Micro: Lecture 2 1/14

Microbial Evolution

Introduction

Microbial evolution explores how microorganisms change over time, leading to the diversity of forms, metabolisms, and ecological niches observed today. This topic is central to understanding the origins, adaptation, and classification of microbes.

The Tree of Life and Microbial Diversity

Historical and Current Views

• Tree of Life: Represents evolutionary relationships among Bacteria, Archaea, and Eukarya.

• Molecular clocks: Use genetic sequence changes to estimate divergence times between species.

• Diversity: Microbes have evolved into many shapes and sizes, as seen in various genera such as Azotobacter.

Current Tree of Life

• Modern phylogenetic trees incorporate genetic data to show relationships among major domains.

• Major groups include Bacteria (e.g., Cyanobacteria, Proteobacteria), Archaea (e.g., Methanogens, Halophiles), and Eukarya (e.g., Fungi, Animals).

Molecular Phylogeny

Molecular Clock Assumptions

• Molecular clock: Assumes constant mutation rates to estimate evolutionary distances.

• Distortions can occur due to horizontal gene transfer, variable mutation rates, or selection pressures.

Horizontal Gene Transfer (HGT)

Mechanisms and Impact

• Definition: Movement of genetic material between organisms other than by vertical transmission (parent to offspring).

• HGT allows microbes to acquire new genes and traits, complicating species definitions and taxonomic relationships.

• DNA sequence data shows genes move freely between species, challenging traditional species concepts.

Evolutionary Trail and Adaptation

• Fossil records and SSU rRNA data generally agree, but HGT is crucial for microbial adaptation.

• HGT occurs between different species and even domains, making evolutionary history complex.

Vertical vs. Horizontal Gene Transfer

• Informational genes (e.g., those involved in transcription, translation) are typically transmitted vertically.

• Operational genes (e.g., metabolic functions) can be gained or lost via HGT.

Adaptive Evolution

Drivers of Diversity

• Diversity in metabolism, morphology, and niche invasion is driven by adaptive evolution.

• Adaptive evolution: The process by which organisms become better suited to their environment through natural selection.

Natural Selection

• Described by Charles Darwin as the mechanism by which advantageous traits become more common in populations.

• Acts on naturally occurring variation, leading to the emergence of new species.

Sources of Genome Variation

• Mutations: Changes in DNA sequence.

• Gene duplications: Can lead to paralogs (genes with similar function).

• Gene loss: Degenerative or reductive evolution.

• Horizontal gene transfer: Acquisition of genes from other organisms.

Studying Adaptive Evolution

• Genome sequences serve as historical records.

• Strongly selective environments (e.g., antibiotic exposure) accelerate observable evolution.

• Experimental evolution uses microbes to test evolutionary hypotheses in the lab.

Case Study: Evolution of Antibiotic Resistance in MRSA

Example

• An elderly patient infected with Staphylococcus aureus (MRSA) was treated with antibiotics.

• After 12 weeks of Linezolid treatment, the bacteria evolved resistance, demonstrating adaptive evolution in a selective environment.

Antibiotic	Original MRSA Isolate	Small-colony Variant
Vancomycin	Partly resistant	Resistant
Rifampin	Sensitive	Resistant
Ciprofloxacin	Sensitive	Resistant
Linezolid	Partly resistant	Resistant

Experimental Evolution

Principles and Methods

• Microbes are ideal for laboratory evolution studies due to short generation times and ease of genetic/environmental manipulation.

• Experimental evolution allows testing of natural selection and adaptation hypotheses.

Stages of Trait Evolution

1. Potentiating mutations: Initial genetic changes that enable future adaptation.

2. Actualization: Emergence of a new phenotype.

3. Refinement: Optimization of the new trait.

Microbial Species and Taxonomy

Defining Species

• Species are defined by phylogeny (DNA relatedness) and ecology (shared traits and niche).

Working Definition of Prokaryotic Species

• SSU (small subunit) rRNA similarity ≥ 97%.

• Average nucleotide identity (ANI) of orthologs ≥ 95%.

• Shared ecotype.

Pan and Core Genomes

• Pan genome: Total genes found in all genomes of a species.

• Core genome: Genes found in every genome of the species.

Genome Type	Description
Pan genome	All genes present in any strain of the species
Core genome	Genes present in every strain of the species

Principles of Taxonomy

Taxonomic Hierarchy

Taxon Rank	Example
Domain	Bacteria
Division (Phylum)	Actinobacteria (Actinomycetota)
Class	Actinobacteria
Subclass	Actinobacteridae
Order	Actinomycetales
Family	Streptomycetaceae
Genus	Streptomyces
Species	Streptomyces coelicolor (1908)

Sequence Analysis and Identification

• Sequence analysis enables identification of unclassified/uncultured organisms, environmental samples, and candidate species.

Nongenetic Categorization

• Microbes can also be classified by phenotypic, ecological, or disease categories.

• Dichotomous keys are still used for classification and identification based on observable traits.

Evolution as a Guiding Principle

Applications Beyond Organisms

• Evolutionary principles apply to protein evolution, machine learning algorithms, and synthetic biology.

• In nature, the primary evolutionary goal is survival and reproduction.

Key Requirements and Study Questions

Adaptive Evolution Requirements

• Variation

• Selection

• Large number of generations

Why Microbes Are Used in Evolution Studies

• Short generation times

• Genetic manipulability

• Controllable environments

Gene Transfer and Classification

• Informational genes are typically subject to vertical transfer.

• Operational genes are more likely to be subject to horizontal gene transfer.

Natural Selection

• Acts on pre-existing variation, not the cause of mutations.

Example Equations

• Molecular clock rate: $K = r imes t$ Where $K$ is the number of substitutions, $r$ is the rate of substitution, and $t$ is time.

• Average Nucleotide Identity (ANI): $ANI = \frac{\text{Number of identical nucleotides}}{\text{Total number of nucleotides compared}} \times 100\%$

Additional info: These notes expand on the provided slides and text, adding definitions, examples, and context for a comprehensive study guide on microbial evolution and taxonomy.