Micro_Chapter_10

Contributions of Key Figures

Carolus Linnaeus (1735)

• Introduced the formal system of biological classification known as binomial nomenclature, which efficiently categorizes organisms using two names: the genus and species.

• Originally classified organisms into two kingdoms: Plantae (plants) and Animalia (animals), establishing a systematic approach to naming and classifying living entities that is still in use today.

Robert H. Whittaker (1969)

• Proposed the five-kingdom system, which expanded biological classification to include:

  • Prokaryotae: Bacteria, organisms without a true nucleus.

  • Protista: Mostly unicellular organisms, including algae and protozoa that do not fit into the other kingdoms.

  • Fungi: Comprised of organisms such as molds, mushrooms, and yeast that absorb nutrients from their environment.

  • Plantae: Multicellular, photosynthetic organisms that play a crucial role in ecosystems and are essential for life on Earth.

  • Animalia: Multicellular organisms that obtain nutrients through ingestion, exhibiting complex behaviors and physiological processes.

Carl Woese (1978)

• Developed the three-domain system, providing a hierarchical framework based on genetic and molecular information rather than just morphological characteristics. The three domains are:

  • Bacteria: True bacteria with a wide range of metabolic capabilities and ecological roles.

  • Archaea: Microorganisms often found in extreme environments, distinguished from bacteria by unique membrane lipids and lack of peptidoglycan in their cell walls.

  • Eukarya: Organisms with complex cells containing a nucleus and organelles, including fungi, plants, and animals.

Definitions

• Taxonomy: The science of classification of living organisms. This discipline categorizes organisms into hierarchical taxa based on genetic, morphological, and ecological similarities and differences.

• Taxon: A group of one or more populations that share common characteristics, used in the classification process (examples include species, genus, and family).

• Phylogeny: The evolutionary history and relationships among individuals or groups of organisms, often represented in phylogenetic trees that correlate with evolutionary lineages.

Classification of Microorganisms

• Over 1,700,000 species of microorganisms have been identified, with estimates suggesting that there could be up to 8,700,000 total species, including between 0.8 to 1,600,000 species of prokaryotes alone.

• Common Characteristics of Organisms:

  • Composed of cells surrounded by a protective plasma membrane that regulates the movement of substances.

  • Utilize ATP (adenosine triphosphate) as the primary energy currency for metabolic processes.

  • Store genetic information in the form of DNA, which contains the instructions for development, functioning, and reproduction.

Domains of Life

1. Bacteria:

   • Consist of prokaryotic cells with peptidoglycan in their cell walls, facilitating structural integrity and protection.

   • Found in diverse environments, including soil, water, and within living hosts, enabling critical roles in nutrient cycling and disease processes.

   • Examples include E. coli (Escherichia coli), Streptococcus, and Bacillus, showcasing vast metabolic diversity.

2. Archaea:

   • Composed of prokaryotic cells that lack peptidoglycan in their cell walls, often living in extreme conditions such as high salinity or temperature.

   • Major groups include:

     • Methanogens: Archaea that produce methane as a metabolic byproduct, often found in anaerobic environments like wetlands.

     • Extreme Halophiles: Require very high salt concentrations for growth, found in areas such as salt lakes and evaporation ponds.

     • Hyperthermophiles: Thrive in extremely high-temperature environments, typically above 80 °C, such as hot springs and hydrothermal vents.

3. Eukarya:

   • Composed of eukaryotic cells with a nucleus and membrane-bound organelles, allowing compartmentalization of cellular processes.

   • Includes distinct kingdoms:

     • Protista: A diverse group of mostly unicellular organisms that can be autotrophic or heterotrophic, such as algae and protozoa.

     • Fungi: Multicellular (molds, mushrooms) and unicellular (yeast) organisms that digest organic matter externally and absorb nutrients through their cell walls.

     • Plantae: Multicellular, predominantly photosynthetic organisms that form the base of most ecosystems as primary producers.

     • Animalia: Multicellular organisms characterized by complex behavior and structures that ingest organic matter, covering a wide range of forms from sponges to mammals.

Identification and Classification of Microorganisms

• Microbial Identification Methods

  • Nomenclature: Uses binomial names (genus + species) for identification and communication, e.g., Salmonella enterica (genus: Salmonella, species: enterica).

Taxonomic Hierarchy

• Ranging from broadest to most specific categories:

  1. Domain

  2. Kingdom

  3. Phylum

  4. Class

  5. Order

  6. Family

  7. Genus

  8. Species

Characteristics of Prokaryotic vs. Eukaryotic Species

• Prokaryotic Species: Defined primarily by genetic similarity rather than reproductive isolation and possess simpler cell structures.

• Eukaryotic Species: Represented by four distinct kingdoms in Domain Eukarya, characterized by complex cell structures and reproductive strategies.

Identification Processes

• Specimen Collection: An essential step that precedes all identification processes to ensure accurate results.

• Phenotypic Identification:

  • Morphology: Examining cell shape and arrangement.

  • Staining Techniques: Includes Gram stain and acid-fast stain to differentiate bacteria based on cell wall characteristics.

  • Biochemical Tests: Analyzing metabolic by-products to determine species identity.

Gram Staining

• A critical method in microbiology that differentiates bacteria into Gram-positive (thick peptidoglycan layer) and Gram-negative (thin peptidoglycan layer); crucial for selecting appropriate antibiotic treatments.

Cultural Characteristics

• Initial identification clues derived from colony morphology (color, shape, size) and characteristics of growth media used (e.g., Blood Agar, MacConkey Agar).

Metabolic Testing

• Identifies biochemical pathways and metabolic functions, such as the catalase test, which determines the presence of the enzyme catalase in bacteria.

Advanced Identification Methods

• Serological Testing: Utilizes antibodies to detect specific antigens present on microbes. Techniques include:

  • Slide Agglutination Tests: Rapid identification method based on agglutination of bacteria with specific antibodies.

  • ELISA (Enzyme-Linked Immunosorbent Assay): A highly sensitive method for detecting and quantifying proteins, antibodies, or hormones.

• Molecular Techniques:

  • Nucleic Acid Amplification: Techniques like PCR (Polymerase Chain Reaction) and RT-PCR (Reverse Transcription PCR) allow for rapid identification of microorganisms based on DNA/RNA sequences.

  • Ribotyping: Classifies organisms based on the patterns of ribosomal RNA, facilitating phylogenetic analysis.

  • Fluorescent In Situ Hybridization (FISH): Employs fluorescent probes that hybridize with specific nucleic acid sequences, allowing visualization of microbes in their natural environment.

  • MALDI-TOF: Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry analyzes unique protein profiles of bacteria for rapid identification.

Conclusion

• Understanding the various classification methods and identification techniques is crucial for microbiology. It aids in accurately identifying microbes for diagnosis, treatment, and further research, ensuring advancements in microbial science and healthcare.