Possible poriferan body fossils in early Neoproterozoic microbial reefs

Abstract

Molecular phylogeny indicates that metazoans (animals) emerged early in the Neoproterozoic era¹, but physical evidence is lacking. The search for animal fossils from the Proterozoic eon is hampered by uncertainty about what physical characteristics to expect. Sponges are the most basic known animal type^2,3; it is possible that body fossils of hitherto-undiscovered Proterozoic metazoans might resemble aspect(s) of Phanerozoic fossil sponges. Vermiform microstructure^4,5, a complex petrographic feature in Phanerozoic reefal and microbial carbonates, is now known to be the body fossil of nonspicular keratosan demosponges^6–10. This Article presents petrographically identical vermiform microstructure from approximately 890-million-year-old reefs. The millimetric-to-centimetric vermiform-microstructured organism lived only on, in and immediately beside reefs built by calcifying cyanobacteria (photosynthesizers), and occupied microniches in which these calcimicrobes could not live. If vermiform microstructure is in fact the fossilized tissue of keratose sponges, the material described here would represent the oldest body-fossil evidence of animals known to date, and would provide the first physical evidence that animals emerged before the Neoproterozoic oxygenation event and survived through the glacial episodes of the Cryogenian period.

Vermiform microstructure in microbial reefs dating to approximately 890 million years ago resembles the body fossils of Phanerozoic demosponges, and may represent the earliest known physical evidence of animals.

Main

Benthic microbial structures (stromatolites and other microbialites) provide conspicuous evidence of pre-Phanerozoic life, but are difficult to understand because they rarely preserve recognizable evidence of the organisms involved. Stromatolitologists have struggled for over a century to decipher their microscopic laminae and clots, which are assumed to have been produced or influenced by in vivo and/or post-mortem biogeochemical activity, and to formalize the ‘taxonomy’ of their morphology and microstructure^5,11.

The existence of metazoans by the Ediacaran period (the last period of the Neoproterozoic) is indicated by bilaterian ‘body’ and trace fossils¹², and geochemical evidence (biomarkers)¹³ provides disputed^14,15, indirect evidence for Cryogenian poriferans. The search for definitive physical evidence of pre-Cryogenian metazoans is confounded by uncertainty about what to look for, but preserved physical evidence should be small, subtle and possibly altogether unfamiliar. Given that sponges are the most basic of known animals^2,3, physical evidence of Neoproterozoic sponges could be sought, but effort focused on the characteristics of mineralized sponge skeletons (siliceous or calcareous spicules)^16–18 overlooks sponges with only proteinaceous (spongin or keratin^19,20) skeletons. Early metazoan evidence might instead resemble taphonomic (preservational) products of sponge soft tissue^21–23 rather than mineralized sponge skeletal components. Although molecular clock data suggest that sponges emerged in the early Neoproterozoic¹, the oldest undisputed sponge body fossils are from the Cambrian period¹⁵.

Recent work^6,7 has shown that vermiform microstructure^4,5—an unusual microscopic feature in Phanerozoic reefs and stromatolites that was initially interpreted as being related to algae⁴ or protozoans^24,25—is instead a keratose sponge body fossil comprising complexly anastomosing cement-filled microtubules enclosed in carbonate microspar. It is produced taphonomically^6,10 in nonspicular keratose demosponges through post-mortem calcification of soft tissue to produce carbonate microspar (automicrite), which surrounds the tough spongin fibres of the ‘skeleton’ of the sponge. Decay of the spongin then produces a network of complexly anastomosing tubular moulds that eventually become passively filled with sparry calcite cement. Although questioned²⁶, the association between vermiform microstructure and sponges has been confirmed in undisputed body fossils of Phanerozoic sponges⁷. Three-dimensional reconstruction of vermiform microstructure has shown that tubule shape and branching configuration are too consistent and complex to be abiogenic (for example, compacted peloids), do not resemble the branching style of other possible organism types (microbial or fungal)⁶ and are identical to the spongin meshworks of keratose sponges⁶. Although the existence of Proterozoic vermiform microstructure has been predicted^6,10,27, published examples are rare^28,29 and difficult to understand.

The calcification of decaying sponge soft tissue has been documented in modern sponges^21,22, and produces sponge ‘mummies’²² as well as a range of subtle carbonate sedimentary textures (such as peloid clusters) in living and Phanerozoic fossil sponges^7,9,21,22. Taphonomic sediment textures (polymuds) that may be poriferan-related have previously been identified in the reefs that are the subject of this Article²³.

Background

This petrographic study presents possible evidence of sponge body fossils in thin sections (30-μm-thick rock slices, viewed microscopically in transmitted light) from the approximately 890-million-year-old (Ma)^30,31 Little Dal reefs (Stone Knife Formation³², northwestern Canada) (Fig. 1a, b). These large (about 500 m in thickness, and kilometres in diameter) microbial reefs^33–36 were built mainly by variably preserved calcimicrobes that have been interpreted as filamentous cyanobacteria (photosynthesizers)^33,35,36, and developed palaeotopographic relief of up to about 100 m above the surrounding subphotic, level-bottom carbonate-mud seafloor. Reef framework, which is generally not discernible in natural exposures, was documented from slabbed hand samples and thin sections³⁵.

Fig. 1. Geographic and stratigraphic location of the study material.

a, Location of Little Dal reefs in northwestern Canada. Scale bar, 100 km. b, Stratigraphic position of the Little Dal reefs in the Stone Knife Formation (Fm)³²; depositional age is known through litho- and chemostratigraphic correlation with the 892 ± 13-Ma (Re–Os black shale)³⁰ Boot Inlet Formation³¹ (Shaler Supergroup (Sg)), together with other geochronological constraints^50,51. Gp, group. c, Reef growth stages^34,35, simplified summary of framework morphologies³⁵ and off-reef cycles³⁴.

The reefs grew in five stages (Fig. 1c), each with different microbialite morphologies: anastomosing millimetre-to-centimetre-scale masses with no consistent shape (stages I–III); centimetre-scale anastomosing columns and digits (stages II, III and V); and steep sheet-like masses at a scale of decimetres to 10 m (stage IV). Stage V includes cement-rich to micritic, domical, turbinate and columnar stromatolites that generally lack calcimicrobes, with associated ooids and stromaclasts. Microbialites of stage I to IV grew predominantly in moderate-energy, illuminated palaeoenvironments^33,35,36, but stage V records a shallow-water, high-energy environment. The microstructure that forms most of the reefal microbialites (especially in stages III and IV) comprises filaments that are about 10 μm in diameter, separated by 10–100-μm masses of marine cement that probably represents the calcified sheath polysaccharide of cyanobacteria^33,36 that was permineralized during microbialite growth. The reef framework, consisting predominantly of this microstructure and its taphonomically degraded equivalents³⁶, defines primary void networks (millimetres to centimetres in size) that are commonly floored with geopetal carbonate mud and lined by isopachous, fibrous marine calcite cement. The relative timing of void-filling by marine cement precipitation versus geopetal sediment accumulation is variable, attesting to the very early timing of marine cement precipitation.

Results

Vermiform microstructure in samples from stages II, III and V of the Little Dal reefs (Fig. 1c) is identifiable only in rare thin sections, in which it forms millimetre-to-centimetre-scale masses of anastomosing tubes that are filled with calcite spar and surrounded by calcite microspar groundmass (Fig. 2a, b). The approximately 20–30-μm-wide tubules have complex, divergent branching and rejoining at a spacing of about 30–100 μm, form very irregular three-dimensional polygonal meshworks, are defined by enclosing microspar, lack walls, and are filled with clear, equant calcite crystals up to 20 μm wide (Fig. 2b). The homogeneous microspar groundmass that encloses the tubules comprises cloudy, equant, interlocking calcite crystals of about 2–8 μm wide, and differs texturally and compositionally from other fine-grained reefal carbonate in its uniform crystal size, lack of sedimentary texture, and dearth of detrital silicate impurities. Vermiform microstructure preservation is good to barely discernible.

Fig. 2. Characteristics and distribution of Little Dal vermiform microstructure in stratigraphically oriented 30-μm-thick thin sections.

a, Well-preserved vermiform microstructure exhibits a polygonal meshwork of anastomosing, slightly curved, approximately 30-μm-diameter tubules embedded in calcite microspar (KEC25). Scale bar, 500 μm. b, Enlarged rectangle from a, showing branching tubules forming three-dimensional polygons intersected at various angles by the thin section; clear calcite crystals, about 10–20 μm in width, fill tubules in groundmass of more finely crystalline calcite (dark grey). Scale bar, 50 μm. c, Three-dimensional fragment of spongin skeleton from a modern keratosan sponge, illustrating its branching and anastomosing network of fibres (incident light). Scale bars, 100 μm (main panel), 20 μm (inset). d, Vermiform microstructure in debris that includes calcimicrobialite and other reef-derived clasts (C) flanking reef stage III (MV63). Scale bars, 1 mm (main panel), 100 μm (inset). e, Vermiform microstructure in shelter pore beneath microbialite clast, in detrital sediment occupying a reef-top depression; pore is thinly lined with marine calcite cement (MC) (indicated with an arrow), and partly filled with geopetal carbonate sediment (GCS) (KEC25; stage-III reef core). Rectangle is enlarged in a. Scale bar, 1 mm. f, Vermiform microstructure in a microbialite (M) framework void is overlain by pore-occluding marine calcite cement; circled area indicates moderately well-preserved tubule meshwork (DL32a; reef stage II; detailed characteristics depicted in Extended Data Fig. 1). Scale bar, 1 mm. g, Patches of vermiform microstructure in various relationships with micritic microbialite masses (white dashed outline) and detrital carbonate sediment (CS) (KES23; resedimented stage-II reef clast). Rectangles are enlarged in i–k. Scale bar, 1 mm. h, Simplified depiction of relationships among vermiform microstructure, microbialite masses and detrital carbonate sediment in g. Scale bar, 1 mm. i, Vermiform microstructure mingled with microbial micrite within a microbialite digit (enlarged from g). Scale bar, 500 μm. j, Vermiform-microstructured mass within sediment between microbialite digits; also contains diagenetic dolomite patches (D) (enlarged from g). Scale bar, 500 μm. k, Vermiform-microstructured mass adhering to the margin of microbialite digit (enlarged from g). Scale bar, 500 μm. All images except c are in plane-polarized transmitted light. Samples from resedimented reef debris are depicted in depositional orientation based on geopetal structures. Reef locations and abbreviations (such as KEC) are described in a previous publication³⁵. Larger versions of vermiform microstructure photomicrographs are provided in Extended Data Figs. 1–5.

Vermiform microstructure is present in three microfacies (i, ii and iii (the last divided into iiia and iiib subsets)), representing three palaeoenvironments (Figs. 2, 3). It is not present in calcimicrobe-dominated stromatolites or level-bottom carbonate mudstone that is distal to reefs.

Fig. 3. Palaeoenvironments occupied by the Little Dal vermiform microstructure interpreted as possible body fossils of keratose sponges.

The organism lived (i) on poorly illuminated to non-illuminated carbonate mud surfaces in depressions on the reef surface and on debris aprons mantling reef flanks; (ii) in voids produced by the growth of the complex microbial framework of the reef; and (iii) interlayered with non-calcimicrobial microbialites (cement-rich and muddy-laminated stromatolites in high-energy reef-capping phase V; irregularly muddy-laminated to clotted microbialites in moderate-energy environments of reef stages II and III). Scale bars, 5 mm.

In microfacies i (Fig. 2d, e, g, j, Extended Data Figs. 1, 2), vermiform microstructure is intercalated with carbonate mud (with or without larger reef-derived clasts and terrigenous impurities) in (1) synsedimentary debris flanking reef stages II and III, and (2) millimetre-to-metre-scale palaeodepressions on reef growth surfaces (stages II and III). It locally encrusts sides of reef-framework clasts in sediment, extends into crevices, and occupies shelter porosity under clasts (Fig. 2e).

Extended Data Fig. 1. Vermiform microstructure of microfacies i.

Elaboration of Fig. 2d. a, Vermiform microstructure is intercalated with detrital sediment (lower 1/3 of image) that includes calcimicrobialite clasts. b, Three-dimensional meshwork of vermiform microstructure transected by the plane of the 30-μm-thick thin section shows anastomosing tubule system; enlarged from a. c, Anastomosing tubules occluded by clear blocky calcite enclosed by cloudy calcite groundmass of slightly smaller crystals; enlarged from b. The tubules have no constructional walls and are defined by the dark enclosing groundmass. Oriented sample MV63 in plane-polarized transmitted light.

Extended Data Fig. 2. Vermiform microstructure of microfacies i.

Elaboration of Fig. 2e. a, Vermiform microstructure in a shelter void beneath an irregular microbialite clast and floored by angular reef clasts in carbonate mud, from a reef-top depression. Fibrous isopachous marine calcite cement lined the pore before its occupation by the vermiform mass. b, Three-dimensional meshwork of vermiform microstructure transected by the plane of the 30-μm-thick thin section shows anastomosing tubule system; enlarged from a. c, Anastomosing tubules occluded by clear blocky calcite enclosed by cloudy calcite groundmass of slightly smaller crystals; enlarged from b. The tubules have no constructional walls and are defined by the dark enclosing groundmass. Oriented sample KEC25 in plane-polarized transmitted light.

In microfacies ii (Fig. 2f, Extended Data Fig. 3), vermiform microstructure occupies millimetre-to-centimetre-scale framework voids of reef stages II and III. Void-filling vermiform microstructure of microfacies i and ii either underlies (Fig. 2f) or overlies (Fig. 2e) isopachous void-lining marine cement.

Extended Data Fig. 3. Spatial–temporal relationships among vermiform microstructure, geopetal detrital sediment and marine cement that collectively fill reef framework voids of microfacies ii.

Elaboration of Fig. 2f. a, Reef framework void among non-calcimicrobial stromatolites of reef stage II. Detrital sediment (DS) occupies lowest part of the void. Much of the void is occupied by vermiform microstructure (V); uppermost parts of the void are occupied by marine cement (MC) and local burial cement (BC). b, Detrital sediment accumulation, which includes quartz silt (transparent white particles); enlarged from a. c, Upper part of void is lined by isopachous cloudy marine calcite cement (arrow) (MC) and the remaining porosity occluded by burial calcite cement (pale) (BC); enlarged from a. d, Enlargement from c to demonstrate cloudy, isopachous, fibrous nature of the marine calcite cement, versus more transparent, equant, blocky shape of burial cement that occupies the small amount of pore space remaining after accumulation of geopetal sediment, growth of vermiform microstructure and precipitation of marine cement. e, Moderately preserved vermiform microstructure; enlarged from a. Oriented sample DL32a from reef stage II, in plane-polarized transmitted light.

In rare microfacies iiia (Fig. 2g–k, Extended Data Fig. 4), vermiform microstructure encrusts non-calcimicrobial microbialite columns and mingles with irregular muddy microbialite microstructure of reef stages II and III. In rare microfacies iiib (Extended Data Fig. 5), vermiform microstructure is sub-millimetrically interlayered with stage-V non-calcimicrobial stromatolites where it locally passes laterally to geopetal peloid accumulations in lenticular voids.

Extended Data Fig. 4. Associations of vermiform microstructure, micritic microbialite columns and detrital sediment in microfacies i and iiia.

Elaboration of Fig. 2g–k. a, Low-magnification image of two irregular microbialite columns and inter-column sediment (outlined by white dashed line). b, Vermiform microstructure is intermingled with muddy microbialite in column interior; enlarged from a. c, Vermiform microstructure intercalated with inter-column sediment; enlarged from a. d, Vermiform microstructure encrusting the margin of a microbialite column; enlarged from a. Sample KES23, from reef stage II, in plane-polarized transmitted light; sample is from a resedimented reef clast and is oriented on the basis of geopetal structures out of the field of view.

Extended Data Fig. 5. Spatial and textural association of vermiform microstructure and geopetal peloids in microfacies iiib.

This association suggests that geopetal peloid accumulations are a taphonomic product derived through poor preservation of vermiform microstructure. a, Poorly preserved vermiform microstructure (arrowed; inset c) adjacent to laminar to lenticular voids containing geopetal peloid accumulations (arrowed; inset b) in cement-rich non-calcimicrobial stromatolites of reef stage V. Oriented IR drillcore sample RT A19-495.4′ in plane-polarized transmitted light.

Discussion

The shape, size, branching style and polygonal meshworks of the Little Dal vermiform tubules closely resemble both spongin fibre networks of modern keratosan sponges (Fig. 2a–c) and vermiform microstructure either demonstrated or interpreted to be sponge-derived in diverse Phanerozoic microbial, reefal and non-reefal carbonate rocks^{6–8,10,24,25,27,37}. The compositional and textural homogeneity of the microspar groundmass supports an origin through permineralization of a pre-existing biological substance⁹, rather than incremental accumulation of detrital sediment or microbial carbonate that passively incorporated complexly anastomosing tubular microfossils. Variable preservation and association with geopetal peloid accumulations are familiar aspects of Phanerozoic sponge taphonomy^9,21,22,38. In previous work, detailed comparison of the three-dimensional characteristics of vermiform microstructure with branching cylindrical organism types yielded no convincing alternative to the sponge interpretation⁶.

The preference of Little Dal vermiform microstructure for environments that were not inhabited by photosynthetic calcimicrobes (reef flanks, depressions on active reef growth surface, and framework and shelter voids), versus its absence from filamentous calcimicrobial reef-framework components, suggests that (1) illumination may not have been a requirement and (2) the organism may have been unable to compete with reef-building photosynthesizers that grew and/or calcified rapidly. The interlayering of vermiform microstructure with calcimicrobe-free microbialite (microfacies iiib) in the high-energy, well-illuminated reef surfaces of reef stage V supports the interpretation that the vermiform-microstructured organism was not capable of competing with reef-building filamentous cyanobacteria, but instead occupied niches in which the filamentous calcimicrobes did not live owing to (1) poor illumination or (2) high hydrodynamic energy. The occupation of cryptic microniches (shelter and reef framework voids) by sponges (for example, microfacies i and ii), is well known in the Phanerozoic^21,37,39,40.

The obligatory spatial association of vermiform microstructure with reefs built by oxygen-producing cyanobacteria may indirectly support a metazoan interpretation. Prior to the Neoproterozoic oxygenation event, marine dissolved oxygen was probably low⁴¹ except perhaps in the vicinity of photosynthesizing microbial communities; the metabolic requirements of metazoans may have limited early animals to localized, comparatively well-oxygenated (for the time) environments (oxygen ‘oases’). Given the approximately 890-Ma depositional age^30,31, the vermiform-microstructured Little Dal organism may been tolerant of ‘low’ oxygen (that is, relative to modern levels), which is a characteristic of some modern and fossil sponges⁴².

If the vermiform-microstructured masses in the Little Dal reefs are accepted as early sponge body fossils, their approximately 890-Ma age would imply that (1) the evolutionary emergence of metazoans was decoupled from the Neoproterozoic oxygenation event^41–45 and (2) early animal life was not catastrophically affected by the Neoproterozoic glacial episodes. If the Little Dal objects are truly sponge body fossils, they are older than the next-youngest undisputed sponge body fossils (Cambrian)¹⁵ by approximately 350 million years.

It would not be surprising to find that the earliest sponges were reef-dwellers; the history of Phanerozoic reefs is rich with reef-building and reef-dwelling sponges⁴⁶. If the masses of vermiform microstructure in the Little Dal reefs were to be accepted as an early Neoproterozoic expression of sponge tissue preservation, their age and proposed identity would be compatible with (1) evidence that the opisthokont (animal + fungus) clade was already established by the time of the Mesoproterozoic–Neoproterozoic transition^47,48, (2) possible evidence of 1-billion-year-old multicellular holozoans⁴⁹, (3) molecular clock estimates for the emergence of the Porifera in the early Neoproterozoic¹ and (4) a revised taxonomy of nonspiculate keratose sponges showing that they are a sister group to other demosponges¹⁹. The Little Dal vermiform microstructure is perhaps exactly what should be expected of the earliest metazoan body fossils: preservation through post-mortem calcification of sponge-grade soft tissue in the decaying bodies of small, shapeless, sessile, epibenthic and cryptic animals most closely affiliated with keratose sponges.

Methods

Field work was done on foot from two-person, backpacking-style camps placed at sites that are accessible only by helicopter. Samples were collected at various times between 1992 and 2018, under all required permits. Recording sample locations using GPS is not possible for most sites owing to the extreme topography of the exposures’ cliffs, pinnacles and canyons, and so sample location was documented using photographs and sketches. Several samples are from a mineral-exploration drill-core stored on-site in the field. Owing to the homogeneous grey weathering of reef surfaces, lithofacies cannot be identified in the field. Instead, hand samples were collected and later slabbed and thin-sectioned. Vermiform microstructure was identified in a small proportion of the samples collected. Repeat visits focused primarily on resampling the rare areas in which vermiform microstructure had been identified.

Standard 30-μm-thick thin sections were examined in plane-polarized transmitted light using a Nikon C-Pol binocular microscope fitted with digital camera and Luminera Infinity Analyze software (for lower-magnification images) and an Olympus BX-51 petrographic microscope equipped with Q-Imaging digital capture system (for higher-magnification images).

Reporting summary

Further information on research design is available in the Nature Research Reporting Summary linked to this paper.

Online content

Any methods, additional references, Nature Research reporting summaries, source data, extended data, supplementary information, acknowledgements, peer review information; details of author contributions and competing interests; and statements of data and code availability are available at 10.1038/s41586-021-03773-z.

Author contributions

E.C.T. conducted all aspects of the study.

Data availability

All relevant data are contained with the Article and its Supplementary Information, or are available from the author upon reasonable request.

Competing interests

The author declares no competing interests.

Extended data

is available for this paper at 10.1038/s41586-021-03773-z.

Supplementary information

The online version contains supplementary material available at 10.1038/s41586-021-03773-z.