Lecture Outline

I. Taxonomy Vs. Systematics

Taxonomy Systematics

Etymology: Etymology:
The term “taxonomy” originates from two The word systematics comes from the word
words, “taxis” meaning arrangement and ‘systema’, meaning the systematic
“nomos” meaning laws. arrangement of the organisms.

Definition: Definition:
Taxonomy is the study of identification, Systematics is the study of diversity and
description, naming and classification of evolutionary relationships of organisms
organisms. through time.

Function: Function:
It helps in the naming and identification of an It gives evolutionary relationships,
organism. classifications, cladistics and phylogeny of an
organism.

Importance: Importance:
Taxonomy is important to all living organisms ● Agriculture and Forestry
because it helps in easy identification of a ● Public Health
species and thus facilitates easy ● Wildlife management
communication of biological information.

Additional information:
● Carolus Linnaeus is the founder of
modern taxonomy
● Taxonomy is a subtype of systematics
that systematically sorts species by
traits.
● Taxonomic rank: Life, Domain,
Kingdom, Phylum, Class, Order,
Family, Genus, Species

II. History of Classification

Aristotle Classified the animal species

Theophr Classified the plant species

astus
 Carolus Regnum Animale (‘animal Regnum Vegetabile (‘vegetable kingdom’, for plants)
Linnaeu kingdom’)
s (1707 -
1778)
Ernst Kingdom Kingdom Plantae Kingdom Protista / Protoctista
Haeckel Animalia
(1886 )
Herbert Kingdom Kingdom Plantae Kingdom Protista / Kingdom Monera
F. Animalia (Eukaryota) Protoctista (Prokaryota)
Copelan (Eukaryota) (Eukaryota)
d (1938)

1937 Édouard Chatton introduced the terms “prokaryote” and “eukaryote” to differentiate these
organisms.

Robert Kingdom Kingdom Kingdom Kingdom Fungi Kingdom Monera

Whittak Animalia Plantae Protista / (Eukaryota) (Prokaryota)
er (Eukaryota (Eukaryota) Protoctista
(1969) ) (Eukaryota)
Carl Kingdo Kingdom Kingdom Kingdom Kingdom Kingdom
Woese m Plantae Protista / Fungi Eubacteria Archaebacteria
and Animali (Eukaryota) Protoctista (Eukaryota) (later called (later called the
colleagu a (Eukaryota) the Bacteria) Archaea)
es (Eukary (Prokaryota) (Prokaryota)
(1977) ota)
Thomas Kingdo Kingdo Kingdom Kingdom Kingdom Kingdo Kingd Kingdo
Cavalier- m m Protista / Chromista Fungi m om m
Smith Animali Plantae Protoctist (Metakaryot (Metakary Archez Eubac Archae
a (Metaka a a) ota) oa teria bacteria
(Metaka ryota) (Protozoa (Arche (Proka (Prokar
ryota) ) zoa) ryota) yota)
(Metakary
ota)

Source: https://encyclopedia.pub/entry/36664
III. Domain Archaea

What are archaea?

In biology, the definition of archaea is that they are prokaryotic forms of life sharing some
features with bacteria and other features with eukarya. Archaea constitute one major domain of
life and comprise only single-celled organisms devoid of nuclei.
Archaea Etymology

Archaea is a modern Latin word derived from the Greek word “arkhaios” meaning ‘primitive’.

Habitats of the Archaea

● Deep’s seas and oceans (archaea form nearly 20% of microbial diversity of the oceans)
● Geysers
● Hot water springs
● Hydrothermal vents
● Volcanoes
● Black smokers
● Mines and oil wells
● Very cold habitats like ice sheaths of tundra
● Highly saline lakes
● Highly acidic places
● Highly alkaline waters
● Swamps, wetlands, and marshlands
● Sewage
● Intestinal tracts of humans and animals
● Highly degraded soils, anoxic muds (archaea in soil)

Types of Archaea

The first archaea described could survive in extremely harsh environments in which no other
organisms could survive. As a result, archaea are often distinguished by the environment in
which they live.

Halophiles
The halophiles, which means "salt-loving," live in environments with high levels of salt (Figure
below). They have been identified in the Great Salt Lake in Utah and in the Dead Sea between
Israel and Jordan, which have salt concentrations several times that of the oceans.

Thermophiles

The thermophiles live in extremely hot environments. For example, they can grow in hot springs,
geysers, and near volcanoes. Unlike other organisms, they can thrive in temperatures near 100°C,
the boiling point of water!

Methanogens
Methanogens can also live in some strange places, such as swamps and inside the guts of cows
and termites. They help these animals break down cellulose, a tough carbohydrate made by
plants (Figure below). This is an example of a mutualistic relationship. Methanogens are named
for their waste product, a gas called methane.

Reproduction
Asexual reproduction is the only way for archaea. They reproduce asexually via binary fission,
budding, or fragmentation. No archaeal member has been reported to undergo endospore
formation.

Energy sources used by archaea

Phototrophic Archaea: Some species of archaea are known to utilize energy from the sun.
Hence they are called phototrophic archaea. Although they can utilize sunlight like the plants,
they can’t fix atmospheric carbon. So, the answer to the query “if archaea photosynthesize” is
NO. They can be “PHOTOTROPHIC” and “NOT PHOTOSYNTHETIC”.Example: Haloarchaea
or Halobacterium.

Lithotrophic Archaea: Some species of archaea are known to utilize inorganic compounds
(chemical energy) to take care of their energy needs like metal ions, hydrogen, ammonia,
etc.Examples: Pyrolobus, Ferroglobus, Methanobacteria, ammonia oxidizing archaea, sulfate
reducing archaea.

Organotrophic Archaea: Some species of archaea are known to utilize organic compounds to
take care of their energy needs like pyruvate, starch, maltose, etc.Examples: Methanosarcinales,
Pyrococcus, Sulfolobus.
Characteristics of Archaebacteria

Following are the important characteristics of archaebacteria:

· Archaebacteria are obligate or facultative anaerobes, i.e., they flourish in the

absence of oxygen and that is why only they can undergo methanogenesis.

· The cell membranes of the Archaebacteria are composed of lipids.

· The rigid cell wall provides shape and support to the Archaebacteria. It also
protects the cell from bursting under hypotonic conditions.

· The cell wall is composed of Pseudomurein, which prevents archaebacteria from

the effects of Lysozyme. Lysozyme is an enzyme released by the immune system of the
host, which dissolves the cell wall of pathogenic bacteria.

· These do not possess membrane-bound organelles such as nuclei, endoplasmic

reticulum, mitochondria, lysosomes, or chloroplast. Its thick cytoplasm contains all the
compounds required for nutrition and metabolism.

· They can live in a variety of environments and are hence called extremophiles.
They can survive in acidic and alkaline aquatic regions, and in temperatures above
boiling point.
 · They can withstand a very high pressure of more than 200 atmospheres.

· Archaebacteria are indifferent towards major antibiotics because they contain

plasmids which have antibiotic resistance enzymes.

· The mode of reproduction is asexual, known as binary fission.

· They perform unique gene transcription.

· The differences in their ribosomal RNA suggest that they diverged from both
prokaryotes and eukaryotes.

Types of Archaebacteria

Archaebacteria are classified based on their phylogenetic relationship. The major types of
Archaebacteria are discussed below:

Crenarchaeota

The Crenarchaeota are Archaea, which exist in a broad range of habitats. They are tolerant to
extreme heat or high temperatures. They have special proteins that help them to function at
temperatures as high as 230 degrees Celsius. They can be found in deep-sea vents and hot
springs, regions with superheated water. These include thermophiles, hyperthermophiles, and
thermoacidophiles.

Euryarchaeota

These can survive under extremely alkaline conditions and can produce methane, unlike any
other living being on earth. These include methanogens and halophiles. Euryarchaeota is
composed of methanogens. The members are critical to geochemical carbon cycling.

Korarchaeota
They possess the genes common with Crenarchaeota and Euryarchaeota. All three are believed
to have descended from a common ancestor. These are supposed to be the oldest surviving
organisms on earth. These include hyperthermophiles. Korarchaeota represents the oldest cell
lineage. Archaea in this phylum are only found in low abundance on the ocean floor near
hydrothermal vents.

Thaumarchaeota

These include archaea that oxidize ammonia. Thaumarchaeota are the most abundant prokaryotes
in soil systems. They are thought to be among the most abundant life forms at 5% of the total
prokaryote population.

Nanoarchaeota

This is an obligate symbiont of archaea belonging to the genus Ignicoccus. Nanoarchaeota are
the smallest known cells and obligate symbionts to other archaea.

IV. Domain Bacteria

Bacteria Domain: Kingdom Eubacteria

Members of eubacteria are unicellular and microscopic. They are referred to as the true
bacteria and are usually called the "bacteria" group. Their cell walls are made of
peptidoglycan, a carbohydrate Bacteria consist of a very diverse group. They can be found in
almost all kinds of places, in soil, water and air. Some are present in raw or spoiled food;
others live in or on other organisms including your body.

How to classify Bacteria:

● By their mode of nutrition, or how they metabolize resources (what they eat)
● By their ability (or not) to produce endospores
● By their means of motility
● By their shape
● By their cell walls

Mode of Nutrition
● Photoautotrophs
● Chemoautotrophs
● Heterotrophs

Presence of Endospores
 ● These are resistant bodies that contain the genetic material and a small amount of
cytoplasm surrounded by a cell wall.

Means of Motility
● Falling leaf motility
● Gliding motility
● Swarming motility
● Darting motility
● Tumbling motility
● Corkscrew motility

Bacteria Shapes
● Cocci
● Bacilli
● Spirilla

Bacterial Cell Walls

● Gram negative cell walls
● Gram positive cell walls

Common Groups of Bacteria

● Cyanobacteria
● Chemosynthetic Bacteria
● Nitrogen-fixing Bacteria
● Spirochetes

Examples of Bacteria:
● Propionibacterium acnes
● Mycobcterium tuberculosis
● Leptospira interrogans
● Streptomyces griseus
● Streptomyces venezuelae
● Escherichia coli
● Lactobacilli bulgaricus

V. Domain Eukarya

As the name suggests, the Eukaryote are eukaryotic cells which have membranes that are pretty
similar to that of bacteria. Eukaryote are further grouped into Kingdom Protista (algae,
protozoans, etc.), Kingdom Fungi (yeast, mold, etc.), Kingdom Plantae (flowering plants, ferns,
etc.) and Kingdom Animalia (insects, vertebrates, etc.). Not all Eukaryotes have a cell wall, and
even if they do they don't contain peptidoglycan as bacteria do. While cells are organized into
tissues in case of kingdom Plantae as well as kingdom Animalia, the presence of cell walls is
only restricted to the members of kingdom Plantae. Each of these three domains of life
recognized by biologists today contain rRNA which is unique to them, and this fact in itself
forms the basis of three-domain system. While the presence of nuclear membrane differentiates
the Eukarya domain from Archaea domain and Bacteria domain - both of which lack nuclear
membrane, the distinct biochemistry and RNA markers differentiate Archaea and Bacteria
domains from each other.

The Eukarya (also spelled Eucarya) possess the following characteristics:

• Eukarya have eukaryotic cells.

• Like the Bacteria, they have membranes composed of unbranched fatty acid chains attached to
glycerol by ester linkages

• Not all Eukarya possess cells with a cell wall, but for those Eukarya having a cell wall, that
wall contains no peptidoglycan.

• Eukarya are resistant to traditional antibacterial antibiotics but are sensitive to most antibiotics
that affect eukaryotic cells.

• Eukarya contain rRNA that is unique to the Eukarya as indicated by the presence molecular
regions distinctly different from the rRNA of Archaea and Bacteria.

The Eukarya are subdivided into the following kingdoms:

a. Protista Kingdom Protista are simple, predominately unicellular eukaryotic organisms.

Examples includes slime molds, euglenoids, algae, and protozoans. (Autotrophs)

b. Fungi Kingdom Fungi are unicellular or multicellular organisms with eukaryotic cell types.
The cells have cell walls but are not organized into tissues. They do not carry out photosynthesis
and obtain nutrients through absorption. Examples include sac fungi, club fungi, yeasts, and
molds. (Autotrophs)
c. Plantae Kingdom Plants are multicellular organisms composed of eukaryotic cells. The cells
are organized into tissues and have cell walls. They obtain nutrients by photosynthesis and
absorption. Examples include mosses, ferns, conifers, and flowering plants. (Autotrophs)

d. Animalia Kingdom Animals are multicellular organisms composed of eukaryotic cells. The
cells are organized into tissues and lack cell walls. They do not carry out photosynthesis and
obtain nutrients primarily by ingestion. Examples include sponges, worms, insects, and
vertebrates. (Heterotrophs)

VI. Viruses
 Viruses

Definition:
Viruses are small obligate intracellular parasites, which by definition contain either a
RNA or DNA genome surrounded by a protective, virus-coded protein coat. Viruses
may be viewed as mobile genetic elements, most probably of cellular origin and
characterized by a long co-evolution of virus and host.

Structure of Viruses:

● Viruses are acellular entities consisting of a protein coat called a capsid and a
nucleic acid core, which contains their genetic material.
● The capsid may have different shapes, such as helical, icosahedral, or complex.
● Some viruses also possess an envelope derived from the host cell's membrane.
● The diverse range of viral structures reflects their adaptation to specific host
organisms.
Classification of Viruses:

● Viruses are classified based on several criteria

● type of nucleic acid they contain (DNA or RNA)
● replication strategy (lytic or lysogenic)
● host specificity
● Baltimore classification system, widely used in virology, categorizes viruses
into seven groups based on their genetic material and replication strategy.

Viral Replication:

-Viruses cannot replicate independently and require a host cell to reproduce.

-The replication cycle typically involves:

● Attachment
● Penetration
● Uncoating
● replication of viral components,
● Assembly
● release.

-Depending on the virus, the replication cycle can be:

● lytic, leading to host cell lysis and death

● lysogenic, where the viral DNA integrates into the host genome, potentially
remaining dormant for an extended period.

Viruses as Pathogens:

- Viruses are responsible for a wide range of human diseases including:

● common cold
● Influenza
● HIV/AIDS
● Hepatitis
● COVID-19

Viruses as Beneficial Agents:

● Bacteriophages- are viruses that infect and kill bacteria, contributing to the
 regulation of microbial populations and ecosystem balance.
● Some viruses can be engineered as gene therapy vectors or used in
biotechnology applications.

Control and Prevention:

Due to the global impact of viral diseases, controlling their spread is of utmost
importance. Vaccines, antiviral drugs, and public health measures such as hygiene
practices and quarantine protocols are key strategies for prevention and control.
Ongoing research is vital to develop novel antiviral therapies and improve our
understanding of viral dynamics.

VII. Viroids

Definition

Viroids are infectious pathogens that affect only plants, therefore are also called plant pathogens.

Structure

Viroids differ from viruses in structure and form. These consist of solely short strands of
circular, and single-stranded RNA without the protein coats.

Some of the plants that are affected by these pathogens are potatoes, tomatoes, cucumbers,
chrysanthemums, coconut palms, avocados, etc.

Viroids were first discovered by T.O. Diener in the year 1971. It was first examined in the potato
spindle tuber viroid that caused a huge loss to the potato industry.

Characteristic Features of Viroids

○Viroids contain only RNA.

○These are known to be smaller in size and infect only the plants.
 ○These are among the smallest known agents causing infectious disease.

○They reproduce within the host cell which they affect and cause variations in them causing
death.

○Viroids are mainly classified into two families namely Pospiviroidae- nuclear viroids and
Avsunviroidae- chloroplastic viroids.

○Viroids are said to move in an intracellular manner, cell to cell through the plasmodesmata, and
long distance through the phloem.

Diseases

Some of the diseases that are caused by the infection of viroids in plants are;

○citrus exocortis

○cucumber pale fruit

○chrysanthemum stunt

(These infectious diseases are spread by the propagation of seeds in plants by cutting, tubers, etc
and also by mishandling the contaminated implements)

○Hepatitis- D is caused in humans by viroid-like particles.

The symptoms that are caused by the infection of viroid in plants include;

○stunting of growth

○stem necrosis

○deformation of the leaves and fruits

Most of the viroids are said to infect the plants, including coconut and apple trees. The (PSTV)
potato spindle tuber viroid causes significant crop damage to the potato yields causing the tubers
to elongate and then crack. The other common type of viroid infection symptoms includes
stunting and leaf epinasty.

VIII. Prions
 PRIONS

(Proteinaceous Infectious Particle)

Definition
A prion is a type of protein that can cause disease in animals and humans by triggering normally
healthy proteins in the brain to fold abnormally.

Structure
Prions are also misfolded proteins. However, prions have the frightening ability to convert
normal proteins into more prion proteins, making them infectious and capable of multiplying.

Forms of Prions

The first, PrPc, is found in abundance in nerve cells. Its exact function is unknown but it is
thought to be innocuous. The second form, PrPsc, is the one that is commonly referred to as
“prion” and is the one that causes the problems.

Prion Disease
 HUMAN PRION DISEASE ANIMAL PRION DISEASE

Creutzfeldt-Jakob Disease (CJD) Bovine Spongiform Encephalopathy (BSE)

Variant Creutzfeldt-Jakob Disease (vCJD) Chronic Wasting Disease (CWD)

Gerstmann-Straussler-Scheinker Syndrome Scrapie

Fatal Familial Insomnia Transmissible mink encephalopathy

Kuru Feline spongiform encephalopathy

Ungulate spongiform encephalopathy

Prions are known to cause various forms of transmissible spongiform encephalopathy (TSE) in
humans and animals. TSE is a rare degenerative disorder that affects the brain and nervous system.

Transmission

● Acquired through contaminated food or medical equipment

● Inherited via mutations in the gene that codes for PrP
● Sporadic, where the misfolded PrP develops without any known cause

Symptoms

● difficulties with thinking, memory, and judgment

● personality changes like apathy, agitation, and depression
● confusion or disorientation
● involuntary muscle spasms (myoclonus)
 ● loss of coordination (ataxia)
● trouble sleeping (insomnia)
● difficult or slurred speech
● impaired vision or blindness

Diagnosis and Treatment

● MRI. An MRI can create a detailed image of your brain.

● Cerebrospinal fluid (CSF) testing. CSF can be collected and tested for markers associated with
neurodegeneration.
● Electroencephalography (EEG). An EEG records electrical activity in your brain.

Medications
– reducing psychological symptoms with antidepressants or sedatives
– providing pain relief using opiate medication
– easing muscle spasms with drugs like sodium valproate and clonazepam

● Assistance. As the disease advances, many people need help taking care of themselves and
performing daily activities.
● Providing hydration and nutrients. In advanced stages of the disease, IV fluids or a feeding
tube may be required.