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

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Baho Ilok
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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.