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The fifth generation (5G) wireless technologies serve as a key propellent to meet the increasing demands of the future Internet of Things (IoT) networks. For wireless communication security in 5G IoT networks, physical-layer security (PLS) has recently received growing interest. This paper aims to provide a comprehensive survey of the PLS techniques in 5G IoT communication systems. The investigation consists of four hierarchical parts. In the first part, we review the characteristics of 5G IoT under typical application scenarios. We then introduce the security threats from the 5G IoT physical-layer and categorize them according to the different purposes of the attacker. In the third part, we examine the 5G communication technologies in 5G IoT systems and discuss their challenges and opportunities when coping with physical-layer threats, including massive multiple-input-multiple-output (MIMO), millimeter wave …