Since, nature microbiology is not a open access journal, but they provided this article as open access, what copyright will these images fall into?

I am not sure, I would consult this in the discord community, you can join here https://discord.gg/mKSKQ7T .

Does that mean this video open to use?

There shouldn't be any problem with the video.

And should I cite NYT or the study if it is open to use?

It would be better if you quoted the study, but NYT is ok too.