Prototaxites

Prototaxites is an extinct genus of terrestrial fossil fungi dating from the Late Silurian until the Late Devonian periods. Prototaxites formed large trunk-like structures up to 1 m wide, reaching 8 m in length, made up of interwoven tubes around 50 um in diameter, making it by far the largest land-dwelling organism of its time.

The taxonomy of Prototaxites has long been the subject of debate. It is widely considered a fungus, but the debate is ongoing. Its exact relationship with extant fungus lineages is uncertain. It was almost certainly a perennial organism that grew over multiple years. Several ecologies have been proposed, including that it was saprotrophic like many modern fungi, or that it was a lichenised autotroph.

Morphology
With a diameter of up to 1 m, and a height reaching 8.8 m, Prototaxites fossils are remnants of by far the largest organism discovered from the period of its existence. Viewed from afar, the fossils take the form of tree trunks, spreading slightly near their base in a fashion that suggests a connection to unpreserved root-like structures. Infilled casts which may represent the spaces formerly occupied by "roots" of Prototaxites are common in early Devonian strata. Concentric growth rings, sometimes containing embedded plant material, suggest that the organism grew sporadically by the addition of external layers. It is probable that the preserved "trunks" represent the fruiting body, or "sporophore", of a fungus, which would have been fuelled by a mycelium, a net of dispersed filaments ("hyphae"). On a microscopic scale, the fossils consist of narrow tube-like structures, which weave around one another. These come in two types: skeletal "tubes", 20–50 micrometres (μm) across, have thick (2–6 μm) walls and are undivided for their length, and generative "filaments", which are thinner (5–10 μm in diameter) and branch frequently; these mesh together to form the organism's matrix. These thinner filaments are septate—that is, they bear internal walls. These septa are perforate—i.e. they contain a germ pore, a trait only present in the modern red algae and fungi.

The similarity of these tubes to structures in the early plant Nematothallus has led to suggestions that the latter may represent leaves of Prototaxites. Unfortunately for this hypothesis, the two have never been found in connection, although this may be a consequence of their detachment after the organisms' death.

History of research
First collected in 1843, it was not until 14 years later that John William Dawson, a Canadian scientist, studied Prototaxites fossils, which he described as partially rotten giant conifers, containing the remains of the fungi which had been decomposing them. This concept was not disputed until 1872, when the rival scientist William Carruthers poured ridicule on the idea. Such was his fervour that he rebuked the name Prototaxites (loosely translated as "first yew" ) and insisted that the name Nematophycus ("stringy alga" ) be adopted, a move strongly against scientific convention. Dawson fought adamantly to defend his original interpretation until studies of the microstructure made it clear that his position was untenable, whence he promptly attempted to rename the genus himself, calling it Nematophyton ("stringy plant"), and denying with great vehemence that he had ever considered it to be a tree. Despite these political attempts to rename the genus, the rules of botanical nomenclature mean that the name "Prototaxites", however inappropriate in meaning, remains in use today.

Despite the overwhelming evidence that the organism grew on land, Carruthers's interpretation that it was a giant marine alga was challenged just once, in 1919, when Arthur Harry Church suggested that Carruthers had been too quick to rule out the possibility that it was a fungus. The lack of any characters diagnostic of any extant group made the presentation of a firm hypothesis difficult; the fossil remained an enigmatic mystery and subject of debate. It was not until 2001, after 20 years of research, that Francis Hueber, of the National Museum of Natural History in Washington, D.C., published a long-awaited paper which attempted to put Prototaxites in its place. The paper deduced, based on its morphology, that Prototaxites was a fungus.

This idea was received with disbelief, denial, and strong scepticism, but further evidence is emerging to support it. In 2007, isotopic analyses by a team including Hueber and Kevin Boyce of the University of Chicago concluded that Prototaxites was a giant fungus. They detected a highly variable range of values of carbon isotope ratios in a range of Prototaxites specimens. Autotrophs (organisms such as plants and algae that make a living via photosynthesis) living at the same time draw on the same (i.e., atmospheric) source of carbon; as organisms of the same type share the same chemical machinery, they reflect this atmospheric composition with a constant carbon isotope trace. The inconsistent ratio observed in Prototaxites appears to show that the organism did not survive by photosynthesis, and Boyce's team deduced that the organism fed on a range of substrates, such as the remains of whichever other organisms were nearby. Nevertheless, the large size of the organism would necessitate an extensive network of subterranean mycelia in order to obtain enough organic carbon to accumulate the necessary biomass. Root-like structures have circumstantially been interpreted as Prototaxites's rhizomorphs, and could support the possibility of the organism transporting nutrients large distances to support its above-ground body.

Other recent research has suggested that Prototaxites represents a rolled-up bundle of liverworts, but this interpretation has substantial difficulties.

A similar genus, Nematasketum, also consists of banded and branching tubes in axial bundles; this seems to be a fungus.

In 2021, Gregory Retallack described the new species Prototaxites honeggeri from the Darriwilian stage of the Middle Ordovician Douglas Lake Member of the Lenoir Limestone, at Douglas Dam, Tennessee, which marks the earliest known appearance of the genus Prototaxites. While an Ordovician origin of the genus is mentioned by some studies, Referring to Retallack′s study, paleobotanist Dianne Edwards commented "When diagnostic features are absent, such fragmentary organic materials can be misinterpreted, leading to implausible attributions". Nelson and Boyce (2022), referring to Retallack′s study, maintained that the first appearance of the genus was in the Late Silurian.

A 2022 paper suggested that Prototaxites was a fungal rhizomorph that grew on its side and likely at least partially underground, as opposed to the traditional view that it grew upright.

Ecological context
The University of Chicago research team has reconstructed Prototaxites as a branchless, columnar structure. It was the tallest living organism in its day by far; in comparison, the contemporary plant Cooksonia only reached 6 cm in height and itself towered over the "moss forests" that grew beneath it, and invertebrates were the only other land-dwelling multi-cellular life. Prototaxites could have used its tall columnar structure for spore dispersal. Alternatively, if Prototaxites contained photosynthetic structures, the height would have increased it ability to capture light. The presence of biomolecules often associated with algae may suggest that Prototaxites was covered by symbiotic or parasitic algae, making it in essence a huge lichen, or even suggesting that it was an alga itself. However, the variability in the ratios in the isotopic signature δ13C between specimens of Prototaxites suggest that it was heterotrophic.

Prototaxites mycelia (strands) were fossilised as they invaded the tissue of vascular plants. In turn, there is evidence of animals inhabiting Prototaxites: Mazes of tubes have been found within some specimens, with the fungus re-growing into the voids, leading to speculation that the extinction of Prototaxites may have been caused by such activity. However, evidence of arthropod boreholes in Prototaxites has been found from the early and late Devonian, suggesting the organism survived the stress of boring for many millions of years. Intriguingly, boreholes appeared in Prototaxites long before plants developed a structurally equivalent woody stem, and it is possible that the borers transferred to plants when these evolved. Prototaxites became extinct in the Late Devonian as vascular plants rose to prominence.