I don’t personally know how the diversity of microorganisms compares with that of macro-organisms. I did a quick search and found this paper discussing “operational taxonomic units” and “species clusters” in bacteria, with the largest survey to date finding 5.6 million OTUs. However I don’t know how that maps onto conventional taxonomy and presumably most of those species are undescribed. It reminds me of this paper estimating that there are 10x more gall midge species than previously expected, also presumably mostly undescribed.
Also I feel like bacteria don’t really fit well with iNaturalist documentation, even other microscopic organisms like diatoms, rotifers, protozoans etc. which are challenging enough on their own are still identifiable to some extent using photography. You might be interested in this recent thread on microorganisms on iNat: How big is the microorganism/microbiology community on iNat?