About Arbuscular Mycorrhizal Fungi (AMF) in Hydroponics

The term “mycorrhiza” literally means fungus-root. It is estimated that 80 to 90 percent of all plant species form mycorrhiza. The relationship between plant and micorrhizae is a symbiosis, the main function of which, while complex, is the transfer of carbon produced by plants to fungi (sugars created in leaves of the plant move downward and into the fungal hyphae via the roots) and the transfer of nutrients acquired by fungi to plants (the plant receives phosphorus, nitrogen, potassium, and micronutrients such as copper, sulfur and zinc).

Elements that are critical in the plant/mycorrhizae symbiosis are CO2 concentration, nitrogen levels, phosphorous levels, soil matrix, pH and carbon.

Phosphorous, Nitrogen and AMF

One of the key functions of AM fungi is they increase the uptake of poorly soluble P sources, such as iron and aluminium phosphate and rock phosphates by converting non bioavailable phosphates in their organic form to inorganic, bioavailable H2PO4 (Pi) and HPO42- phosphorous.

AM fungi colonize the root cortex of the host plant in which the fungi are able to acquire organic carbon as food to build ‘the infrastructure’ for P uptake and transport. The mycorrhizal system is able to take up P more efficiently and transport P over longer distances than the plant root system, overcoming P depletion in soils.1

AM fungi also acquire substantial quantities of N from organic sources and play an important role in the nitrogen cycle, intercepting inorganic N released from decomposing organic matter before roots can acquire it and passing some of this on to plants as arginine (CH2CH2CH2NH-C(NH)NH2). Additionally, a plant ammonium (NH4 N) transporter that is mycorrhiza-specific and preferentially activated in arbusculated cells has recently been discovered, suggesting that N transfer to the plant may operate in a similar manner to P transfer. 2

Pitched this way AM fungi sound impressive.


The benefits of AM fungi are greatest in systems where inputs of phosphorous are low. Heavy usage of phosphorus fertilizer can inhibit mycorrhizal colonization and growth. As a soil’s phosphorus levels available to a plant increases, the amount of phosphorus also increases in the plant’s tissues, and carbon drain on the plant by the AM fungi symbiosis become non-beneficial to the plant. 3

A comprehensive literature review conducted by Kathleen K. Treseder (2004) concludes mycorrhizal abundance declines in response to adequate N (-15%) and P (-32%) fertilization by average across numerous studies.4

Under even moderate P levels that prevail in the majority of field crop systems, early season colonisation by AMF may often be parasitic, creating a carbon drain on crops and reducing yields.5       

In research with AMF (Glomus intraradice), Schenck et al (1993) show citrus grown in adequate P environments had lower relative growth rates than non-mycorrhizal plants of equivalent P status.6 Similar findings have been established in other plant species.7   

Author’s note: Carbon drain occurs when there is adequate available phosphorous, however, AMF continue to metabolise plant produced carbon thus placing unnecessary energy drain/burden on the host plants which are receiving low benefits via the mycorrhizae/plant symbiosis.

Hydroponics and AM Fungi    

Research demonstrates:

1) The benefits of AM fungi are greatest in P deficient environments

2) Where adequate P is present AM fungi colonization is reduced (average 32%)

3) Bioavailable N plays a pivotal role in AM fungi colonization

4) Where high bioavailable N is present, AM fungi colonization is reduced (average 15%)

5) Yields may be detrimentally affected where adequate P exists (due to carbon drain)

H.J. Hawkins et al (2004) note that a nutrient medium containing a P concentration of 0.9 mM (27.876384ppm P) failed to produce viable mycorrhizal colonisation.8 Similar findings by G.Nagahashi (1996) demonstrates that mycorrhizae grown in the presence of P at 1.0mM (30.973ppm) showed significantly less hypal branching than in lower P environments.9

Evaluation of P in Hydroponic Working Solutions 

We evaluated several off the shelf hydroponic nutrients to establish how many ppm of P (phosphorous) would be in working solution by average. It is important to note that the values were established using random mL/L dilution rates and do not reflect values at comparative ECs (although EC should be between approx 1.8 and 2.4). The aim of the analysis was to establish roughly what ppm of P would be in working solution across a broad range of ECs. In all cases ppm of P exceeded 62ppm, which is double the ppm that available research has shown AMF efficiency is reduced. The ppm data was calculated from lab analysis of concentrate formulas once diluted.

Samples (elemental P and not P as P2O5)

AN Sensi Bloom 4ml/L = 81ppm P 

AN Connoisseur Bloom 4ml/L = 90ppm P 

H and G Coco 5ml/L = 75ppm P 

Canna Aqua Flores 5ml/L = 76ppm P 

GH 3 Part = (full strength bloom as per manufacturer recommendations) 330ppm P 

Average = 130.4ppm

Author’s note: When considering that many hydroponic growers use further P through the use of P and K additives during flowerset this too needs to be factored into the P equation. For instance, with a product that contained PK 13- 14 %w/w listed as P2O5 and K2O with a specific gravity of 1.25, used at 1.5mL/L this would equate to an additional 104.8ppm of P in working solution. More simply, additive + nutrient equals over 5 times the P that has been found to be detrimental to AM fungi colonization.


While the symbiosis between plants and AM fungi is complex and while more hydroponic specific research is needed, based on current knowledge it seems probable that any potential benefits of AM fungi in hydroponics is negated by the presence of high bioavailable P in hydroponic solutions. Additionally, high bioavailable N in hydroponic solutions likely reduces the efficiency of AM fungi further. It is also possible the presence of AM fungi in hydroponic settings may be detrimental to growth rates and yields as a result of carbon drain.

Back to the story…

The majority of soil living beneficial bacteria require oxygen for cellular respiration (also termed “oxidative metabolism”). Bacteria that require oxygen are classed as aerobes. Aerobes also require organic material or molecules (such as glucose) to produce energy. For this reason this class of bacteria are also called aerobic heterotrophs (i.e. aerobic heterotrophs are organisms that cannot live without free oxygen and do not produce their own food).

The main elements required for beneficial bacterial nutrition are C, H, O, N, S, P, K, Mg, Fe, Ca, Mn and traces of Zn, Cu and Mo.

‘Aerobic heterotrophs’ require a source of organic carbon, gaseous oxygen (air) and water along with the aforementioned mineral elements.  Their source of energy is produced by the aerobic oxidation of organic material by metabolism to water and carbon dioxide. The energy released is stored in the phosphoanhydride bonds of ATP. When the energy is required it is released from ATP by hydrolysis. Certain environmental conditions are also required for the growth and division of bacteria like O2 concentration, pH and temperature.

ATP stands for Adenosine Tri-Phosphate. ATP consists of an adenosine molecule and three inorganic phosphates . ATP is the most important energy-transfer molecule in all living cells. ATP transports chemical energy within cells for metabolism. ATP is produced during photosynthesis and cellular respiration and used by enzymes and structural proteins in cellular processes, including biosynthetic reactions and cell division.

Phosphorous/phosphate plays a vital role in the ATP chain. Inorganic phosphorus in the form of the phosphate PO43- plays a major role in biological molecules DNA and RNA where it forms part of the molecular structure. Living cells use phosphate to transport cellular energy in the form of ATP. Nearly every cellular process that uses energy obtains it in the form of ATP. ATP ——-> ADP (Adenosine Diphosphate) + Pi (orthophosphate) + energy. 

For beneficial bacteria to survive in a hydroponic environment they will need ideal environmental conditions. Most hydroponic nutrients lack organic carbon sources for beneficial bacteria to survive. They can metabolise humic and fulvic extracts but one of the best sources of food for beneficial bacteria is molasses. Molasses typically contains ‘Total Digestable Nutrients’ (TDN) in excess of 60%, as well as containing a number of the major elements and trace elements required by bacteria, molasses is very high (50%+) in sugars. The sugars contained in molasses are an ideal source of carbon for heterotrophs. Cobalt and molybdenum, which are not usually listed in the typical analysis of molasses, will still be found in small traces. Another property of molasses, due to the high percentage of sugars, is its’ sticking ability when used in foliar sprays. Molasses, along with a wetting agent, increases the coverage and surface holding, optimising foliar nutrition. While discussing foliar sprays and biological inputs, saponins can be used as an organic wetting agent that not only reduces the surface tension of water (i.e. surfactant – surface active agent) it also has bio stimulating properties. Saponins are chemical compounds (phytochemicals) found in abundance in various plant species.  To be specific they are amphipathic glycosides. The foaming ability of saponins is because of their surfactant like structure with hydrophillic (water soluble) and hydrophobic (fat soluble) chains. Their name is derived from the plant soapwort (genus Saponaria). Most commercial saponins are extracted from Yucca schidigera (Spanish Dagger) and Quillaja saponaria (the soap bark tree).

Two other prominent organic additives that act as microbial nutrients/stimulators and plant fertilisers are kelp and fish products.

It is important to note that where hydroponics is concerned, particularly water based systems (e.g. NFT and aeroponics) it’s important not to overdo it with organic matter or additives. In adding too much organics into the hydro system the proliferation of unwanted microbial life may potentially rob oxygen from the root zone creating a situation where roots are suffocated and pathogenic microbe numbers explode under oxygen starved conditions.

Beneficial Bacteria and Fungi Species for Hydroponics


Trichoderma spp. including T. harzianum, T. viride, T. koningii, T. hamatum and other spp.

Trichoderma spp. are free-living fungi that are very common in soil and root ecosystems. Recent discoveries demonstrate that they are opportunistic plant symbionts as well as parasites of other fungi. 1

For many years, the ability of these fungi to increase the rate of plant growth and development, including, especially, their ability to cause the production of more robust roots has been known. The mechanisms for these abilities are only just now becoming understood.

Trichoderma spp. show a high level of genetic diversity, and can be used to produce a wide range of products of commercial and ecological interest. They are prolific producers of extracellular proteins, and are best known for their ability to produce enzymes that degrade cellulose and chitin — although they also produce other useful enzymes.2 In addition, different strains produce more than 100 different metabolites that have known antibiotic activities.3

Trichoderma spp. have been used as biological control agents against a wide range of pathogenic fungi e.g. Rhizoctonia spp., Pythium spp., Botrytis cinerea, and Fusarium spp. Phytophthora palmivora, P. parasitica and different species can be used (e.g. T. harzianum, T. viride, T. virens) to control the various pathogens. Among them, Trichoderma harzianum is reported to be most widely used as an effective bio inoculant.

Some strains of Trichoderma are highly rhizosphere competent (able to colonize and grow on roots as they develop). The most efficient rhizosphere competent strains can be added to soil or seeds by any method. Once they come into contact with the rhizosphere, they colonize the roots. If added as a seed treatment, the best strains will colonize root surfaces even when roots are deep below the soil surface. Trichoderma can colonize for long periods of time in the right environments, so colonization can occur throughout the duration of a crops life cycle. However, in less conducive environments Trichoderma colonization will prove less efficient and reapplication of the fungi is necessary.

To the authors knowledge various strains of Trichoderma control every pathogenic fungus for which control has been sought. However, in contrast to other fungi, Trichoderma spp. have been reported to have limited applications in biocontrol of pathogenic bacteria. An immediate explanation would be that bacteria generally have a faster growth rate (i.e. they multiply faster) than fungi.

This information becomes important when understanding that a broad-spectrum approach to preventing plant pathogens should be incorporated and species of both beneficial bacteria and fungi are likely the ideal.  For instance, a good microbrial product should contain species of Bacillus spp. (bacteria) and Trichoderma spp (fungi). However, it isn’t a simple case of incorporating multiple strains of known to be beneficial bacteria and/or fungi as some species may outcompete others and the combinations may reduce overall efficiency. For instance, Pseudomonas fluorescens strain CHA0 which has demonstrated biofungicide qualities against a range of pathogens releases a compound (Phl) that has antibiotic activity against other beneficial microbes.5 Thus, Incompatibility of co-inoculants can arise because biocontrol agents may also inhibit the growth of each other as well as the target pathogen or pathogens.6

You can read more about how bacteria out-compete fungi here where I cover making your own beneficial bacteria and fungi inoculums (micro teas) for use in hydroponic growing. This article also demonstrates further the complexities of beneficial bacteria and fungi when discussing their correct/optimal use in hydroponic growing systems. 

Trichoderma spp. and Plant Immune Response

Localized and systemic induced resistance occurs in all or most plants due to among other things, response to attack by pathogenic microorganisms, physical damage due to insects and other factors, and the presence of non-pathogenic rhizobacteria.

Trichoderma penetrate the cells of the root system – this triggers a response in the plant that effectively `walls off’ the Trichoderma and prevents it getting any further into the living root tissue. In triggering this response, the plants natural defence mechanism is activated and a systemic resistance is induced.  The relationship between Trichoderma and plant roots is an `opportunistic avirulent symbiotic relationship’ meaning even though the Trichoderma has gained entry to the plant tissue, it does not cause any disease or damage. Both plant and Trichoderma benefit from the symbiosis.

The plant gets protection, while the Trichoderma receives an ecological niche and food from the plant.

The Pathogens Pathogen

In addition to colonizing roots for food, Trichoderma spp. attack, parasitize and gain nutrition from other fungi. Since Trichoderma spp. grow and proliferate best when there are abundant healthy roots, they have evolved numerous mechanisms for both attack of other fungi and for enhancing plant and root growth.

One of the most effective methods of pathogenic fungi control exhibited by Trichoderma is `mycoparasitism’. In this process the Trichoderma detect other fungi, grow towards them, and attach and coil around the fungus, then produce enzymes that destroy the cell walls of the target fungus.

Trichoderma release two types of enzymes in their quest for sustenance – these are cellulase and chitinase. Cellulase enzymes break down cellulose which is a component of plant cells and organic matter. Chitinase breaks down chitin which is a structural component of fungal cell walls.

The production of chitinases has been implicated as a major cause of Trichodermas biocontrol activity against pathogenic fungi.7

Viability and Benefits of Trichoderma Harzianum in Hydroponic Settings

T. harzianum are amongst the most effective of the beneficial microbes in hydroponic settings. Research demonstrates that where T. harzianum has been trialled in hydroponics their presence has controlled or eliminated all manner of pathogens in both inorganic and organic medias. This makes T.harzianum an obvious choice for hydroponic growers. Plant growth promoting benefits are also exhibited by some species of Trichoderma spp.

In research conducted in a controlled hydroponics system, Chet et al (2006) note an increase, at protein level, in the activity of chitinases, b-1,3-glucanases, cellulases and peroxidases in cucumber roots previously inoculated with T. harzianum strain T-203. The capability of T. harzianum to promote increased growth response was verified in the hydroponic system. A 30% increase in seedling emergence was observed and these plants exhibited a 95% increase in root area. Similarly an increase in P and Fe concentration was observed.8

Similarly, research with T.harzianum strain T-203 conducted with cucumbers grown in an axenic (free from other microorganisms) hydroponic system demonstrated increased growth response as early as 5 days post-inoculation resulting in an increase of 25 and 40% in the dry weight of roots and shoots. Similarly, a “significant” increase in the concentration of copper, phosphorous, iron, zinc, manganese and sodium was observed in inoculated roots. In the shoots of these plants, the concentration of zinc, phosphorous and manganese increased by 25, 30 and 70%, respectively.9

Ozbay et al note, T. harzianum strains T95 and T22 increased yield in the presence of measurable disease. Reduction of disease by the use of T. harzianum strains improved tomato yields between 6% and 37% in coir and between 2% and 25% in rockwool. However, Ozbay et al also note, T. harzianum had no effect on yield in the absence of the disease compared with an untreated and uninoculated control. Theses findings suggests that T. harzianum strains used in this experiment act only as biocontrol agents and, beyond this, offer no benefit to yields where disease is not present.10


Trichoderma harzianum are shown across a range of studies to be efficient biocontrol agents.

Additionally, some strains of Trichoderma harzianum are demonstrated to increase the uptake and concentration of a variety of nutrients (copper, phosphorus, iron, manganese and sodium) in hydroponic culture, even under axenic conditions. This increased uptake indicates an improvement in plant active-uptake mechanisms.

However, what is also demonstrated is species, among other factors, will determine whether benefits beyond efficient root disease prevention will be exhibited.

Other Info – Trichoderma spp and Enzymes

Cellulases (enzymes) produced by Trichoderma spp. are the most efficient enzyme system for the complete hydrolysis of cellulosic matter (e.g. decaying root matter) into glucose.11

In research with Trichoderma asperellum, Brotman et al (2008) note the majority of proteins released by T. asperellum could be classified as plant cell wall-degrading enzymes: cellulases (cellobiohydrolase, endoglucanase), hemicellulases (glucan 1,3-β-glucosidase and arabinofuranosidases), and an aspartyl protease (an enzyme that breaks down proteins). glucoamylase, a starch-degrading enzyme, and swollenin, a protein first isolated from T. reesei were also detected.12

Trichoderma viride, T. reesei T. harzianum13 and T. asperellum14 have been demonstrated to produce high levels cellulase enzymes. 

Trichoderma in Coco Substrate 

Inorganic substrates are more effectively colonized by bacteria, while organic substrates are more effectively colonized by fungi. While Trichoderma spp. have been shown to establish and proliferate in a range of mediums, colonization may be greater in organic mediums such as coconut coir. When coconut coir and rockwool were compared after inoculation with T. harzianum it was found that colonization was greater in the coco fibre, while the rockwool system contained the highest amount of fluorescent pseudomonads bacteria.15 When T.harzianum strains were applied at transplanting to the mediums coir and rockwool, Fusarium crown and root rot incidence of greenhouse-grown tomatoes was reduced up to 79% in coir slabs and up to 73% in rockwool slabs with yield increases of 6% and 37% in coir and between 2% and 25% in rockwool.16 

Trichoderma colonization occurs most efficiently where high levels of lignocellulose are present. The term lignocellulose refers to any of several closely related substances constituting the essential part of woody cell walls of plants and consisting of cellulose associated with lignin. The major components of plant cell walls are cellulose, hemicellulose and lignin, with cellulose being the most abundant of these.17

Materials that are high in lignocellulose are the organic medias, straw, wood bark, and coconut fibre. This makes coco fibre an ideal environment for Trichoderma spp. colonization.

Pesticide susceptibility

Trichoderma spp. possess an innate resistance to most agricultural chemicals, including fungicides, although strains differ in their resistance. Most manufacturers with registered Trichoderma products have extensive lists of susceptibilities or resistance to a range of pesticides.

Food for Fungi

Potatoe starch in particular makes a good food for fungi. When they breed fungi in the lab they use potatoe starch to stimulate Trichoderma colonization.

Fulvic/humic acid in solution has been demonstrated in numerous studies to aid micro colonisation in hydroponic settings.

Milk sugar (soluble dissaccharide lactose) has been demonstrated to benefit enzyme production by Trichoderma fungi.

Optimum Nutrient and Media Temperature for Trichoderma

Like many microbial species Trichoderma spp. has temperature optimums for rapid colonization and bioactivity. For most of the commonly applied species this is 25-30o C (77-86 oF) (8) with 28o C (82.4 oF) being the ideal. 18 If conditions are too cold, the colonization of Trichoderma will slow and even cease; if too warm, then die back may occur and the Trichoderma may become out competed, leaving the door open for other forms of microbial species to take hold.


Optimum Water/Media Temp in Hydroponics vs. Optimum Water/Media Temp for Trichoderma


DO Graph

Often hydroponic growers attribute root browning/root disease to water borne pathogens (Pythium) when in fact one of the major causes of root browning is root zone oxygen starvation typically caused through overly warm nutrient or waterlogged media.

Nutrient salts don’t leak into the roots of the plant. Nutrient uptake is an active process which relies on several factors, one of which is that satisfactory levels of oxygen are available to the roots of the plant.

Roots “pump” nutrients from the outside of the root to the inside where they are transported to the leaves. This pumping process requires energy. The roots get their energy from respiration. In turn, respiration requires energy, which is achieved by burning sugar. Part of the sugar made in leaves by photosynthesis is transported to the roots to power the nutrient pumps.

Photosynthesis converts sugar and oxygen from carbon dioxide, nutrition and water using the energy from light.

Respiration is the opposite. Respiration makes energy by burning sugar (supplied by the leaves of the plant) and oxygen to make carbon dioxide. It is this energy that powers (among other things) the root nutrient pumps. In turn these pumps deliver the nutrition that is critical to sugar production within the plant.

Unlike sugar, oxygen is not transported from the leaves to the roots. This means that the roots must get their own oxygen.

If the roots can’t get sufficient amounts of oxygen (because of excessively warm water/nutrient or because there isn’t enough air space in the growing medium) their pumping capacity is significantly reduced. The result of this is that the plant becomes starved of critical nutrition.

While there are various factors that determine dissolved oxygen levels in water, it can be simply stated as fresh (non saline) water can hold 8.26 parts per million of oxygen at 25OC (77 OF), while at 20O C (68 OF),  water can hold as much as 9.09 parts per million of oxygen. The colder water gets the more oxygen it can retain. The warmer water gets the less oxygen it can retain. However, if water is too cold nutrient uptake (hence growth rates) will be reduced.

Oxygen content and water temperature are inextricably linked. As water warms up it loses its capacity to hold oxygen. To avoid root rot as a result of oxygen starvation you will need to keep the nutrient temperature below 25 degrees C (recommended 20 –22°C = 68 – 71.6 °F). In addition to this,
aeration of the nutrient is advised.

Given this information, it is best to maintain optimum oxygen temperatures in solution and media and compromise somewhat on optimum temperature for Trichoderma colonization.

Optimum pH for Trichoderma spp. 

Optimum pH for Trichoderma fungi may vary between species, however fungi thrive in semi acidic conditions. Optimum cellulase production by Trichoderma harzianum is demonstrated at pH 5.0 – 6.0 with 5.5 being the ideal. Above pH 6.0 reduced cellulase production and, therefore, it is advisable that optimum pH for Trichoderma in hydro is 5.5 – 5.8.19

Bacteria in Hydroponics – Bacillus and Pseudomonas spp

Beneficial bacteria, like beneficial fungi, form a symbiotic relationship with the plant (host). The bacteria benefit from the ecological niche provided by the plant, while the plant receives protection from the beneficial bacteria.

Plant growth–promoting rhizobacteria, most of which are Pseudomonas and Bacillus species, are applied to a wide range of agricultural crops to enhance growth and act as disease control.1

Beneficial bacteria suppress pathogens by, among other things, producing hydrolytic enzymes and antibiotics. 

Beneficial bacteria suppress pathogens by, among other things, producing hydrolytic enzymes and antibiotics.


Antibiotics act as micro toxins that can, at low concentrations, poison or kill other microorganisms. It is shown that some antibiotics produced by bacteria are particularly effective against plant pathogens and the diseases they cause.2 It is this antibiotic production that plays a central role in disease control.3

Additionally, these antibiotics are known to induce defence mechanisms in the host plant.4

Bacillus subtilis is able to produce more than two dozen antibiotics with an amazing variety of structures.5  

Biocontrol activity of Bacillus strains against multiple plant pathogens have been widely reported and well documented.6 Their success as a biocontrol agent is associated with the prominent property of producing lipopeptide antibiotics which exhibit wide spectrum antifungal activity.7

Strains of Pseudomonas fluorescence have known biological control activity against certain soil-borne phytopathogenic fungi and are known to produce the antibiotic 2, 4-diacetylphloroglucinol (DAPG) which induces defence mechanisms in the host plant.8

Hydrolytic Enzymes

There is a synergism between the micro toxins (antibiotics) and hydrolytic enzymes produced by bacteria. Firstly, the enzymes degrade the cell wall of the pathogen, and secondly, this enables the toxin to act more efficiently against the pathogen by gaining access at an intracellular level. I.e. bacteria are more able to effectively poison pathogens via the use of cell wall degrading enzymes.

Viability in Hydroponics

Pseudomonas putida strain PCL1760 has been demonstrated to have significant biological control over Fusarium oxysporum in eight independent laboratory experiments conducted in rockwool substrate.9

Similarly Pseudomonas spp. and Bacillus spp. have been demonstrated to have control over Fusarium oxysporum in hydroponic settings.10 

In research with lettuce grown in recirculating gravel bed hydroponic systems Bacillis spp. were shown to control Pythium with Bacillis subtillis demonstrating the highest rate of control. Additionally, B. subtillis consistently enhanced the fresh leaf and root weight by 29.2 and 24.3% compared to the untreated control.11 

Research conducted in inorganic and organic hydroponic medias showed the stimulating effect of Pseudomonas putida and T. atroviride (Trichoderma atroviride) on the reproductive growth of tomato plants in both growing medias. The plant growth stimulation was most likely the result of numerous modes of action exhibited by each microorganism tested. This study concluded that Pseudomonas putida and T. atroviride could be used as plant growth-promoting microorganisms to improve the productivity of greenhouse tomato crops under hydroponic conditions in inorganic or organic media.12 

Pseudomonas putida strain PCL1760 has been shown to exercise significant biological control of tomato foot and root rot (TFRR), a disease caused by Fusarium oxysporum f. sp. radicis-lycopersici (Forl), in eight independent laboratory experiments in hydroponics (stonewool/rockwool substrate). Furthermore, its activity in stonewool was also tested in an industrial certified greenhouse with similar results. The research concluded that Pseudomonas putida strain PCL1760 acted as a bioinoculant via ‘‘competition for nutrients and niches” (CNN).13

Optimum Temperature and pH for Bacillis subtillis

Bacteria species typically thrive best in pH neutral environments. Optimum pH for B. subtillis is 6.5 – 7.0. Optimum temperature is between 40 – 470C. However, as noted with Trichoderma spp., always maintain optimum temperatures and pH for optimal plant growth in hydro systems. I.e. pH 5.5 – 6.0 and nutrient/media temp of 20 – 220C (68 – 71.6 °F)

Food for Bacteria

Bacteria thrives in a high carbon environment. Molasses has been shown to be a cost efficient source of providing this carbon.14

Other sources of food are humates (fulvic and humic acid), kelp, and hydrolysed fish (fish emulsion).

Beneficial Bacteria and Fungi Product Quality

Benefical microbe products are generally formulated as wettable powders (WPs), dusts, granules and aqueous or oil based liquid products using different mineral and organic carriers.

Beneficial microbe products are sold and used, with or without legal registration, for the control of plant diseases. Bio inoculants are either marketed as standalone products or formulated as mixtures with other beneficial bacteria or fungi. Some products with bio inoculant properties may not be registered, and are sold instead as plant strengtheners or growth promoters without any specific claims regarding disease control.15

There are several reputable companies that manufacture government registered products. Government registration ensures that products have been subject to trials and scrutiny where claims made about their efficiency are measured and proven. However, for the most part products sold through the agricultural sector largely remain unregistered or are registered with organic bodies (e.g. OMRI) where products aren’t subject to the same levels of scrutiny .16 Among other reasons that many products remain unregistered are cost of registration and the time required to have the registration approved.

High quality bio innoculants depend on having high concentrations of the microorganism(s), long shelf-life and a formulation appropriate to their use.

Variable results have been reported for all types of microbial products, whether liquid or dry, with variation in their effectiveness attributed to three main causes: (1) presence of an already satisfactory level of the beneficial microbes prior to inoculation; (2) poor survival of the beneficial microbes in their environment; and (3) low quality of the inoculant. Low quality inoculants can be defined as containing insufficient viable cells of the beneficial microbe/s, high numbers of contaminating micro- organisms, or both.17

Olsen et al. (1995) found that only 1 of the 40 commercial North American beneficial products prepared from non-sterile peat contained more benefical microorganisms than contaminants. Contaminant microorganisms in non-sterile conditions often out-compete the beneficial organisms for space and nutrients and may also produce allelopathic (toxic) compounds. Manufacturers also risk incorporating pathogenic organisms into formulations when non-sterile carriers are used.18

To manufacture a high quality microbial product, it is essential (among other things) that the carrier material is sufficiently sterilised. This allows for non-competitive multiplication and maintenance of the microorganisms in a nutrient rich environment.

Molasses and other microbial carriers commonly used for producing liquid beneficial products and peat granule, traditionally used for creating dry micro products, are unique in that they have a high initial ‘bio-burden’ (I.e. high number of contaminating microbes).

These factors dictate the use of autoclaving, in the case of liquids, and irradiation in the case of dry products, to achieve carrier sterility prior to introduction of the beneficial microbes to the carrier. However, while autoclaving or irradiation must be sufficient enough to achieve total “kill” of any contaminating microorganisms, it must not cause substrate/carrier breakdown, the creation of toxins, or adversely affect the carrier’s physical properties in another way. Only through “complete” sterilization can it be guaranteed that unwanted competitive microbes are eliminated from the carrier.19

Some of the beneficial bacteria and fungi that are government registered in various countries




Burkholderia cepacia    –     Soil-borne fungi, nematodes

Pseudomonas fluorescens     –    Soil-borne fungi

P. syringae ESC-10, ESC-11 – Post-harvest fungi

P. chlororaphis   –     Soil-borne fungi

Bacillus subtilis   –    Soil-borne fungi

B. subtilis FZB24   –    Soil-borne

B. subtilis KBC 1010 – Gray mold

B. subtilis GB03 – Soil-borne and wilt

B. subtilis GB07   –     Soil-borne fungi

Rhizobium sp. KR181 – Bio fungicide

Streptomyces griseoviridis K61    –    Various fungi




Trichoderma polysporum, T. harzianum     –      Soil-borne fungi

T. harzianum KRL-AG2    –       Soil-borne fungi

T. harzianum     –       Foliar fungi

T. harzianum, T. viride    –      Various

T. viride     –       Various

T. lignorum    –     Vascular wilt

Trichoderma spp     –     Soil-borne fungi

Ampelomyces quisqualis M-10   –    Powdered mildew

Talaromyces flavus V117b   –    Soil-borne fungi

Gliocladium virens GL-21  –    Soil-borne fungi

G. catenulatum     –     Soil-borne fungi

Fusarium oxysporum   –     non-pathogenic Pathogenic Fusarium


A number of companies are developing new products that are in the process of registration.

Spore Count and CFU (Colony Forming Units)

Spore count and cfu (colony forming units) are used to quantify the microbial content of a liquid or dry beneficial product. Spore count is used with fungi and cfu is used with bacteria. These units indicate the levels of microbes that are present in a given product.

A beneficial bacteria and/or fungi product should contain a level of bacteria or fungi sufficient to inoculate plants and produce gains. The required level of bacteria and/or fungi required cannot be established as a general standard because it varies from one species to another. While it is possible to undersupply beneficial microbes it is not possible to oversupply them. For this reason the higher the cfu and/or spore count the higher the quality of the product (put simply).

Other factors such as bacteria and fungi species (suitability) and contaminants must also be considered in the quality equation.

A quality beneficial bacteria and/or fungi product should list a guaranteed analysis of the cfu and/or spore count. Other things to look for are a use by date and actives.

Species Choice

While some species of fungi and bacteria are demonstrated to produce positive results in both hydroponics and soils (e.g. Trichoderma harzianum, Bacillis subtillis), other species (e.g. Mycorrhizae) may not produce such ubiquitous results. By understanding the science of beneficial bacteria and fungi in hydroponics one can more easily make informed purchasing decisions re products that will produce consistent results (given other factors are in check).

Liquids Products and Sporulation (suspended spores in solution)

Some years ago (2002) I wrote about beneficial bacteria and fungi and the potential they showed for disease control in hydro settings. One point I made was that liquid beneficial microbe products sold through the hydro industry should be avoided and preference should be given to dry micro products instead. This information was oversimplified and was largely based on the quality of liquid products available through the hydro retail sector at that time.

The science….

Bacteria must obtain nutrient materials necessary for their metabolic processes and cell reproduction from their environment. Thus in order microbes to thrive in their environment adequate food and oxygen must be present in solution and media.

A diverse group of gram positive bacteria (e.g. Bacillis spp.) and species of fungi (e.g. Trichoderma) are capable of sporulation as a means of surviving adverse conditions. These specialized bacteria and fungi are able to become dormant under stress and form spores which are resistant to many chemical as well as physical antibacterial measures. Bacterial spores are extremely stable, and resistant to heat, drying, light, disinfectants and other harmful agents than the original living bacterial organism. Spores may survive for many years.

When more suitable conditions present themselves, the spore germinates and again develops a similar cell to the one that originally formed the spore. This new cell, under favourable conditions of moisture, temperature, oxygen, pH and food supply, begins reproduction, antibiotic and enzyme production.

However, other species (gram negative) do not sporulate and their populations typically die out or are significantly reduced when faced with nutritional or oxygen stress.

Put simply – this means is if live sporulating microbes are added to a liquid product they will hibernate if and when faced with nutritional or oxygen stress. The suspended spores can then be regenerated (germinated) when placed in an environment such as a hydroponics system that provides a viable source of oxygen and food.

Other than this, quality liquid products are typically produced using spores that remain suspended due to the presence of antimicrobial preservatives (e.g. Kathon™) that while capable of killing live bacteria and fungi do not harm the more resistant spores.

While different microbes will germinate more readily than others a basic reference is that Bacillis subtillis will germinate within 24 hours of being added to the nutrient solution (fungi will typically germinate sooner).

Liquid products that contain sporulating bacteria and/or fungi are therefore very viable products when they are produced correctly.

Just some of the microbes that sporulate

• Trichoderma harzianum
• Trichoderma viride
• Trichoderma koningii
• Trichoderma polysporum
• Bacillus subtilis
• Bacillus laterosporus
• Bacillus licheniformus
• Bacillus megaterium
• Bacillus pumilus
• Arthrobotrys oligospora
• Hirsutella rhossiliensis
• Acremonium butyri

This Said…..Lab Tests on Hydroponic Store Sold Liquid Bennie Additives


Let me put up some lab tests up that were conducted by the Oregon Department of Agriculture between 2013 – 2015 on just a few beneficial bacteria and fungi products that are sold through hydroponic retail stores. You’ll note that in many cases the bennies that are claimed to be present on labels were either “Not Detected” (i.e. not present at all) or were present at far far lower levels than claimed as per the guaranteed analysis.

In the case of Advanced Nutrients Piranha, Tarantula and Voodoo Juice (see asterisks) you might as well be purchasing bottled water because either none of the stated beneficals are present or they are present at almost non-existent levels.  At over $50.00 USD per litre for each product this makes Advanced Nutrients Piranha, Tarantula and Voodoo Juice the most expensive bottled water money can buy.

So as not to single Advanced Nutrients (AN) out you’ll also note that the General Hydroponics Subculture-B product is every bit as substandard as the AN Piranha, Tarantula and Voodoo Juice snake oils.

See lab tests following. Tests conducted by the Oregon Department of Agriculture (ODA) 2013 – 2015.



You can no doubt see that where the quality of hydroponic store sold liquid bennie additives is concerned it is very much a case of buyer beware.

Don’t despair – there are also many good beneficial bacteria and fungi inoculums available through the Agricultural sector and other. However, as per recommendations I made way back in 2001 – 02 it is perhaps advisable to stear clear of hydroponic (hydro) manufacturer formulated liquid concoctions.

Dry Products – Storage

Dry products consist of spores (inactive bacteria and/or fungi) and a carrier medium. Dry products should be stored out of direct sunlight at between 4oC and 10oC in an airtight container. If the product becomes damp from air moisture the spores will become active and then die out when conditions are not suitable. This will greatly reduce product quality. Packets of bacteria/fungi should not be opened until they are ready to be used.

Water Quality and Beneficial Microbe Viability

Often mains water is treated with monochloramine to kill off undesirable microorganisms. The problem is that monochloramine does not discriminate between undesirable and beneficial microorganisms and therefore residual monochloramine in your tap water supply may also disrupt the viability of beneficial microbes in your hydroponic system (if you are using mains water – this does not apply to RO treated water where carbon filtration is incorporated). Monochloramine is reasonably stable and therefore can persist in tap water for some time. Varying levels of monochloramine can be present in tap water ranging from as low 0.2ppm to much higher; the EPA lists the maximum allowable limit as 4ppm while the World Health Organisation maximum allowable limit is 3ppm.

While both chlorine and monochloramine residuals decrease with time, monochloramine decreases more slowly than chlorine. Chlorine may take days to dissipate in a jug left on a counter and it will take much longer for monochloramine to dissipate. The decomposition rate will be faster when the water is exposed to air and sunlight. Chloramine, like chlorine, will eventually dissipate completely over time but this could take many days.

The easiest way to remove monochloramine from tap water is to first run it through an activated carbon filter. The activated carbon filter can reduce chloramine concentrations of 1 to 2 ppm to less than 0.1 ppm.

Which brings us to our next point… Water Sterilzation methods …..

Read more about beneficial bacteria and fungi (bennies) here. The article covers how to mass produce your own beneficial bacteria and fungi ‘micro teas’ and provides growers with further information on the complexities of beneficial bacteria and fungi.

Sterilization versus Beneficial Micros in Hydroponics

Sterilization is another means to prevent root disease in hydroponics. However, something growers need to be aware of is that oxidixing agents such as monochloramine, chlorine and hydrogen peroxide come with a few problems when applied to hydroponic solutions that comes into contact with the plant’s roots. This relates to the potential phytotoxic potential of these products. You can read more about this here…

Sterilization works by creating an entirely bio-devoid system. This means, sterilization eradicates microflora from the hydro system completely. I.e. by sterilising the nutrient you are killing both beneficial and pathogenic bacteria. UV, ozone, monochloramine, chlorine and hydrogen peroxide are commonly/widely used methods of sterilization in hydroponics.

Products such as Hydrogen Peroxide (Oxy Plus, Hy-Gen Peroxide), or Monochloramine (Pythoff) are useful sterilising agents. Because Pythium is a living organism, sterilization will kill the Pythium spores before they have a chance to enter the plant’s root zone.

It is important to note that both monochloramine and hydrogen peroxide act only as root disease preventatives. I.e. once root disease is present in the crop they are ineffective and other means for controlling the disease should be sort.


WARNING – DO NOT USE OXIDANTS WITH ORGANIC MEDIAS OR ORGANIC ADDITIVES: monochloramine, chlorine and hydrogen peroxide are not suitable for use where organic media (e.g. coco substrate) or organic additives are used. These products are oxidants and oxidants break down organic matter.

Monochloramine in Hydroponics

Inorganic chloramines such as monochloramine are formed when chlorine and ammonia are combined in water. One of the key uses for monochloramine is it is used for disinfecting mains water supplies.

Monochloramine is an oxidant. It kills bacteria by penetration of the cell wall and blockage of the metabolism. Monochloramine is considered to have moderate biocidal activity against bacteria.1 While there are more effective products available for eradicating bacteria (e.g. chlorine) these have been deemed unsuitable for use in treating mains water supplies due to the byproducts they form when interacting with organic matter.2 Monochloramine hydrolyses (breaks down) slowly in aqueous solutions, producing hypochlorite (at alkaline pH) or hypochlorous acid (at acid pH).3

Research into the use of monochloramine in other areas suggests that where bacteria are able to attach to surfaces this provides a primary means for bacteria to survive disinfection. Research of K. pneumoniae grown in a high-nutrient medium attached to glass microscope slides demonstrated a 150-fold increase in disinfection resistance.4

Similar findings have been demonstrated in nursery fertigation systems where organic debris or particles prevented direct contact of chlorine (not to be confused monochloramine) with fungal propagules (Phytophthora spp.) and as a result reduced chlorine efficiency.5

This may have implications in hydroponic systems where hosing, pipes, pots, drip emitters and, for that matter, media may offer pathogens protection.

Because monochloramine hydrolyzes (dissipates) slowly careful use is advised. I.e. monochloramine is an oxidant and overuse can result in build up, resulting in fine root hair burning, which will reduce nutrient uptake.

Use of Chlorine (not to be confused with monochloramine) in Hydroponics

A handy tip. Monochloramine sold through the hydro industry can be replaced by chlorine at greatly reduced cost.

Chlorine (Cl) is demonstrated to be a more effective sterilizing agent than monochloramine.1

Research has demonstrated that 0.5ppm (780 mV) of chlorine in greenhouse irrigation systems at pH 6.0 eliminated Phytophthora sp., Fusarium sp. and bacteria within 0.5 minutes of contact time.2 Chlorine efficiency is pH dependent and efficiency at pH 6.0 – 7.5 has been shown to be the ideal (maximum efficiency of chlorine is 6.5). Below pH 6.0 and toxic chlorine gas will be released. Because optimum pH in hydroponics is pH 5.8 – 6.0 this makes chlorine ideal as an effective and low cost sterilizing agent.

Products such as sodium hypochlorite (liquid typically 12.5% chlorine), calcium hypochlorite (bleaching powder/pool chlorine = approx 65% Cl), and chlorine dioxide are cheap sources of chlorine. Take for example calcium hypochlorite at 65% available chlorine. To achieve 0.5ppm chlorine in 100L of solution 0.08 grams would be required. This would mean that 250 grams of sodium hypochlorite would be good for 3125 treatments. The cost of 250grams of sodium hypochlorite is approximately £12.00 in the UK (in small volume purchased online – far cheaper in volume) or less than $20 USD. Now consider this; you would use only 14.6 grams a year to treat 100L every two days, so 17 years of chlorine treatment would cost less than $20.00 USD. When you consider that a 1L monochloramine product is sold through UK hydroponic stores for £30.00 – £34.99 ($49.00 -$57.00 USD) and is used at 0.2mL/L (50 treatments of 100L) the use of chlorine over monochloramine represents massive savings.

Chlorine – Potential Toxicity to Plants

Chlorine obviously has some potential toxicity (phytotoxicity) issues associated to plants, if used at excessive levels – as does monochloramine and hydrogen peroxide. Sensitive plants such as lettuce may be detrimentally affected if chlorine is present in solution at even 1ppm. Less sensitive plants will be tolerant to higher levels.

Research has demonstrated that 2ppm of chlorine at riser outlet, in fertigation systems poses little  risk of toxicity to the majority of ornamental crops.3 This indicates that treatment with 0.5ppm of chlorine poses very little risk to many  plants.


Chlorine hydrolyzes (dissipates) more quickly than monochloramine and, therefore, treatment should take place every two days. Directly after treatment the chlorinated nutrient should be cycled through the growing system to ensure pipes, pots, channels and media are adequately sterilized.

Measuring Chlorine in Solution

ORP Meters

It’s important to note that simply adding oxidants such monochloramine, chlorine and hydrogen peroxide to solution and hoping for the best can only be described as entering the realms of hydro cowboy country. Numerous factors will influence the levels of oxidant (e.g. temp, pH, ionic strength, organic content, dissipation rates, and existing chlorine or monochloramine in the water supply).

The most efficient means of accurately monitoring oxidant levels is through the use of an ORP meter.

ORP is a measurement of ‘Oxidation Reduction Potential’ (mV) most commonly used to measure the effectiveness of water disinfection systems using sanitizers such as chlorine, bromine, ozone, peroxyacetic acid, hydrogen peroxide etc. ORP standards have been long established for water sanitation and are recommended over ppm measurements with traditional test kits. ORP meters are relatively inexpensive (a handheld pen meter should set you back approximately $100 -150 USD) and easy to operate and should be an essential piece of equipment for people using a chlorination system in hydroponics. Optimal ORP for Pythium control with chlorine = 780 mV at pH 6.0

Desired Chlorine in Solution: 0.5ppm – 780 mV

Optimum pH for chlorine treatment in hydroponics: 6.0 (below pH 6.0 will release chlorine gas – above pH 6.0 is less than optimal for nutrient uptake)

Treatment: every two days – if using an ORP meter maintain at 780 mV

Safety Warnings: Calcium hydrochlorite CAS No: 7778-54-3 has strong oxidizing properties and is a corrosive. Handle with care and store in an airtight, lightproof, sealed container safely out of the reach of children.

Hydrogen Peroxide (H2O2) In Hydroponics

Hydrogen peroxide, as with monochloramine and chlorine, is an oxidant. However, as a benefit it is also a disinfectant. The oxidant and disinfection mechanism of hydrogen peroxide is based on the release of free oxygen radicals:

H2O2 → H2O + O

Free radicals have both oxidising and disinfecting abilities.

Unlike monochloramine, hydrogen peroxide does not produce residues. I.e. Hydrogen peroxide is completely water-soluble.

Hydrogen peroxide hydrolyzes (dissipates) quickly and, therefore, treatment should take place every 2 days.

IMPORTANT NOTES: Sterilizing agents such as monochloramine, chlorine and hydrogen peroxide should not be used in conjunction with beneficial microbes. These compounds do not make a distinction between beneficial and harmful microbes and their use can result in killing off or reducing beneficial microbe numbers. If sterilization is used, it is important to reapply beneficial microbes when the sterilizing agent has completely hydrolyzed/dissipated.

WARNING – DO NOT USE OXIDANTS WITH ORGANIC MEDIAS OR ORGANIC ADDITIVES: monochloramine, chlorine and hydrogen peroxide are not suitable for use where organic media (e.g. coco substrate) or organic additives are used. These products are oxidants and oxidants break down organic matter.

Monochloramine and hydrogen peroxide should never be used together at the same time. Hydrogen peroxide is one method employed by water treatment experts to chase chlorine from mains water supplies. I.e. each product (monochloramine/hydrogen peroxide) renders the other inert.

Pythium – Cure

In 2002 I wrote about using Fongarid (active furalaxyl) as a cure for Pythium with:


“Once you have Pythium, control is not an easy matter. There are off the shelf fungicides that are available in Australia, but they need to be used with caution as they are systemic. I have found that Fongarid – a systemic fungicide that contains active furalaxyl – eradicates Pythium quite successfully. However, if Pythium is able to take hold in the crop this situation may change due to the reproductive cycle of the fungi (genetic mutations and more resistant spore types). For this reason prevention is a far smarter practice than cure.”

[End Quote]

My advice was based on two things. One, research by the CSIRO conducted in 1998 demonstrated the ability of furalaxyl to eradicate pythium 1 and, two, through my own experiences with the product in hydroponics I had/have found that drenching coco coir with a 20ppm solution of furalaxyl for four hours cured Pythium and regenerated healthy root growth within days. To date I haven’t found a better product, hence, still recommending furalaxyl years later. 

Warnings: Furalaxyl is systemic fungicide and should never be used past week 3 of flower.

Use of furalaxyl will also add sodium (Na) to nutrient solution.

For this reason it is recommended that furalaxyl isn’t run constantly through

the growing system. I.e. High levels of sodium are undesirable in solution.



References for this article can be found here