I assume that what you are asking here is more an operational question rather than a conceptual question. Bear in mind that $\phi$ depends on $x$ and $t$, i.e. $\phi = \phi(x,t)$, and that with two variables $t$ and $x = x(t)$:
$D_t = \partial_t + \partial_x \dot{x}$
You can then expand the $\dot{\phi}^2(x,t)$ term into
$\dot{\phi}^2(x,t) = (\partial_t \phi)^2 + 2 (\partial_t \phi) (\partial_x \phi) \dot{x} + (\partial_x \phi)^2 \dot{x}^2$
Now going back to the Lagrangian density $\mathcal{L} = \frac{1}{2} [\mu \dot{\phi}^2(x,t) - Y\partial_x \phi(x,t)]$. Bear in mind that the partial derivatives operates on explicit dependence of variables in question. As an example, let me do the first term of the EL equation here:
$\begin{align*}
\frac{\partial \mathcal{L}}{\partial (\partial_t \phi)} &= \frac{1}{2} \mu \frac{\partial}{\partial (\partial_t \phi)} [(\partial_t \phi)^2 + 2 (\partial_t \phi) (\partial_x \phi) \dot{x} + (\partial_x \phi)^2\dot{x}^2] + \frac{1}{2} Y \frac{\partial}{\partial (\partial_t \phi)} (\partial_x \phi)^2\\
&=\frac{1}{2} \mu [\frac{\partial}{\partial (\partial_t \phi)} (\partial_t \phi)^2 + 2\frac{\partial}{\partial (\partial_t \phi)} (\partial_t \phi) (\partial_x \phi) \dot{x} + \frac{\partial}{\partial (\partial_t \phi)} (\partial_x \phi)^2 \dot{x}^2] + 0 \\
&=\frac{1}{2} \mu [2 (\partial_t \phi) + 2(\partial_x \phi) \dot{x} + 0]\\
&=\mu [(\partial_t \phi) + (\partial_x \phi) \dot{x}]
\end{align*}
$
So far, the point here is that you should treat $\partial_t \phi$ to be an explicit variable, and apply partial derivatives as you normally would just like $x$ or $t$. The term $\frac{1}{2} Y \frac{\partial}{\partial (\partial_t \phi)} (\partial_x \phi)^2$ in the first line, for instance, evaluates to be zero, for there is no dependence on $\partial_t \phi$.
You can halt at this stage and carry on to evaluate the derivative $\frac{\partial \mathcal{L}}{\partial (\partial_x \phi)}$ first, and you should yield something like $\mu [(\partial_t \phi) \dot{x} + (\partial_x \phi) \dot{x}^2] - Y \partial_x \phi$. And since the Lagrangian density does not depend on $\phi$, $\frac{\partial \mathcal{L}}{\partial \phi} = 0$. (Do try to calculate them yourself! I may be wrong here :p)
Combining what you have, you should be able to get the EL equation to be:
$\partial_t \mu [\partial_t \phi + (\partial_x \phi) \dot{x}] + \partial_x \mu [\partial_t \phi + (\partial_x \phi) \dot{x}] \dot{x} - Y \partial_{xx} \phi = 0 $
The third term is obviously the RHS of the equation that you need to prove. What is perhaps messy is the first two terms, but you should refer back to the first equation that we had discussed previously, i.e. $D_t = \partial_t + \partial_x \dot{x}$; with this, it is pretty straightforward to show that
$\mu[\partial_t \dot{\phi} + (\partial_x \dot{\phi}) \dot{x}] = Y \partial_{xx} \phi$
Do the simplification once more and you will obtain the equation that you need to prove :)