For their tests, the researchers used a genetic testing method not employed in clean rooms before, known as ribosomal RNA gene sequence analysis, which allowed them to study and decode a genetic marker common to all bacteria. The unique sequences of each type allowed the researchers to identify a greater number and diversity of bacteria than previously detected in the rooms.

While a few microorganisms, like those common on human skin, were found at all three sites, the study discovered that each room had a bacterial community largely unique to itself. Many factors could be responsible for this diversity, the researchers said, including the differing types of air filters and cleaning agents used and the facilities’ different geographic locations.

“I was surprised by what we found,” Dr. Venkateswaran said in an interview, “and as we continue to sample additional clean rooms, we may be in for even more surprises.”

Dr. Catharine A. Conley, a biologist who is the acting planetary protection officer at NASA headquarters, said the agency had long suspected that the organisms previously detected in clean rooms did not represent the full range that were there. Current cleaning techniques kill most common microbes, she said, and the resulting lack of competition could contribute to the number and diversity of the durable survivors found by the genetic testing approach.

“We know clean rooms can be much cleaner, and some are,” Dr. Conley said, citing some used by the semiconductor and pharmaceutical industries. “The problem is the cost. They are very expensive to build and maintain.”

Spacecraft going to areas where alien life is more likely to be found, like planets or moons with identifiable water, can be sterilized by a heat method that essentially bakes them for hours. But, she said, this runs the risk of damaging components.