There are a number of commercially available temperature sensors which can be located at the reactor core and connected to a data acquisition system. Refer to Echiegu and Ghally (2014) An In-house Computer-based Data Acquisition and Control System for Anaerobic Fermentation Processes. American Journal of Engineering and Applied Science 01/2014; 7(3):313-323. DOI: 10.3844/ajeassp.2014.313.323 which you may download from my Researchgate site.
in a small digester i used thermo-couple in the core of the digester then from the outside i used thermometer to read the temperature daily in the attached image u can c them