As T. thermophilus appeared from FISH to be the dominant popu-lation in both ATAD communities, attempts were made to assess its
substrate uptake patterns in situ with MAR. The incubation temper-ature used in these experiments markedly affected overall levels of
substrate assimilation by the ATAD sludges. As sludge from reactor
2 was used in both aerobic and anaerobic MAR experiments, the
mean operating temperature for this reactor (65 ◦C) was selected
initially for the incubations. However, when FISH/MAR was applied
to the ATAD sludge with the substrates chosen together with the Tth
probe targeting T. thermophilus, none of the substrates were assim-ilated by this population in situ. Therefore, their assimilation was
measured at several temperatures, which produced results sug-gesting that an incubation temperature of 45 ◦C was optimal (data
not presented here), based on −-emission levels. However, when
probe Tth was applied to ATAD samples incubated at 45 ◦C no cells