Darksteel Mutation is one of a rare few class of cards that received errata as soon as it was printed. At a casual glance, you might not be able to tell what the problem is, so let’s reference the errata’d Oracle text:
Enchanted creature is a 0/1 Insect artifact creature with indestructible and loses all other abilities, ***card types, and creature types.***
The bolded part at the end is what makes the card work as intended. For example, suppose your opponent is very devoted to his commander, Nylea, God of the Hunt. You slap Darksteel Mutation on her, and she becomes an artifact creature that’s an Insect, losing her types enchantment and God. (If the above errata wasn’t in place, the fact that Darksteel Mutation makes Nylea “an artifact creature” creates an exception that causes the rest of her types to stay in place. This obviously wasn’t intended, so the additional text was written out on the card.) Note however that Nylea does remain legendary: that is a supertype, and not a card type or subtype.
Nylea remains indestructible by coincidence (if she didn’t already have the ability, she would gain it from the aura), but loses her devotion, trample-granting, and team pump abilities. Notably, this means that Nylea will never become not a creature, regardless of your opponent’s devotion. Darksteel Mutation also doesn’t prevent Nylea from gaining or losing any other abilities. Casting Bow of Nylea afterward will allow Nylea to gain deathtouch when attacking, and casting Turn on her will remove her indestructible ability. It’s important to remember that “being a commander” is not an ability, but an attribute of the card itself, so Darksteel Mutation can never remove her commander-ness.
This becomes important if Nylea somehow becomes able to deal combat damage; it will count toward her commander damage total. Although she becomes a 0/1, effects that change her power and toughness will still be able to affect her. For example, if your opponent activated Nylea’s last ability in response to Darksteel Mutation, she would be a 2/3 (until end of turn). The same is true for +1/+1 counters, such as those put on her with Bow of Nylea.
Today’s Rules Tip written by Jen Wong