Decomposition & Microbes

Let’s take a closer look at the overall process of decomposition of dead plant and animal tissue. The tiniest single-celled microbes, like any living thing, need to eat. What they prefer to consume is organic matter—anything that was once alive or, in the case of some pathogenic microbes, still alive. As microbes decompose organic matter, they break down old cells and convert rigid cell walls and cell contents, often in unusable forms, into liquid nutrients. These nutrients seep into the soil, where plant roots absorb them to build new tissue. As plants grow and die, season after season, the soil is enriched by this recycling method. When animals consume plants, the same process of decomposition occurs internally in their gut, and the nutrients are recycled into bone, muscle, blood, and other tissues. If a carnivore eats an herbivore, the nutrients are recycled once more into the carnivore’s tissues. When the carnivore dies, microbes again recycle its body back into its constituent nutrients, perpetuating the cycle of life.

Nature, in her intricate way, has assigned various microbes different roles in this decomposition and recycling process. Plant nutrients are classified as macronutrients—elements that plants need in large quantities to grow—and micronutrients, which are just as crucial for healthy growth but required in smaller amounts. The macronutrients are nitrogen, phosphorus, and potassium. Here are some of the key types of microbes and their roles in nutrient recycling.

The Nitrogen Recyclers

Certain microbes are responsible for recycling nitrogen in what soil scientists call the nitrogen cycle, transforming yesterday’s plants and animals into food for tomorrow’s plants and animals. All life depends on their work of dismantling old organic matter. Microbiologists know about tens of thousands of these bacteria and other microbes, but there may be many thousands, perhaps millions, still undiscovered and unnamed. Most of them fall into five functional classifications:

1. Ammonifying Bacteria: Living tissue contains proteins made up of nitrogen-containing molecules. When tissue dies, certain microbes use the carbon and water in it as their food, while its nitrogen is a waste product of their metabolism that is converted to ammonium salts and then into ammonia. Nitrifying bacteria take the nitrogen from the ammonia and link it with oxygen atoms to form soluble nitrates, which plants absorb through their roots to make new living tissue.
2. Nitrogen-Fixing Bacteria: These bacteria colonize the roots of certain plants, taking nitrogen molecules from the air (N₂) and splitting them apart by rearranging their electrons. The bacteria then reassemble the nitrogen with oxygen atoms to form soluble nitrates, which plants absorb to create new tissue. The result is the same as with nitrifying bacteria, but the process is different.
3. Denitrifying Bacteria: These usually anaerobic microbes convert the nitrogen in dead plant tissue to nitrogen gas molecules (N₂) that are released into the air. The air we breathe is four-fifths nitrogen, some of which is recycled back into plant nutrients by nitrogen-fixing bacteria. Anaerobic decomposition leads to putrefaction, causing the unpleasant smell of decaying plants.
4. Actinobacteria: These aerobic microbes are essential for decomposing dead plants’ nitrogen-rich amino acids into ammonium salts, which are further converted to ammonia. Their activity transforms dead plant tissue into sweet-smelling humus, a crucial component of healthy soil.
5. Fungi: Fungi play an important role in decomposing organic matter into nitrates that plants can use as food. Different fungal species colonize organic matter during its decomposition, starting with those that break down sugars and starches and followed by those that can decompose tough materials like cellulose and lignin, releasing nitrogen from proteins.

The Phosphorus Scavengers

A special type of fungus called mycorrhizal fungi forms a symbiotic relationship with its host plants. Living in the soil, these fungi colonize plant roots. The plant hosts exude sweet syrup through their roots that the fungi use for food. In return, the fungi send long, threadlike strings called hyphae far into the surrounding soil to gather phosphorus and transport it back to the plant roots, where it’s absorbed. Phosphorus is a macronutrient essential for plant health but is often in short supply in many soils. The valuable service mycorrhizal fungi provide helps maintain a natural ecosystem. If plants are harvested and removed, the phosphorus will eventually be depleted and must be replenished as fertilizer. If plants grow wild, the phosphorus is recycled back into the soil through decomposition.