Ch. 10

Nutrition and Global Distribution of Microorganisms

Types of Nutrition in Microorganisms

Microorganisms obtain energy and carbon through various nutritional strategies, which are fundamental for their survival and ecological roles.

• Autotrophic: Use CO2 as a carbon source.

• Heterotrophic: Obtain carbon from organic compounds.

• Photoautotrophic: Use light energy to fix CO2.

• Chemoautotrophic: Use chemical energy to fix CO2.

• Chemoheterotrophic: Use chemical energy and organic compounds as carbon source.

• Parasitic: Live in or on a host, deriving nutrients at the host's expense.

• Symbiotic: Live in close association with another organism, often benefiting both.

Global Distribution

Microorganisms are distributed globally based on their environmental preferences.

• Mesophiles: Thrive in moderate environments.

• Extremophiles: Thrive in extreme environments.

• Terrestrial: Live on land.

• Aquatic: Live in water.

• Thermophiles: Prefer high temperatures.

• Pyrocophiles: Prefer extremely high temperatures.

• Hypersaline: Prefer high salt concentrations.

• Deep sub-surface: Live in low O2, high pressure, and high temperature environments.

Taxonomy and Phylogeny

Definitions

• Taxonomy: The science of classifying organisms; shows degree of similarity among organisms.

• Phylogeny: The study of the evolutionary history of organisms.

Phylogenetic Trees and Classification

Phylogenetic trees depict evolutionary relationships among organisms based on genetic, morphological, or biochemical data.

• Groups of organisms evolved from a common ancestor.

• Each species retains some characteristics of its ancestor.

• Phylogenetic trees are not 100% accurate.

• Relatedness to ancestors is depicted by distance (time) and branching (last common ancestor).

Historical Milestones in Classification

• 1735 - Linnaeus: Two kingdoms (Plantae and Animalia).

• 1800: Kingdom Protista proposed (bacteria, protozoa, algae, fungi).

• 1937: Prokaryote introduced to distinguish cells without a nucleus.

• 1978 - Woese: Modern three domain system developed.

The Three Domain System

• All organisms evolved from cells that formed over 3 billion years ago.

• Eukaryotes originated from infoldings of prokaryotic plasma membranes.

• Endosymbiotic bacteria developed into organelles.

• Developed by Woese in 1978, based on ribosomal RNA (rRNA) nucleotide sequences.

1. Eukarya

2. Bacteria

3. Archaea

Taxonomic Hierarchy

Levels of Classification

Organisms are classified into a series of subdivisions, from broad to specific.

• Mnemonic: "Dear King Philip Came Over For Good Soup" (Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species)

• Classification is mostly at the genus and species level, but can include families and phyla.

Terms Used for Bacteria

• Prokaryotic species: Population of cells with similar characteristics.

• Culture: Bacteria grown in laboratory media.

• Clone: Population of cells (genetically identical) derived from a single parent cell.

• Strain: Cells that are genetically different within a clone.

Viruses and Classification

• Viruses are not part of the three domain system.

• Viruses are acellular and require a host cell to replicate.

• Viral classification is often based on genetic material.

• A viral species is defined as a population of viruses with similar characteristics occupying a particular ecological niche.

• Viral species can be further grouped into strains.

Classification and Identification of Microorganisms

Identification Methods

Identification involves matching characteristics of unknown organisms to lists of known organisms.

• Use of clinical lab identification.

• Comparison of similarities and differences to categorize organisms.

Methods of Classifying and Identifying Microorganisms

• Morphological characteristics: Useful for identifying eukaryotes; less informative for phylogenetic relationships.

• Differential staining: Stains that differentiate between types of organisms (e.g., Gram stain, acid-fast stain).

• Gram Stain: Differentiates bacteria based on peptidoglycan layer thickness.

Biochemical Tests

• Extremely useful for differentiating/identifying bacteria.

• Bacteria have unique biochemical "signatures" (e.g., presence of certain enzymes).

• Rapid identification methods can perform several tests simultaneously.

Automated Biochemical Tests

• Automated rapid identification systems for medically important bacteria and yeast.

• Mass spectrophotometry: Detects cellular proteins; each bacterium has a unique protein profile.

• MALDI-TOF: Determines unique proteomic fingerprint and matches to a reference library.

Serology

• Analysis of blood serum for antibodies.

• Microorganisms stimulate antibody production, measurable in serum.

Agglutination Tests (Serological Test)

• Sample of unknown bacteria mixed with antibodies specific to known species.

• Presence or absence of agglutination (clumping) indicates identification.

Other Serological Tests

• Enzyme-linked immunosorbent assay (ELISA): Detects antigens or antibodies in a sample.

• Western blotting: Separates and identifies specific antibodies from a sample; used to confirm ELISA results.

DNA Sequencing and Fingerprinting

• Analyzing DNA base composition for identification/classification.

• Guanine (G) + Cytosine (C) % is used to classify Gram+ bacteria.

• Full/partial genome sequencing can identify bacteria/virus/strain by comparison to databases.

• DNA fingerprinting compares fragments for genetic similarities/differences.

• In humans, 99% of genome is the same; 0.1% reveals differences.

Classification Tools: Dichotomous Keys and Cladograms

Combining Laboratory and Observational Data

• Dichotomous Keys: Identification keys based on successive YES/NO questions; help identify organisms in their natural world.

• Cladograms: Maps showing evolutionary relationships among organisms based on rRNA sequences; show ancestral relations and similarity.

• Difference: Dichotomous keys identify organisms; cladograms show evolutionary relationships.

HTML Table: Three Domain System Comparison

Domain	Cell Type	Cell Wall Composition	Examples
Eukarya	Eukaryotic	Varies (cellulose, chitin, none)	Animals, plants, fungi, protists
Bacteria	Prokaryotic	Peptidoglycan	Escherichia coli, Streptococcus
Archaea	Prokaryotic	No peptidoglycan (pseudopeptidoglycan)	Halobacterium, Methanogens

Key Equations and Concepts

• DNA Base Composition:

$\text{G+C\%} = \frac{\text{Number of G and C bases}}{\text{Total number of bases}} \times 100$

• Molecular Clock (rRNA mutations):

$\text{Rate of mutation} = k \times \text{Time}$

Additional info: Some explanations and table entries were expanded for clarity and completeness based on standard microbiology curriculum.