Experimental observation of cyclotron instabilities in a minimum-B confined electron cyclotron resonance ion source plasma is reported. The instabilities are associated with strong microwave emission and a burst of energetic electrons escaping the plasma, and explain the periodic ms-scale oscillation of the extracted beam currents. Such non-linear effects are detrimental for the confinement of highly charged ions due to plasma perturbations at shorter periodic intervals in comparison with their production time. It is shown that the repetition rate of the periodic instabilities in oxygen plasmas increases with increasing magnetic field strength and microwave power and decreases with increasing neutral gas pressure, the magnetic field strength being the most critical parameter. The occurrence of plasma turbulence is demonstrated to restrict the parameter space available for the optimization of extracted currents of highly charged ions.
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