Unraveling the Web of Soil Microbiology


By: Jim Downer

Question: what is the most important concept in soil microbiology? Answer: really complex! We have a better understanding of microbes (as well as pathogens) and the beneficial roles they play in soil. However we are only beginning to understand the complexities of soil microbiology and how intertwined soil life is. This is why we need to understand the role trees play in the lives of microbes and vise versa.

Web of Life

Trees effect microbial communities and at the same time are at the mercy of microbes, which help with nutrient gathering, and water uptake. Soil limits trees growth, which is why the average lifespan of an urban tree is under ten years. Litter-fall or “O” soil horizon (humus rich layer), also called the organic layer is the life blood to a tree. This is why we put mulch around urban trees to try and simulate forest environment. This layer provides a reservoir of organic nutrients which nourishes animals, fungi, bacteria and ultimately the tree that produced it.

Microbes and Their Role

Two broad categories: prokaryotes and eukaryotes

Prokaryotic organisms: are bacteria, simple genetic make up of one chromosome, without a nucleus, single celled and very small.

Eukaryotes: have nucleus (includes fungi, yeast, algae, nematodes, and animals) some are single celled, most are multi-cellular.

Microbes help trees and trees in turn leave behind cells that contain amino acids, proteins, and sugars in the rhizosphere (is an area of high microbial activity adjacent to roots 1 millimeter).

The Role of Roots

Roots secrete a lubricating substance (mucigel.) which allows roots to slip through soil, pushing aside soil particles and leaving behind carbohydrate-rich slime trail. Fine absorbing roots grow and die leaving behind carbon and nutrients allowing room for microorganisms resulting in more porous soils with greater oxygen content that favor microbial growth and health. Roots must balance the ions inside and outside there roots. Bacteria and fungi function in the rhizosphere as heterotrophs, or organisms that derive energy from dead organic matter. In doing so, they convert organically held minerals to ions trees will absorb. Trees maintain balance by importing and excreting ions it needs to maintain its productivity. If litter layer is denied to the tree, there is a greater tendency for mineral nutrient deficiencies to occur.

The Role of Mycorrhizae

Much research has demonstrated the importance of fungal symbionts for the growth of healthy trees mycorrhizal fungi are a diverse group of fungi that occur in all soils and climates around the globe. They colonize and form symbiotic relationships with plant roots and are broadly grouped into 2 categories: ectomycoorrhizea and endomychorrhizea.

Ectomycoorrhizea: form a shield of fungus around the roots of trees they colonize. Trees such as oak, alder, eucalyptus, pines, firs and other conifers in the Pinaceae do not from hairs but instead have intercellular threads (hyphae) called the Hartig net. Hyphae extend out in soil greatly increasing the trees root system

Endomychorrhizea: do not change shape of roots, endomychorrhizea invade the inside of the roots and create an intercellular relationship within the host root cortex. They form globular vesicles and arbuscles. Arbuscle is a tree like structure that forms inside a root cortical cell in order to exchange nutrients and water for carbohydrates from the tree. They also extend out into the soil increasing the absorptive surface area many fold. One of the key effects of the mycorrhizoshere is the area they produce for rhizobacteria, which fix nitrogen solubilize phosphates. They also serve as a biocontrol agents for root pathogenic fungi. The deeper understanding is not how great mycorrihizae are but rather what great gardeners or cultivators of bacteria mycorrihzae are and ultimately how beneficial these bacteria are to the trees in our urban forest. Without them the host tree would certainly languish.

Managing Soil Microbiology

Soil is made up of minerals, solids, air space, water, and all the organisms that live in them. So applications of single species or even small cocktails of microbes to soil, is analogous to adding salt to the ocean. However disturbed or urban soils where the litter layer has been removed or no longer exist can add value to the soil.

What can arborist do to help this process?

  • Prevent compartion- microbial communities need oxygen to thrive.
  • Maintain or add to litter layer that falls under trees and increase square footage areas of mulch under trees.
  • You need to remember that it is not possible to introduce a microbe and have it establish without creating the conditions to support it first. (Mulch)
  • Irrigate do not flood or frequent irrigations. If land is dry irrigate to increase soil moisture levels
  • If a healthy litter layer and or mulch exists under trees, reduce or eliminate fertilization. Grow for quality not quantity

Trees are a part of ecology of the soil. They have a direct effect on the soil and its microbial communities. They are also dependent on soil microbes for nutrients and water.