Microbio Exam 3

16S rRNA

Small-subunit ribosomal RNA in prokaryotes used to infer phylogeny.

18S rRNA

Small-subunit ribosomal RNA in eukaryotes used for phylogeny.

Banded Iron Formation

Layered iron-rich rock formed as oxygen reacted with reduced iron.

Black Queen Theory

Loss of dispensable genes may conserve resources when community members provide the function.

Genetic Drift

Random change in allele/gene frequencies, especially after bottlenecks.

Endosymbiosis

One organism lives inside another; origin of mitochondria and chloroplasts from bacterial partners.

Evolutionary Selection

Differential survival/reproduction favoring traits that increase fitness.

Genome fingerprinting

Comparing characteristic DNA fragment patterns among strains.

Great Oxidation Event

Major rise in atmospheric oxygen ~2.4 billion years ago.

Great Plate Anomaly

Most environmental microbes detected by molecular methods do not grow on routine laboratory plates.

LUCA

Last Universal Common Ancestor of living cells.

Metagenomics

Analysis of DNA recovered from an entire community.

Metatranscriptomics

Analysis of RNA transcripts expressed by an entire community.

Metabolomics

Analysis of metabolites produced in a sample.

Molecular phylogeny

Evolutionary relationships inferred from nucleotide sequences.

Molecular Sequencing

Determining nucleotide order in DNA or RNA.

Phenotypic phylogeny

Evolutionary comparisons based on morphological, physiological, metabolic, and chemical traits.

Phenotypic phylogenic analysis

Comparing multiple observable cell traits to distinguish organisms.

Phylogeny

Evolutionary history of organisms or features.

Phylogenetic Tree

Branching diagram showing inferred evolutionary relationships.

Phylogenetic Species

Cluster of closely related strains sharing ancestry, distinct from other clusters by multiple gene sequences.

Polyphasic Systematics

Classification using molecular and phenotypic evidence together.

rep-PCR

PCR fingerprinting of repetitive genomic sequences.

Ribotyping

DNA fingerprinting focused on ribosomal RNA gene regions.

RNA World

Hypothesis that early RNA acted as both genetic material and catalyst.

SSU rRNA

Small-subunit ribosomal RNA; 16S in prokaryotes and 18S in eukaryotes.

Subsurface Origin Hypothesis

Hypothesis that life originated at stable hydrothermal systems below the ocean surface.

Whole genome sequence analysis

Comparison of complete genomes including gene content, order, and composition.

Ammonification

Conversion of organic nitrogen to ammonium.

Anammox

Anaerobic conversion of nitrite and ammonia to nitrogen gas.

Biogeochemistry

Study of biologically mediated chemical transformations.

Carbon Fixation

Incorporation of inorganic CO₂ into organic compounds.

Climate Change

Long-term environmental shifts including warming, acidification, and altered habitats.

Coupled cycles

Interconnected nutrient cycles that influence one another.

Denitrification

Reduction of nitrate to gaseous nitrogen.

Ecosystem

Organisms and abiotic factors in an environment.

Eutrophication

Excess nutrient enrichment leading to algal blooms and oxygen depletion.

Guild

Metabolically related microbial populations in a community.

Habitat

Part of an ecosystem where a community lives.

Metagenomic analysis

Sequencing/analysis of environmental community DNA.

Microenvironment

Immediate surroundings of a microbe.

Nitrification

Oxidation of ammonium to nitrate.

Nitrogen Fixation

Conversion of atmospheric N₂ into ammonia.

Realized niche or prime niche

Prime niche

Species abundance

Number of individuals of each taxon.

Species richness

Number of different taxa present.Commensalism

Mutualism

Both partners benefit.

Symbioses

Close relationships between different organisms.

Parasitism

One partner benefits at the other’s expense.

Pathogenic

Capable of causing disease.

Antigenic Variation

Changes to microbial surface antigens that reduce immune recognition.

Opportunistic Infection

Disease caused by normally harmless organisms when conditions change.

Parenteral

Entry through broken skin or tissues, such as punctures, bites, or injections.

Infection

Microorganism enters, establishes, and grows in a host; may occur without disease.

Infectious Dose (ID)

Number of organisms needed to establish infection or disease.

Invasive

Able to grow/spread in host tissues in ways that impair function.

Secretion Systems

Microbial machinery for transporting proteins or effectors outside cells or into other cells.

Colonized

Microorganism has established and grown on or in a host.

Disease

Disruption of normal host structure or function.

AB Toxin

Two-part toxin

Acute Infection

Infection with relatively rapid onset and short course; not explicitly defined in these slides.

Antitoxin

Antibodies against a specific toxin.

Attenuation

Decrease or loss of virulence.

Cytopathic Effects (CPE)

Direct damage or functional changes in host cells caused by infection.

Cytotoxin

Toxin that damages or lyses cells.

Endotoxin

Gram-negative bacterial lipopolysaccharide that triggers inflammation.

Enterotoxin

Toxin affecting the intestinal tract.

Exotoxin

Toxic protein released by a pathogen or infected cell.

Hypersensitivity

Excessive immune reaction that can damage host tissue.

Lethal Dose (LD)

Amount of microbe or toxin needed to cause death.

Leukotoxin

Toxin that damages white blood cells; not separately defined in slides.

Mycotoxin

Toxic secondary metabolite produced by fungi.

Pathogenesis

Process by which disease develops.

Pathogenicity

Ability to cause disease.

Pathology

Disease-associated changes to normal tissue or function.

Superantigen

Toxin that broadly activates immune cells and causes excessive inflammation.

Syndrome

Group of signs and symptoms occurring together; not separately defined in slides.

Tissue Specificity

Preference for particular tissues based partly on host receptors.

Toxemia

Presence of toxin in blood.

Toxigenicity

Ability to produce toxins.

Toxoid

Inactivated toxin used in a vaccine.

Virulence

Degree or severity of pathogenicity.Bacteriocytes

Causation

A change in one factor directly produces a change in another.

Coral Bleaching

Loss of coral color due to loss or damage of photosynthetic symbionts.

Correlation

Association between variables without proof of cause.

Ectosymbiosis

Symbiotic partner lives on the exterior of another organism; term not separately defined in slides.

Endomycorrhizae

Fungal mycelium grows deeply into plant root tissues.

Endosymbiosis

One organism lives inside another; origin of mitochondria and chloroplasts from bacterial partners.

Extomycorrhizae

Spelling in guide for ectomycorrhizae

Fecal Microbial Transplantation (FMT)

Transfer of fecal microbiota to restore a recipient gut community.

Foregut Fermentation

Fiber fermentation in a chamber before the small intestine.

Hindgut fermentation

Fiber fermentation in the cecum and/or large intestine.

Lichens

Mutualistic association between fungus and phototrophic alga/cyanobacterium.

Microbial antagonism

Competition between microbes, including occupation of niches and antimicrobial production.

Microbiome

Microbial community plus collective genes and interactions in an environment/host.

Microbiota

Microorganisms living in a particular environment or host site.

Mycorrhizae

Mutualistic associations between fungi and plant roots.

Nitrogenase

Oxygen-sensitive enzyme used to fix N₂ into ammonia.

Nod Factors

Rhizobial signals involved in establishing root-nodule symbiosis.

Prebiotic

Substance that enhances growth of beneficial/normal microbiota.