Lecture 3B.2: Respiration: ETC: H2 Oxidation, Sox System, Fe2+ Oxidation, Nitrification, Anammox Flashcards
Source: PPT and Architecture of bacterial respiratory chains (https://doi.org/10.1038/s41579-020-00486-4)
An organism that switches to alternative electron acceptors when O₂ is limiting
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.
When does a facultative anaerobe switch back to oxygen?
As soon as oxygen becomes available
What types of electron acceptors do facultative anaerobes use? (3)
Inorganic/organic compounds, and metals such as ferric iron (Fe³⁺) and manganese ion (Mn⁴⁺)
Which organisms use more electronegative electron acceptors?
Obligate anaerobes
microorganisms that cannot survive in the presence of oxygen because they lack the enzymes necessary to neutralize the toxic byproducts of oxygen.
Why are obligate anaerobes unable to tolerate oxygen?
Their enzymes are inhibited by oxygen
Alternative Electron Acceptors
What are some examples of highly electronegative electron acceptors? (3)
- Sulfate (SO₄²⁻)
- elemental sulfur (S⁰)
- carbon dioxide (CO₂)
Alternative Electron Acceptors
Why do organisms using SO₄²⁻, S⁰, or CO₂ require an anaerobic lifestyle?
These acceptors are only effective in anaerobic conditions
How does respiration conserve energy?
Through redox reactions, transferring electrons from an electron donor to a final electron acceptor
What are the two major microbial classifications based on electron donors? (2)
Give brief description each.
- Chemoorganotrophs: Oxidize organic compounds
- Chemolithotrophs: Oxidize inorganic compounds and obtain carbon from CO₂
- What happens to electron donors during respiration?
- What happens to electron acceptors?
Mnemonic for redox reactions in respiration?
- They undergo oxidation (lose electrons)
- They undergo reduction (gain electrons)
DORA: Donor is Oxidized, Reduced is Acceptor
What determines how much energy is released in respiration?
The greater the difference in E₀′ between donor and acceptor, the more energy is released.
What are some electron acceptors in anaerobic respiration?
Give four (4)
- Nitrate (NO₃⁻)
- sulfate (SO₄²⁻)
- iron (Fe³⁺)
- carbon dioxide (CO₂)
What type of microbes can switch between aerobic and anaerobic respiration?
Facultative aerobes
What type of microbes cannot tolerate O₂?
Obligate anaerobes
What is the purpose of assimilative reduction?
To reduce NO₃⁻, SO₄²⁻, or CO₂ for biosynthesis (incorporated into biomass)
Does assimilative reduction consume or produce energy?
Consumes energy
What is the purpose of dissimilative reduction?
To reduce NO₃⁻, SO₄²⁻, or CO₂ for energy conservation
What happens to the reduced products in dissimilative reduction?
They are excreted (e.g., N₂, H₂S, CH₄)
Which process is more common in anaerobic respiration?
Dissimilative reduction
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)
- Nitrate (NO₃⁻)
- manganese (Mn⁴⁺)
- iron (Fe³⁺)
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)
- Sulfate (SO₄²⁻)
- elemental sulfur (S⁰)
Which electron acceptor has the lowest E₀′?
E₀′ - reduction potential: a measure of the tendency of a chemical species to gain electrons (be reduced)
CO₂ (reduced to CH₄ in methanogenesis)
How does energy yield change as electron acceptors become less electropositive?
It decreases
Chemolithotrophs that also use organic carbon.
Mixotrophs
One of the simplest chemolithotrophs.
Hydrogen bcteria
A common microbial metabolism product, especially in fermentations.
H₂ (Hydrogen)
Hydrogen Oxidation:
Aerobic hydrogen bacteria oxidize H₂ to form ___ and __.
Water and ATP
Hydrogen Oxidation:
H₂ oxidation by O₂ is highly ___.
exergonic
Hydrogen Oxidation:
Reaction for H₂ oxidation?
H₂ + ½ O₂ → H₂O
Hydrogen Oxidation:
Enzyme that catalyzes H₂ oxidation.
Hydrogenase
Hydrogen Oxidation: Hydrogenases
- Transfers electrons from H₂ to a quinone acceptor.
- Reduces NAD⁺ to NADH directly.
- Membrane-bound hydrogenase or membrane-integrated hydrogenase
- Cytoplasmic hydrogenase
Hydrogen Oxidation:
Model organism for aerobic H₂ oxidation.
Ralstonia eutropha
Hydrogenases:
- Type of hydrogenase that helps in ATP synthesis.
- Hydrogenase that provides reducing power.
- Membrane-bound hydrogenase or membrane-integrated hydrogenase
- cytoplasmic hydrogenase
Hydrogen Oxidation:
Bacteria with a single hydrogenase must rely on ___.
Reverse electron transport
Autotrophy in H₂ Bacteria:
CO₂ fixation pathway in hydrogen bacteria.
Calvin cycle
Autotrophy in H₂ Bacteria:
When growing chemoorganotrophically, hydrogen bacteria repress ___ and ___.
- Calvin cycle
- hydrogenase enzymes
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.
Organisms that switch between chemolithotrophy and chemoorganotrophy.
Facultative chemolithotrophs
Ecological Significance of Hydrogen Bacteria:
H₂ is mainly produced in ___.
Anoxic environments
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.
Ecological Significance of Hydrogen Bacteria:
H₂-consuming microbes prevent H₂ from reaching ___.
oxic zones
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.
Ecological Significance of Hydrogen Bacteria:
Aerobic hydrogen bacteria thrive in ___.
Oxic-anoxic interfaces
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.
Ecological Significance of Hydrogen Bacteria:
Many hydrogen bacteria prefer ___ oxygen levels.
Low (microaerobic)
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.
Microbes that obtain energy by oxidizing reduced sulfur compounds.
Sulfur-oxidizing bacteria (SOB)
Sulfur Oxidation:
Common electron donor in sulfur oxidation.
Give four (4)
- hydrogen sulfide (H₂S)
- elemental sulfur (S⁰)
- thiosulfate (S₂O₃²⁻)
- sulfite (SO₃²⁻)
Sulfur Oxidation:
Final product of sulfur oxidation.
Sulfate (SO₄²⁻)
Sulfur Oxidation:
Process where sulfur oxidation contributes to environmental acidification.
Acid mine drainage (AMD)
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.
Sulfur Oxidation:
General equation for H₂S oxidation.
Partial oxidation to elemental sulfur (S⁰):
H₂S + O₂ → S⁰ + H₂O
Complete oxidation to sulfate (SO₄²⁻):
S⁰ + 1.5 O₂ + H₂O → SO₄²⁻ + 2H⁺
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⁺)
Sulfur Oxidation:
System that catalyzes complete oxidation of sulfur compounds to sulfate.
Sox System
Sulfur-Oxidizing Pathways: Enzyme
Converts intracellular sulfur stores into sulfate.
Reverse-acting dissimilatory sulfite reductase (rDSR)
- 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.
Sulfur-Oxidizing Pathways: Enzymes
Converts sulfite to sulfate.
Name two (2) enzymes
- Adenosine phosphosulfate (APS) reductase
- Sulfite oxidase
Sulfur-Oxidizing Pathways: Enzymes
- Involves an intermediate step where sulfite is first converted to __ before being oxidized to sulfate. What enzyme catalyzes this reaction?
- Directly oxidizes sulfite to sulfate using molecular oxygen or other electron acceptors.
- Adenosine phosphosulfate
- APS reductase (Adenosine phosphosulfate reductase)
- Sulfite oxidase
Energy Conservation in Sulfur Oxidation:
Sulfur oxidation generates electrons that enter the ___.
Electron transport chain (ETC)
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.
Sulfur Oxidation:
ATP synthesis in sulfur oxidation is driven by ___.
Proton motive force (PMF)
Sulfur Oxidation:
Some sulfur oxidizers require this process to generate NADH.
Reverse electron transport
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.
Sulfur Oxidation: Autotrophy and Carbon Fixation:
Most sulfur-oxidizing bacteria fix CO₂ via the ___.
Calvin cycle
Sulfur Oxidation: Autotrophy and Carbon Fixation
Energy from sulfur oxidation supports ___.
Carbon fixation
Bacterium that switches between chemolithotrophy and chemoorganotrophy.
Give one (1) example
Beggiatoa
Sulfur Oxidation: Ecological and Industrial Significance:
Environments where sulfur oxidation is significant.
Name three (3)
- Hydrothermal vents
- Marine sediments
- Sulfur springs
Sulfur Oxidation: Ecological and Industrial Significance:
Acidophilic sulfur bacteria used in biomining.
Acidithiobacillus
Sulfur Oxidation: Ecological and Industrial Significance:
Process where sulfur bacteria help extract metals from ores.
Bioleaching
Sulfur Oxidation: The Sox System
The Sox system is responsible for the oxidation of ___.
reduced sulfur compounds
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.
Sulfur Oxidation: The Sox System
Two (2) bacterial genera with the Sox system.
- Paracoccus
- Thiobacillus
Sulfur Oxidation: The Sox System:
Enumerate the key components of the Sox System (4)
- SoxXA
- SoxYZ (carrier protein)
- SoxB
- SoxCD (Sulfur dehydrogenase)
Additional Info:
SoxX: A cytochrome c protein.
SoxA: A heme-containing enzyme that helps transfer electrons.
Sulfur Oxidation: The Sox System:
Sox component that binds and activates thiosulfate (S₂O₃²⁻).
SoxXA
SoxXA is a periplasmic heme protein complex.
Sulfur Oxidation: The Sox System:
Carrier proteins in the Sox system.
covalently binds sulfur intermediates.
SoxYZ
Acts as a scaffold for sulfur oxidation.
Sulfur Oxidation: The Sox System:
Enzyme that directly oxidizes sulfur to sulfate (SO₄²⁻).
Cleaves and releases sulfate (SO₄²⁻) as the final product.
SoxB
A sulfate-releasing hydrolase that completes the oxidation cycle.
Sulfur Oxidation: The Sox System:
Sox enzyme that further oxidizes sulfite (SO₃²⁻) to sulfate (SO₄²⁻).
Removes electrons from sulfur compounds and transfers them to the ETC.
Functions as a sulfur dehydrogenase, enabling complete oxidation.
SoxCD
Unique Feature of the Sox System:
The Sox system oxidizes sulfur compounds to sulfate without forming ___.
sulfite (SO₃²⁻)
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.
Iron (Fe²⁺) Oxidation:
Electron donor in iron oxidation.
Fe²⁺ (ferrous iron)
Iron (Fe²⁺) Oxidation:
Product of Fe²⁺ oxidation.
Fe³⁺ (ferric iron)
Iron (Fe²⁺) Oxidation:
Fe³⁺ oxidation forms insoluble ___.
Ferric hydroxide (Fe(OH)₃)
Fe3+ + 3H2O → Fe(OH)3 ↓+3H +
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.
Iron (Fe²⁺) Oxidation:
Iron oxidation is most efficient at ___ pH.
Acidic
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.
Iron-Oxidizing Bacteria:
Two acidophilic Fe²⁺-oxidizing bacteria. (2)
- Acidithiobacillus ferrooxidans
- Leptospirillum ferrooxidans
Iron-Oxidizing Bacteria:
Archaeon that oxidizes Fe²⁺ at extremely low pH.
Ferroplasma
Iron-Oxidizing Bacteria:
Three neutral pH iron oxidizers. (3)
- Gallionella ferruginea
- Sphaerotilus natans
- Leptothrix discophora
Energy from Iron Oxidation:
First protein in A. ferrooxidans Fe²⁺ oxidation.
Cytochrome c
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.
Iron (Fe²⁺) Oxidation:
Enumerate the Electron Flow in Fe²⁺ Oxidation (Simplified Pathway)
- Fe²⁺ → Cyc2 (outer membrane cytochrome c)
- Cyc2 → Rusticyanin (periplasmic electron carrier)
- Rusticyanin → Cytochrome c₄ → Cytochrome aa₃ (final electron acceptor: O₂)
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.
Iron (Fe²⁺) Oxidation:
Final electron acceptor in Fe²⁺ oxidation.
O₂
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.
Iron (Fe²⁺) Oxidation:
Key protein transferring electrons to cytochrome c.
Rusticyanin
- 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.
Iron (Fe²⁺) Oxidation:
- Acidithiobacillus ferrooxidans generates ATP through oxidation of __.
- The periplasm of A. ferrooxidans has a pH of __.
- The cytoplasm of A. ferrooxidans has a pH of ___.
- Fe²⁺
- pH: 1-2
- pH: 5.5-6 pH
✔ 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.
Iron (Fe²⁺) Oxidation:
Pathway used by Fe²⁺ oxidizers for carbon fixation.
Calvin cycle
Iron (Fe²⁺) Oxidation:
Reverse electron flow is required to generate ___.
NADH
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.
Ferrous Iron Oxidation Under Anoxic Conditions
Electron acceptor in anaerobic Fe²⁺ oxidation.
Nitrate (NO₃⁻)
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.
Ferrous Iron Oxidation Under Anoxic Conditions
Two types of bacteria that use Fe²⁺ for CO₂ fixation under anoxic conditions. (2)
- Chemolithotrophs
- Phototrophs
- Acidithiobacillus ferrooxidans can fix CO₂ while oxidizing Fe²⁺ anaerobically.
- Rhodopseudomonas palustris can perform anoxygenic photosynthesis using Fe²⁺ as an electron donor while fixing CO₂.
Ferrous Iron Oxidation Under Anoxic Conditions
Fe²⁺ oxidation in anoxic environments leads to the formation of __ and __ when iron(II) sulfide (FeS) is used.
- ferric hydroxide, Fe(OH)₃
- sulfate, SO₄²⁻
Nitrification
What is nitrification?
Oxidation of ammonia (NH₃) and nitrite (NO₂⁻) by nitrifying bacteria
Nitrification
Where are nitrifying bacteria commonly found?
Name four (4)
- Soils
- water
- wastewater
- oceans
Nitrification
What are the two main reactions in nitrification?
- Ammonia oxidation: NH₃ → NO₂⁻
- Nitrite oxidation: NO₂⁻ → NO₃⁻
Nitrification
Name bacteria and archea that oxidizes ammonia to nitrite.
Ammonia Oxidizers
Bacteria: Nitrosomonas
Archae: Nitrosopumilus
Nitrification
Name a bacterium that oxidizes nitrite to nitrate.
Nitrite oxidizer
Nitrobacter
Nitrification
Genus of a bacteria that are dual catalyzers in nitrification?
Can oxidize ammonia and nitrite.
Nitrospira
Nitrification
What do nitrification bioenergetics involve?
Electrons from reduced nitrogen entering an ETC
Nitrification
- E₀′ of the NO₂⁻/NH₃ couple?
- E₀′ of the NO₃⁻/NO₂⁻ couple?
- +0.34 V
- +0.43 V
- 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.
Nitrification: Ammonia Oxidation
Enzyme that catalyzes NH₃ to hydroxylamine (NH₂OH)?
Ammonia Monooxygenase (AMO)
It adds one oxygen atom to ammonia while reducing the other oxygen atom to water (H₂O).
Nitrification: Ammonia Oxidation
Enzyme that converts hydroxylamine to nitrite?
Hydroxylamine Oxidoreductase (HAO)
- Oxidation: Hydroxylamine loses electrons as it converts to nitrite.
- Reduction: These electrons are transferred to a carrier (like cytochrome), reducing it in the process.
Nitrificaation: Ammonia Oxidation
What reaction is catalyzed by AMO?
Reaction
NH₃ + O₂ + 2H⁺ + 2e⁻ → NH₂OH + H₂O
AMO converts ammonia (NH₃) into hydroxylamine (NH₂OH) using oxygen. This is the first step in nitrification, preparing ammonia for further oxidation to nitrite (NO₂⁻).
Nitrification: Nitrite Oxidation
Enzyme that catalyzes NO₂⁻ to NO₃⁻?
Nitrite Oxidoreductase (NXR)
- Oxidation: Nitrite loses electrons as it converts to nitrate.
- Reduction: These electrons are transferred to an electron acceptor (e.g., cytochromes, quinones).
Nitrification: Nitrite Oxidation
Where do electrons from nitrite oxidation travel?
Short electron transport chain to terminal oxidase
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.
Nitrification: Nitrite Oxidation
What types of cytochromes generate PMF during nitrite oxidation?
Cytochromes of a and c types
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.
Nitrification
What cycle do nitrifying bacteria use for CO₂ fixation?
Calvin Cycle
Nitrification
Why is energy yield limited in nitrifying bacteria?
two (2) reasons
High ATP and reducing power requirements
- 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.
- 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.
Nitrification
How do most nitrite oxidizers grow?
Chemoorganotrophically on organic substrates
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.
Nitrification
What types of nutrition do ammonia-oxidizing bacteria prefer?
Obligate chemolithotrophs or mixotrophs
Nitrification: Ecological Roles of Nitrifying Microbes
- What vital nutrient do nitrifiers convert ammonia into?
- What role do nitrifiers play in wastewater treatment?
- In aquatic ecosystems, nitrifiers make nitrogen available to ___ and __.
- Nitrate (NO₃⁻)
- Remove toxic amines and ammonia
- Algae and cyanobacteria
What is Anammox?
A microbial process where __ is oxidized under __ conditions using __ as the electron acceptor
Additional Question: What does the abbreviation mean?
- NH₄⁺
- anoxic
- NO₂⁻
Anaerobic Ammonia Oxidation (Anammox)
Anaerobic Ammonia Oxidation (Anammox)
What is the overall Anammox reaction?
NH₄⁺ + NO₂⁻ → N₂ + 2H₂O
Anaerobic Ammonia Oxidation (Anammox)
What is the ΔG°’ value for the Anammox reaction?
Additional Question: What type of reaction?
-357 kJ (exergonic reaction)
Anaerobic Ammonia Oxidation (Anammox)
Which bacteria catalyze Anammox?
Additional Question: From what phylum?
Obligate anaerobes from the Planctomycetes phylum
Anaerobic Ammonia Oxidation (Anammox)
Name a major species of Anammox bacteria.
Brocadia anammoxidans
Anaerobic Ammonia Oxidation (Anammox)
Name other genera of Anammox bacteria.
Name four (4)
- Kuenenia
- Anammoxoglobus
- Jettenia
- Scalindua
Mnemonic: Ku-An-Jet-Sca
Anaerobic Ammonia Oxidation (Anammox)
What are the characteristics of Anammox bacteria?
Give three (3)
- Obligate anaerobes
- Autotrophic
- Use the reductive acetyl-CoA pathway for CO₂ fixation
Anaerobic Ammonia Oxidation (Anammox)
- A membrane-bound organelle where Anammox reactions occur
- Confines toxic intermediates
Additional:
1. Give one (1) example of toxic intermediate.
2. What does this generate for ATP synthesis?
Anammoxosome
- hydrazine, N₂H₄)
- proton motive force (PMF)
Anaerobic Ammonia Oxidation (Anammox)
What is the structure of the Anammoxosome?
Composed of ladderane lipids
Dense membrane prevents diffusion of toxic intermediates
Anaerobic Ammonia Oxidation (Anammox)
What is the first step of Anammox?
NO₂⁻ is reduced to NO by nitrite reductase (NIR).
Anaerobic Ammonia Oxidation (Anammox)
What enzyme forms hydrazine (N₂H₄)?
Hydrazine synthase (HZS)
Anaerobic Ammonia Oxidation (Anammox)
What enzyme oxidizes hydrazine to N₂?
Hydrazine dehydrogenase (HDH)
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.
Anaerobic Ammonia Oxidation (Anammox)
What happens to the electrons from hydrazine oxidation?
They enter the electron transport chain (ETC), driving ATP synthesis.
Anaerobic Ammonia Oxidation (Anammox)
What does the electron transport chain (ETC) do in Anammox?
Give two (2) reasons
- Regenerates reducing power via cyclic electron transfer
- Electrons reduce NO₂⁻ and NO in earlier steps
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.
Anaerobic Ammonia Oxidation (Anammox)
How is CO₂ fixation achieved in Anammox?
Give three (3)
- Uses reverse electron transport
- Oxidizes NO₂⁻ to NO₃⁻ via nitrite oxidoreductase
- Provides electrons for CO₂ fixation
Anaerobic Ammonia Oxidation (Anammox)
Where are Anammox bacteria found?
Give three (3)
- Anoxic sediments (marine & freshwater)
- Wastewater treatment systems
- Environments where NH₄⁺ and NO₂⁻ coexist
Anaerobic Ammonia Oxidation (Anammox)
How do Anammox bacteria interact with other microbes?
Give two (2)
- Ammonia-oxidizing bacteria and archaea provide NO₂⁻ for Anammox bacteria
- Oxygen levels regulate competition with aerobic ammonia oxidizers
- 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.
- 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.
Anaerobic Ammonia Oxidation (Anammox)
How does Anammox help in wastewater treatment?
Give three (3)
- Removes NH₃ and amines under anoxic conditions
- Reduces nitrogen input into aquatic ecosystems
- Helps maintain water quality
- 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. - 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. - 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.
Anaerobic Ammonia Oxidation (Anammox)
What role does Anammox play in marine nitrogen cycling?
Give two (2)
- Responsible for NH₃ loss in anoxic marine sediments
- Crucial for global nitrogen balance
- Anammox bacteria convert ammonia (NH₄⁺) to nitrogen gas (N₂) in anoxic marine sediments, effectively removing bioavailable nitrogen from the environment and preventing its accumulation.
- 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.
