If you look at the NifH database, you'll notice that the taxonomy only goes to genus level. Thus, I do not think it is possible to obtain species-level assignments with this database, as far as I can tell.
The only thing that might be worth looking into, is to see if your sequences were generated in a mixed orientation? See here. It is not an easy fix, but you can start with vsearch as described in that thread.
I'm not as familiar with the ability of NifH to taxonomically resolve taxa. Perhaps others on the forum can point you in a better direction.