TYPES AND TAXONOMIC GROUPING OF MICROORGANISMS

Taxonomy is the science of classifying, naming and identifying living things. A taxonomic
scheme is used to arrange organisms in groups called taxa (singular: taxon) based on mutual
similarity. Classification is the process of arranging organisms into similar or related groups,
particularly for easy identification. Nomenclature is the branch of taxonomy that deals with
giving names to taxonomic groups in agreement with published rules. Identification is the
process of determining the particular recognized taxon an isolate/organism belong to.
Systematics is the study of organisms and their relationship particularly evolutionary
relationship. It is a general scientific study of organisms with the aim of arranging them in an
orderly manner. This orderly arrangement links phylogeny (evolutionary relationship) with
taxonomy (in taxonomy organisms are characterized, named and grouped according to natural
relationship).

Carolus Linnaeus developed the first natural classification of living things in the eighteenth
century based on anatomical characteristics. Natural classification arranges organisms into
groups whose members share many major characteristics in common. It is based on largely
anatomical characteristics. To know the genius and species of a newly related microbe is based
on polyphasic taxonomy. Polyphasic taxonomy is based on phenotypic, phylogenetic (that is the
evolutionary history) and genotypic features.

2.1 GENERAL SCHEME OF TAXONOMIC HIERARCHY

All microbes are classified into three domains (bacteria, archaea and eukarya). Within each
domain, each microorganism is assigned to a phylum, class, order, family, genius and species.
Some microbes are also given a subspecies designation. A species is a collection of strains that
share stable properties and differ significantly from other groups of strain. A strain consists of
the descendants of single, pure microbial culture. A strain represents a population of individuals
which is distinguishable at least from some other populations of individuals within a species.
Strains within a species may vary slightly from one another in many ways. A genus is a well-
defined group of one or more species that is clearly separate from other genera. Microorganisms
are named using binomial system of Linnaeus (Binomial nomenclature). Using binomial
nomenclature, microorganisms are given two names: a generic and species name. The generic
name begins with a capital letter while the species name begins with a small letter. Both names
are underlined or written in italics.

2.2 TYPES OF CELLS

All living organisms (including microorganisms) are made of two types of cells: Prokaryotic cell
and Eukaryotic cell

Prokaryotic cell

Prokaryotic cells have no true or definite nucleus, that is, their nucleus lack nuclear membrane.
Hence, their nuclear material mixes with cytoplasmic material. Also, their subcellular organelles
are not bounded by membrane and lack internal membranous structure such as endoplasmic
reticulum and Golgi apparatus. Generally, prokaryotic cells range in diameter from 1 – 5µm.
Prokaryotic cells have peptidoglycan cell wall (except archaea) and many have polysaccharides
capsule. Prokaryotes comprise the simpler and most primitive types of microorganisms. They are
mainly unicellular organisms of the domain: bacteria and archaea.

Eukaryotic cell

Eukaryotic cells have a true nucleus and several other distinct subcellular organelles that are
bounded by a membrane; that allow for compartmentalization of functions. Their plasma
membrane is a phospholipid bilayer embedded with proteins. A typical eukaryotic cell is larger
than a prokaryotic. Eukaryotic cells are of the eukarya domain: protist, fungi, plant and animal.
Eukaryotic cell has the following subcellular organelles:

Plasma membrane: It acts as a mechanical cell boundary, a selectively permeable membrane

barrier with transport system, mediate cell-cell interactions and adhesion to surface; secretion;
signal transduction.

Cytoplasm: Composed of cytosol (liquid portion) and organelles; location of many metabolic
processes. The streaming of the cytoplasm helps in distribution of materials within a cell.

Endoplasmic reticulum: Transport of materials, lipid synthesis

Ribosome: Protein synthesis

Golgi apparatus: Packaging and secretion of materials for various purposes; formation of
lysosome

Mitochondrion: Energy production, sites for respiration

Nucleus: Contains the chromosomes that stores genetic information

Nucleolus: Ribosomal RNA synthesis

Chloroplast: Found in plant cell and some protist cell. Site for photosynthesis

Cell wall: Absent in animal cell and some protist cell. Strengthens and give shape to cell

Cilia and flagella: Cell movement

Vacuole: Temporary storage and transport; digestion (food vacuole); water balance (contractile
vacuole)

Table 2.1 Differences between prokaryotic and eukaryotic cell

Prokaryotic cell Eukaryotic cell
Prokaryotic cells are typically 1-5µm in size Eukaryotic cells are typically are 10-100µm in
size
Genetic material are free in cytoplasm Genetic materials are located within membrane-
bound nucleus
Single circular chromosomes or nucleoid Multiple chromosomes, generally in pairs
Membrane –bound organelles absent Several membrane-bound organelles present
Ribosomes are smaller (70S) and are free in Ribosomes are larger (80S) and are free or
cytoplasm attached to membranes
Respiratory enzymes are bound to plasma Respiratory enzymes are located in
membrane mitochondria
Cell wall is made up of peptidoglycan Cell wall contains cellulose or chitin when
(except archaea) present
Cilia absent Cilia may be present
Pili may be present Pili absent

Similarities between prokaryotic cell and eukaryotic cell

 1. Both cell contents are bounded by a plasma membrane
2. DNA stores genetic information in both cells.
3. Ribosomes act as site of protein synthesis in both cells.

Table 2.2 Prokaryotic and eukaryotic organisms

PROKARYOTE EUKARYOTE
Bacteria Protist
Archaea Fungi
Plant
Animal

2.3 BACTERIA

Bacteria are single-celled, prokaryotic, microscopic organisms with peptidoglycan cell wall.
However, some bacteria lack cell wall (that is, the mycoplasma). They have flagella for
movement and reproduce asexually by binary fission.

Bacteria size: Most bacteria fall into a size of about 1-5µm. Some bacteria are smaller, for
example mycoplasma measures less than 1µm, while some are larger, for example
Cyanobacterium oscillatoria which is about 7µm in diameter. A few bacteria are larger than
eukaryotic cells.

2.3.1 BACTERIA SHAPES

The following are the various types of bacterial shapes

1. Rod (Bacillus): A cylindrical shaped bacterium is called a bacillus (plural: bacilla) or rod.
Examples are Escherichia coli, Bacillus anthracis and Salmonella typhi
2. Spherical (Coccus): This is a bacterial cell that is spherical or ovoid in shape. Examples
are Staphylococcus aureus, Neisseria gonorrhoeae and Streptococcus pnuemoniae
3. Spiral (Spirillum/Spirochaetes): Spirillum (plural: spirilla) is a rigid spiral shaped
bacterial cell. Many have tufts of flagella at one or both ends. Spirochaetes are flexible,
spiral-shaped bacteria that have a unique internal arrangement. These bacteria are
 distinctive in other ways but belong to the same phylum, spirochaetes. An example of a
spirochaete is Treponema pallidum.
4. Coccobacillus: They are very short and wide rod. They resemble cocci. An example is
Haemophilus influenzae.
5. Vibrio: They are short, slightly curved rods. They have comma shape. An example is
Vibrio cholerae.
6. Filamentous: The bacteria form long thread called hyphae. The hyphae form a network
called mycelium. An example is actinobacteria

Some bacteria are pleomorphic. They have variable shapes and lack a single characteristic form.
The shape of a bacterium provides certain advantage to the bacteria. For example, rods have
large surface area and are better able to take up nutrients from the environment, cocci are less
prone to drying out while spiral shape aid motility (their shape help their movement through an
aqueous medium).

2.3.2 ARRANGEMENT OF BACTERIA

Cocci can exist singly or associated in characteristic arrangements useful in their identification.
Cocci that divide and form a pair that remain together are diplococci. Cocci that are in long
chairs in one plane are streptococcus while those that divide in random planes forming clusters
are staphylococcus. Divisions in two or three planes can produce symmetrical groupings of
cocci. Division of cocci in two planes to form square group of four cells is called tetrads, an
example is the genus Micrococcus. Some cocci divide in three planes, forming cubical packets of
eight cells (an example is the genus Sarcina)

Rod shaped bacteria only divide in single plane and may therefore form pairs or in chairs
(Bacillus megaterium is found in long chairs). Spiral forms divide in one plane, but tend not to
stick together.

O
Coccus Bacillus Coccobacillus
 Vibrio spirillum spirochete
Figure 2.1 Different Morphology (shapes) of bacteria

Coccus Diplococci Staphylococcus

Streptococci Tetrad cubical packet

Figure 2.2 Various morphology of the bacterium ‘Coccus’
2.3.3 BACTERIA MOTILITY
Some bacteria are motile (that is they move) while other are not. Many bacteria that are motile
have flagella whereas non-motile do not. There are five major methods of movement in bacteria.
Swimming movement conferred by flagella, flagella mediated swarming, corkscrew movement
of spirochetes, twitching motility (associated with pili) and gliding motility.
2.3.4 GENERAL CLASSIFICATION OF BACTERIA
The major lineages or groups in the domain bacteria are
1. The Proteobacteria: This is the largest phylum of bacteria. Many of them are
chemoorganotrophic (organisms that obtain energy from the breakdown of organic compounds)
while some are chemolithotrophic (organisms that obtain energy from the breakdown of
inorganic compounds). This group comprises several soil and water inhabiting bacteria and
parasitic bacteria. Examples of proteobacteria are the genera Escherichia, Rhizobium and
Azotobacter. Some proteobacteria are pathogenic. Examples are Salmonella, Rickettsia and
Neisseria.
2. Gram-Positive Bacteria: This group consists of endospore forming Bacillus and Clostridium
and related spore forming bacteria such as the antibiotic producing Streptomyces. It also includes
lactic acid bacteria such as lactobacillus. streptococcus and the mycoplasma.
3. Cyanobacteria: This group of bacteria is regarded as the first oxygenic phototrophs to evolve
on Earth. This lineage consists of oxygenic phototrophs and are phylogenetically related to
Gram-Positive bacteria. An example of this group is the genus Anabaena.
4. Plantomyces: This lineage consists of bacterial cells with a distinct stalk which helps organism
to attach to a solid substratum.
5. Spirochaetes: This group are helical in morphology. An example is Treponema pallidum that
causes syphilis
6. Green sulphur and green non-sulphur bacteria: They are phototrophic and are autotrophs. An
example is chloroflexus.
7. Dienococcus: This lineage consists of bacteria with unusual cell walls and are innate resistant
to high level of radiation
8. The bacteria belonging to Aquifex andThermotoga. Though they are phylogenetically distinct
from one another, they commonly share the property of growth at high temperature
(thermophiles).
2.4. FUNGI
Fungi are largely terrestrial, spore forming, eukaryotic organisms. They lacking chlorophyll and
are heterotrophs, having absorptive mode of nutrition. Fungi differ from plants in two
fundamental aspects;
i) Plants obtain energy from the sun, fungi do not
ii) Plants utilize carbon (iv) oxide as a carbon sources, fungi do not
True fungi are monophyletic, that is they all have a common ancestor. Fungi are eukaryotes.
2.4.1 SALIENT FEATURES OF FUNGI
1. The vegetative body (thallus) is usually represented by a filament called hypha (Plural:
hyphae). Hyphae are collectively called mycelium. Hyphae are septate or non-septate.
2. Vegetative body (Thallus) is not differentiated into root, stem and leaves and has no special
tissue for internal transport of water and nutrients.
3. Cell wall is mainly made of chitin.
4. All fungi lack chlorophyll. They are heterotrophic; they may be saprophytic, parasitic or
mutualistic.
5. Fungi store carbohydrates in the form glycogen.
6. They reproduce sexually and asexually. Asexual reproduction is more common.
7. Asexual reproduction takes place mostly by sporangiospores and conidia
8. Digestion of food is extracellular.

2.4.2 FUNGI MORPHOLOGY

Fungi range in form and size from unicellular yeasts to large mushroom and puffballs. Yeasts are
unicellular, do not have flagella and reproduce asexually (by budding or transverse fission) or
sexually (by spore formation). Multicellular forms such as moulds have long, branched thread
like filaments called hyphae which aggregate together to form a tangled mycelium. The hyphae
of some fungi have cross walls or septa (singular septum) separating it which may be joined by
more or more pores which allow cytoplasmic streaming; a form of internal transport. This kind
of hyphae are said to be septate. Hyphae without cross walls are coenocytic (that is, having many
nuclei with a single plasma membrane). Hyphae are composed of an outer cell wall and an inner
lumen, which contains the cytosol and organelles.
Many fungi are dimorphic (i.e. they exist in two distinct forms). Their body change from the
yeast form to the mycelial form. (YM shift). In fungi associated with plants, the mycelial form
exists in the plant and the yeast form in the environment.
The cell wall of fungi is made up of principally chitin, a strong but flexible polysaccharide
whose monomer unit is N-acetyl glucosamine. Chitin is found in the exoskeleton of insects.
2.4.3 NUTRITION
Many fungi are saprophytic. They obtain their nutrients from decaying matter on which they
grow. They secrete enzymes extracellular (extracellular digestion) to breakdown complex
molecule to simpler forms that can be absorbed by the hyphae. Most fungi are able to synthesize
their own amino acids and proteins from carbohydrates and simple nitrogenous compounds.
Carbohydrates are stored mainly as glycogen.
2.4.4 RESPIRATION
Many fungi are aerobic, but some yeast can function as facultative anaerobes.
2.4.5 REPRODUCTION
Fungi reproduce sexually and asexually. There are different patterns of reproduction among
fungi. Generally, fungi reproduce by forming spores. Spores are non-motile reproductive cells
and are carried by animals or wind for dispersal.
2.4.6 FUNGI SIZE
It ranges from microscopic fungi such as yeast to large macroscopic ones such as mushroom
2.4.7 FUNGI SHAPE
1. Spherical. An example is yeast
2. Filamentous. An example is mould
2.4.8 ECONOMIC IMPORTANCE OF FUNGI
1. Fungi especially yeasts are essential in industrial fermentation processes such as in the
production of bread, alcohol and cheese.
2. Many antibiotics such as penicillin, griseofulvin is derived from fungi. The immune
suppressive drug cyclosporin is also obtained from fungi.
3. They are responsible for the decomposition and reprocessing of large amounts of
complex organic matter into forms that can be used by other organisms. They help to add
humus to the soil and release carbon (IV) oxide to the atmosphere.
4. They decompose economic important materials such as wood, paper and leather.
5. Some fungi cause disease in crops and human.
6. Fungi are important research tools in the study of fundamental biological processes.
7. Fungi also form beneficial relationships with other organisms. For example, vascular
plant roots form important association with the fungi mycorrhizae. Myccorhizae facilitate
the growth of most plants.
2.4.9 CLASSIFICATION OF FUNGI
2.4.9.1. CHYTRIDIOMYCOTA (CHYTRIDIOMYCETES)
They are also called chytrids. Chytrids are microscopic in size and may consist of single cell, a
small multinucleate mass or a true mycelium. Some members of chytrids are saprophytic while
others are parasites of plants and animals, including insects. A few live anaerobically in the
rumen of herbivores such as sheep and cattle. Chytrids are different from other group of fungi by
producing spores with single, posterior, whiplash flagella (flagellated zoospores). They exhibit
both asexual (by means of motile zoospores) and sexual reproduction. Sexual reproduction may
involve fusion of gametes to produce a diploid zygote, but there is no dikaryotic stage in the life
cycle. An example of a chytrid is Allomyces macrogynus
2.4.9.2 ZYGOMYCOTA (ZYGOMYCETES)
Zygomycota are fungi with coenocytic hyphae (aseptate), with many haploid nuclei. Most of
them are saprophytic while a few are parasites of plants, insects and other animals including
humans. They reproduce asexually under favourable conditions by developing spores in
sporangia (singular sporangium) at the tips of aerial hyphae which are dispersed by wind. Sexual
reproduction produces tough, thick-walled zygote called zygospore that is resistant to
unfavourable environmental conditions. Examples of this group are mucor and the black bread
mould Rhizopus.
Rhizopus are heterothallic, that is, there exist two distinct mating strains known as + and -. These
two mating strains are morphologically identical. A gametangia is formed when two opposite
hyphae (+ and -) come in contact and a cross wall develops behind each top. These fuse together
to form a single large multinucleate cell called dicaryon. A dicaryon is a structure formed by two
cells whose content but not nuclei, have fused. A thick protective covering develops around the
dicaryon in Rhizopus forming the zygospore which can remain dominant for months. The nuclei
from each strain fuse in pairs to give a fully diploid zygote when conditions are favourable. Just
before germination meiosis occurs, an aerial sporangiophore emerges, terminating in a
sporangium. Production and dispersal of haploid spores then occur as in asexual life cycle and
new mycelium forms when the spore germinates.
Figure 2.1 Structure of mould
2.4.9.3 GLOMEROMYCOTA (GLOMEROMYCETES)
This group of fungi forms mycorrhizal symbionts with vascular plant. The fungi mycorrhizae
provide soil nutrients to the plant while the plant provides carbohydrate to the fungus.
Glomeromycetes have aseptate hyphae and produce large multinucleate spores by asexual
reproduction only (precisely by fragmentation of the filaments in the soil or in the plant). Spores
germinate when in contact with the roots of a suitable host plant. Glomeromycetes have evolved
specialized flat hyphae called appressoria to penetrate their host plants.
2.4.9.4 ASCOMYCOTA (ASCOMYCETES)
Ascomycota, also known as sac or cap fungi, is a large and diverse group ranging from
unicellular yeast to filamentous species such mould (e.g. Aspergillus). One of the characteristics
of ascomycetes is the production of haploid ascospores through meiosis of a diploid nucleus in a
small sac called an ascus. Yeast and food spoilage mould belong to this group. Most
ascomycetes produce mycelia that superficially look like those of zygomycetes, however they
are septate; they have cross walls (septa) with pores separating each cell. Asexual reproduction
in most ascomycetes (filamentous) involve the production of airborne spores called conidia.
Sexual reproduction involves two strains of opposite mating types.
The cells of Saccharomyces cerevisiae (brewer’s yeast) are spherical, oval or cylindrical. Under
favourable condition, it reproduces asexually by budding. A new cell forms as a small outgrowth
of the old cell and the bud gradually increases in size and evenyually it separates from the parent
cell. Under unfavourable (limited nutrients) diploid cells undergo meiosis to produce four
daughter cells that remain bound within common cell wall, the ascus. When nutrients become
available, the two haploid cells of different mating types (a and α) fuse to become a diploid
zygote. Meiosis occurs and haploid ascospores are produced.
2.4.9.5 BASIDOMYCOTA (BASIOMYCETES)
They are also called club fungi. Examples include jelly fungi, mush rooms, puffballs, shelf fungi
and lord’s nest fungi. Basidiomycota are named for their characteristics structure or cell called
the basidium which is involved in sexual reproduction. A basidium is produced at the tip of
hyphae and is normally club-shaped. Sexual reproduction results in production of basidiospores
which are formed externally on a base pedestal, producing a club- shape structure called
basidium. Basidia can be found on visible fruiting bodies called basidiocarps which are
positioned on stalks.
2.4.9.6 MICROSPORIDA
Microsporida are obligate endoparasites (intracellular) microbes and are sometimes still
considered as protists. Their genome is highly reduced in size and complexity. Unlike other
fungi, they lack mitochondria, peroxisomes and centrioles but have mitosome, like some protists.
Like most fungi, their cell wall contains chitin and trehalose. Mcirosporidia are different among
eukaryotes by having an organelle called polar tube which is essential for host invasion.
2.5 PROTOZOA
Protozoa are single celled, eukaryotic organisms having animal like characteristics. They belong
to the phylum Protista. The cell is bounded by a typical bilayer plasma membrane. This may be
covered by an envelope or shell. One of the most characteristics structural features of protozoan
is the contractile vacuole, an osmoregulatory organelle. They maintain osmotic balance by
continuous removal of water from the cell. The contractile vacuole is star shaped, the radiating
arms being canals that drain water from the cytoplasm into the vacuole. Protozoans are found in
fresh water, marine or terrestrial habitat.
Most protozoa are heterotrophic typically ingesting and digesting food particles such as bacteria
in phagocytic vacuoles. The have structural features (cilia and flagella) for movement. This is
used to classify protozoans.
2.5.1 CLASSIFICATION OF PROTOZOA
2.5.1.1 ZOOFLAGELLATES (ZOOMASTIGOPHORA)
Zooflagellates are most primitive group of protozoa characterized by having long flagellum for
movement. Typical zooflagellates have a single flagellum while some types have several
flagella. Zooflagellates may be free living, symbiotic or parasitic. Example of zooflagellates is
Trypanosoma brucei, a parasite that causes African sleeping sickness in humans. Other examples
are Giardia lamblia, which causes the intestinal disease giardiasis and Trichomonas vaginalis,
which causes an infection of the female urogenital tract. Reproduction in this group of
protozoans is generally by binary fission.
2.5.1.2 CILIATE (CILIOPHORA)
This is the largest group and also the most complex of protozoan. Most of them are free living
(an example is paramecium) and are characterized by having cilia which may be present all over
the cell surface or arranged in rows or bands. Cilia help to propel the organism or assist in the
ingestion of food. A unique feature of the ciliates is that they have two distinct types of nuclei;
i) Macronuclei: They are concerned with encoding enzymes and other proteins
required for essential metabolic processes in the cell.
ii) Micronuclei: They are solely involved in sexual reproduction by conjugation.
Removal of the macronuclei leads to the death of the cell. Cells without micronuclei can survive
and reproduce by binary fission. Most ciliates possess a mouth structure called cytostome
through which food particles are ingested. Some members of this group have trichocyst,
projecting from the cell surface. It is used for attachment or defense. Some ciliated protozoans
are anaerobic. The only ciliate known to cause disease in humans is Balantidium coli which
causes a form of dysentery.
2.5.1.3 THE AMOEBAS (SARCODINA)
The amoebas are characteristics by having pseudopodia (false feet), a temporary projection from
the cell into which cytoplasm flows until the organism has moved forward. Pseudopodia are also
used to capture and engulf food forming a vacuole around it (holozoic nutrition).
Reproduction in amoebas is by simple binary fission. Most amoebas are free living in aquatic
environment while others are important parasites (an example is Entamoeba histolytica which
causes amoebic dysentery in humans). Some type of amoeba has shell covering it: foraminifera
and radiolarian
2.5.1.4 THE SPOROZOANS (APICOMPLEXA)
The sporozoans are all parasite, infecting a range of vertebrates and invertebrates. Sporozoans
have complex life cycle involving both haploid and diploid phases and infecting more than one
host. Sporozoans are characterized by a spore like stage called a sporozoites, which is involved
in the transmission of the parasite to a new host. A sporozoite is a motile infective stage of the
members of sporozoa that gives rise to asexual stage within the new host. Sporozoans are
generally non-motile and absorb soluble nutrients across the cell surface rather than ingesting
particulate matter. Sporozoites have a complex structure that assist in the penetration of the
host’s tissues. Example is plasmodium, the causative agent of malaria.
2.6 ALGAE
Algae are a group of protists that share a number of common features that differentiate them
from other protists. These features one;
1. Possession of the pigment chlorophyll
2. Deriving energy from the sun by means of oxygenic photosynthesis
3. Fixing carbon from carbon (iv) oxide or dissolved bicarbonate
Algae range from unicellular form to multicellular form such as seaweeds displaying a wide
variety of structure, habitat and life cycle.
2.6.1 STRUCTURAL CHARACTERISTICS OF ALGAE
1. All algae are eukaryotic and therefore contain nucleus, mitochondria, endoplasmic
reticulum, ribosomes and Golgi body
2. All algae (except the euglenophyta) have a cellulose cell wall which contains other
polysaccharides including pectin and alginic acids. The cell wall may also be fortified
with calcium carbonate or silica.
3. They possess flagellum (one or two). They lack cilia.
4. Thy have chloroplast containing chlorophyll for photosynthesis.
2.6.2 CLASSIFICATION OF ALGAE
2.6.2.1 EUGLENOPHYTA
Euglenophyta are unicellular and have flagella. They have a size of 10-500µm. They have a
well-defined nucleus and chloroplast containing chlorophyll a and b. The storage product of
photosynthesis is a β- 1, 3- linked glucan called paramylon. They lack cellulose cell wall but
have a flexible pellicle situated within the plasma membrane. They move towards light with
their eyespot located near the base of the flagellum. Reproduction is by binary fission (asexual
means only). Under unfavourable conditions, they form cyst surrounded by a gelatinous
covering, with no flagella. Under certain conditions, they exist as heterotrophs, they lose their
photosynthetic pigments and feed saprophytically.
2.6.2.2 DINOFLAGELLATE
They are unicellular and their cells are covered with armoured plates known as thecae.
Dinoflagellates are biflagellate. They have two flagella of different lengths and with different
points of insertion into the cell: transverse and longitudinal. The flagella encircle the cell
imparting spinning movement that gives their name (dino means “whirling” in Greek). Most of
them are photosynthetic containing chlorophyll a and c plus certain carotenoids and xanthophyll
which give them a red/golden appearance. Some form endosymbiosis relationships with marine
animals such as corals and sea anemones and are called zooxanthellae. Their chromosomes
contain little or no histone and exist almost permanently in the condensed form. Some tropical
species of dinoflagellate emit light (bioluminescence). Reproduction is by binary fission. Sexual
reproduction occurs in some dinoflagellates.

2.6.2.3 DIATOMS
They belong to the division chrysophyta (the golden-brown algae). They have chlorophyll a and
c. Their colour is due to carotenoids and xanthophyll. Diatoms have silica-based shell known as
frustule surrounding cells. The shell form valuable mineral resource (diatomaceous earth) which
is used in filtration system and also as a light abrasive in products such as silver polish or tooth
paste. Reproduction is usually by binary fission, but a sexual phase with production of haploid
gametes can occur. Asexual reproduction involves mitotic cell division with each daughter cell
receiving one half of the parental frustule and synthesizing a new one to complement it.
2.6.2.4 CHLOROPHYTA (GREEN ALGAE)
They are very similar to plants in terms of ultrastructure, metabolism and photosynthetic
pigments. They have chloroplast containing chlorophyll a and b giving them their characteristic
green colour. The composition of their chlorophyll is similar to plants, to which phylogenetically
they are closely related to. They lack phycobiliproteins. They store carbohydrate in the form of
starch and generally have a rigid cell wall. The starch is stored in structures called pyrenoids,
which are found within chloroplast. Chlorophyta are divided into two main groups: Chlorophytes
which are the unicellular chlamydomonas and dunaliella and the charophyceans, the group that is
actually most closely related to land plants. Most green algae inhabit freshwater, but some are
found in marine habitat while others are found in most soil or growing in snow to which they
impart a pink colour or as symbiont in lichens. Chlorophyta ranges from unicellular to colonial,
filamentous, membranous and tubular forms. An example of unicellular chlorophyta is
chlamydomonas. Reproduction in Chlamydomonas and other unicellular chlorophyta is by
production of zoospores (asexually). Sexual reproduction occurs under less favourable condition.
Most green algae have a complex life cycle, with both asexual and sexual reproductive stage.
2.6.2.5 PHAEOPHYTA
Phaeophyta are the brown algae. They are multicellular, large, complex seaweed. Most of them
are marine organism. Thy contain chlorophyll a and c which is masked by flucoxanthin. They
store photosynthetic product in the form of an unusual polysaccharide called laminarin (β-1, 3-
glucan). The level of tissue organization in brown algae is greatly advanced than the others
mentioned above. They exhibit alternation of generation (sporophyte and gametophyte). An
example of this group is laminaria.
2.6.2.6 RHODOPHYTA
The red colouration of this group is due to the pigments phycoerythrin and phycocyanin which
mask the chlorophyll (a and d) present. They lack flagella at any stage of their life cycle. This
makes them different from any other group of algae. Most rhodophyta are multicellular marine
species, with a few species in fresh water and terrestrial habitat. Life cycle varies among them
and may be quite complex, with variations in the alternation of generation. Premature red algae
reproduce asexually by releasing spores into water. Different species of red algae are
filamentous, leafy or they deposit calcium carbonate, corraline (coral like) in morphology. They
exhibit alternation of multicellular diploid and haploid forms.
Some rhodophytes are source of agar (the polysaccharide solidifying agent used in culture
media) and agarose used in electrophoresis.
2.7 VIRUSES
A virus is a non-cellular, submicroscopic, obligatory intracellular parasites composed of nucleic
acid (either DNA or RNA) surrounded by a protein coat and capable of self-replication within
the living host cell. Viruses are obligate intracellular parasites. They are a unique group of
infections agent with simple, acellular organisation (that is, they lack cell). Viruses can exist
either extracellular or intracellular. When extracellular, they are metabolically inactive (inert)
because they possess little or no enzymes and do not carry out respiratory or biosynthetic
functions. They cannot reproduce outside of living cells. When intracellular, viruses exist
primarily as nucleic acid that can use their host cell to synthesize viral components from which
progeny virions are produced and eventually released.
2.7.1 SALIENT FEATURES OF VIRUS
1. All viruses are obligate parasites
2. They multiply only within their host cell and remain metabolically inactive outside the host
cell.
3. They can only be seen with an electron microscope.
4. Viruses are actually nucleoproteins
5. The viral genetic material may be either RNA or DNA
6. The nucleic acids of viruses are infectious and not the protein coat.
7. Viruses can easily be crystalized
8. They are host specific and are obligate parasite even at genetic level
Viruses are different form bacteria in the following way;
1. They cannot be observed using a light microscope.
2. They have no internal cellular structure.
3. They contain either DNA or RNA, but not both.
4. They are incapable of replication unless when inside an appropriate living host.
5. They are incapable of metabolism.
6. Individuals show no increase in size.
2.7.2 GENERAL STRUCTURAL PROPERTIES
A complete virus particle is called a virion. Virion ranges in size from about 10-400nm in
diameter. The simplest virion consists only of a nucleocapsid, which is composed of a nucleic
acid either DNA or RNA and a protein coat called a capsid. The capsid surrounds the nucleic
acid protects the viral genome and often aid in its transfer between host cells. The nucleocapsid
may be surrounded by an envelope (enveloped virus) or may lack envelope (non-enveloped or
naked virus).
2.7.3 BACTERIOPHAGE
Viruses that infect bacterial cells are called bacteriophage or phages. Bacteriophages literally
mean bacteria eaters. An examples is T.phage which infects Escherichia coli.
2.7.4 VIROID
Viroids are infectious agent that consist only of RNA. Viroid are covalently closed, circular
ssRNA about 250 – 370 nucleotides long. Enzymes in the host’s nucleus are used to replicate the
RNA, which does not appear to be translated into proteins. Viroid are only found in plants where
they cause a variety of diseases.
2.7.4 PRIONS (PROTEINACEOUS INFECTIOUS PARTICLE)
Prions are small self-replicating composed solely of proteins. Prions cause a variety of
neurodegenerative diseases in humans and other animals including scrapie in sheep, mad cow
disease and the human disease kuru and fatal familial insomnia. Prions are altered version of
normal animal proteins and somehow have the ability to cause the normal version to refold itself
into the abnormal form which causes disease. Thus, the prion propagates itself.
2.7.5 SATELLITES
Satellites, like viroid, consist of a nucleic acid. However, the nucleic acid is either DNA or RNA)
They differ from viroid in that their nucleic acid get enclosed in a capsid and they need a helper
virus to replicate. Most satellites use plant viruses as their helper virus.

2.8 ARCHAEA
Archaea are prokaryotes differing from true bacteria in cell wall, plasma membrane chemistry as
well as 16 rRNA sequences. The domain archaea represent prokaryotic cells that have isoprenoid
glycerol diether or diglycerol tetraether lipids in their plasma membrane and have archaea rRNA
2.8.1 GENERAL FEATURES OF THE ARCHAEA
1. Archaea are prokaryotic in cell organization.
 2. Most archaea have cell wall composed of a layer of subunit containing protein and is
known as S-layer, directly associated with the cell membrane. However, some archaeal
cell wall is made up of pseudomurein (i.e. pseudopeptidoglycan).
3. The lipid component of their plasma membrane contains branched isoprenes instead of
fatty acids and these are joined to glycerol by ether-linkages, rather than the ester-linkage
found in true bacteria.
4. Many archaea have flagella for locomotion.
5. Many archaea have pili for attachment to surfaces.
6. Cannulae and Hami are external structures that are unique to archaea. They help to attach
the cell to surfaces including other cells.
7. Many members of the archaea domain are found in extreme environments such as deep-
sea thermal vents, salt ponds, every hot environment (hyperthermophiles and are able to
grow at temperatures over 1000C) and cold Antarctic region (psychrophilic). Some are
symbionts in animal digestive system.
8. Some are unicellular, others filamentous or aggregates.
9. They reproduce mainly by binary fission
10. They may be aerobic, facultative anaerobes or obligate anaerobes
11. Nutritionally, they range from chemolithotrophs to organotrophs
Shapes of Archaea
Archaea exhibit a variety of shape. Cocci and rods are common. Curved rods, spiral shapes,
plate shape, irregular shape or pleomorphic (many shapes) also exist.
Size of Archaea
Archaea also vary in size ranging from 0.1 to over 15µm. Typical rods are 1-2µm by 1-5µm
long; cocci are typically 1-3µm in diameter. However, extremely small and extremely large
archaea also exist.

2.8.2 CLASSIFICATION OF ARCHAEA

Current phylogenetic evidence deduced from comparison of 16S rRNA sequences suggests that
archaea have evolved more slowly than either Bacteria or the Eukaryotes. Archaea consist of
three phyla: the crenarchaeota, Euryarchaeota and Korarchaeota.
Crenarchaeota phylum consists of archaea that are found in extreme hot and cold regions. Most
crenarchaeota are hyperthermophylic. Hyperthermophiles are organism whose optimum
temperature for growth is over is greater than 80 oC. Many hyperthermophiles are
chemolithotrophic autotrophs. They are sole primary producers in such very hot habitats because
phototrophs cannot survive such temperature. The cold dwellers thrive even in frigid water such
as those of the Antarctic region.
Euyarchaeota consist of physiologically diverse group of archaea and many species inhabit
extreme environment. Many of them are extreme halophiles, that is, inhabit very high saline
environment and their requirement for salt is very high. An organism is extreme halophile if it
requires at least 1.5M (about 9%) NaCl for growth. An example of an extreme halophile is
halobacterium. Others are methanogens and still others are mostly acidophiles. Methanogens are
microorganisms that produce methane as an integral part of their energy metabolism. Examples
are methanobacterium and methanosarcina. Methanogens are strictly anaerobic while extreme
halophiles are obligate aerobes. Other groups of euryarchaeota include the hyperthrmophiles
Thermococcus and Pyrococcus and the cell wall less Thermoplasma, an organism phenotypically
similar to the mycoplasma.
Korarchaeota is a newly added phylum. They are hyperthermophilic anaerobes. They are found
in marine and terrestrial geothermal habitat.
Table 2.3 Comparison of features of the three domains of life: Bacteria, Archaea and
Eukarya.
Archaea Bacteria Eukarya
Main genetic material Single closed circle Single closed circle True nucleus with
of dsDNA of dsDNA multiple linear
chromosome
Histones Present Absent Present
Ribosomes 70s 70s 80s
Initiator tRNA Methionine N-formyl methionine Methionine
Membrane fatty acid Ether-linked, Ester-linked, straight Ester-linked, straight
branched chain chain
Cell wall Muramic acid absent Muramic acid present Muramic acid absent
Archaea share some features with true bacteria and others with eukaryotes
 Table 2.4 The three domains of living organisms
Bacteria Archaea Eukarya
Protist
Fungi
Plant
Animal

Figure 2.2 Evolution of archaea