Francis Hueber, a co-author of the new study with the Smithsonian Institution, revived the fungus idea in 2001.
Hueber was among the researchers who, as early as the 1970s, were studying chemical signatures called isotopes in the organism.
In plants like today's trees and flowers, which get energy from the sun and carbon from the air, two particular carbon isotopes should be in balance.
In plants and animals that eat other life-forms, the isotope ratio should vary widely.
That fact turned out to be an important clue: The fossil's combination of isotopes revealed the funguslike habit of feeding on decaying organic matter.
In addition, co-authors at the Carnegie Institution in Washington, D.C., found that Prototaxites fossils contain isotopes from primitive plants of the age as well as certain soil organisms.
Occasional stalks probably sprouted from a vast underground network of hyphae—the fungal equivalent of roots—noted the University of Chicago's Boyce.
The fungus probably grew slowly to attain such large sizes, he added.
It was likely aided by a relatively slow turnover of plant types. In today's world, ecosystems can change quickly, with grasslands giving way to forests in the space of a few years.
Patricia Gensel is a professor of paleobotany at the University of North Carolina at Chapel Hill who was not involved in the new study.
She said the new paper proposes a workable solution to one of science's big hangups about Prototaxites being a fungus: Its reproductive parts seem too big by modern fungus standards.
"If the 'logs' of Prototaxites represent a fruiting body [the fungal reproductive organ], it is huge—bigger than any modern individual fruiting body," she said.
The other plants that coexisted with the massive fungus were at most 6.5 feet (2 meters) tall, meaning their remains wouldn't have provided enough nourishment to support fungi with large fruiting bodies.
"It is felt by some that they alone do not provide a sufficient source of carbon for it," Gensel said.
The study shows that the huge fungus had another source of food: soil microbes called crusts.
"Sucking up carbon from microbial crusts would [make large fruiting bodies] possible."
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