Responsibility to report Health and Safety concerns

Although you say that the university is aware of some of these issues, sometimes action on these matters depends on telling the right people. In particular, if you have not yet told the relevant Health and Safety officers at the university then that might be the reason that no remedial action has been taken. I recommend you report these matters to the Health and Safety office at the university immediately. Indeed, if you have a look at the university policy, there is a good chance that it imposes an obligation on its workers to report safety issues to the Health and Safety office.

Shutting down a lab temporarily to deal with a safety hazard is an annoyance, but it is important to remedy safety problems and could save someone from being seriously injured or killed. If the lab were to be shut permanently as a result of the issue, that would presumably reflect serious safety problems that present a danger to people, or repeated breaches of safety rules. Either way, reporting the issue is appropriate and it is your responsibility to report.

I feel as though I have a responsibility to report these issues to the Health and Safety department, but I'm worried about retribution from my supervisor...

If that is the case then you have big problems --- any supervisor who would retaliate against a lab worker for reporting safety concerns to the university is a menace, and if you are in an environment where that is a possibility then it reflects serious dysfunction at your university. Most occupational health and safety laws prohibit retaliation against workers for reporting safety issues, and in some jurisdictions retaliation against workers in these circumstances can even constitute a criminal offence. In addition to protections in OHS laws, there are also specific provisions for whistleblowers in circumstances where workers suffer retaliation for reporting safety problems.

if the lab is shut down this is likely to have significant negative impacts on a number of other PhD students

Sure, if you leave the lab be managed as it is now, on the other hand, a good percentage of PhD students will think that it is ok to manage dangerous stuff careless and disrespecting rules, because they are (or they become) self-entitled doing more important things than respecting stupid bureaucracy on how to store plutonium and fluoridic acid. They are PhDs after all, expert-to-be on the subject, and they may even become professor, if all things fall in place.

What do you prefer, a negative impact now on them, or a negative impact on society allowing this way of thinking (rules are there for a reason, quite often to protect one from oneself, rather than from the others).

Do yourself a favour: you are a good guy that discovered a number of issues, anybody not complaining is already impacting negatively YOU and a number of honest people.

The same people running the lab this way, supposedly for the greater good of science and consequently of humanity and not for their personal benefit, are doing a disservice to the same humanity at large they claim they are working for.

And being the managers lab or users, they are actually doing a lot for their personal benefits.

So yes, report to the university, but first contact a lawyer. You have to protect yourself and you want to report the violations in the most specific and bureaucratic way possible, please remember that you are going to act against the lab manager and therefore against the university, not for the university.

In the Netherlands they say:

hoge bomen vangen veel wind

Good luck and please remember that the best success is how at peace you are with yourself, not how many succesful papers you churned out while working in dangerous conditions (unless you have an enormous ego that can be at peace only by churning out humongous papers working in dangerous conditions :) ).

PS and side note: regarding safety culture in the UK, an interesting andeoctal point ... maybe there is a foundation acting in the name of John Cockcroft that may help/support you?

Depending on your location, there may be a union representing University staff - for example, in the UK it would be UCU for academic staff, Unite for technical support staff and Unison for clerical staff. Any of these would have specialised Health and Safety reps.

Importantly, unions are used to situations where the employer may not be acting entirely in their staff’s best interest (such as your observation that the University is aware of some violations but turning a blind eye) and will probably be more discreet and understanding of your conundrum. They may also have prior experience of dealing with similar situations and could give you an idea of what the University’s reaction would be depending on which action you choose.

Unions may not be able to act on your behalf unless you are a member, but in most places you should be able to at least speak informally with a rep.