Classification of microorganisms

Systems of classification

1.- Artificial system: Morphological characters like habita, number os stamens, among others are considered to classify organisms., e.g.: Linnaean system.

2.- Natural system: Considers natural relationships to classify organisms., e.g.: George Bentham and Joseph Dalton Hooker's system.

3.- Phylogenetic system: Evolutionary relationships ate taken into account to classify organisms., e.g.: Engler and Prantl's system.

Recently classification of organisms is done based on:

a) Type of cell structure: prokaryotic or eukaryotic.

b) Complexity of organism's body: unicellular or muticellular.

c) Mode of nutrition: autotrophs or heterotrophs.

d) Major ecological role: producer, consumer or decomposer.

e) Phylogenetic relationship: evolutionary relationship, simple or complex.

Over 1.5 million different organisms have been identified to date, this living organisms share many similarities:

Made up of cells surrounded by a plasma membrane.
Use ATP as energy source
Store genetic information as DNA
Ribosomes are the site of protein synthesis

These differences and similarities among organisms are caused by natural selection (Darwin, 1858). Organisms can be classified into taxonomic categories (taxa), based on the difference and similarities among them. The ancient Greeks classified all living organisms into two groups: Kingdom Plantae and Kingdom Animalia. In 1850s bacteria and fungi were incorrectly placed in the Plant Kingdom. In 1860s Kingdom Protista was proposed to include bacteria, fungi, algae and protozoa, but many scientists still classified bacteria and fungi as plants. This disagreement about classification of bacteria and fungi persisted over 100 years.

In 1930s electron microscopy made it clear that bacterial cells lacked a nucleus. The term procaryote was introduced in 1937, by 1959 Kingdom Fungi was established and two years after (1961) the current definition of procaryote was established. In 1968 the Kingdom Procaryotae was accepted by biologist.

In 1969 Robert Whittaker proposed a five kingdom system of biological classification for all living organisms. These five kingdowms were named Monera, Protista, Fungi, Plantae and Animalia. The main criteria for classification used by him include cell structure, thallus organisation, mode of nutrition and phylogenetic relationships. The next table show us the comparative account of different characteristics of the 5 Kingdoms.

Whittaker's Five Kingdoms

Kingdom Monera

Bacteria are the sole member in this kingdom. They are the most abundant microorganisms. Hundreds of bacteria are present in a handful of soil, they also live in extreme habitats such as deserts, snow and deep oceans. They have a procaryotic structure and their mode of nutrition is autotrophic (photosynthetic or chemosynthetic) or heterotrophic (saprophytic or parasitic). The mayor groups of Kingdom Monera are described below.

Archeabacteria: they live in extreme salty areas (halophiles), hot springs (thermoacidophiles) and marshy areas (methanogens). These bacterias differ form others in having a different cell wall estructure and this feature is responsible for their survival in extreme conditions. E.g.: Halobacterium, Thermoplasma and Methanobacterium.

Eubacteria: They are characterized by the presence of a rigid cell wall, and if motile, a flagellum.

Cyanobacteria (blue-green algae) are photosynthetic autotrophs, unicelluar, colonial or filamentous freshwater/marine or terrestrial algae, some of this organisms can fix atmospheric nitrogen. E.g.: Nostoc and Anabaena.
Chemosynthetic autotrophic bacteria oxidase inorganic substances such as nitrates, nitrites and ammonia and use the released energy for their ATP production. The play a great role in recyclying nutrients like nitrogen and phosphorous.
Heterotrophic bacteria are the most abundant in nature. the majority are important decomposers. They are helpful in making curd from milk or production of antibiotics. Some are pathogens causing damage in humans, crops, farm animals and pets. E.g: Escherichia coli, Salmonella typhi, Vibrio cholerae.
Mycoplasma are organisms that completely lack a cell wall. Many mycoplasma are pathogenic in animals and plants.

Kingdom Protista

These are unicellular eukaryotes. some are photosynthetic and others are non-photosynthetic. Some possess cilia or flagella. They reproduce asexually and sexually. Members of Protista are primarily aquatic. This kingdom forms a link with others dealing with living plants, animals and fungi.

Chrysophytes: Includes diatoms and golden algae (desmids). They are microscopic and float passively in water currents (plankton). Most of them are photosynthetic. E.g.: Pinnularia, Navicula, Cytotella.

Dinoflagellates: These organisms are mostly marine and photosynthetic. They appear yellow, green, brown, blue or red depending on the main pigments present in their cells. Most of them has two flagella. E.g.: Gonyaulax, Noctiluca.

Euglenoids: The majority are fresh water organisms found in stagnant water. Instead of a cell wall, they have a protein called pellicle which makes theri body flexible. They act as photosynthetic in the presence of sunlight, but as heterotrophs in absence of it. E.g.: Euglena, Paranema

Slime moulds: These are saprophytics organisms. The body moves along decaying twigs and leaves engulfing organic material. They form aggregations called plasmodium which grow and spread over several feet. During unfavorable conditions, the plasmodium forms fruiting bodies bearing spores at their tips. E.g: Stemonitis, Physarum

Protozoa: All protozoos are heterotophs and live as predators or parasites. There are four major groups of protozoos.

Ameboid protozoos: These organisms live in fresh water, sea water or moist soil. They move and capture their prey by putting out pseudopodia as in Amoeba.
Flagellated protozoos: These organisms are either free-living or parasitic. They have flagella. E.g: Trypanosoma cruzi, Giardia lamblia.
Ciliated protozoos: These are aquatic, actively moving organisms because of the presence of thousands of cilia. Eg: Paramecium
Sporozoos: This includes those that have an infectious spore-like stage in their life cycle. E.g: Plasmodium falciparum.

Kingdom Fungi

They are unicellular (e.g yeast) or muticelullar eukaryotes. With the exception of yeast, fungi are filamentous. Their bodies consist of long, slender thread-like-structures called hyphae. The network of hypae is known as mycelium. Some of these estructures are continuos tubes filled with multinucleated cytoplasm, these are called coenocytic hyphae. Others have septae or cross walls in thier hypae. The cell wall of fungi contains chitin and polysaccharidses. Fungi has an heterotrophic nutrition. Most of them are saprophytes (yeast, Agaricus) and others are parasites e.g Puccina. They reproduce by vegetative (fragmentation, fission, budding) , asexual (formation of spores) and sexual (plasmogamy and karyogamy) methods.

1.- Phycomycetes: They posses an aseptate and coenocytic mycelium. Asexual reproduction takes place by zoospores or by aplanospores. Eg: Mucor, Rhizopus (bread mold)

2.- Ascomycetes: They are mostly multicellular or rarely unicellular. The asexual spores are conidia produced on conidiophores, which on germination produce mycelium. Sexual spores are called ascospores produced in asci, these asci are arranged in ascocarps. E.g: Aspergillus, Penicillium adn Saccharomyces (yeast).

3.- Deuteromycetes: Known as imperfect fungi. The deuteromycetes reproduce only by asexual spores (conidia). The my celium is septate and branched. E.g: Alternaria, Trichoderma and Collectotrichum.

Viruses, Viroid and Prions

In five Kingdom System of classification by Whittaker viruses, vrioids, prions and lichens are not mentioned.

Viruses: These are noncellular, obligate, intracellualar parasites. The viruses contain DNA or RNA as genetic material but not both, apart from nucleic acid viruses posses a capsid which is made of subunits called capsomerees. They show some living characteristics like:

a)They have a genetic material

b) they can multiply inside host cells

c) They exhibit hereditary and the genetic material can undergo mutation

Viroid: The causative agent of potato spindle tuber disease was discovered by Diener and Raymer. It was found to be short strands of RNA without protein coat. Such infectious pathogenic agent of plant that contains only RNA.

Prions: These are proteinaceous infectious particles, first observed by Stanley Prusiner. Prions do not possess nucleic acid. They cause diseases in animals.

Lichens

Lichens: They are the symbiotic associations(mutually beneficial associations) between algae and fungi. The algae component is called phycobiont (autotrophic) and fungal component is called mycobiont (heterotrophic). Phycobiont synthesizes food for fungi and mycobiont absorbs minerals, water etc for the algae. The association is so close that lichen never appears to have two organisms. Lichens are pollution indicators. E.g. Cladonia, Parmelia

Woese's Three Domains System

In 1978 Carl Woese proposed the Domain as the level of classification above kingdom. There are three domains based on the following distinguishing criteria:

Cell wall composition
Membrane lipids
RNA sequence
Protein synthesis
Antibiotic sensitivity

I. Domain Eubacteria: “True bacteria”.

II. Domain Archaeabacteria: “Ancient bacteria”

III. Domain Eucarya: All eucaryotes: Protista, Fungi, Plantae , and Animalia.

Recent developments in molecular biology and biochemistry have revealed that there are two types of procaryotic cells, based on differences in their ribosomes, cell walls, and metabolism.

1. Eubacteria: “True bacteria”.