I suggest to introduce ...

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I suggest to introduce periodic microscopic observations of the sludge, either of the SBR activated sludge and anaerobic digester sludge.  A simple phase contrast microscope, 100 x and 1000 x magnifications, can allow, even to non specialised operators, to evaluate whether the activated sludge to digest changed, containg filamentous bacteria (proliferating and coming from the SBR) that hinder the solid/liquid separation. Problems can rise if Gram positive filamentous bacteria are present, such as Microthrix parvicella and Nocardioforms. They are  quite "robust" not easy to go to anaerobic lysis. Such simple microscopic observations can also conduct you to exclude such phenomena, looking for other ways of investigation, starting from solid mass balances (do the digesters work always in the same conditions in terms of solid loads, retention time, etc.).

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I agree with Valter Tandoi, phase contrast microscopy will help.  I normally jump from 100 to 4-500 times because 1000 times needs to be looked at without a cover slip and under oil immersion, which needs a dry film, whereas the 100 & 500 will use a cover slip.  If you don't know what is normal, then it is difficult to assess what is abnormal.  Do you measure the oxygen during the aeration stage, although this in itself may be mis-leading.  Nocardioforms are easy to identify because they are highly branched, and although some are in the bulk, the majority will be found at the surface of the sludge.  There are a whole range of filamentous, which can cause problems.  If it is anaerobic, then lots of free and flocced spiral bacteria will be present and the dominant filamentous bacteria may be Beggiatoa.  Beggiatoa are large filaments and will be seen moving (gliding motion) and in the event of anaerobic conditions, other sulphur filaments may be present.  Other filaments, which may be present are the mentioned Microthrix, also Sphaerotilus, both of which thrive in the presence of iron or manganese.  

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