Module 8 Flashcards

A set of vocabulary flashcards covering prokaryotic habitats, biogeochemical cycling, symbiotic relationships, human microbiome dynamics, taxonomy, and biochemical identification methods.

Paracoccus denitrificans

A soil-dwelling bacterium capable of surviving hyperacceleration up to $2.4\,g$ (a force equivalent to the surface gravity of Jupiter).

Humus

A nutrient-rich soil component formed when soil bacteria metabolize plant root exudates and release nutrient-rich byproducts back into the soil.

Halobacterium salinarum

A halophilic archaeon that thrives in hypersaline environments like the Dead Sea, decomposing dead brine shrimp to release metabolic products that nourish juvenile brine shrimp and flies.

Carbon Fixation

The process by which prokaryotes convert inorganic carbon dioxide ($\text{CO}_2$) into organic molecules accessible to heterotrophic organisms.

Nitrogen Fixation

The conversion of atmospheric nitrogen ($\text{N}_2$) into ammonia ($\text{NH}_3$), an inorganic form plant species assimilate to synthesize amino acids and nucleic acids.

Rhizobium

A genus of nitrogen-fixing bacteria that resides inside specialized root nodules of legumes to produce ammonia required for plant biomolecule synthesis.

Bioremediation

The process in which prokaryotic communities degrade toxic chemical pollutants contaminating aquatic and terrestrial ecosystems.

Microbial Ecology

The study of interactions between microbial populations and their abiotic and biotic environment.

Mutualism

A symbiotic interaction ($+/+$) in which both participating populations benefit, such as Bacteroides thetaiotaomicron digesting complex plant polysaccharides in the human intestinal tract.

Amensalism

A symbiotic relationship ($-/0$) where Population A is harmed while Population B remains unaffected, such as Staphylococcus epidermidis secreting bacteriocins that destroy competing bacterial species.

Commensalism

A symbiotic relationship ($+/0$) where Population A benefits while Population B is unaffected, such as Staphylococcus epidermidis feeding on sloughed-off dead human skin cells.

Neutralism

A symbiotic interaction ($0/0$) where neither population is affected in any way, such as active vegetative bacterial cells coexisting alongside dormant endospores in soil.

Parasitism

A symbiotic relationship ($+/-$) where Population A benefits at the direct expense and harm of Population B.

Resident Microbiota

Microorganisms that permanently reside in or on the human body.

Transient Microbiota

Microorganisms temporarily located on or within the human body, including potential opportunistic pathogens.

Human Microbiome Project

An initiative launched in $2008$ by the National Institutes of Health (NIH) to map gene sequences from human skin, gut, and oral microbial communities.

Metagenomic Analysis

A methodology that harvests DNA directly from microbial communities without prior isolate culture, addressing the limitation that $99\%$ of environmental and human bacteria cannot be cultured in vitro.

Bergey's Manual of Systematic Bacteriology

A five-volume taxonomic reference for prokaryotes that incorporates nucleotide gene sequencing (such as $16\text{S rRNA}$ sequencing) and official LPSN nomenclature.

Gram-Positive Bacteria

Prokaryotes possessing a thick peptidoglycan cell wall that retains primary crystal violet dye during decolorization, appearing purple under microscopic examination.

Gram-Negative Bacteria

Prokaryotes possessing a thin peptidoglycan layer that loses crystal violet dye during decolorization and accepts safranin counterstain, appearing light red/pink under microscopy.

Deeply Branching Bacteria

Early evolutionary lineages of prokaryotes adapted to extreme environmental conditions resembling early Earth, such as high heat, extreme acidity, high UV exposure, and anoxia.

Low G+C Gram-Positive Bacteria

Gram-positive bacteria whose DNA base composition contains less than $50\%$ guanine and cytosine nucleotides, such as Bacillus anthracis and Clostridium tetani.

High G+C Gram-Positive Bacteria

Gram-positive bacteria whose DNA base composition contains greater than $50\%$ guanine and cytosine nucleotides, such as Corynebacterium diphtheriae and Mycobacterium tuberculosis.

MALDI-TOF MS

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry, a technique where bacterial isolates irradiated by a pulsed UV laser release gaseous ions measured by mass-to-charge ratio ($m/z$) to generate a unique spectrum for identification.

Fatty Acid Methyl Ester (FAME) Analysis

A lipid profiling technique where extracted membrane fatty acids are converted to volatile methyl esters and separated via gas chromatography to produce a unique chromatogram fingerprint.

Phospholipid-Derived Fatty Acids (PLFA) Analysis

An analytical method where membrane phospholipids undergo saponification (alkaline hydrolysis) to release constituent fatty acids prior to FAME gas chromatography analysis.

Cetrimide Agar

A selective growth medium incubated at $42\,^\circ\text{C}$ that inhibits normal cutaneous flora while stimulating Pseudomonas aeruginosa to produce pyocyanin and fluorescein pigments.

Hot Tub Folliculitis

A self-limiting cutaneous infection caused by Pseudomonas aeruginosa that presents as an itchy, bumpy red rash with pus-filled pustules surrounding hair follicles following warm water exposure.