What are good and bad soil microorganisms?

Where do microorganisms come from?

Microorganisms are organisms too small to be viewed solely by the eye, they are everywhere, from the poles to the equators, including deserts, geysers, rocks, volcanos and even in the deep sea. They even live in bigger living organisms, forming part of the microbiota found in and on every multicellular organism. These microscopic organisms can adapt to extreme conditions, such as temperature and pressure and they can even endure high radiation environments. Furthermore, microorganisms were the first live inhabitants of Earth, in fact, a study found that Australian rocks contained microorganisms from 3.45 billion years ago.



The concept of microorganism englobes both unicellular and multicellular organisms, formed by one or multiple cells respectively and these microscopic entities are part of the three domains of life defined by Carl Woese as Archea, Bacteria and Eukaryota. The latter domain includes multicellular microorganisms (micro-animals, some fungi and algae) and unicellular protists and protozoans. Evidences suggest that the most primitive microorganisms found in Earth were prokaryote like (part of the domains of life Archea and Bacteria) and that the development of eukaryotes occurred at a later stage.


The importance of microorganisms is unquestionable, they are part of our culture and health, they ferment foods and drinks (i.e. cheese, yogurt, wine, etc.), treat wastewater, produce fuel, and generate important enzymes and bioactive compounds (i.e. antibiotics). They are in our human body constituting the microbiota, from the gut to the skin flora, generally being good guys, by helping us maintaining the correct functioning of our body, but some can be
nasty or pathogenic and cause infectious diseases. Unsurprisingly, microorganisms are a vital component of fertile soils and their presence is key for maintaining agricultural activities.



Why are microorganisms important for agriculture?

In agriculture, microorganisms are essential for maintaining good soil health, and for promoting sustainable crop production; the soil microorganisms include archaea, bacteria, protozoa, algae, fungi, oomycetes and are all present in a rich ecosystem in which they interact amongst them and with the plant roots forming a complex network. Moreover, these microbes can have both positive and negative effects on soil fertility and on plant health, and their behaviour are heavily influenced by climate, substrate and plant type, oxygen content, pH, and salinity. Here, we will examine the effects of the presence in soils of both, beneficial, and pathogenic microorganisms.



What are beneficial microorganisms?

We consider beneficial microorganisms as those microbes that carry out beneficial activities for the plant health, which include: i) breakdown of organic matter, ii) nutrient cycling, iii) improvement in soil structure, iv)  nitrogen fixation, v) encouragement of plant growth, vi) control of pests and disease, etc. Most microorganisms in the soil have a beneficial effect in the rhizosphere, which is the soil region around the roots and containing the soil microbes. In the rhizosphere plant roots release molecules such as acids and sugars into the surrounding soil, and these root secretions attract a variety of soil microorganisms. 



This microbes/roots relationship tends to have a positive effect on the overall health of the plant. For instance, the plant growth-promoting rhizobacteria (PGPR) promotes plant growth improving infection response, growth rate and overall plant fitness (read more). Moreover, the microorganisms in the rhizosphere promote nutrient turnover and cycling, decomposition of organic matter, and often form symbiotic relationships with the plant, further promoting healthy crop yields, good quality produce and a healthy ecosystem. The symbiotic interaction between fungi and plant roots, known as mycorrhiza, is another example of the beneficial effect that microorganisms have on plant health. The fungi participating in the mycorrhiza promote the absorption of minerals and nutrients from the soil, most notably phosphorus and zinc, while protecting the roots from harmful pathogens; meanwhile, the plant provides the fungi with vital carbohydrates.



The presence of beneficial microorganisms in agricultural soil often implies a lower need to use pesticides and fungicides, as healthy soils promote healthy and disease-resistant crops. This can be seen in occurrences in which pesticides are replaced by bacterial strains for biological pest control, such as the use of Bacillus thuringiensis (BT) in which no harm is brought to the crop, to the surrounding ecosystem or to the human health (read more). Furthermore, biological pest control reduces the environmental strain placed on agricultural practices and contributes towards a healthier ecosystem and more sustainable practices, as there is a reduced need for chemical use. In addition, beneficial microorganisms used for biological pest controls can also improve soil health, promoting soil fertility and consequently increasing crop yields. Not to mention that the improvement in the crop quality will also reach consumer level, as products will retain a higher quality in nutrient and water content.



What are pathogenic microorganisms for crops?

On the other hand, pathogenic microorganisms present in agricultural soils can have a harmful effect on the crop inducing: i) pathogenicity and disease, ii) resistance to crop control products, iii) poor soil health or reduced fertility, iv) poor crop health or poor yields, and lastly v) crop loss. In a nutshell, pathogenic microbes can be detrimental to crop yield, reduce food quality and promote disease spread. These pathogens are often difficult to control and to manage, once widespread. Pathogenic microorganisms include fungi, oomycetes, bacteria and viruses. Some of these pathogenic microorganisms will decompose root nodules, leaching nutrients from the plant, reducing the efficiency of nutrient uptake and mobilisation, and further leading to nutrient deficiency and stunted plant growth. The presence of pathogens can also impact photosynthetic functioning, causing chlorosis and necrosis of leaves and stems resulting in a reduction in the translocation of water and nutrients through the vascular system. This often occurs through the assistance of toxins that colonise the host tissue; these toxins have a negative impact on the host plant and are often host-specific. As a consequence, this will stunt growth and lead to plant death if not managed and treated. Other symptoms of pathogenic invasion include blight, canker, distortion, leaf scorch or spot and gummosis.



Examples of pathogenic microorganism include Phytophthora, Fusarium, Verticillium, Pythium and Rhizoctonia. There are over a 100 species of the pathogenic oomycete Phytophthora, which is also known as the plant destroyer. This pathogenic microorganism can be very damaging to many plants, particularly, ornamental and horticultural crops. Phytophthora spores can survive in plant debris or soil for many years and can infect all parts of the plant, but it usually attacks the roots or stem base.  Fusarium is a fungal genus that is widely distributed in soil. Most species of Fusarium are harmless saprobes (decomposers that feed on decaying organic matter), but some species can have devastating impact on crops. For instance, they can cause Fusarium stem canker, Fusarium root rot, Fusarium wilt in different type of crops, and pathogenic Fusarium species are hardly manageable due to their ability to survive for extended periods in the soil. Verticillium is a soil-borne fungal disease, which causes widespread wilting of affected plants, it pierces host roots to grow into the xylem of the plant, reducing water transport and increasing toxin movement, leading to the death of plant tissues. Pythium causes common crop diseases,
like root rot, often involving seed decay and seedling death. This fungus will reduce root growth, overall plant growth, and lead to the destruction of the hypocotyl (the stem of a germinating seed) and main root system. This will eventually cause infected plants to wilt and die. Lastly, fungal bacteria Rhizoctonia is responsible for many commercially significant crop diseases, for example turfgrass disease, seedling damping, black scurf in potatoes, bare patch, root rot and sheath blight.




The main message is that it is crucial to understand the impact of the microorganisms on soil and on plant health in order to be able to manage and control disease outbreaks. Most plant species have a natural resistance to pathogenic infection, however in some cases, widespread disease will occur. It is therefore critical to understand the biology and impact of pathogenic and beneficial microorganisms in crops. So we need to continue advancing in disease control, focussing on early detection to ensure diagnosis occurs prior to outbreak, enabling more effective and targeted treatments and mitigation measures to be put in place. FungiAlert technology offers for the first time the opportunity to understand both the pathogenic and beneficial microorganisms present in the soil. This tool enables the design of efficient disease control practices to minimise crop losses and to increase plant quality.



Ángela de Manzanos,

CTO at FungiAlert

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