I don't know why the article references "dark matter" but doesn't make the full connection to microbial dark matter: https://en.wikipedia.org/wiki/Microbial_dark_matter

It's not just fungi that are difficult to culture. The (vast?) majority of bacteria, virus, and archae species are undocumented because we don't know how to grow them in a laboratory or even stain them so that they're visible on a microscope slide. Except for the occasional glimpse on an electron microscope slide, most of them are completely invisible to science.