Bacterial Diversity: Cyanobacteria and Gram-Positive

Chapter Overview

• Bacterial diversity varies widely in cell structure and metabolism.
• Species include:
- Heterotrophs
- Lithotrophs
- Phototrophs
• Bacteria exhibit a vast array of life forms that inhabit every habitat on Earth, including human beings.

Bacterial Taxonomy

  • Cyanobacteria: Oxygenic phototrophs

  • Gram-positive: Firmicutes, Tenericutes, and Actinobacteria

  • Gram-negative: Proteobacteria

  • Gram-negative: Spirochetes, Acidobacteria, Bacteroidetes, and Chlorobi

  • Planctomycetes, Verrucomicrobia, and Chlamydiae (PVC Superphylum)

Bacterial Diversity Assessment

• Surveying bacterial diversity in a single chapter is like touring all the countries of a continent in one day.
• Similar to countries, bacterial taxa possess complex traits and histories, with often-contested borders.
• Despite their differences, bacteria exhibit shared major traits.

Common Features of Bacteria

  • Gene Expression Apparatus:

    • RNA polymerase

    • Ribosomal RNAs

    • Translation factors
      Note: Antibiotics often target these components.

  • Cell Walls:

    • Most bacteria possess cell walls made of peptidoglycan.
      Note: They are another target for antibiotics.

  • Phylum Definition: A phylum is a group of bacteria that shares a common ancestor, differentiated based on small-subunit rRNA (SSU rRNA) sequences.

  • Continuous discovery of diverse new bacteria, termed emerging clades.

  • Lineages with genome sequences that diverged early, before well-known phyla, are called deep-branching taxa.

Phylogenetic Relationships

  • A phylogenetic tree demonstrates the relationships amongst representative bacteria, rooted in relation to Archaea and Eukarya.

  • Black labels denote the three domains of life, while blue labels indicate phyla discussed in this chapter.

Well-Studied Bacterial Phyla

  • Cyanobacteria

  • Firmicutes, Tenericutes, and Actinobacteria (Gram-positive bacteria)

  • Proteobacteria (Gram-negative)

  • Deep-branching Gram-negatives

  • PVC superphylum (Planctomycetes-Verrucomicrobia-Chlamydiae)

Deep-Branching Gram-Negative Microbes

  • These bacteria have diverged distantly from Proteobacteria, showcasing diverse metabolism and morphology.

  • Bacteroidetes and Chlorobi (obligate anaerobes):

    • Bacteroides:

      • Ferments complex carbohydrates; typically present in gut microbiome.

      • Characteristics:

        • Gram-negative, non-sporulating rods with gliding motility (though not all).

        • Capable of aerobic or fermentative saccharolytic metabolism.

        • Bacteroidales - obligate anaerobic fermenters that produce acetate and succinate.

        • Typically commensals, aiding in digestion.

        • Synthesize sphingolipids (sphingosine instead of glycerol).

    • Chlorobi:

      • Anaerobic “green sulfur” phototrophs.

      • Utilize H2S as an electron donor (oxidized to SO4²⁻) and deposit S0 extracellularly.

      • May be thermophilic and have pigments stored in chlorosomes.

      • Very efficient in low light intensities and inhabit anoxic, sulfidic environments.

    • Nitrospirae: Oxidize nitrite (NO2⁻) to nitrate (NO3⁻).

    • Acidobacteria: Soil bacteria, make up to 50% of the soil community, involved in nitrogen cycling.

    • Fusobacteria: Includes human pathogens (e.g., septicemia, skin ulcers).

Deep-Branching Thermophiles

  • Cluster near the evolutionary root.

  • Aquificae and Thermotogae:

    • Most extreme bacterial hyperthermophiles.

      • Aquifex pyrophilus: the most thermophilic; it's a flagellated rod and microaerophilic, functioning as a hydrogen chemolithotroph.

      • Thermocrinis ruber:

        • Forms filamentous mats in hydrothermal vents and are chemolithotrophic sulfur oxidizers.

        • Grows optimally at 80°C, known for ‘pink streamers’ of filamentous cells.

      • Thermotoga maritima:

        • Gram-negative, non-sporulating, fermentative anaerobes found in hot springs/hydrothermal vents.

        • Contains a unique sheathed envelope.

        • Shares extensive gene sequences with hyperthermophilic Archaea due to lateral gene transfer (LGT).

      • Typically exhibit fast growth rates and high mutation rates, may appear to have diverged earlier than they actually did.

Deep-Branching Thermophilic Phototrophs

  • Chloroflexi:

    • Photoheterotrophic and moderately thermophilic.

    • Green nonsulfur bacteria with photosynthetic apparatus within chlorosomes.

      • Forms filamentous mats alongside thermophilic cyanobacteria; pigmentation may appear red or yellow due to accessory pigments.

Cyanobacteria: Oxygenic Phototrophs

  • All oxygen gas in Earth’s atmosphere derives from cyanobacteria and plant chloroplasts, which evolved from an ancient cyanobacterium.

  • The phylum Cyanobacteria (Cyanophyta) is named for the blue phycocyanin accessory pigments found in some genera.

  • Genus Synechococcus and Prochlorococcus are the most abundant phototrophs in oceans; Microcystis can form harmful freshwater blooms.

Cyanobacterial Cell Structure

  • Only oxygenic phototrophic prokaryotes.

  • Morphologically diverse, containing chlorophyll and accessory pigments.

  • Conduct photosynthesis within thylakoids.

  • Fix carbon dioxide in specialized structures called carboxysomes.

  • Maintain buoyancy with gas vesicles and many can fix nitrogen in heterocysts.

Types of Cyanobacteria

  • Single-celled: Examples include Synechococcus and Prochlorococcus (ocean dominance) and Microcystis (toxic blooms).

  • Filamentous: Examples include Oscillatoria, Nostoc (differentiated cells), and Anabaena (forms akinetes that resist desiccation).

Cyanobacterial Communities

  • Associated with diverse organisms including animals, plants, fungi, and protists.

  • Sponges in coral reefs may host cyanobacterial communities that provide nutrients.

  • Participates in multilayered microbial mats in environments like salt marshes.

Gram-Positive Bacteria Overview

  • Comprise three major phylogenetic branches:

    • Firmicutes: “Low-GC” species.

    • Actinobacteria: “High-GC” species.

    • Tenericutes: do not possess a cell wall.

Firmicutes - Genus Overview

  • Bacillales:

    • Genus Bacillus:

      • One of the first classified bacterial genera.

        • B. subtilis is a model system for Gram-positive study; B. anthracis is a soil resident and anthrax agent.

        • Develop inert endospores in starvation, germinating in favorable conditions.

        • B. thuringiensis, an effective biological control and produces crystal toxin, delta endotoxin.

Clostridiales - Genus Overview

  • Genus Clostridium:

    • Produces endospores that swell to form a drumstick shape, undergoes fermentation, lacks ETC.

    • Notable species: C. botulinum (botox), C. tetani (tetanus), C. difficile (antibiotic-associated diarrhea).

    • Metabacterium polyspora:

      • Larger anaerobic commensal in the guinea pig GI tract, forms multiple endospores.

Non-Spore-Forming Firmicutes

  • Includes Bacillales, Clostridiales. Comprise many non-spore-forming rods and cocci.

  • Lactic Acid Bacteria: Aerotolerant, low GC, include Lactococcus, Lactobacillus, and Leuconostoc (food production).

  • Listeria monocytogenes:

    • Facultative anaerobe, contaminates food products causing listeriosis (severe gastroenteritis).

    • Propels its way through host cells using an actin propulsion system.

Staphylococcus and Streptococcus

  • Staphylococcus: Cocci in clusters, facultative anaerobes; includes S. aureus (MRSA).

  • Streptococcus: Chain-forming, aerotolerant cocci; includes S. pneumoniae and S. pyogenes.

Other Non-Spore-Forming Firmicutes

  • Dehalobacter: Anaerobic dechlorinators, degrading chlorinated pollutants.

Tenericutes

  • Have completely lost cell walls and peptidoglycan layers.

  • Sterols protect against osmotic stress; known for Mycoplasma, the causative agent of pneumonia and meningitis.

Actinomycetes - Streptomyces Overview

  • Order within Actinobacteria; resembles fungal morphology with filamentous growth.

  • Major soil organisms, aerobic, significant antibiotic producers.

  • Produce geosmin (earthy metabolite), with about 50% antibiotic production.

Actinomycetes Associations

  • Many associate with animals; in marine environments, sponges harbor actinobacteria that produce antibiotics.

  • Leaf-cutter ants cultivate Streptomyces for antifungal purposes.

  • Frankia species form nitrogen-fixing nodules with alder trees.

Nonmycelial Actinobacteria

  • Mycobacterium:

    • Rod-shaped, thick cell walls with mycolic acids; pathogen for tuberculosis and leprosy.

  • Corynebacterium diphtheriae:

    • Causes diphtheria; peculiar cell division via a snapping mechanism.

  • Arthrobacter: Unusual cell cycle with transformations between shapes.

Summary of Chapter 18 Thought Questions

Transition

  1. Discuss structural diversity and ecological function/metabolism divergence in bacteria.

  2. Select a specific organism to exemplify how structure relates to function.

Gram-Negative Overview

  • Share a triple-layered cell envelope; display diverse metabolism through minor biochemical modifications.

  • Alphaproteobacteria: Second-largest class, includes nitrogen-fixers like Rhizobium and Agrobacterium.

  • Betaproteobacteria: Nitrifiers and pathogens such as Neisseria gonorrhoeae.

  • Gammaproteobacteria: Largest and most diverse; includes Pseudomonas (opportunistic pathogen) and Enterobacteriaceae (E. coli).

  • Deltaproteobacteria: Myxobacteria and Bdellovibrio (predatory).

  • Epsilonproteobacteria: Includes Campylobacter (food poisoning) and Helicobacter pylori (gastritis).

Phylogenetic Overview of Spirochetes and Other Classes

  • Spirochetes demonstrate corkscrew motility and diverse ecological roles.

  • Identifiable through a unique cell structure with an outer sheath and endoflagella.

  • Various genera include Treponema (syphilis), Borrelia (Lyme disease), and others that assist in digestion in mutualistic relationships.

Acidobacteria and Bacteroidetes

  • Acidobacteria thrive in diverse conditions, often in soils.

  • Bacteroidetes play essential roles in human gut flora.

PVC Superphylum Highlights

  • Planctomycetes, Verrucomicrobia, and Chlamydiae constitute the PVC superphylum.

  • These phyla exhibit unique cell wall structures and developmental strategies, with Planctomycetes having nucleus-like compartments and Chlamydiae featuring an intracellular lifecycle involving elementary and reticulate bodies.