Microbial Ecology and Immune System Overview

Lecture 20: Horizontal Gene Transfer and Genetic Divergence

Horizontal Gene Transfer

  • Horizontal gene transfer refers to the method by which species pass genes among themselves.

  • This can lead to genetic divergence, which is essential for understanding phylogeny.

Genetic Divergence

  • Genetic divergence generates phylogenetic relationships among species, which can be represented in a phylogenetic tree, a diagram showing the evolutionary relationships among various species based on their phylogeny.

  • A molecular clock helps estimate the time of divergence based on genetic mutations.

    • Example: If two species share 100% of a gene sequence, and another species shares only 50% of the gene with different mutations, this indicates a divergence that has occurred over time.

Features of a Molecular Clock Gene

  • Ideal molecular clock genes exhibit the following characteristics:

    1. Functional Consistency: The gene maintains the same function across different organisms.

    2. Uniform Generation Time: The generation time must be consistent among organisms to ensure comparable mutation rates.

    3. Constant Mutation Rate: The average mutation rate across generations remains constant.

Phylogenetic Tree Components

  • Node: A branch point in a phylogenetic tree that represents a common ancestor.

  • Root: The starting point of a phylogenetic tree from which all branches diverge, marking the initial organism in the evolutionary lineage.

  • Moving from root to tips of the branches indicates evolutionary time progression.

Mechanisms of Evolution and Divergence

  • Random Mutation: Random changes in genetic sequences.

  • Natural Selection: Favorable traits lead to increased offspring in a given environment, influenced by selective pressures.

  • Reductive Evolution: Evolution may favor organisms that reduce their metabolic costs leading to divergence in sequences.

Molecular Techniques for Phylogenetic Studies

Small Subunit rDNA Sequencing

  • Used in bacterial phylogeny, small subunit rDNA (16S rRNA) provides insights into evolutionary relationships.

  • Variable Regions and Constant Regions: Differences are noted in the variable regions of rRNA, while constant regions remain similar across species, aiding in primer design for PCR (Polymerase Chain Reaction).

  • PCR Process: - The process involves

    1. Designing PCR primers to bind to constant regions.

    2. Amplifying the variable regions of rRNA to obtain sequences for analysis.

    3. Employing sequence alignment to establish phylogenetic relationships, where divergence is quantified:

      • % Similarity = 100% - % Divergence.

Understanding Bacterial Diversity

Major Groups of Bacteria

Cyanobacteria

  • Known for oxygenic photosynthesis, have a variety of cell shapes and physiological traits.

  • Found in diverse environments including soil and water.

Actinobacteria

  • Gram-positive bacteria that share common metabolic functions and produce antibiotic compounds (e.g., Streptomyces).

Proteobacteria

  • Classified into classes: alpha, beta, gamma, and others; known for diverse metabolism.

Mycoplasma

  • Related to Firmicutes but lack a cell wall, causing them to be resistant to Gram staining.

Microbial Communities and Their Ecology

Definitions

  • Microbial Communities: Ecosystems formed by organisms interacting with one another.

  • Microbiome (or microbiota): The collection of microbes found in a specific habitat, such as the gut or soil, and reflects a diverse array of species interacting with their environment.

Metagenomics

  • Metagenome: The sum of genetic material recovered directly from environmental samples.

  • Metatranscriptomics: Studying the active genes in a sample by analyzing RNA sequences, revealing currently expressed genes.

Environmental Case Studies

Deepwater Horizon Spill Example

  • The Deepwater Horizon oil spill in the Gulf of Mexico demands a study of microbial responses to anthropogenic environmental changes.

  • Enrichment Culture: Used to favor microbial growth on specific nutrients to observe their efficiency in hydrocarbon degradation.

Class Activity

  1. Identify pairs of organisms more closely related on a phylogenetic tree.

  2. Explain the significance of using small subunit rDNA sequencing.

  3. Categorize bacterial groups as Gram-positive or Gram-negative based on specific characteristics.

Lecture 21: Analysis of Marine Samples and Niche Concept

Understanding Niches

  • Niche: The specific environmental conditions (habitat, resources, interactions) that allow an organism to thrive and reproduce in a given community.

  • Niche Construction: The process by which organisms alter their environment to create preferable biochemical conditions.

Methodologies for Studying Niches

  • FISH (Fluorescence In Situ Hybridization): A technique to visualize and analyze microbial populations spatially within their natural habitat using labeled oligonucleotide probes.

  • Flow Cytometry: Used to sort and analyze the physical properties of cells in a culture, enhancing our understanding of microbial community diversity.

Culturing and Environmental Microbes

Methods for Culturing

  • Techniques must utilize selective growth media to cultivate specific microbial populations and utilize various enrichment strategies.

  • Microfluidic Culture: Employs advanced technologies to maintain microbial interactions in controlled environments.

Environmental Microbes and Substrate Utilization

  • Microbes possess the ability to utilize virtually any organic molecule as a source of carbon or energy, playing a significant role in nutrient cycling.

Microbial Interactions

Benefits and Risks of Microbial Associations

Mutualism, Synergism, Commensalism

  • Mutualism: Interactions where both species benefit.

  • Synergism: Both species benefit but are capable of surviving independently.

  • Commensalism: One species benefits while the other does not receive harm or benefit.

Amensalism and Parasitism

  • Amensalism: One species harms another without a benefit.

  • Parasitism: One species benefits at the expense of another.

Microbial Cycling of Elements

Terrestrial Carbon Cycling

  • Essential Elements: Key elements like Carbon (C), Oxygen (O), Nitrogen (N), Hydrogen (H), Phosphorus (P), and Sulfur (S) are cycled through microbial activity in the ecosystem.

Global Carbon Reservoirs

  • Reservoirs serve as both sources and sinks for essential elements, with atmospheric CO2 acting as a critical component.

Marine Carbon Cycling

  • Impact of anthropogenic activities, such as fossil fuel combustion, increases greenhouse gas concentrations in the atmosphere and contributes to climate change effects such as ocean acidification.

Microbiome and Health

Gut-Brain Axis

  • Dysbiosis can lead to various conditions by disrupting the normal balance of gut microbiota, influencing mood and behavior through biochemical interactions.

  • Gut microbiota may play roles in obesity and metabolic disorders, highlighting the need for further understanding of microbial interactions with the host.

Class Activity

  • Explore the significance of symbiotic relationships involving microbes and design a metagenomic study to assess human gut bacterial digestion of specific foods.

Lecture 22: The Nitrogen Cycle

The Nitrogen Triangle

  • Illustrates the transformations of nitrogen within ecosystems, including fixation of atmospheric N2 into ammonia (NH3).

  • Nitrogenase: The enzyme that catalyzes nitrogen fixation, functioning anaerobically.

Nitrification and Ammonification

  • Nitrification converts NH3 to nitrites and nitrates, whereas ammonification is the breakdown of organic nitrogen into ammonia.

  • Excess nitrogen from fertilizers can lead to ecological imbalances, such as aquatic eutrophication.

Human Microbiome Studies

Benefits and Risks

  • Beneficial Microbiota: Contributes to health by facilitating digestion, producing vitamins, and protecting against pathogens.

  • Dysbiosis Risks: Imbalances can lead to infections or chronic diseases highlighting the dual role of microbiota in health.

Class Activity

  • Discuss examples of symbiotic relationships involving microbes and analyze experimental designs relevant to understanding microbiome effects on human health.

Lecture 24: The Immune System

Cells of the Immune System

  • Overview: The immune system is an integrated network of organs, cells, and tissues responsible for protecting the body from pathogens.

  • Major cell types include white blood cells (WBCs), which are composed of lymphocytes, neutrophils, and others that respond to infections.

Innate vs. Adaptive Immunity

  • Innate Immunity: Immediate, non-specific responses to pathogens through physical barriers and cellular components.

  • Adaptive Immunity: Specific responses involving T cells and B cells, with memory for faster response upon re-exposure to pathogens.

Phagocytosis and Inflammation

Mechanisms of Immune Response

  • Phagocytosis: Process whereby immune cells engulf pathogens, aided by opsonization where antibodies enhance recognition and uptake.

  • Inflammation: A key immune response involving chemical signals, recruitment of cells, and increased blood flow to sites of infection.

Class Activity

  • Examine the role of specific immune cells in recognition and response to infections, and explore the required events for B cell activation during adaptive responses.