We ran mixed microbial cultures, and we ran them on ideas borrowed from fisheries management. A fisheries manager can’t count every fish, so they watch indicators and adjust the rules. We watched what the community was doing and changed conditions to influence what could thrive. We monitored the chemistry, used our noses, and tasted preparations where appropriate. Genetic data came later. Rumens, swamps, and other mixed environments gave us a way to think about the tank. The organisms changed their surroundings, and those surroundings changed which organisms could grow.
Apple feedstocks gave us a clear example. Pectin methylesterase removes methyl ester groups from pectin, releasing methanol. Han and Du followed pectin, enzyme activity, and methanol through apple-wine fermentation and aging, and found methanol still rising during aging. In their spontaneous fermentations, a long lag phase gave the apple’s own pectinases more time to work before the culture took hold. [1] In our apple-pomace work, pectin breakdown started early too. We needed organisms that could metabolize the methanol it released, and we learned that those cultures had to go in at time zero.
Once those cultures were established, fresh pectin no longer caused the methanol buildup we had seen before. Later genetic studies showed populations rising and falling as the fermentation changed. The community did not stay in its starting proportions, but it kept handling new pectin. The organisms carrying a useful metabolism could shrink to a small part of the population while that capability stayed available.
The function persisted at low abundance. Jones and Lennon found evidence that dormancy helped maintain bacterial diversity in lake communities. [2] We never established dormancy as the explanation in our tanks. What we saw was that capacities we needed stayed in the community even at trace populations, and our cultures often recovered from shocks without permanently losing them.
That changed what we tried to hold constant. Genetic data showed us the populations, and the chemistry showed whether the conversions were happening. Like a fisheries manager, we managed for what the system could deliver. The population mix drifted. The conversions held.
Sources
[1] Han and Du (2022). Relationship of the methanol production, pectin and pectinase activity during apple wine fermentation and aging. Food Research International.
https://doi.org/10.1016/j.foodres.2022.111645
[2] Jones and Lennon (2010). Dormancy contributes to the maintenance of microbial diversity. Proceedings of the National Academy of Sciences.
https://doi.org/10.1073/pnas.0912765107