The Soil Is Alive: Fertility & the Biology of Decomposition


If a crumb-like soil structure sets the stage for fertility to occur and chemical reactions are the catalysts, biological organisms are the active agents that create the conditions for plants to thrive in.  Every gram of healthy garden soil contains hundreds of millions of microbes that play a critical role in the breakdown of nutrients and their assimilation by plants.  Fungi, earthworms, sow bugs and a host of other organisms consume decaying plant matter and transform it into fertilizer for plants.


An Ode to Organic Matter

Fertile soils are fostered and maintained by the organisms of the soil food web.  Some of the major players in this system and what gardeners need to know about them are discussed below.  However, the first thing to understand about the soil food web is the role of organic matter as the basic foodstuff of soil organisms and thus the foundation of soil fertility.

In essence, organic matter is the once-living remains of plants and animals.  It is composed primarily of carbon-based compounds, as well as varying degrees of nitrogen.  Most of the nitrogen content dissipates into the atmosphere as the material dries out.  However, some nitrogen also accumulates in the soil during the process of decomposition.  If the source of organic matter is dry and woody, the nitrogen content will be very low and the microbes that breakdown the organic matter will consume any nitrogen that is already in the soil to sustain themselves.  Forms of organic matter like manure, fresh grass clippings, and food scraps that are moist and non-woody have a high nitrogen content and thus add nitrogen to the soil (or compost pile) during decomposition.


Who Creates Humus?

The end product of the decomposition of organic matter is humus, a complex substance that is the basis for long term fertility.  Humus provides little in the way of nutrients directly to plants, but maintains the perfect environment for plants to have the nutrients they need at the right time and in the ideal chemical form.  The presence of humus gives rich topsoil its dark color and crumb-like texture.

Applying organic matter to the soil builds humus content, aided by a medley of micro-organisms.  Four of the major players are:

  • Fungi – responsible for much of the initial breakdown and conditioning of coarse organic matter (i.e. wood chips) so that smaller organisms can start “chewing” on it.  The mats of string-like mycelium (usually white) seen where woody matter contacts the soil is evidence of fungus at work.
  • Insects – from sow bugs to millipedes, compost piles should be full of insects chewing away at dead plant parts, aiding in the mechanical process of decomposition
  • Earthworms – these are the heroes of gardeners everywhere for the work they do in grinding up organic matter, excreting it as enriched “castings.”  Large brown earthworms live in the soil horizon, physically aerating the soil with their worm holes, while little wriggly, red worms can be found on the surface of the soil under the duff.  It is the latter group that is used in worm composting (vermiculture)
  • Bacteria – a myriad of microscopic creatures that are responsible for the chemical decomposition of the tiny bits of organic matter left by the larger decomposers.  There are numerous highly specialized species that each performs a specific function in the reconfiguration of organic molecules that results in humus formation


*For further details on the organisms responsible for decomposition and their roles in a compost pile, see


The Niceties of Nitrogen-Fixation

Many farmers and gardeners are accustomed to applying nitrogen fertilizers for the lush green growth that results.  In the previous posts, we’ve discussed the role if nitrogen in plant growth, its storage in the tissues of plants and animals, and the release of nitrogen into the soil and air during the process of decomposition.  Plants scramble to complete for available nitrogen in the soil, as it is a highly volatile substance that readily loses its soluble form and escapes into the atmosphere.  However, as you may surmise, nature has devised a process to reclaim atmospheric nitrogen and put it back in the soil where plants can use it.

There are bacteria whose job it is to take nitrogen from the air and “fix” it in a soluble form.  They don’t fly around in the sky to do it, but are able to extract nitrogen from the air that’s already mixed in with soil and water (which contains a whopping 79% nitrogen, making plants jealous).  Of most interest to farmers and gardeners are the Rhizobium bacteria that live on the roots of most leguminous plants.  Agriculturalists have essentially domesticated these microbes over the millennia, harnessing their power to increase the nitrogen content in their soils.

If you pull up the roots of a legume – peas, peanuts, clover, beans, etc. – you are likely to see little white or pink nodules on some of the roots.  They look like a tumorous growth, but are actually the factories where nitrogen-fixation takes place.  Rhizobium bacteria have a symbiotic relationship with their host plants – they receive energy and nutrients from the plant and supply nitrogen in return.  The more pinkish in color the nodules are, the greater the quantity of nitrogen transfer. These plants exhibit luxuriant growth and when they die, the remaining nitrogen stored in the nodules is delivered to the soil for other plants to use.

A thorough overview of the nitrogen fixation and its relevance too agriculture can be found here

In the coming weeks, we will share ideas and techniques to improve soil quality so your garden grows more bountiful with less effort – including the use of nitrogen-fixing crops and Rhizobium inoculant to introduce the bacteria to the soil.


Written by Brian Barth