I'm currently a second year PhD student studying microbiology. There's nothing specifically micro related that springs to mind but this is what helped when I applied for my PhD. What I found most helpful when looking at the information on FindaPhD.com website under the advice section, as well as advertised programmes being available there (https://www.findaphd.com/advice/blog/). There's a large number of useful articles that I recommend going through. Other good places to look include your university's careers service and twitter (you'd be surprised the number of PhD and postdoc positions advertised there, as well as general advice under the #phdlife and #phdchat, though these can be US centric).
Depending on where you are from and where you want to study, research council funding (mainly the MRC and BBRC in the UK) is probably the most all encompassing funding you can find, though its also the most competitive. Other than that medical charities' such as the Wellcome foundation have their own PhD funding for numerous different programmes, and individual universities and even projects can come attached with funding.
My best advice would be to cast a wide net when looking for places/funding and to make sure to contact the supervisors of the projects you are interested in. Not having a paper shouldn't be a major disadvantage as most Master's students don't at that stage. The main thing supervisors or admissions staff will be looking for is prior research experience or a good understanding of what research entails (this is as much for your wellbeing as it is theirs). Funding is often competitive so don't be disheartened if you receive rejections. You only need to succeed once.
Best of luck going forward :D
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