Potential pitfalls of FISH microscopy as assessment method for anaerobic digesters

In the present work we investigated how the state of a biogas reactor impacts the enumeration of prokaryotic cells by fluorescencein situhybridisation (FISH). Therefore, the correlation between gas production and FISH hybridisation rates was analysed in different anaerobic digester sludges. High gasification activity coincided with high hybridisation rates. Low hybridisation rates were especially achieved with reactor samples subjected to long starvation periods showing low biogas production.Based on our findings we conclude that samples for FISH analysis should be fixed as soon as possible to prevent a loss of microbial activity resulting in lower FISH signals. Furthermore, the location of sampling is of importance, since samples from different fermenters within the same biogas plant also varied strongly in their FISH hybridisation rate. Our results indicate that FISH could be a useful method for assessing the metabolic state of microorganisms in anaerobic digester plants.