Microbe Science




Beneficial microbe science is an extremely complex subject that is, too often, oversimplified by those with interests in selling beneficial bacteria and fungi products through the hydroponics industry. Just one of the practices that is common is manufacturers/suppliers present positive findings from soil-based research and apply this to an entirely different growing methodology –hydroponics – where, among other things, microflora, pH, EC, media matrix, microbial food levels, nutrient levels, and the bioavailability of nutrients are extremely different from soils. It is important to note that even in soil based research the benefits that a bacteria or fungi species may demonstrate in one soil type may not be replicated in another soil type. Additionally, many biocontrol agents perform well in the laboratory and green house conditions but fail to do so in the field.1 Similar outcomes are also demonstrated in soiless growing where inconsistencies arise between different systems.

What is clear is that beneficial microbes offer hydroponic growers benefits beyond other methods of pathogen control/prevention. I.e. the use of beneficial microbes is not only demonstrated to control/eradicate pathogens but also to enhance yields through hormone stimulation, enzyme production and other mechanisms. The same cannot be said for sterilisation methods such as UV, ozone, monochloramine, chlorine and hydrogen peroxide.

Additionally, It is generally agreed that bio inoculants control diseases more stably under the better controllable conditions than in the open field. Thus, hydroponic systems offer a unique environment for control of pathogens since various parameters can be managed to favour friendly (beneficial) microorganisms over pathogenic bacteria and fungi.3

In the following material I have endeavoured to focus as much as possible on hydroponic specific content. The material covers just some of the ‘beneficials’ that have been shown to colonize efficiently in hydroponic growing environments and are proven to reduce plant disease and/or provide other benefits.

Root disease, root disease prevention, root disease cure, and sterilisation methods are among other subjects covered.

As a warning, this article is long (over 10,000 words). However, root disease, root disease prevention and microbe science are subjects worth coming to terms with.




Pythium is a specific type of organism but the term Pythium has become the generic name for describing a large number of water moulds or damping off fungi. For the purposes of this paper I will refer to many rhizosphere pathogens as Pythium. In other cases where a specific pathologen has been demonstrated to be eradicated or controlled by a given beneficial bacteria or fungi species I will refer to the pathogen using its scientific name. Other names, besides Pythium, that you will find are Fusarium oxysporum, Fusarium spp., Phytophthora spp etc.

spp. refers to species (plural). For instance, if you see Trichoderma spp. this refers to Trichoderma species

Host refers to the plant. I.e. The plant is a host for the beneficial bacteria or fungi

Bioinoculant – A formulation containing one or more beneficial bacterial or fungi strains

When referring to beneficial microbes or beneficial microbe products (bioinoculants) various terminology may be used. E.g. bio inoculant, beneficials, beneficial microbe products, friendly bacteria, beneficial bacteria and beneficial fungi. While the terminology isn’t scientifically correct this terminology is used because it is commonly used throughout the hydroponics retail sector ( is  culturally appropriate to the readership).

Root Disease in Hydroponics (In Brief)

When science first conceived of hydroponics it was believed that the new artificial growing method would exclude soil borne pathogens. This was quickly disproven and it was soon discovered that a microflora, similar to that found in soils, rapidly established itself in hydroponic systems. Among the microflora were the plant pathogens Pythium, Phytophera and Fusarium.


Phytophthora (pronounced Fy-tof-thora – meaning plant destroyer) is a water mould, also known as an oomycete.

Phytophthora is an aggressive plant pathogen. When a plant is infected, it is unable to absorb nutrients.

Fusarium oxysporum

Fusarium oxysporum is a common soil fungus, and can become a pathogen causing a wide variety of wilt diseases in plants (usually called Fusarium wilts). Fusarium wilt can be identified with symptoms such as wilting, chlorosis, necrosis, premature leaf drop, browning of the vascular system, stunting, and damping-off.


The most common root disease found in hydroponics is caused by Pythium. Pythium attacks the root system and severely limits the plant’s capacity to uptake food. What this ultimately means is an unhealthy crop and a low yield. In severe cases it can lead to crop death.

Pythium disease can be recognized by a brown root system that breaks away when pulled. This may also be accompanied by a musty smell as the root system decays.

Pythium can take hold of a weak, stressed crop far more easily than it can a healthy crop. Making sure that your plants remain healthy through the correct nutrition (particularly during heavy fruiting) and optimum conditions (air temp, water/nutrient temp, RH etc) will give your plants increased resistance against Pythium. I.e. plants grown in optimal conditions (i.e. optimal air temperature, optimal water/nutrient/media temperature, optimal nutrition, optimal RH) will be more resistant to root disease than plants that are subjected to stress as a result of less than optimal growing conditions.

Pythium spores are soil inhabitants. This is why hydroponics and soil don’t mix. Avoid introducing soil into your hydroponics environment! This means taking precautions such as not dragging soil from outdoors into your (indoor) growing environment on your shoes, clothes or hands.

Pythium are water moulds. Because of this, untreated water such as stream, dam, and shallow bore water are high-risk products. If you are going to use stream, dam or bore water in your system you will need to sterilise it prior to use. Rainwater should also be treated because of the likelihood of it collecting wind blown soil.

Managing disease suppression in hydroponics represents the best way of controlling Pythium. Three main strategies can be used: (1) increasing the level of suppressiveness by the addition of antagonistic microorganisms; (2) using a mix of microorganisms with complementary ecological traits and antagonistic abilities, combined with disinfection techniques; and (3) amending substrates and nutrient to favour the development of a beneficial microflora. 1

 Friendly Bacteria and Fungi in Hydroponic Settings

Hydroponic systems offer a unique environment for control of pathogens since various parameters can be managed to favour friendly (beneficial) microorganisms over pathogenic bacteria and fungi. Given this, the addition of beneficial bacteria and fungi in hydro systems, when handled correctly, promotes a dynamic microculture that prevents harmful organisms damaging the crop.

While the mechanisms that beneficial microbes use against pathogens are complex these mechanisms can be defined as:

Microbial antagonism

Microbial antagonism results from direct interactions between two microorganisms sharing the same ecological niche. Three main types of direct interaction may be characterized: parasitism, competition for nutrients or plant tissues, and antibiosis.


Parasitism of a plant pathogen by other microorganisms is a widely distributed phenomenon. It involves specific recognition between the antagonist and its target pathogen and several types of cell wall-degrading enzymes (CWDEs) that enable the parasite to penetrate the cell wall (hyphae) of the pathogen.

Competition for nutrients

Competition for nutrients is a general phenomenon regulating the dynamics of microorganisms sharing the same ecological niche and having the same physiological requirements when resources are limited. Competition for nutrients, especially for carbon, is common in as soils and other media, and is considered to be responsible for the phenomenon of fungistasis which is the inhibition of fungal spore germination. Competition for nutrients is one of the modes of action of many beneficial micros.


Antibiosis is the antagonism resulting from the production by one microorganism of secondary metabolites toxic for other microorganisms. Antibiosis is a very common phenomenon responsible for the biocontrol activity of many beneficial microorganisms such as fluorescent Pseudomonas spp., Bacillus spp., Streptomyces spp. and Trichoderma spp. A given strain of beneficial microbe may produce several types of secondary metabolite, having different functions and effective against different species of fungal pathogens.

Induced resistance of the plant

Plants react to physical stresses such as heat, frost, drought, salt, and inoculation with pathogenic or nonpathogenic microorganisms by expressing defence reactions. These defence reactions are SAR (systemic acquired resistance) and ISR (induced systemic resistance). We’ll talk more about this in a moment.

Overview of Microbial Inoculants 

Microbial inoculants are used in agriculture as soil amendments that use beneficial bacteria and fungi to promote plant health and nutrition. Various microbe species can be used as biological control agents and may provide effective activity against various pathogenic microorganisms. Just some examples:

Trichoderma harzianum has biocontrol potential against Botrytis cineria, Fusarium, Pythium and Rhizoctonia; Ampelomyces quisqualis, – a hyperparasite of powdery mildew. Bacillussubtillis has antifungal potential against Phytophthora parasitica Dast, Alternaria solani, Pythium aphanidermatum, C. gloeosporioides, Verticillium dahliae Klebahn, Fusariumoxysporum f.sp melongenae, Botrytis cinerea Pers, Fusarium oxysporum, and Lycopersici.1 Fluorescent pseudomonads produce “highly potent” broad spectrum antifungal molecules against various phytopathogens. 2 Application of Trichoderma viride, Pseudomonas and Bacillus spp. have been found to substantially control seedling, root and stalk rots of maize caused by Fusarium graminearum. Pseudomonas cepacea has been found to inhibit a range of soil borne fungal pathogens including Fusarium graminearum, Fusarium moniliforme and M. phaseolina.3Pseudomonas putida and Trichoderma atroviride have been found to promote the reproductive growth of tomato plants under typical hydroponic growing conditions,4 while numerous studies have demonstrated that rhizosphere bacteria can stimulate plant growth in both soils and hydroponic settings.

Foliar sprays can be used for leaf coverage and they are applied through irrigation to inoculate the soil. While they are applied to improve plant nutrition and health their exudates can also promote hormone production in plants, therefore promoting plant growth.  Many of the beneficial bacteria and fungi form symbiotic relationships within the plant that are mutualistic. Roots themselves release exudates into the soil that are beneficial to the microorganisms which suggests a degree of co-evolution between microorganisms and plants that form the ecosystem of the rhizosphere.

The use of inoculants in agriculture has been shown to extend beyond their benefits as biological fertilizers. Research into the disease resistance of microbioinnoculants in crop species shows they can initiate systemic acquired resistance (SAR) to several common crop diseases.

In plants SAR is a resistance response that occurs following a previous localized exposure to a plant pathogen. Once stimulated SAR can provide resistance for several days to a wide variety of pathogens. When a plant recognizes a pathogen it induces a rapid defence response called the hypersensitive response (HR). HR results in localized cell or tissue death at the site of infection, which limits further spread of infection.

This localized response provides non specific resistance throughout the plant; a phenomenon known as systemic acquired resistance – SAR (Ryals et al 1996).

Plants produce salicylic acid as a result of the HR and this increase in concentration of salicylic acid is an activator of SAR. Research has shown that aspirin (acetyl salicylic acid) can work as a trigger for SAR.

There is also induced systemic resistance (ISR). ISR corresponds to the resistance induced by plant growth-promoting rhizobacteria involving the jasmonic acid (JA) and ethylene (ET) pathways. The two pathways are not independent and there are some commonalities between SAR and ISR. For example, both SAR and ISR are controlled by the same regulatory protein non-expressor in the plant. Cross-communication between defense pathways enables the plant to fine-tune its defense response. Based on recent research, the phenomenon of ‘priming’ defense appears to be a common feature of the plant’s immune system that offers protection against disease. When ISR is induced the plant shows a faster or greater activation of defense responses after infection.5

Put simply….

Beneficial microbes such as plant growth promoting bacteria (PGPB) and fungi can improve plant resistance to pathogens and even some insects by inducing systemic defence responses. Beneficial bacteria and fungi exudates are recognized by the plant, which results in a mild activation of plant immune responses.

Plant Growth Promoting bacteria (PGPB) are considered to promote plant growth directly or indirectly. PGPB can exhibit a variety of characteristics responsible for influencing plant growth. The common traits include production of plant growth regulators (e.g. auxins), siderophores (iron chelating compounds), HCN (amino acid precursor) and antibiotics. Indole acetic acid (IAA) is one of the most physiologically active auxins. IAA is a common product of L-tryptophan metabolism by several microorganisms including PGPB. Microorganisms inhabiting rhizospheres of various plants are likely to synthesize and release auxin as secondary metabolites because of the rich supplies of substrates exuded from the roots compared with non-microbe inhabited soils.

There is evidence that the growth hormones produced by microbes can in some instances increase growth rates and improve yields of the host plants. It is also possible that microbes capable of phosphate solubilization may improve plant productivity both by hormonal stimulation and by supplying phosphate. However, because of the capacity of beneficial microbes to confer plant beneficial effects, efficient colonization of the plant environment is of utmost importance. This is often a fact that is greatly oversimplified by those with interests in selling beneficial microbe products to the agricultural and/or hydroponic sectors. One must consider that many microbes require optimal conditions in which to sufficiently produce benefits and in many instances soil-based research is used to substantiate the merits of bacteria and/or fungi benefits in hydroponics.

Take for example, Arbuscular Mycorrhizal Fungi (AMF) …