DESCRIPTION OF THE KINGDOM FUNGI (LINNAEUS 1753)
| EUKARYA> OPISTHOKONTA> UNIKONTA> FUNGI |
KINGDOM FUNGI LINKS
| Fungi (FUN-zhee) is derived from the Latin word Fungus (Fungi is plural) which means mushroom. Likely, it came fro the older Greek word sphongos (σφογγος), which means sponge. Linnaeus (1753) coined the term Fungi as a plant class. Jahn and Jahn (1949) and later Whittaker (1959) used the term to define the kingdom; however, Moore (1980) was the first to apply a formal diagnosis to Fungi as the name of a kingdom. |
| INTRODUCTION TO THE KINGDOM FUNGI The Fungi have been recognized as a separate kingdom since the work of Whittaker (1957 and 1959). For a time Margulis and Schwartz (1982 and 1988) insisted that the fungi were derived from a lineage that never had flagella. However, the tide of evidence from molecular phylogentic studies demonstrated that the fungi evolved from a flagellated line [see Tudge (2000) and Baldauf (2003a) for a synopsis of the work]. Indeed, that the chytrids were part of that line and that the fungal clade was part of a larger clade called the opisthokonts (animals + fungi in the Unikonta), a group that includes the choanoflagellates and the metazoans, suggests that the fungi and animals are “cousins” (Baldauf and Palmer 1993; Baldauf 1999; and Patterson 1999). Margulis and Schwartz (1998) still maintain that the fungi are a kingdom of conjugating taxa, and, therefore, continue to exclude the chytrids. The most surprising change in fungal taxonomic systems in recent years has been the inclusion of the intracellular parasites of insects and fish called microsporideans (Edlind et al., 1996; Keeling and Doolittle 1996; Fast et al. 1999) based on protein gene comparisons. The unexpected feature of this association was the apparent primitive nature of the microsporideans based on ssu rRNA studies. Indeed, they were usually given at the base of the eukaryote tree along with other putative primitive forms as Giardia and the parabasalids, especially in Archaezoa scenarios (Cavalier-Smith, 1983; see my discussion on this). However, Germot et al. (1997) established that the microsporidians had evolved from a mitochondriate ancestor, and Hirt et al. (1999) then demonstrated their clear affinities with the opisthokonts, particularly the fungi. Since then, independent lines of research have established their association with the fungi (e.g. Fast and Keeling 2001, Keeling 2003, Sokolova et al. 2003, and Ragan et al. 2003). Keeling (2003) argues that the microsporidia are not primitive at all, but evolved from a zygomycete ancestor. Clearly, the microsporidians are fungi; however, their particular location within the kingdom is not clear. Until a few years ago (up to 2004), the taxonomy of Fungi was fairly simple with just four phyla: Chytridiomycota, Zygomycota, Ascomycota, and Basidiomycota (e.g. Hudson 1984, Margulis and Schwartz 1988 and 1998, and Alexopoulos and Mims 1979 and 1996). The classical relationships of the phyla can still be seen in a cladogram of relationships based on mitochondrial DNA sequences by Lang. Schussler et al. (2001) demonstrated that the arbuscular mycorrhizal (AM) fungi, formerly in the order Glomerales of the Zygomycota, are monophyletic and distinctly different (based on ssu r-RNA comparisons) from all other fungal taxa, and they defined a new phylum, Glomeromycota, for them. Their phylum-level status has been confirmed by other studies, particularly Lutzoni et al. (2004, see Figure 1). Schussler et al. (2001) and Lutzoni et al. (2004) also show that the Zygomycota and the Chytridiomycota are paraphyletic. The paraphyly of the basal taxa was confirmed in a series of publications (James et al. 2006a and 2006b; Tanabe et al. 2004; and White et al. 2006). The old phylum, Chytridiomycota s.l. was separated into three phyla: Chytridiomycota (in a much narrower sense), Basicladiomycota, and Neocallimastigomycota (Hibbett et al. 2006). The old phylum Zygomycota, beyond the removal of the Glomeromycota from its ranks (see above), was fragmented into at least three groups (Hibbett et al. 2007) that seem to coalesce into two major groups: the Core Zygomycota (a group that we call Mucoromycota), and a collection of conjugating taxa that have frequent crosswalls: Entomophthoromycota (Humber 2012) and two subphyla from Adl et al. (2012): Kickxellomycotina and Zoopagomycotina in an emended phylum that we call Kickxellomycota. The general structure of the Ascomycota and Basidiomycota has not changed very much. Molecular work (summarized by Lutzoni et al. 2004; and Hibbett et al. 2007) confirms that the two phyla are sister-taxa in a group that Hibbett et al. (2007) call subkingdom Dikarya. As the name implies, both phyla have dikaryotic hyphae, however, they tend to be long-lived and persistent only in the Basidiomycota. Both taxa tend to cluster their sexual spore-bearing structures in sporocarps. The form taxa (Form-Phyla, etc.) of the older taxonomies (e.g. Bold et al. 1987 and Alexopolous and Mims 1979) are not natural and have been sorted out according to their lineages. These include some of the non-sexual fungi, forms in which sexual reproduction has become lost or significantly modified such that meiosis doe not occur. Others are chimeroid organisms called lichens. These do occupy a “no man’s land” of taxonomic uncertainty (although there are many who claim to be certain enough) because lichens are entities that develop as a symbiosis between free-living taxa, a fungus (the mycobiont) and an alga (the phycobiont). Current convention places the lichens within the Kingdom Fungi, and classifies them according to the species of the mycobiont (mostly ascomycetous fungi). |
FIGURE 1. This figure is a modification of the SSU and LSU r-RNA analyses of Lutzoni et al. (2004) for the Kingdom Fungi.
The groups within traditional phyla have been color-coded:
CHYTRIDIOMYCOTA (brown)
ZYGOMYCOTA (orange)
GLOMEROMYCOTA (green)
BASIDIOMYCOTA (red)
ASCOMYCOTA (blue)
FIGURE 2. This figure is a synopsis of James et al. (2006) as abstracted in McLaughlin et al. (2009).
| PHYLA OF THE KINGDOM FUNGI |
- THE BASAL FUNGI
MICROSPORIDIA (Balbiani 1882)
CHYTRIDIOMYCOTA (Powell 2007)
NEOCALLIMASTIGOMYCOTA (James et al. 2007)
BLASTOCLADIOMYCOTA (James et al. 2007)
MUCOROMYCOTA (em. Benny 2007)
KICKXELLOMYCOTA (em. Benny 2007)
ENTOMOPHTHOROMYCOTA (Humber 2012)
GLOMEROMYCOTA (James et al. 2006)
- THE DIKARYA
ASCOMYCOTA (James et al. 2006)- BASIDIOMYCOTA (Moore 1980)
LICHENS
| LITERATURE CITED Alexopoulos, C. J. and C. W. Mims. 1979. Introductory Mycology. 3rd ed. John Wiley and Sons. New York. Alexopoulos, C. J., C. W. Mims, and M. Blackwell. 1996. Introductory Mycology. 4th ed., John Wiley & Sons, New York. Baldauf, S. L. 1999. A Search for the origins of animals and fungi: comparing and combining molecular data. American Naturalist. 154: S178-S188. Baldauf, S. L. 2003a. The deep roots of eukaryotes. Science. 300(5626): 1701-1703. Baldauf, S. L. and J. D. Palmer. 1993. Animals and fungi are each other’s closest relatives: Congruent evidence from multiple proteins. Proceedings of the National Academy of Science USA. 90: 11558-11562. Bold, H. C., C. J. Alexopoulos, and T. Delevoryas. 1987. Morphology of Plants and Fungi. 5th Edition. HarperCollins Publishers, Inc. New York. Cavalier-Smith, T. 1983. A six-kingdom classification and a unified phylogeny. In: Schenk, H.E.A. and W.S. Schwemmler, eds. Endocytobiology II. de Gruyter , Berlin . pp. 1027-1034. Edlind, T. D., J. Li, G. S. Visvesvara, and M. H. Vodkin. G. L. McLaughlin, and S. K. Katiyar. 1996. Phylogenetic analysis of b-Tubulin sequences from amitochondrial protozoa. Molecular Phylogenetics and Evolution. 5(2): 359-367. Fast, N. M. and P. J. Keeling. 2001. Alpha and beta subunits of pyruvate dehydrogenase E1 from the microsporidian Nosema locustae mitochondrion-derived carbon metabolism in microsporidia. Molecular and Biochemical Parasitology. 117(2):201-209. Fast, N. M., J. M. Logsdon Jr., and W. F. Doolittle. 1999. Phylogenetic analysis of the TATA box binding protein (TBP) gene from Nosema locustae: evidence for a Microsporidia-Fungi relationship and spliceosomal intron loss. Molecular Biology and Evolution. 16(10):1415-1419. Germot, A., H. Philippe, and H. Le Guyader. 1997.Evidence for loss of mitochondria in Microsporidia from a mitochondrial-type HSP70 in Nosema locustae. Molecular and Biochemical Parasitology. 87: 159–168. Hibbett, D. S., M. Binder, J. F. Bischoff, M. Blackwell, P. F. Cannon, O. E. Eriksson, S. Huhndorf, T. James, P. M. Kirk, R. Lücking, T. Lumbsch, F. Lutzoni, P. B. Matheny, D. J. Mclaughlin, M. J. Powell, S. Redhead, C. L. Schoch, J. W. Spatafora, J. A. Stalpers, R. Vilgalys, M. C. Aime, A. Aptroot, R. Bauer, D. Begerow, G. L. Benny, L. A. Castlebury, P. W. Crous, Y.-C. Dai, W. Gams, D. M. Geiser, G. W. Griffith, C. Gueidan, D. L. Hawksworth, G. Hestmark, K. Hosaka, R. A. Humber, K. Hyde, J. E. Ironside, U. Kõljalg, C. P. Kurtzman, K.-H. Larsson, R. Lichtwardt, J. Longcore, J. Miądlikowska, A. Miller, J.-M. Moncalvo, S. Mozley-Standridge, F. Oberwinkler, E. Parmasto, V. Reeb, J. D. Rogers, C. Roux, L. Ryvarden, J. P. Sampaio, A. Schüßler, J. Sugiyama, R. G. Thorn, L. Tibell, W. A. Untereiner, C. Walker, Z. Wang, A. Weir, M. Weiß, M. M. White, K. Winka, Y.-J. Yao, and N. Zhang. 2007. A higher-level phylogenetic classification of the Fungi. Mycological Research. 111: 509-547. Hirt, R. P., J. M. Logdon Jr., B. Healey, M. W. Dorey, W.F. Doolittle, and T. M. Embley. 1999. Microsporidia are related to Fungi: evidence from the largest subunit of RNA polymerase II and other proteins. Proceedings of the National Academy of Sciences USA . 96(2): 580-585. James, T. Y., P. M. Letcher, J. E. Longcore, S. E. Mozley-Standridge, D. Porter, M. J. Powell, G. W. Griffith, and R.Vilgalys. 2006a. A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota). Mycologia. 98(6): 860-871. James, Y. T., K. Kauff, C. L. Scoch, P. B. Matheny, V. Hofstetter, C. J. Cox, G. Celio, C. Gueidan1, E. Fraker, J. Miadlikowska1, H. T. Lumbsch, A. Rauhut, V. Reeb, A. E. Arnold, A. Amtoft, J. E. Stajich, K. Hosaka, G.-H. Sung, D. Johnson, B. O’Rourke, M. Crockett, M. Binder, J. M. Curtis, J. C. Slot, Z. Wang, A. W. Wilson, A. Schüßler, J. E. Longcore, K. O’Donnell, S. Mozley-Standridge, D. Porter, P. M. Letcher, M. J. Powell, J. W. Taylor, M. M. White, G. W. Griffith, D. R. Davies, R. A. Humber, J. B. Morton, J. Sugiyama, A. Y. Rossman, J. D. Rogers, D. H. Pfister, D. Hewitt, K. Hansen, S. Hambleton, R. A. Shoemaker, J. Kohlmeyer, B. Volkmann-Kohlmeyer, R. A. Spotts, M. Serdani, P. W. Crous, K. W. Hughes, K. Matsuura, E. Langer, G. Langer, W. A. Untereiner, R. Lücking, B. Büdel, D. M. Geiser, A. Aptroot, P. Diederich, I. Schmitt, M. Schultz, R. Yahr, D. S. Hibbett, F. Lutzoni, D. J. McLaughlin, J. W. Spatafora, and Rytas Vilgalys. 2006b. Restructuring the the early evolution of Fungi using a six gene phylogeny. Nature. 443: 818-822. Keeling, P. J . 2003. Congruent evidence from α-tubulin and β-tubulin gene phylogenies for a zygomycete origin of microsporidia. Fungal Genetics and Biology. 38: 298-309. Keeling, P. J., and W. F. Doolittle. 1996. Alpha-tubulin from early-diverging eukaryotic lineages and the evolution of the tubulin family. Molecular Biology and Evolution 13: 1297-1305. Lutzoni, F. F. Kauff, C.J. Cox, D. McLaughlin, G. Celio, B. Dentinger, M. Padamsee, D. Hibbett, T.Y. James, E. Baloch, M. Grube, V. Reeb, V. Hofstetter, C. Schoch, A.E. Arnold, J. Miadlikowska, J. Spatafora, D. Johnson, S. Hambleton, M. Crockett, R. Shoemaker, G, Sung, R. Lucking, T. Lumbsch, K. O’Donnell, M. Binder, P. Diederich, D. Ertz, C. Gueidan, K. Hansen, R.C. Harris, K. Hosaka, Y.W. Lim, B. Matheny, H Nishida, D. Pfister, J. Rogers, A. Rossman, I. Schmitt, H. Sipman, J. Stone, J. Sugiyama, R, Yahr, R, Vilgalys. 2004. Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. American Journal of Botany. 91(10): 1446-1480. Margulis, L. and K. Schwartz. 1982. Five kingdoms, an illustrated guide to the phyla of life on earth. W.H. Freeman and Co. New York. Margulis, L. and K. Schwartz. 1988. Five kingdoms, an illustrated guide to the phyla of life on earth. 2nd Edition. W.H. Freeman and Co. New York. Margulis, L. and K. Schwartz. 1998. Five kingdoms, an illustrated guide to the phyla of life on earth. 3rd Edition. W. H. Freeman and Company. New York. Moore, R. T. 1980. Taxonomic proposals for the classification of marine yeasts and other yeast-like fungi including the smuts. Botanica Marina. 23: 361–373. Patterson, D. J. 1999. The diversity of eukaryotes. American Naturalist. 154 (Suppl.): S96–S124. Ragan, M.A., C.A. Murphy, and T. G. Rand. 2003. Are Ichthyosporea animals or fungi? Baysean phylogenetic analysis of elongation factor 1α of Ichthyophonus irregularis. Molecular Phylogenetics and Evolution. 29: 550-562. Schüßler, A. D. Schwarzott, and C. Walker. 2001. A new fungal phylum, the Glomeromycota: phylogeny and evolution. Mycological Research. 105(12): 1413-1421. Sokolova, Y. Y., V. V. Dolgikh, E. V. Morzhina, E. S. Nassonova, I. V. Issi, R. S. Terry, J. E. Ironside, J. E. Smith, and C. R. Vossbrinck. 2003. Establishment of the new genus Paranosema based on the ultrastructure and molecular phylogeny of the type species Paranosema grylli Gen. Nov., Comb. Nov. (Sokolova, Selezniov, Dolgikh, Issi 1994), from the cricket Gryllus bimaculatus. Journal of Invertebrate Pathology. 84: 159-172. Tanabe, Y., M. Saikawa, M. M. Watanabe, and J. Sugiyama. 2004. Molecular phylogeny of Zygomycota based on EF-1 and RPB-1 sequences: limitations and utility of alternative markers to rDNA. Molecular Phylogenetics and Evolution. 30:438-449. Tudge, C. 2000. The Variety of Life, A Survey and a Celebration of all the Creatures That Have Ever Lived. Oxford University Press. New York. White, M. M., T. Y. James, K. O’Donnell, M. J. Cafaro, Y. Tanabe, and J. Sugiyama. 2006. Phylogeny of the Zygomycota based on nuclear ribosomal sequence data. Mycologia. 98(6): 872-881. Whittaker, R. H. 1957. The kingdoms of the living world. Ecology. 38(3): 536-538. Whittaker, R. H. 1959. On the broad classification of organisms. The Quarterly Review of Biology. 34(3): 210-226. |
| By Jack R. Holt. Last revised: 03/28/2017 |
