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Abundant cell-like organic structures have been proposed as microfossils in Paleoarchean (3.2–3.5Ga) cherts. The wide range of δ¹³C(C-org) values recorded in Paleoarchean organic matter (OM), including some of these possible microfossils, is difficult to reconcile with the smaller range observed in living cells and younger microfossils. Metamorphic and metasomatic effects on δ¹³C(C-org) have been recognized in Paleoarchean rocks, but have never been assessed for cell-like structures. Migrations of OM, of which the textures can mimic microfossils, are also difficult to constrain in Paleoarchean cherts that are often cut by sub-millimeter- to meter-scale OM-bearing veins. Here, we present the results of petrography, Raman microspectroscopy, and in situ analyses of δ¹³C(C-org) and H/C using secondary ion mass spectrometry (SIMS) of diverse organic microstructures, including possible microfossils, from two localities of the 3.4-billion-year-old Strelley Pool Formation (Western Australia, SPF).For the first time, we show that the wide range of δ¹³C(C-org) values recorded at the micrometer scale correlates with specific OM-texture types in the SPF. The crosscutting texture and lower structural order show that the OM in micro-veins of one sample from the Goldsworthy greenstone belt (WF4) post-dates all other OM-texture types. Possible microfossils (spheres, lenses), clots and micrometer-scale globules all show a higher structural order reached during peak metamorphism. Other than late micro-veins, textures indicative of OM migration beyond the millimeter-scale are absent; hence the source of clots, lenses, spheres and globules is indigenous to the cherts. A weak positive relation between δ¹³C(C-org) and H/C demonstrates that the 10‰ range in δ¹³C(C-org) recorded in indigenous OM is not metamorphic or metasomatic in origin. Texture-specific isotopic compositions strongly argue against fully abiotic OM synthesis. Spherical cell-like structures have distinct δ¹³C(C-org) values compared to all other organic textures: their distribution peaks between -35 and -36‰ in WF4 and averages -35.7‰ in sample PAN1-1A from the Panorama greenstone belt. Lenses are composed of a network of nanoscale OM with a relatively high H/C and δ¹³C(C-org) (average= -32‰ inWF4), and include globules with lower H/C and δ¹³C(C-org) down to -40‰. Similar globules also appear as isolated clusters. In both WF4 and PAN1-1A, δ¹³C(C-org) of OM clots shows a bimodal distribution, the lower values overlapping with those of lenses. These heterogeneities can be explained by different carbon-fixation metabolisms, e.g., photosynthetic high δ¹³C(C-org) lenses versus methanogenic low δ¹³C(C-org) spheres. Alternatively, heterogeneities can be explained by selective diagenetic preservation of the distinct isotopic fractionations inherited from different precursor biomolecules. Selective preservation is supported by (i) coupled δ¹³C(C-org)–H/C heterogeneities, (ii) the δ¹³C(C-org) differences between cell-like structures and recondensed clots, (iii) internal isotopic heterogeneities in SPF lenses similar to heterogeneities in modern and fossil cells. These results support the interpretation of biogenicity of morphologically cellular structures in the SPF.