Soil Microbes

The natural world is built upon a system of reliance. Nearly every living creature and organism on earth relies on others within its ecosystem to perform certain evolutionarily driven tasks that help fuel the natural progression of life.

A coyote hunts down and kills a rabbit. After the coyote consumes its fill of flesh and protein, it leaves the carcass behind and moves on. Though the coyote has discarded what remains of the dead rabbit, it is not the end of the story. It is actually just the beginning: a forward to the complex story of natural decomposition. As the rabbit carcass sits, it will begin to attract smaller animals and insects that will continue to break down what remains including bones, tendons, vascular tissues and proteins. This decomposition continues all the way down to the smallest, microscopic organisms in the soil that consume the last of the deceased rabbit’s organic matter. Just as many animals, insects, and soil microbes have relied on the consumption of the rabbit to obtain vital nutrients for survival, plants rely on those tiny soil microbes to further break down organic matter. This breakdown eventually improves soil fertility by converting the organic matter into an elemental ion form, which is readily taken in by the roots of a needy plant. The following is a brief overview of two soil microbes that can directly affect the growth of a plant, soil bacteria and fungi.

Bacteria are the most populous microorganism found in healthy soils. These tiny, single-celled creatures are microscopic in size and generally anywhere from 300,000 to 500,000 of them can fit into a period at the end of a sentence. Bacteria are the oldest, most primitive forms of life and come in three styles or shapes: spiral, coccus (oval) and bacillus (rod-shaped). All types are active in the soil. In nature, bacteria serve as one of the main decomposers of organic matter, second only to fungi. This makes them a vital member of the soil food web. By decomposing plant and animal materials, the bacteria in turn ingests organic carbon compounds, such as nitrogen and any other elemental nutrients present. The nutrients are then held or immobilized within the bacteria to be released when the bacteria itself dies. The process in which the nutrients are converted and released in plant accessible forms is called mineralization.

A favorite food source for soil bacteria is fresh, young plant material, or green matter, which the bacteria can easily break down because of its high sugar content. Older plant material (brown matter) contains more complex organic carbon compounds that require initial decomposition by other organisms before bacteria can benefit. The green matter they consume contains the carbohydrate cellulose, which is comprised of chains of carbon-based glucose. Half of a plant’s mass is made up of cellulose, so bacteria have a plentiful food source when they colonize the soil near it. Another popular food source that bacteria are attracted to is root exudates. Because of this, large numbers of bacteria will populate a plant’s rhizosphere, where they will break down organic matter and help feed the plant.

A main element that bacteria help make available from organic matter is nitrogen (N). Through decomposition, specialized bacteria (Bacillus included) have the ability to change the amino acids found in the organic material into ammonia in a process termed ammonification. Plants have the ability to take in nitrogen from ammonia in the form of ammonium nitrogen. Furthermore, other specialized bacteria (Nitrosomonas included) can convert the ammonia to nitrite, which in turn is oxidized by nitrite-oxidizing bacteria (Nitrobacter included). This oxidation finally converts the nitrite into the nitrate form of nitrogen, a form that is readily taken in by a plants root. This transformation is collectively referred to as part of the nitrogen cycle, in which bacteria play a crucial role. Bacteria will be found in larger numbers, in comparison to fungi, in gardens or fields that are tilled on a regular seasonal basis. This is because fungi are much more delicate and need more time in an undisturbed soil to grow and populate.

Fungi are usually not as numerous as bacteria in the soil, mainly because of their size. However, their numbers can still be rather high given the right conditions. Like bacteria, they too play an important role in the decomposition of organic matter and the recycling of nutrients in the soil food web. Though larger in size than bacteria, fungi are still microscopic cells. They grow in long hair-like structures called hyphae, which join together and form mycelium that can colonize the roots of a plant.

The visible part of fungi is the mushroom, which is the fruiting/flowering body that contains the spores for reproduction. A big difference between bacteria and fungi is the fact that fungi not only decompose cellulose (bacteria’s main food source), but they can also decompose more complex plant tissues such as lignin and pectin. Some fungi possess particular enzymes that can digest or breakdown the organic matter, immobilizing the nutrients within the soil. This initial decomposition of complex organic matter makes it possible for smaller organisms like bacteria to feed from it as well.

When fungal hyphae grow in length, they have the ability to sort of traverse the surrounding soil in search of more organic matter to consume. The same cannot be said about bacteria, which are more or less immobile in the soil. In nature, fungi are heavy consumers of organic matter such as dead leaves, plants and animal material. Without fungi and its ability to effectively decompose and recycle these materials, they would just continue to accumulate on the forest floor.
Some fungi even have the ability to form symbiotic relationships with the roots of vascular plants in an association that is termed mycorrhiza. The mycorrhizal relationship is one that is mutually beneficial to both the plant and the fungi. After colonizing the roots, the fungi receive a steady and direct supply of carbohydrates, such as glucose and sucrose, which are translocated from the leaves of the plants to the roots. In turn, the plant receives elemental nutrient ions that its own roots, for a variety of reasons, may not be able to uptake. The fungal hyphae have the ability to access these hard to reach nutrients, such as the phosphate ion, and deliver them directly to the roots.

Plant roots that are colonized by mycorriza fungi greatly benefit from the funguses ability to enhance and expand the surface area and reach of the original root structure. As was eluded earlier, fungi are slower growing and more delicate than their bacterial counter parts and they thrive in a soil that is relatively undisturbed, such as no-till and permiculture gardens. As they live and work on decomposing organic matter, fungi also release nitrogen in the ammonium form, which given the presence of specialized bacteria, can be converted to nitrate in two steps.

Outdoor soil growers that practice the organic method of gardening have been benefiting from, or relying on, the presence of soil microbes in their garden (many without even knowing). An important aspect to remember when discussing these tiny, living creatures in our gardens is the fact that every living creature requires a food/energy source to survive and reproduce. Soil microbes feed and obtain energy from the organic matter in the soil. Organic gardening methods are based upon this very principle. Most organic fertilizers and amendments are in a form where they must be further decomposed before they will be of any benefit to the plant. The microbes feed on this organic matter, breaking the complex carbon bonds and, for lack of a better word, release the elemental nutrients help within the bond. However, if the soil does not contain enough organic matter for microbes to feed sufficiently, their numbers will undoubtedly be lower and they will likely congregate within a plants rhizosphere. They will then consume any root exudates and dead root cells that they can.

Outdoor soil gardeners are not the only growers that can benefit from microbes in the soil. Both outdoor and indoor container growers can as well. The growers that utilize an organic soil-less potting mix and some form of organic fertilizer, be it liquid or granular, stand to benefit greatly from the inoculation of beneficial microbes to the rooting media. A majority of organic fertilizers contain small amounts of elemental nutrients that are readily available to plant roots, but most of the nutrients will still be trapped within a carbon bond. The addition of soil microbes to the rooting medium will help the grower obtain a higher level of soil fertility and plant development.

Soil microbes have also been shown to help water retention and disease suppression within the root zone. I personally do not recommend the addition of beneficial microbes or any potentially living biological to traditional hydroponic growing systems; especially, those that incorporate an inert substrate like perlite or rockwool as a growing medium. These systems usually utilize inorganic fertilizer sources that are designed for immediate uptake by the roots. Without a proper source of organic matter for them to feed from, most will likely never inoculate or die from starvation. Those that do survive will likely gather within the rhizosphere where they could potentially cause more harm than good, especially if the conditions in the root zone become anerobic or lacking in oxygen.

As natural evolution has progressed in our world, it has embraced both competition and reliance as a way to cycle energy and nutrition throughout the land, sea, and sky. The microorganisms in the soil and the plants we grow are constantly involved in an often mutually beneficial game of give and take. And it is this reliance they have developed with on another that keeps life complex and perpetual.

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