Ingredients for microbial life preserved in 3.5 billion-year-old fluid inclusions

Multienergy Codriven Electron Transfer Across the Nano-Bio Interface for Efficient Photobiocatalysis

Integrating biocatalysis with nanophotocatalysis provides a promising pathway to address the knotty environmental and energy problems. However, energy loss during the transfer of extracellular electrons across the nano-bio interface seriously limits the efficiency of whole-cell-based photobiocatalytic systems. Herein, we demonstrate an integrated multienergy codriven reaction platform containing BaTiO3 nanoparticles (BTO) for harvesting mechanical energy from flowing water to elevate the interfacial electric field, BiVO4 quantum dots (BQD) for harvesting light energy to generate photocarriers, and Geobacter sulfurreducens (GS) for accepting photoelectrons to accomplish the biocatalytic reactions. The synergism between the piezoelectric and photoelectric fields significantly promotes the cross-membrane transport of photoelectrons, contributing to enhanced acetate metabolism, electron transfer, and energy synthesis of GS microbes. Such well-designed BQD/BTO-GS hybrids result in the simultaneous degradation of organic contaminants and detoxification of heavy metals in water with approximately 100% treatment efficiency. The rates of tetracycline (TC) oxidation and Cr(VI) reduction are determined to be 32.8 and 9.58 times higher than that of GS biocatalysis, respectively. Our photobiocatalytic platform exhibits an exceptional apparent quantum yield of 15.54% at 400 nm, exceeding those of most reported abiotic-biotic photobiocatalytic systems. Further investigation verifies the extensibility of our multienergy codriven strategy to the other nano-bio hybrids for enhancing the biocatalytic efficiencies (such as methanogenesis, CO2 fixation, and denitrification), thus offering an inspiring platform for energy and environmental applications. This work not only presents crucial insights into the mechanism of the water-energy nexus but also provides a paradigm for the construction of sustainable reaction systems via multienergy harnessing.

Volatile organic compounds (VOCs) in terrestrial extreme environments: implications for life detection beyond Earth

Covering: 1961 to 2024Discovering and identifying unique natural products/biosignatures (signatures that can be used as evidence for past or present life) that are abundant, and complex enough that they indicate robust evidence of life is a multifaceted process. One distinct category of biosignatures being explored is organic compounds. A subdivision of these compounds not yet readily investigated are volatile organic compound (VOCs). When assessing these VOCs as a group (volatilome) a fingerprint of all VOCs within an environment allows the complex patterns in metabolic data to be unravelled. As a technique already successfully applied to many biological and ecological fields, this paper explores how analysis of volatilomes in terrestrial extreme environments could be used to enhance processes (such as metabolomics and metagenomics) already utilised in life detection beyond Earth. By overcoming some of the complexities of collecting VOCs in remote field sites, a variety of lab based analytical equipment and techniques can then be utilised. Researching volatilomics in astrobiology requires time to characterise the patterns of VOCs. They must then be differentiated from abiotic (non-living) signals within extreme environments similar to those found on other planetary bodies (analogue sites) or in lab-based simulated environments or microcosms. Such an effort is critical for understanding data returned from past or upcoming missions, but it requires a step change in approach which explores the volatilome as a vital additional tool to current 'Omics techniques.

Amide groups in 3.7 billion years old liquid inclusions

Carbon with depleted d13C (down to - 25.6‰ VPDB) found in > 3.7 billion year old metamorphic sediments from the Isua Supracrustal Belt, Southwestern Greenland, has been proposed to represent the oldest remains of life on Earth. Graphitic inclusions within garnet porphyroblasts from this locality have been shown to associate with elements consistent with biogenic remains. In this report, we focus on certain liquid inclusions found in the Isua garnets, characterizing their chemical composition using atomic force microscopy, AFM-based infrared spectroscopy, optical photothermal infrared spectroscopy, Raman spectroscopy, and time-of-flight secondary ion mass spectrometry. Our results show that the liquid inclusions contain functional groups consisting of carbon, nitrogen, and oxygen in a configuration similar to amide functional groups. We suspect that the amide groups formed from N, O and C-containing volatile components that were released from the original kerogenous material enclosed in the garnets, as this was graphitized during thermal maturation. This is consistent with the observed inclusion assemblage of solid graphitic and viscous fluid inclusions alike. Our observations are compatible with the inclusions forming from biogenic precursor material, and when considered alongside previous reports on the carbonaceous material in the Isua metamorphic sediments, these and our study collectively indicate that the carbonaceous material in the Isua metasediments represents the oldest traces of life on Earth.

Evidence for nontraditional mcr-containing archaea contributing to biological methanogenesis in geothermal springs

Recent discoveries of methyl-coenzyme M reductase-encoding genes (mcr) in uncultured archaea beyond traditional euryarchaeotal methanogens have reshaped our view of methanogenesis. However, whether any of these nontraditional archaea perform methanogenesis remains elusive. Here, we report field and microcosm experiments based on ¹³C-tracer labeling and genome-resolved metagenomics and metatranscriptomics, revealing that nontraditional archaea are predominant active methane producers in two geothermal springs. Archaeoglobales performed methanogenesis from methanol and may exhibit adaptability in using methylotrophic and hydrogenotrophic pathways based on temperature/substrate availability. A five-year field survey found Candidatus Nezhaarchaeota to be the predominant mcr-containing archaea inhabiting the springs; genomic inference and mcr expression under methanogenic conditions strongly suggested that this lineage mediated hydrogenotrophic methanogenesis in situ. Methanogenesis was temperature-sensitive , with a preference for methylotrophic over hydrogenotrophic pathways when incubation temperatures increased from 65° to 75°C. This study demonstrates an anoxic ecosystem wherein methanogenesis is primarily driven by archaea beyond known methanogens, highlighting diverse nontraditional mcr-containing archaea as previously unrecognized methane sources.

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.

Aliphatic Aldehydes in the Earth's Crust-Remains of Prebiotic Chemistry?

The origin of life is a mystery that has not yet been solved in the natural sciences. Some promising interpretative approaches are related to hydrothermal activities. Hydrothermal environments contain all necessary elements for the development of precursor molecules. There are surfaces with possible catalytic activity, and wide ranges of pressure and temperature conditions. The chemical composition of hydrothermal fluids together with periodically fluctuating physical conditions should open up multiple pathways towards prebiotic molecules. In 2017, we detected potentially prebiotic organic substances, including a homologous series of aldehydes in Archean quartz crystals from Western Australia, more than 3 billion years old. In order to approach the question of whether the transformation of inorganic into organic substances is an ongoing process, we investigated a drill core from the geologically young Wehr caldera in Germany at a depth of 1000 m. Here, we show the existence of a similar homologous series of aldehydes (C₈ to C₁₆) in the fluid inclusions of the drill core calcites, a finding that supports the thesis that hydrothermal environments could possibly be the material source for the origin of life.

Palaeoecological Implications of Lower-Middle Triassic Stromatolites and Microbe-Metazoan Build-Ups in the Germanic Basin: Insights into the Aftermath of the Permian–Triassic Crisis

Following the end-Permian crisis, microbialites were ubiquitous worldwide. For instance, Triassic deposits in the Germanic Basin provide a rich record of stromatolites as well as of microbe-metazoan build-ups with nonspicular demosponges. Despite their palaeoecological significance, however, all of these microbialites have only rarely been studied. This study aims to fill this gap by examining and comparing microbialites from the Upper Buntsandstein (Olenekian, Lower Triassic) and the lower Middle Muschelkalk (Anisian, Middle Triassic) in Germany. By combining analytical petrography (optical microscopy, micro X-ray fluorescence, and Raman spectroscopy) and geochemistry (δ13Ccarb, δ18Ocarb), we show that all the studied microbialites formed in slightly evaporitic environments. Olenekian deposits in the Jena area and Anisian strata at Werbach contain stromatolites. Anisian successions at Hardheim, in contrast, host microbe-metazoan build-ups. Thus, the key difference is the absence or presence of nonspicular demosponges in microbialites. It is plausible that microbes and nonspicular demosponges had a mutualistic relationship, and it is tempting to speculate that the investigated microbial-metazoan build-ups reflect an ancient evolutionary and ecological association. The widespread occurrence of microbialites (e.g., stromatolites/microbe-metazoan build-ups) after the catastrophe may have resulted from suppressed ecological competition and the presence of vacant ecological niches. The distribution of stromatolites and/or microbe-metazoan build-ups might have been controlled by subtle differences in salinity and water depth, the latter influencing hydrodynamic processes and nutrient supply down to the microscale. To obtain a more complete picture of the distribution of such build-ups in the earth’s history, more fossil records need to be (re)investigated. For the time being, environmental and taphonomic studies of modern nonspicular demosponges are urgently required.

Contrasting Modes of Carbonate Precipitation in a Hypersaline Microbial Mat and Their Influence on Biomarker Preservation (Kiritimati, Central Pacific)

Microbial mats represented the earliest complex ecosystems on Earth, since fossil mineralized examples (i.e., microbialites) date back to the Archean Eon. Some microbialites contain putative remains of organic matter (OM), however the processes and pathways that lead to the preservation of OM within microbialite minerals are still poorly understood. Here, a multidisciplinary study is presented (including petrographic, mineralogical and organic geochemical analyses), focusing on a modern calcifying mat from a hypersaline lake in the Kiritimati atoll (Central Pacific). The results show that this mat has a complex history, with two main growth phases under hypersaline conditions, separated by an interruption caused by desiccation and/or freshening of the lake. The mineral precipitates of the mat are predominantly aragonitic and two contrasting precipitation modes are observed: the main growth phases of the mat were characterized by the slow formation of irregular micritic particles with micropeloidal textures and subspherical particles, linked to the degradation of the exopolymer (EPS) matrix of the mat; whereas the interruption period was characterized by the rapid development of a thin but laterally continuous crust composed of superposed fibrous aragonite botryoids that entombed their contemporaneous benthic microbial community. These two precipitation modes triggered different preservation pathways for the OM of the mat as the thin crust shows a particular lipid biomarker signature, different from that of other layers and the relatively rapid precipitation of the crust protecting the underlying lipids from degradation, causing them to show a preservation equivalent to that of a modern active microbial community, despite them being >1100 years old. Equivalent thin mineral crusts occur in other microbialite examples and, thus, this study highlights them as excellent targets for the search of well-preserved biomarker signatures in fossil microbialites. Nevertheless, the results of this work warn for extreme caution when interpreting complex microbialite biomarker signatures, advising combined petrographic, mineralogical and geochemical investigations for the different microbialite layers and mineral microfabrics.

Water is a preservative of microbes

Water is the cellular milieu, drives all biochemistry within Earth's biosphere and facilitates microbe-mediated decay processes. Instead of reviewing these topics, the current article focuses on the activities of water as a preservative-its capacity to maintain the long-term integrity and viability of microbial cells-and identifies the mechanisms by which this occurs. Water provides for, and maintains, cellular structures; buffers against thermodynamic extremes, at various scales; can mitigate events that are traumatic to the cell membrane, such as desiccation-rehydration, freeze-thawing and thermal shock; prevents microbial dehydration that can otherwise exacerbate oxidative damage; mitigates against biocidal factors (in some circumstances reducing ultraviolet radiation and diluting solute stressors or toxic substances); and is effective at electrostatic screening so prevents damage to the cell by the intense electrostatic fields of some ions. In addition, the water retained in desiccated cells (historically referred to as 'bound' water) plays key roles in biomacromolecular structures and their interactions even for fully hydrated cells. Assuming that the components of the cell membrane are chemically stable or at least repairable, and the environment is fairly constant, water molecules can apparently maintain membrane geometries over very long periods provided these configurations represent thermodynamically stable states. The spores and vegetative cells of many microbes survive longer in the presence of vapour-phase water (at moderate-to-high relative humidities) than under more-arid conditions. There are several mechanisms by which large bodies of water, when cooled during subzero weather conditions remain in a liquid state thus preventing potentially dangerous (freeze-thaw) transitions for their microbiome. Microbial life can be preserved in pure water, freshwater systems, seawater, brines, ice/permafrost, sugar-rich aqueous milieux and vapour-phase water according to laboratory-based studies carried out over periods of years to decades and some natural environments that have yielded cells that are apparently thousands, or even (for hypersaline fluid inclusions of mineralized NaCl) hundreds of millions, of years old. The term preservative has often been restricted to those substances used to extend the shelf life of foods (e.g. sodium benzoate, nitrites and sulphites) or those used to conserve dead organisms, such as ethanol or formaldehyde. For living microorganisms however, the ultimate preservative may actually be water. Implications of this role are discussed with reference to the ecology of halophiles, human pathogens and other microbes; food science; biotechnology; biosignatures for life and other aspects of astrobiology; and the large-scale release/reactivation of preserved microbes caused by global climate change.

Microbial processes during deposition and diagenesis of Banded Iron Formations

Banded Iron Formations (BIFs) are marine chemical sediments consisting of alternating iron (Fe)-rich and silica (Si)-rich bands which were deposited throughout much of the Precambrian era. BIFs represent important proxies for the geochemical composition of Precambrian seawater and provide evidence for early microbial life. Iron present in BIFs was likely precipitated in the form of Fe3+ (Fe(III)) minerals, such as ferrihydrite (Fe(OH)3), either through the metabolic activity of anoxygenic photoautotrophic Fe2+ (Fe(II))-oxidizing bacteria (photoferrotrophs), by microaerophilic bacteria, or by the oxidation of dissolved Fe(II) by O2 produced by early cyanobacteria. However, in addition to oxidized Fe-bearing minerals such as hematite (FeIII 2O3), (partially) reduced minerals such as magnetite (FeIIFeIII 2O4) and siderite (FeIICO3) are found in BIFs as well. The presence of reduced Fe in BIFs has been suggested to reflect the reduction of primary Fe(III) minerals by dissimilatory Fe(III)-reducing bacteria, or by metamorphic (high pressure and temperature) reactions occurring in presence of buried organic matter. Here, we present the current understanding of the role of Fe-metabolizing bacteria in the deposition of BIFs, as well as competing hypotheses that favor an abiotic model for BIF deposition. We also discuss the potential abiotic and microbial reduction of Fe(III) in BIFs after deposition. Further, we review the availability of essential nutrients (e.g. P and Ni) and their implications on early Earth biogeochemistry. Overall, the combined results of various ancient seawater analogue experiments aimed at assessing microbial iron cycling pathways, coupled with the analysis of the BIF rock record, point towards a strong biotic influence during BIF genesis.

Phase transitions in natural C-O-H-N-S fluid inclusions - implications for gas mixtures and the behavior of solid H2S at low temperatures

C-O-H-N-S-bearing fluids are known as one of the most challenging geochemical systems due to scarcity of available experimental data. H₂S-rich fluid systems were recognized in a wide array of world-class mineral deposits and hydrocarbon reservoirs. Here we report on a nature of low-temperature (T ≥ -192 °C) phase transitions observed in natural CH₄-H₂S-CO₂-N₂-H₂O fluid inclusions, which are modeled as closed thermodynamic systems and thus serve as natural micro-laboratories representative of the C-O-H-N-S system. For the first time, we document solid-solid H₂S (α ↔ β ↔ γ) transitions, complex clathrates and structural transformations of solid state H₂S in natural inclusion gas mixtures. The new data on Raman spectroscopic features and a complete sequence of phase transition temperatures in the gas mixtures contribute to scientific advancements in fluid geochemistry. Enhanced understanding of the phase equilibria in the C-O-H-N-S system is a prerequisite for conscientious estimation of P-T-V-X properties, necessary to model the geologic evolution of hydrocarbon and mineral systems. Our findings are a driver for the future research expeditions to extraterrestrial H₂S-rich planetary systems owing to their low temperature environments.

Bad Smells and Broken DNA: A Tale of Sulfur-Nucleic Acid Cooperation

Hydrogen sulfide (H2S) is a gasotransmitter that exerts numerous physiologic and pathophysiologic effects. Recently, a role for H2S in DNA repair has been identified, where H2S modulates cell cycle checkpoint responses, the DNA damage response (DDR), and mitochondrial and nuclear genomic stability. In addition, several DNA repair proteins modulate cellular H2S concentrations and cellular sulfur metabolism and, in turn, are regulated by cellular H2S concentrations. Many DDR proteins are now pharmacologically inhibited in targeted cancer therapies. As H2S and the enzymes that synthesize it are increased in many human malignancies, it is likely that H2S synthesis inhibition by these therapies is an underappreciated aspect of these cancer treatments. Moreover, both H2S and DDR protein activities in cancer and cardiovascular diseases are becoming increasingly apparent, implicating a DDR-H2S signaling axis in these pathophysiologic processes. Taken together, H2S and DNA repair likely play a central and presently poorly understood role in both normal cellular function and a wide array of human pathophysiologic processes. Here, we review the role of H2S in DNA repair.