*Warning! This post gets a bit technical. We chose not to simplify the language too much because we didn’t want to compromise any of the rich scientific research that Sarah Taber conducted. Exploring facts behind an argument such as the one against organic hydroponics requires some technical detail. If you have questions, please leave them in the comments!

Here are a few terms to help you out if you're new to the hydroponics scene:

Sterility is a lack of micro-organisms. This is considered a negative trait in agriculture, where micro-organisms like bacteria support not only plant health but ecosystem health.

Bacteria play a crucial role in nutrient processing and uptake by plants. Without them, plants are more vulnerable to disease, and have difficulty taking up nutrients.  

Hydroponics has a reputation for being sterile. 

This may include real consequences for farmers who use these techniques to make a living. The danger is that a failed bid for organic certification could set a dangerous precedent, leading to a large scale devaluation of the industry.  Ultimately, the skewed reputation of the hydroponic growing method affects the livelihood of farmers.

Let me stop you there if you’re thinking of large scale commodity crop farmers. That's not who we're talking about here. More and more small farmers are choosing hydroponics as the method with which to serve their communities on a local scale. 

Hydroponics offers a variety of benefits, and opposition to the technique affects these small farmers. That’s something we want to avoid, since small farmers are bringing back transparent local food to strengthen their communities, physically, socially, and economically.

Triple Threat hydroponic farm pours generously into its community with youth programs and community gardening.

Of course, if the reputation for sterility of hydroponics is true to the facts, then it is a valid and real concern. Sterile growing environments fail to meet the goals of the Organic program. (Like  preserving natural resources and biodiversity.)

Soil plays host to a robust community of microbes, bacteria, and fungi. These ecosystems support the Organic programs goal of preserving natural resources and biodiversity. The question is,

“Do hydroponic growing environments boast the same number and variety of microbes, or are they truly more sterile than soil environments?”

Studies show that they are not more sterile, when treated with proper management. Let’s look at the facts.

Studies that look at the microbiology in hydroponics systems find about 10,000,000 bacteria per milliliter of nutrient solution (1, 29).

Those are big bacteria numbers, but how do they stack up to soil?  

Soil microbiology varies quite a bit, but compost consistently comes in at 100,000 to 1,000,000,000 colony forming units - or cfu- a measure of the viable bacterial and fungal cells - per milliliter of dry compost (2, 3, 10, 30). (It’s a weird comparison since water vs dry dirt is apples to oranges, but it’s the best we’ve got. Unfortunately, there are no studies with a direct comparison to soil.)

In other words, the bacterial populations in conventional hydroponic systems are right in the normal range for compost. Not soil. Compost.

These systems are also rich in fungi-- a study that looked at both fungi and bacteria in hydroponic systems found 1,000,000 cfu/ml bacteria and 10 to 1000 fungi cfu/ml in the system (29).

A hydroponic system gains that microbial flora very quickly. A study watching the growth of bacteria in a hydroponic system started with a nutrient solution that had 500-900 cfu/ml bacteria in it. Within 20 hours of running the solution through tomatoes in rockwool, the bacterial population rose to 1,000,000 cfu/ml. Analysis showed most of these bacteria were plant root symbionts like Pseudomonas fluorescens (a bacteria which aids the plant in defense and nutrient uptake).

Meanwhile, the control solution stayed at the original 500-900 cfu/ml.

Microbe populations in hydroponics aren’t just high—they’re also diverse. There aren’t a ton of studies looking at the diversity of microbes in hydroponics, but what we have shows a diversity in hydroponics equivalent to what is found in soil (4).
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What about mycorrhizae? Mycorrhizae are the equivalent of a root for fungi, and they play a key role in plant growth by a strong symbiotic (mutually beneficial) relationship with the plant roots. Hydroponic plants with mycorrhizae tend to be healthier and yield better than those without, just as in soil (17).

Mycorrhizae thrive in hydroponics. In fact, they do so well that when people need to raise mycorrhizae to make spores for inoculum (for example, the inocula used by organic farmers), they raise those mycorrhizae on plants in hydroponic systems (12, 14).

True, you don’t get as many mycorrhizae with high nutrient concentrations (25). The good news is you don’t need high nutrient concentrations for hydroponics—in fact you can get away with a lot lower nutrient levels than you could in soil.
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Root surfaces are a “hot spot” of microbial activity (11) both in soil and hydroponics. The microbe populations immediately surrounding the roots are much higher than the surrounding area.

Root zone bacteria in hydroponics were found at 10,000,000,000 cfu per gram of roots (4)—a thousandfold increase over the 10,000,000 cfu milliliter populations in the solution (1, 29). This pattern of relatively low microbial populations in the surrounding environment, but high populations immediately around the roots, is similar to what is found in soil.

It’s these root-zone microbes, or PGPR (plant growth promoting rhizobacteria) that are most responsible for disease suppression, signaling plants to create more secondary metabolites (like flavonoids and other antioxidants), etc.

This difference in population is because plant roots exude mucilage—a complex mix of carbohydrates, amino acids, and organic acids—into the environment. This is a key food source for microbes and a major driver of soil ecology.

In other words, a lot of the “soil flora” that organic agriculture relies on is actually root flora. Microbes will live anywhere there are roots-- not just in soil. 

Allelopathy is when one plant species inhibits the growth of the other to compete for resources. Allelopathic compounds inhibit the growth of the other species by negatively impacting their function.

The root exudates of most crops include allelopathic compounds to help plants compete with their neighbors. Without a surrounding microflora, these compounds can build up to levels that are toxic to the plants that create them (6, 18, 29)—in both soil and hydroponic systems.

Plant health depends on a strong microflora around the roots to break these compounds down (24, 32). The fact that it’s possible to grow plants in hydroponics at all without them killing themselves by allelopathy is pretty good evidence that there are very active root flora in most systems, even conventional ones.

A review of these studies in 2011 found suppressive flora in rockwool, NFT, peat, and other hydroponic methods (5, 9, 15, 16, 20, 21, 22, 26, 27, 28, 31). It should be noted that compared to soil, there haven’t been many studies on suppressive flora in hydroponics. The fact that of these few studies, so many have found strong evidence of suppressive flora in hydroponics is important.

One possible explanation for the sterility rumor is the fact that new and poorly-managed hydroponic systems can have very little microflora, leading to disease susceptibility (19). However, since this also occurs in poorly-managed soil farms, this isn’t a reason to consider hydroponics different from soil farms.
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Another myth that supports the sterility rumor is that hydroponics is more prone to disease than other techniques. Hydroponics isn’t “more prone to disease” than soil. It’s more prone to one disease—Pythium root rot. Pythium has a spore that swims. So the reason it’s more prominent in hydroponics isn’t because hydroponics has no microbiota—it’s just because it’s easier for the spores to get around in an aquatic environment than in soil. (Even then you can still manage hydroponic systems for disease suppression, so hydroponics aren’t doomed to always have Pythium.)
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Soil-based organic agriculture has had nearly 15 years of R&D since the USDA put out the organic regulations in 2002. The proficiency of organic farming has come a long way since then. Having an organic market meant there was incentive to learn how to do organic management methods, and for crop care companies to develop products and tools that are compatible with organic philosophies. Hydroponics and aquaponics haven’t had this benefit of 15 years of R&D investment. Hydroponic and aquaponic growers in 2016 lag behind soil growers in using organic techniques because they haven’t been developed yet. And if hydroponics and aquaponics are banned from organic certification, they never will be. 

As we’ve seen, the well managed hydroponic system can be just as diverse and rich in microbial communities as a well managed soil system. Poorly managed systems of either hydroponic or soil techniques will suffer, but farmers have a plethora of management principles and information from invested parties (such as the USDA) to help improve that diversity and quantity of microbes.

Here are some easy ways to manage hydroponic and aquaponic systems for healthy root flora:
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The urban farming movement and other sustainable socio-economic trends depend on alternative growing techniques like hydroponics.

Photo: Fable: From Farm to Table urban farm. Doesn't look sterile to me.

Hydroponics and aquaponics can support social sustainability in ways that no other technique can, but portions of that sustainability may rely on organic certification. For instance, urban agriculture is often forced to be soilless (because of space and/or contaminated soil). Organic certification allows a premium price, which can be critical for urban operations’ survival because of high land prices. In other words: a “soil-only” organic rule may eliminate urban agriculture, an important source of urban employment and upward mobility. 

Hydroponics and aquaponics, due to both higher yields and more space-conservative equipment, can produce significantly more food for a given area than soil-based agriculture. A “soil-only” organic philosophy requires habitat destruction to make room for organic agriculture.
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An additional problem with land use in soil-based organic agriculture: it’s an important and under-discussed driver of habitat loss. The three-year period to transition current farmland to organic is costly, so a popular organic farming technique is to plow up land that had previously been designated as wildlife habitat (source). Unlike farmland, land that used to be wildlife habitat can be certified organic immediately.

The science is clear that hydroponic and aquaponic systems can be managed organically (e.g. by fostering a beneficial root flora). However, translating that knowledge to tools & practices lags far behind-- just like it did for soil-based organic growers prior to 2002. The establishment of USDA organic regulations in 2002 created an important marketplace and set of incentives to develop and implement sustainable technologies in soil.

Hydroponics and aquaponics have developed to where they’re ready for the same growth in sustainable practice. Organic certification is an important driver of adopting sustainability practices. Without a price premium to aim for, aquaponics and hydroponics are unlikely to ever achieve their full potential as sustainable technologies.