An introduction to the root zone microbiome

Thanks to ongoing research, in recent years there have been huge advances in the scientific understanding of the root zone microbiome – in other words, the microbial life on and around the roots of a plant. But how does the root zone microbiome develop in stone wool, and what is really going on in this fascinating, invisible world?

“The root zone in a non-organic growing medium like stone wool can contain just as many bacteria as an organic substrate – up to and sometimes more than a billion per millilitre of stone wool,” says Marta Streminska, a microbial ecologist based in the Wageningen University & Research, Business Unit Greenhouse Horticulture and Flower Bulbs in Bleiswijk, the Netherlands.

Definition: A microbiome is a characteristic microbial community that occupies a reasonably well-defined habitat which has distinct physio-chemical properties. The microbiome not only refers to the microorganisms involved, but also encompasses their theatre of activity, which results in the formation of specific ecological niches. In the case of the root zone microbiome, that theatre of activity is the area directly around the roots of a plant the rhizosphere, and the microorganisms in the wider root zone.

Clean and disease-free at the point of manufacture

It’s not hard to imagine organic growing media such coco peat teeming with microbial life. But what about non-organic growing media such as stone wool? Do they contain microbes in the root zone too? “Grodan’s stone wool growing media is clean and disease-free at the point of manufacture. However, as soon as water, nutrients, seeds and plants are added, microbes immediately start to spread, quickly establishing a diverse root zone microbiome (see Graph 1).

How does the microbiome develop in stone wool?

“When we plant a young seedling in a stone wool block or slab, the microbes quickly colonise the root zone, where they thrive on root exudates: organic matter such as glucose, organic acids and secondary metabolites that are constantly secreted by the plant roots during growth. In terms of the numbers of bacteria, there’s not a huge difference between stone wool or organic growing media,” she says. “Those numbers are mind-blowing, with more than a billion cells made up from 600 – 700 different genera per millilitre of stone wool”.

“It is even more clear now that there is a difference between the microbial populations developing directly in the rhizosphere and in the rest of the root zone. So even on such a small spatial scale, there are measurable and defined microbial differences,” comments Marta.

“One key difference between the microbiome in stone wool and organic growing media is the presence of fungi. Fungi prefer complex organic matter such as cellulose and lignin which is more abundant in organic growing media. The reason for this is that organic growing media is made from dead plant material,” she adds. This simple explanation is why higher levels of fungi are found in organic growing media compared to stone wool, because fungi have the ability to degrade complex organic compounds and make carbon available again.

Intensive research

For many years, the importance of microorganisms in plant growth was underestimated and often completely overlooked. “Around 20 or 30 years ago, microorganisms in cultivation systems were often overlooked, simply because scientists were unable to see the diversity of microbes, as they could not be cultured in the laboratory ,” she continues. Since then, thanks to advances in molecular biology, microbiologists have been able to study the role of microbes in plants more intensively, both in the  phyllosphere (the above ground plant parts) and the rhizosphere (the below-ground plant parts).

It is also known today that in addition to  precise irrigation management, a balanced root zone microbiome makes an important contribution to maintaining the strength, health, resilience and the production potential of a plant. “Using the new scientific techniques, we are now looking at two things: which microbes are there and what is their function ” says Marta. 

The good, the bad and the ugly

When talking about the functions of root zone microbes, the microbiologist groups them into three categories (Table 1). From the plant cultivation perspective, they can be  called “the good, the bad and the ugly”. The ‘good’ ones have a positive impact on the plant, the ‘bad’ ones have a negative impact on the plant, and the ‘uglies’ are possible human pathogens, although they have a neutral effect on the plant. Examples of ‘uglies’ are E. coli that can be introduced in crops through human contact, and L. pneumophila  that can thrive in water systems. However, this categorisation process is not always easy, as some of the microbes from the same genus can be good, bad and ugly. “For example the bacterium Pseudomonas fluorescens is good. It can suppress fungal plant pathogens and is used as a bio-control agent in the root zone. Pseudomonas syringae is a common, if not the most common plant pathogen. In tomato it causes leaf-speck.  Finally Pseudomonas aeruginosa can cause pneumonia in humans.

We see the same for some types of fungi, such as Fusarium. Many species of Fusarium cause wilting and root rots in different plants, on the other hand there are Fusarium isolates such as Fusarium oxysporum isolate Fo47 which are not plant pathogenic at all and actually protect plant from attack by pathogenic Fusarium oxysporum, by occupying the roots and influencing the induced resistance of the plant” she comments.

Most growers are all too familiar with examples of ‘bad’ root zone microbes: plant pathogens such as  Fusarium oxysporum and Pythium aphanidermatum that make plants sick. “In nature, these support the natural selection process by eliminating weak plants, but of course they are undesirable in today’s large scale commercial greenhouses, which tend to cultivate monoculture crops with a high level of uniformity within the population due to the use of F1 hybrid seeds,” adds Marta.

Thanks to the ongoing research, it’s now known that some ‘good’ microbes (see examples in Table 1) can help to protect a plant against such pathogens. “Some of them will actually directly attack the pathogen to prevent it from affecting the plant. Other modes of action can include triggering the plant to prime itself for a pathogen attack, such as by producing hormones like salicylic acid or jasmonic acid. Some Bacillus strains often do both. For example they produce metabolites that kill plant pathogens directly as well as inducing the plants systemic resistance by influencing the production of salicylic and jasmonic acid.  By colonising the rhizosphere in this way  ‘good’ microbes can limit the pathogen’s access to the roots,” she comments.

Contribution to resilient growing

“Unlike beneficial insects, bacteria and fungi can’t be seen or counted on the plant or in the water sample directly. But they are there and they can really make a huge difference to plant resilience,” states the microbial ecologist. That’s why it is important is to steer the root zone microbiome in the growing medium towards a stable and beneficial balance.

In the context of the current shift to resilient growing systems in Controlled Environment Agriculture, microbes can also make an important contribution to reducing the use of chemicals in the transition to natural pathogen and pest control.

Besides this, ‘good’ microbes can perform various other functions in the root zone. “Some microbes – especially fungi – feed on the cellulose in decaying roots in the growing medium,  degrading the organic matter to make the organic carbon available again. Others play a role in the availability and uptake of nutrients such as nitrogen, phosphorus and  micronutrients. At the moment, in hydroponic systems all nutrients are provided continuously in mineral form to the plant with irrigation. However, that does not mean that the microorganisms cannot help the plants with uptake of these nutrients whilst helping protect against disease. Microbes in the root zone microbiome secrete compounds called ‘sideropores’ which chelate iron meaning the iron is no longer available for other potentially pathogenic micro-organisms thus lowering their virulence towards plants.  Another important function of microbes in the root zone, such as some Trichoderma or Pseudomonas species, is the production of various metabolites. These organic molecules can include plant hormones such as auxins and cytokinins that promote plant growth and development,” she explains.

Clearly, the root zone in both organic media and stone wool growing media is home to hundreds of genera of microorganisms. Even though research is still ongoing to better understand their individual functions, there is no doubt that the right balance in the root zone microbiome can contribute to a stronger, healthier, more resilient and more productive plant. But how can the root zone microbiome be steered? And what are the advantages of stone wool in this context? Read Part 2 of this series to find out.