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Do all living entities, even microorganisms like the single-cell amoeba or virus, have both soul and Supersoul?

Hare Krishna! Thanks for this question. It's clear you're thinking deeply on these topics.

Yes EVERY living entity has a soul and a Supersoul. Actually Paramatma, (Krishna) is within every ATOM, but the jiva soul is within every living entity.

Laxmimoni dasi