Use of Fungi Biodegradation Environmental Microbiology
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The following chapter: Use of Fungi Biodegradation by J. W. BENNET, K. G. WUNCH, AND B. D. FAISON Has been taken from the book: Manual of Environmental Microbiology Second Edition Editor in Chief Christon J. Hurst ASM Press Washington, D.C. 2002. Useof Fungiin Biodeadation l. \7. BENNETI K. G.\yUNCH, AND B. D. FAISON 87 In nature, fungi do much of the dirty work. Th"y are par- Stramenopila, and four protist phyla. ln this classification, ticularly efficient at degrading the major plant polymers, the kingdom Fungi encompassesfour phyla: Chytridiomy- cellulose and lignin, but they also decomposea huge array cota, Zygomycota, Ascomycota, and Basidiomycota (18, of other organic molecules including waxes, rubber, feath- 26). The Stramenopila encompassesthree phyia' Oomy- ers, insect cuticles, and animal flesh. Although industrial cota, Hyphochytriomycota, and Labyrinthulornycota. From microbiologists regularly hamess fungal metabolism for the perspectiveof researchon fungal degradation,most of brewing, baking, cheesepreparation, and for production of the speciesof interest are in the kingdom Fungi. antibiotics, commercial enzymes, and a number of com- In filamentous forms, the individual thread-like cells are modity chemicals, fungi are best known for their dirry called hyphae. A fungal colony, or porrion of a colony, work. They spoil our foods, blight our crops, rot our build- composed of many hyphae together is called a mycelium. ings, contaminate our petri dishes, and cause some rather The filamentous/mycelial growth form poses problems in loathsome diseases.Paradoxically, despite this notoriety, determining the sizeof a single organism and in measuring "thal- the use of fungi in bioremediation has been limited com- the growth of fungi. In the older literarure, the term pared to that of bacteria. Here we present a brief intro- lus" is often used to describe macroscopic mycelial forma- duction to fungal taxonomy and mycological techniques, tions. introduce methods for isolating fungi and for growing them Fungal taxonomy is based on reproducrive morphology, in the laboratory, define some important terms, review ex, which consists of both meiotic and mitotic spore-bearing amples of the successfulapplications of fungal organisms structures. Both sexual and asexual spores are typically and enzymesfor biodegradation, and point out the advan- made in vast numbers. Many fungi have more than one tages and disadvantagesof fungi as agents of bioremedia- morphologically distinct spore rype ar different phasesin tion. their life cycles. Further complicating rhis fungal pleomor- phism is the fact that some fungi exist as either yeasror filamentous forms depending on the environmental milieu, A LITTLETAXONOMY a phenomenon called dimorphism, best known from med- Like rnany other higher-order raxonornic units, the term ically important species. "fungus" is difficult to define. It embracesa large group of Like other eukaryotes,fungi have nuclei, mitochondria, nonphotosynthetic lower eukaryotesonce consideredpart B0S ribosomes,and chromosomes.Fungal cells may be hap- of the plant kingdom and later afforded srarusin their own loid or diploid; the nuclei within a mycelium rnay all be "Fifth kingdom, the Kingdom," on the basisof their char- genetically identical (monokaryotic) or may be a mixture acteristic absorptive mode of nutrition (102, 117, 168). of different genetic types (heterokaryotic). Basidiomycetes taditionally, the Myxomycora, or slirne molds, and the often have a special form of heterokaryon called a dikar- "true Eumycota, or fungi," comprised the two major sub- yon. Although rnany fungi are microscopic,the best-known divisions within this fungal kingdom. A plasmodium or speciesform macroscopicfruiting structuressuch as mush- pseudoplasmodiumcharacterized the Myxomycota, a group rooms and truffles. Fungi are ubiquitous in terrestrial en- rvhich included well-known senera such as Dict^tosielium vironments, and many fungi are capable of growing in and Physarum,while in the Eumycora the assimilative environments hostile ro mosr other forms of life (97). For phase was usually {ilamentous or yeasr-like.More recenrly, example, fungi are the only eukaryotesthat include mem- classificationbased on evolutionary relationships(i.e., phy- bers with thermophilic (60 to 62'C) oprimal growrh tem- logenetic classification) has led to a realization rhar the peratures(158). organismsthat have traditionally been called fungi, on the In summary, the broadly understood concept of fungi basis of shared nutritional modes and morphological char- comprisesa polyphyletic group of eukaryotic, heterotrophic acters, do not represenr a monophyletic lineage. Derived organisms that absorb their food. Mycology texts such as primarily from data on small-ribosomal-subunit(rDNA) se- those by Alexopoulos, Mims, and Blackwell (10), Ross quence analysis,the assemblageof traditional fungi is noiv ( 143), Moore-Landecker(124), and Carlile and Watkinson placed in three groups: the kingdom Fungi, rhe kingdom (10) are helpful introductions ro this economically impor' 960 87. Use of Funsi in Biodesradation I 961 rant group. Another useful tool is Ainsw,orth6 Blsbi''s Moreover, dormant ftrngal sp()resmay prrlduce nlllnerous Dictionaryof ilrc Fungi (83). General trrx.rnonricprinciples, colonies ri'hile thri'u'ing nonsporulating colonies may not as rvell as a guicle to the sometimes arcllne principles of be recoveredat all. ln licluidshake culture, many filamen- fungal nomenclature, which are govcrned by the lnterna- tous ftrngi form pellets, thus rnaking direct turbidity assays tional Code of Botanical Nomenclature, are presented by impractical and making dry weights the most cornmonly Havyksworth(79). The last volumes (in two parts) of the used measure.in batcl'rculture, the synthesisof m:rny fun- classicseries, The Fungl: an AduancedTreatise,provide com- gal procluctsand en:ymes is not correlated with growth but prehensivetaxonomic coverage(2,3), rvhile the hrst vol- is triggereclby the lin-rit:rtionof an essentialnutrient. The "trophophase" "idiophase," umes (4-0) give an almost encyclopedic revierv of the terms and roughly comparable classicalmycological literature. Anotl-rer useful resource is to bacterial log phase and stationary phase, respectively, the multivolume seriesentitled The Mycota, an Encyclopedia havc been used to describe {ilamentous growth. Both of Fungi (50). Volume VII addressesfungal classilication secondary-metabolite production and the ligninolytic- and taxonomy (120). enzyme production are correlated u'itl-r idiophase. Enrichment cultures arc a classicalmicrobiological tech- nique, commonly used ftrr hnding a specific microbe to de- grade a certain toxic waste. Enrichment cultures favor the ACQUtStilON,CARE, AND FEEDING growth of a particular speciesbasecl on its nutritional re- OF FUNGI quirements. h-r the most colnmon application of this Filamentous fungi have more described speciesthan any method, aliquots of rvater, soil, leaf litter, or other mixed other group of microorganisms,with :rbotrt 80,000 already inocula arc placed into a medium containing the targeted named and approximately 1,800 new species published cornpound as the sole carbon source.Only organismswith each year. As with bacteria, it is believed that only a small degradativeability will grow. In liquid cttlture, competition proportion of extant species are known tt-r science. The for the substratewill leacl to enrichment of the microbial total number of fungal species,both knorvn and unknorvn, strain that is able to grorv fastest.On petri plates, colonies has been estimatedat more than 1.5 million (80, BZ). representing many species are usually isolated; these are About 170,000 pure strains of fungi are maintained in then subcultured and tested further. With ferv exceptions, culture collections internationally, representingan esti- this approach leads to the isolation of bacteria. In general, mated 7,000 different species(Bi ). Information about these fungi are slower growing and produce fewer propagulesthan resources can be accessed through the World l)irectory of do bacteria. In addition, fungi are less likely than bacteria CoLlectionsof Cukure.s of Microorganisms(156). One of the to have the capracity to use xenobirttics as sole carbon oldest and largest fungal collections is the Centrarrlburear sources.Many fungi need a supplemental carbon source to voor Schemmelculturesin the Netherlands. The major col- sustain growth, i.e., their tlegradative potential is cometa- lection in the United States is the Atnerican Type Culture bolic. Collection (98). In addition, the collection at the Thus, the key to successftrlisolation of fungi for xeno- Northern Regional Research Laboratory of the U.S. De- biotic clegradatic-rnis trvofcrld:(i) the recognition that fungi partment of Agriculture in Peoria, lll., housesa large nLrm- are easily outgrown by bacteria and (ii) the recognition ber of economically important fungi, ancl the Forest that they produce many potent biodcgradativeenzymes ca- Products Laboratory in Madison, Wis., holds a major col- pable of degrading toxic pollutants yet do not use these lection of wood-rotting species.Major culture collections breakdon'nproJucts to sustaingrowth. To successfullyiso- maintain \Veb sites with information about holdings and late fungi with potential for bioremediation, it is necessary instructions about ordering. As with bacterial and viral to impose imaginative enrichment conditions, including strains, a fee is usua[y charged for obtaining cultures.