How to Measure Biomass Yield in a Non-Homogeneous Anammox Bioreactor?

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The discussion revolves around challenges in measuring biomass yield in a continuous anammox bioreactor that suffers from poor mixing, with biomass settling at the bottom. Participants suggest agitation as a potential solution to achieve better mixing, which would facilitate easier sampling. However, concerns about shear stress on the biomass are raised, indicating that agitation methods should be chosen carefully to avoid negatively impacting biological processes. Alternatives like ultrasound depth measurements, akin to fish finders, are proposed as non-invasive techniques to assess biomass distribution without disturbing the reactor environment. The conversation emphasizes the need to balance effective mixing with the preservation of biological activity.
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We have in our lab a continuous anammox bioreactor, however, it is not well mixed, i.e. all the biomass is concentrated at the bottom of the reactor. We're interested in quantifying the biomass yield. Does anybody know of any techniques to measure this in a continuous non-homogeneous bioreactor? Thanks!
 
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Agitate it? Then it would be a homogeneous bioreactor, and you could easily pull out a sample. If shear is a problem, know that agitation can be low shear or high shear or in between.

Would the biology work better or worse if the reactor was agitated? If worse, maybe you could just agitate it when you needed to pull a sample.
 
Ultrasound depth measurements, similar to a "Fish Finder" as used on fishing boats.
 

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