Notes on Microbial Taxonomy: Major Characteristics and Principles

The below mentioned article provides a note on the microbial taxonomy. Learn about the major characteristics used in microbial taxonomy and principles of microbial taxonomy.

Notes on Taxonomy:

The classification of microorganisms is a complex and often perplexing enterprise. Our systems of classification are imposed upon the natural variety of microorganisms to serve our particular needs, and older systems of classification are abandoned if they cease to serve us well.

Diverse criteria may be used to classify microorganisms- Morphology, means of propagation and sexual cycle, physiology, genetic or evolutionary relation-ship habitat, or more pragmatic criteria such as industrial, agricultural or medical importance. In practice, classification is based on several criteria, and the Sting system, while useful, lacks clarity and uniformity.

A system of numerical taxonomy may be based on similarity matrices or it may be based on the ratio of the bases guanine + cytosine/adenine + thymine (% GC) as a percentage of total DNA bases of the microorganism. For instance for several genera of enterobacteria the % GC is between 50 and 60%, while for Staphylococcus it is between 30 and 40% and for Lacto- bacillus between 40 and 50%.

A basic distinction may be made between prokaryotic and eukaryotic cells Eukaryotic cells are distinguished, as the name implies, by a distinct nucleus which is surrounded by a membrane. Nuclear DNA is associated with proteins and is present in definite structures; the chromosomes, Eu­karyotic cells contain other structures such as mitochondria which are the loci of energy-producing metabolism. Photosynthetic eukaryotes contain separate chloroplasts which produce energy from sunlight. All eukaryotes require oxygen. During cell division, meiosis permits the transmission of genetic material to daughter cells.

In contrast, prokaryotes lack a well-defined nucleus. The genetic material in the form of double stranded DNA is attached to the plasma membrane but is not separated from the cell content by its own membrane. Mito­chondria chondria are absent and the enzymes required for energy metabolism are distributed throughout the plasma.

Photosynthesis where it occurs is also based on photosynthetic molecules associated with membranes. Prokaryotes may be obligate anaerobes, facultative anaerobes, or fully aerobic organisms. In many instances facultative anaerobes grow best in the pres­ence of an atmosphere containing less than 20% oxygen.

Bacteria and the blue-green algae (Cyanobacteria) are prokaryotes Fungi (including yeasts), algae, protists, and all plants and animals have eukaryotic cells. The above description indicates that prokaryotes are more primitive organisms and that their evolutionary development preceded that of the eukaryotes. It is thought that aerobic bacteria developed about 3.5 billion years ago in the anoxic atmosphere of the earth.

Cyano­bacteria, which are largely responsible for the development of oxygen in the – atmosphere by aerobic photosynthesis, may have appeared about 2 billion years ago. Eukaryotes, which depend on the presence of oxygen in the atmosphere, developed about 1 to 1.5 billion years ago. The evolutionary development of microorganisms has been described in a most lucid manner by schopf (1978).

The following brief outline places some of the more important microbes into appropriate taxa. It is not meant as a description of the various sub­divisions of microbes, nor is it in any sense complete. However, it may aid the reader m realizing taxonomic relationships, and it may serve as an aid to memory.

For a comprehensive and authoritative treatment of the subject of tax- anomy the reader is referred to the following – Sneath (1957); Sokal and Sneath (1963); Thimann (1963); Hawker (1966); Lodder (1970); Moore Landecker (1972); Mandelstam and McQuillan (1973); Colwell (1973); Las- kinand Lechevalier (1973) Breed et al (1957); Buchanan and Gibbons (1974); and Beuchat (1978).

Phycomycotina:

Phycomycetes are a diverse group of lower, filamentous fungi. Most species are aquatic and have motile cells. However, the group of greatest industrial interest, the pin molds or bread molds (Zygomycetes), is terrestrial and has non-motile zygospores. These include the genera Rhizopua and Mucor.

Rhizopus arrhizae is one of the molds responsible for tempe fermen­tations. R. stolonifer is known as the black bread mold. Mucor pusillus and Mmiehei are used for the production of microbial rennets, and M, miehei is flavors production of an esterase which forms desirable cheese flavors.

Ascomycotina:

The ascomycetes are characterized by a special sac-like structure (ascus) which contains the spores (ascospores). These are sexual spores resulting from the fusion of 2 nuclei followed by meiosis. The haploid ascospores, often 8 per ascus, contain 1 or several haploid nuclei. On germination, these spores develop into the typical, vegetative filaments which are called hyphae or mycelia. If the vegetative cells occur principally as single cells, they are generally designated as yeasts.

This is a very large class of microorganisms which includes many soil microbes, among them Chaetomium, a wood rotting fungus whose species are excellent producers of cellulases. lt includes fungi living in plants or animals and in fresh and salt water. Many of these fungi are well known plant pathogens or food spoilage organisms responsible for the powdery mildew of fruits or the soft rot of vegetables. The red bread mold, Neurospora sitophila, is well known. Endothia parasitica is a commercial source of microbial rennet. The true morel mushroom, Morchella esculenta, belongs to the Ascomycotina.

Basidiomycotina:

The basidiomycetes are the most highly evolved group of fungi. They are characterized by the fact that spores (basidiospores) are borne externally on a basidium. The latter is a structure in which nuclear fusion and reductive division occurs and which bears the externally located spores. This large group of organisms includes the mushrooms, puffballs, bracket fungi, rusts, smuts, jelly fungi, stinkhorns, and others.

The cultivated mushroom, Agaricus bisporus, carries 2 spores on the basidium, in contrast to the wild .species, A. campestris, which carries 4 spores. Another mushroom, Lentinus edodes, is grown commercially in Japan on wooden logs. This “shiitake” mushroom has been one of the earli­est sources of 5′-nucleotides.

Deuteromycotina:

This subdivision of the fungi contains all organisms for which a true sexual stage (perfect stage) does not exist or has not been recognized. These Deuteromycetes or Fungi Imperfecti is difficult to classify and probably lack any common phylogenetic origin. Many of them have counterparts in the Ascomycetes. For instance, the red bread mold, Neurospora sitophila, (see under Ascomycotina), is known in its imperfect state as Manilla sito­phila.

The genus Aspergillus is widely used for the production of organic acids and enzymes. It is a major contributor in the ripening of Oriental foods. A. oryzae, A. niger, and A. awamori are widely used species.

The genus Penicillium, which is used for the production of antibiotics, is also used for the production of organic acids. P. roqueforti and P. camemberti are used for the production of mold ripened cheeses. A species of Botrytis, B. cinerea, is responsible for the noble rot of grapes.

Yeasts:

Yeasts are fungi which exist generally in the form of single cells and which reproduce by budding or by fission. Yeasts which form ascospores or basidiospores are properly classified with the sporogenous fungi, and asporogenous yeasts should be classified with the Fungi Imperfecti. It must be understood that grouping of these organisms as “yeasts” cuts across the classification of fungi which has been outlined above.

Some examples of ascomycetous and asporogenous yeasts follow.

Ascomycetous Yeasts:

Species of Saccharomyces are used widely for the leavening of baked goods, and for the production of wine, beer, and distilled beverages. In all of these commercial processes S. cerevisiae is used, with the exception of lager beer (S. uvarum), some sourdoughs (S. exiguus), and some wine fermentations (S. uvarum, S. fermentati).

Kluyveromyces species are used for the production of alcohol from dairy products (K. fragilis). The following genera are present in much “natural” wine fermentation- Han­senula, Pichia, Dekkera, Saccharomycodes and Schizosaccharomyces. Saccharomycopsis fibuligera is used in the saccharification of starch.

Asporogenous Yeasts:

Candida utilis is used for the production of inac­tive dry yeast for food and feed. C. lipolytica and C. tropicalis are used for the same purpose. A Brettanomyces is used in the production of Belgian Iambic beer. Species of Kloeckera and Metschnikowia occur in spontaneous wine fermentations.

This short enumeration gives some idea of the diversity of industrially useful yeasts.

Chemoautotrophic Bacteria:

These organisms are called chemoautotrophic because of their ability to grow by oxidation of inorganic compounds. One of the groups, the hydrogen bacteria, can oxidize hydrogen. 0₂ is the terminal electron acceptor. But the hydrogen bacteria are quite versatile in utilizing various carbon com­pounds, and show great similarity to heterotrophic organisms with similar nutritional requirements or capabilities.

Other groups of chemoautotrophic bacteria are the thiobacilli, which oxidize reduced sulfur compounds, and the nitrifying bacteria, which oxi­dize NH₃ or NO₂^-2.

Phototrophic Bacteria:

These purple, green, or brown bacteria carry out anaerobic photosynthe­sis, that is, without the formation of oxygen. This is in contrast to the Cyanobacteria, the algae, and the higher green plants, which produce oxy­gen during photosynthesis. The photosynthetic pigments are bacterio-chlorophylls. All of them can fix molecular nitrogen.

Cyanobacteria:

These important microorganisms have previously been included in the algae (blue-green algae or Cyanophyta), but they are prokaryotes which lack a nucleus. Their photosynthetic ability is based on the presence of chlorophyll a and phycobiliproteins. However, these are not present in a chloroplast but adhere to 2 membranes in the cell. The Cyanobacteria produce oxygen during photosynthesis, an ability they share with the algae and higher green plants. This clearly distinguishes them from the photo- trophic bacteria.

Bacteria:

The cells of these non-filamentous and non-photosynthetic organisms are relatively simple and quite small. Cocci have a diameter of about 0.5 to 1 μ; rods rarely exceed 1 μ. in width but may attain a length of up to 20 μ. They are generally classified on the basis of their shape with subdivisions based on other morphological characteristics, on aerobic or anaerobic growth, on retention of the Gram stain, on physiological reactions, or on other criteria. Therefore, it is not surprising that schemes of classification by taxonomists differ appreciably depending on the weight given to one or other criteria used in classification.

Bacteria divide by fission, and some bacteria may produce asexual spores. These are formed within the bacterial cell (endospores), and they show greater resistance to heating than the bacterial cells. Cells shapes are distinguished as spherical (cocci), as rod-shaped (bacilli) or as curved rods. The cocci may be divided into diplococci (2 adhering cells), streptococci (a straight chain of cells), staphylococci (a sheet of cells), or sarcina (a three- dimensional arrangement or packet of cells).

The rods are divided into non-sporeforming rods, which include both Gram-positive and Gram-negative forms, and the sporeforming rods (bacil­lus). The sporeforming rods may be further divided into the aerobic genus Bacillus and the anaerobic genus Clostridium.

Curved rods are Gram-negative. They may be divided into those with a simple curved shape, the genus Vibrio, and those with a screw-shaped rod, the genus Spirillum.

Actinomycetes:

These bacteria form mycelia. In contrast to fungal mycelia, the broadest filaments are quite thin with a diameter of less than 0.5 μ. The soil or oxidative forms include the genera Streptomyces, Nocarcdia, and Mycobacte­rium. The parasitic or fermentative forms include the genus Actinomyces proper.

Lactic Acid Bacteria:

The trivial name “lactic acid bacteria” describes a number of bacteria both cocci and rods, which are characterized by the production of lactic acid by fermentation of carbohydrates. They warrant special consideration because of their great importance in food fermentations.

Apart from their well-known use in the fermentation of dairy products (cheese, buttermilk, yoghurt, sour cream) they form the basis of the fermentation of sauerkraut fermented pickles, fermented sausage, sourdough bread, and soda crackers as well as the malo-lactic fermentation of wines.

Homofermentative species produce lactic acid principally, while heterofermentative species produce lactic acid, ethanol, acetic acid, glycerol, mannitol, and CO₂ anaerobically from fermentable carbohydrates.

Algae:

These photosynthetic organisms resemble green plants, but they lack roots, stems, and leaves. They may be unicellular organisms or the cells may form branched or un-branched filaments. Algae are eukaryotes with a well-defined nucleus. In contrast to photosynthetic bacteria, photosynthesis is localized in specific bodies, the chromatophores. Most algae multiply vegetatively or asexually by spore formation. But sexual reproduction is fairly frequent in grass-green, brown and red algae. It is rare in yellow- green and golden-brown algae.

Most marine algae are of macroscopic size. Some are used as food, for instance- Porphyra, which is consumed in the Orient. Gelidium is used for the extraction of agar, Chondrus cryptus (Irish moss) is the source of carrageenin, and the giant kelp of the Pacific coast of North America, Macrocystis pyrifera, is the source of alginates.

Some freshwater algae are of particular interest for the production of biomass (and single cell protein). These belong to the group Chlorophyta, green algae whose food reserve is starchy. Examples are the unicellular genus Chlorella and the genus Scenedesmus, which grows in non-filamentous colonies. Spirulina, which is of equal interest, is a “blue green alga”; i.e., it belongs to the Cyanobacteria.