Design and Construction of an Experimental Setup to Enhance Mineral Weathering through the Activity of Soil Organisms

Enhanced weathering (EW) is an emerging carbon dioxide (CO2) removal technology that can contribute to climate change mitigation. This technology relies on accelerating the natural process of mineral weathering in soils by manipulating the abiotic variables that govern this process, in particular mineral grain size and exposure to acids dissolved in water. EW mainly aims at reducing atmospheric CO2 concentrations by enhancing inorganic carbon sequestration. Until now, knowledge of EW has been mainly gained through experiments that focused on the abiotic variables known for stimulating mineral weathering, thereby neglecting the potential influence of biotic components. While bacteria, fungi, and earthworms are known to increase mineral weathering rates, the use of soil organisms in the context of EW remains underexplored. This protocol describes the design and construction of an experimental setup developed to enhance mineral weathering rates through soil organisms while concurrently controlling abiotic conditions. The setup is designed to maximize weathering rates while maintaining soil organisms' activity. It consists of a large number of columns filled with rock powder and organic material, located in a climate chamber and with water applied via a downflow irrigation system. Columns are placed above a fridge containing jerrycans to collect the leachate. Representative results demonstrate that this setup is suitable to ensure the activity of soil organisms and quantify their effect on inorganic carbon sequestration. Challenges remain in minimizing leachate losses, ensuring homogeneous ventilation through the climate chamber, and avoiding flooding of the columns. With this setup, an innovative and promising approach is proposed to enhance mineral weathering rates through the activity of soil biota and disentangle the effect of biotic and abiotic factors as drivers of EW.

Chemical Gardens Mimic Electron Paramagnetic Resonance Spectra and Morphology of Biogenic Mn Oxides

Manganese (Mn) oxides are ubiquitous in nature and occur as both biological and abiotic minerals, but empirically distinguishing between the two remains a problem. Recently, electron paramagnetic resonance (EPR) spectroscopy has been proposed for this purpose. It has been reported that biogenic Mn oxides display a characteristic narrow linewidth in contrast to their pure abiotic counterparts, which is explained in part by the large number of cation vacancies that form within the layers of biogenic Mn oxides. It was, therefore, proposed that natural samples that display a narrow EPR linewidth, ΔHpp < 580G, could be assigned to a biogenic origin. However, in poorly crystalline or amorphous solids, both dipolar broadening and exchange narrowing simultaneously determine the linewidth. Considering that the spectral linewidth is governed by several mechanisms, this approach might be questioned. In this study, we report synthetic chemical garden Mn oxide biomorphs that exhibit both morphologically life-like structures and narrow EPR linewidths, suggesting that a narrow EPR line may be unsuitable as reliable evidence in assessment of biogenicity.

Detection of porphyrins in vertebrate fossils from the Messel and implications for organic preservation in the fossil record

Organic molecules preserved in fossils provide a wealth of new information about ancient life. The discovery of almost unaltered complex organic molecules in well-preserved fossils raise the question of how common such occurrences are in the fossil record, how to differentiate between endogenous and exogenous sources for the organic matter and what promotes such preservation. The aim of this study was the in-situ analysis of a well-preserved vertebrate fossil from 48 Ma Eocene sediments in the Messel pit, Germany for preservation of complex biomolecules. The fossil was characterized using a variety of techniques including time-of-flight secondary ion mass spectrometry (ToF-SIMS), scanning electron microscopy/energy dispersive x-ray spectroscopy (SEM/EDX), x-ray diffraction (XRD) and Raman spectroscopy. A suite of organic molecules was detected, including porphyrins, which given the context of the detected signal are most probably diagenetically altered heme originating from the fossil though a microbial contribution cannot be completely ruled out. Diagenetic changes to the porphyrin structure were observed that included the exchange of the central iron by nickel. Further analyses on the geochemistry of the fossil and surrounding sediments showed presence of pyrite and aluminosilicates, most likely clay. In addition, a carbonate and calcium phosphate dominated crust has formed around the fossil. This suggests that several different processes are involved in the preservation of the fossil and the organic molecules associated with it. Similar processes seem to have also been involved in preservation of heme in fossils from other localities.

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.

Is the climate change mitigation effect of enhanced silicate weathering governed by biological processes?

A number of negative emission technologies (NETs) have been proposed to actively remove CO₂ from the atmosphere, with enhanced silicate weathering (ESW) as a relatively new NET with considerable climate change mitigation potential. Models calibrated to ESW rates in lab experiments estimate the global potential for inorganic carbon sequestration by ESW at about 0.5-5 Gt CO₂  year^-1 , suggesting ESW could be an important component of the future NETs mix. In real soils, however, weathering rates may differ strongly from lab conditions. Research on natural weathering has shown that biota such as plants, microbes, and macro-invertebrates can strongly affect weathering rates, but biotic effects were excluded from most ESW lab assessments. Moreover, ESW may alter soil organic carbon sequestration and greenhouse gas emissions by influencing physicochemical and biological processes, which holds the potential to perpetuate even larger negative emissions. Here, we argue that it is likely that the climate change mitigation effect of ESW will be governed by biological processes, emphasizing the need to put these processes on the agenda of this emerging research field.

On Topological Analysis of fs-LIMS Data. Implications for in Situ Planetary Mass Spectrometry

In this contribution, we present results of non-linear dimensionality reduction and classification of the fs laser ablation ionization mass spectrometry (LIMS) imaging dataset acquired from the Precambrian Gunflint chert (1.88 Ga) using a miniature time-of-flight mass spectrometer developed for in situ space applications. We discuss the data generation, processing, and analysis pipeline for the classification of the recorded fs-LIMS mass spectra. Further, we define topological biosignatures identified for Precambrian Gunflint microfossils by projecting the recorded fs-LIMS intensity space into low dimensions. Two distinct subtypes of microfossil-related spectra, a layer of organic contamination and inorganic quartz matrix were identified using the fs-LIMS data. The topological analysis applied to the fs-LIMS data allows to gain additional knowledge from large datasets, formulate hypotheses and quickly generate insights from spectral data. Our contribution illustrates the utility of applying spatially resolved mass spectrometry in combination with topology-based analytics in detecting signatures of early (primitive) life. Our results indicate that fs-LIMS, in combination with topological methods, provides a powerful analytical framework and could be applied to the study of other complex mineralogical samples.

Isotope abundance ratio measurements using femtosecond laser ablation ionization mass spectrometry

Accurate isotope ratio measurements are of high importance in various scientific fields, ranging from radio isotope geochronology of solids to studies of element isotopes fractionated by living organisms. Instrument limitations, such as unresolved isobaric inferences in the mass spectra, or cosampling of the material of interest together with the matrix material may reduce the quality of isotope measurements. Here, we describe a method for accurate isotope ratio measurements using our laser ablation ionization time-of-flight mass spectrometer (LIMS) that is designed for in situ planetary research. The method is based on chemical depth profiling that allows for identifying micrometer scale inclusions embedded in surrounding rocks with different composition inside the bulk of the sample. The data used for precise isotope measurements are improved using a spectrum cleaning procedure that ensures removal of low quality spectra. Furthermore, correlation of isotopes of an element is used to identify and reject the data points that, for example, do not belong to the species of interest. The measurements were conducted using IR femtosecond laser irradiation focused on the sample surface to a spot size of ~12 μm. Material removal was conducted for a predefined number of laser shots, and time-of-flight mass spectra were recorded for each of the ablated layers. Measurements were conducted on NIST SRM 986 Ni isotope standard, trevorite mineral, and micrometer-sized inclusions embedded in aragonite. Our measurements demonstrate that element isotope ratios can be measured with accuracies and precision at the permille level, exemplified by the analysis of B, Mg, and Ni element isotopes. The method applied will be used for in situ investigation of samples on planetary surfaces, for accurate quantification of element fractionation induced by, for example, past or present life or by geochemical processes.

Sulfur Chemistry May Have Paved the Way for Evolution of Antioxidants

The first organisms on the young Earth, just 1-1.5 billion years old, were likely chemolithoautotrophic anaerobes, thriving in an anoxic world rich in water, CO₂, and N₂. It is generally assumed that, until the accumulation of O₂ in the atmosphere, life was exempted from the oxidative stress that reactive oxygen species (ROS) impose on hydrocarbon-based life. Therefore, it is perplexing to note that life on the early Earth already carried antioxidants such as superoxide dismutase enzymes, catalase, and peroxiredoxins, the function of which is to counteract all forms of ROS, including H₂O₂. Phylogenetic investigations suggest that the presence of these enzymes in the last universal common ancestor, far predating the great oxygenation event (GOE) sometime between 2.3 and 2.7 billion years ago, is thought to be due to the appearance of oxygen-producing microorganisms and the subsequent need to respond to the appearance of ROS. Since the metabolic enzymes that counteract ROS have been found in all domains of life, they are considered of primitive origin. Two questions arise: (1) Could there be a nonbiological source of ROS that predates the oxygenic microbial activity? (2) Could sulfur, the homologue of oxygen, have played that role? Reactive sulfur species (RSS) may have triggered the evolution of antioxidants such that the ROS antioxidants started out as "antisulfur" enzymes developed to cope with, and take advantage of, various forms of RSS that were abundantly present on the early Earth.

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.

Serpentinization: Connecting Geochemistry, Ancient Metabolism and Industrial Hydrogenation

Rock⁻water⁻carbon interactions germane to serpentinization in hydrothermal vents have occurred for over 4 billion years, ever since there was liquid water on Earth. Serpentinization converts iron(II) containing minerals and water to magnetite (Fe₃O₄) plus H₂. The hydrogen can generate native metals such as awaruite (Ni₃Fe), a common serpentinization product. Awaruite catalyzes the synthesis of methane from H₂ and CO₂ under hydrothermal conditions. Native iron and nickel catalyze the synthesis of formate, methanol, acetate, and pyruvate-intermediates of the acetyl-CoA pathway, the most ancient pathway of CO₂ fixation. Carbon monoxide dehydrogenase (CODH) is central to the pathway and employs Ni⁰ in its catalytic mechanism. CODH has been conserved during 4 billion years of evolution as a relic of the natural CO₂-reducing catalyst at the onset of biochemistry. The carbide-containing active site of nitrogenase-the only enzyme on Earth that reduces N₂-is probably also a relic, a biological reconstruction of the naturally occurring inorganic catalyst that generated primordial organic nitrogen. Serpentinization generates Fe₃O₄ and H₂, the catalyst and reductant for industrial CO₂ hydrogenation and for N₂ reduction via the Haber⁻Bosch process. In both industrial processes, an Fe₃O₄ catalyst is matured via H₂-dependent reduction to generate Fe₅C₂ and Fe₂N respectively. Whether serpentinization entails similar catalyst maturation is not known. We suggest that at the onset of life, essential reactions leading to reduced carbon and reduced nitrogen occurred with catalysts that were synthesized during the serpentinization process, connecting the chemistry of life and Earth to industrial chemistry in unexpected ways.

Chemical and Optical Identification of Micrometer-Sized 1.9 Billion-Year-Old Fossils by Combining a Miniature Laser Ablation Ionization Mass Spectrometry System with an Optical Microscope

The recognition of biosignatures on planetary bodies requires the analysis of the putative microfossil with a set of complementary analytical techniques. This includes localized elemental and isotopic analysis of both, the putative microfossil and its surrounding host matrix. If the analysis can be performed with spatial resolution at the micrometer level and ppm detection sensitivities, valuable information on the (bio)chemical and physical processes that influenced the sample material can be gained. Our miniaturized laser ablation ionization mass spectrometry (LIMS)-time-of-flight mass spectrometer instrument is a valid candidate for performing the required chemical analysis in situ. However, up until now it was limited by the spatial accuracy of the sampling. In this contribution, we introduce a newly developed microscope system with micrometer accuracy for Ultra High Vacuum application, which allows a significant increase in the measurement capabilities of our miniature LIMS system. The new enhancement allows identification and efficient and accurate sampling of features of micrometer-sized fossils in a host matrix. The performance of our system is demonstrated by the identification and chemical analysis of signatures of micrometer-sized fossil structures in the 1.9 billion-year-old Gunflint chert.

Searching for Biosignatures in Exoplanetary Impact Ejecta

With the number of confirmed rocky exoplanets increasing steadily, their characterization and the search for exoplanetary biospheres are becoming increasingly urgent issues in astrobiology. To date, most efforts have concentrated on the study of exoplanetary atmospheres. Instead, we aim to investigate the possibility of characterizing an exoplanet (in terms of habitability, geology, presence of life, etc.) by studying material ejected from the surface during an impact event. For a number of impact scenarios, we estimate the escaping mass and assess its subsequent collisional evolution in a circumstellar orbit, assuming a Sun-like host star. We calculate the fractional luminosity of the dust as a function of time after the impact event and study its detectability with current and future instrumentation. We consider the possibility to constrain the dust composition, giving information on the geology or the presence of a biosphere. As examples, we investigate whether calcite, silica, or ejected microorganisms could be detected. For a 20 km diameter impactor, we find that the dust mass escaping the exoplanet is roughly comparable to the zodiacal dust, depending on the exoplanet's size. The collisional evolution is best modeled by considering two independent dust populations, a spalled population consisting of nonmelted ejecta evolving on timescales of millions of years, and dust recondensed from melt or vapor evolving on much shorter timescales. While the presence of dust can potentially be inferred with current telescopes, studying its composition requires advanced instrumentation not yet available. The direct detection of biological matter turns out to be extremely challenging. Despite considerable difficulties (small dust masses, noise such as exozodiacal dust, etc.), studying dusty material ejected from an exoplanetary surface might become an interesting complement to atmospheric studies in the future. Key Words: Biosignatures-Exoplanets-Impacts-Interplanetary dust-Remote sensing. Astrobiology 17, 721-746.

Effect of Nickel Levels on Hydrogen Partial Pressure and Methane Production in Methanogens

Hydrogen (H₂) consumption and methane (CH₄) production in pure cultures of three different methanogens were investigated during cultivation with 0, 0.2 and 4.21 μM added nickel (Ni). The results showed that the level of dissolved Ni in the anaerobic growth medium did not notably affect CH₄ production in the cytochrome-free methanogenic species Methanobacterium bryantii and Methanoculleus bourgensis MAB1, but affected CH₄ formation rate in the cytochrome-containing Methanosarcina barkeri grown on H₂and CO₂. Methanosarcina barkeri also had the highest amounts of Ni in its cells, indicating that more Ni is needed by cytochrome-containing than by cytochrome-free methanogenic species. The concentration of Ni affected threshold values of H₂ partial pressure (pH₂) for all three methanogen species studied, with M. bourgensis MAB1 reaching pH₂ values as low as 0.1 Pa when Ni was available in amounts used in normal anaerobic growth medium. To our knowledge, this is the lowest pH₂ threshold recorded to date in pure methanogen culture, which suggests that M.bourgensis MAB1 have a competitive advantage over other species through its ability to grow at low H₂ concentrations. Our study has implications for research on the H₂-driven deep subsurface biosphere and biogas reactor performance.

Anaerobic Fungi: A Potential Source of Biological H2 in the Oceanic Crust

The recent recognition of fungi in the oceanic igneous crust challenges the understanding of this environment as being exclusively prokaryotic and forces reconsiderations of the ecology of the deep biosphere. Anoxic provinces in the igneous crust are abundant and increase with age and depth of the crust. The presence of anaerobic fungi in deep-sea sediments and on the seafloor introduces a type of organism with attributes of geobiological significance not previously accounted for. Anaerobic fungi are best known from the rumen of herbivores where they produce molecular hydrogen, which in turn stimulates the growth of methanogens. The symbiotic cooperation between anaerobic fungi and methanogens in the rumen enhance the metabolic rate and growth of both. Methanogens and other hydrogen-consuming anaerobic archaea are known from subseafloor basalt; however, the abiotic production of hydrogen is questioned to be sufficient to support such communities. Alternatively, biologically produced hydrogen could serve as a continuous source. Here, we propose anaerobic fungi as a source of bioavailable hydrogen in the oceanic crust, and a close interplay between anaerobic fungi and hydrogen-driven prokaryotes.

Chemical Composition of Micrometer-Sized Filaments in an Aragonite Host by a Miniature Laser Ablation/Ionization Mass Spectrometer

Detection of extraterrestrial life is an ongoing goal in space exploration, and there is a need for advanced instruments and methods for the detection of signatures of life based on chemical and isotopic composition. Here, we present the first investigation of chemical composition of putative microfossils in natural samples using a miniature laser ablation/ionization time-of-flight mass spectrometer (LMS). The studies were conducted with high lateral (∼15 μm) and vertical (∼20-200 nm) resolution. The primary aim of the study was to investigate the instrument performance on micrometer-sized samples both in terms of isotope abundance and element composition. The following objectives had to be achieved: (1) Consider the detection and calculation of single stable isotope ratios in natural rock samples with techniques compatible with their employment of space instrumentation for biomarker detection in future planetary missions. (2) Achieve a highly accurate chemical compositional map of rock samples with embedded structures at the micrometer scale in which the rock matrix is easily distinguished from the micrometer structures. Our results indicate that chemical mapping of strongly heterogeneous rock samples can be obtained with a high accuracy, whereas the requirements for isotope ratios need to be improved to reach sufficiently large signal-to-noise ratio (SNR).

Formation of H2 and CH4 by weathering of olivine at temperatures between 30 and 70°C

Hydrocarbons such as CH4 are known to be formed through the Fischer-Tropsch or Sabatier type reactions in hydrothermal systems usually at temperatures above 100°C. Weathering of olivine is sometimes suggested to account for abiotic formation of CH4 through its redox lowering and water splitting properties. Knowledge about the CH4 and H2 formation processes at low temperatures is important for the research about the origin and cause of early Earth and Martian CH4 and for CO2 sequestration. We have conducted a series of low temperature, long-term weathering experiments in which we have tested the CH4 and H2 formation potential of forsteritic olivine.The results show low temperature CH4 production that is probably influenced by chromite and magnetite as catalysts. Extensive analyses of a potential CH4 source trapped in the crystal structure of the olivine showed no signs of incorporated CH4. Also, the available sources of organic carbon were not enough to support the total amount of CH4 detected in our experiments. There was also a linear relationship between silica release into solution and the net CH4 accumulation into the incubation bottle headspaces suggesting that CH4 formation under these conditions could be a qualitative indicator of olivine dissolution.It is likely that minerals such as magnetite, chromite and other metal-rich minerals found on the olivine surface catalyze the formation of CH4, because of the low temperature of the system. This may expand the range of environments plausible for abiotic CH4 formation both on Earth and on other terrestrial bodies.

Reduction of nitrogen compounds in oceanic basement and its implications for HCN formation and abiotic organic synthesis

Hydrogen cyanide is an excellent organic reagent and is central to most of the reaction pathways leading to abiotic formation of simple organic compounds containing nitrogen, such as amino acids, purines and pyrimidines. Reduced carbon and nitrogen precursor compounds for the synthesis of HCN may be formed under off-axis hydrothermal conditions in oceanic lithosphere in the presence of native Fe and Ni and are adsorbed on authigenic layer silicates and zeolites. The native metals as well as the molecular hydrogen reducing CO2 to CO/CH4 and NO3-/NO2- to NH3/NH4+ are a result of serpentinization of mafic rocks. Oceanic plates are conveyor belts of reduced carbon and nitrogen compounds from the off-axis hydrothermal environments to the subduction zones, where compaction, dehydration, desiccation and diagenetic reactions affect the organic precursors. CO/CH4 and NH3/NH4+ in fluids distilled out of layer silicates and zeolites in the subducting plate at an early stage of subduction will react upon heating and form HCN, which is then available for further organic reactions to, for instance, carbohydrates, nucleosides or even nucleotides, under alkaline conditions in hydrated mantle rocks of the overriding plate. Convergent margins in the initial phase of subduction must, therefore, be considered the most potent sites for prebiotic reactions on Earth. This means that origin of life processes are, perhaps, only possible on planets where some kind of plate tectonics occur.