–30 headline crop diseases, 370 Pleuricospora spp., 343 physical weathering, 6 hemibiotrophs, 376–8 Pleurotus ostreatus, 195, 406–7, 444 physiological species concept, 74 horizontal resistance, 387 genome, 546 Physoderma spp., 47 host penetration through stomata, Pleurotus pulmonarius, 311 phytoalexins, 386, 387 379–81 bioremediation of pentachlorophenol phytoanticipins, 386 host-selective toxins, 384 (PCP), 334–6 phytodebris, 31–4 host-specific toxins, 378 Pleurotus pulmonarius fruit body Phytophthora cactorum, 514 hypersensitive response in the host, formation of gills, 297–8 Phytophthora infestans, 75, 368, 370, 376, 384–5, 386, 388 Pleurotus spp., 71, 277 512, 522 induction of programmed cell death, cultivation, 278 Phytophthora megasperma, 75, 387 384–5 remediation of agricultural waste, 278 Phytophthora palmivora,75 insertional mutagenesis, 389 ploidy and nuclear number, 117 Phytophthora parasitica, 353 integrated pest management, 376–7 plus end tracking proteins (þTIPs), 127 Phytophthora spp., 29, 30, 75, 384 leaf spot diseases (Cercospora spp.), 372 Pneumocystis carinii, 30, 56, 431 Piedraia hortae, 426 losses to world agricultural production, genome, 546 pigmenation of fungal cell walls, 167–8 368–70 Pneumocystis jirovecii, 30, 56, 431 Pilaira spp., 442 molecular studies of pathogen virulence, pneumocystis pneumonia (PCP), 30, 56, 431 pileipellis, 291 389 Pneumocystis spp., 30, 55, 56, 438 pili, 107 necrotrophs, 376–8 pneumocystosis, 431, 522 Pilobolus spp., 442 oxidative burst in the host, 384–5 Podospora anserina, 185, 186, 195, 203 pine (Pinus), 346, 347, 349, 351, 354 pathogen–host–environment clock mutant, 215–16 mycorrhizal associations, 338 relationships, 374–6 het loci, 188 Piptocephalis spp., 440, 442 pathogens that produce haustoria, 371–2 post-fusion incompatibility response, 188 Piptoporus betulinus, 78, 273 pre-formed and induced defence prion protein, 196 PIR proteins, 165 mechanisms, 385–7 Podospora spp., 203, 210 Piromyces spp., 46, 401, 403 rice blast fungus (Magnaporthe grisea), poisoning from fungal toxins, 433–6 Pityopus spp., 343 370 poly-A polymerase, 111 plant disease rust fungi, 371–2, 379–81 polyacetylenes, 264 disease triangle, 374–6 smut fungi, 371–2 polychlorinated biphenyls (PCBs), 245 pathogen–host–environment symptoms of disease in plants, 377–9 polyenes, 514–17, 523 relationships, 374–6 systemic acquired resistance in plants, polygalacturonases, 241 plant pathogens, 367–89 386–7 polyketides, 260, 261–3 Armillaria spp., 370–2 tolerance in plants, 387 polymerase chain reaction (PCR), 25, 33 avoiding nutrient or water stress in using disease resistant cultivars, 376 soil microbes, 8 plants, 376 vertical resistance, 387 Polymyxa spp., 77 barley powdery mildew (Blumeria plants polyoxins, 171 graminis), 371 benefits of mycorrhizal associations, 325 polyoxorims, 521, 526 biological control methods, 377 dependence on mycorrhizal associations, polyphyletic group, 28 biotrophs, 376–8 325 Polyporaceae, 66 black stem rust of wheat (Puccinia plasma membrane, 133–6 Polyporales, 67 graminis tritici), 373–4 active transport processes, 133 polypores changing host metabolism, 378–9 electrochemical proton gradient, 133 pore (tube) formation, 301 co-evolution of plant–pathogen disease facilitated diffusion, 133 Polyporus hispidus, 263 systems, 387–9 GPI-anchors, 135 Polyporus mylittae, 227 comparison with animal pathogens, 436–9 ion channels, 133–4 polysaccharides defence mechanisms in plants, 384–5, ion pumping, 133 breakdown by fungi, 239–42 385–7 signalling pathways, 134–5 Polystictus versicolor,94

622 Index

Polystictus xanthopus, 301 prokaryotes pullulanase, 242 polystyrene cell membrane, 107 PVC microbial degradation, 334 cell structure, 107–8 microbial degradation, 334 polyurethanes DNA, 107 pycnidia, 198, 223–4 microbial degradation, 334 extrachromosomal DNA, 108 pyrenomycetes, 60 Pontisma spp., 75 plasmids, 108 pyridines, 518 poplar (Populus), 346 prosenchyma, 225 pyrimidine analogues, 518 porcini. See Boletus edulis proteasomal proteolysis, 121 pyrogallol, 263 pore space in soil, 6–7 proteasomes, 246 Pyrola spp., 343 posaconazole, 524 protective antifungal agents, 512 Pyrolaceae, 343 positive autotropism, 96–7, 181 protein Pyronema spp., 60 post-fusion incompatibility response, 185, as nitrogen and carbon source, 246, pyruvate carboxylase, 253 186, 188 256–7, 327 pyruvate formation potato blight, 75, 368, 522 digestion by fungi, 246–7 glycolysis, 251–2 powdery mildews, 327, 382–3, 389 protein-coding genes, 33, 115 pyruvate kinase, 253 pravastatin, 473 protein prenylation, 135 Pythiales, 75 predatory fungi protein sequences Pythiogeton spp., 75 nematode-trapping fungi, 405–8 phylogenetic studies, 25–6 Pythium aphanidermatum,75 pre-mRNA, 111, 113 protein sorting/targeting mechanism, Pythium spp., 30, 75, 199, 327, 331, 440 splicing, 111–12 119–21 Pyxidiophora spp., 60 pre-ribosomal RNAs (pre-rRNAs), 112 proteinaceous hereditary elements. Pyxidiophorales, 60 primary homothallism See prion proteins Neurospora spp., 203 proteinases, 246–7, 327 Quorn™ myco-protein, 56, 274 primary metabolism, 251–6 extracellular, 246–7 production, 473 acetyl-CoA, 252 intracellular, 246 Quorn™ fermentation, 487–92 ATP synthesis, 251, 253 proteins Quorn™ fungus, 461 basic function, 251 chloroplast protein transport, 121 catabolism of carbohydrate, 251–2 destruction, 121 r-selected species, 354 Embden–Meyerhof–Parnass (EMP) fungal cell wall, 163–5 Raffaelea spp., 399, 400 pathway, 251 mitochondrial protein transport, 120 rainfall Entner–Doudoroff (ED) pathway, 252 mRNA translation, 118–19 effects on soil formation, 6 excretion of excess nitrogen, 256–7 proteolysis, 121 Raistrick, Harold, 480 fats, 254–5 signal peptides, 119–20 Ran protein, 113 formation of NADH and NADPH, 251 synthesis, 107 RAS protein activation, 134–5 gluconeogenesis, 253–4 synthesis in the cytoplasm, 118–19 ravuconazole, 524 glutamate decarboxylation loop, 253 targeting peptides, 119–20 Rayner, Alan, 214 glutamine synthetase/glutamate synthase transmembrane proteins, 120 reactive oxygen species (ROS), 384 system, 256 transport into the nucleus, 121 recalcitrant waste glycolysis, 251–2, 254 proteome analysis, 559 remediation by fungi, 334–6 hexose monophosphate pathway (HMP), proteomics, 557 recombinant protein production by 252 protobasidia, 292 filamentous fungi, 557 Krebs (TCA) cycle, 252 proton gradients, 253 recombinant vectors, 552 mannitol, 254 Prototaxites spp., 31–4 Red Data lists, 563 NADP-GDH, 255–6 protozoa red pepper mites (Pygmephorus spp.), 270 nitrogen, 254–7 numbers in soil, 7 regional patterning (regional specification), oxidative phosphorylation, 253 pseudoparenchyma, 225 283, 290–1 pentose phosphate pathway (PPP), 252 pseudorhizas, 227 reishi, 279 protein as a carbon source, 256–7 pseudosclerotial plate, 227 remediation of agricultural/industrial proton gradients, 253 Pseudosphaerita spp., 75 wastes, 278, 334–6 pyruvate formation, 251–2 pseudothecia, 60 renewed fruiting, 315 TCA (tricarboxylic acid) cycle, 252 Psilocybe cubensis,62 rescue (microtubule switch), 126 trehalose, 254 Psilocybe spp., 263 resistance (R) proteins, 387 urea production, 256–7 psilocybin, 263 resistance to antifungal agents, 430–1, primary pathways Pterospora spp., 343, 344 522–6 definition, 251 Pterulaceae, 396 resupinate fruit body, 332 primordium of a structure, 283 Puccinia coronata f. sp. avenae, 389 reverse genetics, 550, 554 prion proteins, 188 Puccinia graminis, 62, 199, 512 Rhipidiales, 75 propagation and transmission, 196 genome, 557 Rhipidium spp., 75 prochloraz, 518 Puccinia graminis tritici, 373–4 Rhizanthella spp., 346 profilin, 145 Puccinia spp., 62 Rhizidiomyces spp., 77 programmed cell death, 185, 315–16, 376 Pucciniales, 62–3 Rhizoctonia solani, 69, 186, 440, 444 in cultures, 465–6 Pucciniomycotina, 62–3 Rhizoctonia spp., 78, 91, 327, 337, 344, 345 prokaryote/eukaryote distinction, 23 puffballs, 66, 228, 288 rhizomorphs, 226–7

Index 623

Rhizomucor pusillus, 431 transcription and processing, 112–13 Schizosaccharomyces pombe, 56, 93, 105, Rhizophlyctis spp., 43 Ruminantia, 403 118, 127, 475 Rhizophydiales, 45 ruminants chitin synthase gene, 160 Rhizophydium spp., 43 anaerobic chytrids in, 45–6, 400–5 mating types, 200 Rhizopus arrhizus, 54, 431 digestion, 493–4 molecular motors, 128 Rhizopus nigricans,54 evolution, 403–4 Schizosaccharomyces spp., 116 Rhizopus oligosporus, 54, 274 foregut fermentation, 403 Schleiden, Matthias Jakob, 107 Rhizopus oryzae,54 Ruminococcus albus, 402 Schwann, Theodor, 107 Rhizopus rot, 54 Russula bella, 330 Sclerocystis spp., 441 Rhizopus sexualis, 199 Russulales, 67, 72 Scleroderma bovista, 328 Rhizopus spp., 55, 247 rust fungi, 62–3, 199, 371–2, 373–4 Scleroderma citrinum, 442 Rhizopus stolonifer,54 Sclerospora spp., 75 Rhododendron spp., 341 Saccharomyces carlsbergensis, 476 Sclerosporales, 75 Rhodosporidium sphaerocarpum, 150 Saccharomyces cerevisiae, 55, 56, 105, 116, sclerotia, 198, 227–8 Rhodosporidium spp., 63 117, 127, 475 Sclerotinia sclerotiorum, 384, 385, 493 Rhodotorula spp., 63 actin gene mutations, 126 Sclerotinia spp., 60 Rhynchonectria spp., 60 bread-making, 499–501 Sclerotinia trifoliorum, 202 rhythmic growth chitin synthases 161, 162 Scolytinae, 399 mycelium, 214–16 chromosome and genome sequencing, scrapie disease in sheep, 196 ribosomal DNA (rDNA) sequencing, 25 105 Scutellospora spp., 52, 340, 441 ribosomal gene cluster fermentation, 105–6 seasons on the Earth, 23 externally transcribed spacer region genome, 113, 537 Sebacinales, 67 (ETS), 25 killer/immunity phenotype, 196 seborrhoeic dermatitis, 62 intergenic spacer regions (IGS), 25 mating process, 200–1 secondary homothallism internally transcribed spacers (ITS), 25 mating types, 199, 200, 201–3 Neurospora tetrasperma, 203 non-transcribed spacer region (NTS), 25 mitochondrial genes, 194 secondary metabolism phylogenetic studies, 25 model organism for research, definition, 257 spacer regions, 25 105–7 secondary metabolites, 257 ribosomal protein factors, 25 molecular motors, 128 aflatoxins, 262 ribosomal RNA. See rRNA Sup35p prion protein, 196 agaritine, 263 ribosome assembly, 112–13 virus-like particles, 196 Amanita toxins, 264 ribosomes, 107 Saccharomyces ellipsoideus, 477 carotenes, 260 mitochondrial, 195 Saccharomyces rouxii, 505 carotenoids, 258, 260 mRNA translation, 118–19 Saccharomyces spp., 56–8 cephalosporins, 264–3 protein synthesis, 118–19 Saccharomycetales, 56 cyclopentanes, 264 rice Saccharomycotina, 56–9 diterpenes, 259 bakanae disease, 379 salami, 495, 503–4 ergosterol, 259–61 rice blast fungus, 327, 370, 379, 382, 389, Salilagenidiales, 75 ergot alkaloids, 263 545 Salmonella spp., 106 fatty acid synthesis, 261–3 rice sheath blight, 521 Salvarsan, 512 gibberellins, 259 Rigidoporus ulmarius,71 Saprolegnia ferax, 138, 141 growth inhibition, 91 ringworm, 425 growth mechanism, 160 iron-binding compounds, 264 RNA, 107 Saprolegnia spp., 31, 75, 85 latex, 264 features of the universal ancestor, 24 Saprolegniales, 75, 514 muscarines and muscaridines, 263 RNA polymerases, 109 saprotrophic fungi, 62, 238, 326, 327 nature of secondary metabolism, 257 RNA probes decay of structural timber, 331–3 penicillins, 264–3 soil microbes, 8 dry rot, 331–3 polyacetylenes, 264 RNA-processing machines, 111 inorganic transformations, 327 polyketides, 260, 261–3 RNP machines, 118 nitrogen sources in plant litter, 327 precursors, 257 ro (ropy) genes, 117 physical power of growing fungi, sesquiterpenes, 259 rock surfaces 328–30 shikimate-chorismate derivatives, 263–1 fungal growth, 10 range of substrate materials, 327 siderophores, 264 rodents release of chlorohydrocarbons, 336 statins, 263 target of aflatoxins, 330 toxins produced by, 328–31 steroids, 258 root rots, 327 waste remediation, 334–6 sterols, 259–61 root–soil interface sap-stain fungi, 333 strobilurins, 263 importance of fungi, 10 Sarcodes spp., 343, 344 terpenes, 258–9 rose handler’s disease, 427 satratoxins, 432 triterpenes, 259 Royal Botanic Gardens, Kew, 71 Scheele, Karl William, 477 zearalenone, 262 Rozella spp., 35 Schizophyllum commune, 170, 180, 189, secondary pathways Rozellopsidales, 75 195, 210, 311 definition, 251 Rozellopsis spp., 75 genome, 546 secretory vesicles, 161–2 rRNA, 107, 109, 113 tetrapolar heterothallism, 206–10 sedges (Cyperaceae), 62

624 Index

sedimentary rocks, 6 shiroshimeji (Pleurotus ostreatus), 277 dynamic matrix, 7 selective toxicity concept, 512 shmoos, 118 effects of living organisms, 6 self/non-self recognition. See vegetative Siberian Traps ﬂood basalts, 37 organic matter, 6 compatibility sick building syndrome, 432 soil tilth, 6 self-fertilisation, 180 siderophores, 264 temperature effects, 6 self-incompatibility, 180 signal peptides, 119–20 weathering processes, 6 self-sterility, 180 signal recognition particle, 120 soil geochemistry septation, 92–3, 99–100 signalling pathways, 134–5 geomycology, 9–10 and branching, 97–8 GPI anchors, 135 soil solution, 5, 6–7 comparison with cytokinesis, 145–6 G-proteins, 134–5 soil structure formation of septa, 100 MAP kinase, 135, 143 contribution of fungi, 11, 326 multinucleate hyphae, 146–8 RAS protein activation, 134–5 effects of glomalin, 171 nature of the fungal cell, 99–100 signal ampliﬁcation, 135 soil tilth, 6 orientation of septa, 100 silicon in soil minerals, 6 soil types process, 144–5 simvastatin, 473 nutrient cycling, 6 septal band, 147 sinapyl alcohol, 242 organic soil, 6 septal form, 144 sirenin, 47, 48, 199 solar wind, 22–3 septal pores, 99 Sirolpidium spp., 75 solid substrates types of septa, 99 sitosterol, 512 advantages of mycelial growth, 100–1 septins, 145 slime moulds, 23, 29, 52 somatic incompatibility. See vegetative Septoria spp., 223, 327 slugs and snails compatibility Sericomyrmex spp., 396 fungi as food, 271 Sordaria brevicollis, 186 serine proteinases, 247 small mammals Sordaria spp., 60, 228 Serpula lacrymans, 78, 226, 250, 331–3 fungi as food of, 271–2 Sordariales, 522 sesquiterpenes, 259 small subunit ribosomal RNA (SSU rRNA) sordarins, 522 sex pheromones in fungi, 48 genes Sordariomycetes, 60, 61, 438 sexual behaviour phylogenetic studies, 24, 33 Sordariomycetidae, 399 creation of a dikaryon, 180 smut fungi, 62, 371–2 sorus, 62 creation of a monokaryon, 180 SNARE proteins, 124, 146 soy foods, 504–6 sexual reproduction, 198–211 snoRNA, 113 soy sauce, 274, 495 anamorphic fungi, 198–9 snoRNP, 113 production, 504–6 biology of mating type factors, 210–11 snRNA, 112, 113 soya bean (Glycine max), 387 diversity of behaviours in fungi, 180 snRNP, 112 spalting, 333 duration of stages, 199 soft rots, 238, 384 species concept in fungi, 71–5 fungi which lack sexual reproduction, soil biological species concept, 71–4 198–9 amount of land used to supply food, 5 ecological species concept, 74 genetic control of mating, 201 association of fungi with, 5 evolutionary species concept, 74 heterothallic fungi, 180, 199–200 importance as a terrestrial habitat, 5 molecular phylogenetic approach, 74–5 homothallic fungi, 180, 199, 200 soil atmosphere, 5, 6–7 morphological species concept, 71 hormones involved, 199 soil biota phylogenetic species concept, 74–5 hyphal fusion, 142 diversity and quantity, 7 physiological species concept, 74 incompatibility systems, 199 effects of soil formation on, 6 spindle apparatus, 116 karyogamy, 198 microarthopod fungivores, 267 spindle checkpoint, 116 mating in budding yeast, 200–1 microbial diversity in soil, 7–8 spindle pole body, 115, 116, 145 mating systems, 199–200 organic matter food source, 6 Spinellus spp., 440 mating type switching in budding yeast, soil components, 5–7 Spitzenko¨rper, 125, 139, 141, 142, 161, 162 201–3 clays, 6 Spizellomycetales, 45 mating types, 199 dynamic matrix, 7 spliceosomes, 112 mating types in Basidiomycota, 205–10 elements found in soil minerals, 6 splicing of pre-mRNA, 111–12 mating types in Neurospora spp., 203–5 gaseous phase, 5 Spongospora spp., 77 meiosis, 198 humic substances (humus), 6 spores mitosporic fungi, 198–9 liquid phase, 5 dispersal, 214 morphology of structures involved, 199 minerals, 5–6 dormancy, 86 phenotype of sexual reproduction, 199 organic matter, 5, 6 emergence of germ tubes (hyphal tips), 86 plasmogamy, 198 pore space, 6–7 formation, 216–20 process, 199–200 sand, 6–7 germination, 86–7 spore production, 199 soil atmosphere, 5 initiation, 92 stages, 198 soil solution, 5, 6–7 multinucleate, 183 Sheehan, John, 478 solid phase, 5–6 production, 199, 214 shiitake. See Lentinula edodes soil food web, 7 spherical growth stage, 86 shikimate-chorismate derivatives, 263–1 soil formation uninucleate, 183 shikimic acid pathway, 252 and rainfall, 6 Sporidiobolus spp., 63 shimejitake (Hypsizygus tessulatus), 71 climatic effects, 6 Sporobolomyces spp., 63

Index 625

sporodochium, 223 systematics access to information about, 513 sporopollenin, 401 definition, 27 toxins produced by fungi, 331, 433–6 Sporothrix schenckii, 167, 427 systemic acquired resistance in plants, Trachipleistophora anthropophthera, 413 sporotrichosis, 427 386–7 Trachipleistophora hominis, 413 spruce (Picea), 346, 347, 351, 354 systemic antifungal agents, 512–13 Trachymyrmex spp., 396 squalene, 259 systemic mycoses trama, 292 Squamanita odorata, 442 clinical control of, 522–6 Trametes versicolor,78 SR proteins, 112 systems biology approach, 531, 557 transcription factors, 109–10 St Anthony’s fire, 434–5 transcription research, 107 Stachybotrys chartarum, 432–3 tannins, 238 transcriptome analysis, 559 Stachybotrys elegans, 440 Taphrina betulina,56 transcriptomics, 557 stachylysin, 432 Taphrina deformans,56 transfer RNA. See tRNA starch breakdown, 241–2 Taphrina spp., 56–7 transformation of cells, 551 statins, 4, 55, 263, 331, 473 Taphrinomycetes, 438 transgenic plants, 422 steady state (soft spot) model of hyphal tip Taphrinomycotina, 30, 56, 431 translational triggering, 222 extention, 139 targeting peptides, 119–20 translocase of inner membrane (TIM), 120 Stemonitales, 77 Tarsonemus myceliophagus, 270 translocase of outer membrane (TOM), 120 Stemonitis spp., 77 TATA-box binding protein-associated transmembrane glycoproteins, 248 Stereaceae, 66 factor(s) (TAFs), 109, 111 transmembrane proteins, 120, 162 steroids, 258 Tatum, Edward, 106 transplant patients derivatives, 473 taxon prevention of organ rejection, 4 manufacture, 486–7 definition, 27 See also immunocompromised patients sterols, 133, 199, 259–61, 512 taxonomic ranks for fungi, 28 transport vesicles, 124 stigmasterol, 512 taxonomy transportation of nutrients, 247–51 stinkhorns, 66, 228, 288 definition, 27 active transport, 249 stinking smut, 62 fungal cell wall structure, 158–9 bulk flow, 248 stipes of fruiting bodies, 227 fungi, 27 effects on water potential, 249–51 stramenopiles, 31 TCA (tricarboxylic acid) cycle, 252, 477 facilitated diffusion, 248–9 Streptomyces tea production, 496 ion pumps, 249 symbiosis with gardening ants, 397–8 teleomorph (sexual stage), 42 mass flow, 248 Streptomyces cacaoi var. asoensis, 521 tempeh, 54, 274, 506 simple diffusion, 248 Streptomyces coelicolor genome, 536, 537 temperature solute transport systems, 248 Streptomyces noursei, 515 effects on soil formation, 6 transmembrane glycoproteins, 248 Streptomyces tendae, 521 tendril hyphae, 225 transporter molecules, 248 streptomycete bacteria, 85, 86 termites, 62 Trechisporales, 69 stringy oak rot, 332 and fungi, 279 Tree of Life Project, 26, 31 strobilurins, 4, 263, 331, 526–9 gardening, 279–80, 398–9 trehalose, 254 Strobilurus ohshimae, 331 Termitomyces spp., 280, 398–9 Tremella spp., 208 stromata, 198, 223–4 Termitomyces titanicus, 398 Tremellales, 66 Strongwellsea spp., 418 terpenes Tremellomycetes, 66 structural timber secondary metabolites, 258–9 triadimefon, 518 dry rot, 331–3 tetrapolar mating system, 205–6 triarimol, 518 effects of wood-decay fungi, 331–3 Ustilago maydis, 205–6 triazbutil, 518 subsistence diet Thallophyta, 23 triazoles, 518 land required per person, 5 Thanatephorus cucumeris,69 Trichloma spp., 353 succinate dehydrogenase, 252 Theia–Earth impact, 21, 22, 23 Trichoderma harzianum, 493 sudden infant death syndrome (SIDS), 431 Thelephorales, 69 Trichoderma pleuroticola, 444 sufu, 506 thigmotropism, 379 Trichoderma pleurotum, 444 sugar beet leaf disease (Cercospora beticola), Thraustochytriales, 77 Trichoderma reesei, 240, 474 372 Thraustochytrium spp., 77 Trichoderma spp., 270, 440, 442, 444, 493 sulfatases, 247 thrush (fungal infection), 429 biological control, 444 sulfur in the soil, 239 thyriothecia, 60 Trichoderma virens, 484 superoxide, 384 Tieghemomyces spp., 440 Trichoderma viride, 444 surface tension catapult, 229 Tilletia spp., 62 Trichoglossum spp., 60 symbiosis. See mutualism, mycorrhizas Tilletia tritici, 264 Tricholoma fumosum, 338, 349 symport, 249 tinder bracket fungus, 273 Tricholoma matsutake, 71, 272, 273 synchronous division of nuclei, 146–8 toadstools, 228 Tricholoma spp., 78, 338, 347 synchronous mitosis tofu, 506 Tricholomataceae, 246, 280, 398 hyphal growth, 93 tolypophagy, 346 Trichomycetes, 53, 414–16 Synchytrium spp., 43 toxic waste Trichophyton rubrum, 425 synnemata, 223 breakdown by fungi, 238 Trichophyton spp., 247, 425, 426 syntaxins, 146 remediation by fungi, 334–6 Trichosporon cutaneum, 426 synthetic biology, 560 toxicity tricyclazole, 526

626 Index

trisporic acid, 199 post-fusion incompatibility response, ang-kak, 506 triterpenes, 259 185, 186 arachidonic acid, 482–3 tRNA, 107, 109, 113, 118 vegetative compatibility (v-c) group, 185 autolysis in cultures, 465–6 truffie`res (truffle groves), 279 vegetative compatibility reactions, 441 batch culture, 452–69 truffles, 56, 272, 288, 337, 346 vegetative incompatibility beer-making, 475–6 cultivation in truffle groves, 279 barrage formation, 188 bioreactors, 496 See also Tuber spp. cell death caused by, 185 bread-making, 499–501 tryptophan, 263 clear zone formation, 188 cheese production, 501–5 Tuber magnatum, 56, 272 See also vegetative compatibility chemostats, 470–3 Tuber melanosporum, 56, 272 Venus, 22 chocolate production, 495 Tuber spp., 60 veratryl alcohol, 244, 245, 336 citric acid biotechnology, 468, 477–8 See also truffles Verrucalvus spp., 75 coffee production, 495–6 Tubeufia spp., 60 Vertalac, 422 culturing fungi, 452–6 Tunbridge ware, 333 vertical mitochondrial transmission, 195 digestion of lignocellulosic residues, turbidostat cultures, 472–3 Verticillium dahliae, 185 497–9 turgor pressure, 250 Verticillium fungicola, 443–4 evolution in fermenters, 487–92 two-dimensional gel electrophoresis, 559 Verticillium lecanii, 418, 422 fabric manufacture, 483–4, 484–6 Tylopoda (pseudoruminants), 403 Verticillium spp., 60, 330, 442 fed-batch culture, 451–70 Tyrannosorus spp., 60 vesicles, 162 fermented foods, 504–6 Tyromyces placentus, 332 in arbuscular mycorrhizas, 338 fermented meat products, 503–4 tyrosine, 263 types of, 161–2 fermented soy foods, 504–6 vesicular-arbuscular mycorrhizas (VAM), fermenter engineering, 458–60 ubiquitin, 121 51, 326, 337, 338 fermenter growth kinetics, 462–4 Ulocladium atrum, 493 vessel hyphae, 225 fermenters, 451–2 ultraviolet (UV) radiation, 22–3 victorin, 378 food processing, 484–6 shielding from, 167 Virtual Library, 562 fungal biological control agents, 492–3 unifactorial incompatibility, 199 virulence, 437 fungal fermentations in submerged liquid United Kingdom National Culture virus-like particles cultures, 452 Collection, 562 cytoplasmic segregation, 196 fungal growth in liquid cultures, 460–3 universal ancestor concept, 24 Vittaforma corneae, 413 glucose-stats, 473 universal common descent theory, 28 Volvariella bombycina, 312 growth as pellets, 466–9 untrue fungi, 75–7 Volvariella fruit body growth yield, 464–5 urea, 311 formation of gills, 296–7 mycoherbicides, 492–3 osmotic metabolite, 308, 311 Volvariella spp. mycopesticides, 492–3 production in fungi, 256–7 use of protein, 246 myco-protein, 487–92 Urediniomycetes, 62 Volvariella volvacea, 71, 210, 443 natural digestive fermentations in urediospores, 380 cultivation, 279 herbivores, 493–4 Uromyces appendiculatus,62 voriconazole, 431, 524 nutristats, 473 Uromyces fabae open (continuous) systems, 453 host penetration through stomata, 379– Walksman, Selman, 480 oxygen demand of the culture, 456–8 81 waste remediation by fungi, 334–6 oxygen supply to the culture, 456–8 Uromyces spp., 62, 379–81 water distribution in soils penicillin history and production, 478–82 Usnea spp., 60 effects on fungal growth, 10 permittistats, 473 Ustilaginomycetes, 62 water moulds, 75–7 pH auxostats, 473 Ustilaginomycotina, 62 water potential, 249–51 pharmaceuticals, 473, 478–83 Ustilago hordei, 389 water relationships in the fungal cell, programmed cell death in cultures, 465–6 Ustilago maydis, 62, 127, 132, 150 249–51 Quorn™ fermentation, 487–92 genome, 546 weathering processes, 6 range of uses of submerged pheromone signalling, 209 chemical weathering, 6 fermentations, 473–4 tetrapolar mating system, 205–6 leaching, 6 ruminant digestion, 493–4 Ustilago spp., 62, 371 physical weathering, 6 salami production, 503–4 Ustilago violacea, 195 wet-rot fungi, 332 solid state fermentations, 494–7 wheat soy sauce, 504–6 Vaccinium (bilberry) black stem rust (Puccinia graminis tritici), spore and inocula production, 492–3 mycorrhizas, 337, 341 373–4 stationary phase, 465–6 vacuoles, 128–9 wheat (Triticum), 11 steroid manufacture, 486–7 valley fever, 428 white-rot fungi, 62, 78, 238, 240, 244–6, surface fermentation, 477 variotin, 263 336, 345 tea production, 496 Vegemite, 274 white rust, 379 turbidostat cultures, 472–3 vegetative compatibility, 180, 185–8 Whitfields ointment, 512 use of fungi to make chemical compatibility test, 185 Whittaker, R. H., 23 transformations, 486–7 het loci, 185–6, 188 whole organism biotechnology, 451–506 wine-making, 476–7 alcoholic fermentations, 474–7 Wilcoxina spp., 351

Index 627

wild mushrooms Woronin bodies, 99, 144 yeast research commercial exploitation, 272–4 Wurzelpilze, 336 breeding experiments, 106 willow (Salix), 346 Wurzelsymbiose, 336 contribution to eukaryote cell biology, wine making, 476–7 105–7 witches’ broom disease of birch, 56 Xerocomus parasiticus, 442 fermentation, 105–6 Woese, Carl, 24 xylanases, 241 genetics, 106 wood ear fungus (Auricularia polytricha) xylans, 240 yeast–mycelial dimorphism, 150–1 trade, 273 Xylaria polymorpha,78 ‘wood-wide-web’ Xylaria spp., 60 zearalenone, 262 ectomycorrhizas, 338 xylosidase, 240 zinc finger protein, 221 mycorrhizas, 349 zoonoses, 425 wood-decay fungi, 78, 238, 327, 345 yeast, 55, 56–9 Zoopagales, 52 chlorohydrocarbon release, 336 basidiomycetous, 63 Zoopagomycotina, 30, 52, 442 decay of structural timber, 331–3 cell cycle genetic studies, 149–50 zoospores dry rot, 331–3 cell cycle in budding yeast, 150 free cell formation, 48–50 woodland mushrooms, 347 definition, 105 zygomycetes, 52 ectomycorrhizas, 338 epiphytes, 79 zygomycosis, 53, 54, 431–2 World Data Centre for Microorganisms genome, 537 Zygomycota, 29, 30, 35, 50, 52–5, 414 (WDCM), 562 lipophilic, 62 meiosis, 118 World Federation of Culture Collections, number of protein coding genes, 115 polyphyletic nature, 52 562 switching mating types, 200 zygosporangium, 52 world’s largest individual organism, 370 yeast artificial chromosome (YAC), 532, 552 zymogen, 136