The Internet of Things (IoT) is innovative, intensive technology and supports wide areas of application, such as Smart environment, Healthcare, Security, industrial environment, and massive technology that inaugurate associated with real things. It also improves the living standard of society. These smart things are revolutionary and helping human beings in different ways but on the other hand security threats are growing rapidly and attackers are influencing the life of a man. Whereas, when technologies become developed, it carries a weakness that are continuously exploited and targeted. Security risk and threats directly concern with IoT environment and one of the main challenges of today, numerous issues need to be addressed within a physical layer of IoT Environment. In this paper, we have discussed the risk assessments and specifically pointed out the physical layer. We proposed a detailed ontology and highlighted the challenges, threats and different types of attacks in the IoT environment. We briefly debate the importance of the physical layer and emphasis the challenges it faces in the IoT environment and how hackler can attack this layer using tapping and QoS attacks.