Rockin’ the Rhizosphere: The Benefits of Microbial Life in the Rhizosphere

By Lynette Morgan
Published: November 28, 2018 | Last updated: December 7, 2021 10:32:01
Key Takeaways

Understanding the benefits of microbial life in the rhizosphere of your hydroponic plants will go a long to growing healthy, productive crops. But how do you monitor and adjust something you can’t see? Lynette Morgan explains.

Plants have developed a good working relationship with many of the microbes naturally present in their growing environment, and this is not limited to just soil-based crops. Anywhere there is moisture, nutrients, and a supply of organic carbon, microbes will thrive, and hydroponic systems are no exception. In the early days of soilless systems, it was thought that a clean and sterile approach to hydroponic cropping was ideal, with the elimination, or at least reduction, in fungi and bacteria, in general, is the objective. However, a more modern approach has embraced microbial diversity and now hydroponic growers have a wide selection of inoculant products for use in their production systems. While this has been a significant step forward in understanding and utilizing nature’s forces to overcome pathogens and enhance growth, there is still a lot to learn about microbial interactions and how we may harness these to our best advantage.


Plant Growth Promoting Rhizobacteria

Plant growth-promoting rhizobacteria (PGPR) are bacteria capable of promoting plant growth by colonizing the plant root system. They can be divided into two groups: symbiotic bacteria that form an association with the plant, and free-living rhizobacteria that are present in the root zone but not reliant on a direct association with the root system or plant. Beneficial microbes may be most well known for their protection against a number of root pathogens, however, they have a much greater potential under hydroponic production.

Relationships with beneficial microbe populations in the rhizosphere occur in hydroponics just as they do out in the field, with diverse and beneficial microbe species present in a wide range of different soilless systems. Root exudates, which are the release of organic compounds from the root system, were once seen as a potential problem in hydroponics due to the belief that they would build up in the root system and restrict plant growth. However, root exudates, which represent between five and 21 percent of the photosynthetically fixed carbon, are used by the plant to attract and select certain microorganisms in the rhizosphere. These microbes can then work, via different mechanisms, to influence plant health and growth. For example, root exudates act as signals that encourage and initiate a relationship or symbiosis with rhizobia and mycorrhizal fungi, as well as rhizobacteria, which is beneficial for both microbes and plants.


When plant roots sense an attack by pathogenic microbes, they release certain exudates called phytoalexins (defense proteins) and other unknown compounds, engaging in a process of underground chemical warfare. For example, the roots of sweet basil plants have been shown to release rosmarinic acid, an antimicrobial compound, in response to attacks by Phytophthora cinnamoni disease, which is possibly just one of many such defense responses we are yet to identify and understand.

Microbes and Hydroponic Systems

While a new hydroponic system may start off with very little in the way of microbial life, as soon as moisture and an organic carbon source (plants) are present, inoculation naturally begins. Microflora develop rapidly after planting a crop in a hydroponic system and consume plant exudates, compounds in the nutrient solution, and dead plant materials. Some of the microspecies may be pathogenic, however, these are generally outnumbered and outcompeted by populations of non-pathogenic organisms. In most hydroponic systems, the species of beneficial resident microflora most commonly found are Bacillus spp. Gliocladium spp, Trichoderma spp, and Pseudomonas spp.

Hydroponic studies into the effects of various species of beneficial bacteria have found several positive results. Bacillus amyloliquefaciens has been shown to increase vitamin C content and water-use efficiency in tomatoes, while Bacillus licheniformis increased fruit diameter and weight of tomatoes and peppers while promoting higher yields. A strain of Pseudomonas sp. has been found to promote the growth of hydroponic tomato crops and increase the uptake of calcium, which in turn reduced blossom end rot of tomato fruit. In hydroponic strawberries, inoculation with plant growth promoting rhizobacteria (Azospirillum brasilense) resulted in a higher sweetness index and a greater concentration of flavonoids and flavonols in the fruit as well as increasing the concentration of micronutrients (iron). In hydroponic tomato studies evaluating a number of different plant growth promoting rhizobacteria, it was found that Bacillus spp. (strain 66/3) was effective in increasing tomato yield significantly — this increase in marketable yield was 37 and 18 percent compared to untreated control plants in fall and spring crops respectively.


These effects of increased yield and improved compositional quality in hydroponic crops from microbial interactions are likely to have occurred via complex processes, some of which are still not fully understood. Some species of beneficial rhizospheric bacteria are known to improve plant performance in stressful environments, improving yields either directly or indirectly. Some studies have shown that growth-promoting rhizobacteria may provide a direct boost to plant growth by providing fixed nitrogen, phytohormones, and iron that has been sequestered by bacterial siderophores and soluble phosphate. Other species may protect the plant from potentially highly damaging pathogens that would otherwise limit plant growth, quality, and yields. However, it’s likely the majority of root-associated bacteria that play a beneficial role in hydroponic plant growth do so by producing the plant hormone auxin as indole-3-acetic acid (IAA). Studies have shown that inoculating hydroponic systems and different plant species with these bacteria led to increased root growth and enhanced formation of lateral roots and root hairs, which may be at least partially attributed to bacterial IAA. This results in an enhanced tolerance to plant stress and improved ability to take up water and nutrients.

While a large number of proven beneficial bacteria exist, fungi also contain some highly effective species that have been proven in both soil and hydroponic systems. One of the most significant of these is Trichoderma. Others are arbuscular mycorrhizal fungi such as Gliocladium virens, non pathogenic F. oxysporum, Paecilomyces lilacinus, Penicillium chrysogenum, and a number of others identified in studies as having an antagonistic effect on pathogenic fungi. In many of these studies, it has been discovered that combinations of synergistic fungi species often have a greater effect on disease control than when used singly.


Inoculation of Microbes

While naturally occurring, beneficial microbes do typically self-inoculate into new hydroponic systems, however, this can be a slow process and species diversity may be limited. Well-established hydroponic systems, where microbial life is not being continually killed with the use of sterilant, biocide chemicals such as chlorine or hydrogen peroxide, ultraviolet or ozone treatment, or other methods, tend to have a greater diversity of beneficial microbial species than newer systems. Microbes can be introduced through several different methods. Commercial, packaged inoculant products designed for hydroponics are now widely available and since these contain species known to be beneficial, they are a good place to start. Ideally, since different microbial species carry out different roles and have varying effects on growth, disease control, and other factors, using a product that has a diverse mix of species as a general first inoculant is a good idea. Such inoculate products are often designed to be added directly to the nutrient solution, however, some are in more widespread use as substrate inoculant products incorporated into the growing medium before planting. If using inoculants such as Trichoderma, it’s often easier to establish beneficial microbes into a new substrate as little competition exists from microorganisms already present. But if the substrate is relatively inert, such as stonewool or other synthetic growing mediums, this is initially a difficult environment for microbial life to take hold. Once plants are established, carbon exudates from the roots and sloughed off root material begin to provide organic substances for microbes to grow and population numbers then begin to build over time. Some microbial inoculants may also be applied as seed coatings and commercially obtained seed lots may be treated with inoculants aimed to improve germination and seedling establishment rates through a range of different processes including rot pathogen prevention and root growth promotion.

Alongside commercial mixes of inoculants, microbes may be introduced in a number of other ways — organic growers are usually well-versed in the benefits of a fully mature compost to provide beneficial microbial life and a well-processed vermicast (worm castings) is an even richer source of microflora. These can be mixed as a small percentage (10-15 percent) into hydroponic substrates such as coconut fiber for use in hydroponic and hydro-organic systems to provide an initial source of naturally occurring beneficial microbes. In commercial production, and more commonly these days with some smaller hydroponic systems, the use of a slow sand filter system for disease suppression and inoculation with beneficial microbes is one of the most effective ways of obtaining a diverse population of beneficial microflora. The sand filter system acts as a continuous source of inoculation with beneficial species and is particularly useful for solution culture systems where microbial life can be more limited than in substrate-based hydroponic systems.

While inoculation with commercial microbial mixes are a great step forward for soilless growers, these may not always result in a large and diverse microfloral population. Several issues and environmental effects can restrict, delay, and prevent colonization by this method. The presence of a sufficient carbon food source, correct environmental conditions, and competition from any pre-existing microbes can all limit the inoculation process. For this reason, regular addition of microbe mixes can assist and using as diverse a range of species as possible can help with establishment.

Maintaining diversity of beneficial microbial life in the rhizosphere of hydroponic plants may seem a rather difficult task as the presence or absence of these can’t be seen to be checked and adjusted. However, a basic understanding and a little consideration for what can’t be observed, but may be occurring in the rhizosphere, can go a long way to getting that high-yielding, healthy, and problem-free crop everyone aspires to.


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Written by Lynette Morgan | Author, Partner at SUNTEC International Hydroponic Consultants

Profile Picture of Lynette Morgan

Dr. Lynette Morgan holds a B. Hort. Tech. degree and a PhD in hydroponic greenhouse production from Massey University, New Zealand. A partner with SUNTEC International Hydroponic Consultants, Lynette is involved in remote and on-site consultancy services for new and existing commercial greenhouse growers worldwide as well as research trials and product development for manufacturers of hydroponic products. Lynette has authored five hydroponic technical books and is working on her sixth.

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