Lecture 3B.2: Respiration: ETC: H2 Oxidation, Sox System, Fe2+ Oxidation, Nitrification, Anammox

Question 1

An organism that switches to alternative electron acceptors when O₂ is limiting

Answer 1

Facultative anaerobes

• an organism that survives with or without molecular oxygen.
• capable of switching between aerobic and anaerobic modes of respiration in order to generate energy.

Question 2

When does a facultative anaerobe switch back to oxygen?

Answer 2

As soon as oxygen becomes available

Question 3

What types of electron acceptors do facultative anaerobes use? (3)

Answer 3

Inorganic/organic compounds, and metals such as ferric iron (Fe³⁺) and manganese ion (Mn⁴⁺)

Question 4

Which organisms use more electronegative electron acceptors?

Answer 4

Obligate anaerobes

microorganisms that cannot survive in the presence of oxygen because they lack the enzymes necessary to neutralize the toxic byproducts of oxygen.

Question 5

Why are obligate anaerobes unable to tolerate oxygen?

Answer 5

Their enzymes are inhibited by oxygen

Question 6

Alternative Electron Acceptors

What are some examples of highly electronegative electron acceptors? (3)

Answer 6

• Sulfate (SO₄²⁻)
• elemental sulfur (S⁰)
• carbon dioxide (CO₂)

Question 7

Alternative Electron Acceptors

Why do organisms using SO₄²⁻, S⁰, or CO₂ require an anaerobic lifestyle?

Answer 7

These acceptors are only effective in anaerobic conditions

Question 8

How does respiration conserve energy?

Answer 8

Through redox reactions, transferring electrons from an electron donor to a final electron acceptor

Question 9

What are the two major microbial classifications based on electron donors? (2)

Give brief description each.

Answer 9

• Chemoorganotrophs: Oxidize organic compounds
• Chemolithotrophs: Oxidize inorganic compounds and obtain carbon from CO₂

Question 10

1. What happens to electron donors during respiration?
2. What happens to electron acceptors?

Mnemonic for redox reactions in respiration?

Answer 10

1. They undergo oxidation (lose electrons)
2. They undergo reduction (gain electrons)

DORA: Donor is Oxidized, Reduced is Acceptor

Question 11

What determines how much energy is released in respiration?

Answer 11

The greater the difference in E₀′ between donor and acceptor, the more energy is released.

Question 12

What are some electron acceptors in anaerobic respiration?

Give four (4)

Answer 12

• Nitrate (NO₃⁻)
• sulfate (SO₄²⁻)
• iron (Fe³⁺)
• carbon dioxide (CO₂)

Question 13

What type of microbes can switch between aerobic and anaerobic respiration?

Answer 13

Facultative aerobes

Question 14

What type of microbes cannot tolerate O₂?

Answer 14

Obligate anaerobes

Question 15

What is the purpose of assimilative reduction?

Answer 15

To reduce NO₃⁻, SO₄²⁻, or CO₂ for biosynthesis (incorporated into biomass)

Question 16

Does assimilative reduction consume or produce energy?

Answer 16

Consumes energy

Question 17

What is the purpose of dissimilative reduction?

Answer 17

To reduce NO₃⁻, SO₄²⁻, or CO₂ for energy conservation

Question 18

What happens to the reduced products in dissimilative reduction?

Answer 18

They are excreted (e.g., N₂, H₂S, CH₄)

Question 19

Which process is more common in anaerobic respiration?

Answer 19

Dissimilative reduction

Question 20

Which electron acceptors are the most electropositive (highest E₀′)?

Give three (3)

E₀′ - reduction potential: a measure of the tendency of a chemical species to gain electrons (be reduced)

Answer 20

• Nitrate (NO₃⁻)
• manganese (Mn⁴⁺)
• iron (Fe³⁺)

Question 21

Which electron acceptors have a moderate E₀′?

Give two (2)

E₀′ - reduction potential: a measure of the tendency of a chemical species to gain electrons (be reduced)

Answer 21

• Sulfate (SO₄²⁻)
• elemental sulfur (S⁰)

Question 22

Which electron acceptor has the lowest E₀′?

E₀′ - reduction potential: a measure of the tendency of a chemical species to gain electrons (be reduced)

Answer 22

CO₂ (reduced to CH₄ in methanogenesis)

Question 23

How does energy yield change as electron acceptors become less electropositive?

Answer 23

It decreases

Question 24

Chemolithotrophs that also use organic carbon.

Answer 24

Mixotrophs

Question 25

One of the simplest chemolithotrophs.

Answer 25

Hydrogen bcteria

Question 26

A common microbial metabolism product, especially in fermentations.

Answer 26

H₂ (Hydrogen)

Question 27

# Hydrogen Oxidation: Aerobic hydrogen bacteria oxidize H₂ to form ___ and __.

Answer 27

Water and ATP

Question 28

# Hydrogen Oxidation: H₂ oxidation by O₂ is highly ___.

Answer 28

exergonic

Question 29

# Hydrogen Oxidation: Reaction for H₂ oxidation?

Answer 29

H₂ + ½ O₂ → H₂O

Question 30

# Hydrogen Oxidation: Enzyme that catalyzes H₂ oxidation.

Answer 30

Hydrogenase

Question 31

# Hydrogen Oxidation: Hydrogenases 1. Transfers electrons from H₂ to a quinone acceptor. 2. Reduces NAD⁺ to NADH directly.

Answer 31

1. Membrane-bound hydrogenase or membrane-integrated hydrogenase 2. Cytoplasmic hydrogenase

Question 32

# Hydrogen Oxidation: Model organism for aerobic H₂ oxidation.

Answer 32

*Ralstonia eutropha*

Question 33

# Hydrogenases: 1. Type of hydrogenase that helps in ATP synthesis. 2. Hydrogenase that provides reducing power.

Answer 33

1. Membrane-bound hydrogenase or membrane-integrated hydrogenase 2. cytoplasmic hydrogenase

Question 34

# Hydrogen Oxidation: Bacteria with a single hydrogenase must rely on ___.

Answer 34

Reverse electron transport

Question 35

# Autotrophy in H₂ Bacteria: CO₂ fixation pathway in hydrogen bacteria.

Answer 35

Calvin cycle

Question 36

# Autotrophy in H₂ Bacteria: When growing chemoorganotrophically, hydrogen bacteria repress ___ and ___.

Answer 36

- Calvin cycle - hydrogenase enzymes ## Footnote Why? because these pathways are primarily used for chemolithotrophic growth (using inorganic compounds like hydrogen as an energy source). * Calvin cycle: Normally used for carbon fixation when the bacteria grow autotrophically using CO₂. Since organic compounds provide carbon, this cycle is unnecessary. * Hydrogenase enzymes: Usually involved in oxidizing hydrogen (H₂) for energy production. When organic molecules serve as the energy source, hydrogen oxidation is not needed, so these enzymes are downregulated.

Question 37

Organisms that switch between chemolithotrophy and chemoorganotrophy.

Answer 37

Facultative chemolithotrophs

Question 38

# Ecological Significance of Hydrogen Bacteria: H₂ is mainly produced in ___.

Answer 38

Anoxic environments ## Footnote Exaplanation H₂ is mainly produced in anoxic environments (environments without oxygen) because many anaerobic microorganisms generate hydrogen gas as a byproduct of fermentation and other metabolic processes. Examples of H₂ production: * Fermentative bacteria break down organic matter, releasing H₂. * Methanogens and sulfate-reducing bacteria participate in hydrogen cycling. * Decomposition of organic matter in environments like wetlands, sediments, and the digestive tracts of animals produces H₂. Since oxygen can rapidly react with hydrogen, significant accumulation of H₂ typically occurs in environments where oxygen is absent or very low.

Question 39

# Ecological Significance of Hydrogen Bacteria: H₂-consuming microbes prevent H₂ from reaching ___.

Answer 39

oxic zones ## Footnote H₂-consuming microbes prevent H₂ from reaching oxic zones (oxygen-rich environments) by rapidly utilizing hydrogen gas in anaerobic processes. * Why? Hydrogen is a key energy source for anaerobic microorganisms like methanogens, sulfate-reducing bacteria, and acetogens, which consume H₂ to drive their metabolism. * Effect: By depleting H₂ in anoxic zones, these microbes prevent its diffusion into oxygen-rich areas, where it could otherwise react with oxygen in abiotic or aerobic microbial processes. * Importance: This maintains redox balance in microbial ecosystems and supports anaerobic energy generation in environments like sediments, deep soils, and intestines.

Question 40

# Ecological Significance of Hydrogen Bacteria: Aerobic hydrogen bacteria thrive in ___.

Answer 40

Oxic-anoxic interfaces ## Footnote Explanation: Aerobic hydrogen bacteria thrive in oxic-anoxic interfaces, where they access both H₂ from anoxic zones and oxygen for respiration. These zones occur in soils, sediments, wetlands, and microbial mats, allowing efficient H₂ oxidation.

Question 41

# Ecological Significance of Hydrogen Bacteria: Many hydrogen bacteria prefer ___ oxygen levels.

Answer 41

Low (microaerobic) ## Footnote Additional info: * Hydrogen bacteria that prefer low (microaerobic) oxygen levels are called microaerophilic hydrogen bacteria. * They thrive in environments with suboptimal oxygen concentrations (not fully aerobic but not completely anaerobic). * High oxygen levels can inhibit their hydrogenase enzymes, affecting H₂ metabolism. * Common habitats include oxic-anoxic interfaces, such as soils, sediments, and microbial mats.

Question 42

Microbes that obtain energy by oxidizing reduced sulfur compounds.

Answer 42

Sulfur-oxidizing bacteria (SOB)

Question 43

# Sulfur Oxidation: Common electron donor in sulfur oxidation. | Give four (4)

Answer 43

* hydrogen sulfide (H₂S) * elemental sulfur (S⁰) * thiosulfate (S₂O₃²⁻) * sulfite (SO₃²⁻)

Question 44

# Sulfur Oxidation: Final product of sulfur oxidation.

Answer 44

Sulfate (SO₄²⁻)

Question 45

# Sulfur Oxidation: Process where sulfur oxidation contributes to environmental acidification.

Answer 45

Acid mine drainage (AMD) ## Footnote Explanation: The process where sulfur oxidation contributes to environmental acidification is called acid mine drainage (AMD). * Cause: Sulfide minerals (e.g., pyrite, FeS₂) react with oxygen and water, producing sulfuric acid (H₂SO₄). * Effect: Lowers pH, making water highly acidic and leaching toxic metals into the environment. * Common in: Mining sites, abandoned mines, and areas with exposed sulfide-rich rocks. AMD is a major environmental issue, harming aquatic ecosystems, soil quality, and water sources.

Question 46

# Sulfur Oxidation: General equation for H₂S oxidation.

Answer 46

Partial oxidation to elemental sulfur (S⁰): H₂S + O₂ → S⁰ + H₂O Complete oxidation to sulfate (SO₄²⁻): S⁰ + 1.5 O₂ + H₂O → SO₄²⁻ + 2H⁺ ## Footnote Step 1: Hydrogen sulfide (H₂S) reacts with oxygen, forming elemental sulfur and water. Step 2: Elemental sulfur further oxidizes, producing sulfate (SO₄²⁻) and releasing protons (H⁺)

Question 47

# Sulfur Oxidation: System that catalyzes complete oxidation of sulfur compounds to sulfate.

Answer 47

Sox System

Question 48

# Sulfur-Oxidizing Pathways: Enzyme Converts intracellular sulfur stores into sulfate.

Answer 48

Reverse-acting dissimilatory sulfite reductase (rDSR) ## Footnote * Function: Catalyzes the oxidation of stored elemental sulfur (S⁰) into sulfite (SO₃²⁻), which is then converted to sulfate (SO₄²⁻). * Importance: Helps sulfur-oxidizing bacteria efficiently use stored sulfur for energy production. * Occurs in: Sulfur-oxidizing bacteria like *Beggiatoa* and *Thiobacillus*.

Question 49

# Sulfur-Oxidizing Pathways: Enzymes Converts sulfite to sulfate. | Name two (2) enzymes

Answer 49

- Adenosine phosphosulfate (APS) reductase - Sulfite oxidase

Question 50

# Sulfur-Oxidizing Pathways: Enzymes 1. Involves an intermediate step where sulfite is first converted to __ before being oxidized to sulfate. What enzyme catalyzes this reaction? 2. Directly oxidizes sulfite to sulfate using molecular oxygen or other electron acceptors.

Answer 50

1. * Adenosine phosphosulfate * APS reductase (Adenosine phosphosulfate reductase) 2. Sulfite oxidase

Question 51

# Energy Conservation in Sulfur Oxidation: Sulfur oxidation generates electrons that enter the ___.

Answer 51

Electron transport chain (ETC) ## Footnote Explanation: * Process: Sulfur-oxidizing bacteria oxidize compounds like H₂S, S⁰, or SO₃²⁻, releasing electrons. * Electron flow: These electrons pass through the ETC, driving proton motive force (PMF) and ATP synthesis via oxidative phosphorylation. * Key organisms: *Thiobacillus*, *Beggiatoa*, and other sulfur-oxidizing bacteria.

Question 52

# Sulfur Oxidation: ATP synthesis in sulfur oxidation is driven by ___.

Answer 52

Proton motive force (PMF)

Question 53

# Sulfur Oxidation: Some sulfur oxidizers require this process to generate NADH.

Answer 53

Reverse electron transport ## Footnote Explanation: * Why? Sulfur oxidation donates electrons to the electron transport chain (ETC) at a low energy level, insufficient to reduce NAD⁺ to NADH. * Solution: Cells use reverse electron transport, where electrons move uphill (against the redox gradient) using energy from the proton motive force (PMF). * Importance: NADH is essential for biosynthesis and carbon fixation in sulfur-oxidizing bacteria like *Thiobacillus* and *Beggiatoa*.

Question 54

# Sulfur Oxidation: Autotrophy and Carbon Fixation: Most sulfur-oxidizing bacteria fix CO₂ via the ___.

Answer 54

Calvin cycle

Question 55

# Sulfur Oxidation: Autotrophy and Carbon Fixation Energy from sulfur oxidation supports ___.

Answer 55

Carbon fixation

Question 56

Bacterium that switches between chemolithotrophy and chemoorganotrophy. | Give one (1) example

Answer 56

*Beggiatoa*

Question 57

# Sulfur Oxidation: Ecological and Industrial Significance: Environments where sulfur oxidation is significant. | Name three (3)

Answer 57

* Hydrothermal vents * Marine sediments * Sulfur springs

Question 58

# Sulfur Oxidation: Ecological and Industrial Significance: Acidophilic sulfur bacteria used in biomining.

Answer 58

*Acidithiobacillus*

Question 59

# Sulfur Oxidation: Ecological and Industrial Significance: Process where sulfur bacteria help extract metals from ores.

Answer 59

Bioleaching

Question 60

# Sulfur Oxidation: The Sox System The Sox system is responsible for the oxidation of ___.

Answer 60

reduced sulfur compounds ## Footnote Explanation: * A reduced compound has more electrons and less oxygen. * An oxidized compound has fewer electrons and more oxygen. The Sox system is used by sulfur-oxidizing bacteria to extract electrons from reduced sulfur compounds (like H₂S, S⁰, and SO₃²⁻) and transfer them to the electron transport chain (ETC) to generate ATP. * H₂S (highly reduced) → loses electrons → becomes oxidized * The Sox system captures these electrons and channels them into the ETC for energy production. * The final product is SO₄²⁻ (sulfate), which is fully oxidized and cannot donate more electrons.

Question 61

# Sulfur Oxidation: The Sox System Two (2) bacterial genera with the Sox system.

Answer 61

* *Paracoccus* * *Thiobacillus*

Question 62

# Sulfur Oxidation: The Sox System: Enumerate the key components of the Sox System (4)

Answer 62

* SoxXA * SoxYZ (carrier protein) * SoxB * SoxCD (Sulfur dehydrogenase) ## Footnote Additional Info: SoxX: A cytochrome c protein. SoxA: A heme-containing enzyme that helps transfer electrons.

Question 63

# Sulfur Oxidation: The Sox System: Sox component that binds and activates thiosulfate (S₂O₃²⁻).

Answer 63

SoxXA | SoxXA is a periplasmic heme protein complex.

Question 64

# Sulfur Oxidation: The Sox System: Carrier proteins in the Sox system. | covalently binds sulfur intermediates.

Answer 64

SoxYZ ## Footnote Acts as a scaffold for sulfur oxidation.

Question 65

# Sulfur Oxidation: The Sox System: Enzyme that directly oxidizes sulfur to sulfate (SO₄²⁻). | Cleaves and releases sulfate (SO₄²⁻) as the final product.

Answer 65

SoxB ## Footnote A sulfate-releasing hydrolase that completes the oxidation cycle.

Question 66

# Sulfur Oxidation: The Sox System: Sox enzyme that further oxidizes sulfite (SO₃²⁻) to sulfate (SO₄²⁻). ## Footnote Removes electrons from sulfur compounds and transfers them to the ETC. Functions as a sulfur dehydrogenase, enabling complete oxidation.

Answer 66

SoxCD

Question 67

# Unique Feature of the Sox System: The Sox system oxidizes sulfur compounds to sulfate without forming ___.

Answer 67

sulfite (SO₃²⁻) ## Footnote Explanation: * Many sulfur oxidation pathways go through an intermediate step where sulfite (SO₃²⁻) is formed before being converted to sulfate (SO₄²⁻). * The Sox system is different because it directly oxidizes sulfur compounds to sulfate (SO₄²⁻) without accumulating sulfite. * This makes the Sox pathway more efficient and less toxic for the cell, as sulfite can be harmful in high concentrations.

Question 68

# Iron (Fe²⁺) Oxidation: Electron donor in iron oxidation.

Answer 68

Fe²⁺ (ferrous iron)

Question 69

# Iron (Fe²⁺) Oxidation: Product of Fe²⁺ oxidation.

Answer 69

Fe³⁺ (ferric iron)

Question 70

# Iron (Fe²⁺) Oxidation: Fe³⁺ oxidation forms insoluble ___.

Answer 70

Ferric hydroxide (Fe(OH)₃) | Fe3+ + 3H2O → Fe(OH)3 ↓+3H + ## Footnote Explanation: * When Fe²⁺ (ferrous iron) is oxidized to Fe³⁺ (ferric iron), it reacts with water to form ferric hydroxide (Fe(OH)₃). * Fe(OH)₃ is insoluble and precipitates, often giving water a reddish-brown color, commonly seen in acid mine drainage.

Question 71

# Iron (Fe²⁺) Oxidation: Iron oxidation is most efficient at ___ pH.

Answer 71

Acidic ## Footnote Explanation: * Iron oxidation (Fe²⁺ → Fe³⁺) is most efficient in acidic environments (low pH) because Fe³⁺ remains soluble in acidic conditions. * At neutral or alkaline pH, Fe³⁺ forms insoluble ferric hydroxide (Fe(OH)₃), slowing down oxidation. * Many iron-oxidizing bacteria (e.g., *Acidithiobacillus ferrooxidans*) thrive in acidic environments (pH 1-3) to efficiently oxidize Fe²⁺ and generate energy.

Question 72

# Iron-Oxidizing Bacteria: Two acidophilic Fe²⁺-oxidizing bacteria. (2)

Answer 72

* *Acidithiobacillus ferrooxidans* * *Leptospirillum ferrooxidans*

Question 73

# Iron-Oxidizing Bacteria: Archaeon that oxidizes Fe²⁺ at extremely low pH.

Answer 73

Ferroplasma

Question 74

# Iron-Oxidizing Bacteria: Three neutral pH iron oxidizers. (3)

Answer 74

* Gallionella ferruginea * Sphaerotilus natans * Leptothrix discophora

Question 75

# Energy from Iron Oxidation: First protein in *A. ferrooxidans* Fe²⁺ oxidation.

Answer 75

Cytochrome c ## Footnote Explanation: * The outer membrane cytochrome c (Cyc2) is the initial Fe²⁺ oxidizer. * It accepts electrons from Fe²⁺ in the periplasmic space. * These electrons are then transferred to the ETC, driving ATP synthesis and NADH production.

Question 76

# Iron (Fe²⁺) Oxidation: Enumerate the Electron Flow in Fe²⁺ Oxidation (Simplified Pathway)

Answer 76

1. Fe²⁺ → Cyc2 (outer membrane cytochrome c) 2. Cyc2 → Rusticyanin (periplasmic electron carrier) 3. Rusticyanin → Cytochrome c₄ → Cytochrome aa₃ (final electron acceptor: O₂) ## Footnote Explanation: 1. * Fe²⁺ (ferrous iron) donates electrons to Cyc2, an outer membrane cytochrome c. * Cyc2 is the first electron acceptor in the pathway, directly interacting with Fe²⁺ in the environment. * This oxidizes Fe²⁺ to Fe³⁺, which then precipitates as ferric hydroxide (Fe(OH)₃) in acidic conditions. 2. * The electrons from Cyc2 are transferred to rusticyanin, a small blue copper protein in the periplasm. * Rusticyanin has a very high redox potential, making it an efficient electron carrier. * This step helps channel electrons deeper into the electron transport chain (ETC). 3. * Rusticyanin passes electrons to cytochrome c₄, another periplasmic cytochrome. * Cytochrome c₄ transfers electrons to cytochrome aa₃ (a terminal oxidase). * Cytochrome aa₃ donates electrons to O₂, reducing it to H₂O. * This final step creates a proton gradient, which drives ATP synthesis via ATP synthase.

Question 77

# Iron (Fe²⁺) Oxidation: Final electron acceptor in Fe²⁺ oxidation.

Answer 77

O₂ ## Footnote Additional Info: Where Iron-Oxidizing Bacteria Access O₂ ✔ Acidic Mine Drainage → Oxygen from cracks, rainwater. ✔ Hydrothermal Vents → Oxygen from seawater mixing. ✔ Freshwater Sediments → Oxygen diffuses from water. ✔ Wetlands & Peat Bogs → Plant roots release O₂. ✔ Wastewater Treatment → Artificial aeration.

Question 78

# Iron (Fe²⁺) Oxidation: Key protein transferring electrons to cytochrome c.

Answer 78

Rusticyanin ## Footnote * Fe²⁺ oxidation occurs in the periplasm (outside the cytoplasmic membrane). * Rusticyanin accepts electrons from Fe²⁺. * Rusticyanin then transfers electrons to periplasmic cytochrome c. * Cytochrome c passes the electrons to cytochrome aa₃ oxidase (complex IV), which reduces O₂ to H₂O. * This electron flow helps generate a proton gradient for ATP synthesis.

Question 79

# Iron (Fe²⁺) Oxidation: 1. *Acidithiobacillus ferrooxidans* generates ATP through oxidation of __. 2. The periplasm of *A. ferrooxidans* has a pH of __. 3. The cytoplasm of *A. ferrooxidans* has a pH of ___.

Answer 79

1. Fe²⁺ 2. pH: 1-2 3. pH: 5.5-6 pH ## Footnote ✔ Periplasm → Exposed to external acidic conditions (pH ~2). ✔ Cytoplasm → Maintained at near-neutral pH (~6.5-7.0). **Effect of pH Gradient on Iron Oxidation** ✔ Fe²⁺ Oxidation Occurs in the Periplasm * Fe²⁺ is unstable in neutral pH but soluble in acidic pH. * A. ferrooxidans oxidizes Fe²⁺ in the periplasm at pH ~2, preventing iron precipitation as Fe(OH)₃. ✔ Rusticyanin and Electron Transfer Efficiency * Rusticyanin and cytochrome c function optimally in the periplasmic acidic environment. * The large pH gradient (ΔpH) helps drive proton motive force (PMF), boosting ATP synthesis. ✔ Prevents Fe³⁺ Hydrolysis in the Periplasm * Fe³⁺ is produced in the periplasm, where it remains soluble. * If Fe³⁺ entered the cytoplasm (~pH 7), it would form insoluble ferric hydroxide (Fe(OH)₃), disrupting metabolism.

Question 80

# Iron (Fe²⁺) Oxidation: Pathway used by Fe²⁺ oxidizers for carbon fixation.

Answer 80

Calvin cycle

Question 81

# Iron (Fe²⁺) Oxidation: Reverse electron flow is required to generate ___.

Answer 81

NADH ## Footnote Function of NADH: NADH serves as a reducing agent that provides the necessary electrons for converting 3-phosphoglycerate (3-PGA) into glyceraldehyde-3-phosphate (G3P) during the Calvin cycle.

Question 82

# Ferrous Iron Oxidation Under Anoxic Conditions Electron acceptor in anaerobic Fe²⁺ oxidation.

Answer 82

Nitrate (NO₃⁻) ## Footnote Explanation: * In anaerobic conditions, iron-oxidizing bacteria can use nitrate (NO₃⁻) as an electron acceptor instead of oxygen. This process allows them to oxidize Fe²⁺ while reducing nitrate to nitrite (NO₂⁻) or further to nitrogen gas (N₂). This adaptation enables these bacteria to thrive in environments where oxygen is limited, supporting their energy production and growth. Iron-oxidizing bacteria obtain nitrate (NO₃⁻) from several sources: * Nitrate is naturally present in soils and water bodies due to the decomposition of organic matter and the activities of nitrifying bacteria. * In the nitrogen cycle, nitrifying bacteria convert ammonium (NH₄⁺) into nitrate (NO₃⁻) * Wastewater effluent often contains nitrates due to the treatment processes that promote nitrification. * In environments with limited oxygen (like wetlands, sediments, or anaerobic zones), nitrate can accumulate as a product of microbial nitrogen transformations.

Question 83

# Ferrous Iron Oxidation Under Anoxic Conditions Two types of bacteria that use Fe²⁺ for CO₂ fixation under anoxic conditions. (2)

Answer 83

* Chemolithotrophs * Phototrophs ## Footnote * *Acidithiobacillus ferrooxidans* can fix CO₂ while oxidizing Fe²⁺ anaerobically. * *Rhodopseudomonas palustris* can perform anoxygenic photosynthesis using Fe²⁺ as an electron donor while fixing CO₂.

Question 84

# Ferrous Iron Oxidation Under Anoxic Conditions Fe²⁺ oxidation in anoxic environments leads to the formation of __ and __ when iron(II) sulfide (FeS) is used.

Answer 84

- ferric hydroxide, Fe(OH)₃ - sulfate, SO₄²⁻

Question 85

# Nitrification What is nitrification?

Answer 85

Oxidation of ammonia (NH₃) and nitrite (NO₂⁻) by nitrifying bacteria

Question 86

# Nitrification Where are nitrifying bacteria commonly found? | Name four (4)

Answer 86

- Soils - water - wastewater - oceans

Question 87

# Nitrification What are the two main reactions in nitrification?

Answer 87

1. Ammonia oxidation: NH₃ → NO₂⁻ 2. Nitrite oxidation: NO₂⁻ → NO₃⁻

Question 88

# Nitrification Name bacteria and archea that oxidizes ammonia to nitrite. | Ammonia Oxidizers

Answer 88

Bacteria: *Nitrosomonas* Archae: *Nitrosopumilus*

Question 89

# Nitrification Name a bacterium that oxidizes nitrite to nitrate. | Nitrite oxidizer

Answer 89

*Nitrobacter*

Question 90

# Nitrification Genus of a bacteria that are dual catalyzers in nitrification? | Can oxidize ammonia and nitrite.

Answer 90

*Nitrospira*

Question 91

# Nitrification What do nitrification bioenergetics involve?

Answer 91

Electrons from reduced nitrogen entering an ETC

Question 92

# Nitrification 1. E₀′ of the NO₂⁻/NH₃ couple? 2. E₀′ of the NO₃⁻/NO₂⁻ couple?

Answer 92

1. +0.34 V 2. +0.43 V ## Footnote * NO₂⁻/NH₃ (+0.34 V): Nitrite reduction to ammonia is possible but less favorable. * NO₃⁻/NO₂⁻ (+0.43 V): Nitrate reduction to nitrite is more favorable, making nitrate the preferred electron acceptor.

Question 93

# Nitrification: Ammonia Oxidation Enzyme that catalyzes NH₃ to hydroxylamine (NH₂OH)?

Answer 93

Ammonia Monooxygenase (AMO) ## Footnote It adds one oxygen atom to ammonia while reducing the other oxygen atom to water (H₂O).

Question 94

# Nitrification: Ammonia Oxidation Enzyme that converts hydroxylamine to nitrite?

Answer 94

Hydroxylamine Oxidoreductase (HAO) ## Footnote * Oxidation: Hydroxylamine loses electrons as it converts to nitrite. * Reduction: These electrons are transferred to a carrier (like cytochrome), reducing it in the process.

Question 95

# Nitrificaation: Ammonia Oxidation What reaction is catalyzed by AMO? | Reaction

Answer 95

NH₃ + O₂ + 2H⁺ + 2e⁻ → NH₂OH + H₂O ## Footnote AMO converts ammonia (NH₃) into hydroxylamine (NH₂OH) using oxygen. This is the first step in nitrification, preparing ammonia for further oxidation to nitrite (NO₂⁻).

Question 96

# Nitrification: Nitrite Oxidation Enzyme that catalyzes NO₂⁻ to NO₃⁻?

Answer 96

Nitrite Oxidoreductase (NXR) ## Footnote * Oxidation: Nitrite loses electrons as it converts to nitrate. * Reduction: These electrons are transferred to an electron acceptor (e.g., cytochromes, quinones).

Question 97

# Nitrification: Nitrite Oxidation Where do electrons from nitrite oxidation travel?

Answer 97

Short electron transport chain to terminal oxidase ## Footnote Electrons from nitrite oxidation (NO₂⁻ → NO₃⁻), catalyzed by Nitrite Oxidoreductase (NXR), enter a short electron transport chain (ETC). These electrons are eventually transferred to a terminal oxidase, where they reduce O₂ to H₂O, generating a proton gradient for ATP synthesis.

Question 98

# Nitrification: Nitrite Oxidation What types of cytochromes generate PMF during nitrite oxidation?

Answer 98

Cytochromes of a and c types ## Footnote Cytochrome c * Function: A mobile electron carrier that shuttles electrons from one protein complex to another in the ETC. * Role in PMF: When cytochrome c transfers electrons to terminal oxidases, it facilitates the pumping of protons into the periplasmic space, contributing to the PMF. Terminal Oxidase (e.g., Cytochrome aa₃) * Function: Accepts electrons from cytochromes and reduces O₂ to H₂O. * Role in PMF: This process actively pumps protons out of the cytoplasm, increasing the proton gradient across the membrane, which is essential for ATP synthesis.

Question 99

# Nitrification What cycle do nitrifying bacteria use for CO₂ fixation?

Answer 99

Calvin Cycle

Question 100

# Nitrification Why is energy yield limited in nitrifying bacteria? | two (2) reasons

Answer 100

High ATP and reducing power requirements ## Footnote 1. High ATP Demand: Nitrification involves multiple steps (oxidizing ammonia to nitrite and then nitrite to nitrate), each requiring energy input. The overall process demands significant ATP for cellular maintenance, growth, and biosynthetic processes. 1. Need for Reducing Power: Nitrifying bacteria also require reducing power (NADH or NADPH) for biosynthetic reactions. This additional need competes for the energy generated during nitrification, limiting the overall energy available for ATP production.

Question 101

# Nitrification How do most nitrite oxidizers grow?

Answer 101

Chemoorganotrophically on organic substrates ## Footnote Most nitrite oxidizers, particularly those in environments with low inorganic nitrogen, utilize organic substrates as their primary energy and carbon source. They grow chemoorganotrophically by oxidizing organic compounds to obtain energy, which supports their metabolism and allows them to convert nitrite (NO₂⁻) to nitrate (NO₃⁻). This ability to utilize organic matter enhances their growth and survival in various ecological niches.

Question 102

# Nitrification What types of nutrition do ammonia-oxidizing bacteria prefer?

Answer 102

Obligate chemolithotrophs or mixotrophs

Question 103

# Nitrification: Ecological Roles of Nitrifying Microbes 1. What vital nutrient do nitrifiers convert ammonia into? 2. What role do nitrifiers play in wastewater treatment? 3. In aquatic ecosystems, nitrifiers make nitrogen available to ___ and __.

Answer 103

1. Nitrate (NO₃⁻) 2. Remove toxic amines and ammonia 3. Algae and cyanobacteria

Question 104

# What is Anammox? A microbial process where __ is oxidized under __ conditions using __ as the electron acceptor | Additional Question: What does the abbreviation mean?

Answer 104

- NH₄⁺ - anoxic - NO₂⁻ | Anaerobic Ammonia Oxidation (Anammox)

Question 105

# Anaerobic Ammonia Oxidation (Anammox) What is the overall Anammox reaction?

Answer 105

NH₄⁺ + NO₂⁻ → N₂ + 2H₂O

Question 106

# Anaerobic Ammonia Oxidation (Anammox) What is the ΔG°' value for the Anammox reaction? | Additional Question: What type of reaction?

Answer 106

-357 kJ (exergonic reaction)

Question 107

# Anaerobic Ammonia Oxidation (Anammox) Which bacteria catalyze Anammox? | Additional Question: From what phylum?

Answer 107

Obligate anaerobes from the *Planctomycetes* phylum

Question 108

# Anaerobic Ammonia Oxidation (Anammox) Name a major species of Anammox bacteria.

Answer 108

*Brocadia anammoxidans*

Question 109

# Anaerobic Ammonia Oxidation (Anammox) Name other genera of Anammox bacteria. | Name four (4)

Answer 109

* Kuenenia * Anammoxoglobus * Jettenia * Scalindua | Mnemonic: Ku-An-Jet-Sca

Question 110

# Anaerobic Ammonia Oxidation (Anammox) What are the characteristics of Anammox bacteria? | Give three (3)

Answer 110

* Obligate anaerobes * Autotrophic * Use the reductive acetyl-CoA pathway for CO₂ fixation

Question 111

# Anaerobic Ammonia Oxidation (Anammox) * A membrane-bound organelle where Anammox reactions occur * Confines toxic intermediates ## Footnote Additional: 1. Give one (1) example of toxic intermediate. 2. What does this generate for ATP synthesis?

Answer 111

Anammoxosome ## Footnote 1. hydrazine, N₂H₄) 2. proton motive force (PMF)

Question 112

# Anaerobic Ammonia Oxidation (Anammox) What is the structure of the Anammoxosome?

Answer 112

Composed of ladderane lipids | Dense membrane prevents diffusion of toxic intermediates

Question 113

# Anaerobic Ammonia Oxidation (Anammox) What is the first step of Anammox?

Answer 113

NO₂⁻ is reduced to NO by nitrite reductase (NIR).

Question 114

# Anaerobic Ammonia Oxidation (Anammox) What enzyme forms hydrazine (N₂H₄)?

Answer 114

Hydrazine synthase (HZS)

Question 115

# Anaerobic Ammonia Oxidation (Anammox) What enzyme oxidizes hydrazine to N₂?

Answer 115

Hydrazine dehydrogenase (HDH) ## Footnote Why "Dehydrogenase"? * Removes electrons: HDH extracts electrons from hydrazine, transferring them to the electron transport chain. * Does not transfer oxygen: Unlike oxygenases, HDH does not incorporate oxygen into the substrate.

Question 116

# Anaerobic Ammonia Oxidation (Anammox) What happens to the electrons from hydrazine oxidation?

Answer 116

They enter the electron transport chain (ETC), driving ATP synthesis.

Question 117

# Anaerobic Ammonia Oxidation (Anammox) What does the electron transport chain (ETC) do in Anammox? | Give two (2) reasons

Answer 117

* Regenerates reducing power via cyclic electron transfer * Electrons reduce NO₂⁻ and NO in earlier steps ## Footnote Explanation: 1. The ETC facilitates cyclic electron transfer, which helps regenerate reducing power (NADH/NADPH) needed for biosynthetic processes and maintaining metabolic functions. 2. Electrons from the ETC are used to reduce nitrite (NO₂⁻) to nitric oxide (NO) and potentially further to dinitrogen gas (N₂). This is crucial for the anammox process, where ammonium (NH₄⁺) is oxidized anaerobically.

Question 118

# Anaerobic Ammonia Oxidation (Anammox) How is CO₂ fixation achieved in Anammox? | Give three (3)

Answer 118

* Uses reverse electron transport * Oxidizes NO₂⁻ to NO₃⁻ via nitrite oxidoreductase * Provides electrons for CO₂ fixation

Question 119

# Anaerobic Ammonia Oxidation (Anammox) Where are Anammox bacteria found? | Give three (3)

Answer 119

* Anoxic sediments (marine & freshwater) * Wastewater treatment systems * Environments where NH₄⁺ and NO₂⁻ coexist

Question 120

# Anaerobic Ammonia Oxidation (Anammox) How do Anammox bacteria interact with other microbes? | Give two (2)

Answer 120

* Ammonia-oxidizing bacteria and archaea provide NO₂⁻ for Anammox bacteria * Oxygen levels regulate competition with aerobic ammonia oxidizers ## Footnote 1. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) oxidize ammonia (NH₄⁺) to nitrite (NO₂⁻), which is essential for Anammox bacteria, as they utilize NO₂⁻ as a substrate in their metabolic process. 2. Anammox bacteria thrive in anoxic (low oxygen) conditions, whereas aerobic ammonia oxidizers require oxygen for their metabolism. The availability of oxygen influences the competition between these groups. In oxygen-rich environments, aerobic ammonia oxidizers may outcompete Anammox bacteria, while in anoxic conditions, Anammox bacteria can flourish, effectively reducing nitrogen compounds in the ecosystem.

Question 121

# Anaerobic Ammonia Oxidation (Anammox) How does Anammox help in wastewater treatment? | Give three (3)

Answer 121

* Removes NH₃ and amines under anoxic conditions * Reduces nitrogen input into aquatic ecosystems * Helps maintain water quality ## Footnote 1. Removal of NH₃ and Amines: Anammox bacteria convert ammonia (NH₄⁺) and amines into nitrogen gas (N₂) under anoxic conditions, effectively removing these nitrogen compounds from wastewater. 2. Reduction of Nitrogen Input: By transforming nitrogenous compounds into inert nitrogen gas, Anammox reduces the nitrogen loading into receiving water bodies, preventing eutrophication (excessive nutrient enrichment) that can lead to algal blooms. 3. Maintenance of Water Quality: The anammox process contributes to the overall removal of nitrogen from wastewater, helping to maintain water quality and support the health of aquatic ecosystems by ensuring balanced nutrient levels.

Question 122

# Anaerobic Ammonia Oxidation (Anammox) What role does Anammox play in marine nitrogen cycling? | Give two (2)

Answer 122

* Responsible for NH₃ loss in anoxic marine sediments * Crucial for global nitrogen balance ## Footnote 1. Anammox bacteria convert ammonia (NH₄⁺) to nitrogen gas (N₂) in anoxic marine sediments, effectively removing bioavailable nitrogen from the environment and preventing its accumulation. 2. The anammox process contributes significantly to the global nitrogen cycle by reducing the levels of reactive nitrogen in marine ecosystems. This process is crucial for maintaining the nitrogen balance, as it helps regulate the availability of nitrogen in the ocean, impacting primary production and overall ecosystem health.