Reconstructing Deep-Time Biology with Molecular Fossils

Phylogenomic Evidence for the Origin of Obligate Anaerobic Anammox Bacteria Around the Great Oxidation Event

The anaerobic ammonium oxidation (anammox) bacteria can transform ammonium and nitrite to dinitrogen gas, and this obligate anaerobic process accounts for up to half of the global nitrogen loss in surface environments. Yet its origin and evolution, which may give important insights into the biogeochemistry of early Earth, remain enigmatic. Here, we performed a comprehensive phylogenomic and molecular clock analysis of anammox bacteria within the phylum Planctomycetes. After accommodating the uncertainties and factors influencing time estimates, which include implementing both a traditional cyanobacteria-based and a recently developed mitochondria-based molecular dating approach, we estimated a consistent origin of anammox bacteria at early Proterozoic and most likely around the so-called Great Oxidation Event (GOE; 2.32-2.5 Ga) which fundamentally changed global biogeochemical cycles. We further showed that during the origin of anammox bacteria, genes involved in oxidative stress adaptation, bioenergetics, and anammox granules formation were recruited, which might have contributed to their survival on an increasingly oxic Earth. Our findings suggest the rising levels of atmospheric oxygen, which made nitrite increasingly available, was a potential driving force for the emergence of anammox bacteria. This is one of the first studies that link the GOE to the evolution of obligate anaerobic bacteria.

Geological alteration of Precambrian steroids mimics early animal signatures

The absence of unambiguous animal body fossils in rocks older than the late Ediacaran has rendered fossil lipids the most promising tracers of early organismic complexity. Yet much debate surrounds the various potential biological sources of putative metazoan steroids found in Precambrian rocks. Here we show that 26-methylated steranes-hydrocarbon structures currently attributed to the earliest animals-can form via geological alteration of common algal sterols, which carries important implications for palaeo-ecological interpretations and inhibits the use of such unconventional 'sponge' steranes for reconstructing early animal evolution.

Testing Flight-like Pyrolysis Gas Chromatography-Mass Spectrometry as Performed by the Mars Organic Molecule Analyzer Onboard the ExoMars 2020 Rover on Oxia Planum Analog Samples

The Mars Organic Molecule Analyzer (MOMA) onboard the ExoMars 2020 rover (to be landed in March 2021) utilizes pyrolysis gas chromatography-mass spectrometry (GC-MS) with the aim to detect organic molecules in martian (sub-) surface materials. Pyrolysis, however, may thermally destroy and transform organic matter depending on the temperature and nature of the molecules, thus altering the original molecular signatures. In this study, we tested MOMA flight-like pyrolysis GC-MS without the addition of perchlorates on well-characterized natural mineralogical analog samples for Oxia Planum, the designated ExoMars 2020 landing site. Experiments were performed on an iron-rich shale (that is rich in Fe-Mg-smectites) and an opaline chert, with known organic matter compositions, to test pyrolytic effects related to heating in the MOMA oven. Two hydrocarbon standards (n-octadecane and phytane) were also analyzed. The experiments show that during stepwise pyrolysis (300°C, 500°C, and 700°C), (1) low-molecular-weight hydrocarbon biomarkers (such as acyclic isoprenoids and aryl isoprenoids) can be analyzed intact, (2) discrimination between free and complex molecules (macromolecules) is principally possible, (3) secondary pyrolysis products and carryover may affect the 500°C and 700°C runs, and (4) the type of the organic matter (functionalized vs. defunctionalized) governs the pyrolysis outcome rather than the difference in mineralogy. Although pyrosynthesis reactions and carryover clearly have to be considered in data interpretation, our results demonstrate that pyrolysis GC-MS onboard MOMA operated under favorable conditions (e.g., no perchlorates) will be capable of providing important structural information on organic matter found on Mars, particularly when used in conjunction with other techniques on MOMA, including derivatization and thermochemolysis GC-MS and laser desorption/ionization-MS.

Investigating the Effect of Perchlorate on Flight-like Gas Chromatography-Mass Spectrometry as Performed by MOMA on board the ExoMars 2020 Rover

The Mars Organic Molecule Analyzer (MOMA) instrument on board ESA's ExoMars 2020 rover will be essential in the search for organic matter. MOMA applies gas chromatography-mass spectrometry (GC-MS) techniques that rely on thermal volatilization. Problematically, perchlorates and chlorates in martian soils and rocks become highly reactive during heating (>200°C) and can lead to oxidation and chlorination of organic compounds, potentially rendering them unidentifiable. Here, we analyzed a synthetic sample (alkanols and alkanoic acids on silica gel) and a Silurian chert with and without Mg-perchlorate to evaluate the applicability of MOMA-like GC-MS techniques to different sample types and assess the impact of perchlorate. We used a MOMA flight analog system coupled to a commercial GC-MS to perform MOMA-like pyrolysis, in situ derivatization, and in situ thermochemolysis. We show that pyrolysis can provide a sufficient overview of the organic inventory but is strongly affected by the presence of perchlorates. In situ derivatization facilitates the identification of functionalized organics but showed low efficiency for n-alkanoic acids. Thermochemolysis is shown to be an effective technique for the identification of both refractory and functional compounds. Most importantly, this technique was barely affected by perchlorates. Therefore, MOMA GC-MS analyses of martian surface/subsurface material may be less affected by perchlorates than commonly thought, in particular when applying the full range of available MOMA GC-MS techniques.

Bisnorgammacerane traces predatory pressure and the persistent rise of algal ecosystems after Snowball Earth

Eukaryotic algae rose to ecological relevance after the Neoproterozoic Snowball Earth glaciations, but the causes for this consequential evolutionary transition remain enigmatic. Cap carbonates were globally deposited directly after these glaciations, but they are usually organic barren or thermally overprinted. Here we show that uniquely-preserved cap dolostones of the Araras Group contain exceptional abundances of a newly identified biomarker: 25,28-bisnorgammacerane. Its secular occurrence, carbon isotope systematics and co-occurrence with other demethylated terpenoids suggest a mechanistic connection to extensive microbial degradation of ciliate-derived biomass in bacterially dominated ecosystems. Declining 25,28-bisnorgammacerane concentrations, and a parallel rise of steranes over hopanes, indicate the transition from a bacterial to eukaryotic dominated ecosystem after the Marinoan deglaciation. Nutrient levels already increased during the Cryogenian and were a prerequisite, but not the ultimate driver for the algal rise. Intense predatory pressure by bacterivorous protists may have irrevocably cleared self-sustaining cyanobacterial ecosystems, thereby creating the ecological opportunity that allowed for the persistent rise of eukaryotic algae to global importance.

Cryogenian evolution of stigmasteroid biosynthesis

Sedimentary hydrocarbon remnants of eukaryotic C₂₆-C₃₀ sterols can be used to reconstruct early algal evolution. Enhanced C₂₉ sterol abundances provide algal cell membranes a density advantage in large temperature fluctuations. Here, we combined a literature review with new analyses to generate a comprehensive inventory of unambiguously syngenetic steranes in Neoproterozoic rocks. Our results show that the capacity for C₂₉ 24-ethyl-sterol biosynthesis emerged in the Cryogenian, that is, between 720 and 635 million years ago during the Neoproterozoic Snowball Earth glaciations, which were an evolutionary stimulant, not a bottleneck. This biochemical innovation heralded the rise of green algae to global dominance of marine ecosystems and highlights the environmental drivers for the evolution of sterol biosynthesis. The Cryogenian emergence of C₂₉ sterol biosynthesis places a benchmark for verifying older sterane signatures and sets a new framework for our understanding of early algal evolution.

Enhanced procedural blank control for organic geochemical studies of critical sample material

Organic contamination of sedimentary rocks can produce artefacts in studies of hydrocarbon composition, and this can have significant negative consequences for interpretations of the geobiological record. False positives - that is cases of non-syngenetic hydrocarbon biomarkers - are common in Precambrian studies, and significant challenges persist despite the intensive effort devoted to these studies. Efforts to standardize the 'burden of proof' for distinguishing between contamination and syngenetic material have to date failed to yield a simple or universal protocol, yet the need remains great, as both bitumen-lean rocks and bitumen-rich samples can be vulnerable to the accumulation of false-positive signals. In an effort to determine the best approach to quality control, we tested the capability of different blank materials to collect ambient contamination by assessing their capacity to adsorb hydrocarbons during storage in plastic bags and found that commonly used Quartz sand does not provide an adequate measure of storage- or laboratory-induced contamination. Brick blanks, having the advantage that they can parallel rock samples even during the sawing process, are characterized by similar poor adsorption properties. Primarily steered by mineralogy, organic carbon content and surface area, model-black shales can adsorb up to 20 times more contaminants than sand blanks and up to 200 times more contaminants than organic-free model-carbonates. This observation provides an explanation for reports and observations of seemingly systematic stratigraphic variation of contaminants, but mostly should raise awareness for the evaluation of procedural blanks, in particular of sample-to-blank ratios, when studying bitumen-lean rock samples of varying lithologies. Additionally, differences between the hydrocarbon profiles in plastic bags and the hydrocarbon signatures transferred to blank materials emphasize difficulties in the unequivocal detection of contamination sources. Artificial black shale pellets can provide enhanced contamination control in biomarker studies - particularly for exceptionally vulnerable samples such as Precambrian rocks, meteorites or extraterrestrial sample-return material.