Name: microbial carbon fixation pathways
Uploaded: 2025-06-12T09:37:09.000Z
Duration: 1 min 28 s
Channel: JoVE

K12 Standards

north-carolina-k-12-science-standard-course-of-study

NC K-12 Science Standard Course of Study

9-12

Earth and Environmental Science

Earth's Systems

ESS.EES.4.2

Carbon-dioxide Fixation

Carbon dioxide fixation occurring in autotrophs is the process of converting inorganic carbon into organic molecules.The Calvin cycle, the most common carbon fixation pathway, occurs in the carboxysomes of cyanobacteria. In eukaryotic autotrophs, this pathway occurs in the cytoplasm or the chloroplast stroma.It has three phases: carboxylation, where RuBisCO attaches carbon dioxide to ribulose-1,5-bisphosphate, forming 3-phosphoglycerate; reduction, where ATP and NADPH convert 3-phosphoglycerate to glyceraldehyde-3-phosphate; and regeneration, reforming ribulose-1,5-bisphosphate.Some bacteria use the reductive TCA cycle to produce organic compounds using carbon dioxide and water. This cycle operates in reverse of the oxidative TCA cycle, which releases carbon dioxide molecules.In certain bacteria, the Wood-Ljungdahl pathway uses hydrogen as an electron donor and carbon dioxide as &#8211; an electron acceptor and a carbon source &#8211; to produce acetate.Meanwhile, in some archaea and bacteria, the 3-hydroxypropionate cycle fixes carbon dioxide and bicarbonate for metabolism.

carbon-dioxide fixation

Carbon dioxide fixation in prokaryotes enables the assimilation of inorganic carbon into organic molecules, supporting biosynthetic pathways, sustaining ecosystems, and contributing to the global carbon cycle. It also has industrial applications in carbon capture and bioproduct synthesis. Autotrophic organisms rely on this process to utilize CO&#8322; as a carbon source in diverse environments.The Calvin CycleThe Calvin cycle is the most widespread carbon fixation mechanism, primarily used by cyanobacteria and autotrophic prokaryotes. It is integrated with photosynthesis but requires 9 ATP and 6 NADPH per CO&#8322; molecule, making it energy-intensive compared to alternatives like the reductive TCA cycle, which requires only 5 ATP. Despite this, its adaptability makes it the dominant pathway in many ecosystems.This cycle occurs in carboxysomes, specialized microcompartments that enhance efficiency by concentrating CO&#8322; and minimizing oxygen interference. The key enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), catalyzes the initial carboxylation reaction. The cycle has three phases:<ul><li>Carboxylation: RuBisCO attaches CO&#8322; to ribulose-1,5-bisphosphate (RuBP), forming two molecules of 3-phosphoglycerate (3-PGA).</li><li>Reduction: ATP and NADPH convert 3-PGA into glyceraldehyde-3-phosphate (G3P), a carbohydrate precursor.</li><li>Regeneration: Enzymatic reactions regenerate RuBP from G3P, maintaining the cycle.</li></ul>Alternative Carbon Fixation PathwaysSome autotrophic bacteria use alternative pathways suited to specific ecological niches.Reductive Tricarboxylic Acid (TCA) CycleAnaerobic and microaerophilic bacteria employ the reductive TCA cycle, which runs in reverse to the oxidative TCA cycle. It incorporates CO&#8322; into organic molecules through reduction reactions, synthesizing key metabolic intermediates.Wood&#8211;Ljungdahl PathwayAcetogenic and methanogenic bacteria use this pathway, where hydrogen serves as an electron donor while CO&#8322; functions as both an electron acceptor and carbon source. The primary end product, acetate, is used for biomass synthesis or energy generation.3-Hydroxypropionate CycleThis pathway, found in certain archaea and bacteria, fixes CO&#8322; and bicarbonate through carboxylation and rearrangement reactions, incorporating inorganic carbon into organic intermediates essential for metabolism.Environmental AdaptationsThese diverse fixation pathways allow prokaryotes to thrive in extreme environments, including deep-sea hydrothermal vents (e.g., Hydrogenobacter), acidic hot springs (e.g., Sulfolobus acidocaldarius), anoxic sediments (e.g., Desulfobacter), and polar ice regions (e.g., Psychromonas). These environments present challenges such as high temperatures, low oxygen, and extreme pH, where specialized carbon fixation mechanisms enable survival and contribute to global carbon cycling.

Carbon dioxide fixation in prokaryotes enables the assimilation of inorganic carbon into organic molecules, supporting biosynthetic pathways, sustaining ...

Education

JoVE Core

Microbiology

Unit

Microbial Metabolism

KEY TERMS AND CONCEPTS

microbial carbon fixation pathways

Microbial carbon fixation pathways let prokaryotes turn carbon dioxide into organic molecules. This process supports biosynthesis, helps sustain ecosystems, and plays a role in the global carbon cycle. It also has industrial uses in carbon capture and bioproduct synthesis. Autotrophic organisms depend on this process to use CO2 as a carbon source in many environments.

The Calvin cycle is the most common carbon fixation pathway. Cyanobacteria and other autotrophic prokaryotes use it, and it works with photosynthesis. It is energy-intensive because each CO2 molecule requires 9 ATP and 6 NADPH, but its flexibility makes it the main pathway in many ecosystems. The cycle occurs in carboxysomes, which are specialized microcompartments that concentrate CO2 and reduce oxygen interference.

RuBisCO, or ribulose-1,5-bisphosphate carboxylase/oxygenase, starts the Calvin cycle by adding CO2 to ribulose-1,5-bisphosphate, or RuBP. This forms two molecules of 3-phosphoglycerate, or 3-PGA. In the reduction phase, ATP and NADPH convert 3-PGA into glyceraldehyde-3-phosphate, or G3P, which is a carbohydrate precursor. In the regeneration phase, enzymes rebuild RuBP so the cycle can continue.

Some autotrophic bacteria use other carbon fixation pathways that fit specific habitats. The reductive tricarboxylic acid, or TCA, cycle is used by anaerobic and microaerophilic bacteria. It runs in reverse of the oxidative TCA cycle and uses reduction reactions to add CO2 to organic molecules. This pathway makes key metabolic intermediates and uses only 5 ATP, which is less than the Calvin cycle.

The Wood-Ljungdahl pathway is used by acetogenic and methanogenic bacteria. In this pathway, hydrogen acts as the electron donor. CO2 serves as both an electron acceptor and a carbon source. The main product is acetate, which can support biomass synthesis or energy generation.

Some archaea and bacteria use the 3-hydroxypropionate cycle. This pathway fixes CO2 and bicarbonate through carboxylation and rearrangement reactions. It adds inorganic carbon to organic intermediates that are important for metabolism.

These different pathways help prokaryotes survive in extreme environments. Examples include deep-sea hydrothermal vents, acidic hot springs, anoxic sediments, and polar ice regions. Organisms such as Hydrogenobacter, Sulfolobus acidocaldarius, Desulfobacter, and Psychromonas live in these settings. Their carbon fixation systems help them cope with high temperatures, low oxygen, and extreme pH while also contributing to the global carbon cycle.

Microbial Carbon Fixation Pathways

microbial nutrition

Microbial Energy and Carbon Sources

Microbial energy and carbon sources determine how microorganisms live and grow. These metabolic strategies help microbes survive in many habitats and keep energy moving through ecosystems. They also support nutrient cycling in nature. Microbes are grouped by where they get energy, electrons, and carbon. Phototrophs use light, while chemotrophs use chemical compounds for energy. Lithotrophs take electrons from reduced inorganic substances, and organotrophs take them from organic compounds.

atp and energy production

How Cells Make and Use ATP

ATP is the main energy carrier in cells. It is made of adenosine, which includes adenine and ribose, plus three phosphate groups. The bonds between the phosphate groups hold a large amount of potential energy. When ATP is hydrolyzed, it becomes ADP or AMP and releases energy for cell work. Cells use that energy for many essential tasks. It supports macromolecule synthesis, intracellular transport, and mechanical movement. ATP also acts as an energy manager by linking catabolic and anabolic...

redox reactions

Electron Carriers in Redox Metabolism

Redox reactions move electrons through metabolic pathways in cells. Oxidation is the loss of electrons, and reduction is the gain of electrons. These two steps happen together, which keeps electron flow moving through metabolism. A clear example appears in bacterial metabolism. Glucose is oxidized to carbon dioxide, while oxygen is reduced to water. This shows how one molecule loses electrons as another gains them. Cells use special electron carriers to make these transfers happen.

introduction to metabolism

Metabolism: Energy Use and Biomolecule Synthesis

Metabolism is the set of chemical reactions that keep living cells working. It includes reactions that break down biomolecules and reactions that build them up. These two sides of metabolism work together to support energy balance and cell function. Catabolic pathways break large molecules into smaller parts. Carbohydrates, lipids, and proteins can be broken down into monosaccharides, fatty acids, and amino acids. These reactions release energy, and cells store much of that energy as ATP, or...

carbohydrate catabolism

Glucose Breakdown and ATP Production

Glucose breakdown is a key part of cell metabolism that lets cells make ATP, the usable form of energy. The process follows two main paths: cellular respiration and fermentation. Both start with glycolysis, which does not require oxygen. Glycolysis splits one glucose molecule into two molecules of pyruvic acid. It also produces a net gain of two ATP molecules and two NADH molecules. This step sets up the cell to continue with respiration or switch to fermentation, depending on whether oxygen...

glycolysis

Glycolysis and Pyruvate Fate

Glycolysis is a central pathway in glucose catabolism and a major way cells make energy. It is also called the Embden-Meyerhof pathway. This process takes place in the cytoplasm and can work with or without oxygen, which makes it useful in many organisms and conditions. Glycolysis has ten steps and turns one glucose molecule into two pyruvate molecules. It has two phases. In the preparatory phase, the cell uses two ATP to add phosphate groups to glucose and split it into two three-carbon...

other glycolytic pathways

Pentose Phosphate Pathway and Entner-Doudoroff

The pentose phosphate pathway works alongside glycolysis in cells that need both sugar breakdown and building blocks for growth. It handles pentoses, which are five-carbon sugars, and also uses glucose as a starting point. The pathway has two parts, an oxidative phase and a non-oxidative phase. It does not make ATP directly, but its products can feed back into glycolysis when the cell needs them. The oxidative phase mainly makes NADPH, a reduced electron carrier. In this phase,...

cellular respiration

Cellular Respiration: ATP Production Pathways

Cellular respiration is the process cells use to turn glucose into ATP, the main energy molecule in the cell. It depends on oxidation and the transfer of electrons to a separate electron acceptor. This sequence of reactions supports energy production in both aerobic and anaerobic settings. Glycolysis is the first step. It takes place in the cytoplasm of both prokaryotic and eukaryotic cells. One glucose molecule is broken into two pyruvate molecules, and the cell gains a net 2 ATP and 2 NADH.

electron transport chain components

Electron Transport Chain and ATP Production

The electron transport chain helps cells make ATP by moving electrons through membrane protein complexes. In eukaryotic cells, it sits in the inner mitochondrial membrane. In prokaryotic cells, it is found in the plasma membrane and can differ in the number and type of complexes, depending on the organism and its environment. The chain uses several electron carriers to pass electrons along in redox reactions, which are reactions that involve oxidation and reduction. These carriers include...

chemiosmosis and atp synthesis

Electron Transport Chain Powers ATP Output

The electron transport chain powers ATP production during cellular respiration. It sits in the inner mitochondrial membrane and moves high-energy electrons from NADH and FADH2 to molecular oxygen, the final electron acceptor. As electrons move through the chain, protons are pushed across the membrane to build the gradient needed for ATP synthesis. Electrons from NADH enter the chain at Complex I, also called NADH: ubiquinone oxidoreductase. In prokaryotes, this step helps pump protons from the...

respiration pathways

TCA Cycle and Energy Pathways

Cellular respiration uses the TCA cycle, also called the Krebs cycle, to help cells make usable energy from organic molecules. This pathway is a central part of aerobic respiration and also supports biosynthesis. It links the breakdown of food molecules to the cell's energy needs. Pyruvate from glycolysis enters this process first. The pyruvate dehydrogenase complex converts pyruvate into acetyl-CoA through oxidative decarboxylation. This step produces one NADH and one carbon dioxide molecule.

microbial fermentation

Fermentation Products in Microbes

Fermentation is an anaerobic process that lets microbes make energy from sugar without oxygen or an electron transport chain. It is important in both biology and industry. The process is grouped by the products it makes. Pyruvate and its derivatives act as key electron acceptors in fermentative pathways. This step helps oxidize NADH back to NAD+, which is needed for glycolysis to keep running. Without NAD+ regeneration, glycolysis would stop and the cell would lose its main source of ATP under...

metabolism of chemolithotrophs

How Chemolithotrophs Make ATP

Chemolithotrophs make ATP by using inorganic chemicals as an energy source. They oxidize molecules such as hydrogen gas, ammonia, reduced sulfur compounds, and ferrous iron. Instead of relying on organic carbon like heterotrophs, they move electrons from these inorganic donors into the electron transport chain, or ETC. That electron flow builds a proton motive force, or PMF. The PMF drives ATP synthesis through oxidative phosphorylation. Because inorganic electron donors usually release less...

amino acid catabolism

Microbes Use Proteins for Energy

Microbes can use proteins as a carbon and energy source, especially when polysaccharides or lipids are scarce. But proteins are too large to pass through the plasma membrane on their own. To solve this, microbes secrete extracellular proteases and peptidases that break proteins into peptides. The peptides are then transported into the cell, where intracellular proteases cut them into free amino acids. Once amino acids are available, microbes break them down in two main ways: deamination and...

lipid catabolism

How Microbes Break Down Fats for Energy

Microbes break down triglycerides and fatty acids to make energy. Triglycerides are important long-term energy storage molecules in microorganisms. Lipases hydrolyze, or split with water, triglycerides into glycerol and free fatty acids. Each product then enters a different metabolic route that helps the cell make ATP, the main energy currency. Glycerol metabolism begins after glycerol is released from triglyceride hydrolysis. Glycerol kinase adds a phosphate group to form glycerol-3-phosphate.

oxygenic photosynthesis

How Plants Make Oxygen and ATP

Oxygenic photosynthesis is the process plants, algae, and cyanobacteria use to capture light energy and turn it into chemical energy. It uses water as the source of electrons and releases molecular oxygen, or O2. The process also produces ATP and NADPH, which cells need for later energy use and carbon fixation. The main reactions happen in the thylakoid membranes, where chlorophyll pigments absorb light. In cyanobacteria, these membranes come from folds in the plasma membrane. Two photosystems...

anoxygenic photosynthesis

Bacterial Light Capture Without Oxygen

Anoxygenic photosynthesis is a bacterial way to capture light energy without making oxygen. It supports carbon fixation, but it does not use water as the electron donor. Instead, these phototrophs use other electron donors such as hydrogen sulfide, elemental sulfur, thiosulfate, or organic compounds. This process is carried out by several groups of bacteria, including purple bacteria, green sulfur bacteria, heliobacteria, and other anoxygenic phototrophs. These organisms have evolved a...

biosynthesis in bacteria

How Bacteria Build Key Macromolecules

Bacteria build essential macromolecules through tightly controlled biosynthetic pathways. These anabolic reactions make proteins, nucleic acids, lipids, and polysaccharides. The products support growth, cell division, and normal cell function. Bacterial biosynthesis starts with precursor metabolites from glycolysis, the pentose phosphate pathway, and the Krebs cycle. Important precursors include pyruvate, acetyl-CoA, and glucose-6-phosphate. Cells use these compounds to make the monomers that...

Microbial carbon fixation pathways let prokaryotes turn carbon dioxide into organic molecules. This process supports biosynthesis, helps sustain ecosystems, and plays a role in the global carbon cycle. It also has industrial uses in carbon capture and bioproduct synthesis. Autotrophic organisms depend on this process to use CO2 as a carbon source in many environments. The Calvin cycle is the most common carbon fixation pathway. Cyanobacteria and other autotrophic prokaryotes use it, and it...

biosynthesis of polysaccharides

Activated Sugars for Polysaccharide Synthesis

Activated sugars drive polysaccharide synthesis in cells. Glycogen and starch are built from nucleoside diphosphate sugars, mainly uridine diphosphate glucose (UDPG) and adenosine diphosphate glucose (ADPG). These sugar donors act as high-energy intermediates in carbohydrate metabolism and biosynthesis. UDPG supports glycogen synthesis in animals and many bacteria. It forms when glucose-1-phosphate reacts with uridine triphosphate (UTP). UDP-glucose pyrophosphorylase catalyzes this reaction.

inorganic nitrogen assimilation

Nitrogen Uptake by Microbes

Nitrogen uptake by microbes is essential for making proteins, nucleic acids, and other cell parts. Many bacteria and archaea take in nitrogen as nitrate or ammonia. They then convert it into forms that can be built into biomolecules. When nitrate enters a cell, it goes through assimilatory nitrate reduction. This is a two-step process. First, nitrate reductase changes nitrate to nitrite using NADH or FAD as an electron donor, depending on environmental and cellular conditions. Then nitrite...

sulfur assimilation

Sulfur Uptake and Cysteine Synthesis

Sulfur uptake and cysteine synthesis are key parts of microbial metabolism. Sulfur is needed to build important biomolecules, including the amino acids cysteine and methionine, as well as cofactors such as coenzyme A and biotin. Microorganisms usually take in sulfur from the environment as sulfate, but sulfate must be changed before cells can use it. Because sulfate is highly oxidized, it must go through assimilatory sulfate reduction to become biologically useful. Some microorganisms can also...

amino acid biosynthetic pathways

Amino Acid Building from Cell Metabolites

Amino acid biosynthesis lets cells build amino acids from common metabolic intermediates. These amino acids support cell growth, protein synthesis, and metabolic regulation. The main source molecules come from glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway. Key precursors include alpha-ketoglutarate, pyruvate, oxaloacetate, phosphoenolpyruvate, and erythrose-4-phosphate. They supply the carbon skeletons needed to form amino acids. Nitrogen must also be added...

biosynthesis of nucleic acids

Nucleotide Building Blocks for DNA and RNA

Nucleotide biosynthesis makes the building blocks needed for DNA and RNA. Cells use this pathway to make purine and pyrimidine nucleotides and keep their supply balanced. That balance helps protect genetic integrity and supports normal cell function. Purine nucleotide synthesis starts with ribose-5-phosphate, a sugar made in the pentose phosphate pathway. PRPP synthetase adds phosphate groups to form phosphoribosyl pyrophosphate, or PRPP, which is the activated starting point for the pathway.

biosynthesis of lipids

How Membrane Lipids Vary Across Life

Membrane lipids vary across Bacteria, Archaea, and Eukarya, and these differences help cells survive in different environments. The three domains of life make lipids through distinct biosynthetic pathways. Those pathways create membranes with different stability, permeability, and flexibility. Bacteria and eukaryotes both build fatty acid-based lipids from acetyl-CoA and malonyl-CoA. The pathway includes condensation, reduction, and dehydration steps. Bacteria use a type II fatty acid...

formation of lipopolysaccharides

Lipopolysaccharides and Gram-Negative Defense

Lipopolysaccharides (LPS) are important parts of the outer membrane of Gram-negative bacteria. They help stabilize the membrane and help protect bacteria from host immune responses. LPS has three main parts: lipid A, a core oligosaccharide, and an O antigen. LPS biosynthesis and assembly depend on a coordinated set of enzymes and transport steps. The molecule is also known as an endotoxin. It can activate Toll-like receptor 4 (TLR4) in the host and trigger strong immune responses. In severe...

key terms and concepts

Explore how prokaryotes fix carbon dioxide using the Calvin cycle, reductive TCA cycle, Wood-Ljungdahl pathway, and 3-hydroxypropionate cycle.

Microbial Carbon Fixation Pathways | JoVE K12

JoVE Core Microbiology provides an engaging introduction to the microbial world and its influence on health, industry, and the environment. This comprehensive collection covers key concepts such as microbial structure, metabolism, genetics, and ecology. It introduces essential laboratory techniques and microscopy methods through visually engaging animations. Corresponding scientist-in-action videos bridge classroom concepts with real-world research and applications.

microbiology

Pennsylvania State Academic Standards

Earth and Space Science

3.3.9-12.L

3.3.9-12.N

Louisiana Student Standards for Science

High School

Earth Science

Earth’s Systems

HS-ESS2-4

HS-ESS2-6

HS-ESS2-7

Igneous Volcanic Rock

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The Carbon Cycle

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Igneous Intrusive Rock

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using-topographic-maps-to-generate-topographic-profiles

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determining-spatial-orientation-rock-layers-with-brunton

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Making a Geologic Cross Section

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Use models to explain how mantle convection powers plate tectonics.

ESS.EES.2.1

Analyze and interpret data to predict locations of volcanoes and earthquakes based on plate boundaries.

ESS.EES.2.2

an-overview-of-alkenone-biomarker-analysis-for-paleothermometry

An Overview of Alkenone Biomarker Analysis for Paleothermometry

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Topographic Surveying and Contours

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Plotting of Topographic Maps

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Methods of Obtaining Topography

Topography involves measuring and mapping land elevations, natural features, and artificial structures to create accurate representations of the terrain. ...

Use models to explain how plate tectonics influence topography.

ESS.EES.2.3

The Soil Ecosystem

Plants obtain inorganic minerals and water from the soil, which acts as a natural medium for land plants. The composition and quality of soil depend not ...

Conditions on Early Earth

What are Biogeochemical Cycles?

The most common elements in organic molecules, carbon, hydrogen, oxygen, nitrogen, sulfur, and phosphorus, are only available in the ecosystem in limited ...

The Water Cycle

The Earth&rsquo;s hydrosphere includes all of the areas where the storage and movement of water occurs. Since water is the basis of all living processes, ...

The Nitrogen Cycle

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The Phosphorus Cycle

Unlike carbon, water, and nitrogen, phosphorus is not present in the atmosphere as a gas. Instead, most phosphorus in the ecosystem exists as compounds, ...

The Sulfur Cycle

Sulfur, an important element in the chemical makeup of proteins, is recycled through the atmosphere and aquatic and terrestrial environments. Found in the ...

Bioremediation

Bioremediation is the use of prokaryotes, fungi, or plants to remove pollutants from the environment. This process has been used to remove harmful toxins ...

Carry out investigations to explain how the rock cycle and rates of weathering, erosion, and soil formation influence Earth's systems.

ESS.EES.2.4

What is Climate?

Climate refers to the prevailing weather conditions in a specific area over an extended period. As the saying goes, &#8220;Climate is what you expect. ...

What is Weather?

Overview

Weather refers to the current state of atmospheric conditions at a specific time and place. Weather is temporary and is influenced by the ...

Variation of Atmospheric Pressure

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ESS.EES.2.5

States of Water

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The potential of hydrogen (pH) is a measure of the acidity or basicity of a water-based solution determined by the concentration of hydronium ions (H3O+). ...

Solvents

A solvent is a substance, most often a liquid, that can dissolve other substances. Here, the substance being dissolved is called a solute. When a solvent ...

Redox Reactions

Oxidation-reduction or redox reactions involve the transfer of electrons from one molecule or atom to another. When an atom gains an electron, another ...

Adhesion

Adhesion occurs when one type of molecule is attracted to a different molecule. Water exhibits adhesive properties in the presence of polar surfaces, such ...

Cohesion

Cohesion is the attraction between molecules of the same type, such as water molecules. Water molecules have an overall neutral charge but are polar ...

Specific Heat

The specific heat capacity of a substance refers to the energy required to increase the temperature of one gram of that substance by one degree Celcius. ...

Vaporization

The physical form of a substance changes by changing its temperature. For example, raising the temperature of a liquid causes the liquid to vaporize ...

Role of Water in Human Biology

Water is the one of the most significant components of the human body; it plays a crucial role in several physiological activities because of its unique ...

solubility-equilibria-ionic-product-of-water

Solubility Equilibria: Ionic Product of Water

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Carry out investigations to explain the properties of water.

ESS.EES.3.1

Energy

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Energy Basics

Chemical reactions, such as those that occur when you light a match, involve changes in energy as well as matter.

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Climate Change

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Enthalpy

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Mechanism of heat transfer

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Use models to explain how water is an agent of energy transfer.

ESS.EES.3.2

Analyze how the geosphere is shaped by plate tectonics and the rock cycle.

Microbial Carbon Fixation Pathways

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