Microbial Classification and Nomenclature — Study Notes

Binomial nomenclature and naming conventions

• Organisms are named using binomial nomenclature: two names, genus and species (epithet).

• Genus name is capitalized; species name is not.

• First mention uses the full genus name; subsequent mentions may abbreviate the genus to its initial (e.g., Escherichia coli → E. coli).

• Example: Saccharomyces cerevisiae is the same organism as baker's yeast used in baking; common store names label it as baker's yeast, but the scientific name is $extit{Saccharomyces cerevisiae}$.

• In the supermarket, packaging may list a common name (baker's yeast) rather than the scientific binomial.

• Review question format shown: which of A, B, C, or D is the correct scientific name? (illustrates correct capitalization and two-name format)

Timeline and evolution of classification of microorganisms

• Bacteria were present on Earth around $3.5 imes 10^9$ years ago.

• Unicellular organisms (prokaryotes) preceded multicellular organisms; eukaryotes appeared around $2.5 imes 10^9$ years ago.

• There was a long timespan between these events (roughly a billion years) before complex cellular life dominated.

• The first microscope emerged roughly $3.5 imes 10^2$ years ago (about 350 years ago), enabling the discovery of microorganisms and subsequent taxonomic updates.

• Classification systems evolved as more organisms were discovered; the modern three-domain system was proposed about $47 ext{ years ago}$ by Carl Woese based on DNA sequencing.

• The three domains are: Domain Bacteria, Domain Archaea, and Domain Eukarya (also called Eukaryota).

• The three-domain system relies on sequencing specific regions of DNA to group organisms by evolutionary relationships.

Three-domain system and what each domain indicates

• Domain one: $extbf{Bacteria}$ – prokaryotic organisms with no nucleus, no membranous organelles, and usually a thick cell wall containing peptidoglycan.

• Domain two: $extbf{Archaea}$ – prokaryotes with some distinct features (cell walls lacking peptidoglycan in most species) and often extreme metabolic capabilities; many produce methane as a metabolic by-product.

• Domain three: $extbf{Eukarya}$ – eukaryotes with a true nucleus and membrane-bound organelles; includes fungi, protozoa, algae, plants, and animals.

• Prokaryotes (Domains Bacteria and Archaea) are characterized by:

  • Lack of a true nucleus; DNA is typically located in the cytoplasm as a single circular chromosome.

  • Absence of membranous organelles such as mitochondria, Golgi apparatus, and endoplasmic reticulum.

  • A cell wall that provides structural support and osmotic protection; in bacteria, this wall is normally composed of peptidoglycan.

  • Generally unicellular (single-celled) organisms.

• Eukaryotes (Domain Eukarya) are characterized by:

  • A membrane-bound nucleus containing linear DNA.

  • Membranous organelles (e.g., mitochondria, endoplasmic reticulum, Golgi apparatus).

  • Can be unicellular or multicellular.

Prokaryotes: core features and structure

• Key traits of prokaryotes (Domains Bacteria and Archaea):

  • Single cell (unicellular).

  • No nucleus; DNA resides in the cytoplasm as a circular chromosome.

  • No membranous organelles (no true mitochondria, no Golgi, no endoplasmic reticulum).

  • Thick cell wall that protects against osmotic pressure.

  • Most bacterial cell walls contain peptidoglycan (a polymer of sugars with peptide cross-links).

• Peptidoglycan structure (conceptual): the cell wall is made of a polymer with two components:

  • Peptide (amino acid) portion

  • Glycan (sugar) portion

  • This combination provides rigidity and shape to bacterial cells.

• Important terminology:

  • Prokaryote: literally "before nucleus" (from Greek protos = first, karyon = nucleus).

  • Karyon means nucleus; pro- means before.

• DNA organization in prokaryotes:

  • DNA is circular and resides in the cytoplasm (not inside a nucleus).

• Osmotic protection:

  • The thick cell wall helps protect against lysis when cells are in hypotonic environments.

• Binary fission:

  • Prokaryotes divide by binary fission: $ext{Binary fission: } 1 <br>ightarrow 2.$

Bacterial morphology: shapes

• Bacteria come in three major shapes (and a few variations):

  • Coccus (cocci, plural): spherical/rounded cells.

  • Bacillus (bacilli, plural): rod-shaped cells.

  • Spiral forms: includes spirilla and spirochetes; a common simple spiral is Vibrio, which is comma-shaped.

• These shapes account for the vast majority of bacterial forms (roughly 99.99% in the lecture's phrasing).

Archaea: distinctive traits and extremophiles

• Archaea are prokaryotes but differ biochemically from Bacteria:

  • Their cell walls do not typically contain peptidoglycan; some have pseudopeptidoglycan or other polymers.

  • Membrane lipids and metabolic pathways differ from bacterial counterparts.

• Metabolic and environmental diversity:

  • Methanogens produce methane as a by-product of their metabolism (CO2 + H2 → CH4 + H2O, for example).

  • Halophiles thrive in extremely salty environments.

  • Hyperthermophiles thrive in extremely high temperatures.

• Extremophiles expand our understanding of the limits of life and have implications in geology and industrial biotechnology.

Eukaryotes: diversity and key features

• Eukaryotes possess a true nucleus and membrane-bound organelles (e.g., mitochondria, Golgi, endoplasmic reticulum).

• They can be unicellular or multicellular.

• Major groups of microbial eukaryotes include:

  • Fungi

  • Protozoa (protozoans)

  • Algae

Fungi: structure and life cycles

• Fungi include:

  • Unicellular yeasts (e.g., budding yeasts)

  • Multicellular molds and mushrooms

• Growth form:

  • Mycelium: a network of hyphae (filaments) that spread through the substrate.

  • The fuzzy appearance of mycelia is due to abundant hyphae.

• Not plants; fungi are heterotrophs that absorb nutrients from their surroundings.

• Cell wall composition:

  • Chitin (not cellulose) is a key component of many fungal cell walls.

• Reproduction:

  • Fungi exhibit both sexual and asexual reproduction; spores produced by the mycelium enable propagation.

Protozoa: single-celled, ingestive eukaryotes

• Protozoa are single-celled eukaryotes (though some form colonies or complex life cycles).

• They possess specialized structures for ingesting food:

  • A mouth-like opening (ingestion) that allows them to take in food.

  • Pseudopods (false feet) used for feeding and locomotion; pseudopod formation involves cytoplasmic streaming and extension of the cell membrane.

• Movement organelles:

  • Cilia: numerous short hair-like structures; used for movement and feeding.

  • Flagella: usually one or two long tails; used for locomotion.

• Reproduction:

  • Protozoa can reproduce both sexually and asexually (depends on species and conditions).

• The term "protozoa" historically means "first animals" and reflects early classifications of these single-celled organisms as primitive animal-like protists.

Algae: photosynthetic eukaryotes

• Algae are diverse photosynthetic eukaryotes:

  • Green algae are often single-celled.

  • Brown and red algae are typically multicellular.

• They contribute to primary production and oxygen generation in aquatic environments.

• They can reproduce sexually or asexually, depending on species and environmental conditions.

Practical implications and connections

• The three-domain system reshaped biology by grouping life into Bacteria, Archaea, and Eukarya based on genetic data rather than solely on morphology.

• Differences between Bacteria and Archaea have implications for antibiotic targeting (peptidoglycan in bacteria makes them susceptible to certain antibiotics; many archaea lack this component).

• Prokaryotic cell structure (circular DNA, lack of membrane-bound organelles, peptidoglycan walls) supports rapid growth by binary fission and adapts to diverse environments, including extreme habitats (in Archaea).

• Eukaryotic microorganisms (fungi, protozoa, algae) introduce complexity through membrane-bound organelles, linear DNA in a nucleus, and more complex life cycles, including sexual reproduction and multicellularity (in some groups).

• Methanogenesis (Archaea) versus respiration in bacteria and eukaryotes illustrates diverse metabolic strategies and ecological roles in carbon cycling.

• Fungi, protozoa, and algae illustrate the spectrum of microbial eukaryotes from unicellular to multicellular, each with distinct cell wall components (chitin in fungi; cellulose in some algae), modes of nutrition (absorptive vs photosynthetic), and life cycles.

Quick reference: key terms and concepts

• Binomial nomenclature: two-part naming system for organisms; Genus (capitalized) + species epithet (lowercase).

• Genus abbreviation: once the full genus name has been written, it may be abbreviated to the initial (e.g., $extit{Escherichia coli} <br>ightarrow E. coli$).

• Domain: highest taxonomic rank in Woese’s three-domain system.

• Prokaryote: organisms lacking a nucleus and membranous organelles; include Bacteria and Archaea.

• Eukaryote: organisms with a nucleus and membranous organelles; include fungi, protozoa, and algae.

• Peptidoglycan: the bacterial cell wall polymer composed of peptide cross-links and glycan chains.

• Pseudopod: a temporary cytoplasmic projection used for movement and food capture in some protozoa.

• Mycelium and hyphae: the filamentous network and its branches in many fungi.

• Methanogens, Halophiles, Hyperthermophiles: archaeal groups adapted to methane production, high-salt, and high-temperature environments respectively.

• Binary fission: asexual reproduction in prokaryotes, resulting in two daughter cells; represented as $1 <br>ightarrow 2$.

Connections to foundational principles and real-world relevance

• The binomial naming system reflects the Linnaean tradition combined with modern taxonomy to provide a universal language for biology.

• The three-domain system emphasizes evolutionary relationships inferred from genetic data, aligning classification with phylogeny rather than solely morphology.

• Understanding prokaryotic cell structure and metabolism is foundational for fields like microbiology, medicine, environmental science, and biotechnology.

• Studying extremophiles (Archaea) broadens our understanding of the limits of life and informs industrial applications such as biocatalysts and bioenergy.

• Fungi, protozoa, and algae illustrate how eukaryotic microorganisms contribute to ecosystems, human health, agriculture, and industry (e.g., fermentation, biofuels, and bioremediation).