When there is a need to determine which bacteria or fungi are present (in agriculture, medicine, or biotechnology), scientists can also turn to other tools besides cultures, such as nucleic acid tests (which instead detect that organism's DNA or RNA, even if only in fragments or spores as opposed to entire cells) or immunologic tests (which instead detect its antigens, even if only in fragments or spores as opposed to entire cells).
The latter tests may be helpful in addition to (or instead of) culture, although circumspection is required in interpreting their results, too, because the DNA, RNA, and antigens of many different bacteria and fungi are often much more prevalent (in air, soil, water, and human bodies) than is popularly imagined—at least in tiny amounts.
Lewis Thomas put fastidiousness and the challenge of culturing isolates into logical context in his 1974 book Lives of a Cell: "It has been estimated that we probably have real knowledge of only a small proportion of the microbes of the earth, because most of them cannot be cultivated alone.
They live together in dense, interdependent communities, feeding and supporting the environment for each other, regulating the balance of populations between different species by a complex system of chemical signals.
Regarding Lewis's point about the limits of humans' ability to discover greater knowledge of microbes—from individual species and strains to whole microbial communities—another pair of facts is relevant.