Metallomics in deep time and the influence of ocean chemistry on the metabolic landscapes of Earth's earliest ecosystems

Abstract

Modern biological dependency on trace elements is proposed to be a consequence of their enrichment in the habitats of early life together with Earth's evolving physicochemical conditions; the resulting metallic biological complement is termed the metallome. Herein, we detail a protocol for describing metallomes in deep time, with applications to the earliest fossil record. Our approach extends the metallome record by more than 3 Ga and provides a novel, non-destructive method of estimating biogenicity in the absence of cellular preservation. Using microbeam particle-induced X-ray emission (µPIXE), we spatially quantify transition metals and metalloids within organic material from 3.33 billion-year-old cherts of the Barberton greenstone belt, and demonstrate that elements key to anaerobic prokaryotic molecular nanomachines, including Fe, V, Ni, As and Co, are enriched within carbonaceous material. Moreover, Mo and Zn, likely incorporated into enzymes only after the Great Oxygenation Event, are either absent or present at concentrations below the limit of detection of µPIXE, suggesting minor biological utilisation in this environmental setting. Scanning and transmission electron microscopy demonstrates that metal enrichments do not arise from accumulation in nanomineral phases and thus unambiguously reflect the primary composition of the carbonaceous material. This carbonaceous material also has δ¹³C between -41.3‰ and 0.03‰, dominantly -21.0‰ to -11.5‰, consistent with biological fractionation and mostly within a restricted range inconsistent with abiotic processes. Considering spatially quantified trace metal enrichments and negative δ¹³C fractionations together, we propose that, although lacking cellular preservation, this organic material has biological origins and, moreover, that its precursor metabolism may be estimated from the fossilised "palaeo-metallome". Enriched Fe, V, Ni and Co, together with petrographic context, suggests that this kerogen reflects the remnants of a lithotrophic or organotrophic consortium cycling methane or nitrogen. Palaeo-metallome compositions could be used to deduce the metabolic networks of Earth's earliest ecosystems and, potentially, as a biosignature for evaluating the origin of preserved organic materials found on Mars.

Figure 1

Sampling location maps (a,b) and petrographic context of the microstructures of interest; irregular clots (c,d) and volcanic particle coatings (e,f) sourced from the 3.33 Ga Josefsdal Chert (Barberton greenstone belt, South Africa). (a) Map of southern Africa showing the location of the Barberton greenstone belt. (b) Map of the southern portion of the Barberton greenstone belt; white box indicates the location of the Josefsdal Chert, near the border of South Africa and Eswatini, from which all studied samples were collected. (c) Thin section of weakly laminated clotted carbonaceous chert corresponding to black massive chemical chert observed in the field (see Fig. S2). Carbonaceous clots are distributed throughout a silica matrix; other phases include scattered microminerals including pyrite and chromite spinel (see Fig. 2). (d) High-resolution photomicrograph showing irregular, stellate carbonaceous clots of up to ~1 mm diameter. (e) Thin section of laminated black and white banded chert corresponding to laminated chert observed in the field (see Fig. S2). (f) High-resolution photomicrograph showing sub-rounded and sub-angular pseudomorphed and silicified volcanic particles coated and impregnated with carbonaceous material (dark regions).

Figure 2

Selected geochemical analyses relevant to the palaeoenvironmental characterisation of the 3.33 Ga Josefsdal Chert. (a) REE+Y compositions of various samples from the studied horizons of the Josefsdal Chert normalised to Mud from Queensland (MuQ), a mixed mafic-felsic shale estimate of Archaean continental composition. HREE enrichment and positive La and Y anomalies indicates hydrogenous, thalassogenic contributions (marine), whereas positive Eu anomalies indicate hydrothermal fluid contributions. (b,c) Raman spectroscopy mapping of a representative irregular clot (b) and carbon-impregnated volcanic particle (c). Inset optical images show the regions of analysis; field of view = 1 mm. Green = carbonaceous material; yellow-orange = quartz; blue = anatase. Anatase can be considered a proxy for the alteration of volcanic particles associated with carbonaceous material. (d) Average Raman spectra for carbonaceous material in four studied samples (99SA07, black; 12SA09, green; 12SA16, blue; 14SA01, red). (e,f) SEM-EDS analyses of non-silicified mineral phases associated with carbonaceous material. Spectra are colour-correspondent to points within the regions of analysis shown. Red spectra = Ni-rich pyrite; beige spectra = K-Al phyllosilicate. Extensive SEM-EDS analyses are shown in Figs. S4-S8. (g,h) TEM micrographs from within clotted microstructures (sample 99SA07) showing the discontinuous distribution of carbonaceous material (black) within the microquartz matrix (grey).

Figure 3

Box-plot representations of SIMS δ¹³C data for irregular clots, particle coatings/impregnations and generic carbonaceous material (other CM) in the studied samples of the Josefsdal Chert. Comparisons are given with well-defined carbon isotope fractionations for the products of anoxygenic and oxygenic photosynthesisers, and methane and sulphur-cycling organisms (compiled after McCandless and Gurney; Schidlowski; Londry and Des Marais; Vieth and Wilkes). Well-defined microstructures (clots and coatings) have negative and restricted δ¹³C ranges consistent with biological mediation by multiple pathways. Coatings are characterised by δ¹³C values slightly more negative than clots (averaging −15.16‰ versus −9.44‰). Generic CM (other CM) in the same samples is characterised by a wide range of positive and negative δ¹³C values (between −47.4 ± 8.3‰ and +13.5 ± 2.0‰) bearing less resemblance to products resulting from specific biological pathways.

Figure 4

µPIXE spatially quantified elemental mapping within irregular clots. (a) µPIXE optical image of representative irregular clot. White box indicates the region for which the spectrum (b) and element maps (c) are given. (b) µPIXE spectrum with peak identification for the energy range 0–18 keV. (c) Element heat maps (black = low concentration, white = high concentration) for the region indicated in A, showing localised significant enrichments corresponding to entrained micromineral particles such as those identified by SEM-EDS in Fig. 2, but also a general enrichment within carbonaceous material (outlined by dotted white line) relative to the matrix.

Figure 5

µPIXE spectra after mapping within carbon-rich volcanic particle coatings (a) and generic carbonaceous material in the form of flakes (b). (a) µPIXE optical image of representative particle coating and accompanying spectra with peak identification for the energy range 0–18 keV. (b) µPIXE optical image of a representative carbonaceous flake and accompanying spectra with peak identification for the energy range 0–18 keV. Note the very strong enrichments in certain transition metals within the flake (Fe, Ni, Ti) corresponding to their spatially restricted accumulation within micro-mineral particles as shown in Fig. S15-S16.

Figure 6

Systematic approach to calculating the palaeo-metallome with reference to modern organisms. (a) Comparison between fractional contributions of elements of interest in Josefsdal Chert carbonaceous material and reported prokaryotic metallomes (e.g. Zerkle et al.). A metallomic contribution of V, Co, Ni, Cu and As (with bio-essential Fe, not shown) is frequently seen in irregular clots and particle coating morphologies. The least deviating pattern is seen between that of M. jannaschii and Josefadal Chert carbonaceous material: V, Ni, Co, Cu and Fe, together with reduced (or absent) requirements of Mn and Mo. The higher dependency on Cu seen for S. tepidum and S. meliloti more closely aligns its intracellular metal abundances with carbonaceous material in particle coatings, but we suggest that Cu may not be integral to the Josefsdal Chert carbonaceous material, but instead be the result of non-specific uptake due to extracellular polymer-driven resistance to toxicity (after Hickman-Lewis et al.). In most cases, the concentrations in putative biomass is lower than that for in vivo cells. This is consistent with degradation of biomass during the decay of cellular components. (b) Metal:metal ratios for the studied microstructures against values in the matrix demonstrating statistically distinct enrichments of V, Co, Ni, Cu, K and Ca. Enrichments in transition metals and depletions in Ca and K are consistent with bio-accumulation (i.e., in molecular nanomachines) and toxicity mitigation (i.e., against salt stress). The overall differences between significant metal enrichments in clots and coatings (highlighted in green) with respect to flakes and the matrix (highlighted in grey) implies that the accumulation of transition metals in flakes occurs by a different, less efficient process. We propose bio-accumulation for the effective accumulation of metals in clots and coatings, but passive, non-specific accumulation in the case of flakes. Passive accumulation is consistent with the similarity in metal:metal ratios in flakes and the matrix. Where no box plot is shown, either one or both of the elements in question were not present in the region of interest.