Biogeochemical Cycles and Environmental Bioremediation

Vocabulary flashcards detailing microbial stratification, the carbon, nitrogen, and sulfur cycles, hazardous environmental contaminants, and physical and biological remediation methods.

Stratified Microbial Community

A layered arrangement of microbial populations in soil, lake, or ocean sediments, organized vertically based on the sequence of available terminal electron acceptors (ranging from $O_2$ at the surface to $NO_3^-$, manganese, iron, sulfate, and $CO_2$ at the deepest levels).

Hydrogen Sulfide ($H_2S$)

A rotten-egg-smelling gas produced by sulfate-reducing bacteria at the bottom of sediment columns that reacts with reduced iron ($Fe^{2+}$) to precipitate black iron sulfide.

Winogradsky Column

A classic microbial culture device (typically a glass cylinder filled with soil, shredded newspaper, carbonate, and a water layer) that establishes light and oxygen gradients to display stratified bands of aerobic, photosynthetic, and anaerobic organisms.

Methanogenesis

An anaerobic reduction process carried out by methanogens at the bottom of sediment or inside anoxic animal guts, reducing $CO_2$ to methane ($CH_4$).

Methane Oxidizers

Microorganisms that usually live aerobically (such as around plant roots) and oxidize upward-migrating methane ($CH_4$) back into carbon dioxide ($CO_2$).

Nitrous Oxide ($N_2O$) Potency

A potent greenhouse gas intermediate produced during denitrification that is approximately $20$ times more potent than carbon dioxide.

Diazotrophs

Specialized microorganisms (such as cyanobacteria and rhizobia) capable of biological nitrogen fixation, converting inert atmospheric $N_2$ into bioavailable ammonia ($NH_3$).

Biological Nitrogen Fixation Cost

An energetically demanding biochemical reduction requiring $12\,\text{NADH}$ and $18\,\text{ATP}$ to break the triple bond of a single $N_2$ molecule.

Nitrification

A two-step aerobic oxidation carried out by lithotrophic bacteria in which ammonia ($NH_3$) is first oxidized to nitrite ($NO_2^-$) and then further oxidized to nitrate ($NO_3^-$).

Denitrification

An anaerobic respiratory process in which bacteria use nitrate ($NO_3^-$) as a terminal electron acceptor, reducing it sequentially through intermediates such as $NO$ and $N_2O$ back to $N_2$ gas.

Anammox

Anaerobic ammonia oxidation; a biological process where ammonia is oxidized anaerobically to nitrogen gas.

Dissimilatory Sulfate Reduction

An anaerobic respiration pathway used by bacteria like Desulfovibrio, where sulfate ($SO_4^{2-}$) serves strictly as a terminal electron acceptor for energy metabolism and is reduced to $H_2S$, rather than incorporated into biomass.

Bay Region

A specific curved bend found in polycyclic aromatic hydrocarbons containing four or more rings that is enzymatically converted in the liver to a reactive three-membered epoxide, causing covalent DNA adducts and frameshift mutations.

Three-Metal Catalyst

The metallic components of an automotive catalytic converter consisting of palladium, rhodium, and platinum that can abrade over time into environmental soot and road dust.

BTEX

An acronym for benzene, toluene, ethylbenzene, and xylene; volatile organic solvents widely used to wash oils off metals during manufacturing and welding that degrade over time in the environment.

Plume

An underground body of contaminated groundwater that migrates away from a point source leak across property lines.

Vadose Zone

The aerated, unsaturated soil zone located above the water table where aerobic microbial degradation typically proceeds at higher rates.

Air Sparging

A physical remediation technique (also called air stripping) where air is pumped into a well to volatilize volatile organic compounds (VOCs), which are pulled out and condensed at the surface via a cold finger.

Soil Flushing

A physical remediation method where water is pumped underground through injection wells and extracted to wash out water-soluble contaminants.

Solidification

A physical remediation containment process in which concrete and water are injected underground to immobilize contaminants for approximately $200$ years.

Vitrification

A containment method that adds specific chemical compounds to an underground contamination site to fuse the hazardous materials into a stable, supercooled glass structure.

Enhanced Bioremediation

The subsurface injection of oxygen or air, water, and limiting nutrients (such as fixed nitrogen, phosphorus, and iron) or reductants to stimulate the growth and degradation rates of native microbial populations.

Recalcitrant Compounds

Chemical contaminants that inherently resist environmental and microbial degradation, frequently encompassing the most carcinogenic substances such as multi-ring polycyclic aromatic hydrocarbons.