Classification and Microbial Growth - Study Notes (copy)
Overview
Classification and Microbial Growth surveys the diversity of living organisms, why we classify them, and how classification systems have evolved from ancient ideas to modern, genome-informed frameworks. It also covers foundational concepts in microbiology, including how bacteria grow, how we culture and count them, and how binomial nomenclature and taxonomic practices are applied in the lab. The content emphasizes the shift from morphology-based groupings (e.g., Plants vs Animals) to phylogenetic and domain-based systems, and it introduces core lab techniques used to study microbial life, from growth media to dilution methods and generation time.
Major groups and the rationale for classification
Biologists have identified over 1.5 million unique organisms, with many more species likely awaiting discovery. Despite immense diversity, all living things share fundamental cellular features such as DNA, ribosomes, and plasma membranes. Classification provides universal criteria for identifying new organisms, helps arrange related organisms into groups, sheds light on evolutionary relationships, and promotes unity within the scientific community.
Taxonomy vs. Phylogenetics
Two main approaches underpin classification: Taxonomy is the science of organizing living organisms into groups based on similarities and differences. Phylogenetics involves tracking evolutionary descent by studying genetic material to infer relationships and history.
Cell theory and its historical development
The Cell Theory emerged from key historical figures: Robert Hooke in the 1600s introduced the term “cell.” Matthias Schleiden proposed that all plants are composed of cells, and Theodor Schwann asserted that all animals are composed of cells. Rudolf Virchow added a crucial principle: the cell is the basic unit of life, and all living things are made of cells; all cells arise from pre-existing cells. Together, these ideas established cells as the fundamental units of life and foundational for biology, including taxonomy and evolutionary studies.
Development of the taxonomy/classification system
Original classifications traced back to Aristotle, who split life into plants and animals based on observable features. Over time, the plant/animal dichotomy proved insufficient as microscopic organisms revealed complexities beyond movement or energy source. Movement and energy acquisition (cellular respiration vs photosynthesis) were used to distinguish early plant-like from animal-like organisms. Microscopic discoveries revealed organisms that did not fit neatly into the two groups, prompting the creation of new kingdoms and, later, more nuanced classification schemes.
Original classifications: Plantae vs Animalia
Groups were defined largely by mobility and how organisms obtained energy:
Organisms that move and derive energy through cellular respiration were grouped with animals.
Organisms that don’t move and use light energy to generate their own food via photosynthesis were grouped with plants.
As knowledge advanced, this dichotomy proved too simplistic, leading to new kingdoms and reclassifications.
Protista and Fungi: responses to microscopic diversity
Microscopic discoveries showed single-celled organisms that looked plant-like but could move, and others that defied easy placement. Protista (1866) emerged as a catch-all kingdom for such organisms, including green algae, diatoms, and dinoflagellates. Protista became the most controversial group with significant reclassifications in recent years. Fungi were originally placed with Protista due to their lack of photosynthesis and their absorptive nutrition, but later insights into their biochemistry and distinct lifestyles led to a separate Kingdom Fungi in 1959. Fungi can be macroscopic or microscopic, act as decomposers recycling nutrients by breaking down dead matter, and differ from plants (photosynthesis) and animals (ingestion).
Prokaryotic vs. Eukaryotic cells
The advent of the electron microscope revealed two major cellular architectures: Prokaryotic and Eukaryotic. Prokaryotes (including bacteria) lack a true nucleus, whereas eukaryotes possess a true nucleus. Based on these distinctions and molecular data, a new level of classification—Domain—was introduced, separating organisms into Bacteria, Archaea, and Eukarya. The term “prokaryotic” reflects the absence of a nucleus, while “eukaryotic” indicates a true nucleus.
Recent taxonomic changes: genome-based taxonomy
Taxonomic revisions moved away from relying solely on physical characteristics to assessing relationships through comparisons of genomic DNA, RNA, and protein sequences. This shift yielded more accurate evolutionary relationships and led to major reorganization, including:
Separation of Bacteria and Archaea into distinct domains.
Reorganization of many eukaryotic lineages within Domain Eukarya.
Domain classification and the three-domain system
A key refinement is the Domain-level framework, now comprising:
Domain Bacteria,
Domain Archaea,
Domain Eukarya.
Within this system, kingdoms such as Fungi, Animalia, and Plantae are contained within Domain Eukarya, and Protists are no longer a single kingdom but are distributed across the eukaryotic supergroups. Archaea share more similarities with eukaryotes in certain molecular features and membrane lipids than with bacteria, and their membranes typically feature ether-linked lipids, unlike the ester-linked lipids of bacteria and eukaryotes. Archaea and bacteria are thus kept in separate domains due to fundamental molecular differences.
Domain Archaea: biology and ecology
Archaea were first identified in extreme environments (halophiles in high salt, methanogens that produce methane, thermophiles in high temperatures). They are now known to inhabit diverse habitats — soil, water, and within organisms — including extreme environments. Interestingly, archaea are considered more closely related to humans than to bacteria in some molecular analyses, and none have been shown to cause disease in humans.
Phylogenetic Tree of Life
The phylogenetic framework presents Bacteria, Archaea, and Eukarya as major domains, with subdivisions that include bacteria such as Spirochetes, Proteobacteria, and Cyanobacteria; archaea such as Methanosarcina and Halophiles; and eukaryotic lineages including plants, animals, fungi, and diverse protists (e.g., ciliates, flagellates, and amoebae). The diagram centers on LUCA (the Last Universal Common Ancestor) and reflects deep evolutionary relationships rather than strict, fixed taxonomic ranks. This tree underpins modern thinking about evolutionary history and relationships among life forms.
Reorganization of eukaryotic organisms into supergroups
To better reflect protist diversity, eukaryotes have been reorganized into several supergroups: Excavata (e.g., Euglena); SAR (Stramenopiles, Alveolata, Rhizaria; e.g., kelp, dinoflagellates); Archaeplastida (algae and land plants, including those in Plantae); Amoebozoa (amoebas and slime molds); and Opisthokonta (animals and fungi). This classification system is widely used but remains the subject of debate among scientists.
How does an individual organism get classified?
Classification combines morphology, genetics, biochemistry, and evolutionary relationships. It involves choosing the most informative features and placing organisms within a hierarchical framework—from domain down to species—while recognizing that our understanding can change with new data.
Carl Linnaeus and the foundation of taxonomy
Carl Linnaeus (1707–1778) is regarded as the Father of Taxonomy. He popularized binomial nomenclature (Genus species) and developed a hierarchical classification system based on shared physical characteristics. A classic example is the Strawberry Tree; its formal name is Arbutus unedo. In this system, the Genus is capitalized, the species is lowercase, and the name is italicized or underlined. The standard taxonomic ranks—Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species—reflect a nested structure from broad to specific. Modern practice retains binomial nomenclature but has expanded the framework to incorporate supergroups and the three-domain concept.
Nomenclature and practical examples
Binomial nomenclature is typically used as Genus species (e.g., Arbutus unedo for the strawberry tree). The genus may be abbreviated after first use (e.g., A. unedo). In bacteria, names like Staphylococcus aureus are written in italics, with the genus capitalized and the species lowercase. The genus and species can be abbreviated as S. aureus in text. For bacteria, there is an additional layer of specificity: strains are subgroups within a species identified by numbers or letters that follow the species (e.g., Escherichia coli O157:H7). Strains may carry additional virulence factors encoded on plasmids.
Baker’s yeast as an example
A classic example of binomial nomenclature in fungi is Baker’s yeast, referred to scientifically as Saccharomyces cerevisiae. The yeast is commonly described by common names such as “sugar fungi.” In practice, the binomial name is used for precise identification, with the genus capitalized, species lowercase, and both in italics: Saccharomyces cerevisiae (often abbreviated as S. cerevisiae).
Strains and virulence factors
A strain is a subgroup of a species distinguished by one or more characteristics. Strains are denoted by additional identifiers after the epithet. For example, Escherichia coli O157:H7 produces Shiga toxin and may carry virulence plasmids that encode extra factors that enhance pathogenicity. Strains thus represent meaningful genetic and phenotypic diversity within a species.
How bacteria grow
Bacteria grow by increasing cell number through cell division, not by increasing cell size. The primary mode is binary fission, in which a single cell duplicates its DNA, elongates the cytoplasmic membrane, partitions DNA, forms a cross wall, and finally splits into two genetically identical daughter cells. The time required for division, the generation time, typically ranges from about 1 ext{ to } 3 ext{ hours} for many bacteria, though it varies by species and conditions. A standard growth model expresses the number of cells after n generations as N = N_0 2^n, though the text notes the expression as “2n” in places; the widely used form is with the exponent.
Growth requirements and environmental factors
Growth depends on physical factors:
Temperature (each species has an optimal growth temperature),
pH, and
Osmotic pressure (salt levels).
Chemical requirements include:Carbon sources (e.g., glucose), and
Inorganic nutrients (e.g., water, nitrogen, phosphorus, sulfur).
Oxygen requirements categorize organisms as:Obligate aerobes (must have oxygen),
Facultative anaerobes (can use oxygen but can grow without it),
Obligate anaerobes (prefer no oxygen and may be harmed by oxygen), and
Aerotolerant anaerobes (do not use oxygen but tolerate it).
Culturing microbes in the lab
Microorganisms grow in culture media that provide the right nutrients, salt balance, and pH. Media are sterilized, typically by steam autoclaving at temperatures between 121^ ext{C} and 134^ ext{C} for about 20 ext{ min}. Growth can occur on solid agar (in slants or plates) or in liquid nutrient broth.
Growth patterns and measurement
Bacteria multiply by binary fission, not by increasing cell size. The generation time defines how long a cell takes to divide, typically 1 ext{–} 3 ext{ hours}. Growth over generations follows the exponential pattern described by N = N_0 2^n, where N is the number of cells after n generations. The bacterial growth curve tracks population size over time and comprises four phases: Lag, Log (exponential), Stationary, and Death.
The four phases of growth
Lag phase: cells are not yet dividing; they adjust to the environment and build up energy and materials for division.
Log (exponential) phase: cells divide rapidly; population increases exponentially.
Stationary phase: nutrients become limiting; growth slows and division roughly balances cell death.
Death phase: waste products accumulate and cells die faster than they are formed.
Controlling bacterial growth and counting cells
Growth can be limited by refrigeration or freezing, heating, acidity (e.g., vinegar for pickling), or high salt (brine for preservation). Counting bacteria in a culture is challenging because numbers are enormous; common counting methods include hemocytometer counts and plate counts. Plate counting involves spreading diluted cultures on agar and counting resulting colonies.
Plate counts and their limitations
Reliable plate counts come from plates with about 30–300 colonies. Plates with more than roughly 300 colonies become too crowded to count accurately, while plates with fewer than about 30 colonies lack statistical reliability. To achieve countable plates, a dilution or dilution series is performed to reduce cell concentration before plating.
Dilutions and dilution factors
A dilution reduces concentration of a substance, whether bacterial cells or a chemical. A diluent (e.g., water, saline, or buffer) is used. A familiar example is diluting fruit punch: 1 part concentrate to 9 parts water yields a final concentration of rac{1}{10} of the original, i.e., a dilution factor of 1:10. The general dilution factor is defined as
DF = \frac{V{ ext{stock}}}{V{ ext{stock}} + V_{ ext{diluent}}}.
For a 1:10 dilution, with 1 part stock and 9 parts diluent, this becomes DF = \frac{1}{1+9} = \frac{1}{10} = 0.1 = 10^{-1}. For a 1:100 dilution, DF = \frac{1}{100} = 0.01 = 10^{-2}.
A practical example: if you dilute 1 mL of stock into 99 mL of diluent, the dilution factor is
DF = \frac{1}{1+99} = \frac{1}{100} = 0.01 = 10^{-2}.
Note that the stock (undiluted) solution has a dilution factor of 1 by definition, and later dilutions reduce the factor accordingly. In some notations, dilutions are written as 1:10, 1:100, etc.
Summary of key formulas and conventions
Generation growth: N = N_0 2^n (N0 is initial count, n is the number of generations).
Dilution factor: DF = \frac{V{ ext{stock}}}{V{ ext{stock}} + V_{ ext{diluent}}}.
For a 1:10 dilution, DF = 1/10; for a 1:100 dilution, DF = 1/100.
Temperature, pH, osmotic pressure, carbon source, and inorganic nutrients determine growth viability and rate.
Practical lab takeaways
Use selective media to inhibit some organisms while allowing others to grow, and differential media to visualize specific metabolic capabilities.
Employ a combination of morphological observations, biochemical tests, and genetic data to identify bacterial species, recognizing that horizontal gene transfer can blur species boundaries in bacteria.
Remember that binomial nomenclature and proper formatting (Genus capitalized, species lowercase, both italicized) are essential in lab reports and scientific communication.
Notes on formatting conventions used in this document
Genus species names are written with the genus capitalized and the species lowercase and italicized (e.g., Staphylococcus aureus). Abbreviations such as S. aureus may be used after the full name has been introduced.
When discussing growth equations, LaTeX formatting is used for clarity and consistency, enclosed in double dollar signs, e.g., N = N0 2^n and DF = \frac{V{ ext{stock}}}{V{ ext{stock}} + V{ ext{diluent}}}.