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Soil health, crop nutrition and microbes

Growers and farmers would often read or hear about soil health or healthy soil. What does healthy soil mean?

In simple terms it is when soils are supporting plant health, plants are supporting animal health, are stable or improving environmental aspects, and are actively sustaining a balanced population of beneficial microbes. Healthy soil is productive, sustainable and profitable. i

Most of the common farming techniques employed in industrial crop production; such as continued or overuse of synthetic fertilisers and pesticides, monocropping and intensive tillage, will degrade soil over time, resulting in new problems which are solved through the use of more synthetic inputs, resulting in a continual cascade of issues and use of chemicals. As an example, research has found that the application of synthetic nitrogen fertiliser decreases a soil’s microbiological diversity or alters its natural microbiological composition in favour of more pathological strains. ii iii Excessive fertiliser use can also result in the build-up of salts in soil, heavy metal contamination and accumulation of nitrate, a source of water pollution and also harmful to humans. iv

Even though soil microbial communities are negatively impacted by application of synthetic chemicals, growers continue to use synthetic water soluble fertilisers because they supply water soluble nutrients that can be immediately accessed by plants.

Until fairly recently, we did not understand the role that soil microbes play in plant health and productivity and many of the competing reactions in the soil that lock up water soluble nutrients.

Why does soil biology matter?

We have known about the role that rhizobia and other bacteria play in nitrogen fixation and plant growth for decades. What is less understood is the influence that other microbes have on soil and plant health, growth and sustainability. These microbes are now recognised as improving retention and access to moisture, enhancing stress tolerance, providing disease resistance, aid in balanced nutrient availability and uptake, and promote biodiversity in the soil.

Soil microbes and their microbial activity have a tremendous influence on plant health and productivity. One benefit for the plant is access to a balanced nutritional food supply. The most intense interactions between microbes and plants take place at the rhizosphere, which is the interface between plant roots and the soil.

Beneficial properties of healthy soils


Nutrient cycling
Nitrogen fixation and mineralisation
Antagonism of pathogens and pests
Breakdown of organic matter to humus
Degrades pollutants
Nutrient retention


Improved water infiltration
Improved holding capacity
Improved root proliferation
Resistance to erosion
Aerobic environment


Improved nutrient storage
A balanced supply of nutrients
Bind and buffer heavy metals
Immobilises pollutants
Reduced impact of soil antagonists
Buffering of pH

A snap shot of soil microbes

There are basically four functional soil bacteria groups including decomposers, mutualists, pathogens and lithotrophs.

Decomposer bacteria consume simple sugars and simple carbon compounds, while mutualistic bacteria form partnerships with plants including the nitrogen-fixing bacteria (Rhizobia). Bacteria can also become pathogens to plants and lithotrophic bacteria convert nitrogen, sulfur, or other nutrients for energy and are important in nitrogen cycling and pollution degradation.

Actinomycetes, well-known as decomposers, have large filaments or hyphae and act similar to fungus in processing soil organic residues which are hard to decompose (chitin, lignin, etc.). They also produce more than 50 different antibiotics to protect plants from pathogenic bacteria. Actinomycetes are important in forming stable humus, which enhances soil structure, improves nutrient storage, and increases water retention. v

Soils contain an abundance of symbiotic microbes. Included in these are four bacteria types that convert atmospheric nitrogen (N2) into nitrogen for plants. Of these, three types can fix nitrogen without a plant host, and live freely in the soil, these include Azotobacter, Azospirillum and Clostridium. vi In addition Bacteria of the Azospirillum genus promote increased root mass and more efficient nitrogen uptake from the soil.

Flourishing microbial populations increase soil productivity and crop yields. Bacteria perform many important roles in the soil ecosystem including improved soil structure, soil aggregation and recycling of soil nutrients. Soil bacteria form microaggregates in the soil by binding soil particles together with their secretions. These microaggregates are like the building blocks for improving soil structure. Improved soil structure increases water infiltration and increases the water holding capacity of the soil. vii

Arbuscular mycorrhizal fungi form an intricate relationship with the roots of most flowering plants, increase nutrient accessibility and are associated with the provision of phosphorus to the plant.

Bacteria and fungi are typically consumed by protozoa and nematodes and the microbial waste excreted is ammonium (NH4+) which is plant available nitrogen. viii

Hover over the yellow circles below for more information

Not all microbes are beneficial

Anaerobic bacteria are generally found in compacted soil, deep inside soil particles (microsites), and hydric soils where oxygen is limiting. Many pathogenic bacteria prefer anaerobic soil conditions and are known to outcompete or kill off aerobic bacteria in the soil. Anaerobic bacteria favour wet, poorly drained soils and can produce toxic compounds that can limit root growth and predispose plants to root diseases. Many anaerobic bacteria are found in the intestines of animals and are associated with manure and foul odour’s. ix

For denitrification to occur, a lack of oxygen or anaerobic conditions (heavy clay soil, water logging) must exit to enable bacteria to cleave off the oxygen from nitrates to form nitrous oxide or dinitrogen gas. These conditions are common in ponded or saturated fields, compacted fields, or deep inside the microaggregates of soil where oxygen is limited. Denitrifying bacteria decrease the nitrogen level in soils directing nitrogen back into the atmosphere. On a saturated clay soil, as much as 40 to 60 percent of the soil nitrogen may be lost by denitrification to the atmosphere. x

Anaerobic conditions can be combatted in a number of ways and is a core outcome of improving soil structures.

Best of both worlds

How can we maintain fast access to nutrients applied through fertilisers, while not killing off the soil microbes that make for a stronger and healthier plant? This is exactly what we have designed a BioAg program to achieve.

BioAg products contain bacterial and fungal cultures. As soils become more biologically active growers see more efficient utilisation of the applied nutrients. This can lead to a reduction in the amount of nitrogen and phosphorus fertiliser required. An increase in beneficial microbes creates healthy and productive soils that enhance plant health and growth along with sustainability.

With BioAg’s approach it is easy to convert a high-input conventional farming system into a more sustainable farming system with improvements in crop nutrition and improving soil properties as well as reducing impact on the environment.

Talk to a BioAg Area Manager about how our programs, combined with conventional nutrients, improve the ability of pasture and crops to access nutrients and moisture. Ask your Area Manager to explain how our programs can reduce the impact of pests, disease, heat and frost stresses.

See our resources page for more information about the effectiveness of BioAg programs and products.

Beneficial microorganisms for sustainable agriculture

From a CSIRO paper by Dr. Vadakattu Gupta xi

It is essential to enhance the activities of microbes that benefit plant nutrition, control diseases and assist plants to cope with a variety of abiotic stresses to sustain and improve global food production in future climate scenarios while maintaining environmental health. A diverse range of beneficial microorganisms have been found but their reliable use in field environments is yet to be fully realised. New knowledge on soil microbial diversity can lead to the discovery of new generation inoculants as well as improve survival and performance of beneficial microbes in situ following their introduction into foreign environments.

Dr. Vadakattu Gupta is a principal research scientist in CSIRO Ecosystem Sciences at Waite campus in Adelaide. His research interests are in the areas of functional microbial ecology and plant-microbe-soil interactions with current focus on unravelling the genetic and functional diversity of disease suppressive microbial communities and rhizosphere dynamics of microbiota and biological functions.


[i] vro.agriculture.vic.gov.au

[ii] Zhou, Jing et al. “Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China.” Scientific Reports 7, 3267 (2017).

[iii] Paungfoo-Lonhienne, Chanyarat et al. “Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere.” Science Reports, 5(8678) (March 2, 2015).

[iv] Rodriguez-Eugenio, Natalia et al. “Soil Pollution: A Hidden Reality.” United Nations Food and Agriculture Organization, 2018.

[v] Sylvia, D.M., Hartel, P.G. Fuhrmann, J.J. and Zuberer, D.A. (2005). Principles and Applications of Soil Microbiology (2nd ed.). Edited by David M. Sylva, Pearson Prentice Hall, Upper Saddle River, New Jersey.

[vi] Wagner, S. C.. (2011) Biological Nitrogen Fixation. Nature Education Knowledge 3(10):15

[vii] Ingham, E.R. (2009). Soil Biology Primer, Chapter 4: Soil Fungus. Ankeny IA: Soil & Water
Conservation Society. Pg. 22-23.

[viii] Hoorman, J. (2016) Role of Soil Bacteria. Assistant Professor and Extension Educator, Agriculture and Natural Resources. ohioline.osu.edu

[ix] Lowenfels, J. and Lewis, W. (2006). Teaming with Microbes: A Gardener’s Guide to the Soil Food Web, Chapter 3: Bacteria, Timber Press, Portland, Oregon.

[x] Dick, W. (2009). Lecture on Biochemistry Process in Soil Microbiology, Personal collection of W. Dick, The Ohio State University School of Environment and Natural Resources.

[xi] Beneficial microorganisms for sustainable agriculture by Dr V Gupta, viewed 27/08/2014.