Final answer:
The primary challenge in culturing prokaryotes in laboratory settings is the lack of suitable nutrients and the specific growth requirements that scientists have yet to determine for many species.
Step-by-step explanation:
The most substantial difficulty in culturing prokaryotes in laboratory settings is related to a lack of suitable nutrients. Over 99 percent of bacteria and archaea cannot be successfully cultured because many have specific requirements for growth that are still unknown to scientists. For example, they may need certain micronutrients, ideal pH conditions, precise temperature, correct pressure, or specific co-factors and co-metabolites that are not provided in laboratory cultures.
Furthermore, some bacteria are obligate intracellular parasites and cannot be cultured outside a host cell, making it challenging to grow them in a typical laboratory environment. The diverse conditions required by prokaryotes, including sources of energy and carbon as well as specific nutrients, are often difficult to replicate outside of their natural ecosystems.