At long last, Boyce, an assistant professor of paleontology, and his collaborators claim to have solved the taxonomic riddle of Prototaxites. From an analysis of carbon isotopes trapped in these ancient fossils, they conclude that Prototaxites was a fungus.

Their study also sheds light on the biological complexity of the long-gone Devonian epoch, 416 to 359 million years ago, and offers new guidance for astrobiologists as they prepare to explore the universe.

The Devonian was a transitional period, when evolution was rapidly solving the problems of living on land. "At the beginning of the Devonian, there are vascular plants, but they are 2 feet tall at the most, with no leaves and no wood," says Boyce. "At the end of the Devonian, there are big trees and ferns with leaves. This happened over about 60 million years."

The discoverer of Prototaxites thought it was a vascular plant, and chose a name that means "early yew." But well-preserved sections of the fossil showed a filamentous structure with numerous small tubes that were not at all typical of vascular plants, Boyce says. (Vascular plants, including all flowering plants, are more complex than non-vascular plants. This latter group, including mosses, lack xylem and phloem, tissues that vascular plants use to circulate water and nutrients.)

Plant fossils are commonly infiltrated by minerals such as silica or calcite, and they often retain organic matter and microstructure. "That's a great thing about plant fossils," says Boyce. "Paleobotanists [can] take for granted that we have cellular preservation." To understand Prototaxites's place in taxonomy, Boyce and collaborators relied on isotopic analysis - an examination of two common forms of carbon -- carbon-12 and carbon-13. As photosynthetic plants ingest and metabolize carbon dioxide, their composition correlates with the isotopic composition of the carbon dioxide in the atmosphere.

Samples from a particular species of plant in a particular environment vary by at most 2 to 4 parts per thousand in the C-12/C-13 ratio, Boyce says. "In general, you won't get much more than that."

Prototaxites broke the mold. Even in a particular locality, "We find a difference of 12 parts per thousand," says Boyce, which means Prototaxites was not photosynthetic, and therefore was not an autotroph - a primary producer. Instead, it was a heterotroph - a consumer of biological material made by other organisms. "If you are a heterotroph, you can be all over the place" in the C-12/C-13 ratio, Boyce says. But which heterotroph? Prototaxites was large and filamentous, but large, filamentous organisms are photosynthetic - except for fungi. Therefore Prototaxites had to be a fungus.

And what did Prototaxites, the fungus, actually eat? Modern fungi consume many types of decaying organic material, and Prototaxites may have eaten whatever it could get its hyphae (feeding tubes) on. Although terrestrial plants were developing fast when Prototaxites was around, some of the Prototaxites fossils have isotopes inconsistent with consuming vascular plants. The most likely alternative food source is a type of soil crust called cryptobiotic soil that is now found primarily in deserts. Cryptobiotic soil contains bacteria (including cyanobacteria), lichens, mosses, green algae and fungi. (Even though most of these organisms are photosynthetic, different species, even in a particular location, have different ratios of carbon isotopes, Boyce says, which explains the varying C-12/C-13 ratios in Prototaxites.) Because cryptobiotic crusts do not fossilize, isotopic analysis of Prototaxites becomes a unique lens into the Devonian landscape, Boyce says. "These fungi show us that well into the period of diversification of vascular plants, there are still large areas of microbial activity." Today, by contrast, cryptobiotic soil has largely retreated to deserts.

One of the first implications for astrobiology concerns technique, Boyce says. Scientists often measure the chemistry of samples by grinding multiple samples into one batch, "But we have found that it is very important to do comparative analysis. We are not the first to look at the chemistry of Prototaxites, but what was different was that we grabbed as many fossils as we could, from individual locations, and compared each fossil. What mattered was the variance."

Robert Hazen, a staff scientist at the Carnegie Institution in Washington who also contributed to the report, stresses the importance of difference. "In other worlds, even if the biota is non-obvious or extinct, we have a very good chance of recovering samples with tell-tale isotopic, elemental, or biomolecular signatures." New, miniaturized instruments offer the promise of making on-site detections of these anomalies, he says, reinforcing the importance of determining in advance exactly what to search for.

The Prototaxites results also stress the hazard of preconceptions about forms of life: What we see and know can narrow our expectations and allow us to miss evidence of life, Hazen says. "There is an intrinsic fascination with the dominant life forms, dinosaurs, trilobites, giant mammals. But here was a landscape where there wasn't much animal biota. It was dominated by a giant organism, but it's counterintuitive, it was a giant fungus. This gives us a broader sense of what is possible, of the richness, the abundance of life. It puts the whole richness of evolution in a new perspective."

The Prototaxites research may also help astrobiologists "understand the emergence of biocomplexity," Hazen says, "from the simplicity of the geochemical world, to a microbial-dominated world, to one dominated by macrofauna. We see a forest today, and photosynthetic plants are dominant, with a few fungi and microbes in the soil that are not obvious or dominant. Here is an ecosystem where the ground cover is microbes, and the things that look like trees are fungi! It shows we have a lot to learn."

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