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Oxygen is absorbed also from the soil atmosphere by the root.
Obtainable under the proprietary name Chlordane, the toxin gradually works down into the soil diffusing into the soil atmosphere.
There is also the possibility that gene transfer could increase the efficiency of nitrogen fixation in symbiotic bacteria and promote fixation under nitrogen-rich soil atmosphere conditions.
This is a much slower atmospheric change than lungs, of course, and is suited to the confined and restricted conditions of a 'soil atmosphere', which is just what we need for them to breathe in poison.