Classification & identification of Fungi

Classification & identification of Fungi

Classification vs. identification

Before going further it is worth pointing out the difference between classification and identification.

Classification answers questions of the sort: How is this fungus related to other fungi?

Identification addresses the more immediate question: What's the name of the specimen in front of me?

Classification therefore deals with evolutionary history and a good classification scheme should group evolutionarily close organisms near one another. This demands a good understanding of many different aspects of fungal structure (both macroscopic and microscopic) and fungal biology, since the different aspects provide different types of evidence regarding relationships. In order to develop a sound classification, all the evidence must be assessed.

The classification hierarchy

There are different degrees of relatedness in the living world and these varying degrees of relatedness lead to the concept of a hierarchy of different levels of classification - kingdom, division (or phylum), class, order, family, genus, species. That sequence goes from broad to fine. That is, a kingdom contains a number of divisions, each division contains a number of classes, each class contains a number of orders and so on.

A species name is a unique combination of two Latin (or pseudo-Latin) words. That combination is called a binomial. When photos on this website are labelled with species names, those names (such as Schizophyllum commune in this instance) <<042>> are examples of binomials. Going back to the earlier pigeonhole analogy, we could say one of our pigeonholes has the label Schizophyllum commune on it.

As noted in the {{ASCOMYCETES AND BASIDIOMYCETES SECTION}} those (macro) fungi can be divided into two groups, depending on whether spores are produced in asci or on basidia. Within the classification hierarchy, fungi that have asci constitute a Division called the Ascomycota and those with basidia constitute a Division called the Basidiomycota. These two technical names are obviously very similar to the ordinary English words ascomycete and basidiomycete. People often talk of "high level" or "low level" classificatory features. The former are used in the definition of higher groupings such as division and class while the latter are used at lower levels - for example, to define genera and species. In these terms asci and basidia are very high level classificatory features.

There are microfungal basidiomycetes and ascomycetes, but they are beyond the scope of this website.

While the (macro) fungi are contained within two divisions of kingdom Eumycota, the full range of organisms (macro and micro) that are likely to be called "fungi" are found in three kingdoms. Many of the features or techniques used in classification are also used routinely in specimen identification and often that is inevitable. For example, luminosity is one of the defining characteristics of the genus Omphalotus, an example of which is shown in the accompanying photos. <<001, 002>> This easily observable classificatory feature is obviously a very useful identification feature as well.

However, classificatory features are not always necessary in day-to-day identification work. For example, DNA analysis is now in widespread use for the investigation of relationships between different organisms. DNA analysis is often in the news because of its use as a forensic tool in criminal investigations. There will be a little bit more about DNA analysis later. For the moment it is enough to know that DNA analysis is a powerful classification tool but it does require specialist equipment and is impractical in much routine identification work. So mycologists often use the more easily observed features for much of the day-to-day identification work.

Classification and identification - final words

Sometimes the evidence from one approach may contradict the evidence from another approach. For example, the old classification (relying on "inkiness" as an important feature) put all the Inkcaps into the genus Coprinus - but DNA analysis says the Inkcaps don't all belong in the one genus - in fact, not even in the one family. What do you do when you get conflicting evidence? Obviously, re-check the methods to see if there have been any mistakes. If not, you can either accept one lot of evidence as more reliable than the other or leave the issue unresolved. Not necessarily a very happy result, but sometimes it's necessary to put a problem aside and wait for future developments to resolve the issue.

In the case of Coprinus, people redid the DNA analysis, using improved techniques, and still came up with the same conclusion. One thing to note is that the DNA evidence didn't come as a great surprise to some mycologists, since there had been considerable debate (over a hundred years) about the correct relationships between the Coprinus species. The DNA results prompted re-examination of the macroscopic and microscopic structures in various Coprinus species.

The DNA evidence indicates that Coprinus comatus and a few other species form a closely related group, so there's a good argument for grouping those species into a genus of their own. Apart from the DNA evidence, the species in this group share some microscopic and macroscopic features that aren't found in other Coprinus species. One macroscopic feature is very easy to see. The stem of Coprinus comatus is pipelike, rather than solid, but the pipe isn't empty. There's a wispy cord, composed of a bundle of hyphae, that runs the length of the hollow centre and has no known purpose. This photo shows a dried specimen of Coprinus comatus, with the stem cut open to reveal the wispy central cord. The cord is present in the other species that the DNA evidence groups with Coprinus comatus - but the cord is absent from those Coprinus species that are not grouped with Coprinus comatus.

At present, the status of the species in Coprinus is being debated and more work is needed before the debate is settled and any new genera agreed to.

However the Coprinus work does show that whenever a specialised technique is used to help classify fungi, it is essential to re-examine other features to see if there is anything that is correlated with the results from the specialised technique. That may not always happen but, in the current example, the cord in the hollow stem is an easily observed feature that is correlated with the genetic evidence. Therefore the cord would be ideal for identification purposes, assuming the Coprinus comatus group is placed in its own genus.

B vitamins

B vitamins are a group of water-soluble vitamins that play important roles in cell metabolism. The B vitamins were once thought to be a single vitamin, referred to as vitamin B (much as people refer to vitamin C). Later research showed that they are chemically distinct vitamins that often coexist in the same foods. In general, supplements containing all eight are referred to as a vitamin B complex. Individual B vitamin supplements are referred to by the specific name of each vitamin (e.g., B₁, B₂, B₃ etc.).

List of B vitamins

·         Vitamin B₁ (thiamine)

·         Vitamin B₂ (riboflavin)

·         Vitamin B₃ (niacin or niacinamide)

·         Vitamin B₅ (pantothenic acid)

·         Vitamin B₆ (pyridoxine, pyridoxal, or pyridoxamine, or pyridoxine hydrochloride)

·         Vitamin B₇ (biotin)(vitamin H)

·         Vitamin B₉ (folic acid)

·         Vitamin B₁₂ (various cobalamins; commonly cyanocobalamin in vitamin supplements)

B vitamin molecular functions Vitamin	Name	Structure	Molecular Function
Vitamin B1	Thiamine		Thiamine plays a central role in the generation of energy from carbohydrates. It is involved in RNA and DNA production, as well as nerve function. Its active form is a coenzyme called Thiamine pyrophosphate (TPP), which takes part in the conversion of pyruvate to acetyl Coenzyme A (CoA) in metabolism.
Vitamin B2	Riboflavin		Riboflavin is involved in the energy production for the electron transport chain, the citric acid cycle, as well as the catabolism of fatty acids (beta oxidation)
Vitamin B3	Niacin		Niacin is composed of two structures: nicotinic acid and nicotinamide. There are two co-enzyme forms of niacin: nicotinamide adenine dinucleotide(NAD) and nicotinamide adenine dinucleotide phosphate (NADP). Both play an important role in energy transfer reactions in the metabolism of glucose, fat and alcohol. NAD carries hydrogens and their electrons during metabolic reactions, including the pathway from the citric acid cycle to the electron transport chain. NADP is a coenzyme in lipid and nucleic acid synthesis
Vitamin B5	Pantothenic acid		Pantothenic acid is involved in the oxidation of fatty acids and carbohydrates. Coenzyme A, which can be synthesised from panothenic acid, is involved in the synthesis of amino acids, fatty acids, ketones, cholesterol, phospholipids, steroid hormones, neurotransmitters (such as acetylcholine) andantibodies.
Vitamin B6	Pyridoxine		Pyridoxine is usually stored in the body as pyridoxal 5'-phosphate (PLP), which is the co-enzyme form of vitamin B6. Pyridoxine is involved in the metabolism of amino acids and lipids; in the synthesis of neurotransmitters  and hemoglobin, as well as in the production of nicotinic acid (vitamin B3). Pyridoxine also plays an important role in gluconeogenesis
Vitamin B7	Biotin		Biotin plays a key role in the metabolism of lipids, proteins and carbohydrates. It is a critical co-enzyme of four carboxylases: acetyl CoA carboxylase, which is involved in the synthesis of fatty acids from acetate; propionyl CoA carboxylase, involved in gluconeogenesis; β-methylcrotonyl Coa carboxylase, involved in the metabolism of leucin; and pyruvate CoA carboxylase, which is involved in the metabolism of energy, amino acids and cholesterol.
Vitamin B9	Folic Acid		Folic acid acts as a co-enzyme in the form of tetrahydrofolate (THF), which is involved in the transfer of single-carbon units in the metabolism of nucleic acids and amino acids. THF is involved in pyrimidine nucleotide synthesis, so is needed for normal cells division, especially during pregnancy and infancy, which are times of rapid growth. Folate also aids in erythropoiesis, the production of red blood cells.
Vitamin B12	Cobalamin		Vitamin B12 is involved in the cellular metabolism of carbohydrates, proteins and lipids. It is essential in the production of blood cells in bone marrow, nerve sheaths and proteins. Vitamin B12 functions as a co-enzyme in intermediary metabolism for the methionine synthase reaction withmethylcobalamin, and the methylmalonyl CoA mutase reaction with adenosylcobalamin

B vitamin deficiency

Several named vitamin deficiency diseases may result from the lack of sufficient B-vitamins. Deficiencies of other B vitamins result in symptoms that are not part of a named deficiency disease.

Vitamin	Name	Deficiency effects
Vitamin B1	thiamine	Deficiency causes beriberi. Symptoms of this disease of the nervous system include weight loss, emotional disturbances, Wernicke's encephalopathy (impaired sensory perception), weakness and pain in the limbs, periods of irregular heartbeat, and edema (swelling of bodily tissues). Heart failure and death may occur in advanced cases. Chronic thiamine deficiency can also cause Korsakoff's syndrome, an irreversible psychosis characterized by amnesia and confabulation.
Vitamin B2	riboflavin	Deficiency causes ariboflavinosis. Symptoms may include cheilosis (cracks in the lips), high sensitivity to sunlight, angular cheilitis, glossitis (inflammation of the tongue),seborrheic dermatitis or pseudo-syphilis (particularly affecting the scrotum or labia majora and the mouth), pharyngitis (sore throat), hyperemia, and edema of thepharyngeal and oral mucosa.
Vitamin B3	niacin	Deficiency, along with a deficiency of tryptophan causes pellagra. Symptoms include aggression, dermatitis, insomnia, weakness, mental confusion, and diarrhea. In advanced cases, pellagra may lead to dementia and death (the 3(+1) Ds: dermatitis, diarrhea, dementia, and death).
Vitamin B5	pantothenic acid	Deficiency can result in acne and paresthesia, although it is uncommon.
Vitamin B6	pyridoxine	Deficiency may lead to microcytic anemia (because pyridoxyl phosphate is the cofactor for heme synthesis), depression, dermatitis, high blood pressure (hypertension), water retention, and elevated levels of homocysteine.
Vitamin B7	biotin	Deficiency does not typically cause symptoms in adults but may lead to impaired growth and neurological disorders in infants. Multiple carboxylase deficiency, an inborn error of metabolism, can lead to biotin deficiency even when dietary biotin intake is normal.
Vitamin B9	folic acid	Deficiency results in a macrocytic anemia, and elevated levels of homocysteine. Deficiency in pregnant women can lead to birth defects. Supplementation is often recommended during pregnancy. Researchers have shown that folic acid might also slow the insidious effects of age on the brain.
Vitamin B12	cobalamin	Deficiency results in a macrocytic anemia, elevated homocysteine, peripheral neuropathy, memory loss and other cognitive deficits. It is most likely to occur among elderly people, as absorption through the gut declines with age; the autoimmune disease pernicious anemia is another common cause. It can also cause symptoms of mania andpsychosis. In rare extreme cases, paralysis can result.

B vitamin side effects

Because water-soluble B vitamins are eliminated in the urine, taking large doses of certain B vitamins may produce transient effects.

Vitamin	Name	Tolerable Upper Intake Level	Harmful effects
Vitamin B1	thiamine	None	No known toxicity from oral intake. There are some reports of anaphylaxis caused by high-dose thiamine injections into the vein or muscle. However, the doses were greater than the quantity humans can physically absorb from oral intake.
Vitamin B2	riboflavin	None	No evidence of toxicity based on limited human and animal studies. The only evidence of adverse effects associated with riboflavin comes from in vitrostudies showing the production of reactive oxygen species (free radicals) when riboflavin was exposed to intense visible and UV light.[14]
Vitamin B3	niacin	35 mg/day from supplements, drugs or fortified food	Intake of 3000 mg/day of nicotinamide and 1500 mg/day of nicotinic acid are associated with nausea, vomiting, and signs and symptoms of liver toxicity. Other effects may include glucose intolerance, and (reversible) ocular effects. Additionally, the nicotinic acid form may cause vasodilatory effects, also known as flushing, including redness of the skin, often accompanied by an itching, tingling, or mild burning sensation, which is also often accompanied by pruritus, headaches, and increased intracranial blood flow, and occasionally accompanied by pain. Medical practitioners prescribe recommended doses up to 2000 mg per day of niacin, usually in time release format, to combat arterial plaque development in cases of high lipid levels.
Vitamin B5	pantothenic acid	None	No known toxicity
Vitamin B6	pyridoxine	100 mg/day from supplements, drugs or fortified food[17]	Intake of more than 1000 mg/day is associated with peripheral sensory neuropathy; other effects are unconfirmed: dermatological lesions [causal association is unlikely]; B6 dependency in newborns [causal association is also unlikely].
Vitamin B7	biotin	None	No known toxicity
Vitamin B9	folic acid	1 mg/day	Masks B12 deficiency, which can lead to permanent neurological damage
Vitamin B12	cyanocobalamin	None established.	Acne-like rash [causality is not conclusively established].

B vitamin sources

B vitamins are found in whole unprocessed foods. Processed carbohydrates such as sugar and white flour tend to have lower B vitamin than their unprocessed counterparts. For this reason, it is required by law in the United States (and many other countries) that the B vitamins thiamine, riboflavin, niacin, and folic acid be added back to white flour after processing. This is sometimes called "Enriched Flour" on food labels. B vitamins are particularly concentrated in meat such as turkey, tuna and liver. Good sources for B vitamins include kombucha, whole grains, potatoes, bananas, lentils, chili peppers, tempeh, beans, nutritional yeast, brewer's yeast, and molasses. Although the yeast used to make beer results in beers being a source of B vitamins,^[22] their bioavailability ranges from poor to negative as drinking ethanol inhibits absorption of thiamine (B₁), riboflavin (B₂), niacin (B₃), biotin (B₇), and folic acid (B₉). In addition, each of the preceding studies further emphasizes that elevated consumption of beer and other ethanol-based drinks results in a net deficit of those B vitamins and the health risks associated with such deficiencies.

The B₁₂ vitamin is of note because it is not available from plant products, making B₁₂ deficiency a legitimate concern for vegans. Manufacturers of plant-based foods will sometimes report B₁₂content, leading to confusion about what sources yield B₁₂. The confusion arises because the standard US Pharmacopeia (USP) method for measuring the B₁₂ content does not measure the B₁₂directly. Instead, it measures a bacterial response to the food. Chemical variants of the B₁₂ vitamin found in plant sources are active for bacteria, but cannot be used by the human body. This same phenomenon can cause significant over-reporting of B₁₂ content in other types of foods as well.

Another popular means of increasing one's vitamin B intake is through the use of dietary supplements. B vitamins are also commonly added to energy drinks, many of which have been marketed with large amounts of B vitamins with claims that this will cause the consumer to "sail through your day without feeling jittery or tense."Some nutritionists have been critical of these claims, pointing out for instance that while B vitamins do "help unlock the energy in foods," most Americans acquire the necessary amounts easily in their diets

Because they are soluble in water, excess B vitamins (such as may be ingested via supplements) are generally readily excreted, although individual absorption, use and metabolism may vary… The elderly and athletes may need to supplement their intake of B₁₂ and other B vitamins due to problems in absorption and increased needs for energy production. In cases of severe deficiency B vitamins, especially B₁₂, may also be delivered by injection to reverse deficiencies. Both type 1 and type 2 diabetics may also be advised to supplement thiamine based on high prevalence of low plasma thiamine concentration and increased thiamine clearance associated with diabetes. Also, Vitamin B₉ (folic acid) deficiency in early embryo development has been linked to neural tube defects. Thus, women planning to become pregnant are usually encouraged to increase daily dietary folic acid intake and/or take a supplement.