lecture 12 bio200

Comprehensive vocabulary flashcards covering microbial nutritional categories, oxygen requirements, laboratory techniques, domain differences, and major bacterial and archaeal groups.

Photoautotroph

An organism that utilizes light as its energy source and carbon dioxide ($CO_2$) as its carbon source.

Chemoautotroph

An organism that uses chemicals as its energy source and carbon dioxide ($CO_2$) as its carbon source.

Photoheterotroph

An organism that uses light as its energy source and organic compounds as its carbon source; some use $H_2S$ instead of water as an electron donor and may release sulfur instead of oxygen.

Chemoheterotroph

An organism that uses chemicals for energy and organic compounds for carbon, obtaining both from food or other organic material (e.g., animals, fungi, many protists, bacteria, and archaea).

Pathogen

An organism that obtains nutrients from living hosts and has the capacity to cause disease.

Obligate Aerobe

An organism that requires oxygen to survive and grow; in a culture tube, it gathers at the top where oxygen concentration is highest.

Obligate Anaerobe

An organism for which oxygen is toxic or damaging, lacking sufficient protective mechanisms against oxygen-related toxic compounds; found growing at the bottom of a culture tube.

Facultative Anaerobe

An organism that can survive with or without oxygen, preferring aerobic respiration when oxygen is present but capable of switching to anaerobic pathways; grows throughout a culture tube but is denser near the top.

Aerotolerant Anaerobe

An organism that cannot use oxygen for metabolism but tolerates its presence without harm, continuing anaerobic metabolism and growing relatively evenly throughout a culture tube.

Bacterial Oxygen Tolerance Tube Growth Patterns

Test tube patterns showing microbial oxygen requirements: A: obligate aerobes (top), B: obligate anaerobes (bottom), C: facultative anaerobes (concentrated near top and throughout), D: aerotolerant anaerobes (evenly distributed), E: microaerophiles (middle band).

Pure Culture

A laboratory culture containing only one single species of microorganism.

Metagenomics

A technique in which genetic material is collected and analyzed directly from an environmental sample without prior laboratory culturing, revealing unculturable organisms and novel evolutionary lineages.

Gram-Positive Bacteria

Bacteria possessing a cell wall with a thick peptidoglycan layer that retains crystal violet dye, staining purple/blue.

Gram-Negative Bacteria

Bacteria possessing a thin peptidoglycan layer enclosed by an outer membrane, which stains pink/red during Gram staining.

Vertical Gene Transfer

The transmission of genetic material directly from parent organism to offspring.

Lateral Gene Transfer

The movement of genetic material between distinct individual organisms, sometimes crossing species barriers.

Plasmid

A small circular piece of DNA separate from the chromosomal DNA that can replicate independently and carry specific genes, including those for antibiotic resistance.

Hadobacteria and Hyperthermophilic Bacteria

Bacterial lineages characteristically associated with and adapted to high-temperature environments.

Deinococcus radiodurans

A bacterium renowned for its extraordinary resistance to lethal levels of radiation and capacity to survive harsh environmental extremes.

Thermotoga maritima

A thermophilic, heat-loving bacterium that serves as a classic example of extensive lateral gene transfer.

Aquifex

A genus of heat-loving bacteria inhabiting extremely hot environments, including conditions near boiling temperatures.

Firmicutes

A diverse group of Gram-positive bacteria, many of which form durable endospores; contains genera such as Bacillus, Clostridium, and cell-wall-lacking Mycoplasmas.

Endospore

A dormant, highly heat-resistant structure formed inside certain bacterial cells (notably Firmicutes) to endure extreme environmental conditions until favorable conditions return.

Actinobacteria

A phylum of Gram-positive, filamentous bacteria that reproduce by binary fission; notable for soil decomposition and the commercial synthesis of antibiotics.

Cyanobacteria

Gram-negative, photosynthetic bacteria ('blue-green algae') that perform oxygen-producing photosynthesis, contributed to oxygenating Earth's atmosphere, and are evolutionary ancestors to modern plant chloroplasts.

Spirochetes

Gram-negative, spiral-shaped heterotrophic bacteria equipped with internal axial filaments for motility; includes pathogens responsible for syphilis and Lyme disease.

Treponema pallidum

A spirochete bacterium that acts as the causative pathogen of syphilis.

Borrelia burgdorferi

A spirochete bacterium that causes Lyme disease.

Chlamydias

Extremely small, Gram-negative obligate intracellular parasites that cannot reproduce independently outside of their host cells and possess two distinct developmental forms.

Proteobacteria

The largest group of Gram-negative bacteria by number of species described, exhibiting high metabolic diversity and containing representatives of all four nutritional categories.

Features of the Tree of Life

A phylogenetic comparison of cellular domains showing key synapomorphies: Bacteria possess peptidoglycan cell walls, initiate translation with formylmethionine, and have unbranched lipids; Archaea feature branched membrane lipids, lack peptidoglycan, and initiate translation with methionine; Eukarya feature membrane-bounded organelles, linear chromosomes, and unbranched lipids.

Asgard Archaea

An archaeal lineage closely related to eukaryotes that encodes genes for eukaryotic-like traits, such as cytoskeleton formation, cell shape regulation, and membrane functioning.

Lokiarchaeota

A candidate phylum of Asgard archaea identified from genetic material collected near the Loki's Castle hydrothermal vent system, offering essential insight into eukaryotic origins.

Crenarchaeota

A major group of archaea in which many members are extremophiles, such as thermophiles and acidophiles that can withstand pH values approaching zero, as well as species living in marine habitats.

Euryarchaeota

A major archaeal group composed of methanogens, extreme thermophiles, and extreme halophiles.

Methanogens

Organisms within Euryarchaeota that produce methane as a metabolic byproduct, frequently residing in animal digestive tracts and contributing to greenhouse gas emissions.

Halophiles

Salt-tolerant or salt-requiring organisms within Euryarchaeota that thrive in high-salinity aquatic environments, such as the Dead Sea.

Mycoplasmas

A group of bacteria categorized under Firmicutes that are unique for completely lacking a cell wall.

Methanopyrus kandleri

A species belonging to Euryarchaeota that is characterized as both a methanogen and an extreme thermophile.