Lake sediments contain viable allochthonous bacteria that can be cultured and used for palaeoecological studies. To be a good palaeoindicator, a bacterium must be able to survive in sediments for long periods of time, but also be unable to reproduce in the lake bottom. Bacteria can survive the unfavourable environmental conditions in lake sediments as resting cells. The endospore is the most specialized form and gives the bacterium an extreme longevity. The oldest viable endospores isolated from lake sediments that we are aware of are about 9000 years old.
Several species, mainly in the genera Thermoactinomyces, Bacillus and Clostridium, form endospores. Clostridium perfringens has been used as palaeoindicator for sewage pollution, while Thermoactinomyces vulgaris is an indicator for past agricultural activity in the boreal forest zone and a potential climatic indicator in other vegetation zones. Although isolation and enumeration of bacterial endospores from lake sediments is rather easy and has considerable potential as a powerful tool in palaeoecology, the number of studies using palaeoecological approaches is limited.