Microbial Diversity and Metagenomics Classification and taxonomy of bacteria, archaea, fungi, and extremophiles –

Microbial Diversity and Metagenomics
Classification and taxonomy of bacteria, archaea, fungi, and
extremophiles

1. Microbial Diversity:
Classification and
Taxonomy
An Exploration for Undergraduate Biology Students and Early-Career
Microbiology Learners

2. Chapter 1:
Foundations
Introduction to Microbial Diversity
Defining the Unseen
World
Microbial diversity encompasses the vast array of microscopic
organisms, including bacteria, archaea, fungi, protists, and
viruses. These organisms are the most abundant life forms on
Earth.
The Importance of
Microbes
Microorganisms drive global biogeochemical cycles (carbon,
nitrogen, sulfur), sustain the health of all ecosystems, and play
crucial roles in human health, industry, and agriculture.

3. The Major Microbial
Groups
Microbes are broadly categorised into several primary groups, each possessing distinct cellular, genetic, and ecological characteristics.
Bacteria
Prokaryotic, single-celled organisms with a wide range of
metabolic capabilities. They are ubiquitous and include both
pathogens and beneficial species.
Archaea
Prokaryotic organisms, genetically distinct from bacteria, often
found in extreme environments. They are known for unique
membrane lipids and metabolic pathways.
Fungi
Eukaryotic organisms, including yeasts, moulds, and mushrooms.
They are primarily decomposers and play vital roles in nutrient
recycling.
Extremophiles
Organisms, mainly Archaea and some Bacteria, that thrive in
physically or geochemically extreme conditions that are
detrimental to most life forms.

4. Chapter 2: Organising LifeClassification and
Taxonomy
Taxonomy is the science of defining groups of biological organisms on the basis of shared characteristics and giving names to those
groups. It is fundamental to understanding microbial relationships.
Principles of
Taxonomy
Involves three core activities: Classification (grouping based on
similarities), Nomenclature (assigning names), and Identification
(determining an isolate's identity).
Binomial
Nomenclature
The standardised system of naming organisms using two parts: the
Genus (capitalised) and the species (lowercase), for example, Escherichia
coli.

5. Woese's Three-Domain
System
The current universally accepted classification system, proposed by Carl Woese in 1977, redefines life into three fundamental domains based on ribosomal RNA (rRNA) analysis.
Eukarya
— —
Prokaryoti
—

6. The Taxonomic
Hierarchy
Microorganisms are organised into a nested hierarchy, progressing from the broadest grouping to the most specific, reflecting evolutionary relationships.
Domain
The highest rank; includes Bacteria, Archaea, and Eukarya.
Kingdom
The next level, such as Protista, Fungi, Plantae, Animalia (for Eukarya).
Phylum
A major division within a Kingdom; sometimes called Division in botany/mycology.
Class
A grouping of related Orders.
Order
A grouping of related Families, often ending in "-ales" for bacteria.
Family
A grouping of related Genera, often ending in "-aceae" for bacteria.
Genus
A group of closely related species.
Species
The fundamental rank; a group of strains sharing many stable properties.

7. Chapter 3: Deep
Dive
Characteristics of Bacteria
Cell Wall Structure and Gram Staining
The bacterial cell wall is critical for protection and classification. The Gram
stain is a differential staining technique that separates bacteria into two
large groups based on cell wall composition:
Gram-Positive: Possess a thick peptidoglycan layer that retains the
purple crystal violet stain.
Gram-Negative: Have a thin peptidoglycan layer and an outer membrane,
causing them to stain pink/red with safranin counterstain.
Morphology
Basic bacterial shapes include Coccus (spherical), Bacillus (rod-shaped),
and Spirillum (spiral).

8. Unique Features of
Archaea
Though superficially resembling bacteria, Archaea possess several distinct molecular
features that place them in a separate domain.
Ether-Linked Lipids
Their cell membranes contain unique
lipids with ether linkages (instead of
ester linkages found in Bacteria and
Eukarya), often forming lipid
monolayers for stability in high heat.
Extreme
Environments
Archaea are famous for inhabiting
harsh conditions like hot springs, salt
lakes, and deep-sea vents. Examples
include methanogens and extreme
halophiles.
Diverse Metabolic
Pathways
They exhibit unusual metabolic traits, such as methanogenesis (producing methane)
and chemolithotrophy, leveraging inorganic chemicals for energy.

9. Fungi: The Great
Decomposers
Fungi are eukaryotic organisms that are essential for decomposition and nutrient cycling in terrestrial ecosystems.
Morphology
Most are filamentous, forming a network of
thread-like structures called hyphae, which
collectively form a mycelium. Yeasts are an
exception, existing as single cells.
Reproduction
They reproduce sexually and asexually,
primarily through the formation of spores,
which are highly resistant and easily
dispersed into the environment.
Ecological Role
Fungi are the primary agents for breaking
down complex organic materials like
cellulose and lignin, making nutrients
available to other organisms.

10. Extremophiles: Masters of Survival
Extremophiles are microbes, predominantly Archaea, that have adapted to flourish under conditions that would kill most other life.
Thermophiles
Thrive in extremely high temperatures (e.g., hot springs, deep-sea
vents). Adaptation: Heat-stable enzymes and membrane structures.
Halophiles
Require high salt concentrations (e.g., Dead Sea, saline
environments). Adaptation: Mechanisms to prevent water loss and
balance osmotic pressure.
Acidophiles
Live in highly acidic environments (low pH) (e.g., mine drainage).
Adaptation: Proton pumps and stable internal pH regulators.
Psychrophiles
Flourish in extremely cold environments (e.g., Arctic/Antarctic ice).
Adaptation: Anti-freeze proteins and fluid membranes at low
temperatures.
Understanding extremophiles provides valuable insights into the limits of life and the potential for life to exist on other planets.

11. Thank you