Microbial Ecology of our Aquaponics System

NASA syringe sampling

Angela Detweiler takes sample. Photo by Sander Van den Groenendaal

Learning more about the microbes in our aquaponics system and how we can improve or encourage those actors to do their jobs more efficiently has always been a goal of the Symbi Biological program. Put another way, we’re talking about the microbiome and microbiome eco system services that are performed. We know that there are certain nitrifying bacteria doing most of the heavy lifting in aquaponics, but what others are present and what role to do they play in nutrient cycling? 

We volunteered to provide samples as part of a very exciting NASA study of the microbial ecology of food production systems. Scientists from the Microbial Ecology / Biogeochemistry Research Laboratory at NASA Ames Research Center will determine the


Photo from nanporetech.com

microbiome of our aquaponics system using a DNA sequencer called the minION, which is the size of a cell phone from the late 90s or early 2000s. It’s really tiny!

Scientists Brad Bebout, Leslie Bebout, Angela Detweiler and NASA Intern Sander Van den Groenendaal brought several sampling kits, which included syringes to draw the sample water/biofilm and then it was pressed into a micro filter to collect the sample for analysis. They took samples from the plant roots,

NASA roots

Taking samples from plant roots. Photo by Sander Van den Groenendaal.

biofilter, system water, and the periphyton (biofilm inside of deep water culture troughs) similar to what was tested in a recently released paper where they found the bacteria around the fish feces was dominated by one group of bacteria from Cetobacterium, whereas the rest of the system had similar microbial communities and were more diverse.

NASAbiofilter sampling

Taking sample from biofilter net tank. Photo by Sander Van den Groenendaal.

One difference from the paper is that we are testing system water since it is ubiquitous in the system to see if there are common organisms distributed throughout the system amongst the tested compartments.


Aquaponics has come a long way since the days of “I dunno, it just seems to work!” to a more advanced science seriously looking at food production, food safety, and optimization of nutrient cycling to improve nutrient density of the crops being grown.

NASA Water quality

Brad and Leslie Bebout taking water quality measurements. Photo by Sander Van den Groenendaal.


Aquaponics can never replace soil, but where arable land is not present, like deserts, old lava fields, and urban locations, it begins to make a lot of economical sense. Especially, if you’re thinking of going to Mars! I would like to thank Jon Parr of Schoolgrown for connecting me with such amazing scientists that also happen to be a lot of fun. I look forward to sharing our findings and hope to keep moving the needle forward for Aquaponics.

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