The nature and origin of nucleus-like intracellular inclusions in Paleoproterozoic eukaryote microfossils

Polysphaeroides filiformis, a proterozoic cyanobacterial microfossil and implications for cyanobacteria evolution

Deciphering the fossil record of cyanobacteria is crucial to understand their role in the chemical and biological evolution of the early Earth. They profoundly modified the redox conditions of early ecosystems more than 2.4 Ga ago, the age of the Great Oxidation Event (GOE), and provided the ancestor of the chloroplast by endosymbiosis, leading the diversification of photosynthetic eukaryotes. Here, we analyze the morphology, ultrastructure, chemical composition, and metals distribution of Polysphaeroides filiformis from the 1040-1006 Ma Mbuji-Mayi Supergroup (DR Congo). We evidence trilaminar and bilayered ultrastructures for the sheath and the cell wall, respectively, and the preservation of Ni-tetrapyrrole moieties derived from chlorophyll in intracellular inclusions. This approach allows an unambiguous interpretation of P. filiformis as a branched and multiseriate photosynthetic cyanobacterium belonging to the family of Stigonemataceae. It also provides a possible minimum age for the emergence of multiseriate true branching nitrogen-fixing and probably heterocytous cyanobacteria.

Colonial green algae in the Cambrian plankton

The fossil record indicates a major turnover in marine phytoplankton across the Ediacaran-Cambrian transition, coincident with the rise of animal-rich ecosystems. However, the diversity, affinities and ecologies of Cambrian phytoplankton are poorly understood, leaving unclear the role of animal interactions and the drivers of diversification. New exceptionally preserved acritarchs (problematic organic-walled microfossils) from the late early Cambrian (around 510 Ma) reveal colonial organization characterized by rings and plates of interconnected, geometrically arranged cells. The assemblage exhibits a wide but gradational variation in cell size, ornamentation and intercell connection, interpreted as representing one or more species with determinate (coenobial) colony formation via cell division, aggregation and growth by cell expansion. An equivalent strategy is known only among green algae, specifically chlorophycean chlorophytes. The fossils differ in detail from modern freshwater examples and apparently represent an earlier convergent radiation in marine settings. Known trade-offs between sinking risk and predator avoidance in colonial phytoplankton point to adaptations triggered by intensifying grazing pressure during a Cambrian metazoan invasion of the water column. The new fossils reveal that not all small acritarchs are unicellular resting cysts, and support an early Palaeozoic prominence of green algal phytoplankton as predicted by molecular biomarkers.

Distinguishing cellular from abiotic spheroidal microstructures in the ca. 3.4 Ga Strelley Pool Formation

The morphogenesis of most carbonaceous microstructures that resemble microfossils in Archean (4-2.5 Ga old) rocks remains debated. The associated carbonaceous matter may even-in some cases-derive from abiotic organic molecules. Mineral growths associated with organic matter migration may mimic microbial cells, some anatomical features, and known microfossils-in particular those with simple spheroid shapes. Here, spheroid microstructures from a chert of the ca. 3.4 Ga Strelley Pool Formation (SPF) of the Pilbara Craton (Western Australia) were imaged and analyzed with a combination of high-resolution in situ techniques. This provides new insights into carbonaceous matter distributions and their relationships with the crystallographic textures of associated quartz. Thus, we describe five new types of spheroids and discuss their morphogenesis. In at least three types of microstructures, wall coalescence argues for migration of carbonaceous matter onto abiotic siliceous spherulites or diffusion in poorly crystalline silica. The nanoparticulate walls of these coalescent structures often cut across multiple quartz crystals, consistent with migration in/on silica prior to quartz recrystallization. Sub-continuous walls lying at quartz boundaries occur in some coalescent vesicles. This weakens the "continuous carbonaceous wall" criterion proposed to support cellular inferences. In contrast, some clustered spheroids display wrinkled sub-continuous double walls, and a large sphere shows a thick sub-continuous wall with pustules and depressions. These features appear consistent with post-mortem cell alteration, although abiotic morphogenesis remains difficult to rule out. We compared these siliceous and carbonaceous microstructures to coalescent pyritic spheroids from the same sample, which likely formed as "colloidal" structures in hydrothermal context. The pyrites display a smaller size and only limited carbonaceous coatings, arguing that they could not have acted as precursors to siliceous spheroids. This study revealed new textural features arguing for abiotic morphogenesis of some Archean spheroids. The absence of these features in distinct types of spheroids leaves open the microfossil hypothesis in the same rock. Distinction of such characteristics could help addressing further the origin of other candidate microfossils. This study calls for similar investigations of metamorphosed microfossiliferous rocks and of the products of in vitro growth of cell-mimicking structures in presence of organics and silica.

Eukaryogenesis and oxygen in Earth history

The endosymbiotic origin of mitochondria during eukaryogenesis has long been viewed as an adaptive response to the oxygenation of Earth's surface environment, presuming a fundamentally aerobic lifestyle for the free-living bacterial ancestors of mitochondria. This oxygen-centric view has been robustly challenged by recent advances in the Earth and life sciences. While the permanent oxygenation of the atmosphere above trace concentrations is now thought to have occurred 2.2 billion years ago, large parts of the deep ocean remained anoxic until less than 0.5 billion years ago. Neither fossils nor molecular clocks correlate the origin of mitochondria, or eukaryogenesis more broadly, to either of these planetary redox transitions. Instead, mitochondria-bearing eukaryotes are consistently dated to between these two oxygenation events, during an interval of pervasive deep-sea anoxia and variable surface-water oxygenation. The discovery and cultivation of the Asgard archaea has reinforced metabolic evidence that eukaryogenesis was initially mediated by syntrophic H₂ exchange between an archaeal host and an α-proteobacterial symbiont living under anoxia. Together, these results temporally, spatially and metabolically decouple the earliest stages of eukaryogenesis from the oxygen content of the surface ocean and atmosphere. Rather than reflecting the ancestral metabolic state, obligate aerobiosis in eukaryotes is most probably derived, having only become globally widespread over the past 1 billion years as atmospheric oxygen approached modern levels.

Intracellular bound chlorophyll residues identify 1 Gyr-old fossils as eukaryotic algae

The acquisition of photosynthesis is a fundamental step in the evolution of eukaryotes. However, few phototrophic organisms are unambiguously recognized in the Precambrian record. The in situ detection of metabolic byproducts in individual microfossils is the key for the direct identification of their metabolisms. Here, we report a new integrative methodology using synchrotron-based X-ray fluorescence and absorption. We evidence bound nickel-geoporphyrins moieties in low-grade metamorphic rocks, preserved in situ within cells of a ~1 Gyr-old multicellular eukaryote, Arctacellularia tetragonala. We identify these moieties as chlorophyll derivatives, indicating that A. tetragonala was a phototrophic eukaryote, one of the first unambiguous algae. This new approach, applicable to overmature rocks, creates a strong new proxy to understand the evolution of phototrophy and diversification of early ecosystems.

Nuclear preservation in the cartilage of the Jehol dinosaur Caudipteryx

Previous findings on dinosaur cartilage material from the Late Cretaceous of Montana suggested that cartilage is a vertebrate tissue with unique characteristics that favor nuclear preservation. Here, we analyze additional dinosaur cartilage in Caudipteryx (STM4-3) from the Early Cretaceous Jehol biota of Northeast China. The cartilage fragment is highly diagenetically altered when observed in ground-sections but shows exquisite preservation after demineralization. It reveals transparent, alumino-silicified chondrocytes and brown, ironized chondrocytes. The histochemical stain Hematoxylin and Eosin (that stains the nucleus and cytoplasm in extant cells) was applied to both the demineralized cartilage of Caudipteryx and that of a chicken. The two specimens reacted identically, and one dinosaur chondrocyte revealed a nucleus with fossilized threads of chromatin. This is the second example of fossilized chromatin threads in a vertebrate material. These data show that some of the original nuclear biochemistry is preserved in this dinosaur cartilage material and further support the hypothesis that cartilage is very prone to nuclear fossilization and a perfect candidate to further understand DNA preservation in deep time.

Cryptic terrestrial fungus-like fossils of the early Ediacaran Period

The colonization of land by fungi had a significant impact on the terrestrial ecosystem and biogeochemical cycles on Earth surface systems. Although fungi may have diverged ~1500-900 million years ago (Ma) or even as early as 2400 Ma, it is uncertain when fungi first colonized the land. Here we report pyritized fungus-like microfossils preserved in the basal Ediacaran Doushantuo Formation (~635 Ma) in South China. These micro-organisms colonized and were preserved in cryptic karstic cavities formed via meteoric water dissolution related to deglacial isostatic rebound after the terminal Cryogenian snowball Earth event. They are interpreted as eukaryotes and probable fungi, thus providing direct fossil evidence for the colonization of land by fungi and offering a key constraint on fungal terrestrialization.

Radiation of nitrogen-metabolizing enzymes across the tree of life tracks environmental transitions in Earth history

Nitrogen is an essential element to life and exerts a strong control on global biological productivity. The rise and spread of nitrogen-utilizing microbial metabolisms profoundly shaped the biosphere on the early Earth. Here, we reconciled gene and species trees to identify birth and horizontal gene transfer events for key nitrogen-cycling genes, dated with a time-calibrated tree of life, in order to examine the timing of the proliferation of these metabolisms across the tree of life. Our results provide new insights into the evolution of the early nitrogen cycle that expand on geochemical reconstructions. We observed widespread horizontal gene transfer of molybdenum-based nitrogenase back to the Archean, minor horizontal transfer of genes for nitrate reduction in the Archean, and an increase in the proliferation of genes metabolizing nitrite around the time of the Mesoproterozoic (~1.5 Ga). The latter coincides with recent geochemical evidence for a mid-Proterozoic rise in oxygen levels. Geochemical evidence of biological nitrate utilization in the Archean and early Proterozoic may reflect at least some contribution of dissimilatory nitrate reduction to ammonium (DNRA) rather than pure denitrification to N₂ . Our results thus help unravel the relative dominance of two metabolic pathways that are not distinguishable with current geochemical tools. Overall, our findings thus provide novel constraints for understanding the evolution of the nitrogen cycle over time and provide insights into the bioavailability of various nitrogen sources in the early Earth with possible implications for the emergence of eukaryotic life.

Nucleus preservation in early Ediacaran Weng'an embryo-like fossils, experimental taphonomy of nuclei and implications for reading the eukaryote fossil record

The challenge of identifying fossilized organelles has long hampered attempts to interpret the fossil record of early eukaryote evolution. We explore this challenge through experimental taphonomy of nuclei in a living eukaryote and microscale physical and chemical characterization of putative nuclei in embryo-like fossils from the early Ediacaran Weng'an Biota. The fossil nuclei exhibit diverse preservational modes that differ in shape, presence or absence of an inner body and the chemistry of the associated mineralization. The nuclei are not directly fossilized; rather, they manifest as external moulds. Experimental taphonomy of epidermal cells from the common onion (Allium cepa) demonstrates that nuclei are more decay resistant than their host cells, generally maintaining their physical dimensions for weeks to months post-mortem, though under some experimental conditions they exhibit shrinkage and/or become shrouded in microbial biofilms. The fossil and experimental evidence may be rationalized in a single taphonomic pathway of selective mineralization of the cell cytoplasm, preserving an external mould of the nucleus that is itself resistant to both decay and mineral replication. Combined, our results provide both a secure identification of the Weng'an nuclei as well as the potential of a fossil record of organelles that might help arbitrate in long-standing debates over the relative and absolute timing of the evolutionary assembly of eukaryote-grade cells.

Identifying microbial life in rocks: Insights from population morphometry

The identification of cellular life in the rock record is problematic, since microbial life forms, and particularly bacteria, lack sufficient morphologic complexity to be effectively distinguished from certain abiogenic features in rocks. Examples include organic pore-fillings, hydrocarbon-containing fluid inclusions, organic coatings on exfoliated crystals and biomimetic mineral aggregates (biomorphs). This has led to the interpretation and re-interpretation of individual microstructures in the rock record. The morphologic description of entire populations of microstructures, however, may provide support for distinguishing between preserved micro-organisms and abiogenic objects. Here, we present a statistical approach based on quantitative morphological description of populations of microstructures. Images of modern microbial populations were compared to images of two relevant types of abiogenic microstructures: interstitial spaces and silica-carbonate biomorphs. For the populations of these three systems, the size, circularity, and solidity of individual particles were calculated. Subsequently, the mean/SD, skewness, and kurtosis of the statistical distributions of these parameters were established. This allowed the qualitative and quantitative comparison of distributions in these three systems. In addition, the fractal dimension and lacunarity of the populations were determined. In total, 11 parameters, independent of absolute size or shape, were used to characterize each population of microstructures. Using discriminant analysis with parameter subsets, it was found that size and shape distributions are typically sufficient to discriminate populations of biologic and abiogenic microstructures. Analysis of ancient, yet unambiguously biologic, samples (1.0 Ga Angmaat Formation, Baffin Island, Canada) suggests that taphonomic effects can alter morphometric characteristics and complicate image analysis; therefore, a wider range of microfossil assemblages should be studied in the future before automated analyses can be developed. In general, however, it is clear from our results that there is great potential for morphometric descriptions of populations in the context of life recognition in rocks, either on Earth or on extraterrestrial bodies.

1 billion-year-old cell contents preserved in monazite and xenotime

Exceptional microfossil preservation, whereby sub-cellular details of an organism are conserved, remains extremely rare in the Precambrian rock record. We here report the first occurrence of exceptional cellular preservation by the rare earth element (REE) phosphates monazite and xenotime. This occurs in ~1 billion-year-old lake sediments where REEs were likely concentrated by local erosion and drainage into a closed lacustrine basin. Monazite and xenotime preferentially occur inside planktonic cells where they preserve spheroidal masses of plasmolyzed cell contents, and occasionally also membranous fragments. They have not been observed associated with cell walls or sheaths, which are instead preserved by clay minerals or francolite. REE phosphates are interpreted to be the earliest minerals precipitated in these cells after death, with their loci controlled by the micro-scale availability of inorganic phosphate (P_i) and REEs, probably sourced from polyphosphate granules within the cells. The strong affinity of REEs for phosphate and the insolubility of these minerals once formed means that REE phosphates have the potential for rapid preservation of cellular morphology after death and durability in the rock record. Hence, authigenic REE phosphates provide a promising new target in the search for the preservation of intra-cellular components of fossilised microorganisms.

After the boring billion and before the freezing millions: evolutionary patterns and innovations in the Tonian Period

The Tonian Period (ca. 1000–720 Ma) follows the ‘boring billion' in the Mesoproterozoic Era and precedes ‘snowball Earth' glaciations in the Cryogenian Period. It represents a critical transition in Earth history. Geochemical data indicate that the Tonian Period may have witnessed a significant increase in atmospheric pO2 levels and a major transition from predominantly sulfidic to ferruginous mid-depth seawaters. Molecular clock estimates suggest that early animals may have diverged in the Tonian Period, raising the intriguing possibility of coupled environmental changes and evolutionary innovations. The co-evolution of life and its environment during the Tonian Period can be tested against the fossil record by examining diversity trends in the Proterozoic and evolutionary innovations in the Tonian. Compilations of Proterozoic microfossils and macrofossils apparently support a Tonian increase in global taxonomic diversity and morphological range relative to the Mesoproterozoic Era, although this is not reflected in assemblage-level diversity patterns. The fossil record suggests that major eukaryote groups (including Opisthokonta, Amoebozoa, Plantae, and SAR) may have diverged and important evolutionary innovations (e.g. multicellularity and cell differentiation in several groups, eukaryovory, eukaryote biomineralization, and heterocystous cyanobacteria) may have arisen by the Tonian Period, but thus far no convincing animal fossils have been found in the Tonian. Tonian paleontology is still in its nascent stage, and it offers many opportunities to explore Earth-life evolution in this critical geological period.

Three-dimensional preservation of cellular and subcellular structures suggests 1.6 billion-year-old crown-group red algae

The ~1.6 Ga Tirohan Dolomite of the Lower Vindhyan in central India contains phosphatized stromatolitic microbialites. We report from there uniquely well-preserved fossils interpreted as probable crown-group rhodophytes (red algae). The filamentous form Rafatazmia chitrakootensis n. gen, n. sp. has uniserial rows of large cells and grows through diffusely distributed septation. Each cell has a centrally suspended, conspicuous rhomboidal disk interpreted as a pyrenoid. The septa between the cells have central structures that may represent pit connections and pit plugs. Another filamentous form, Denaricion mendax n. gen., n. sp., has coin-like cells reminiscent of those in large sulfur-oxidizing bacteria but much more recalcitrant than the liquid-vacuole-filled cells of the latter. There are also resemblances with oscillatoriacean cyanobacteria, although cell volumes in the latter are much smaller. The wider affinities of Denaricion are uncertain. Ramathallus lobatus n. gen., n. sp. is a lobate sessile alga with pseudoparenchymatous thallus, “cell fountains,” and apical growth, suggesting florideophycean affinity. If these inferences are correct, Rafatazmia and Ramathallus represent crown-group multicellular rhodophytes, antedating the oldest previously accepted red alga in the fossil record by about 400 million years.

The last common ancestor of modern eukaryotes is generally believed to have lived during the Mesoproterozoic era, about 1.6 to 1 billion years ago, or possibly somewhat earlier. We studied exquisitely preserved fossil communities from ~1.6 billion-year-old sedimentary rocks in central India representing a shallow-water marine environment characterized by photosynthetic biomats. We discovered amidst extensive cyanobacterial mats a biota of filamentous and lobate organisms that share significant features with modern eukaryotic algae, more specifically red algae. The rocks mainly consist of calcium and magnesium carbonates, but the microbial mats and the fossils are preserved in calcium phosphate, letting us view the cellular and subcellular structures in three dimensions with the use of synchrotron-radiation X-ray tomographic microscopy. The most conspicuous internal objects in the cells of the filamentous forms are rhomboidal platelets that we interpret to be part of the photosynthetic machinery of red algae. The lobate forms grew as radiating globular or finger-like protrusions from a common centre. These fossils predate the previously earliest accepted red algae by about 400 million years, suggesting that eukaryotes may have a longer history than commonly assumed.

Molecular preservation of 1.88 Ga Gunflint organic microfossils as a function of temperature and mineralogy

The significant degradation that fossilized biomolecules may experience during burial makes it challenging to assess the biogenicity of organic microstructures in ancient rocks. Here we investigate the molecular signatures of 1.88 Ga Gunflint organic microfossils as a function of their diagenetic history. Synchrotron-based XANES data collected in situ on individual microfossils, at the submicrometre scale, are compared with data collected on modern microorganisms. Despite diagenetic temperatures of ∼150–170 °C deduced from Raman data, the molecular signatures of some Gunflint organic microfossils have been exceptionally well preserved. Remarkably, amide groups derived from protein compounds can still be detected. We also demonstrate that an additional increase of diagenetic temperature of only 50 °C and the nanoscale association with carbonate minerals have significantly altered the molecular signatures of Gunflint organic microfossils from other localities. Altogether, the present study provides key insights for eventually decoding the earliest fossil record.

Thermal diagenesis is generally seen as detrimental to the preservation of organic biosignatures. Using synchrotron-based XANES data, Alleon et al. find preservation of the molecular signatures of organic microfossils from the 1.88 Ga Gunflint cherts.

Decimetre-scale multicellular eukaryotes from the 1.56-billion-year-old Gaoyuzhuang Formation in North China

Fossils of macroscopic eukaryotes are rarely older than the Ediacaran Period (635–541 million years (Myr)), and their interpretation remains controversial. Here, we report the discovery of macroscopic fossils from the 1,560-Myr-old Gaoyuzhuang Formation, Yanshan area, North China, that exhibit both large size and regular morphology. Preserved as carbonaceous compressions, the Gaoyuzhuang fossils have statistically regular linear to lanceolate shapes up to 30 cm long and nearly 8 cm wide, suggesting that the Gaoyuzhuang fossils record benthic multicellular eukaryotes of unprecedentedly large size. Syngenetic fragments showing closely packed ∼10 μm cells arranged in a thick sheet further reinforce the interpretation. Comparisons with living thalloid organisms suggest that these organisms were photosynthetic, although their phylogenetic placement within the Eukarya remains uncertain. The new fossils provide the strongest evidence yet that multicellular eukaryotes with decimetric dimensions and a regular developmental program populated the marine biosphere at least a billion years before the Cambrian Explosion.

Macroscopic organisms are rare in the fossil record until the Ediacaran Period, beginning 635 million years ago. Here, Zhu et al. report the discovery of 1.56-billion-year-old carbonaceous compression fossils that provide evidence of the evolution of macroscopic, multicellular eukaryotes long before the Ediacaran Period.

On the age of eukaryotes: evaluating evidence from fossils and molecular clocks

Our understanding of the phylogenetic relationships among eukaryotic lineages has improved dramatically over the few past decades thanks to the development of sophisticated phylogenetic methods and models of evolution, in combination with the increasing availability of sequence data for a variety of eukaryotic lineages. Concurrently, efforts have been made to infer the age of major evolutionary events along the tree of eukaryotes using fossil-calibrated molecular clock-based methods. Here, we review the progress and pitfalls in estimating the age of the last eukaryotic common ancestor (LECA) and major lineages. After reviewing previous attempts to date deep eukaryote divergences, we present the results of a Bayesian relaxed-molecular clock analysis of a large dataset (159 proteins, 85 taxa) using 19 fossil calibrations. We show that for major eukaryote groups estimated dates of divergence, as well as their credible intervals, are heavily influenced by the relaxed molecular clock models and methods used, and by the nature and treatment of fossil calibrations. Whereas the estimated age of LECA varied widely, ranging from 1007 (943-1102) Ma to 1898 (1655-2094) Ma, all analyses suggested that the eukaryotic supergroups subsequently diverged rapidly (i.e., within 300 Ma of LECA). The extreme variability of these and previously published analyses preclude definitive conclusions regarding the age of major eukaryote clades at this time. As more reliable fossil data on eukaryotes from the Proterozoic become available and improvements are made in relaxed molecular clock modeling, we may be able to date the age of extant eukaryotes more precisely.

Paleobiological perspectives on early eukaryotic evolution

Eukaryotic organisms radiated in Proterozoic oceans with oxygenated surface waters, but, commonly, anoxia at depth. Exceptionally preserved fossils of red algae favor crown group emergence more than 1200 million years ago, but older (up to 1600-1800 million years) microfossils could record stem group eukaryotes. Major eukaryotic diversification ~800 million years ago is documented by the increase in the taxonomic richness of complex, organic-walled microfossils, including simple coenocytic and multicellular forms, as well as widespread tests comparable to those of extant testate amoebae and simple foraminiferans and diverse scales comparable to organic and siliceous scales formed today by protists in several clades. Mid-Neoproterozoic establishment or expansion of eukaryophagy provides a possible mechanism for accelerating eukaryotic diversification long after the origin of the domain. Protists continued to diversify along with animals in the more pervasively oxygenated oceans of the Phanerozoic Eon.