Filamentous microstructures in mineral-filled vesicles of the ~2.4-billion-year-old (Ga) Palaeoproterozoic Ongeluk Formation basalt branch, anastomose, and form mycelium-like networks indistinguishable from Phanerozoic deep-biosphere fossils attributed to fungi. Bengtson and colleagues, who described them in 2017, left their nature explicitly open: unless these filaments represent an unknown branch of fungus-like organisms, the fungal clade would be two to three times older than current molecular estimates, and fungal origin and early evolution may have occurred in the oceanic deep biosphere rather than on land. Nearly a decade of follow-up work has sharpened rather than settled the question: the filaments are completely replaced by clay minerals with no preserved organic matter, abiotic chemical-garden precipitates and bacterial protoplasts can reproduce the same morphology, and cavity-dwelling structures are vulnerable to contamination by younger organisms. The problem is to determine the origin of these structures — fungal, other (extinct or prokaryotic) fungus-like organisms, or abiotic — and thereby what follows for the age and environmental setting of fungal origins.

Background

Fungi are not confined to soils and surfaces: their tubular filaments (hyphae), which branch and re-fuse (anastomose) into a network called a mycelium, have repeatedly colonized fractures and pores in igneous rock. Fossils occupying such cavities in Phanerozoic (541 million years ago, Ma, to present) volcanic rocks show that this endolithic ('within-rock') deep-biosphere habitat has been occupied by fungus-like organisms for at least ~400 Ma. In submarine basalt, gas bubbles frozen during cooling leave vesicles that are later filled with minerals (amygdales), and it is on the walls of such vesicles that these fossil filaments grow.

The Ongeluk Formation of South Africa is a ~2.4 Ga (billion years ago) package of submarine basalt deposited during the Palaeoproterozoic era (the earliest division of the Proterozoic eon, roughly 2.5–1.6 billion years ago). Bengtson and colleagues (2017) described filaments 2–12 micrometres wide and up to hundreds of micrometres long inside amygdales of this basalt: solid, apparently non-septate tubes that branch at Y- and T-shaped junctions, anastomose, carry bulbous protrusions, form tangled, diverging 'broom' structures anchored in a jumbled basal film lining the cavity walls, and are composed of iron-rich chlorite, a clay mineral interpreted as a replacement of the original filament walls. Synchrotron X-ray tomography of discrete rock blocks established this organization in three dimensions. In much younger deep-biosphere occurrences, comparable mycelial fossils are attributed to fungi on the basis of chemical and morphological similarity to living fungi; the Ongeluk filaments, however, preserve no residual organic matter, so the attribution rests entirely on morphology and growth organization.

Why the attribution matters: relaxed molecular-clock dating (estimating divergence times from DNA-sequence differences) places the origin of the fungal clade at roughly 1.0–1.5 Ga — published estimates for deep fungal divergences span about 0.75–2.7 Ga — and the oldest widely accepted fungal body fossils are organic-walled filaments with preserved chitin from the ~1010–890 Ma Grassy Bay Formation of Arctic Canada (Loron et al. 2019), followed by fungus-like fossils from the early Ediacaran (~635 Ma; Gan et al. 2021) onward. If the Ongeluk filaments are fungi, the fungal clade — and with it the crown of eukaryotic life — must be at least 2.4 Ga old, and fungal origins may lie in the oceanic deep biosphere rather than on land.

The evidential basis has, however, been contested since publication. McMahon (2019) showed that laboratory 'chemical gardens' — self-organized mineral tubes that precipitate where silica- or carbonate-bearing alkaline fluids react with dissolved metal salts — produce curvilinear, branching, anastomosing filaments with circular cross-sections and bulbous protrusions, and argued that the biological case for the Ongeluk filaments 'rests largely on their morphological and organizational resemblance' to younger fossils while their composition is 'compatible with both biotic and abiotic interpretations'. Kanaparthi and colleagues (2024, non-peer-reviewed preprint) reported that bacteria exposed to conditions resembling these cavity settings transform into protoplasts whose shapes mimic presumed fungal microfossils, concluding that morphology alone cannot indicate phylogeny for Proterozoic microfossils. Head et al. (2024) further cautioned that cavity-dwelling structures in crystalline rock can be contaminated by deep penetration of much younger (even modern) fungi. The question is therefore no longer simply 'fungi or not', but a three-way discrimination among fungal, other-biogenic, and abiotic origins, resolvable only by evidence beyond gross morphology.

Problem Statement

Determine the origin and biological affinity of the mycelium-like filamentous structures preserved in vesicles (amygdales) of the ~2.4-billion-year-old Ongeluk Formation basalt, South Africa. Specifically, resolve which of the alternatives posed by the primary source and sharpened by subsequent work holds: (i) the filaments are fungi, in which case the fungal clade is at least ~2.4 Ga old — two to three times older than current molecular estimates — and fungal origin and early evolution may lie in the oceanic deep biosphere rather than on land; (ii) they are biogenic but not fungi, that is, fossils of an unknown branch of fungus-like organisms (prokaryotic or eukaryotic) whose morphology converges on mycelia; or (iii) they are abiotic structures, such as chemical-garden precipitates. A resolution must discriminate among these alternatives with evidence capable of withstanding the known confounds — the complete clay-mineral replacement of the filaments (no preserved organic matter), the demonstrated morphological convergence of fungal, bacterial and abiotic filamentous forms, and the possibility of contamination by younger endolithic organisms — and must state explicitly what follows for the age and environmental setting of fungal origins.

References

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