Ted Floyd Creekcare

Urban Soils

drawingHealthy Microbes Create Healthy Soils

by Ted Floyd
Sept. 2012

Keywords: Soil microbes, Soil organic matter, Soil carbon, Global warming, Climate change, Food security

Healthy soils with high organic matter will help to maintain food security and reduce global warming.

Why healthy microbes?

Soil microbes are an essential component of the natural carbon cycle. Living carbon compounds are manufactured by photosynthesis in plants when carbon dioxide from the atmosphere is synthesised into organic plant martial. When the plant dies the carbon compounds are incorporated into the soil.

During photosynthesis sunlight energy is transformed into chemical energy and stored in the chemical bonds of organic compounds in plants. Carbon and energy are linked in all living organisms and ecosystems.

The soil is natures recycling center where microbes eat dead plants and during respiration carbon dioxide is released back into the atmosphere. To maintain a balance in the earths carbon ecosystem the growth, death and decay of plants occurs in a cycle and microbes are essential for the decay of dead plants. If soil microbes did not exist, the world would be covered by a deep layer of dead plants.

Abundant plant growth occurs in healthy soils and microorganisms build up healthy soils. There is a two way process where plants encourage microbes to grow and microbes encourage plants to grow. There is a mutual benefit relationship.

white lichen growning on 10cm diameter branch

Lichen growing on a melaleuca (Tea Tree/Bottlebrush) branch which blew down in a storm in August 2012 - Photograph Marghnanita da Cruz 3 September 2012

Soil Microorganisms

A gram of healthy soil contains up to 3,000 million bacteria and 500,000 fungi plus actinomycetes, algae and protozoa. Bacteria have a diameter of approximately 0.001 mm and fungi filaments about 0.005 mm. In comparison clay particles are less than 0.002 mm.

Bacteria prefer to grow in the thin layer of moisture surrounding clay particles and fungi grow better in large soil pores and can survive in dry conditions. Bacteria prefer to eat smaller soluble compounds, especially sugars and starch.


Fungi are able to feed on hard to decompose plant fibers and woody material including cellulose, lignin and plant fibers. The fruiting body of fungi is often seen growing on fallen dead tree branches. Toadstools and mushrooms are the fruiting body of a large network of fungi hyphae in the soil.

Favorable environment for microbes.


Organic matter formed from dead plants containing Carbon, Oxygen and Hydrogen is the basic food and energy source for soil microorganisms.


The essential minerals required for the growth of soil microorganisms is similar to the needs of plants. Many minerals are needed in small amounts and are mainly found in proteins and nucleic acids of microbes.

Nitrogen Phosphorus Potassium Sulphur Sodium Calcium Magnesium Manganese Iron Zinc Copper and Cobalt are essential minerals required by microorganisms.


Thiamine B1, Riboflavin, Niacin, Pyridoxine B6 are essential vitamins.

Different microbe species can synthesise some vitamins.

Nutrients for decomposition

drawing nitrogen cycle

An adequate supply of nitrogen is needed for the rapid decomposition of organic matter. Optimum carbon/nitrogen ratio is 25-30/1. Straw and similar mulches have a high C/N ratio of 100/1 and when the soil is covered with a dense straw mulch, plant growth is retarded because of a nitrogen deficiency. Microbes growing on the straw consume most of the available nitrogen and small plants suffer from nitrogen deficiency. Leaf litter under pine or casurina formed from high lignin needles will retard growth of grasses and other small plants.

Optimum Phosphorus content for decomposition is 100/1. Many Australian soils have a low Phosphorus content and gum leaves are low in phosphorus.


Optimum at field capacity. Most bacteria grow in moist conditions, some bacteria survive in dry conditions by forming spores. Fungi are more tolerant of dry conditions. In anaerobic, waterlogged soils, microbe activity is low and peat is formed.

When a soil is very dry microbial activity slows down and many individual microbes die. Some species survive harsh conditions by forming spores. When suitable moist conditions return spores germinate into rapidly growing microbes.


Most microbes are aerobic and need gaseous oxygen to grow. Oxygen needs to flow from the atmosphere down into the soil and carbon dioxide needs to rise into the atmosphere. Some microbes are anaerobic and survive in poorly aerated soils.

For good aeration soils need to be drained and have a stable structure with large interconnecting pores. Waterlogged soils are anaerobic.


The growth rate of microorganisms increases with a rise in temperature.

A ten degrees rise in temperature doubles the decomposition rate of soil organic matter. Preferred temperature range 25-35 degrees. Tropical, soils have higher temperature, increased microbial activity and low soil organic matter. Alpine soils have low microbial activity and contain high organic matter.


Most soil microbes preffer a neutral pH. Optimum for molds 5.6 and bacteria 6.5-7.5.

Sometimes fertilizers decrease soil pH and reduce microbe activity.

Stable soil structure

Soil structure controls access of microbes to organic matter. Porous structure improves the movement of air and water necessary for microbial growth.


Organic matter can be stabilized by clay particles, Calcium, Iron and aluminum can form bridges between organic matter and clay.

Plant root exudates

Root exudates provide many nutrients stimulating microbial growth in rhyzosphere surrounding the root tip. The microbes break down organic matter converting nutrients into soluble forms able to be absorbed by plant roots.

white specks and splotches, soil and wood

White fungi breaking down wood, Garden Annandale, Photograph Marghanita da Cruz 3 September 2012

Tillage and stubble mulching.

Tillage can disrupt soil aggregates and this can increase access of microbes to organic matter and increase rate of decay. Tillage removes plants and the supply of leaf litter and the addition of food for microbes is interrupted. Tillage breaks up fungi hyphae. Aeration is increased by tillage and this stimulates microbial decay.

An old farm management practice was to plough the soil and to regularly cultivate to kill weeds. A bare fallow of up to a year was maintained so as to increase soil moisture for the benefit of a wheat crop. After the wheat was harvested the stuble was burnt to enable ease of ploughing and to kill wheat diseases. After many years these management practices destroyed soil organic matter and serious erosion occurred.

Decreased tillage and stubble mulching is practiced by many modern farms.

Decay of soil organic matter

Hot dry desert soils have low organic matter. High rainfall and high plant growth increase soil organic matter. Cold climates reduce organic decay and increase soil organic matter.

Striped Fungi Brackets

Fungi brackets breaking down dead melaleuca branch. 14 October 2008

Fungi growing in Mulch

Bright Yellow Fungi. 24 February 2005

Fungi growing in Mulch

Opened overnight and turned pale yellow. 25 Februrary 2005.

Tiny white toadstool shaped fungi growing in leaf litter, next to secateurs

White Fungi, Annandale. 18 April 2009

These and more Fungi at Annandale on the Web (Photographs Marghanita da Cruz)

Plant litter

10% of plants are eaten by animals.

90% of dead plant material is decomposed by soil microbes.

Soils are dominated by fungi under trees and shrubs. Fungi can decompose cellulose and lignin and grow better in well aerated soils and in surface soils. Fungi account for 60 - 90% of microbial mass in forest soils.

Bacteria dominate in grasses and pasture soils.

Bacteria can tolerate poor aeration and can grow deeper in soils.

Permanent grasses with no tillage, develop deep roots and allocate more photosynthetic material below ground.

Organic matter is transformed into material of greater recalicitrance as decomposition continues along the decay chain. Easily decomposed materials including sugars are decomposed first leaving hard to decompose compounds like lignin.

Nitrogen and phosphorus content of soil organic matter increases as material progresses along decay chain.

Soil animals eat plant litter and break it up into smaller pieces more readily decomposed by microbes. The fecal pellets from animals may also be decomposed by microbes or small animals. Mites and coleambola graze on bacteria or suck on fungi hyphae. Springtails and millipedes browse on fungi. Centipedes and some mites are carnivores.

Humus is formed when organic matter is broken down and difficult to decompose molecules are polymerized into large humic molecules.

Soil Action

Deep down in the dark, soils are buzzing with action. Invisible microbes are eating dead plant litter and animal remains. Microbes eat microbes.

The growth of all living matter is linked. Every plant, animal and microbe is dependent on many other organisms for food, energy and nutrients.

Plants gain energy by photosynthesis from the sun. When plants die, leaf, stem and root litter becomes organic matter in soils. Different microorganisms and animals eat different parts of the plant litter and there is a chain of different microbes eating smaller and smaller bits of litter. Sugars are eaten first and lignin is very difficult to break down and is eaten very slowly. Humus is formed from hard to decompose compounds.

In the natural carbon cycle no extra carbon is added to the ecosystem. In the modern world carbon dioxide is added to the worlds ecosystem when fossil fuels are burnt.

Microbes and plants living together

Plants and microbes help each other, dead plants provide food for soil microbes and microbes provide minerals for plants.

Plants and microbes sometimes form very special relations when plants and microbes help each other. This is symbiosis.

In the rhyzosphere surrounding the growing tips of plant roots, microbes are stimulated by root exudates. Food is exchanged from plant roots to microbes and microbes decay nutrients into forms available to plant roots.

Mycorrhiza fungi grow hyphae into root hairs. The fungi obtain sugar and other nutrients from the plant. The fungi absorb mineral nutrients, especially phosphorus from distant parts of the soil and transports the mineral directly into the plant root.

Rhizobium bacteria grow in nodules inside the roots of legume plants. These bacteria are able to use gaseous nitrogen in the soil atmosphere for growth and to provide nitrogen for the growth of host plants.


Healthy soils with high organic matter will help to maintain food security and reduce global warming.

Increasing soil organic matter is a powerful weapon to help reduce atmospheric carbon dioxide. The Australian Government has introduced the Carbon Farming Initiative. (link Carbon Farming Initiative) Landholders are now able to gain carbon credits and sell these credits on the carbon markets.

There are many different techniques farmers and backyard gardeners can use to improve soil health. Generally healthy soils have adequate organic matter and abundant microorganisms. Plants and microorganisms interact with each other to produce healthy soils.

Carbon Farmers of Australia are a leading farmers organization promoting the use of soil to store carbon and helping to reduce global warming.


The Carbon Farming Handbook, 2012

An Introduction to Soil Carbon, Land Management and Climate Change.

Carbon Farmers of Australia

This book describes many carbon farming techniques, including, grazing management, conservation tillage, biological and organic farming, biodynamic farming and biochar. The carbon cycle is described with information on microbes, plant roots, earthworms and humus.

The Carbon Farming Initiative (www.cleanenergyfuture.gov.au/carbon-farming-initiative/) is not restricted to farms. Their is potential for this scheme to be used by many different landowners. For example Local Councils in urban areas should be able to become involved in this scheme.