Chapter 11 Prokaryotes: The archaea and bacteria domain

Introduction to Domains

• Study of the domains of Archaea and Bacteria

• Focus on characteristics of Bacteria and Archaea

• Differentiation among various members of the Bacteria domain

Classification of Bacteria

Overview of Bacteria and Archaea

• Domains categorized into Bacteria and Archaea

• Subclassification within Bacteria: phyla, and selected classes

  • Gram Positive Bacteria

    • Phyla: Firmicutes and Actinobacteria

      • Firmicutes

        • Low GC content

        • Classes: Bacilli and Clostridia

      • Actinobacteria

        • High GC content

  • Gram Negative Bacteria

    • Phylum: Proteobacteria

      • Classes: Alpha to Epsilon Proteobacteria

• In Archaea: Phylum Crenarchaeota

  • Class: Thermoprotei (thermophiles, hyperthermophiles)

Metabolic Diversity in Bacteria

• Photosynthetic bacteria: Cyanobacteria (oxygenic) vs Chlorobi (anoxygenic)

  • Cyanobacteria: Use oxygen

  • Chlorobi: Do not use oxygen

• Chloroflexi: Another group of anoxygenic photosynthetic bacteria

  • Distinction: Chloroflexi are green non-sulfur bacteria while Chlorobi are green sulfur bacteria

• Chlamydia: Intracellular parasites, reproducing within eukaryotic cells

Classification Techniques

• Use of ribosomal RNA sequences for classification

• Dichotomous tree reflects classification of prokaryotes

  • Peptidoglycan signature for Bacteria

  • Pseudomurein signature for Archaea

Gram Reaction and Classification

Gram-negative Bacteria

• Subdivided into Gram negatives (red stain) and Gram positives (purple stain)

  • Gram positive:

    • Firmicutes (low GC) and Actinobacteria (high GC)

  • Gram negative: Morphological classification into Proteobacteria or non-Proteobacteria

• Proteobacteria

  • Largest group, diverse shapes

  • Types: Alpha, Beta, Gamma, Delta, Epsilon

Alpha Proteobacteria Characteristics

• High adaptability in low-nutrient environments

• Can exist in symbiotic relationships, some pathogenic to humans

• Dichotomous classification based on metabolic activity

  • Some produce (e.g., Rickettsia) and some are non-pathogenic (e.g., Wolbachia)

• Chemoautotrophic plant pathogens: e.g., Rhizobia fix nitrogen in legume roots

Noteworthy Members of Alpha Proteobacteria

• Pelagibacter ubique: Prolific in oceans, termed ubiquitous

• Pathogeic Members:

  • Bartonella: Cat scratch disease (Bartonella henselae)

  • Brucella: Causes brucellosis

  • Rickettsia: Transmitted by arthropods, causes spotted fevers

    • Examples include Rickettsia prowazekii and Rickettsia rickettsii

Environmental Members

• Caulobacter: Has prosthecae extensions for nutrient absorption

• Hyphomicrobium: Forms hyphae-like structures for nutrient uptake

• Nitrogen fixers: Azospirillum, Rhizobium, and Bradyrhizobium forming nodules in plant roots

Beta Proteobacteria Characteristics

• Utilize nutrients from decaying organic matter

• Pathogenic Members:

  • Azoarcus: Oxidizes sulfur compounds

  • Sphaerotilus and Spirillum: Adapt to freshwater and sewage environments

  • Bordetella: Causes whooping cough, with vaccination available

Gamma Proteobacteria Characteristics

• Largest subgroup with various physiological traits

• Pseudomonas: Notorious for hospital infections, diverse metabolism

• Legionella pneumophila: Causes Legionnaires' disease, discovered in cooling towers

• Vibrionales: Includes Vibrio cholerae, causes cholera

• Enterobacteriaceae: Ferment carbohydrates in intestines, include Enterobacter and Escherichia

Delta Proteobacteria Characteristics

• Few members focus on predation of other bacteria and sulfur cycling

  • Bdellovibrio: Predatory bacteria attacking others

  • Desulfovibrio: Reduces sulfur, found in anaerobic environments

Epsilon Proteobacteria Characteristics

• Microaerophilic and helical bacteria include:

  • Campylobacter: Causes gastroenteritis

  • Helicobacter: Known for stomach infections and ulcers, only bacterium known to cause stomach cancer

Gram-positive Bacteria Overview

Classification of Gram-positive Bacteria

• Actinobacteria: High GC content; includes pathogenic members like Corynebacterium diphtheriae

• Firmicutes: Low GC content; examples include Clostridium species

  • Notable pathogens: Clostridium botulinum, Clostridium perfringens, Clostridium difficile

Unique Characteristics of Actinobacteria

• Form filaments and conidia (e.g., Streptomyces)

• Include nitrogen-fixing bacteria (e.g., Frankia)

• Mycoplasma: Unique in lacking a cell wall, causes atypical pneumonia

Characteristics of Non-Proteobacteria Gram Negatives

• Include various bacteria like Chlamydia, Bacteroidetes, Cytophaga, Fusobacteria

Photosynthetic Bacteria

Types of Photosynthetic Processes

• Oxygenic Photosynthesis: Involves water and CO2 to produce glucose, water, and O2

• Anoxygenic Photosynthesis: Uses compounds like hydrogen sulfide, produces carbohydrates and sulfur

• Notable examples include Anabaena and green sulfur bacteria

Domain Archaea Overview

• Extremophiles like hyperthermophiles (e.g., Pyrodictium), methanogens (e.g., Methanobacterium), and extreme halophiles (e.g., Halobacterium)

Conclusion

• Diversity of microorganisms comes from mutations and horizontal gene transfer

• Adaptations to varied microenvironments reinforce bacterial diversity throughout this chapter.

Introduction to Domains

• Study of the Domains of Archaea and Bacteria: An exploration into the classification and characteristics of prokaryotic life forms, specifically focusing on the two distinct domains: Bacteria and Archaea.

• Focus on Characteristics of Bacteria and Archaea: Understanding the structural, metabolic, and reproductive traits that differentiate these two domains, alongside their ecological roles.

• Differentiation Among Various Members of the Bacteria Domain: Delve into the vast diversity and specific traits that characterize different bacterial species, which are essential for identifying their function and interaction in ecosystems.

Classification of Bacteria

• Overview of Bacteria and Archaea: Both domains are categorized into various phyla, and special attention is given to their unique attributes.

• Domains Categorized into Bacteria and Archaea: This bifurcation reflects significant evolutionary divergences, highlighting distinct characteristics such as cellular structure, membrane composition, and genetic material.

Subclassification within Bacteria: Phyla and Selected Classes

Gram Positive Bacteria

• Phyla: Firmicutes and Actinobacteria: These phyla include bacteria with unique cell wall properties that affect their staining in Gram staining processes.

• Firmicutes: Characterized by low guanine-cytosine (GC) content; includes notable classes such as:

  • Bacilli: Rod-shaped bacteria that often form endospores, enhancing survival.

  • Clostridia: Anaerobic, spore-forming bacteria often associated with fermentation and pathogenic properties.

• Actinobacteria: Showcasing high GC content, this phylum includes:

  • Streptomyces: Known for their filamentous structures and antibiotic production.

  • Pathogenic members such as Corynebacterium diphtheriae.

Gram Negative Bacteria

• Phylum: Proteobacteria: One of the largest and most diverse groups with varied shapes and metabolic capabilities, including classes:

  • Alpha to Epsilon Proteobacteria: With grades of oxygen requirements and ecological roles.

• Gram Negative: Identified by their thin peptidoglycan layer and outer membrane, affecting their resistance to antibiotics. They exhibit diverse morphologies, categorized into:

  • Proteobacteria: Includes significant pathogens and environmental bacteria.

  • Non-Proteobacteria: Encompassing distinct bacterial families that thrive in various ecological niches.

Metabolic Diversity in Bacteria

• Photosynthetic Bacteria: Distinction is made between:

  • Cyanobacteria: Oxygenic, using sunlight, releasing oxygen as a byproduct.

  • Chlorobi and Chloroflexi: Anoxygenic, utilizing sulfide or organic compounds in their photosynthesis, with specific characteristics promoting their differentiation.

• Chlamydia: Known as intracellular parasites, they depend entirely on host cells for nutrients and reproduction.

Classification Techniques

• Ribosomal RNA Sequences for Classification: Employing molecular techniques based on the sequencing of ribosomal RNA genes to elucidate phylogenetic relationships among prokaryotes.

• Peptidoglycan Signature for Bacteria: The presence of peptidoglycan in bacterial cell walls serves as a critical taxonomic tool.

• Pseudomurein Signature for Archaea: Distinctive to archaeal domains, helping to further classify and differentiate.

Gram Reaction and Classification

• Gram-negative Bacteria: Divided into groups based on their Gram staining behavior, influencing pathogenicity and treatment methodologies.

• Gram-positive Bacteria: Undergo staining into categories based on their peptidoglycan content; includes essential pathogens.

Noteworthy Members of Proteobacteria

Alpha Proteobacteria

• Characteristics: Exhibit high adaptability, often found in low-nutrient environments. Notably form symbiotic relationships or exhibit pathogenic behaviors.

• Key Members:

  • Pelagibacter ubique: Ubiquitous in ocean environments, contributing to marine ecosystems.

  • Pathogenic Members: Include Bartonella (Causing cat scratch fever) and Rickettsia (Transmitted via arthropods, responsible for spotted fevers).

Beta Proteobacteria

• Characteristics: Often involved in nutrient cycling within ecosystems.

• Pathogenic Members:

  • Bordetella: Notorious for causing whooping cough.

Gamma Proteobacteria

• Diversity: The largest subgroup, encompassing varied physiological traits and notable pathogens.

Delta Proteobacteria

• Focus on Predation: A unique ecological role in predating on other bacteria.

Epsilon Proteobacteria

• Microaerophilic and Helical Characteristics: Key members include Helicobacter known for its role in stomach ulcers and cancer.

Gram-positive Bacteria Overview

• Significant Pathogens: Such as Clostridium species, which can cause severe diseases ranging from botulism to colitis.

Characteristics of Non-Proteobacteria Gram Negatives

• Diverse Forms: Include notable groups like Chlamydia responsible for sexually transmitted infections.

Photosynthetic Bacteria

• Oxygenic vs. Anoxygenic: Compounds utilized for photosynthesis vary, showcasing their ecological adaptations.

Domain Archaea Overview

• Extremophiles: Includes various groups such as hyperthermophiles and halophiles, exhibiting remarkable adaptations to extreme environments.

Conclusion

• Bacterial Diversity: Driven by environmental pressures, mutations, and horizontal gene transfer, reinforcing the complex interactions within microbial communities.