The main new things that you are asked to learn in graduate school are:
1.
Taking more responsibility for yourself and your career.
In addition to effectively managing time, you should also learn more about how universities and academic careers work (e.g. by reading the pages on this website carefully, including the ones for postdocs, but also by asking more of your senior colleagues about it), and develop professional habits of interaction (see the networking page; do not underestimate this part). You should be spending a lot of time reading. You need to master a field of literature by the end of your PhD, in the sense of knowing the paradigms.
2.
How to pick research projects and bring them to a published outcome.
This is of course what doing research is about. But generally: do not underestimate how important and difficult picking the right project is. The hard part is that you have to nevertheless decide something even when you don't know what you need to know, including whether you're more into field or lab work, collaboration or independence, whether your project is very or just moderately risky, whether other people consider this an unfilled niche or an esoteric side issue.
3.
The broader picture that your research fits into.
You should be spending a lot of time reading. You need to master a field of literature by the end of your PhD, in the sense of knowing the paradigms, where the holes are, the commonly studied organisms, the well-known authors and seminal papers as well as who is working in your area right now (this is also what your >comprehensive exam (='prelim exam') is about). You should be spending a lot of time reading. You need to master a field of literature by the end of your PhD, in the sense of knowing the paradigms.