The economy is a fantastically complex mechanism made up of billions of individual players, acting in their own best interest. At least, that is how it works in theory. 

It turns out that a vastly more complex, far more sustainable economy is thriving beneath our feet. Soil farmers know this well. The microbial economy is a diverse mechanism of billions of microscopic creatures engaged in a constant nutrient exchange. In microbial economics, one microbe’s waste is another microbes treasure. Each genus has its particular niche, thriving on specific nutrients and expelling others.

An interesting note about microbes is that they come in two broad categories, aerobic and anaerobic microbes. Aerobic means air loving, specifically oxygen rich air. We are aerobic creatures and partner best with aerobic microbes. The same goes for our fish and plants. Meanwhile, anaerobic microbes thrive in oxygen-poor environments. An example of this is the deadly botulism bacteria that grow in the airless environment of a soup can. There are beneficial anaerobes that can come into play in more advanced aquaponic ecosystems. 

In healthcare, there is a growing appreciation for the microbiome and probiotics, the complex network of microbes that lives in and on all of us. Each person’s microbiome is unique and plays a wide variety of roles in maintaining good health. These benefits range from healthy, radiant skin, to healthy digestion, to improved mental health. Likewise, the probiotic microbiomes of both fish and plants are of vital importance in maintaining the healthiest stock. For fish, microbes help maintain digestion, promote full absorption of nutrients from feed, and help protect the outside of the fish in their slime coating. For plants, microbes help protect leaves from pathogens and pests and coat the roots to provide nutrients like nitrogen, in the form of nitrate (NO3-). The study of the microbiome for humans, plants, and fish alike is really still in its infancy. The future holds many exciting possibilities, like creating specific flavor profiles in crops from notable farming regions, known as terroir. By cultivating microbial blends from specific locations, an enterprising farmer might recreate that indescribable flavor in an aquaponics system from anywhere in the world.

In aquaponics, most of the focus to date has been on two primary “teams” of nitrifying bacteria, the nitrosomonas genus (Team 1) and the nitrobacter genus (Team 2). These two genus of bacteria work in conjunction with the fish and plants to help create the nitrogen cycle. The two teams of chemolithotrophic bacteria convert Ammonia (NH3) from the fish into Nitrites and then into Nitrates (NO2->NO3-). There is also another classification of bacteria that uses carbon as a food source to mineralize the solid fish waste in the system, known as heterotrophic bacteria.

Team 1 - Nitrosomonas
Ammonia oxidizing bacteria (AOB) like the nitrosomonas genus consume ammonia NH3 and excrete nitrites NO2-. Nitrosomonas prefers an optimum pH range of 6.0-9.0 and a temperature range of 68 to 86°F.

Team 2 - Nitrobacter
Nitrite-oxidizing bacteria (NOB) like the nitrobacter genus consume nitrites NO2 and excrete nitrates NO3-. Nitrobacter have an optimum pH range of 7.3 - 7.5 and a temperature range of 32 to 120 °F. 

Both teams also consume plant exudates, or the sugars released by plant roots. There is a hypothesis that root exudates actually inhibit the growth of plants and removal via microbes is highly beneficial. In exchange for this tasty treat, both teams of bacteria help deliver nitrogen directly to the plants. 


Note for Commercial Growers: Go beyond the nitrogen cycle
Healthy aquaponics systems require more than just nitrates to thrive. Other nutrients are needed in various different forms, including dissolved ions like iron, calcium, and potassium. Different types of microbes like heterotrophic bacteria break down the suspended waste and convert them into ionic form, allowing the plants to easily absorb them. Nutrient needs are covered in a later section.

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