Android wizard Chainfire has released an experimental root method for Marshmallow, currently only compatible with Nexus devices. The new method works in a fairly interesting way. The new method mounts an ext4 image file with /su as a mount point through /data/, with a few modifications to necessary files outside of /system. For the uninitiated, it basically means a virtual drive is linked to the system data folder and given root privileges. This allows the init script, which is run on boot, to run the root program despite it not being loaded into /system.
This new method has a few interesting benefits and caveats. To name a few, you'll have to reflash your system partition to use it and older root apps with hardcoded paths for superuser access won't work with it. The way this new method avoids using the /system partition also means that a standard factory reset will unroot the device in question and erase all the root files, leaving basically no evidence of mucking around. This could be a boon for those who are scared to root for fear of voiding their warranties, but it also means flashing new partitions of custom ROMs through this method could become some convoluted business unless new methods that piggyback this are developed soon. On the other hand, this also means that scary procedures like changing a kernel lose some of their risk; what would cause a soft or hard brick before will now just cause a rooting failure.
This method is still highly experimental, so if you own a Nexus and feel like giving it a try, be warned. You also should be very careful not to change things around to mount the new method's files as read only on boot, or to change system to read/write. Carrying out normal root tasks, such as theming and allowing access for apps to modify protected files, will require workarounds for the new method, but this could just become the future of Android rooting. Chainfire's revolutionary idea seems set to usher in a new era for Android modders, keeping up with Google's new protections in a much less invasive way.