Challenges in evidencing the earliest traces of life

Dating Ammonia-Oxidizing Bacteria with Abundant Eukaryotic Fossils

Evolution of a complete nitrogen (N) cycle relies on the onset of ammonia oxidation, which aerobically converts ammonia to nitrogen oxides. However, accurate estimation of the antiquity of ammonia-oxidizing bacteria (AOB) remains challenging because AOB-specific fossils are absent and bacterial fossils amenable to calibrate molecular clocks are rare. Leveraging the ancient endosymbiosis of mitochondria and plastid, as well as using state-of-the-art Bayesian sequential dating approach, we obtained a timeline of AOB evolution calibrated largely by eukaryotic fossils. We show that the first AOB evolved in marine Gammaproteobacteria (Gamma-AOB) and emerged between 2.1 and 1.9 billion years ago (Ga), thus postdating the Great Oxidation Event (GOE; 2.4 to 2.32 Ga). To reconcile the sedimentary N isotopic signatures of ammonia oxidation occurring near the GOE, we propose that ammonia oxidation likely occurred at the common ancestor of Gamma-AOB and Gammaproteobacterial methanotrophs, or the actinobacterial/verrucomicrobial methanotrophs which are known to have ammonia oxidation activities. It is also likely that nitrite was transported from the terrestrial habitats where ammonia oxidation by archaea took place. Further, we show that the Gamma-AOB predated the anaerobic ammonia-oxidizing (anammox) bacteria, implying that the emergence of anammox was constrained by the availability of dedicated ammonia oxidizers which produce nitrite to fuel anammox. Our work supports a new hypothesis that N redox cycle involving nitrogen oxides evolved rather late in the ocean.

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.

Chapter 1: The Astrobiology Primer 3.0

The Astrobiology Primer 3.0 (ABP3.0) is a concise introduction to the field of astrobiology for students and others who are new to the field of astrobiology. It provides an entry into the broader materials in this supplementary issue of Astrobiology and an overview of the investigations and driving hypotheses that make up this interdisciplinary field. The content of this chapter was adapted from the other 10 articles in this supplementary issue and thus represents the contribution of all the authors who worked on these introductory articles. The content of this chapter is not exhaustive and represents the topics that the authors found to be the most important and compelling in a dynamic and changing field.

The time of appearance of the genetic code

I support the hypothesis that the origin of the genetic code occurred simultaneously with the evolution of cellularity. That is to say, I favour the hypothesis that the origin of the genetic code is a very, very late event in the history of life on Earth. I corroborate this hypothesis with observations favouring the progenote's stage for the Last Universal Common Ancestor (LUCA), for the ancestor of bacteria and that of archaea. Indeed, these progenotic stages would imply that - at that time - the origin of the genetic code was still ongoing simply because this origin would fall within the very definition of progenote. Therefore, if the evolution of cellularity had truly been coeval with the origin of the genetic code - at least in its terminal part - then this would favour theories such as the coevolution theory of the origin of the genetic code because this theory would postulate that this origin must have occurred in extremely complex protocellular conditions and not concerning stereochemical or physicochemical interactions having to do with other stages of the origin of life. In this sense, the coevolution theory would be corroborated while the stereochemical and physicochemical theories would be damaged. Therefore, the origin of the genetic code would be linked to the origin of the cell and not to the origin of life as sometimes asserted. Therefore, I will discuss the late hypothesis of the origin of the genetic code in the context of the theories proposed to explain this origin and more generally of its implications for the early evolution of life.

Studying the Human Microbiota: Advances in Understanding the Fundamentals, Origin, and Evolution of Biological Timekeeping

The recently observed circadian oscillations of the intestinal microbiota underscore the profound nature of the human-microbiome relationship and its importance for health. Together with the discovery of circadian clocks in non-photosynthetic gut bacteria and circadian rhythms in anucleated cells, these findings have indicated the possibility that virtually all microorganisms may possess functional biological clocks. However, they have also raised many essential questions concerning the fundamentals of biological timekeeping, its evolution, and its origin. This narrative review provides a comprehensive overview of the recent literature in molecular chronobiology, aiming to bring together the latest evidence on the structure and mechanisms driving microbial biological clocks while pointing to potential applications of this knowledge in medicine. Moreover, it discusses the latest hypotheses regarding the evolution of timing mechanisms and describes the functions of peroxiredoxins in cells and their contribution to the cellular clockwork. The diversity of biological clocks among various human-associated microorganisms and the role of transcriptional and post-translational timekeeping mechanisms are also addressed. Finally, recent evidence on metabolic oscillators and host-microbiome communication is presented.

Is There Such a Thing as a Biosignature?

The concept of a biosignature is widely used in astrobiology to suggest a link between some observation and a biological cause, given some context. The term itself has been defined and used in several ways in different parts of the scientific community involved in the search for past or present life on Earth and beyond. With the ongoing acceleration in the search for life in distant time and/or deep space, there is a need for clarity and accuracy in the formulation and reporting of claims. Here, we critically review the biosignature concept(s) and the associated nomenclature in light of several problems and ambiguities emphasized by recent works. One worry is that these terms and concepts may imply greater certainty than is usually justified by a rational interpretation of the data. A related worry is that terms such as "biosignature" may be inherently misleading, for example, because the divide between life and non-life-and their observable effects-is fuzzy. Another worry is that different parts of the multidisciplinary community may use non-equivalent or conflicting definitions and conceptions, leading to avoidable confusion. This review leads us to identify a number of pitfalls and to suggest how they can be circumvented. In general, we conclude that astrobiologists should exercise particular caution in deciding whether and how to use the concept of biosignature when thinking and communicating about habitability or life. Concepts and terms should be selected carefully and defined explicitly where appropriate. This would improve clarity and accuracy in the formulation of claims and subsequent technical and public communication about some of the most profound and important questions in science and society. With this objective in mind, we provide a checklist of questions that scientists and other interested parties should ask when assessing any reported detection of a "biosignature" to better understand exactly what is being claimed.

Isotopic Signatures of Carbon Transfer in a Proterozoic Analogue Microbial Mat

Modern microbial mats are potential analogues for Proterozoic ecosystems, yet only a few studies have characterized mats under low-oxygen conditions that are relevant to Proterozoic environments. Here, we use protein-stable isotope fingerprinting (P-SIF) to determine the protein carbon isotope (δ13C) values of autotrophic, heterotrophic, and mixotrophic organisms in a benthic microbial mat from the low-oxygen Middle Island Sinkhole, Lake Huron, USA (MIS). We also measure the δ13C values of the sugar moieties of exopolysaccharides (EPS) within the mat to explore the relationships between cyanobacterial exudates and heterotrophic anabolic carbon uptake. Our results show that Cyanobacteria (autotrophs) are 13C-depleted, relative to sulfate-reducing bacteria (heterotrophs), and 13C-enriched, relative to sulfur oxidizing bacteria (autotrophs or mixotrophs). We also find that the pentose moieties of EPS are systematically enriched in 13C, relative to the hexose moieties of EPS. We hypothesize that these isotopic patterns reflect cyanobacterial metabolic pathways, particularly phosphoketolase, that are relatively more active in low-oxygen mat environments, rather than oxygenated mat environments. This results in isotopically more heterogeneous C sources in low-oxygen mats. While this might partially explain the isotopic variability observed in Proterozoic mat facies, further work is necessary to systematically characterize the isotopic fractionations that are associated with the synthesis of cyanobacterial exudates. IMPORTANCE The δ13C compositions of heterotrophic microorganisms are dictated by the δ13C compositions of their organic carbon sources. In both modern and ancient photosynthetic microbial mats, photosynthetic exudates are the most likely source of organic carbon for heterotrophs. We measured the δ13C values of autotrophic, heterotrophic, and mixotrophic bacteria as well as the δ13C value of the most abundant photosynthetic exudate (exopolysaccharide) in a modern analogue for a Proterozoic environment. Given these data, future studies will be better equipped to estimate the most likely carbon source for heterotrophs in both modern environments as well as in Proterozoic environments preserved in the rock record.

The symbiotic origin of the eukaryotic cell

Eukaryogenesis represented a major evolutionary transition that led to the emergence of complex cells from simpler ancestors. For several decades, the most accepted scenario involved the evolution of an independent lineage of proto-eukaryotes endowed with an endomembrane system, including a nuclear compartment, a developed cytoskeleton and phagocytosis, which engulfed the alphaproteobacterial ancestor of mitochondria. However, the recent discovery by metagenomic and cultural approaches of Asgard archaea, which harbour many genes in common with eukaryotes and are their closest relatives in phylogenomic trees, rather supports scenarios based on the symbiosis of one Asgard-like archaeon and one or more bacteria at the origin of the eukaryotic cell. Here, we review the recent discoveries that led to this conceptual shift, briefly evoking current models of eukaryogenesis and the challenges ahead to discriminate between them and to establish a detailed, plausible scenario that accounts for the evolution of eukaryotic traits from those of their prokaryotic ancestors.

Microbial biosignatures in ancient deep-sea hydrothermal sulfides

Deep-sea hydrothermal systems provide ideal conditions for prebiotic reactions and ancient metabolic pathways and, therefore, might have played a pivotal role in the emergence of life. To understand this role better, it is paramount to examine fundamental interactions between hydrothermal processes, non-living matter, and microbial life in deep time. However, the distribution and diversity of microbial communities in ancient deep-sea hydrothermal systems are still poorly constrained, so evolutionary, and ecological relationships remain unclear. One important reason is an insufficient understanding of the formation of diagnostic microbial biosignatures in such settings and their preservation through geological time. This contribution centers around microbial biosignatures in Precambrian deep-sea hydrothermal sulfide deposits. Intending to provide a valuable resource for scientists from across the natural sciences whose research is concerned with the origins of life, we first introduce different types of biosignatures that can be preserved over geological timescales (rock fabrics and textures, microfossils, mineral precipitates, carbonaceous matter, trace metal, and isotope geochemical signatures). We then review selected reports of biosignatures from Precambrian deep-sea hydrothermal sulfide deposits and discuss their geobiological significance. Our survey highlights that Precambrian hydrothermal sulfide deposits potentially encode valuable information on environmental conditions, the presence and nature of microbial life, and the complex interactions between fluids, micro-organisms, and minerals. It further emphasizes that the geobiological interpretation of these records is challenging and requires the concerted application of analytical and experimental methods from various fields, including geology, mineralogy, geochemistry, and microbiology. Well-orchestrated multidisciplinary studies allow us to understand the formation and preservation of microbial biosignatures in deep-sea hydrothermal sulfide systems and thus help unravel the fundamental geobiology of ancient settings. This, in turn, is critical for reconstructing life's emergence and early evolution on Earth and the search for life elsewhere in the universe.

Abiogenesis through gradual evolution of autocatalysis into template-based replication

How life emerged from inanimate matter is one of the most intriguing questions posed to modern science. Central to this research are experimental attempts to build systems capable of Darwinian evolution. RNA catalysts (ribozymes) are a promising avenue, in line with the RNA world hypothesis whereby RNA pre-dated DNA and proteins. Since evolution in living organisms relies on template-based replication, the identification of a ribozyme capable of replicating itself (an RNA self-replicase) has been a major objective. However, no self-replicase has been identified to date. Alternatively, autocatalytic systems involving multiple RNA species capable of ligation and recombination may enable self-reproduction. However, it remains unclear how evolution could emerge in autocatalytic systems. In this review, we examine how experimentally feasible RNA reactions catalysed by ribozymes could implement the evolutionary properties of variation, heredity and reproduction, and ultimately allow for Darwinian evolution. We propose a gradual path for the emergence of evolution, initially supported by autocatalytic systems leading to the later appearance of RNA replicases.

Mechanisms shaping the gypsum stromatolite-like structures in the Salar de Llamara (Atacama Desert, Chile)

The explanation of the origin of microbialites and specifically stromatolitic structures is a problem of high relevance for decoding past sedimentary environments and deciphering the biogenicity of the oldest plausible remnants of life. We have investigated the morphogenesis of gypsum stromatolite-like structures currently growing in shallow ponds (puquíos) in the Salar de Llamara (Atacama Desert, Northern Chile). The crystal size, aspect ratio, and orientation distributions of gypsum crystals within the structures have been quantified and show indications for episodic nucleation and competitive growth of millimetric to centimetric selenite crystals into a radial, branched, and loosely cemented aggregate. The morphogenetical process is explained by the existence of a stable vertical salinity gradient in the ponds. Due to the non-linear dependency of gypsum solubility as a function of sodium chloride concentration, the salinity gradient produces undersaturated solutions, which dissolve gypsum crystals. This dissolution happens at a certain depth, narrowing the lower part of the structures, and producing their stromatolite-like morphology. We have tested this novel mechanism experimentally, simulating the effective dissolution of gypsum crystals in stratified ponds, thus providing a purely abiotic mechanism for these stromatolite-like structures.

Factors affecting the independence and reliability of Science and how these are perceived

Science studies natural phenomena or uses laws, theories, models and mechanisms to explain them, which are revised when new evidence emerges. However, Science cannot give answer to all questions that may arise. The benefits of science are well known and there is no reason to expand on them. It is of interest though to examine the structure and factors that influence the scientific world and may hold it back from offering greater benefits to mankind. The current study is concerned with the question whether or not Science is independent and reliable. Social and political reasons can direct substantive research in specific areas, but they can also encourage the promotion of unfounded theories. External factors such as prejudice against new ideas and understanding of natural happenings can negatively affect the objectivity of Science. Such factors examined in this paper and influence Science are: Research funding, policy makers and industry; Journal editors; Dogma; Theories declared as Conspiracies; Mutual interests in Academia; Knowledge control, cover ups and war superiority. The above factors can be used negatively to restrain serious scientists from expressing educated opinions and publishing them in scientific journals. In this way healthy discussions between 'opposing parties' are restricted, with Science being the victim as no sound conclusions and consensus on important subjects are reached. To check how the above positions are perceived by the scientific community, a questionnaire was circulated among scientists in 11 countries. Analyzing the 106 responds that were anonymously received, indicated that the respondents were largely in line with the expressed positions of the present paper. It is proposed that the real answer to minimize the effect of the factors that influence Science negatively, is educating people's critical abilities and considering nothing for granted-especially under the influence of powerful Media-unless its validity is independently checked and verified.

Radical change in tectonic regime and paleo-environment at the end of Neoarchean evidenced by a unique metal co-existing deposit

Banded iron formation and Cu-Zn sulfide deposits within volcanic-argillaceous sequences (as volcanogenic massive sulphide deposits (VMS)-like type) occur together in the Qingyuan greenstone belt of the North China Craton, recording the first appearance of oxidized ores and sulfide ores co-existing in the early Earth. The unique metal co-existing deposits should meet two requirements: tectonic setting and sedimentary environment. As regards to tectonic setting, plate-like tectonics might have started since the end of the Neoarchean because continents had grown large enough and there occurred volcanic arcs and backarc basins similar to modern ones in a way. Partial melting of subducted continental crust is conductive to providing ore-forming elements. As for sedimentary environment, late Neoarchean seawater was rich in Fe²⁺ and anoxic. Instantaneous oxidation of the seawater resulted possibly from frequent submarine volcanic eruptions and facilitated precipitation of the banded iron formation. At this point, it is also favorable for the enrichment of Cu and Zn ions in seawater. The VMS-like deposits tended to form when the seawater was reduced again. Studies of isotopic elements like sulfur, oxygen, iron and silicon support the above geological processes. It is shown that the geologic conditions only existed in the late Neoarchean and Paleoproterozoic for a short period of time. The banded iron formations disappeared around 1.85 Ga, and the associated sulfide metal deposits also became dominant sedimentary exhalative deposits in the meso-Neoproterozoic Boring Billion, as a result of increasing oxidation of the oceans and the increasing maturity of the continental crust. This study is significant not only for decoding metallogenic genesis but also helping understand rapid change in Precambrian tectonic regimes and Earth's environments.

Characterization of ancestral Fe/Mn superoxide dismutases indicates their cambialistic origin

Superoxide dismutases (SODs) are critical metalloenzymes mitigating the damages of the modern oxygenated world. However, the emergence of one family of SODs, the Fe/Mn SOD, has been recurrently proposed to predate the great oxygenation event (GOE). This ancient family lacks metal binding selectivity, but displays strong catalytic selectivity. Therefore, some homologues would only be active when bound to Fe or Mn, although others, dubbed cambialistic, would function when loaded with either ion. This posed the longstanding question about the identity of the cognate metal ion of the first SODs to emerge. In this work, we utilize ancestral sequence reconstruction techniques to infer the earliest SODs. We show that the “ancestors” are active in vivo and in vitro. Further, we test their metal specificity and demonstrate that they are cambialistic in nature. Our findings shed light on how the predicted Last Common Universal Ancestor was capable of dealing with decomposition of the superoxide anion, and the early relationship between life, oxygen, and metal ion availability.

Fe-Rich Fossil Vents as Mars Analog Samples: Identification of Extinct Chimneys in Miocene Marine Sediments Using Raman Spectroscopy, X-Ray Diffraction, and Scanning Electron Microscopy-Energy Dispersive X-Ray Spectroscopy

On Earth, the circulation of Fe-rich fluids in hydrothermal environments leads to characteristic iron mineral deposits, reflecting the pH and redox chemical conditions of the hydrothermal system, and is often associated with chemotroph microorganisms capable of deriving energy from chemical gradients. On Mars, iron-rich hydrothermal sites are considered to be potentially important astrobiological targets for searching evidence of life during exploration missions, such as the Mars 2020 and the ExoMars 2022 missions. In this study, an extinct hydrothermal chimney from the Jaroso hydrothermal system (SE Spain), considered an interesting geodynamic and mineralogical terrestrial analog for Mars, was analyzed using Raman spectroscopy, X-ray diffraction, and scanning electron microscopy coupled with energy dispersive X-ray spectroscopy. The sample consists of a fossil vent in a Miocene shallow-marine sedimentary deposit composed of a marl substrate, an iron-rich chimney pipe, and a central space filled with backfilling deposits and vent condensates. The iron crust is particularly striking due to the combined presence of molecular and morphological indications of a microbial colonization, including mineral microstructures (e.g., stalks, filaments), iron oxyhydroxide phases (altered goethite, ferrihydrite), and organic signatures (carotenoids, organopolymers). The clear identification of pigments by resonance Raman spectroscopy and the preservation of organics in association with iron oxyhydroxides by Raman microimaging demonstrate that the iron crust was indeed colonized by microbial communities. These analyses confirm that Raman spectroscopy is a powerful tool for documenting the habitability of such historical hydrothermal environments. Finally, based on the results obtained, we propose that the ancient iron-rich hydrothermal pipes should be recognized as singular terrestrial Mars analog specimens to support the preparatory work for robotic in situ exploration missions to Mars, as well as during the subsequent interpretation of data returned by those missions.

Genes encoding the photosystem II proteins are under purifying selection: an insight into the early evolution of oxygenic photosynthesis

The molecular evolution concerns coding sequences (CDSs) of genes and may affect the structure and function of proteins. Non-uniform use of synonymous codons during translation, known as codon usage bias (CUB), depends on the balance between mutations bias and natural selection. We estimated different CUB indices, i.e. the effective number of codons (ENC), G + C content in the 3rd codon positions (GC₃), and codon adaptation index for CDSs of intrinsic proteins of photosystem II (PSII), such as psbA (D1), psbD (D2), psbB (CP47), psbC (CP43), and CDSs of the extrinsic protein psbO (PsbO). These genes occur in all organisms that perform oxygenic photosynthesis (OP) on Earth: cyanobacteria, algae and plants. Comparatively, a similar analysis of codon bias for CDSs of L and M subunits that constitute the core proteins of the type II reaction centre (RCII) in anoxygenic bacteria was performed. Analysis of CUB indices and determination of the number of synonymous (d_S) and nonsynonymous substitutions (d_N) in all analysed CDSs indicated that the crucial PSII and RCII proteins were under strong purifying (negative) selection in course of evolution. Purifying selection was also estimated for CDSs of atpA, the α subunit of ATP synthase, an enzyme that was most likely already present in the last universal common ancestor (LUCA). The data obtained point to an ancient origin of OP, even in the earliest stages of the evolution of life on Earth.

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.

Origin and evolution of nitrogen fixation in prokaryotes

The origin of nitrogen fixation is an important issue in evolutionary biology. While nitrogen is required by all living organisms, only a small fraction of bacteria and archaea can fix nitrogen. The prevailing view is that nitrogen fixation first evolved in archaea and was later transferred to bacteria. However, nitrogen-fixing (Nif) bacteria are far larger in number and far more diverse in ecological niches than Nif archaea. We, therefore, propose the bacteria-first hypothesis, which postulates that nitrogen fixation first evolved in bacteria and was later transferred to archaea. As >30,000 prokaryotic genomes have been sequenced, we conduct an in-depth comparison of the two hypotheses. We first identify the six genes involved in nitrogen fixation in all sequenced prokaryotic genomes and then reconstruct phylogenetic trees using the six Nif proteins individually or in combination. In each of these trees, the earliest lineages are bacterial Nif protein sequences and in the oldest clade (group) the archaeal sequences are all nested inside bacterial sequences, suggesting that the Nif proteins first evolved in bacteria. The bacteria-first hypothesis is further supported by the observation that the majority of Nif archaea carry the major bacterial Mo (molybdenum) transporter (ModABC) rather than the archaeal Mo transporter (WtpABC). Moreover, in our phylogeny of all available ModA and WtpA protein sequences, the earliest lineages are bacterial sequences while archaeal sequences are nested inside bacterial sequences. Furthermore, the bacteria-first hypothesis is supported by available isotopic data. In conclusion, our study strongly supports the bacteria-first hypothesis.

Biogeochemical fingerprinting of magnetotactic bacterial magnetite

Biominerals are important archives of the presence of life and environmental processes in the geological record. However, ascribing a clear biogenic nature to minerals with nanometer-sized dimensions has proven challenging. Identifying hallmark features of biologically controlled mineralization is particularly important for the case of magnetite crystals, resembling those produced by magnetotactic bacteria (MTB), which have been used as evidence of early prokaryotic life on Earth and in meteorites. We show here that magnetite produced by MTB displays a clear coupled C-N signal that is absent in abiogenic and/or biomimetic (protein-mediated) nanometer-sized magnetite. We attribute the presence of this signal to intracrystalline organic components associated with proteins involved in magnetosome formation by MTB. These results demonstrate that we can assign a biogenic origin to nanometer-sized magnetite crystals, and potentially other biominerals of similar dimensions, using unique geochemical signatures directly measured at the nanoscale. This finding is significant for searching for the earliest presence of life in the Earth's geological record and prokaryotic life on other planets.

From the origin of life to pandemics: emergent phenomena in complex systems

When a large number of similar entities interact among each other and with their environment at a low scale, unexpected outcomes at higher spatio-temporal scales might spontaneously arise. This non-trivial phenomenon, known as emergence, characterizes a broad range of distinct complex systems-from physical to biological and social-and is often related to collective behaviour. It is ubiquitous, from non-living entities such as oscillators that under specific conditions synchronize, to living ones, such as birds flocking or fish schooling. Despite the ample phenomenological evidence of the existence of systems' emergent properties, central theoretical questions to the study of emergence remain unanswered, such as the lack of a widely accepted, rigorous definition of the phenomenon or the identification of the essential physical conditions that favour emergence. We offer here a general overview of the phenomenon of emergence and sketch current and future challenges on the topic. Our short review also serves as an introduction to the theme issue Emergent phenomena in complex physical and socio-technical systems: from cells to societies, where we provide a synthesis of the contents tackled in the issue and outline how they relate to these challenges, spanning from current advances in our understanding on the origin of life to the large-scale propagation of infectious diseases. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.

The Origin of Life: What Is the Question?

The question of the origin of life is a tenacious question that challenges many branches of science but is also extremely multifaceted. While prebiotic chemistry and micropaleontology reformulate the question as that of explaining the appearance of life on Earth in the deep past, systems chemistry and synthetic biology typically understand the question as that of demonstrating the synthesis of novel living matter from nonliving matter independently of historical constraints. The objective of this contribution is to disentangle the different readings of the origin-of-life question found in science. We identify three main dimensions along which the question can be differently constrained depending on context: historical adequacy, natural spontaneity, and similarity to life-as-we-know-it. We argue that the epistemic status of what needs to be explained-the explanandum-varies from approximately true when the origin-of-life question is the most constrained to entirely speculative when the constraints are the most relaxed. This difference in epistemic status triggers a shift in the nature of the origin-of-life question from an explanation-seeking question in the most constrained case to a fact-establishing question in the lesser-constrained ones. We furthermore explore how answers to some interpretations of the origin-of-life questions matter for other interpretations.

On the Pathogenicity of the Oral Biofilm: A Critical Review from a Biological, Evolutionary, and Nutritional Point of View

Plaque control is one of the most recommended approaches in the prevention and therapy of caries and periodontal diseases. However, although most individuals in industrialized countries already perform daily oral hygiene, caries and periodontal diseases still are the most common diseases of mankind. This raises the question of whether plaque control is really a causative and effective approach to the prevention of these diseases. From an evolutionary, biological, and nutritional perspective, dental biofilms have to be considered a natural phenomenon, whereas several changes in human lifestyle factors during modern evolution are not “natural”. These lifestyle factors include the modern “Western diet” (rich in sugar and saturated fats and low in micronutrients), smoking, sedentary behavior, and continuous stress. This review hypothesizes that not plaque itself but rather these modern, unnatural lifestyle factors are the real causes of the high prevalence of caries and periodontal diseases besides several other non-communicable diseases. Accordingly, applying evolutionary and lifestyle medicine in dentistry would offer a causative approach against oral and common diseases, which would not be possible with oral hygiene approaches used on their own.

Protocells: Milestones and Recent Advances

The origin of life is still one of humankind's great mysteries. At the transition between nonliving and living matter, protocells, initially featureless aggregates of abiotic matter, gain the structure and functions necessary to fulfill the criteria of life. Research addressing protocells as a central element in this transition is diverse and increasingly interdisciplinary. The authors review current protocell concepts and research directions, address milestones, challenges and existing hypotheses in the context of conditions on the early Earth, and provide a concise overview of current protocell research methods.

Active Microbial Airborne Dispersal and Biomorphs as Confounding Factors for Life Detection in the Cell-Degrading Brines of the Polyextreme Dallol Geothermal Field

Determining the precise limits of life in polyextreme environments is challenging. Studies along gradients of polyextreme conditions in the Dallol proto-volcano area (Danakil salt desert, Ethiopia) showed the occurrence of archaea-dominated communities (up to 99%) in several hypersaline systems but strongly suggested that life did not thrive in the hyperacidic (pH ∼0), hypersaline (∼35% [wt/vol],) and sometimes hot (up to 108°C) ponds of the Dallol dome. However, it was recently claimed that archaea flourish in these brines based on the detection of one Nanohaloarchaeotas 16S rRNA gene and fluorescent in situ hybridization (FISH) experiments with archaea-specific probes. Here, we characterized the diversity of microorganisms in aerosols over Dallol, and we show that, in addition to typical bacteria from soil/dust, they transport halophilic archaea likely originating from neighboring hypersaline ecosystems. We also show that cells and DNA from cultures and natural local halophilic communities are rapidly destroyed upon contact with Dallol brine. Furthermore, we confirm the widespread occurrence of mineral particles, including silica-based biomorphs, in Dallol brines. FISH experiments using appropriate controls show that DNA fluorescent probes and dyes unspecifically bind to mineral precipitates in Dallol brines; cellular morphologies were unambiguously observed only in nearby hypersaline ecosystems. Our results show that airborne cell dispersal and unspecific binding of fluorescent probes are confounding factors likely affecting previous inferences of archaea thriving in Dallol. They highlight the need for controls and the consideration of alternative abiotic explanations before safely drawing conclusions about the presence of life in polyextreme terrestrial or extraterrestrial systems.

Prebiotic Aggregates (Tissues) Emerging from Reaction-Diffusion: Formation Time, Configuration Entropy and Optimal Spatial Dimension

For the formation of a proto-tissue, rather than a protocell, the use of reactant dynamics in a finite spatial region is considered. The framework is established on the basic concepts of replication, diversity, and heredity. Heredity, in the sense of the continuity of information and alike traits, is characterized by the number of equivalent patterns conferring viability against selection processes. In the case of structural parameters and the diffusion coefficient of ribonucleic acid, the formation time ranges between a few years to some decades, depending on the spatial dimension (fractional or not). As long as equivalent patterns exist, the configuration entropy of proto-tissues can be defined and used as a practical tool. Consequently, the maximal diversity and weak fluctuations, for which proto-tissues can develop, occur at the spatial dimension 2.5.

Precambrian Paleobiology: Precedents, Progress, and Prospects

In 1859, C. R. Darwin highlighted the “inexplicable” absence of evidence of life prior to the beginning of the Cambrian. Given this lack of evidence and the natural rather than theological unfolding of life’s development Darwin espoused, over the following 50 years his newly minted theory was disputed. At the turn of the 19th century, beginning with the discoveries of C. D. Walcott, glimmerings of the previously “unknown and unknowable” early fossil record came to light – but Walcott’s Precambrian finds were also discounted. It was not until the breakthrough advances of the 1950’s and the identification of modern stromatolites (1956), Precambrian phytoplankton in shales (1950’s), stromatolitic microbes in cherts (1953), and terminal-Precambrian soft-bodied animal fossils (1950’s) that the field was placed on firm footing. Over the following half-century, the development and application of new analytical techniques coupled with the groundbreaking contributions of the Precambrian Paleobiology Research Group spurred the field to its international and distinctly interdisciplinary status. Significant progress has been made worldwide. Among these advances, the known fossil record has been extended sevenfold (from ∼0.5 to ∼3.5 Ga); the fossil record has been shown consistent with rRNA phylogenies (adding credence to both); and the timing and evolutionary significance of an increase of environmental oxygen (∼2.3 Ga), of eukaryotic organisms (∼2.0 Ga), and of evolution-speeding and biota-diversifying eukaryotic sexual reproduction (∼1.2 Ga) have been identified. Nevertheless, much remains to be learned. Such major unsolved problems include the absence of definitive evidence of the widely assumed life-generating “primordial soup”; the timing of the origin of oxygenic photosynthesis; the veracity of postulated changes in global photic-zone temperature from 3.5 Ga to the present; the bases of the advent of eukaryotic sexuality-requiring gametogenesis and syngamy; and the timing of origin and affinities of the small soft-bodied precursors of the Ediacaran Fauna.

Fossil cells

Philip Donoghue introduces the fossil record of cells.

Timing the evolution of antioxidant enzymes in cyanobacteria

The ancestors of cyanobacteria generated Earth's first biogenic molecular oxygen, but how they dealt with oxidative stress remains unconstrained. Here we investigate when superoxide dismutase enzymes (SODs) capable of removing superoxide free radicals evolved and estimate when Cyanobacteria originated. Our Bayesian molecular clocks, calibrated with microfossils, predict that stem Cyanobacteria arose 3300-3600 million years ago. Shortly afterwards, we find phylogenetic evidence that ancestral cyanobacteria used SODs with copper and zinc cofactors (CuZnSOD) during the Archaean. By the Paleoproterozoic, they became genetically capable of using iron, nickel, and manganese as cofactors (FeSOD, NiSOD, and MnSOD respectively). The evolution of NiSOD is particularly intriguing because it corresponds with cyanobacteria's invasion of the open ocean. Our analyses of metalloenzymes dealing with reactive oxygen species (ROS) now demonstrate that marine geochemical records alone may not predict patterns of metal usage by phototrophs from freshwater and terrestrial habitats.

Cyanobacteria and biogeochemical cycles through Earth history

Cyanobacteria are the only prokaryotes to have evolved oxygenic photosynthesis, transforming the biology and chemistry of our planet. Genomic and evolutionary studies have revolutionized our understanding of early oxygenic phototrophs, complementing and dramatically extending inferences from the geologic record. Molecular clock estimates point to a Paleoarchean origin (3.6-3.2 billion years ago, bya) of the core proteins of Photosystem II (PSII) involved in oxygenic photosynthesis and a Mesoarchean origin (3.2-2.8 bya) for the last common ancestor of modern cyanobacteria. Nonetheless, most extant cyanobacteria diversified after the Great Oxidation Event (GOE), an environmental watershed ca. 2.45 bya made possible by oxygenic photosynthesis. Throughout their evolutionary history, cyanobacteria have played a key role in the global carbon cycle.

Cellular remains in a ~3.42-billion-year-old subseafloor hydrothermal environment

Subsurface habitats on Earth host an extensive extant biosphere and likely provided one of Earth's earliest microbial habitats. Although the site of life's emergence continues to be debated, evidence of early life provides insights into its early evolution and metabolic affinity. Here, we present the discovery of exceptionally well-preserved, ~3.42-billion-year-old putative filamentous microfossils that inhabited a paleo-subseafloor hydrothermal vein system of the Barberton greenstone belt in South Africa. The filaments colonized the walls of conduits created by low-temperature hydrothermal fluid. Combined with their morphological and chemical characteristics as investigated over a range of scales, they can be considered the oldest methanogens and/or methanotrophs that thrived in an ultramafic volcanic substrate.

Builders, tenants, and squatters: the origins of genetic material in modern stromatolites

Micro-organisms have long been implicated in the construction of stromatolites. Yet, establishing a microbial role in modern stromatolite growth via molecular analysis is not always straightforward because DNA in stromatolites can have multiple origins. For example, the genomic material could represent the microbes responsible for the construction of the stromatolite (i.e., "builders"), microbes that inhabited the structure after it was built (i.e., "tenants"), or microbes/organic matter that were passively incorporated after construction from the water column or later diagenetic fluids (i.e., "squatters"). Disentangling the role of micro-organisms in stromatolite construction, already difficult in modern systems, becomes more difficult as organic signatures degrade, and their context is obscured. To evaluate our ability to accurately decipher the role of micro-organisms in stromatolite formation in geologically recent settings, 16/18S SSU rRNA gene sequences were analyzed from three systems where the context of growth was well understood: (a) an actively growing stromatolite from a silicic hot spring in Yellowstone National Park, Wyoming, where the construction of the structure is controlled by cyanobacteria; (b) a mixed carbonate and silica precipitate from Little Hot Creek, a hot spring in the Long Valley Caldera of California that has both abiogenic and biogenic components to accretion; and (c) a near-modern lacustrine carbonate stromatolite from Walker Lake, Nevada that is likely abiogenic. In all cases, the largest percentage of recovered DNA sequences, especially when focused on the deeper portions of the structures, belonged to either the tenant or squatter communities, not the actual builders. Once removed from their environmental context, correct interpretation of biology's role in stromatolite morphogenesis was difficult. Because high-throughput genomic analysis may easily lead to incorrect assumptions even in these modern and near-modern structures, caution must be exercised when interpreting micro-organismal involvement in the construction of accretionary structures throughout the rock record.

The metabolic network of the last bacterial common ancestor

Bacteria are the most abundant cells on Earth. They are generally regarded as ancient, but due to striking diversity in their metabolic capacities and widespread lateral gene transfer, the physiology of the first bacteria is unknown. From 1089 reference genomes of bacterial anaerobes, we identified 146 protein families that trace to the last bacterial common ancestor, LBCA, and form the conserved predicted core of its metabolic network, which requires only nine genes to encompass all universal metabolites. Our results indicate that LBCA performed gluconeogenesis towards cell wall synthesis, and had numerous RNA modifications and multifunctional enzymes that permitted life with low gene content. In accordance with recent findings for LUCA and LACA, analyses of thousands of individual gene trees indicate that LBCA was rod-shaped and the first lineage to diverge from the ancestral bacterial stem was most similar to modern Clostridia, followed by other autotrophs that harbor the acetyl-CoA pathway.

Emergy unsustainability index for agricultural systems assessment: A proposal based on the laws of thermodynamics

The anthropic effects of agriculture call for more sustainable systems. Agricultural sustainability conventionally communicates an idea of perennity. However, the sustainability of living open systems, like agricultural systems, can be regarded as a mere utopian idea when the effects of the laws of thermodynamics are taken into account. Under such physical laws, what really exists is the fact that any system alone has the property of unsustainability. The rate of entropy production can denote the potential level of the unsustainability of a system. The higher the rate of entropy production in an agricultural system, the higher its potential for unsustainability. Directly measuring entropy in living open systems is unfeasible. Even so, such systems are subject to the laws of thermodynamics. Indirect measurements of entropy in living open systems can be assessed by approximation through an analysis of the energy flows of the system. We used emergy analysis to account for the energy flows and compare the unsustainability among agricultural systems. However, the indicators proposed by emergy analysts have been more aligned with the perspective of sustainability. To change this perspective, we propose an emergy unsustainability index applied in this paper specifically to agricultural systems (EUI_AS). EUI_AS is not a simple inversion of the ESI obtained by the ratio between the Emergy Yield Ratio (EYR) and the Environmental Loading Ratio (ELR). The use of renewable exergy stored from one production cycle to another is one of the peculiarities of long-term agricultural systems. Therefore, quantifying the renewable and non-renewable fractions of resources used is fundamental to the EUI_AS. A higher EUI_AS means that an agricultural system is more dependent on non-renewable economic resources than renewable resources, and, in general, environmental impacts are higher due to the use of non-renewable resources.

The 'classic stromatolite' Cryptozoön is a keratose sponge-microbial consortium

Animal evolution transformed microbial mat development. Canonically inferred negative effects include grazing, disturbance and competition for space. In contrast, ancient examples of cooperation between microbial mats and invertebrates have rarely been reported. Late Cambrian (~485 million years) Cryptozoön is widely regarded as the first stromatolite to have received a taxonomic name and has been compared with present-day examples at Shark Bay, Australia. Here, we show that Cryptozoön is an interlayered consortium of keratose ('horny') sponge and microbial carbonate in roughly equal proportions. Cryptozoön's well-defined layering reflects repeated alternation of sponge and microbial mat. Its distinctive lateral growth is due to the ability of keratosans to colonize steep and overhanging surfaces. Contrary to the perception of Phanerozoic stromatolites as anachronistic survivors in a eukaryotic world, Cryptozoön suggests mutualistic behaviour in which sponges and microbial mats cooperated to gain support, stability and relief, while sharing substrates, bacteria and metabolites. Keratosan-microbial consortia may have been mistaken for stromatolites throughout the record of the past 500 million years, and possibly longer.

Trace Element Concentrations Associated with Mid-Paleozoic Microfossils as Biosignatures to Aid in the Search for Life

Identifying microbial fossils in the rock record is a difficult task because they are often simple in morphology and can be mimicked by non-biological structures. Biosignatures are essential for identifying putative fossils as being definitively biological in origin, but are often lacking due to geologic effects which can obscure or erase such signs. As such, there is a need for robust biosignature identification techniques. Here we show new evidence for the application of trace elements as biosignatures in microfossils. We found elevated concentrations of magnesium, aluminum, manganese, iron, and strontium colocalized with carbon and sulfur in microfossils from Drummond Basin, a mid-Paleozoic hot spring deposit in Australia. Our results also suggest that trace element sequestrations from modern hot spring deposits persist through substantial host rock alteration. Because some of the oldest fossils on Earth are found in hot spring deposits and ancient hot spring deposits are also thought to occur on Mars, this biosignature technique may be utilized as a valuable tool to aid in the search for extraterrestrial life.

Embryo-Like Features in Developing Bacillus subtilis Biofilms

Correspondence between evolution and development has been discussed for more than two centuries. Recent work reveals that phylogeny-ontogeny correlations are indeed present in developmental transcriptomes of eukaryotic clades with complex multicellularity. Nevertheless, it has been largely ignored that the pervasive presence of phylogeny-ontogeny correlations is a hallmark of development in eukaryotes. This perspective opens a possibility to look for similar parallelisms in biological settings where developmental logic and multicellular complexity are more obscure. For instance, it has been increasingly recognized that multicellular behavior underlies biofilm formation in bacteria. However, it remains unclear whether bacterial biofilm growth shares some basic principles with development in complex eukaryotes. Here we show that the ontogeny of growing Bacillus subtilis biofilms recapitulates phylogeny at the expression level. Using time-resolved transcriptome and proteome profiles, we found that biofilm ontogeny correlates with the evolutionary measures, in a way that evolutionary younger and more diverged genes were increasingly expressed toward later timepoints of biofilm growth. Molecular and morphological signatures also revealed that biofilm growth is highly regulated and organized into discrete ontogenetic stages, analogous to those of eukaryotic embryos. Together, this suggests that biofilm formation in Bacillus is a bona fide developmental process comparable to organismal development in animals, plants, and fungi. Given that most cells on Earth reside in the form of biofilms and that biofilms represent the oldest known fossils, we anticipate that the widely adopted vision of the first life as a single-cell and free-living organism needs rethinking.

The structure of autocatalytic networks, with application to early biochemistry

Metabolism across all known living systems combines two key features. First, all of the molecules that are required are either available in the environment or can be built up from available resources via other reactions within the system. Second, the reactions proceed in a fast and synchronized fashion via catalysts that are also produced within the system. Building on early work by Stuart Kauffman, a precise mathematical model for describing such self-sustaining autocatalytic systems (RAF theory) has been developed to explore the origins and organization of living systems within a general formal framework. In this paper, we develop this theory further by establishing new relationships between classes of RAFs and related classes of networks, and developing new algorithms to investigate and visualize RAF structures in detail. We illustrate our results by showing how it reveals further details into the structure of archaeal and bacterial metabolism near the origin of life, and provide techniques to study and visualize the core aspects of primitive biochemistry.

Deconstructing Earth's oldest ichnofossil record from the Pilbara Craton, West Australia: Implications for seeking life in the Archean subseafloor

Microtextures of titanite (CaTiSiO₅ ) in exceptionally preserved Archean pillow lavas have been proposed as the earliest examples of microbial ichnofossils. An origin from microbial tunneling of seafloor volcanic glass that is subsequently chloritized and the tunnels infilled by titanite has been argued to record the activities of subseafloor microbes. We investigate the evidence in pillow lavas of the 3.35 Ga Euro Basalt from the Pilbara Craton, Western Australia, to evaluate the biogenicity of the microtextures. We employ a combination of light microscopy and chlorite mineral chemical analysis by EPMA (electron probe micro-analysis) to document the environment of formation and analyze their ultrastructure using FIB-TEM (focussed ion beam combined with transmission electron microscopy) to investigate their mode of growth. Petrographic study of the original and re-collected material identified an expanded range of titanite morphotypes along with early anatase growth forming chains and aggregates of coalesced crystallites in a sub-greenschist facies assemblage. High-sensitivity mapping of FIB lamellae cut across the microtextures confirm that they are discontinuous chains of coalesced crystallites that are highly variable in cross section and contain abundant chlorite inclusions, excluding an origin from the mineralization of previously hollow microtunnels. Comparison of chlorite mineral compositions to DSDP/IODP data reveals that the Euro Basalt chlorites are similar to recent seafloor chlorites. We advance an abiotic origin for the Euro Basalt microtextures formed by spontaneous nucleation and growth of titanite and/anatase during seafloor-hydrothermal metamorphism. Our findings reveal that the Euro Basalt microtextures are not comparable to microbial ichnofossils from the recent oceanic crust, and we question the evidence for life in these Archean lavas. The metamorphic reactions that give rise to the growth of the Euro Basalt microtextures could be commonplace in Archean pillow lavas and need to be excluded when seeking traces of life in the subseafloor on the early Earth.

The Construction of Biological 'Inter-Identity' as the Outcome of a Complex Process of Protocell Development in Prebiotic Evolution

The concept of identity is used both (i) to distinguish a system as a particular material entity that is conserved as such in a given environment (token-identity: i.e., identity as permanence or endurance over time), and (ii) to relate a system with other members of a set (type-identity: i.e., identity as an equivalence relationship). Biological systems are characterized, in a minimal and universal sense, by a highly complex and dynamic, far-from-equilibrium organization of very diverse molecular components and transformation processes (i.e., 'genetically instructed cellular metabolisms') that maintain themselves in constant interaction with their corresponding environments, including other systems of similar nature. More precisely, all living entities depend on a deeply convoluted organization of molecules and processes (a naturalized von Neumann constructor architecture) that subsumes, in the form of current individuals (autonomous cells), a history of ecological and evolutionary interactions (across cell populations). So one can defend, on those grounds, that living beings have an identity of their own from both approximations: (i) and (ii). These transversal and trans-generational dimensions of biological phenomena, which unfold together with the actual process of biogenesis, must be carefully considered in order to understand the intricacies and metabolic robustness of the first living cells, their underlying uniformity (i.e., their common biochemical core) and the eradication of previous -or alternative- forms of complex natural phenomena. Therefore, a comprehensive approach to the origins of life requires conjugating the actual properties of the developing complex individuals (fusing and dividing protocells, at various stages) with other, population-level features, linked to their collective-evolutionary behavior, under much wider and longer-term parameters. On these lines, we will argue that life, in its most basic sense, here on Earth or anywhere else, demands crossing a high complexity threshold and that the concept of 'inter-identity' can help us realize the different aspects involved in the process. The article concludes by pointing out some of the challenges ahead if we are to integrate the corresponding explanatory frameworks, physiological and evolutionary, in the hope that a more general theory of biology is on its way.

Chasing Synthetic Life: A Tale of Forms, Chemical Fossils, and Biomorphs

This Essay focuses briefly on early studies elaborated by natural and chemical philosophers, and the once-called synthetic biologists, who postulated the transition from inanimate to animate matter and even foresaw the possibility of creating artificial life on the basis of physical and chemical principles only. Such ideas and speculations, ranging from soundness to weirdness, paved however the way to current developments in areas like abiotic pattern formation, cell compartmentalization, biomineralization, or the origin of life itself. In particular, the generation of biomorphs and their relationship to microfossils represents an active research domain and seems to be the logical way to bring the historical work up to the future, as some scientists are trying to make artificial cells. The last sections of this essay will also highlight modern science aimed at understanding what life is and, whether or not, it can be redefined in chemical terms.

Chemical Origins of Life: Its Engagement with Society

Comprehending the origin of life on Earth is intriguing and its scientific endeavors have engaged society while guiding the search for life elsewhere. However, some persistently question the science and support for such endeavors. This Science & Society article attempts to put this in context and contemplates how engagement could prevent misunderstandings.

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

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.

The Future of Origin of Life Research: Bridging Decades-Old Divisions

Research on the origin of life is highly heterogeneous. After a peculiar historical development, it still includes strongly opposed views which potentially hinder progress. In the 1st Interdisciplinary Origin of Life Meeting, early-career researchers gathered to explore the commonalities between theories and approaches, critical divergence points, and expectations for the future. We find that even though classical approaches and theories-e.g. bottom-up and top-down, RNA world vs. metabolism-first-have been prevalent in origin of life research, they are ceasing to be mutually exclusive and they can and should feed integrating approaches. Here we focus on pressing questions and recent developments that bridge the classical disciplines and approaches, and highlight expectations for future endeavours in origin of life research.