Microbially Mediated Redox Reactions

A set of practice flashcards focused on terms and definitions related to microbially mediated redox reactions and biogeochemical cycles from the lecture transcript.

Acid-base reactions

Chemical reactions, such as the reaction between sodium bicarbonate and acetic acid, that occur rapidly and reach equilibrium immediately without the help of living organisms.

Sodium bicarbonate

The chemical name for baking soda, which reacts with vinegar in an immediate acid-base reaction.

Acetic acid

The chemical name for vinegar, which reacts with sodium bicarbonate to reach equilibrium as sodium acetate in water.

Sodium acetate

The product formed when baking soda and vinegar react and reach equilibrium.

Redox reactions

Oxidation-reduction reactions that entail the transfer of electrons and are often slow and out of equilibrium.

Photosynthesis

The process where organisms capture light energy and convert it to chemical energy stored in reduced organic compounds.

Aerobic respiration

A biologically mediated redox reaction where heterotrophic organisms oxidize organic matter to yield energy with $CO_2$ as a by-product.

Phototrophic organisms

Organisms that convert carbon in $CO_2$ to more reduced organic forms by capturing light energy.

Herbivory

A direct process where photosynthetically produced organic matter supports heterotrophic organisms via consumption of plants.

Detritivory

A direct process where heterotrophic organisms are supported by photosynthetically produced organic matter via the consumption of detritus.

Consumer food webs

Indirect pathways through which photosynthetically produced organic matter ultimately supports various life forms, including humans.

Bacteria and archaea

The primary groups of microorganisms responsible for most microbially mediated redox reactions in ecosystems.

Symbiotic association

A relationship where microorganisms, such as certain bacteria or fungi, live in close association with eukaryotes.

Candidatus Desulforudis audaxviator

A bacterium found 2.8 km beneath the Earth's surface in a South African gold mine that survives without photosynthesis by oxidizing molecular hydrogen.

Bold traveler

The English translation of the specific name 'audaxviator' for the bacterium found deep in the Earth's crust.

2.8 km

The depth beneath the Earth's surface where the bacterium Candidatus Desulforudis audaxviator was the only organism found in water samples.

60°C

The temperature of the anoxic water habitat in the South African gold mine 2.8 km deep.

pH 9.3

The pH level of the water samples where Candidatus Desulforudis audaxviator was discovered.

Radioactive decay

The energy source in the parent rock of deep subterranean habitats that produces molecular hydrogen and sulfate from dissolution.

Molecular hydrogen ($H_2$)

The primary electron donor used by Candidatus Desulforudis audaxviator for survival in deep groundwater.

Barite

Barium sulfate ($BaSO_4$) in parent rock that provides sulfate through dissolution to be used as an electron acceptor by deep-living microbes.

Gibbs free energy ($\Delta G$)

A quantify used to measure chemical potential energy; if negative, the reaction yields energy.

Negative $\Delta G$

Indicates that a reaction yields energy which can potentially be captured by organisms.

Positive $\Delta G$

Indicates that a reaction will only proceed with external energy input, such as light.

Chemosynthesis

The process of $CO_2$ fixation into organic matter using energy from strong electron donors in the absence of light.

Half-reactions

The two components of a redox reaction that divide the process into one element losing electrons and another gaining electrons.

$$-181\,kJ/4\,e^-$$

The association $\Delta G$ value for the oxidation of carbon in organic matter during aerobic respiration.

$$-313\,kJ/4\,e^-$$

The associated $\Delta G$ value for the reduction of oxygen during aerobic respiration.

$$-494\,kJ$$

The total energy yield per mole of organic matter ($CH_2O$) oxidized during aerobic respiration.

Reduced

The state of an element or compound when its oxidation state goes down, meaning it has gained electron(s).

Oxidized

The state of an element or compound when its oxidation state goes up, meaning it has lost electron(s).

Anaerobic degradation

Metabolism largely performed by specialized microorganisms to break down and recirculate organic matter in anoxic environments.

Anoxic microsites

Small environments, such as decaying organic matter in soils, where anaerobic metabolism occurs despite broader oxygen presence.

Alternative electron acceptors

Substances other than oxygen, such as nitrate or sulfate, used in anaerobic respiration.

Hydrolysis

The first step in anaerobic decomposition where polymers are broken down into monomers.

Fermentation

The step in anaerobic degradation following hydrolysis that generates simple products like $H_2$ and acetate.

Terminal electron accepting process (TEAP)

The final oxidation step in the anaerobic food chain that converts organic carbon to $CO_2$.

Denitrification

The reduction of nitrate ($NO_3^-$) to $N_2$, which serves as a TEAP yielding less energy than aerobic respiration.

Iron reduction

A terminal electron accepting process where ferric iron ($Fe^{3+}/Fe(OH)_3$) is reduced to ferrous iron ($Fe^{2+}$).

Manganese reduction

A TEAP where $MnO_2$ is reduced to $Mn^{2+}$, occurring in marine sediments and groundwaters.

Sulfate reduction

A terminal electron accepting process where sulfate ($SO_4^{2-}$) is reduced to sulfide forms like $H_2S$, predominant in marine environments.

Methanogenesis

The dominant process for anaerobic degradation of organic matter when alternative electron acceptors are absent, producing $CH_4$.

Dissimilatory processes

Redox reactions where reduced products are released to the environment rather than being assimilated into organic matter.

Energy hierarchy

The predictable sequence in which redox reactions occur based on decreasing energy yield and reactant availability.

Redox potential

A field measurement that roughly indicates which anaerobic degradation processes are likely to dominate in an environment.

Chemolithotrophs

Organisms that harness energy from purely inorganic redox reactions, such as the oxidation of sulfide or iron.

Nitrification

The chemolithotrophic oxidation of ammonium ($NH_4^+$) to nitrate ($NO_3^-$).

$$-347\,kJ/mole$$

The energy yield ($\Delta G$) from the oxidation of ammonium to nitrate during nitrification.

Sulfide oxidation

The conversion of $H_2S$ and $O_2$ to $H_2SO_4$, typically occurring at interfaces between anoxic and oxic zones.

Ferrous oxidation

The oxidation of ferrous iron ($Fe(HCO_3)_2$) to ferric hydroxide ($Fe(OH)_3$).

Manganous oxidation

The oxidation of manganese carbonate ($MnCO_3$) to manganese oxide ($Mn_2O_3$).

Oxygenic photosynthesis

The light-driven production of organic matter and oxygen from $CO_2$ and water.

Anoxygenic photosynthesis

A process by sulfur bacteria using light to react $CO_2$ and $H_2S$ to produce organic matter and sulfuric acid.

Nitrogen fixation

The reaction converting $N_2$ and energy into $NH_3$, performed when reactive nitrogen is scarce.

Soil acidification

The lowering of soil pH, often caused by nitrification in intensively fertilized agricultural systems.

Lime

A substance added periodically to agricultural soils to maintain favorability for crop growth by counteracting soil acidification.

ATP

Adenosine triphosphate, the form of energy captured during electron transport and used in biosynthesis.

$$(CH_2O)_n$$

The chemical abbreviation used for complex organic matter in ecosystem science redox equations.

Acetate

A simple carbon compound produced during fermentation and further oxidized in anaerobic respiration.

Methane ($CH_4$)

A gas produced in methanogenic environments where alternative electron acceptors are exhausted.

Nitrate ($NO_3^-$)

A mobile form of dissolved inorganic nitrogen that can be readily lost from fertilized agricultural soils.

Ammonium ($NH_4^+$)

An inorganic nitrogen species that serves as the electron donor for nitrifying bacteria.

Sulfuric acid ($H_2SO_4$)

A product of sulfide oxidation and anoxygenic photosynthesis by sulfur bacteria.

Ferric iron ($Fe^{3+}$)

The oxidized form of iron used as an electron acceptor in anoxic environments.

Ferrous iron ($Fe^{2+}$)

The reduced form of iron that accumulates during iron reduction in habitats like wetlands.

Manganese dioxide ($MnO_2$)

The oxidant used in manganese reduction processes.

Bisulfide ($HS^-$)

A common form of sulfide produced during sulfate reduction depending on the environmental pH.

Formate ($HCOO^-$)

A fermentation product mentioned as part of the anaerobic breakdown of organic matter.

Methanol ($CH_3OH$)

A simple alcohol produced during fermentation in anoxic environments.

$0.02$$ percent

A quantitative value not in text, replaced with verbatim duration: 'fast' for acid-base vs 'slow' for redox.

$4\,e^-$$ transfer

The number of electrons transferred in the aerobic respiration half-reactions depicted in the text.

Hydraulic forces

Examples like currents or gravity that can move organisms away from essential resources, limiting biological activity.

Competitive equilibration

The process which may be precluded by microscale spatiotemporal variability, leading to overlapping redox zones.

Groundwater flow paths

Environmental settings where the sequence of redox reactions is observed over meters to kilometers.

Hydrothermal vents

Habitats where sulfide emerging into oxygen-rich water provides energy for symbiotic microorganisms via chemolithotrophy.

Hot springs

Habitats where chemolithotrophs exploit energy-releasing inorganic redox reactions at the interface of oxic and anoxic conditions.

Eutrophic lakes

Water bodies whose thermoclines serve as typical locations for chemolithotrophic sulfide oxidation.

Salt marshes

Coastal ecosystems where sulfate reduction typically predominates due to available sulfate and organic matter.

Recalcitrant organic matter

Complex, hard-to-degrade materials whose digestion is facilitated by anaerobic metabolism in animal gastrointestinal systems.

Biogeochemical cycles

Cycles of elements like C, O, N, S, Fe, Mn, and P that are driven by microbially mediated redox transformations.

Terminal food chain step

Anaerobic respiration of simple fermentation products following the hydrolysis of polymers.

Dissolved inorganic N

Form of nitrogen, specifically nitrate, characterized by its mobility and likelihood of escaping soil ecosystems.

Protons ($H^+$)

Particles whose consumption or production in biologically mediated redox reactions determines environmental pH.

Biosynthesis

The biological process for which energy captured as ATP is utilized.

Electron transport

The pathway involving enzymes that acts as 'teeth on gears' to convert chemical potential energy into usable energy.

Microscale spatiotemporal variability

Environmental heterogeneity that causes theoretical redox hierarchies to appear to overlap in space or time.

Stumm and Morgan (1995)

A work cited as the source for modified examples of ecologically important biologically mediated redox reactions.

$5CH_2O + 4NO_3^- + 4H^+ \rightarrow 5CO_2 + 7H_2O + 2N_2$

The chemical reaction equation for microbially mediated denitrification.

$2CH_2O + SO_4^{2-} + H^+ \rightarrow 2CO_2 + 2H_2O + HS^-$

The chemical reaction equation for microbially mediated sulfate reduction.

$4Fe(HCO_3)_2 + O_2 + 6H_2O \rightarrow 4Fe(OH)_3 + 4H_2CO_3 + 4CO_2$

The chemical reaction equation for the chemolithotrophic oxidation of ferrous iron.