Final answer:
Proton pumps across all domains of organisms suggest they were present in the last universal common ancestor, supporting the idea that cells from all domains share an evolutionary origin in proton gradient utilization.
Step-by-step explanation:
The presence of proton pumps in all three domains of organisms — Bacteria, Archaea, and Eukarya — suggests a shared evolutionary origin. These proton pumps are integral to chemiosmosis and the generation of a proton motive force (PMF), which is fundamental for cellular processes like ATP synthesis. Considering the ubiquity and essential function of proton pumps, it is most likely that they were present in the last universal common ancestor (LUCA) of all three domains, and thus, option B (Proton gradients across a membrane were used by cells that were the common ancestor of all three domains of life) is the correct answer.