how to store Time Machine backups on NFS and keep metadata?
If you're explicitly looking to make a copy of the existing backups (a backup of the backups), you will need to make a disk image with Disk Utility. Time Machine uses hardlinked directories which are only supported by HFS+, so you need HFS+ in a container.

You'd be much better off running netatalk on the Ubuntu server, which will share the disk over AFP, allowing Time Machine to back up directly to it. Here's one guide: http://pwntr.com/2012/03/03/easy-mac-os-x-lion-10-7-time-machine-backup-using-an-ubuntu-linux-server-11-10-12-04-lts-and-up/