Organic geochemical approaches to understanding early life

Standard Candles for Dating Microbial Lineages

Molecular clock analyses are challenging for microbial phylogenies, due to a lack of fossil calibrations that can reliably provide absolute time constraints. An alternative source of temporal constraints for microbial groups is provided by the inheritance of proteins that are specific for the utilization of eukaryote-derived substrates, which have often been dispersed across the Tree of Life via horizontal gene transfer. In particular, animal, algal, and plant-derived substrates are often produced by groups with more precisely known divergence times, providing an older-bound on their availability within microbial environments. Therefore, these ages can serve as "standard candles" for dating microbial groups across the Tree of Life, expanding the reach of informative molecular clock investigations. Here, we formally develop the concept of substrate standard candles and describe how they can be propagated and applied using both microbial species trees and individual gene family phylogenies. We also provide detailed evaluations of several candidate standard candles and discuss their suitability in light of their often complex evolutionary and metabolic histories.

In search of the RNA world on Mars

Advances in origins of life research and prebiotic chemistry suggest that life as we know it may have emerged from an earlier RNA World. However, it has been difficult to reconcile the conditions used in laboratory experiments with real-world geochemical environments that may have existed on the early Earth and hosted the origin(s) of life. This challenge is due to geologic resurfacing and recycling that have erased the overwhelming majority of the Earth's prebiotic history. We therefore propose that Mars, a planet frozen in time, comprised of many surfaces that have remained relatively unchanged since their formation > 4 Gya, is the best alternative to search for environments consistent with geochemical requirements imposed by the RNA world. In this study, we synthesize in situ and orbital observations of Mars and modeling of its early atmosphere into solutions containing a range of pHs and concentrations of prebiotically relevant metals (Fe²⁺ , Mg²⁺ , and Mn²⁺ ) spanning various candidate aqueous environments. We then experimentally determine RNA degradation kinetics due to metal-catalyzed hydrolysis (cleavage) and evaluate whether early Mars could have been permissive toward the accumulation of long-lived RNA polymers. Our results indicate that a Mg²⁺ -rich basalt sourcing metals to a slightly acidic (pH 5.4) environment mediates the slowest rates of RNA cleavage, though geologic evidence and basalt weathering models suggest aquifers on Mars would be near neutral (pH ~ 7). Moreover, the early onset of oxidizing conditions on Mars has major consequences regarding the availability of oxygen-sensitive metals (i.e., Fe²⁺ and Mn²⁺ ) due to increased RNA degradation rates and precipitation. Overall, (a) low pH decreases RNA cleavage at high metal concentrations; (b) acidic to neutral pH environments with Fe²⁺ or Mn²⁺ cleave more RNA than Mg²⁺ ; and (c) alkaline environments with Mg²⁺ dramatically cleaves more RNA while precipitates were observed for Fe²⁺ and Mn²⁺ .

Pushing Raman spectroscopy over the edge: purported signatures of organic molecules in fossil animals are instrumental artefacts

Widespread preservation of fossilized biomolecules in many fossil animals has recently been reported in six studies, based on Raman microspectroscopy. Here, we show that the putative Raman signatures of organic compounds in these fossils are actually instrumental artefacts resulting from intense background luminescence. Raman spectroscopy is based on the detection of photons scattered inelastically by matter upon its interaction with a laser beam. For many natural materials, this interaction also generates a luminescence signal that is often orders of magnitude more intense than the light produced by Raman scattering. Such luminescence, coupled with the transmission properties of the spectrometer, induced quasi-periodic ripples in the measured spectra that have been incorrectly interpreted as Raman signatures of organic molecules. Although several analytical strategies have been developed to overcome this common issue, Raman microspectroscopy as used in the studies questioned here cannot be used to identify fossil biomolecules.

Evolutionary History of Bioessential Elements Can Guide the Search for Life in the Universe

Our understanding of life in the universe comes from one sample, life on Earth. Current and next-generation space missions will target exoplanets as well as planets and moons in our own solar system with the primary goal of detecting, interpreting and characterizing indications of possible biological activity. Thus, understanding life's fundamental characteristics is increasingly critical for detecting and interpreting potential biological signatures elsewhere in the universe. Astrobiologists have outlined the essential roles of carbon and water for life, but we have yet to decipher the rules governing the evolution of how living organisms use bioessential elements. Does the suite of life's essential chemical elements on Earth constitute only one possible evolutionary outcome? Are some elements so essential for biological functions that evolution will select for them despite low availability? How would this play out on other worlds that have different relative element abundances? When we look for life in the universe, or the conditions that could give rise to life, we must learn how to recognize it in extremely different chemical and environmental conditions from those on Earth. We argue that by exposing self-organizing biotic chemistries to different combinations of abiotic materials, and by mapping the evolutionary history of metalloenzyme biochemistry onto geological availabilities of metals, alternative element choices that are very different from life's present-day molecular structure might result. A greater understanding of the paleomolecular evolutionary history of life on Earth will create a predictive capacity for detecting and assessing life's existence on worlds where alternate evolutionary paths might have been taken.

Mineral self-organization on a lifeless planet

It has been experimentally demonstrated that, under alkaline conditions, silica is able to induce the formation of mineral self-assembled inorganic-inorganic composite materials similar in morphology, texture and nanostructure to the hybrid biomineral structures that, millions of years later, life was able to self-organize. These mineral self-organized structures (MISOS) have been also shown to work as effective catalysts for prebiotic chemical reactions and to easily create compartmentalization within the solutions where they form. We reason that, during the very earliest history of this planet, there was a geochemical scenario that inevitably led to the existence of a large-scale factory of simple and complex organic compounds, many of which were relevant to prebiotic chemistry. The factory was built on a silica-rich high-pH ocean and powered by two main factors: a) a quasi-infinite source of simple carbon molecules synthesized abiotically from reactions associated with serpentinization, or transported from meteorites and produced from their impact on that alkaline ocean, and b) the formation of self-organized silica-metal mineral composites that catalyze the condensation of simple molecules in a methane-rich reduced atmosphere. We discuss the plausibility of this geochemical scenario, review the details of the formation of MISOS and its catalytic properties and the transition towards a slightly alkaline to neutral ocean.

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.

Organo-mineral associations in chert of the 3.5 Ga Mount Ada Basalt raise questions about the origin of organic matter in Paleoarchean hydrothermally influenced sediments

Hydrothermal and metamorphic processes could have abiotically produced organo-mineral associations displaying morphological and isotopic characteristics similar to those of fossilized microorganisms in ancient rocks, thereby leaving false-positive evidence for early life in the geological record. Recent studies revealed that geologically-induced alteration processes do not always completely obliterate all molecular information about the original organic precursors of ancient microfossils. Here, we report the molecular, geochemical, and mineralogical composition of organo-mineral associations in a chert sample from the ca. 3.47 billion-year-old (Ga) Mount Ada Basalt, in the Pilbara Craton, Western Australia. Our observations indicate that the molecular characteristics of carbonaceous matter are consistent with hydrothermally altered biological organics, although significantly distinct from that of organic microfossils discovered in a chert sample from the ca. 3.43 Ga Strelley Pool Formation in the same area. Alternatively, the presence of native metal alloys in the chert, previously believed to be unstable in such hydrothermally influenced environments, indicates strongly reducing conditions that were favorable for the abiotic formation of organic matter. Drawing definitive conclusions about the origin of most Paleoarchean organo-mineral associations therefore requires further characterization of a range of natural samples together with experimental simulations to constrain the molecular composition and geological fate of hydrothermally-generated condensed organics.

Challenges in evidencing the earliest traces of life

Earth has been habitable for 4.3 billion years, and the earliest rock record indicates the presence of a microbial biosphere by at least 3.4 billion years ago-and disputably earlier. Possible traces of life can be morphological or chemical but abiotic processes that mimic or alter them, or subsequent contamination, may challenge their interpretation. Advances in micro- and nanoscale analyses, as well as experimental approaches, are improving the characterization of these biosignatures and constraining abiotic processes, when combined with the geological context. Reassessing the evidence of early life is challenging, but essential and timely in the quest to understand the origin and evolution of life, both on Earth and beyond.

Cyanobacteria evolution: Insight from the fossil record

Cyanobacteria played an important role in the evolution of Early Earth and the biosphere. They are responsible for the oxygenation of the atmosphere and oceans since the Great Oxidation Event around 2.4 Ga, debatably earlier. They are also major primary producers in past and present oceans, and the ancestors of the chloroplast. Nevertheless, the identification of cyanobacteria in the early fossil record remains ambiguous because the morphological criteria commonly used are not always reliable for microfossil interpretation. Recently, new biosignatures specific to cyanobacteria were proposed. Here, we review the classic and new cyanobacterial biosignatures. We also assess the reliability of the previously described cyanobacteria fossil record and the challenges of molecular approaches on modern cyanobacteria. Finally, we suggest possible new calibration points for molecular clocks, and strategies to improve our understanding of the timing and pattern of the evolution of cyanobacteria and oxygenic photosynthesis.