Micro: lecture 3: 1/16

Microbial Diversity

Introduction to the Microbial World

Microbial diversity encompasses the vast variety of microorganisms, including Bacteria, Archaea, and Eukaryotic microbes (such as yeasts, protists, and algae). These organisms vary greatly in their structure, metabolism, and ecological roles.

• Free-living and symbiotic lifestyles

• Colonize every habitat on Earth

• Majority exist in complex communities

• Most have not yet been characterized

Comparing Domains of Life

Three Domains: Bacteria, Archaea, Eukarya

All living organisms are classified into three domains based on genetic and cellular characteristics. The table below summarizes key differences and similarities:

Characteristic	Bacteria	Archaea	Eukarya
Cell volume	1-100 μm3	1-100 μm3	1-106 μm3
DNA organization	Circular (usually)	Circular	Linear, with histones
Gene organization	Operons	Operons	Single genes
Metabolism	Diverse: denitrification, N2 fixation, lithotrophy, respiration, fermentation	Diverse: methanogenesis, lithotrophy, respiration, fermentation	Respiration and fermentation
Multicellularity	Simple	Simple	Simple or complex

Additional info: Archaea share some traits with eukaryotes (e.g., similar RNA polymerase and ribosomal proteins), but also have unique features such as methanogenesis and the ability to thrive in extreme environments.

Bacteria vs. Archaea & Eukaryotes

Key Differences

• Central apparatus for gene expression differs between Bacteria, Archaea, and Eukaryotes.

• Most bacteria have a cell wall of peptidoglycan, absent in Archaea and Eukaryotes.

Importance: Understanding these differences is crucial for developing antibiotics (which often target bacterial-specific features) and for biotechnological applications.

Problematic similarity: The similarity between eukaryotes (e.g., fungi and humans) can complicate the development of antifungal drugs, as these may also affect human cells.

Bacterial Phylogeny and Diversity

Bacterial Phyla

Bacterial phylogeny is based on genetic sequencing, especially of SSU rRNA. Many phyla remain incomplete or are only provisionally identified.

• Many bacteria are uncultured or unclassified

• Environmental sequencing helps identify new candidate phyla

• The majority of bacterial species remain unidentified

Deep-Branching Thermophiles

Characteristics

These are extremophiles that share traits and habitats with archaea. They exhibit rapid growth and high mutation rates, which can affect phylogenetic conclusions.

• Aquificae (e.g., Aquifex pyrophilus): Flagellated rods, hyperthermophilic

• Thermotogae (e.g., Thermotoga maritima): Anaerobic respiration, extensive archaeal gene transfer

• Chloroflexi: Photoheterotrophic, moderately thermophilic, form filamentous mats with cyanobacteria

• Deinococcus-Thermus: Ornithine in peptidoglycan, includes radiation-resistant Deinococcus radiodurans

Cyanobacteria

Oxygenic Phototrophic Prokaryotes

• Conduct photosynthesis in thylakoids

• Fix CO2 in carboxysomes

• Many fix nitrogen in specialized cells called heterocysts

Example: Cyanobacteria played a key role in oxygenating Earth's early atmosphere.

Gram-Positive Bacteria

Major Groups

• Firmicutes (Low-GC): Includes spore-formers (e.g., Clostridium, Bacillus) and non-spore formers (e.g., Lactobacillus, Staphylococcus, Streptococcus, Mycoplasma)

• Actinobacteria (High-GC): Includes Streptomyces (filamentous), Mycobacterium (TB, leprosy), Corynebacterium diphtheriae

Both groups have thick cell walls that retain the Gram stain (crystal violet).

Gram-Negative Bacteria: Proteobacteria

Classes and Characteristics

• Alphaproteobacteria: Photoheterotrophs, oligotrophs, methylotrophs, endosymbionts, rickettsias

• Betaproteobacteria: Photoheterotrophs, lithotrophs (nitrifiers, sulfur/iron oxidizers), pathogens

• Gammaproteobacteria: Sulfur/iron phototrophs, enterobacteria (e.g., Escherichia coli), aerobic rods, plant pathogens

• Deltaproteobacteria: Sulfur/iron reducers, myxobacteria, bacterial parasites

• Epsilonproteobacteria: Sulfur oxidizers/reducers, microaerophilic helical pathogens (e.g., Helicobacter pylori)

Deep-Branching Gram-Negative Phyla

• Acidobacteria: Many species live in extreme conditions

• Bacteroidetes: Major inhabitants of the human colon

• Chlorobi: Green sulfur bacteria

Other Bacterial Phyla

• Spirochetes: Sheathed spiral cells with internalized flagella

• Chlamydiae: Intracellular parasites

• Planctomycetes: Nucleus-like compartment

• Verrucomicrobia: Wrinkled microbes

Archaeal Diversity

Ecological and Physiological Diversity

Archaea are the most ecologically diverse domain, thriving in a wide range of pH, temperature, and salt concentrations. These adaptations have been exploited in biotechnology and industry.

• Major groups: Crenarchaeota, Thaumarchaeota, Euryarchaeota

• Include methanogens, thermophiles, halophiles

Eukaryotic Microbes

Major Groups

• Fungi

• Algae

• Protists

Saccharomyces cerevisiae is a model eukaryote, widely used in research to study cell biology, genetics, and metabolism.

Expanding Understanding of the Microbial World

Our knowledge of microbial diversity continues to grow, especially with advances in sequencing technologies. Many microbes remain unculturable, and the role of viruses in microbial ecosystems is an active area of research.

Sample Questions for Review

1. Considering the phylogenetic tree of life generated from SSU rRNA sequences, pathogenic bacteria cluster throughout the tree of life, indicating their diverse evolutionary origins.

2. The Bacteroidetes phylum is significant as major inhabitants of the human colon.

3. Cyanobacteria are the only oxygenic phototrophic prokaryotes that produce O2.