The question arises from "Geometry of Algebraic Curves" from Arbarello, Cornalba, Griffiths and Harris. I wrote something down in my master's thesis that I admittedly don't completely understand, and I wanna figure it out now that I have some time on my hands!
Page 311 claims the following, which I expanded a bit to make the question self-contained :
Let $A$ and $B$ be algebraic vector bundles over a complex algebraic variety $W$ and let $\mathbb P \overset{def}= \mathbb P(\mathrm{Hom}(B,A)) \to W$ be the associated projective bundle. Let $\sigma : A \to B$ be a morphism of vector bundles ; by composition, $\sigma$ induces a map $$ \widetilde{\sigma} : \mathrm{Hom}(B,A) \to \mathrm{Hom}(A,A). $$ We consider the composition of bundle maps on $\mathbb P$ : $$ \mathcal O_{\mathbb P}(-1) \overset{i}{\to} \pi^* \mathrm{Hom}(B,A) \overset{\pi^* \widetilde{\sigma}}{\to} \pi^* \mathrm{Hom}(A,A) \overset{\mathrm{tr}}{\to} \mathcal O_{\mathbb P} $$ where $i$ is the standard inclusion and $\mathrm{tr}$ is the trace functional. (...)
What is this standard inclusion? I can't even deal with the case where $W$ is a point (which would at least let me understand the map on the fibers...). In this case vector bundles are vector spaces $V_A, V_B$, so I am looking for a map of varieties $\mathcal O_{\mathbb P(\mathrm{Hom}(V_B,V_A))}(-1) \to \pi_{\mathbb P}^* \mathrm{Hom}(V_B,V_A)$, and by the universal property of the pullback, since I already have a map $\mathcal O_{\mathbb P}(-1) \to \mathbb P$, all I need is a map $\mathcal O_{\mathbb P}(-1) \to \mathrm{Hom}(V_B,V_A)$. But even that map I don't see it!
It's pretty much the same as what happens for the tautological bundle over projective space.
Recall that if $\mathbb P^n$ is the projective space of lines in $V := \mathbb C^{n+1}$, the tautological bundle $\mathcal O(-1)$ is the bundle of lines in $V$, so we get an inclusion $$ 0 \to \mathcal O(-1) \to \underline V $$ of vector bundles over $\mathbb P^n$, where $\underline V$ is the trivial vector bundle over $\mathbb P^n$ with fiber $V$. The inclusion maps a line in $\mathcal O(-1)$ (which is the space of lines in $V$) to the line in $\underline V$, tautologically.
Passing now to your situation, suppose $E \to X$ is a holomorphic vector bundle of rank $r+1$ over a complex manifold $X$. We then construct the projective bundle $\pi : \mathbb P(E) \to X$ of lines in $E$, and get an inclusion $$ 0 \to \mathcal O(-1) \to \pi^* E $$ of vector bundles over $\mathbb P^n$, in exactly the same way as before. You have $E = \mathrm{Hom}(B,A)$, which doesn't really matter since the inclusion exists for any vector bundle.
Note that the first situation is just the case where $X$ is a point, because we can interpret a vector space $V$ as a vector bundle over a point, and then $\underline V = \pi^* V$, where $\pi : \mathbb P^n \to \{\mathrm{pt}\}$ is the constant map.