Without using the Wave Beam, one must fire down at it from above to kill it, the orifice at the top is its weak point. The most efficient way to kill it is to wait for it to stop throwing blobs, then, once it stops and retracts into the ground a small bit, then repeatedly jump over it while shooting down. The plants found between the platforms during the Nettori battle in Metroid Fusion greatly resemble Blob Throwers in regard to their appearance and their ability to launch projectiles, though they behave like Samus Eaters in that they trap their prey and do not appear to extend at all.
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