Changing the picture of Earth's earliest fossils (3.5-1.9 Ga) with new approaches and new discoveries

Physicochemical origins of prokaryotic and eukaryotic organisms

Origins research currently rests on a vitalistic foundation and requires reconceptualization. From a cellular perspective, prokaryotic cells grow and divide in stable, colloidal processes, throughout which the cytoplasm remains crowded (concentrated) with closely interacting proteins and nucleic acids. Their functional stability is ensured by repulsive and attractive non-covalent forces, especially van der Waals forces, screened electrostatic forces, and hydrogen bonding (hydration and the hydrophobic effect). On average, biomacromolecules are crowded at above 15% volume fraction, surrounded by up to 3 nm layer of aqueous electrolyte at ionic strength above 0.01 molar; they are energized by biochemical reactions coupled to nutrient environments. During cellular growth, non-covalent molecular forces and biochemical reactions stabilize the cytoplasm as a two-phase, colloidal system comprising vectorially structured cytogel and dilute cytosol. From a geochemical perspective, Earth's rotation kept prebiotic molecules in continuous cyclic disequilibria in Usiglio-type intertidal pools, rich in potassium and magnesium ions, the last cations to precipitate from evaporatig seawater. These ions impart biochemical functionality to extant proteins and RNAs. The prebiotic molecules were repeatedly purified by phase separation in response to tidal drying and rewetting; they were chemically evolving as briny, carbonaceous inclusions in tidal sediments until the crowding transition allowed chemical evolution to proceeed toward Woesian progenotes, the Last Universal Common Ancestors (LUCAs) and the first prokaryotes. These cellular and geochemical processes are summarized as a jigsaw puzzle of the emerging and evolving prokaryotes. Their unavoidable cyclic fusions and rehydrations along Archaean coastlines initiated the emergence of complex Precambrian eukaryotes.

Chapter 4: A Geological and Chemical Context for the Origins of Life on Early Earth

Within the first billion years of Earth's history, the planet transformed from a hot, barren, and inhospitable landscape to an environment conducive to the emergence and persistence of life. This chapter will review the state of knowledge concerning early Earth's (Hadean/Eoarchean) geochemical environment, including the origin and composition of the planet's moon, crust, oceans, atmosphere, and organic content. It will also discuss abiotic geochemical cycling of the CHONPS elements and how these species could have been converted to biologically relevant building blocks, polymers, and chemical networks. Proposed environments for abiogenesis events are also described and evaluated. An understanding of the geochemical processes under which life may have emerged can better inform our assessment of the habitability of other worlds, the potential complexity that abiotic chemistry can achieve (which has implications for putative biosignatures), and the possibility for biochemistries that are vastly different from those on Earth.

Multi-Technique Characterization of 3.45 Ga Microfossils on Earth: A Key Approach to Detect Possible Traces of Life in Returned Samples from Mars

The NASA Mars 2020 Perseverance rover is actively exploring Jezero crater to conduct analyses on igneous and sedimentary rock targets from outcrops located on the crater floor (Máaz and Séítah formations) and from the delta deposits, respectively. The rock samples collected during this mission will be recovered during the Mars Sample Return mission, which plans to bring samples back to Earth in the 2030s to conduct in-depth studies using sophisticated laboratory instrumentation. Some of these samples may contain traces of ancient martian life that may be particularly difficult to detect and characterize because of their morphological simplicity and subtle biogeochemical expressions. Using the volcanic sediments of the 3.45 Ga Kitty's Gap Chert (Pilbara, Australia), containing putative early life forms (chemolithotrophs) and considered as astrobiological analogues for potential early Mars organisms, we document the steps required to demonstrate the syngenicity and biogenicity of such biosignatures using multiple complementary analytical techniques to provide information at different scales of observation. These include sedimentological, petrological, mineralogical, and geochemical analyses to demonstrate macro- to microscale habitability. New approaches, some unavailable at the time of the original description of these features, are used to verify the syngenicity and biogenicity of the purported fossil chemolithotrophs. The combination of elemental (proton-induced X-ray emission spectrometry) and molecular (deep-ultraviolet and Fourier transform infrared) analyses of rock slabs, thin sections, and focused ion beam sections reveals that the carbonaceous matter present in the samples is enriched in trace metals (e.g., V, Cr, Fe, Co) and is associated with aromatic and aliphatic molecules, which strongly support its biological origin. Transmission electron microscopy observations of the carbonaceous matter documented an amorphous nanostructure interpreted to correspond to the degraded remains of microorganisms and their by-products (extracellular polymeric substances, filaments…). Nevertheless, a small fraction of carbonaceous particles has signatures that are more metamorphosed. They probably represent either reworked detrital biological or abiotic fragments of mantle origin. This study serves as an example of the analytical protocol that would be needed to optimize the detection of fossil traces of life in martian rocks.

Microbially mediated fossil concretions and their characterization by the latest methodologies: a review

The study of well-preserved organic matter (OM) within mineral concretions has provided key insights into depositional and environmental conditions in deep time. Concretions of varied compositions, including carbonate, phosphate, and iron-based minerals, have been found to host exceptionally preserved fossils. Organic geochemical characterization of concretion-encapsulated OM promises valuable new information of fossil preservation, paleoenvironments, and even direct taxonomic information to further illuminate the evolutionary dynamics of our planet and its biota. Full exploitation of this largely untapped geochemical archive, however, requires a sophisticated understanding of the prevalence, formation controls and OM sequestration properties of mineral concretions. Past research has led to the proposal of different models of concretion formation and OM preservation. Nevertheless, the formation mechanisms and controls on OM preservation in concretions remain poorly understood. Here we provide a detailed review of the main types of concretions and formation pathways with a focus on the role of microbes and their metabolic activities. In addition, we provide a comprehensive account of organic geochemical, and complimentary inorganic geochemical, morphological, microbial and paleontological, analytical methods, including recent advancements, relevant to the characterization of concretions and sequestered OM. The application and outcome of several early organic geochemical studies of concretion-impregnated OM are included to demonstrate how this underexploited geo-biological record can provide new insights into the Earth's evolutionary record. This paper also attempts to shed light on the current status of this research and major challenges that lie ahead in the further application of geo-paleo-microbial and organic geochemical research of concretions and their host fossils. Recent efforts to bridge the knowledge and communication gaps in this multidisciplinary research area are also discussed, with particular emphasis on research with significance for interpreting the molecular record in extraordinarily preserved fossils.

Archean (3.3 Ga) paleosols and paleoenvironments of Western Australia

The Pilbara craton of northwestern Australia is known for what were, when reported, the oldest known microfossils and paleosols on Earth. Both interpretations are mired in controversy, and neither remain the oldest known. Both the microfossils and the paleosols have been considered hydrothermal artefacts: carbon films of vents and a large hydrothermal cupola, respectively. This study resampled and analyzed putative paleosols within and below the Strelley Pool Formation (3.3 Ga), at four classic locations: Strelley Pool, Steer Ridge, Trendall Ridge, and Streckfuss, and also at newly discovered outcrops near Marble Bar. The same sequence of sedimentary facies and paleosols was newly recognized unconformably above the locality for microfossils in chert of the Apex Basalt (3.5 Ga) near Marble Bar. The fossiliferous Apex chert was not a hydrothermal vein but a thick (15 m) sedimentary interbed within a sequence of pillow basalts, which form an angular unconformity capped by the same pre-Strelley paleosol and Strelley Pool Formation facies found elsewhere in the Pilbara region. Baritic alluvial paleosols within the Strelley Pool Formation include common microfossil spindles (cf. Eopoikilofusa) distinct from marine microfossil communities with septate filaments (Primaevifilum) of cherts in the Apex and Mt Ada Basalts. Phosphorus and iron depletion in paleosols within and below the Strelley Pool Formation are evidence of soil communities of stable landscapes living under an atmosphere of high CO2 (2473 ± 134 ppmv or 8.8 ± 0.5 times preindustrial atmospheric level of 280 ppm) and low O2 (2181 ± 3018 ppmv or 0.01 ± 0.014 times modern).

Phylogenomics of five Pseudanabaena cyanophages and evolutionary traces of horizontal gene transfer

BACKGROUND

Along with the fast development and urbanization in developing countries, the waterbodies aside the growing cities become heavily polluted and highly eutrophic, thus leading to the seasonal outbreak of cyanobacterial bloom. Systematic isolation and characterization of freshwater cyanophages might provide a biological solution to control the awful blooms. However, genomic sequences and related investigations on the freshwater cyanophages remain very limited to date.

RESULTS

Following our recently reported five cyanophages Pam1~Pam5 from Lake Chaohu in China, here we isolated another five cyanophages, termed Pan1~Pan5, which infect the cyanobacterium Pseudanabaena sp. Chao 1811. Whole-genome sequencing showed that they all contain a double-stranded DNA genome of 37.2 to 72.0 kb in length, with less than half of the putative open reading frames annotated with known functions. Remarkably, the siphophage Pan1 encodes an auxiliary metabolic gene phoH and constitutes, together with the host, a complete queuosine modification pathway. Proteomic analyses revealed that although Pan1~Pan5 are distinct from each other in evolution, Pan1 and Pan3 are somewhat similar to our previously identified cyanophages Pam3 and Pam1 at the genomic level, respectively. Moreover, phylogenetic analyses suggested that Pan1 resembles the α-proteobacterial phage vB_DshS-R5C, revealing direct evidence for phage-mediated horizontal gene transfer between cyanobacteria and α-proteobacteria.

CONCLUSION

In addition to the previous reports of Pam1~Pam5, the present findings on Pan1~Pan5 largely enrich the library of reference freshwater cyanophages. The abundant genomic information provides a pool to identify novel genes and proteins of unknown function. Moreover, we found for the first time the evolutionary traces in the cyanophage that horizontal gene transfer might occur at the level of not only inter-species, but even inter-phylum. It indicates that the bacteriophage or cyanophage could be developed as a powerful tool for gene manipulation among various species or phyla.

In Situ Identification of Paleoarchean Biosignatures Using Colocated Perseverance Rover Analyses: Perspectives for In Situ Mars Science and Sample Return

The NASA Mars 2020 Perseverance rover is currently exploring Jezero crater, a Noachian-Hesperian locality that once hosted a delta-lake system with high habitability and biosignature preservation potential. Perseverance conducts detailed appraisals of rock targets using a synergistic payload capable of geological characterization from kilometer to micron scales. The highest-resolution textural and chemical information will be provided by correlated WATSON (imaging), SHERLOC (deep-UV Raman and fluorescence spectroscopy), and PIXL (X-ray lithochemistry) analyses, enabling the distributions of organic and mineral phases within rock targets to be comprehensively established. Herein, we analyze Paleoarchean microbial mats from the ∼3.42 Ga Buck Reef Chert (Barberton greenstone belt, South Africa)-considered astrobiological analogues for a putative ancient martian biosphere-following a WATSON-SHERLOC-PIXL protocol identical to that conducted by Perseverance on Mars during all sampling activities. Correlating deep-UV Raman and fluorescence spectroscopic mapping with X-ray elemental mapping, we show that the Perseverance payload has the capability to detect thermally and texturally mature organic materials of biogenic origin and can highlight organic-mineral interrelationships and elemental colocation at fine spatial scales. We also show that the Perseverance protocol obtains very similar results to high-performance laboratory imaging, Raman spectroscopy, and μXRF instruments. This is encouraging for the prospect of detecting microscale organic-bearing textural biosignatures on Mars using the correlative micro-analytical approach enabled by WATSON, SHERLOC, and PIXL; indeed, laminated, organic-bearing samples such as those studied herein are considered plausible analogues of biosignatures from a potential Noachian-Hesperian biosphere. Were similar materials discovered at Jezero crater, they would offer opportunities to reconstruct aspects of the early martian carbon cycle and search for potential fossilized traces of life in ancient paleoenvironments. Such samples should be prioritized for caching and eventual return to Earth.

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.

Multiwavelength Ablation/Ionization and Mass Spectrometric Analysis of 1.88 Ga Gunflint Chert

The investigation of chemical composition on planetary bodies without significant sample processing is of importance for nearly every mission aimed at robotic exploration. Moreover, it is a necessary tool to achieve the longstanding goal of finding evidence of life beyond Earth, for example, possibly preserved microbial remains within martian sediments. Our Laser Ablation Ionization Mass Spectrometer (LIMS) is a compact time-of-flight mass spectrometer intended to investigate the elemental, isotope, and molecular composition of a wide range of solid samples, including e.g., low bulk density organic remains in microfossils. Here, we present an overview of the instrument and collected chemical spectrometric data at the micrometer level from a Precambrian chert sample (1.88 Ga Gunflint Formation, Ontario, Canada), which is considered to be a martian analogue. Data were collected from two distinct zones-a silicified host area and a carbon-bearing microfossil assemblage zone. We performed these measurements using an ultrafast pulsed laser system (pulse width of ∼180 fs) with multiple wavelengths (infrared [IR]-775 nm, ultraviolet [UV]-387 nm, UV-258 nm) and using a pulsed high voltage on the mass spectrometer to reveal small organic signals. We investigated (1) the chemical composition of the sample and (2) the different laser wavelengths' performance to provide chemical depth profiles in silicified media. Our key findings are as follows: (1) microfossils from the Gunflint chert reveal a distinct chemical composition compared with the host mineralogy (we report the identification of 24 elements in the microfossils); (2) detection of the pristine composition of microfossils and co-occurring fine chemistry (rare earth elements) requires utilization of the depth profiling measurement protocol; and (3) our results show that, for analysis of heterogeneous material from siliciclastic deposits, siliceous sinters, and cherts, the most suitable wavelength for laser ablation/Ionization is UV-258 nm.

The tumor suppression theory of aging

Despite continued increases in human life expectancy, the factors determining the rate of human biological aging remain unknown. Without understanding the molecular mechanisms underlying aging, efforts to prevent aging are unlikely to succeed. The tumor suppression theory of aging introduced here proposes somatic mutation as the proximal cause of aging, but postulates that oncogenic transformation and clonal expansion, not functional impairment, are the relevant consequences of somatic mutation. Obesity and caloric restriction accelerate and decelerate aging due to their effect on cell proliferation, during which most mutations arise. Most phenotypes of aging are merely tumor-suppressive mechanisms that evolved to limit malignant growth, the dominant age-related cause of death in early and middle life. Cancer limits life span for most long-lived mammals, a phenomenon known as Peto's paradox. Its conservation across species demonstrates that mutation is a fundamental but hard limit on mammalian longevity. Cell senescence and apoptosis and differentiation induced by oncogenes, telomere shortening or DNA damage evolved as a second line of defense to limit the tumorigenic potential of clonally expanding cells, but accumulating senescent cells, senescence-associated secretory phenotypes and stem cell exhaustion eventually cause tissue dysfunction and the majority, if not most, phenotypes of aging.

Fossil cells

Philip Donoghue introduces the fossil record of cells.

Ancient Oil as a Source of Carbonaceous Matter in 1.88-Billion-Year-Old Gunflint Stromatolites and Microfossils

The 1.88-billion-year-old Gunflint carbonaceous microfossils are renowned for their exceptional morphological and chemical preservation, attributed to early and rapid entombment in amorphous silica. The carbonaceous matter lining and partly filling filamentous and spherical structures is interpreted to be indigenous, representing thermally altered relicts of cellular material (i.e., kerogen). Here we show that stromatolitic black cherts from the Gunflint Formation, Schreiber Beach, Ontario, Canada, were saturated in syn-sedimentary oil. The thermally altered oil (pyrobitumen), which occurs in the stromatolites and intercolumn sediments, fills pores and fractures, and coats detrital and diagenetic grain surfaces. The occurrence of detrital bitumen grains in the stromatolites points to the proximity of shallow seafloor oil seeps and hence the possible existence of chemosynthetic microbes degrading hydrocarbons. We suggest that hydrocarbons that migrated through the silicifying stromatolites infiltrated semi-hollow microbial molds that formed following silica nucleation on the walls or sheaths of decayed cells. Upon heating, the hydrocarbons were transformed to nanoporous pyrobitumen, retarding silica recrystallization and enhancing detailed preservation of the carbon-rich microfossils. Hydrocarbon infiltration of silicified microbes offers a new explanation for the preservation of the Gunflint microfossils and may have played a role in the formation of some of Earth's oldest microfossils.

A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids

In modern oceans, eukaryotic phytoplankton is dominated by lineages with red algal-derived plastids such as diatoms, dinoflagellates, and coccolithophores. Despite the ecological importance of these groups and many others representing a huge diversity of forms and lifestyles, we still lack a comprehensive understanding of their evolution and how they obtained their plastids. New hypotheses have emerged to explain the acquisition of red algal-derived plastids by serial endosymbiosis, but the chronology of these putative independent plastid acquisitions remains untested. Here, we establish a timeframe for the origin of red algal-derived plastids under scenarios of serial endosymbiosis, using Bayesian molecular clock analyses applied on a phylogenomic dataset with broad sampling of eukaryote diversity. We find that the hypotheses of serial endosymbiosis are chronologically possible, as the stem lineages of all red plastid-containing groups overlap in time. This period in the Meso- and Neoproterozoic Eras set the stage for the later expansion to dominance of red algal-derived primary production in the contemporary oceans, which profoundly altered the global geochemical and ecological conditions of the Earth.

Bone metabolism and evolutionary origin of osteocytes: Novel application of FIB-SEM tomography

Lacunae and canaliculi spaces of osteocytes are remarkably well preserved in fossilized bone and serve as an established proxy for bone cells. The earliest bone in the fossil record is acellular (anosteocytic), followed by cellular (osteocytic) bone in the jawless relatives of jawed vertebrates, the osteostracans, about 400 million years ago. Virtually nothing is known about the physiological pressures that would have initially favored osteocytic over anosteocytic bone. We apply focused ion beam-scanning electron microscopy tomography combined with machine learning for cell detection and segmentation to image fossil cell spaces. Novel three-dimensional high-resolution images reveal areas of low density around osteocyte lacunae and their canaliculi in osteostracan bone. This provides evidence for demineralization that would have occurred in vivo as part of osteocytic osteolysis, a mechanism of mineral homeostasis, supporting the hypothesis that a physiological demand for phosphorus was the principal driver in the initial evolution of osteocytic bone.

New preparation techniques for molecular and in-situ analysis of ancient organic micro- and nanostructures

Organic microfossils preserved in three dimensions in transparent mineral matrices such as cherts/quartzites, phosphates, or carbonates are best studied in petrographic thin sections. Moreover, microscale mass spectrometry techniques commonly require flat, polished surfaces to minimize analytical bias. However, contamination by epoxy resin in traditional petrographic sections is problematic for the geochemical study of the kerogen in these microfossils and more generally for the in situ analysis of fossil organic matter. Here, we show that epoxy contamination has a molecular signature that is difficult to distinguish from kerogen with time-of-flight secondary ion mass spectrometry (ToF-SIMS). This contamination appears pervasive in organic microstructures embedded in micro- to nano-crystalline carbonate. To solve this problem, a new semi-thin section preparation protocol without resin medium was developed for micro- to nanoscale in situ investigation of insoluble organic matter. We show that these sections are suited for microscopic observation of Proterozoic microfossils in cherts. ToF-SIMS reveals that these sections are free of pollution after final removal of a <10 nm layer of contamination using low-dose ion sputtering. ToF-SIMS maps of fragments from aliphatic and aromatic molecules and organic sulfur are correlated with the spatial distribution of organic microlaminae in a Jurassic stromatolite. Hydrocarbon-derived ions also appeared correlated with kerogenous microstructures in Archean cherts. These developments in analytical procedures should help future investigations of organic matter and in particular, microfossils, by allowing the spatial correlation of microscopy, spectroscopy, precise isotopic microanalyses, and novel molecular microanalyses such as ToF-SIMS.

Nanoscale 3D quantitative imaging of 1.88 Ga Gunflint microfossils reveals novel insights into taphonomic and biogenic characters

Precambrian cellular remains frequently have simple morphologies, micrometric dimensions and are poorly preserved, imposing severe analytical and interpretational challenges, especially for irrefutable attestations of biogenicity. The 1.88 Ga Gunflint biota is a Precambrian microfossil assemblage with different types and qualities of preservation across its numerous geological localities and provides important insights into the Proterozoic biosphere and taphonomic processes. Here we use synchrotron-based ptychographic X-ray computed tomography to investigate well-preserved carbonaceous microfossils from the Schreiber Beach locality as well as poorly-preserved, iron-replaced fossil filaments from the Mink Mountain locality, Gunflint Formation. 3D nanoscale imaging with contrast based on electron density allowed us to assess the morphology and carbonaceous composition of different specimens and identify the minerals associated with their preservation based on retrieved mass densities. In the Mink Mountain filaments, the identification of mature kerogen and maghemite rather than the ubiquitously described hematite indicates an influence from biogenic organics on the local maturation of iron oxides through diagenesis. This non-destructive 3D approach to microfossil composition at the nanoscale within their geological context represents a powerful approach to assess the taphonomy and biogenicity of challenging or poorly preserved traces of early microbial life, and may be applied effectively to extraterrestrial samples returned from upcoming space missions.

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.

The degradation of organic compounds impacts the crystallization of clay minerals and vice versa

Expanding our capabilities to unambiguously identify ancient traces of life in ancient rocks requires laboratory experiments to better constrain the evolution of biomolecules during advanced fossilization processes. Here, we submitted RNA to hydrothermal conditions in the presence of a gel of Al-smectite stoichiometry at 200 °C for 20 days. NMR and STXM-XANES investigations revealed that the organic fraction of the residues is no longer RNA, nor the quite homogeneous aromatic-rich residue obtained in the absence of clays, but rather consists of particles of various chemical composition including amide-rich compounds. Rather than the pure clays obtained in the absence of RNA, electron microscopy (SEM and TEM) and diffraction (XRD) data showed that the mineralogy of the experimental residues includes amorphous silica and aluminosilicates mixed together with nanoscales phosphates and clay minerals. In addition to the influence of clay minerals on the degradation of organic compounds, these results evidence the influence of the presence of organic compounds on the nature of the mineral assemblage, highlighting the importance of fine-scale mineralogical investigations when discussing the nature/origin of organo-mineral microstructures found in ancient rocks.

Evaluating Biogenicity on the Geological Record With Synchrotron-Based Techniques

The biogenicity problem of geological materials is one of the most challenging ones in the field of paleo and astrobiology. As one goes deeper in time, the traces of life become feeble and ambiguous, blending with the surrounding geology. Well-preserved metasedimentary rocks from the Archaean are relatively rare, and in very few cases contain structures resembling biological traces or fossils. These putative biosignatures have been studied for decades and many biogenicity criteria have been developed, but there is still no consensus for many of the proposed structures. Synchrotron-based techniques, especially on new generation sources, have the potential for contributing to this field of research, providing high sensitivity and resolution that can be advantageous for different scientific problems. Exploring the X-ray and matter interactions on a range of geological materials can provide insights on morphology, elemental composition, oxidation states, crystalline structure, magnetic properties, and others, which can measurably contribute to the investigation of biogenicity of putative biosignatures. Here, we provide an overview of selected synchrotron-based techniques that have the potential to be applied in different types of questions on the study of biosignatures preserved in the geological record. The development of 3rd and recently 4th generation synchrotron sources will favor a deeper understanding of the earliest records of life on Earth and also bring up potential analytical approaches to be applied for the search of biosignatures in meteorites and samples returned from Mars in the near future.

Paleo-Rock-Hosted Life on Earth and the Search on Mars: A Review and Strategy for Exploration

Here we review published studies on the abundance and diversity of terrestrial rock-hosted life, the environments it inhabits, the evolution of its metabolisms, and its fossil biomarkers to provide guidance in the search for life on Mars. Key findings are (1) much terrestrial deep subsurface metabolic activity relies on abiotic energy-yielding fluxes and in situ abiotic and biotic recycling of metabolic waste products rather than on buried organic products of photosynthesis; (2) subsurface microbial cell concentrations are highest at interfaces with pronounced chemical redox gradients or permeability variations and do not correlate with bulk host rock organic carbon; (3) metabolic pathways for chemolithoautotrophic microorganisms evolved earlier in Earth's history than those of surface-dwelling phototrophic microorganisms; (4) the emergence of the former occurred at a time when Mars was habitable, whereas the emergence of the latter occurred at a time when the martian surface was not continually habitable; (5) the terrestrial rock record has biomarkers of subsurface life at least back hundreds of millions of years and likely to 3.45 Ga with several examples of excellent preservation in rock types that are quite different from those preserving the photosphere-supported biosphere. These findings suggest that rock-hosted life would have been more likely to emerge and be preserved in a martian context. Consequently, we outline a Mars exploration strategy that targets subsurface life and scales spatially, focusing initially on identifying rocks with evidence for groundwater flow and low-temperature mineralization, then identifying redox and permeability interfaces preserved within rock outcrops, and finally focusing on finding minerals associated with redox reactions and associated traces of carbon and diagnostic chemical and isotopic biosignatures. Using this strategy on Earth yields ancient rock-hosted life, preserved in the fossil record and confirmable via a suite of morphologic, organic, mineralogical, and isotopic fingerprints at micrometer scale. We expect an emphasis on rock-hosted life and this scale-dependent strategy to be crucial in the search for life on Mars.

Organic geochemical approaches to understanding early life

Here we discuss the early geological record of preserved organic carbon and the criteria that must be applied to distinguish biological from non-biological origins. Sedimentary graphite, irrespective of its isotopic composition, does not constitute a reliable biosignature because the rocks in which it is found are generally metamorphosed to the point where convincing signs of life have been erased. Rather, multiple lines of evidence, including sedimentary textures, microfossils, large accumulations of organic matter and isotopic data for co-existing carbon, nitrogen and sulfur are required before biological origin can be convincingly demonstrated.

A New Frontier for Palaeobiology: Earth's Vast Deep Biosphere

Diverse micro-organisms populate a global deep biosphere hosted by rocks and sediments beneath land and sea, containing more biomass than any other biome except forests. This paper reviews an emerging palaeobiological archive of these dark habitats: microfossils preserved in ancient pores and fractures in the crust. This archive, seemingly dominated by mineralized filaments (although rods and coccoids are also reported), is presently far too sparsely sampled and poorly understood to reveal trends in the abundance, distribution, or diversity of deep life through time. New research is called for to establish the nature and extent of the fossil record of Earth's deep biosphere by combining systematic exploration, rigorous microanalysis, and experimental studies of both microbial preservation and the formation of abiotic pseudofossils within the crust. It is concluded that the fossil record of Earth's largest microbial habitat may still have much to tell us about the history of life, the evolution of biogeochemical cycles, and the search for life on Mars.

Extracellular and Intracellular Biomineralization Induced by Bacillus licheniformis DB1-9 at Different Mg/Ca Molar Ratios

Biomineralization has become a research hotspot and attracted widespread attention in the field of carbonate sedimentology. In this study, precipitation of carbonate minerals was induced by Bacillus licheniformis DB1-9 bacteria, (identity confirmed with its phylogenetic tree), to further explore the biomineralization mechanisms. During experiments, lasting up to 24 days with varying Mg/Ca molar ratios and regular monitoring of conditions, ammonia and carbonic anhydrase are released by the bacteria, resulting in a pH increase. Carbonic anhydrase could have promoted carbon dioxide hydration to produce bicarbonate and carbonate ions, and so promoted supersaturation to facilitate the precipitation of carbonate minerals. These include rhombohedral, dumbbell-shaped, and elongated calcite crystals; aragonite appears in the form of mineral aggregates. In addition, spheroidal and fusiform minerals are precipitated. FTIR results show there are organic functional groups, such as C–O–C and C=O, as well as the characteristic peaks of calcite and aragonite; these indicate that there is a close relationship between the bacteria and the minerals. Ultrathin slices of the bacteria analyzed by HRTEM, SAED, EDS, and STEM show that precipitate within the extracellular polymeric substances (EPS) has a poor crystal structure, and intracellular granular areas have no crystal structure. Fluorescence intensity and STEM results show that calcium ions can be transported from the outside to the inside of the cells. This study provides further insights to our understanding of biomineralization mechanisms induced by microorganisms.

The Ladder of Life Detection

We describe the history and features of the Ladder of Life Detection, a tool intended to guide the design of investigations to detect microbial life within the practical constraints of robotic space missions. To build the Ladder, we have drawn from lessons learned from previous attempts at detecting life and derived criteria for a measurement (or suite of measurements) to constitute convincing evidence for indigenous life. We summarize features of life as we know it, how specific they are to life, and how they can be measured, and sort these features in a general sense based on their likelihood of indicating life. Because indigenous life is the hypothesis of last resort in interpreting life-detection measurements, we propose a small but expandable set of decision rules determining whether the abiotic hypothesis is disproved. In light of these rules, we evaluate past and upcoming attempts at life detection. The Ladder of Life Detection is not intended to endorse specific biosignatures or instruments for life-detection measurements, and is by no means a definitive, final product. It is intended as a starting point to stimulate discussion, debate, and further research on the characteristics of life, what constitutes a biosignature, and the means to measure them.

Improving preservation state assessment of carbonate microfossils in paleontological research using label-free stimulated Raman imaging

In micropaleontological and paleoclimatological studies based on microfossil morphology and geochemistry, assessing the preservation state of fossils is of the highest importance, as diagenetic alteration invalidates textural features and compromises the correct interpretation of stable isotope and trace elemental analysis. In this paper, we present a novel non-invasive and label-free tomographic approach to reconstruct the three-dimensional architecture of microfossils with submicron resolution based on stimulated Raman scattering (SRS). Furthermore, this technique allows deciphering the three-dimensional (3D) distribution of the minerals within these fossils in a chemically sensitive manner. Our method, therefore, allows to identify microfossils, to chemically map their internal structure and eventually to determine their preservation state. We demonstrate the effectiveness of this method by analyzing several benthic and planktonic foraminifera, obtaining full 3D distributions of carbonate, iron oxide and porosity for each specimen. Subsequently, the preservation state of each microfossil can be assessed using these 3D compositional maps. The technique is highly sensitive, non-destructive, time-efficient and avoids the need for sample pretreatment. Therefore, its predestined application is the final check of the state of microfossils before applying subsequent geochemical analyses.

Changes of aliphatic C-H bonds in cyanobacteria during experimental thermal maturation in the presence or absence of silica as evaluated by FTIR microspectroscopy

Aliphatic C-H bonds are one of the major organic signatures detected in Proterozoic organic microfossils, and their origin is a topic of interest. To investigate the influence of the presence of silica on the thermal alteration of aliphatic C-H bonds in prokaryotic cells during diagenesis, cyanobacteria Synechocystis sp. PCC6803 were heated at temperatures of 250-450°C. Changes in the infrared (IR) signals were monitored by micro-Fourier transform infrared (FTIR) spectroscopy. Micro-FTIR shows that absorbances at 2,925 cm^-1 band (aliphatic CH₂ ) and 2,960 cm^-1 band (aliphatic CH₃ ) decrease during heating, indicating loss of the C-H bonds, which was delayed by the presence of silica. A theoretical approach using solid-state kinetics indicates that the most probable process for the aliphatic C-H decrease is three-dimensional diffusion of alteration products under both non-embedded and silica-embedded conditions. The extrapolation of the experimental results obtained at 250-450°C to lower temperatures implies that the rate constant for CH₃ (k_CH3 ) is similar to or lower than that for CH₂ (k_CH2 ; i.e., CH₃ decreases at a similar rate or more slowly than CH₂ ). The peak height ratio of 2,960 cm^-1 band (CH₃ )/2,925 cm^-1 band (CH₂ ; R_3/2 values) either increased or remained constant during the heating. These results reveal that the presence of silica does affect the decreasing rate of the aliphatic C-H bonds in cyanobacteria during thermal maturation, but that it does not significantly decrease the R_3/2 values. Meanwhile, studies of microfossils suggest that the R_3/2 values of Proterozoic prokaryotic fossils from the Bitter Springs Group and Gunflint Formation have decreased during fossilization, which is inconsistent with the prediction from our experimental results that R_3/2 values did not decrease after silicification. Some process other than thermal degradation, possibly preservation of specific classes of biomolecules with low R_3/2 values, might have occurred during fossilization.

Exoplanet Biosignatures: A Review of Remotely Detectable Signs of Life

In the coming years and decades, advanced space- and ground-based observatories will allow an unprecedented opportunity to probe the atmospheres and surfaces of potentially habitable exoplanets for signatures of life. Life on Earth, through its gaseous products and reflectance and scattering properties, has left its fingerprint on the spectrum of our planet. Aided by the universality of the laws of physics and chemistry, we turn to Earth's biosphere, both in the present and through geologic time, for analog signatures that will aid in the search for life elsewhere. Considering the insights gained from modern and ancient Earth, and the broader array of hypothetical exoplanet possibilities, we have compiled a comprehensive overview of our current understanding of potential exoplanet biosignatures, including gaseous, surface, and temporal biosignatures. We additionally survey biogenic spectral features that are well known in the specialist literature but have not yet been robustly vetted in the context of exoplanet biosignatures. We briefly review advances in assessing biosignature plausibility, including novel methods for determining chemical disequilibrium from remotely obtainable data and assessment tools for determining the minimum biomass required to maintain short-lived biogenic gases as atmospheric signatures. We focus particularly on advances made since the seminal review by Des Marais et al. The purpose of this work is not to propose new biosignature strategies, a goal left to companion articles in this series, but to review the current literature, draw meaningful connections between seemingly disparate areas, and clear the way for a path forward. Key Words: Exoplanets-Biosignatures-Habitability markers-Photosynthesis-Planetary surfaces-Atmospheres-Spectroscopy-Cryptic biospheres-False positives. Astrobiology 18, 663-708.

Constraining the Time Interval for the Origin of Life on Earth

Estimates of the time at which life arose on Earth make use of two types of evidence. First, astrophysical and geophysical studies provide a timescale for the formation of Earth and the Moon, for large impact events on early Earth, and for the cooling of the early magma ocean. From this evidence, we can deduce a habitability boundary, which is the earliest point at which Earth became habitable. Second, biosignatures in geological samples, including microfossils, stromatolites, and chemical isotope ratios, provide evidence for when life was actually present. From these observations we can deduce a biosignature boundary, which is the earliest point at which there is clear evidence that life existed. Studies with molecular phylogenetics and records of the changing level of oxygen in the atmosphere give additional information that helps to determine the biosignature boundary. Here, we review the data from a wide range of disciplines to summarize current information on the timings of these two boundaries. The habitability boundary could be as early as 4.5 Ga, the earliest possible estimate of the time at which Earth had a stable crust and hydrosphere, or as late as 3.9 Ga, the end of the period of heavy meteorite bombardment. The lack of consensus on whether there was a late heavy meteorite bombardment that was significant enough to prevent life is the largest uncertainty in estimating the time of the habitability boundary. The biosignature boundary is more closely constrained. Evidence from carbon isotope ratios and stromatolite fossils both point to a time close to 3.7 Ga. Life must have emerged in the interval between these two boundaries. The time taken for life to appear could, therefore, be within 200 Myr or as long as 800 Myr. Key Words: Origin of life-Astrobiology-Habitability-Biosignatures-Geochemistry-Early Earth. Astrobiology 18, 343-364.

Experimental precipitation of apatite pseudofossils resembling fossil embryos

Certain phosphatic grains preserved in the rock record are interpreted as microfossils representing a diversity of microorganisms from bacteria to fossil embryos. In addition to bona fide primary biological features, phosphatic microfossils and fossil embryos commonly exhibit features that result from abiotic precipitation or diagenetic alteration. Distinguishing between abiotic and primary biological features can be difficult, and some features thought to represent biological tissue could instead be artifacts that are unrelated to the original morphology of a preserved organism. Here, we present experimentally generated, abiotically produced mineral precipitates that morphologically resemble biologically produced features, some of which may be observed in the rock record or noted in extant organisms, including embryos. These findings extend the diversity of biomorphic features known to result from abiotic precipitation.

SIMS analyses of the oldest known assemblage of microfossils document their taxon-correlated carbon isotope compositions

Analyses by secondary ion mass spectroscopy (SIMS) of 11 specimens of five taxa of prokaryotic filamentous kerogenous cellular microfossils permineralized in a petrographic thin section of the ∼3,465 Ma Apex chert of northwestern Western Australia, prepared from the same rock sample from which this earliest known assemblage of cellular fossils was described more than two decades ago, show their δ¹³C compositions to vary systematically taxon to taxon from -31‰ to -39‰. These morphospecies-correlated carbon isotope compositions confirm the biogenicity of the Apex fossils and validate their morphology-based taxonomic assignments. Perhaps most significantly, the δ¹³C values of each of the five taxa are lower than those of bulk samples of Apex kerogen (-27‰), those of SIMS-measured fossil-associated dispersed particulate kerogen (-27.6‰), and those typical of modern prokaryotic phototrophs (-25 ± 10‰). The SIMS data for the two highest δ¹³C Apex taxa are consistent with those of extant phototrophic bacteria; those for a somewhat lower δ¹³C taxon, with nonbacterial methane-producing Archaea; and those for the two lowest δ¹³C taxa, with methane-metabolizing γ-proteobacteria. Although the existence of both methanogens and methanotrophs has been inferred from bulk analyses of the carbon isotopic compositions of pre-2,500 Ma kerogens, these in situ SIMS analyses of individual microfossils present data interpretable as evidencing the cellular preservation of such microorganisms and are consistent with the near-basal position of the Archaea in rRNA phylogenies.

Exploring the interior of cuticles and compressions of fossil plants by FIB-SEM milling and image microscopy

We present the first study of cuticles and compressions of fossil leaves by Focused Ion Beam Scanning Electron Microscopy (FIB-SEM). Cavities preserved inside fossil leaf compressions corresponding to substomatal chambers have been observed for the first time and several new features were identified in the cross-section cuts. These results open a new way in the investigation of the three-dimensional structures of both micro- and nanostructural features of fossil plants. Moreover, the application of the FIB-SEM technique to both fossils and extant plant remains represent a new source of taxonomical, palaeoenvironmental and palaeoclimatic information.

VIRTUAL PALEONTOLOGY—AN OVERVIEW

Virtual paleontology is the study of fossils through three-dimensional digital visualizations; it represents a powerful and well-established set of tools for the analysis and dissemination of fossil data. Techniques are divisible into tomographic (i.e., slice-based) and surface-based types. Tomography has a long predigital history, but the recent explosion of virtual paleontology has resulted primarily from developments in X-ray computed tomography (CT), and of surface-based technologies (e.g., laser scanning). Destructive tomographic methods include forms of physical-optical tomography (e.g., serial grinding); these are powerful but problematic techniques. Focused Ion Beam (FIB) tomography is a modern alternative for microfossils; it is also destructive but is capable of extremely high resolutions. Nondestructive tomographic methods include the many forms of CT, which are the most widely used data-capture techniques at present, but are not universally applicable. Where CT is inappropriate, other nondestructive technologies (e.g., neutron tomography, magnetic resonance imaging, optical tomography) can prove suitable. Surface-based methods provide portable and convenient data capture for surface topography and texture, and might be appropriate when internal morphology is not of interest; technologies include laser scanning, photogrammetry, and mechanical digitization. Reconstruction methods that produce visualizations from raw data are many and various; selection of an appropriate workflow will depend on many factors, but is an important consideration that should be addressed prior to any study. The vast majority of three-dimensional fossils can now be studied using some form of virtual paleontology, and barriers to broader adaptation are being eroded. Technical issues regarding data sharing remain problematic. Technological developments continue; those promising tomographic recovery of compositional data are of particular relevance to paleontology.

Illusory Late Heavy Bombardments

The Late Heavy Bombardment (LHB), a hypothesized impact spike at ∼3.9 Ga, is one of the major scientific concepts to emerge from Apollo-era lunar exploration. A significant portion of the evidence for the existence of the LHB comes from histograms of (40)Ar/(39)Ar "plateau" ages (i.e., regions selected on the basis of apparent isochroneity). However, due to lunar magmatism and overprinting from subsequent impact events, virtually all Apollo-era samples show evidence for (40)Ar/(39)Ar age spectrum disturbances, leaving open the possibility that partial (40)Ar* resetting could bias interpretation of bombardment histories due to plateaus yielding misleadingly young ages. We examine this possibility through a physical model of (40)Ar* diffusion in Apollo samples and test the uniqueness of the impact histories obtained by inverting plateau age histograms. Our results show that plateau histograms tend to yield age peaks, even in those cases where the input impact curve did not contain such a spike, in part due to the episodic nature of lunar crust or parent body formation. Restated, monotonically declining impact histories yield apparent age peaks that could be misinterpreted as LHB-type events. We further conclude that the assignment of apparent (40)Ar/(39)Ar plateau ages bears an undesirably high degree of subjectivity. When compounded by inappropriate interpretations of histograms constructed from plateau ages, interpretation of apparent, but illusory, impact spikes is likely.

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.

Limited influence of Si on the preservation of Fe mineral-encrusted microbial cells during experimental diagenesis

The reconstruction of the history of microbial life since its emergence on early Earth is impaired by the difficulty to prove the biogenicity of putative microfossils in the rock record. While most of the oldest rocks on Earth have been exposed to different grades of diagenetic alterations, little is known about how the remains of micro-organisms evolve when exposed to pressure (P) and temperature (T) conditions typical of diagenesis. Using spectroscopy and microscopy, we compared morphological, mineralogical, and chemical biosignatures exhibited by Fe mineral-encrusted cells of the bacterium Acidovorax sp. BoFeN1 after long-term incubation under ambient conditions and after experimental diagenesis. We also evaluated the effects of Si on the preservation of microbial cells during the whole process. At ambient conditions, Si affected the morphology but not the identity (goethite) of Fe minerals that formed around cells. Fe-encrusted cells were morphologically well preserved after 1 week at 250 °C-140 MPa and after 16 weeks at 170 °C-120 MPa in the presence or in the absence of Si. Some goethite transformed to hematite and magnetite at 250 °C-140 MPa, but in the presence of Si more goethite was preserved. Proteins-the most abundant cellular components-were preserved over several months at ambient conditions but disappeared after incubations at high temperature and pressure conditions, both in the presence and in the absence of Si. Other organic compounds, such as lipids and extracellular polysaccharides seemed well preserved after exposure to diagenetic conditions. This study provides insights about the composition and potential preservation of microfossils that could have formed in Fe- and Si-rich Precambrian oceans.