Does database systems use basic system calls of local file system?
What mysql_user wrote is probably true for all systems using files to store data as those just have to communicate with the filesystem used and it does not make sense to rewrite the "drivers" for all known filesystems just to manage them directly (and would collide with the OS drivers anyway).

But some DBMS allow the use of disks/partitions directly. It allows to skip one layer of indirection and buffering, to manage caches directly.., but loses the benefits of using files (simpler backup etc.).

It is often called raw partition


MySQL InnoDB
SQL Server
Oracle used to support it but seems to be desupported - probably getting replaces by Oracle ASM which looks more like a dedicated filesystem, but in the end has similar benefits - being optimized for databases instead of universal files.
Firebird
raw devices deprecated in DB2, but it can use Linux block devices instead which is still quite low-level