Microorganism Classification: Taxonomy, Domains, and Characteristics

Taxonomy

the science of biological classification

Classification

grouping organisms into taxa based on mutual similarity or evolutionary relatedness

Identification

characterization of an isolate to determine what species it is

Nomenclature

assignment of names to taxonomic groups in agreement with published rules

Anaerobic Jar and Chamber

used to hold petri plates supporting cultures

Carolus Linnaeus

developed a new way to categorize plants and animals

Ernst Haeckel

wrote General Morphology of Organisms, proposing four kingdoms

Robert Whittaker

proposed adding a fifth kingdom (fungi) to the tree of life

Systematics

study of the diversity of life (both past and present) and the relationships among living things through time

Species (in prokaryotes)

collection of strains that share stable properties in common and differ significantly from other group of strains

Species (in eukaryotes)

a group of closely related organisms that breed among themselves

Strain

population of organisms that descends from a pure culture isolate or from a species

Carolus Linnaeus

The most famous early taxonomist was a Swedish botanist, zoologist, and physician named ________ (1701-1778)

Systema Naturae

Published by Carolus Linnaeus, it proposed the Linnaean taxonomy

Haeckel Tree

1st attempt to depict the common evolutionary history of all living cells (by Ernst in 1866)

Three Kingdom Tree

Included Protista for unicellular organisms and Monera for unicellular organisms whose cells lack nuclei

Protista

for unicellular organisms

Monera

unicellular organisms whose cells. lack nuclei; ancestral to other forms of life

Whittaker Tree

Five-Kingdom Tree proposed adding another Kingdom (Fungi)

Prokaryota

Contained just the Kingdom Monera in the Whittaker Tree

Eukaryota

Contained the kingdoms: Fungi, Protista, Plantae, and Animalia in the Whittaker Tree

Carl Woese

Proposed a genetics-based tree of life with 6 Kingdoms: Eubacteria, Archaebacteria, Protista, Fungi, Plantae, Animalia

Archaebacteria

Significantly different from other bacteria and eukaryotes in terms of 16S rRNA gene sequences

Three Domains of Life

Divides cellular life forms into Archaea, Bacteria, and Eukaryote domains.

16S rRNA gene

Differences in ribosomal RNAs that synthesize new proteins.

Binomial Nomenclature

A two-word naming system for identifying organisms by genus and species.

Generic Name

Can change if the organism is assigned to another genus because of new information.

Specific Name

Stable; the oldest epithet for a particular organism takes precedence and must be used.

Candidatus

Provisional taxonomic name appended to candidate taxonomic ranks.

Thiomargarita namibiensis

Known as the Sulfur Pearl of Namibia.

Taxon

group

Taxa

groups

Species

Each distinct kind of organism is designated as a species.

Bergey's Manual of Systematic Bacteriology

A standard reference for identifying and classifying different prokaryotes.

Bergey's Manual of Determinative Bacteriology

A standard reference for identifying and classifying different prokaryotes.

International Code for the Nomenclature of Bacteria

Established in 1991, it provides rules for naming bacteria.

International Journal of Systematic Bacteriology (IJSB)

A publication related to the taxonomy and classification of bacteria.

International Journal of Systematic and Evolutionary Microbiology (IJSEM)

Official publication of record for taxonomy and classification of Bacteria, Archaea, and microbial eukaryotes.

Characterization and Identification

Involves the study of a population of identical cells, not a single cell.

Pure culture

A prerequisite for characterization and identification.

Reasons for doing characterization

Identification purposes, comparison with other organisms, and exploiting beneficial characteristics.

Cultural characteristics

Affected by the nutrients required for growth and the physical conditions of an environment that will favor growth.

Nutritional types

Based on energy source and carbon source.

Photoautotroph

Uses sunlight as energy source and CO2 as carbon source.

Photoheterotroph

Uses sunlight as energy source and organic compounds as carbon source.

Chemoautotroph

Uses inorganic chemicals (H2, NH3, NO2-, Fe2+, H2S) as energy source and CO2 as carbon source.

Chemoheterotroph

Uses organic compounds (sugars, amino acids, etc.) as energy source.

Psychrophile

Grows between -5 and 15°C.

Psychrotroph

Grows between 20 and 30°C but grows well at lower temperatures.

Mesophile

Grows between 25 and 45°C.

Thermophile

Grows between 45 and 70°C.

Hyperthermophile

Grows between 70 and 110°C.

Acidophile

Optimal pH below 5.5.

Neutrophile

Optimal pH between 5 and 8.

Alkaliphile

Optimal pH above 8.5.

Metabolic characteristics

Biochemical/physiological characteristics, i.e., presence of enzymes, fermentation of sugar.

Citrate Test

A test used to determine the ability of an organism to utilize citrate as its sole carbon source.

Methyl Red reaction

A test that indicates the production of stable acid end products from glucose fermentation.

Gram Negative

Refers to bacteria that stain pink in the Gram staining procedure, indicating a thin peptidoglycan layer.

Gram Positive

Refers to bacteria that stain violet in the Gram staining procedure, indicating a thick peptidoglycan layer.

Cell Wall Chemistry

The chemical composition and structure of the cell wall that determines the classification of bacteria.

Cell Membrane Chemistry

The chemical composition and structure of the cell membrane that regulates the entry and exit of substances.

Capsule Chemistry

The chemical composition of the capsule surrounding some bacteria, which can protect against phagocytosis.

Antigen

A molecule that binds to a specific antibody, often stimulating a response in the immune system.

Antigenic

Describing a substance that can provoke an immune response.

DNA Hybridization

A technique used to identify the presence of specific DNA sequences by hybridizing complementary strands.