I have to store users in different OU, because there is two separate
Units running inside one organization. They have nothing to do with
each other and their parent organization is same and their is only one
Server to manage both.


I don't quite understand what is your problem here.
You can a "ou" inside another "ou" and then search the user base dn with a scope of "sub".
Let's say:

ou=Users
ou=Users,ou=Organization1
ou=Users,ou=Organization2

Then, in /etc/ldap.conf, you would specify:

nss_base_passwd ou=Users,dc=domain,dc=com?sub

instead of

nss_base_passwd ou=Users,dc=domain,dc=com?one

Did I understand your question wrongly?

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