Taxonomy of Life
Humans have too often fancied themselves to be the centre of Creation. As in so many other examples of such hubris in the past, the idea could not last. The Creator has bestowed upon us a more humbling place in the scheme of things. Just as Earth is not the centre of the Universe, mankind is not the central branch on the Tree of Life.
D. Andrew White M.Sc. 04/04/2009
Phylogeny is nowadays generally interpreted as the science of determining the evolutionary relatedness of organisms. Taxonomy was the science of discovering the order in the great scheme of biological Creation. Traditionally taxonomy was based mostly on the visible morphologies, anatomies and histologies of creatures. Nowadays the genetic comparison of organisms is considered to be more significant than the comparison of visible features. Genetics also has shown that visible similarity is not a perfect guide to relatedness. Nevertheless, these genetic comparisons suggest that all earthly creatures are related through common descent.
Where do plants and animals figure, genetically, in relationship to other living things? At one time this question was wide open. Since the 1990s, the question has been answered to a large extent. The DNA sequences of many organisms have been decoded and compared. The experimental results suggest that plants and animals are genetically similar to protozoa, but they are as one tiny twig on the Tree of Life. Furthermore, animals, plants, fungi and protozoa are not single entities, they are composites (Collins & Jegalian 1999, Doolittle 2000 ).
From the time of Carl von Linné, in the 1730s, biologists have tended to classify all life into two taxonomic ‘Kingdoms’: Plantae (plants) and Animalia (animals). This scheme crammed most bacteria, yeasts, fungi, lichen, seaweed and green plants into the Plantae Kingdom. The animals, and certain motile protozoa, were all shoehorned into the Animalia Kingdom. In the 1870s Ernst Haeckel added another kingdom, the ‘Protista’ - the microbe group. Even by the turn of the last century most taxonomists still crammed everything non-animal into the Plantae. These assumptions did not survive the century. Herbert F. Copeland suggested that the monera and protozoa be separated. Many taxonomists left the fungi in the Plantae Kingdom. But Copeland thought of the fungi as advanced protoctista. By the 1970s there were five recognised taxonomic Kingdoms. Basically, fungi were recognised as a kingdom. This system was developed by R.H. Whittaker in the 1950s. Even this did not last. Thomas Cavalier-Smith suggested that most algae were distinct enough to warrant being called the Kingdom Chromista (‘coloured ones’). Eventually, the Monera had proven to be too diverse to be seriously considered one single kingdom.
Carl Woese during the 1980s suggested that there were at least three ‘kingdoms’, or perhaps there were tens of them. Woese planted the seed of the idea that the Kingdom (Regnum) taxon should be retired. He proposed a more encompassing scheme grouping all kingdoms into three ‘Domains’. After 2003, there were suspicions that the viruses are also a separate domain. Although, most taxonomists still include viruses with the bacteria. Nowadays the number of Kingdoms is again uncertain.
Modern taxonomy is arranged somewhat as in the table below:
| DOMAIN | KINGDOM: Sub-Kingdom, {Super-Group} | Phylum or Super-Phylum |
| VIRUS: | Mimivirus Virus, Viroids |
|
BACTERIA:  |
Eubacteria |
Acidobacteria (Acidobacteria, Solibacter etc.)
Actinobacteria (Mycobacterium, Streptomyces, Bifidobacterium etc.) Aquificae (Aquifex) Bacteroidetes (Bacteroidetes, Flavobacteria, Sphingobacteria etc.) Chlamydiae (Chlamydia, Chlamydophila etc.) Chlorobi (Chlorobium) Chloroflexi (Dehalococcoidetes) Cyanobacteria (Anabaena, Gloeobacter, Nostoc, Prochlorococcus etc.) Chloroplast (endosymbiont) Deinococcus-Thermus (Deinococcus, Thermus) Firmicutes (Bacillus, Listeria, Staphylococcus, Clostridium, Streptococcus, Mycoplasma, etc.) Fusobacteria (Fusobacterium) Planctomycetes (Rhodopirellula) Proteobacteria (Nitrobacter, Brucella, Agrobacterium, Magnetospirillum, Rickettsia, Wolbachia, Novosphingobium, Bdellovibrio, Myxococcus, Anaeromyxobacter, Candidatus, Phytoplasma, Escherichia, Erwinia, Salmonella, Legionella, Yersinia, Pseudomonas, Chromohalobacter, Rhodospirillium, Chromatium, Photobacterium, Vibrio, Xylella etc.) Mitochondria (endosymbiont) Spirochaetes (Leptospira, Borrelia, Treponema) Thermotogae (Thermotoga) |
| . | ||
| ARCHAEA: | Archaebacteria | Euryarchaeota (halobacters & methanobacters) Koryarchaeota (Thermococcus) Nanoarchaeota (symbionts of archaes) |
| Eocyta | Crenarchaeota (thermobacters) | |
| . | ||
| PROTOZOA: Archaezoa {Excavata} |
Diplomona (giardia) Parabasalida (trichomonas) |
|
| Discicristata {Excavata} | Euglenozoa (euglenoids) Heterolobosea (amoeboflagellates) Acrasiomycota (cellular slime moulds) | |
| Bikonta {Rhizaria} | Foraminifera (foraminifers) Radiolaria (radiolarians) Rhizopoda (amoebae) |
|
| Amoebozoa {Amoebozoa} | Naegleria (flagellated amoebae) Entamoeba (parasitic amoebae) Myxogastria (plasmoidial slime moulds) Protoselidia (protostelid slime moulds) Dictyosteliomycota (dictyostelid slime moulds) |
|
| Alveoles {Chromalveolata} | Ciliophora (ciliates) Apicomplexa (plasmoidia) Dinophyta (dinoflagellate algae) |
|
| Chromista outliers {Chromalveolata} | Telonemia (flagellate protists) Haptista (haptophytes) Cryptophyta (nucleomorph flagellates) |
|
EUCARYA  |
CHROMISTA: Stramenophiles {Chromalveolata} |
Ochrophyta (synurophytes) Phaeophyta (brown seaweed) Bacillariophyta (diatoms) Xanthophyta (yellow algae) Chrysophyta (golden algae) Sagenista (bicoecea unicells) Hyphochytridiomycota (water fungoids) Labyrinthula (slime nets) Oomycota (water moulds) |
| PLANTAE: {Archaeplastida} red seaweed & plants |
Glaucophyta (syncyanotic algae) Rhodophyta (red seaweed) Chloroplastida (green algae & plants) |
|
| ANIMALIA: {Opisthokonta} zooids |
Animalia (metazoa & animals) Choanoflagellida (choanoflagellates) Mesomycetozoea (Amoebidium spp.) |
|
| FUNGI: {Opisthokonta} fungoids |
Fungi (moulds & toadstools) Microsporida (nosema) Discocristea (nucleariid amoebae) |
References
Adl, Sina M. et al. 2005. The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists. Journal of Eukaryotic Microbiology. 52(5): 399-451.
Bhattacharya, D. and Medlin, L.K. 2004. Dating Algal Origin Using Molecular Clock Methods. Protist. 155: 9-10.
Cavalier-Smith, Thomas. 2004. Only six kingdoms of life. Proceedings of the Royal Society, London. (B): 1251-1262.
Collins, Francis S. and Jegalian, Karin G. 1999. Deciphering the code of life. Scientific American. 281 (6): 86-91.
Doolittle, W. Ford. 2000. Uprooting the Tree of Life. Scientific American. 282, (2): 90-97.
Lee, Robert Edward. 1999. Phycology. 3rd Edition. Cambridge University Press. Cambridge.
Margulis, Lynn and Schwartz, Karlene V. 1982. Five Kingdoms - an illustrated guide to the phyla of life on Earth. 2nd Edition. W.H. Freeman and Company. New York.
Tudge, Colin. 2000. The Variety of Life. Oxford University Press. Oxford.
Truffles & Tuckahoes
Truffles are fungi that form their fruiting bodies underground. The spores remain in the ‘toadstool’ until disseminated by animals. Several fungi of the genus Tuber are sought as food items in the forested regions of southern Europe. Dogs can be trained to detect truffles by smell. However, the detection of the truffle odour comes quite naturally to pigs. Traditionally pigs were, and still sometimes are, used in truffle hunting (Del Conte & Læssøe 2008).
(1) Tartufo d'Alba: White truffle (Tuber magnatum) is one example of a highly prized underground mushroom. It is smooth, soft, marbled, and it tastes both spicy and mushroomy. Only a tiny amount is sufficient to flavour food. It grows mostly in calcareous soil, mostly in the Piedmont region of Italy. It is mostly mycorrhizal on beech and oak roots.
(2) Perigord truffle: Perigord truffle (Tuber melanosporum) has a dark scaly exterior and marbled interior. It is found throughout the southern Mediterranean area, mostly in reddish pedalfer soils. It grows mostly near oak roots.
(3) Pine truffles:. Truffles do occur in the Americas. The Oragon truffle (Tuber gibbosum) is delicious like its Old World counterpart. In grows mostly under Douglas fir. The west coast pine truffle (Geopora cooperi) is also very similar to a truffle. Pine truffles are eaten by squirels (Loeb et al 2000).
(4) Deer truffles: Various truffle-like fungi are fairly common in eastern North America. The genera Elaphomyces, Gymnomyces and Rhizopogon all produce truffle-like bodies. Some truffle-like fungi are edible, others are tough in texture, and yet others engulf the sand in which they grow. Deer truffles are not only eaten by deer, they are also eaten by squirrels (Loeb et al 2000). These animals find the fruiting bodies by their distinctive odour.
(5) Pseudo-truffles: Basidiomycete false-truffles do occur. The conifer forest false truffles (Truncocolumella spp.) are a club fungi. The bolete false-truffles (Gastroboletus spp.) produce bolete-like mushrooms which do not usually break through the leaf litter. Many false truffles appear to be derived from above ground toadstools. They are structured very much like toadstools with an ‘aborted’ forms. They remain in the budding stage without opening their caps. Most of these basidiomycete false-truffles are more common in the western conifer forests.
(6) Tuckahoes: Some false-truffles form an underground sclerotium. A sclerotium is a means by which a fungus survives drought or winter. It is not a fruiting body, the actual toadstool is aboveground. The commonest tuckahoe (Wolfiporia cocos) looks very much like a truffle. It can be as large as a coconut. These tuckahoes were eaten by the Algonquins and other Amerindian peoples. Another tuckahoe species (Polyporus tuberaster) is similar, but its aboveground toadstool is more often found. Its sclerotium tends to be sandy and is semi-edible at best. The Australian version of the tuckahoe (Laccocephalum mylittae), once called Mylitta australis, is very similar. This fungus was also once used as a food source. Hypogeous sclerotia are fairly common in dry environments, such as the American prairies and the Australian outback.
References
Del Conte, Anna and Læssøe, Thomas. 2008. The Edible Mushroom Book. DK Publishing. New York.
Loeb, S.C., Tainter, F.H. and Cazares, E. 2000. Habitat associations of hypogeous fungi in the southern appalachians: Implications for the endangered northern flying squirrel (Glaucomys sabrinus coloratus). America Midland Naturalist. 144(2):286-296.
Thomas, William S. 2003. Field Guide to Mushrooms. Sterling Publishing Co., Inc. New York.
Bioluminescent Fungi
There is a catch-all rural American term for weird glowing spots in in the wilderness: “foxfire”. Foxfire is sometimes just will-o’-the-wisp, or natural flames of burning methane (swamp gas). Other times the spooky lights are caused by bioluminescent organisms. Many organisms can produce visible light. Firefly beetles, many algae, and a host of fungi can glow in the dark.
Masses of the honey mushroom’s mycelium can glow eerily on dark nights. Mostly this mycelial mat is hidden under bark, but on occasion it is noticeable. Jack-o’-lantern toadstools also can glow in the dark. In this case, a whole group of fungal fruiting bodies may be seen glowing feebly on dark nights. In both cases, the chemical reaction radiates a bluish-green light. The glow is ‘cool’, except perhaps at a micro-molecular level. Of course, immobile glowing fungi cannot explain all will-o’-the-wisp sightings. Some spook lights move, and hence must have another explanation.
The adaptive function of fungal bioluminescence is not fully known. It is most common in wood rotting fungi. In many cases bioluminescence seems to be a side effect of oxygen respiration. The light producing enzymatic reactions are also involved in the creation of metabolic water. In some species, the glowing tissues may attract insects, which help to disperse the spores. In actual fact, even though the biochemical process is fairly well understood, its full biological role is still an enigma.
I remember my first encounter with luminous fungi, probably a soil Mycena. When I was a child I found a glowing patch in the grass. At the time I tried to convince myself that it was a glowworm. However, when I went to grab it, I fetched up an off-centre glowing segmented structure. Apparently, these segments were the gills of the toadstool!
Endophytic Fungi
Endophytic fungi are a group of fungi which live asymptomatically inside plant tissues. These fungi were first noticed in the 1940s, but only at the turn of the 21st century was the ubiquity of these fungi fully recognised. They live like fungi imperfecti, much of the time, producing mostly conidial spores or simply cloning themselves. They are between benign parasites and true symbionts in their behaviour. Although, many endophytic fungi become rotting agents upon the death of their host plant. Sometimes they may produce toxins in response to pests which feed on their host’s tissues. These toxins benefit the host plant. For example, there are endophytes which make grass poisonous to grazing animals. Other endophytes, in oak leaves, ward off gall midges. In the sense that these ‘endophytes’ can protect their host, they are symbionts. Endophytes are low-key examples of symbiosis (Heinrich 1997, Schardl et al 1997, Meijer & Leuchtmann 1999).
Endophytes belong to several fungal taxonomic groups, but most are ascomycetes. Many of the needle cast fungi (e.g. Phomopsis spp. & Lophoderma spp.), have endophytic relatives. Even some of the leaf spot diseases (e.g. Rhytisma spp.) have endophytic relations. Most of the endophytes which infect pines are members of the Rhytismataceae family. Since there are rhytismataceous parasites, mycologist have wondered if endophytes are not just the old familiar parasites in dormancy mode. Genetic studies show that the rhytismataceous endophytes are not the same as their pathogenic cousins. They are members of the same genera, but they are not identical species (Ganley et al 2004). Endophyticity seems to be a niche different from parasitism. Possibly this mode of life developed from true parasitism.
In theory parasites can evolve to become ever more benign to their host. If a parasite does not harm its host, it has a more secure food supply than if it weakens the host. Severe plant diseases may often be due to parasites in novel hosts. Novel hosts may lack resistance to the ‘new’ parasite. In the long run, both host and parasite may co-evolve into an asymptomatic relationship. Probably a fungus would evolve quicker than a long-lived tree. Highly virulent strains of a parasite would have an initial advantage in its new frontier. The advantage would become a detriment after the contagion’s food supply is consumed. Natural selection would then favour the less virulent strains of the parasite. This co-evolution seems to have happened in many cases. Dutch elm disease (Ceratocystis novo-ulmi) was relatively benign in Asian elms. But when it reached Europe and the Americas, it encountered hosts which were not equipped to deal with the fungus. Similarly, the potato blight (Phytophthora infestans) is relatively harmless to the potatoes of the Andes. When potatoes were cultivated in Europe they lost their tolerance of the fungoid. When the fungoid was introduced to Ireland in the 1840s, the results were devastating. There are many other examples of diseases which only become problems for host species which have not co-evolved mutual tolerance.
An Example of an Endophytic Fungus
Matthew 13:24-25.
‘Tares’ is an old name for the darnel ryegrass (Lolium temulentum) of Eurasia and North Africa. It is widely considered a weed, even being despised as a source of fodder. This little divertimento into agronomy does relate to mycology somehow – bear with me.
Darnel ryegrass, or tares, was a scourge of cereal farmers and haymakers alike. In the olden days wheat, and other cereals, were often contaminated by the seeds of wild grasses. Darnel contaminants often made wheat flour both poisonous and distasteful. Cattle sometimes became ill from too much darnel in their hay. In sheep it could cause staggers disease. Tares seldom infest hay and cereal crops nowadays. Seed-corn is cleaner now than it was in yesteryear. This is why the word ‘tares’ is not so familiar to twenty-first century folks.
Darnel gets its toxicity from temuline, an alkaloid. This poison is produced by an endophytic fungus (teleomorph: Gloeotinia temulenta). In darnel ryegrass, the fungus occurs mostly in its asexual form (anamorph: Endoconidium temulentum). However, the fungus does produce sexual ascomata when it grows on other species of ryegrass. In these other hosts it causes the blind seed disease, or seed abortion. In effect, outside of its native host this endophytic fungus becomes a pathogenic fungus.
References
Coder, Kim D. 2004. Foxfire - secret lights in the chipper box. I.S.A. Arborist News. 13 (5): 5-8.
Corliss, William R. 1983. Hand Book of Unusual Natural Phenomena. Anchor Press. Garden City New York.
Ganley, Rebecca J., Brunsfeld, Steven J. and Newcombe, George. 2004. A community of unknown, endophytic fungi in western white pine. PNAS, July 6, 101 ( 27):| 10107-10112
Heinrich, Bernd. 1997. The Trees of My forest. Cliff Street Books. New York.
Holliday, Paul. 1989. A Dictionary of Plant Pathology. Cambridge University Press. Cambridge.
Lee, Robert Edward. 1999. Phycology. 3rd Edition. Cambridge University Press. Cambridge.
McLoughlin, Stephan and Vajda, Vivi. 2005. Ancient wollemi pines resurgent. American Scientist. 93 (6): 540-547.
Meijer, G. and Leuchtmann, A. 1999. Multistrain infections of the grass Brachypodium sylvaticum by its fungal endophyte Epichloë sylvatica. New Phytologist, 141: 355-368.
Schardl, C. L., Leuchtmann, A., Chung, K.-R., Penny, D., and Siegel, M. R. 1997. Coevolution by common descent of fungal symbionts (Epichloë spp.) and grass hosts. Molecular Biology and Evolution. 14: 133-143.
Schwarze, F.W.M.R., Engels, J. and Mattheck, C. 2004. Fungal Strategies of Wood Decay in Trees. Springer. Berlin.