The externalized cost of carbon released into the atmosphere is an interesting problem in that we need to define where and when it should be paid. As an illustrated early sample of this, the burning of biomass is considered carbon neutral because all the carbon released was once absorbed by the plant when it grew.
In agricultural, we have added carbon which starts out as natural gas. It then get used to create synthetic fertilizer. The fertilizer is used to grow feed crops, which then the animals eat. The manure is then either dumped or kept for creating new bio gas or sold to organic farms that uses it as an alternative to synthetic fertilizer. The organic farms can then sell feed to more farms, but at lower and lower yields given the same input carbon from the first synthetic fertilizer, or crops that people eat.
One alternative is that each instance pay for carbon it handles, in which case we don't care if carbon is added or not. We could also tax the first instance where the carbon is introduced to the system. A different system could attempt to tax what we find to be the incentive for the system.
Personally I would tax the externalities of synthetic fertilizer because that is instance where extra carbon get added, and it solves part of the controversial issue of biomass production being labeled as carbon neutral when using fertilizer. It will also make animal feed more expensive for factory farms, while grazing animals farms in low population areas can benefit from being more ecological to the environment.