You'll want to get rid of Yellow Witherbloom in Creatures of Ava as soon as you can. These rotting bulbs will block pathways, hide treasures, and generally cause a huge annoyance as you try to see the whole map. You won't be able to use the first abilities your staff has to take them down, but luckily you will unlock the spell you need to get rid of Yellow Witherbloom for good as you make your way through the story.
The standard witherbloom buds you'll encounter around the grasslands are a reddy orange, so it's easy to notice the difference between the two, since the yellow are bright and surrounded by spores. The health bar of a Yellow Witherbloom is also solid yellow and won't deplete until you use the appropriate spell. That's because Yellow Witherbloom bulbs are essentially armoured, which makes them immune to your staff's absorption abilities. Fortunately, you'll be able to unlock the means to get rid of them pretty quickly.
You'll need to unlock the Krist ability before you can get rid of Yellow Witherbloom. After exploring the Weeping Rock civilization and completing the sagestone puzzle with Nim'ar, the Nafitar (your staff) will gain the ability to cast the Krist spell. You complete this mission within the grasslands, which is the first area of the map you encounter in Creatures of Ava. So, you'll unlock this ability quite early in the game. You can't skip ahead to complete this puzzle, so you'll need to work through the mainline quests and then retrace your steps to destroy Yellow Witherbloom around the starting zone.
To activate Krist, you need to create a connection ring around the Yellow Witherbloom by clicking and holding the left mouse button, before hitting the E key. This will send a blue light barreling toward the bloom and remove the yellow outer layer. From here, you can continue to use your standard weakening spell on the bloom to remove it. The effects of Krist only last for a limited amount of time, though, so you'll need to act fast to stop the bloom from re-growing its protective layer.
Yellow Witherblooms are found throughout Creatures of Ava and are well worth stripping away, even if they don't lead you to the next part of the story. Sometimes you'll uncover a pathway or free a creature, but there are also some valuable collectibles hidden behind the withering such as backpack pockets or health brews—well worth going back and exploring older areas to find.