22.3 Prokaryotic Metabolism

Prokaryotic Macronutrients and Metabolism

Prokaryotes are essential for life on Earth because of their roles in nutrient cycling and energy acquisition. Their metabolic strategies are remarkably diverse, which is how they manage to thrive in environments ranging from deep-sea vents to soil to the human gut. From photosynthetic cyanobacteria to chemoheterotrophic decomposers, prokaryotes drive the biogeochemical cycles that keep ecosystems functioning.

Essential Macronutrients for Prokaryotes

Like all living things, prokaryotes need specific elements to build their cellular machinery. Here are the big ones:

• Carbon — The backbone of organic molecules (proteins, nucleic acids, lipids). Prokaryotes get carbon either from organic compounds or by fixing inorganic $CO_2$ from the atmosphere.
• Nitrogen — Required for amino acids and nucleic acids. Some prokaryotes absorb nitrogen from organic sources, while others can fix atmospheric $N_2$ directly, a trick that eukaryotes cannot do on their own.
• Phosphorus — Used to build nucleic acids (DNA, RNA) and phospholipids, and critical for energy-transfer molecules like $ATP$ and $GTP$.
• Sulfur — A component of certain amino acids (cysteine, methionine) and enzyme cofactors. Prokaryotes obtain sulfur from organic compounds or inorganic sulfate.
• Other elements — Potassium, magnesium, calcium, and iron are needed in smaller quantities. These support enzyme function, maintain cell structure, and participate in various metabolic reactions.

Energy Acquisition in Prokaryotes

Prokaryotes are classified by how they get energy and where they get carbon. These two criteria combine to produce the major metabolic categories you need to know.

• Phototrophy — Energy comes from light. Photosynthetic prokaryotes like cyanobacteria capture light energy and use it to fix carbon.
• Chemotrophy — Energy comes from chemical compounds rather than light. This splits into two subcategories:
  • Chemoautotrophs — Fix inorganic $CO_2$ using energy released from inorganic chemical reactions (e.g., oxidizing hydrogen sulfide or ammonia).
  • Chemoheterotrophs — Get both energy and carbon from organic compounds. Most bacteria you encounter in everyday life fall into this group.
• Lithoautotrophy — A specific type of chemotrophy where energy is derived from inorganic molecules. Examples include sulfur-oxidizing bacteria, hydrogen-oxidizing bacteria, and ammonia-oxidizing archaea.
• Organoheterotrophy — Energy and carbon both come from organic molecules. This category includes organisms that use fermentation, aerobic respiration, or anaerobic respiration.

Prokaryotic Energy Metabolism

Once prokaryotes acquire nutrients, they need to extract usable energy. The main metabolic pathways are:

1. Glycolysis — The initial breakdown of glucose into pyruvate. This pathway is common to nearly all prokaryotes and does not require oxygen. It yields a small amount of $ATP$ directly.

2. Aerobic respiration — Uses $O_2$ as the final electron acceptor. After glycolysis, pyruvate enters further oxidation steps. The electron transport chain embedded in the plasma membrane generates a proton gradient, and oxidative phosphorylation uses that gradient to produce large amounts of $ATP$. This is the most energy-efficient pathway.

3. Anaerobic respiration — Follows the same general logic as aerobic respiration, but uses alternative electron acceptors instead of $O_2$. Common alternatives include nitrate ($NO_3^-$) and sulfate ($SO_4^{2-}$). This yields less $ATP$ than aerobic respiration but allows prokaryotes to survive in oxygen-free environments.

4. Fermentation — Produces $ATP$ without any external electron acceptor. Organic molecules serve as both electron donors and acceptors. The $ATP$ yield is low (only what glycolysis produces), but fermentation lets organisms generate energy when neither oxygen nor alternative electron acceptors are available.

Prokaryotes in Global Nutrient Cycles

Prokaryotic metabolism doesn't just matter for the organisms themselves. It drives the planet-wide cycling of elements that all life depends on.

Carbon Cycle

1. Carbon fixation — Photosynthetic prokaryotes (especially cyanobacteria) fix atmospheric $CO_2$ into organic molecules, contributing significantly to global primary production.
2. Decomposition — Chemoheterotrophic prokaryotes break down dead organic matter, releasing $CO_2$ back into the atmosphere.
3. Methanogenesis — Methanogenic archaea produce methane ($CH_4$) during anaerobic metabolism. Methane is a potent greenhouse gas, roughly 80 times more effective at trapping heat than $CO_2$ over a 20-year period.

Nitrogen Cycle

The nitrogen cycle has several distinct steps, each carried out by different prokaryotes:

1. Nitrogen fixation — Certain prokaryotes (e.g., Rhizobium in root nodules of legumes) convert atmospheric $N_2$ into ammonia ($NH_3$). This is the only biological way to make atmospheric nitrogen available to living organisms.
2. Nitrification — A two-step process. First, ammonia-oxidizing bacteria and archaea convert $NH_3$ to nitrite ($NO_2^-$). Then, nitrite-oxidizing bacteria convert $NO_2^-$ to nitrate ($NO_3^-$), which plants can absorb.
3. Denitrification — Under anaerobic conditions, some prokaryotes reduce $NO_3^-$ all the way back to atmospheric $N_2$, completing the cycle.
4. Ammonification — When prokaryotes decompose organic matter (dead organisms, waste), they release $NH_3$. That ammonia can then be taken up by plants directly or enter nitrification.

Without prokaryotes performing these transformations, essential elements like carbon and nitrogen would remain locked in forms that most organisms can't use. Prokaryotic metabolism is what keeps these nutrients cycling and ecosystems in balance.