Microbial Metabolism, Respiration, Phototrophy, and Symbiosis

Vocabulary flashcards covering microbial nutrition, energetics, respiration types, chemolithotrophy, phototrophy, global cycles, and host-microbe symbioses.

Prototroph

An organism that can synthesize all necessary organic compounds from inorganic substances, requiring nothing added to minimal medium (MM) containing only carbon, water, and salt.

Auxotroph

A mutant organism that has lost the ability to synthesize specific essential compounds, requiring them to be added to its growth medium.

Enrichment medium

A growth medium that favors the proliferation of fastidious microbes requiring specific and complex nutrition.

Fastidious

A description of microbes that require specific and complex nutritional components to grow.

Selective medium

A medium formulated to grow a target microbe while inhibiting non-target microbes, typically by bacteriostatic action (e.g., AIA agar, Mossel EE broth).

Differential medium

A growth medium that distinguishes between different groups of microbes growing on the same plate (e.g., MAC agar).

Viable Plate Count (VPC)

An indirect cell counting method that involves diluting a sample, counting colony-forming units (CFU), and back-calculating cell numbers.

$$\text{OD}_{600}$$

An indirect method of estimating cell density by measuring cell turbidity at $600\,\text{nm}$, which cannot differentiate between living and dead cells.

Growth rate

A measure of the number of generations per unit of time in the exponential (log) phase, calculated using the equation $N = N_0 2^n$.

Diauxic growth

A biphasic growth pattern characterized by a hump in the growth curve, occurring when an organism completely exhausts one carbon source, adapts, and begins consuming a second.

Prosthetic group

A non-protein cofactor that is permanently attached to an enzyme to enable its catalytic function.

Coenzyme

A free-floating, non-protein organic cofactor that transiently interacts with an enzyme to assist its function.

Chemolithotroph

An organism that derives its metabolic energy by utilizing inorganic molecules as electron donors.

Chemoorganotroph

An organism that obtains its metabolic energy and electron donors from organic chemical compounds.

Autotroph

An organism capable of fixing its own carbon, utilizing $\text{CO}_2$ as its primary carbon source.

Heterotroph

An organism that obtains its required carbon externally from preformed organic compounds.

ATP synthase

A reversible rotary motor enzyme that can harness the proton motive force (PMF) to produce ATP or hydrolyze ATP to generate a PMF.

Oxidative phosphorylation

The synthesis of ATP driven by the proton motive force (PMF) generated across a membrane by an electron transport chain.

Substrate-level phosphorylation

The direct transfer of a high-energy phosphate group to ADP to form ATP without requiring an electron transport chain or proton motive force.

Fermentation

A cytoplasmic metabolic process relying on substrate-level phosphorylation where an organic compound is oxidized to an energy-rich intermediate, generating ATP, and subsequently reduced into various fermentation products to reoxidize $\text{NADH}$.

Dissimilative reduction

A high-flux respiratory pathway in which an element (such as $\text{SO}_4^{2-}$) serves as a terminal electron acceptor for energy generation and is subsequently excreted as waste.

Assimilative reduction

The reduction of an inorganic compound where the reduced element is incorporated as a permanent structural or functional component of cellular biomass.

Methanogens

Archaea that carry out an exergonic pathway using unusual electron carriers to reduce $\text{CO}_2$ into methane ($\text{CH}_4$).

Nanowires

Cellular structures used by microbes to shuttle electrons externally to insoluble electron acceptors, such as $\text{Fe}^{3+}$.

Siderophores

Iron-binding compounds secreted by cells to scavenge and import iron into the cell for reduction.

Hydrogenases

Enzymes in chemolithotrophs that catalyze the reversible oxidation of $\text{H}_2$ gas, feeding electrons into the electron transport chain or directly reducing $\text{NAD}^+$.

Anammoxosome

A bacterial membrane-bound organelle specialized for anaerobic ammonium oxidation, where nitrite ($\text{NO}_2^-$) and ammonium ($\text{NH}_4^+$) react to produce $\text{N}_2\text{H}_4$, nitrogen gas ($\text{N}_2$), and water.

Chemolithoautotroph

An organism that generates energy from the oxidation of inorganic chemicals and fixes its own carbon, usually from $\text{CO}_2$, requiring high amounts of $\text{NADH}$.

Antennae pigments

Light-harvesting pigments, such as chlorophylls (oxygenic) and bacteriochlorophylls (anoxygenic), that collect photons at diverse wavelengths and transfer the energy to the reaction center.

Accessory pigments

Molecules such as phycobilins and carotenoids that capture additional wavelengths of light and safeguard the photosynthetic apparatus against photooxidation.

Reaction center (RC)

The specialized photosynthetic complex (PSI or PSII) where light energy drives the excitation of electrons.

Anoxygenic phototrophy

A photosynthetic process relying on cyclic photophosphorylation to produce ATP without generating oxygen or reducing equivalents ($\text{NADH}$) directly.

Chlorosomes

Specialized reaction center complexes found in green bacteria that enable efficient phototrophy under extremely low-light conditions.

Oxygenic phototrophy

A linear photosynthetic pathway that uses water ($\text{H}_2\text{O}$) as an electron donor, generates a proton motive force, and reduces $\text{NADP}^+$ to $\text{NADPH}$ as the terminal electron acceptor.

Rhodopsin-based phototrophy

A simplified phototrophic mechanism that produces ATP using bacteriorhodopsin to drive a light-activated cis-trans retinal isomerization that pumps protons, bypassing reaction centers and chlorophyll.

Calvin cycle

A stromal carbon fixation pathway that utilizes the enzyme RuBisCO, consuming $3\,\text{ATP}$ and $2\,\text{NADPH}$ per molecule of $\text{CO}_2$ to yield glyceraldehyde-3-phosphate (G3P) for sugar synthesis.

RuBisCO

The key stromal enzyme of the Calvin cycle that catalyzes the primary carbon fixation step by attaching $\text{CO}_2$ to build organic precursors.

Methylotrophs

Microorganisms capable of utilizing methane ($\text{CH}_4$) as a source of carbon and energy for biosynthesis and bioremediation.

Methane hydrates

Ice-like crystalline solids composed of methane molecules trapped within cages of water molecules, serving as a vast reservoir of greenhouse gas.

Dead zones

Hypoxic aquatic regions caused by eutrophication, where nutrient influx triggers massive microbial growth that consumes dissolved oxygen and suffocates macrofauna.

Nitrogenase

An enzyme that reduces atmospheric dinitrogen ($\text{N}_2$) into bioavailable ammonia, requiring an input of $8$ electrons and $16\,\text{ATP}$.

Syntrophy

A mutualistic cross-feeding interaction where one organism survives by consuming the metabolic waste product of another, such as a methanogen consuming the $\text{H}_2$ produced by a fermenter.

Quorum sensing

A bacterial cell-to-cell communication mechanism involving the secretion and accumulation of signaling molecules that allows populations to coordinate group behaviors.

Rhizosphere

The soil zone immediately surrounding plant roots where roots secrete nutrients and metabolites to stimulate and nourish microbial growth.

Nod factors

Signaling molecules produced by rhizosphere bacteria that stimulate host plant roots to develop nodules, facilitating symbiotic nitrogen-fixing infections.

Human milk oligosaccharides (HMOs)

Complex sugars found in breast milk that selectively serve as a nutrient source for Bifidobacterium, promoting the establishment of a healthy infant gut microbiome.

Dysbiosis

A state of gut microbiome disruption wherein bacteria breach the epithelial barrier due to the loss of tight junctions, thinning of the mucus layer, and low antimicrobial peptides.