A fluid-structure interaction (FSI) methodology is presented for simulating elastic bodies embedded and/or encapsulating viscous incompressible fluid. The fluid solver is based on finite volume and the large eddy simulation approach to account for turbulent flow. The structural dynamic solver is based on the combined finite element method-discrete element method (FEM-DEM). The two solvers are tied up using an immersed boundary method (IBM) iterative algorithm to improve information transfer between the two solvers. The FSI solver is applied to submerged vegetation stems and blades of small-scale horizontal axis kinetic turbines. Both bodies are slender and of cylinder-like shape. While the stem mostly experiences a dominant drag force, the blade experiences a dominant lift force. Following verification cases of a single-stem deformation and a spinning Magnus blade in laminar flows, vegetation flexible stems and flexible rotor blades are analysed, while they are embedded in turbulent flow. It is shown that the single stem's flexibility has higher effect on the flow as compared to the rigid stem than when in a dense vegetation patch. Making a marine kinetic turbine rotor flexible has the potential of significantly reducing the power production due to undesired twisting and bending of the blades. These studies point to the importance of FSI in flow problems where there is a noticeable deflection of a cylinder-shaped body and the capability of coupling FEM-DEM with flow solver through IBM.