It is not possible to mute the microphone system wide as that is controlled by the driver. (unless I am wrong)
You can however, disable the microphone completely by interacting with the Audio Manager/Mixer class - AudioSystem.
I don't recommend this approach.
If you are coding your own application, muting the microphone is simple and only a matter of manipulating the TargetDataLine to stop buffering output by just reading the data and not sending it across the wire.
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