Alternative Pathways of Carbon Dioxide Fixation: Insights into the Early Evolution of Life?

Electron flow dynamics in sulfur-based autotrophic bioreduction of Cr(VI) mediated by inorganic carbon species: Insights for environmental remediation

The deployment of sulfur-based autotrophic bioremediation for in situ groundwater remediation faces hurdles due to electron competition among electron acceptors, impacting contaminant removal efficiency and causing pH instability. Notably, the sulfur-based bioreduction of Cr(VI) [Cr(VI)-SAR] exemplifies gaps in our comprehension of electron competition dynamics with inorganic carbon (IC), and its subsequent influence on pH. Herein, we established a Cr(VI)-SAR system interfaced with diverse IC species, providing definitive insights into electron transfer mechanisms through rigorous multi-biocycle analysis and thermodynamically consistent half-reaction calculations. Through quantification of electron transfer pathways, we derived reaction equations for Cr(VI) reduction in conjunction with various IC species. Furthermore, metagenomics were used to quantify functional enzymes and identify diverse electron transport patterns alongside IC fixation pathways. Notably, the enrichment of genes associated with electron shuttles and conductive pili expands the paradigm of extracellular electron transfer, while the Wood-Ljungdahl pathway streamlines microbial metabolic proliferation with reduced energy expenditure. Quantitative analysis of these functional genes offers a plausible mechanism underlying the observed shifts in electron competition between IC and Cr(VI). This research marks an advancement in the Cr(VI)-SAR foundational theory, with a particular focus on the dynamics of electron competition, contributing to a deeper understanding of this environmentally significant process.

Simulated early Earth geochemistry fuels a hydrogen-dependent primordial metabolism

Molecular hydrogen is the electron donor for the ancient exergonic reductive acetyl-coenzyme A pathway (acetyl-CoA pathway), which is used by hydrogenotrophic methanogenic archaea. How the presence of iron-sulfides influenced the acetyl-CoA pathway under primordial early Earth geochemistry is still poorly understood. Here we show that the iron-sulfides mackinawite (FeS) and greigite (Fe3S4), which formed in chemical garden experiments simulating geochemical conditions of the early Archaean eon (4.0-3.6 billion years ago), produce abiotic H2 in sufficient quantities to support hydrogenotrophic growth of the hyperthermophilic methanogen Methanocaldococcus jannaschii. Abiotic H2 from iron-sulfide formation promoted CO2 fixation and methanogenesis and induced overexpression of genes encoding the acetyl-CoA pathway. We demonstrate that H2 from iron-sulfide precipitation under simulated early Earth hydrothermal geochemistry fuels a H2-dependent primordial metabolism.

Cascade Catalytic Systems for Converting CO2 into C2+ Products

The excessive emission and continuous accumulation of CO2 have precipitated serious social and environmental issues. However, CO2 can also serve as an abundant, inexpensive, and non-toxic renewable C1 carbon source for synthetic reactions. To achieve carbon neutrality and recycling, it is crucial to convert CO2 into value-added products through chemical pathways. Multi-carbon (C2+) products, compared to C1 products, offer a broader range of applications and higher economic returns. Despite this, converting CO2 into C2+ products is difficult due to its stability and the high energy required for C-C coupling. Cascade catalytic reactions offer a solution by coordinating active components, promoting intermediate transfers, and facilitating further transformations. This method lowers energy consumption. Recent advancements in cascade catalytic systems have allowed for significant progress in synthesizing C2+ products from CO2. This review highlights the features and advantages of cascade catalysis strategies, explores the synergistic effects among active sites, and examines the mechanisms within these systems. It also outlines future prospects for CO2 cascade catalytic synthesis, offering a framework for efficient CO2 utilization and the development of next-generation catalytic systems.

Inorganic Carbon Acquisition and Photosynthetic Metabolism in Marine Photoautotrophs: A Summary

The diffusive availability of CO2 for photosynthesis is orders of magnitude lower in water than in air. This, and the low affinity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) for CO2, implies that most marine photoautotrophs (cyanobacteria, microalgae, macroalgae and marine angiosperms or seagrasses) would be severely restricted were they to rely only on dissolved CO2 for their photosynthetic performance. On the other hand, the ~120 times higher concentration of bicarbonate (HCO3-) makes this inorganic carbon (Ci) form more available for utilisation by marine photosynthesisers. The most common way in marine macrophytes to utilise HCO3- is to convert it to CO2 within acidic micro-zones of diffusion boundary layers (DBLs), including the cell walls, as catalysed by an outwardly acting carbonic anhydrase (CA). This would then generate an intra-chloroplastic (or for cyanobacteria intra-carboxysomal) CO2-concentrating mechanism (CCM). Some algae (e.g., the common macroalgae Ulva spp.) and most cyanobacteria and microalgae feature direct HCO3- uptake as the most efficient CCM, while others (e.g., some red algae growing under low-light conditions) may rely on CO2 diffusion only. We will in this contribution summarise our current understanding of photosynthetic carbon assimilation of submerged marine photoautotrophs, and in particular how their 'biophysical' CCMs differ from the 'biochemical' CCMs of terrestrial C4 and Crassulacean Acid Metabolism (CAM) plants (for which there is very limited evidence in cyanobacteria, algae and seagrasses).

Carbon fluxes rewiring in engineered E. coli via reverse tricarboxylic acid cycle pathway under chemolithotrophic condition

BACKGROUND

A transgenic strain of Escherichia coli has been engineered to directly assimilate gaseous CO2 into its biomass through hydrogen-powered anaerobic respiration. This was achieved by expressing key components of the reverse tricarboxylic acid (rTCA) cycle, including genes encoding α-ketoglutarate: ferredoxin oxidoreductase (KOR) and ATP-dependent citrate lyase (ACL) from Chlorobium tepidum. These enzymes were selected for their essential roles in enabling CO2 fixation and integration into central metabolism.

RESULTS

This study found that KOR alone can support cellular maintenance under chemolithotrophic conditions, while additional expression of ACL enhances CO2 assimilation. Using isotopic 13CO2 tracing, it was demonstrated that KOR alone facilitates CO2 assimilation into TCA metabolites. However, co-expression of ACL with KOR redirected carbon fluxes from TCA cycle toward essential metabolic pathways, particularly those involved in protein and nucleotide biosynthesis. Compared to KOR alone, ACL co-expression significantly increased isotopic enrichments in amino acids (e.g., methionine, threonine, glycine) and nucleotides (e.g., deoxythymidine, deoxycytidine). These results suggest that ACL supports the synthesis of nitrogen-containing metabolites when inorganic nitrogen is sufficient, while KOR alone sustains core metabolic functions under chemolithotrophic conditions.

CONCLUSIONS

This study demonstrates a novel strategy to engineer E. coli for CO2 fixation using only one or two heterologous enzymes under chemolithotrophic conditions. These findings reveal the minimal genetic and nutritional requirements for CO2 assimilation and provide insights into metabolic flux partitioning in engineered strains. This research paves the way for sustainable applications in carbon fixation and biotechnological innovation.

Bioenergetic trade-offs can reveal the path to superior microbial CO2 fixation pathways

A comprehensive optimization of known prokaryotic autotrophic carbon dioxide (CO2) fixation pathways is presented that evaluates all their possible variants under different environmental conditions. This was achieved through a computational methodology recently developed that considers the trade-offs between energy efficiency (yield) and growth rate, allowing us to evaluate candidate metabolic modifications in silico for microbial conversions. The results revealed the superior configurations in terms of both yield (efficiency) and rate (driving force). The pathways from anaerobic organisms appear to fix carbon at lower net ATP cost than those found in aerobic organisms, and the reverse TCA cycle pathway shows the lowest overall energy cost and maximum adaptability across a broad range of CO2 and electron donor (H2) concentrations. The reverse tricarboxylic acid cycle and Wood-Ljungdahl pathways appear highly efficient under a broad range of conditions, while the 3-hydroxypropionate 4-hydroxybutyrate cycle and the 3-hydroxypropionate bicycle appear capable of generating large thermodynamic driving forces at only moderate ATP yield losses.IMPORTANCEBiotechnology can lead to cost-effective processes for capturing carbon dioxide using the natural or genetically engineered metabolic capabilities of microorganisms. However, introducing desirable genetic modifications into microbial strains without compromising their fitness (growth yield and rate) during industrial-scale cultivation remains a challenge. The approach and results presented can guide optimal pathway configurations for enhanced prokaryotic carbon fixation through metabolic engineering. By aligning strain modifications with these theoretically revealed near-optimal pathway configurations, we can optimally engineer strains of good fitness under open culture industrial-scale conditions.

Microbial drivers of biogeochemical cycles in deep sediments of the Kathiawar Peninsula Gulfs of India

Deep marine sediments are rich in microbial diversity, which holds metabolic repertoire to modulate biogeochemical cycles on a global scale. We undertook the environmental microbiome inhabiting the Gulf of Kathiawar Peninsula as a model system to understand the potential involvement of the deep marine sediment microbial community and as a cohort in the carbon, nitrogen, and sulfur biogeochemical cycles. These gulfs are characterized by dynamic tidal variations, diverse sediment textures, and nutrient-rich waters, driven by coastal processes and the interaction between natural coastal dynamics and anthropogenic inputs that shape its microbial community diversity. Our findings suggest that carbon fixation was carried out by Gamma-proteobacteria with CBB cycle-related genes or by microbial participants with Wood-Ljungdahl pathway-related genes. Microbial communities involved in nitrogen metabolism were observed to be rich and diverse, and most microbial communities potentially contribute to the nitrogen cycle via processing nitrogen oxides. Bacteria belonging to the KSB1 phylum were also found to fix nitrogen. The sulfur cycle was spread throughout, with Verrucomicrobiota phylum being a major contributor. The varying napAB genes, significantly lower in the Gulf of Kutch compared to the Gulf of Cambay and the Arabian Sea, mediated nitrate reduction. Dynamics between these pathways were mutually exclusive, and organic carbon oxidation was widespread across the microbial community. Finally, the proteobacteria phylum was highly versatile and conceivably contributed to biogeochemical flux with exceptionally high abundance and the ability to form metabolic networks to survive. The work highlights the importance of critical zones and microbial diversity therein, which needs further exploration.

Self-sensitized Cu(ii)-complex catalyzed solar driven CO2 reduction

Developing a self-sensitized catalyst from earth-abundant elements, capable of efficient light harvesting and electron transfer, is crucial for enhancing the efficacy of CO2 transformation, a critical step in environmental cleanup and advancing clean energy prospects. Traditional approaches relying on external photosensitizers, comprising 4d/5d metal complexes, involve intermolecular electron transfer, and attachment of photosensitizing arms to the catalyst necessitates intramolecular electron transfer, underscoring the need for a more integrated solution. We report a new Cu(ii) complex, K[CuNDPA] (1[K(18-crown-6)]), bearing a dipyrrin amide-based trianionic tetradentate ligand, NDPA (H3L), which is capable of harnessing light energy, despite having a paramagnetic Cu(ii) centre, without any external photosensitizer and photocatalytically reducing CO2 to CO in acetonitrile : water (19 : 1 v/v) with a TON as high as 1132, a TOF of 566 h-1 and a selectivity of 99%. This complex also shows hemilability in the presence of water, which not only plays a role in the proton relay mechanism but also helps stabilize a crucial Cu(i)-NDPA intermediate. The hemilability was justified by the formation of N3O (2) and N2O2 (3) coordinated congeners of the N4 bound complex 1. The overall mechanism was further investigated via spectroscopic techniques such as EPR, UV-vis, and spectroelectrochemistry, culminating in the justification of a single electron-reduced Cu(i)NDPA species as a proposed intermediate. In the next step, the binding of CO2 to the Cu(i) complex and subsequent electron transfer to form Cu(ii)-COO·- was indirectly probed by a radical trapping experiment via the addition of p-methoxy-2,6-di-tert-butylphenol that led to the formation of a phenoxyl radical. This work provides new strategies for designing earth-abundant robust molecular catalysts that can function as photocatalysts without the aid of any external photosensitizers.

Metabolic redundancy and specialisation of novel sulfide-oxidizing Sulfurimonas and Sulfurovum along the brine-seawater interface of the Kebrit Deep

BACKGROUND

Members of the Campylobacterota phylum are dominant key players in sulfidic environments, where they make up a stable portion of sulfide-oxidizing bacterial communities. Despite the significance of these bacteria in primary production being well recognised in several ecosystems, their genomic and metabolic traits in sulfidic deep hypersaline anoxic basins (DHABs) remain largely unexplored. This knowledge gap not only hampers our understanding of their adaptation and functional role in DHABs but also their ecological interactions with other microorganisms in these unique ecosystems.

RESULTS

Metabolic reconstructions from metagenome-assembled genomes (MAGs) of sulfide-oxidizing Campylobacterota were conducted at 10 cm spatial resolution within the halocline of the brine-seawater interface (BSI, salinity 91-155 PSU) of the 1466 m deep sulfidic Kebrit Deep in the Red Sea. Fifty-four Campylobacterota MAGs were assembled and dereplicated into three distinct groups, with the highest-quality genome retained as representative. These genomes represent novel sulfide-oxidizing species within the Sulfurimonas and Sulfurovum genera, which differ from those found in mildly saline deep-sea sulfidic pools. They are stratified along the BSI and utilise the reductive tricarboxylic acid cycle to fix carbon dioxide, acting as primary producers. Their energy generation processes include aerobic or anaerobic-nitrate-dependent sulfide oxidation, as well as hydrogen oxidation. In addition to the osmoprotectant pathways commonly observed in Campylobacterota, such as the synthesis and uptake of proline and glutamate, the two Kebrit Deep Sulfurovum species exhibit genomic signatures for ectoine synthesis, further aiding their adaptation to high salinity. This combination of metabolic redundancy and specialisation within the confined spatial boundaries (~1 m) of the BSI is pivotal in governing microbial interactions, including those with sulfate-reducers, heterotrophs, and other primary producers.

CONCLUSIONS

These results show how the selective pressures mediated by the sulfidic and hypersaline conditions of Kebrit Deep have resulted in novel, adapted and metabolically redundant Sulfurimonas and Sulfurovum species that contribute to the energy coupling, nutrient turnover and metabolic continuity along the physico-chemical gradient of the BSI.

Differential diversity and structure of autotrophs in agricultural soils of Qinghai Province

The biodiversity of CO2-assimilating bacterial communities is pivotal for carbon sequestration in agricultural systems. Changes in the diversity, structure, and activity of the soil chemolithoautotrophic bacteria were examined in four agricultural areas, Dulan (DL), Gonghe (GH), Huzhu (HZ), and Datong (DT) counties in Qinghai Province, where wheat, oilseed rape, and barley were planted. This process was performed using Illumina amplicon sequencing of the ribulose-1,5-bisphosphatecarboxylase/oxygenase (RubisCO) gene (cbbL Form I) and activity data. The diversity, community, and activity of soil autotrophic CO2-fixing bacteria differed significantly across soil sites, whereas cbbL-bearing bacterial diversity and activity were similar across different crop types. RubisCO activity in the HZ region was significantly greater than in the other three regions (P < 0.001). The overall relative abundance trend of the bacterial taxa was similar among the three crop samples. Moreover, 31, 27, 10, and 8 significant linear discriminant analysis effect sizes were identified in the four regions collected from HZ, DL, DT, and GH, respectively. No significant biomarkers were detected in any of the crop groups. Some soil properties had significant relationships with the autotrophic bacterial community composition.

IMPORTANCE

Agricultural soil plays important roles in carbon fixation during carbon capture and storage. Autotrophic bacteria that utilize inorganic compounds as electron donors for growth fix CO2 photosynthetically or chemo-autotrophically in diverse ecosystems and affect soil organic carbon sequestration. Soil properties, agronomic management measures, and environmental factors can influence the community composition, abundance, and activity of CO2-assimilating bacteria. This study aims at evaluating the effects of different regions and crop types on the abundance, composition, and activity of CO2-fixing bacteria in agricultural soil.

Evidence for corrin biosynthesis in the last universal common ancestor

Corrinoids are cobalt-containing tetrapyrroles. They include adenosylcobalamin (vitamin B12) and cobamides that function as cofactors and coenzymes for methyl transfer, radical-dependent and redox reactions. Though cobamides are the most complex cofactors in nature, they are essential in the acetyl-CoA pathway, thought to be the most ancient CO2-fixation pathway, where they perform a pterin-to-cobalt-to-nickel methyl transfer reaction catalyzed by the corrinoid iron-sulphur protein (CoFeS). CoFeS occurs in H2-dependent archaeal methanogens, the oldest microbial lineage by measure of physiology and carbon isotope data, dating corrinoids to ca. 3.5 billion years. However, CoFeS and cobamides are also essential in the acetyl-CoA pathway of H2-dependent bacterial acetogens. To determine whether corrin biosynthesis was established before archaea and bacteria diverged, whether the pathways arose independently or whether cobamide biosynthesis was transferred from the archaeal to the bacterial lineage (or vice versa) during evolution, we investigated phylogenies and structural data for 26 enzymes of corrin ring and lower ligand biosynthesis. The data trace cobamide synthesis to the common ancestor of bacteria and archaea, placing it in the last universal common ancestor of all lifeforms (LUCA), while pterin-dependent methyl synthesis pathways likely arose independently post-LUCA in the lineages leading to bacteria and archaea. Enzymes of corrin biosynthesis were recruited from preexisting ancient pathways. Evolutionary forerunners of CoFeS function were likely Fe-, Ni- and Co-containing solid-state surfaces, which, in the laboratory, catalyze the reactions of the acetyl-CoA pathway from CO2 to pyruvate under serpentinizing hydrothermal conditions. The data suggest that enzymatic corrin biosynthesis replaced insoluble solid-state catalysts that tethered primordial CO2 assimilation to the Earth's crust, suggesting a role for corrin synthesis in the origin of free-living cells.

Catching carbon fixation without fixing

Structural snapshots of an enzyme complex reveal missing pieces of a biological process.

Assessing environmental gradients in relation to dark CO2 fixation in estuarine wetland microbiomes

The rising atmospheric concentration of CO2 is a major concern to society due to its global warming potential. In soils, CO2-fixing microorganisms are preventing some of the CO2 from entering the atmosphere. Yet, the controls of dark CO2 fixation are rarely studied in situ. Here, we examined the gene and transcript abundance of key genes involved in microbial CO2 fixation along major environmental gradients within estuarine wetlands. A combined multi-omics approach incorporating metabarcoding, deep metagenomic, and metatranscriptomic analyses confirmed that wetland microbiota harbor four out of seven known CO2 fixation pathways, namely, the Calvin cycle, reverse tricarboxylic acid cycle, Wood-Ljungdahl pathway, and reverse glycine pathway. These pathways are transcribed at high frequencies along several environmental gradients, albeit at different levels depending on the environmental niche. Notably, the transcription of the key genes for the reverse tricarboxylic acid cycle was associated with high nitrate concentration, while the transcription of key genes for the Wood-Ljungdahl pathway was favored by reducing, O2-poor conditions. The transcript abundance of the Calvin cycle was favored by niches high in organic matter. Taxonomic assignment of transcripts implied that dark CO2 fixation was mainly linked to a few bacterial phyla, namely, Desulfobacterota, Methylomirabilota, Nitrospirota, Chloroflexota, and Pseudomonadota.

IMPORTANCE

The increasing concentration of atmospheric CO2 has been identified as the primary driver of climate change and poses a major threat to human society. This work explores the mostly overlooked potential of light-independent CO2 fixation by soil microbes (a.k.a. dark CO2 fixation) in climate change mitigation efforts. Applying a combination of molecular microbial tools, our research provides new insights into the ecological niches where CO2-fixing pathways are most active. By identifying how environmental factors, like oxygen, salinity and organic matter availability, influence these pathways in an estuarine wetland environment, potential strategies for enhancing natural carbon sinks can be developed. The importance of our research is in advancing the understanding of microbial CO2 fixation and its potential role in the global climate system.

Gut microbiota and quantitative traits divergence at different altitude of long-tailed dwarf hamsters, Cricetulus longicaudatus

To investigate the community structure and diversity of gut microflora and their function in body mass regulation, as well as the effects of various locations on gut microbiota and Cricetulus longicaudatus body mass regulation at various elevations. We examined the diversity, abundance, and community structure of the gut microbiota of long-tailed dwarf hamsters from eight regions in Shanxi province during summer using 16S rDNA sequencing technology and analyzed the relationships between these microbiota and environmental variables as well as morphological indicators. The results revealed Firmicutes and Bacteroidetes as the dominant phyla at the phylum level, with Lactobacillus emerging as the predominant genus. We observed differences of gut microflora between different areas, and this diversity is affected by altitude. The high-altitude areas individuals had lower β diversity of gut microbiota than the low-altitude area. Moreover, the body and skull indexes of long-tailed dwarf hamsters also changed with altitude. The result presented in this study indicated that the body size of long-tailed dwarf hamsters conforms to Bergmann's law. And Providencia had significant correlation with body size. Finally, functional analysis of the gut microbiota showed changes in metabolic function that depended on elevation, and collinear network analysis showed how the gut microbiota interacts with each other. All of these results suggest that long-tailed hamsters are different depending on their altitude, with altitude being the main factor affecting both the structure of microbes and the way their metabolism works. This study shows that altitude has a big effect on the gut microbiota and phenotypic traits of long-tailed hamsters. It also shows how well this species can adapt to changes in altitude.

Core cooperative metabolism in low-complexity CO2-fixing anaerobic microbiota

Biological conversion of carbon dioxide into methane has a crucial role in global carbon cycling and is operated by a specialised set of anaerobic archaea. Although it is known that this conversion is strictly linked with cooperative bacterial activity, such as through syntrophic acetate oxidation, there is also a limited understanding on how this cooperation is regulated and metabolically realised. In this work, we investigate the activity in a microbial community evolved to efficiently convert carbon dioxide into methane and predominantly populated by Methanothermobacter wolfeii. Through multi-omics, biochemical analysis and constraint-based modelling, we identify a potential formate cross-feeding from an uncharacterised Limnochordia species to M. wolfeii, driven by the recently discovered reductive glycine pathway and upregulated when hydrogen and carbon dioxide are limited. The quantitative consistency of this metabolic exchange with experimental data is shown by metagenome-scale metabolic models integrating condition-specific metatranscriptomics, which also indicate a broader three-way interaction involving M. wolfeii, the Limnochordia species, and Sphaerobacter thermophilus. Under limited hydrogen and carbon dioxide, aspartate released by M. wolfeii is fermented by Sphaerobacter thermophilus into acetate, which in turn is convertible into formate by Limnochordia, possibly forming a cooperative loop sustaining hydrogenotrophic methanogenesis. These findings expand our knowledge on the modes of carbon dioxide reduction into methane within natural microbial communities and provide an example of cooperative plasticity surrounding this process.

GTP before ATP: The energy currency at the origin of genes

Life is an exergonic chemical reaction. Many individual reactions in metabolism entail slightly endergonic steps that are coupled to free energy release, typically as ATP hydrolysis, in order to go forward. ATP is almost always supplied by the rotor-stator ATP synthase, which harnesses chemiosmotic ion gradients. Because the ATP synthase is a protein, it arose after the ribosome did. What was the energy currency of metabolism before the origin of the ATP synthase and how (and why) did ATP come to be the universal energy currency? About 27 % of a cell's energy budget is consumed as GTP during translation. The universality of GTP-dependence in ribosome function indicates that GTP was the ancestral energy currency of protein synthesis. The use of GTP in translation and ATP in small molecule synthesis are conserved across all lineages, representing energetic compartments that arose in the last universal common ancestor, LUCA. And what came before GTP? Recent findings indicate that the energy supporting the origin of LUCA's metabolism stemmed from H2-dependent CO2 reduction along routes that strongly resemble the reactions and transition metal catalysts of the acetyl-CoA pathway.

Desulfosporosinus paludis sp. nov., an acidotolerant sulphate-reducing bacterium isolated from moderately acidic fen soil

An obligately anaerobic, spore-forming sulphate-reducing bacterium, strain SB140T, was isolated from a long-term continuous enrichment culture that was inoculated with peat soil from an acidic fen. Cells were immotile, slightly curved rods that stained Gram-negative. The optimum temperature for growth was 28 °C. Strain SB140T grew at pH 4.0-7.5 with an optimum pH of 6.0-7.0 using various electron donors and electron acceptors. Yeast extract, sugars, alcohols and organic acids were used as electron donors for sulphate reduction. SB140T additionally used elemental sulphur and nitrate as electron acceptors but not sulphite, thiosulphate or iron(III) provided as ferrihydrite and fumarate. The 16S rRNA gene sequence placed strain SB140T in the genus Desulfosporosinus of the phylum Bacillota. The predominant cellular fatty acids were iso-C15 : 0 (52.6%) and 5,7 C15 : 2 (19.9%). The draft genome of SB140T (5.42 Mbp in size) shared 77.4% average nucleotide identity with the closest cultured relatives Desulfosporosinus acididurans M1T and Desulfosporosinus acidiphilus SJ4T. On the basis of phenotypic, phylogenetic and genomic characteristics, SB140T was identified as a novel species within the genus Desulfosporosinus, for which we propose the name Desulfosporosinus paludis sp. nov. The type strain is SB140T (=DSM 117342T=JCM 39521T).

Conversion of pyridoxal to pyridoxamine with NH3 and H2 on nickel generates a protometabolic nitrogen shuttle under serpentinizing conditions

Serpentinizing hydrothermal vents are likely sites for the origin of metabolism because they produce H2 as a source of electrons for CO2 reduction while depositing zero-valent iron, cobalt, and nickel as catalysts for organic reactions. Recent work has shown that solid-state nickel can catalyze the H2-dependent reduction of CO2 to various organic acids and their reductive amination with H2 and NH3 to biological amino acids under the conditions of H2-producing hydrothermal vents and that amino acid synthesis from NH3, H2, and 2-oxoacids is facile in the presence of Ni0. Such reactions suggest a metallic origin of metabolism during early biochemical evolution because single metals replace the function of over 130 enzymatic reactions at the core of metabolism in microbes that use the acetyl-CoA pathway of CO2 fixation. Yet solid-state catalysts tether primordial amino synthesis to a mineral surface. Many studies have shown that pyridoxal catalyzes transamination reactions without enzymes. Here we show that pyridoxamine, the NH2-transferring intermediate in pyridoxal-dependent transamination reactions, is generated from pyridoxal by reaction with NH3 (as little as 5 mm) and H2 (5 bar) on Ni0 as catalyst at pH 11 and 80 °C within hours. These conditions correspond to those in hydrothermal vents undergoing active serpentinization. The results indicate that at the origin of metabolism, pyridoxamine provided a soluble, organic amino donor for aqueous amino acid synthesis, mediating an evolutionary transition from NH3-dependent amino acid synthesis on inorganic surfaces to pyridoxamine-dependent organic reactions in the aqueous phase.

All-in-One CO2 Capture and Transformation: Lessons from Formylmethanofuran Dehydrogenases

Carbon-one-unit (C1) feedstocks are generally used in the chemical synthesis of organic molecules, such as solvents, drugs, polymers, and fuels. Contrary to the dangerous and polluting carbon monoxide mostly coming from fossil fuels, formate and formamide are attractive alternative feedstocks for chemical synthesis. As these are currently mainly obtained from the oil industry, novel synthetic routes have been developed based on the transformation of the greenhouse gas CO2. Such developments are motivated by the urgent need for carbon chemical recycling, leading to a sustainable future. The inert nature of CO2 represents a challenge for chemists to activate and specifically convert the molecule through an affordable and efficient process. The chemical transformation could be inspired by biological CO2 activation, in which highly specialized enzymes perform atmospheric CO2 fixation through relatively abundant metal catalysts. In this Account, we describe and discuss the potential of one of the most efficient biological CO2-converting systems: the formylmethanofuran dehydrogenase (abbreviated as FMD).FMDs are multienzymatic complexes found in archaea that capture CO2 as a formyl group branched on the amine moiety of the methanofuran (MFR) cofactor. This overall reaction leading to formyl-MFR production does not require ATP hydrolysis as compared to the CO2-fixing microbes relying on the reductive Wood-Ljungdahl pathway, highlighting a different operative mode that saves cellular energy. FMD reaction represents the entry point in hydrogenotrophic methanogenesis (H2 and CO2 dependent or formate dependent) and operates in reverse in other methanogenic pathways and microbial metabolisms. Therefore, FMD is a key enzyme in the planetary carbon cycle. After decades of investigations, recent studies have provided a description of the FMD structure, reaction mechanism, and potential for the electroreduction of CO2, to which our laboratory has been actively contributing. FMD is an "all-in-one" enzyme catalyzing a redox-active transformation coupled to a redox-neutral transformation at two very different metal cofactors where new C-H and C-N bonds are made. First, the principle of the overall reaction consisting of an exergonic CO2 reduction coupled with an endergonic formate condensation on MFR is resumed. Then, this Account exposes the molecular details of the active sites and provides an overview of each catalytic mechanism. It also describes the natural versatility of electron-delivery modules fueling CO2 reduction and extends it to the possibilities of using artificial systems such as electrodes. A perspective concludes on how the mechanistic of FMD could be applied to produce CO2-based chemical intermediates to synthesize organic molecules. Indeed, through its biochemical properties, the enzyme opens opportunities for CO2 electroreduction to generate molecules such as formate and formamide derivatives, which are all intermediates for synthesizing organic compounds. Transferring the chemical knowledge acquired from these biological systems would provide coherent models that can lead to further development in the field of synthetic biology and bio-inspired synthetic chemistry to perform large-scale CO2 conversion into building blocks for chemical synthesis.

Repurposing First-Row Transition Metal Carbon Dioxide Reduction Electrocatalysts for Electrochemical Carboxylation of Benzyl Chloride

Carbon dioxide (CO2) is an abundant and useful C1 feedstock for electrocarboxylation, a process that incorporates a carboxyl moiety into an organic molecule. In this work, three first-row transition metal CO2 reduction electrocatalysts, NiPDIiPr (1), NiTPA (2), and Fe(salenCl4) (3), were explored as electrocarboxylation catalysts with benzyl chloride as a substrate. The cyclic voltammograms of all three catalysts showed current enhancements in the presence of benzyl chloride under a CO2 atmosphere. Introduction of DMAP as additives showed further current enhancement. Electrolyses with one-compartment cell generated a moderate yield of phenylacetic acid. Addition of MgBr2 was proven to be crucial to the formation of the carboxylate product. While the yield of carboxylation was moderate, this work showed an example of electrocarboxylation of benzyl chloride without using a metal electrode or sacrificial anode, which could lead to a more sustainable carboxylation methodology.

Synthetic biology of metabolic cycles for Enhanced CO2 capture and Sequestration

In most organisms, the tri-carboxylic acid cycle (TCA cycle) is an essential metabolic system that is involved in both energy generation and carbon metabolism. Its uni-directionality, however, restricts its use in synthetic biology and carbon fixation. Here, it is describing the use of the modified TCA cycle, called the Tri-carboxylic acid Hooked to Ethylene by Enzyme Reactions and Amino acid Synthesis, the reductive tricarboxylic acid branch/4-hydroxybutyryl-CoA/ethylmalonyl-CoA/acetyl-CoA (THETA) cycle, in Escherichia coli for the purposes of carbon fixation and amino acid synthesis. Three modules make up the THETA cycle: (1) pyruvate to succinate transformation, (2) succinate to crotonyl-CoA change, and (3) crotonyl-CoA to acetyl-CoA and pyruvate change. It is presenting each module's viability in vivo and showing how it integrates into the E. coli metabolic network to support growth on minimal medium without the need for outside supplementation. Enzyme optimization, route redesign, and heterologous expression were used to get over metabolic roadblocks and produce functional modules. Furthermore, the THETA cycle may be improved by including components of the Carbon-Efficient Tri-Carboxylic Acid Cycle (CETCH cycle) to improve carbon fixation. THETA cycle's promise as a platform for applications in synthetic biology and carbon fixation.

Functional redundancy buffers the effect of poly-extreme environmental conditions on southern African dryland soil microbial communities

Drylands' poly-extreme conditions limit edaphic microbial diversity and functionality. Furthermore, climate change exacerbates soil desiccation and salinity in most drylands. To better understand the potential effects of these changes on dryland microbial communities, we evaluated their taxonomic and functional diversities in two Southern African dryland soils with contrasting aridity and salinity. Fungal community structure was significantly influenced by aridity and salinity, while Bacteria and Archaea only by salinity. Deterministic homogeneous selection was significantly more important for bacterial and archaeal communities' assembly in hyperarid and saline soils when compared to those from arid soils. This suggests that niche partitioning drives bacterial and archaeal communities' assembly under the most extreme conditions. Conversely, stochastic dispersal limitations drove the assembly of fungal communities. Hyperarid and saline soil communities exhibited similar potential functional capacities, demonstrating a disconnect between microbial structure and function. Structure variations could be functionally compensated by different taxa with similar functions, as implied by the high levels of functional redundancy. Consequently, while environmental selective pressures shape the dryland microbial community assembly and structures, they do not influence their potential functionality. This suggests that they are functionally stable and that they could be functional even under harsher conditions, such as those expected with climate change.

An integrated transcriptome and physiological analysis of nitrogen use efficiency in rice (Oryza sativa L. ssp. indica) under drought stress

Nitrogen is a critical nutrient vital for crop growth. However, our current understanding of nitrogen use efficiency (NUE) under drought remains inadequate. To delve into the molecular mechanisms underlying NUE under drought, a transcriptome and physiological co-expression analysis was performed in rice, which is particularly sensitive to drought. We conducted a pot experiment using rice grown under normal irrigation, mild drought stress, and severe drought stress. Compared to the normal treatment, drought stress led to a significant reduction in NUE across growth stages, with decreases ranging from 2.18% to 31.67%. Totals of 4,424 and 2,452 genes were identified as NUE-related DEGs that showed differential expressions (DEGs) and significantly correlated with NUE (NUE-related) under drought in the vegetative and reproductive stages, respectively. Interestingly, five genes involved in nitrogen metabolism were found in the overlapped genes of these two sets. Furthermore, the two sets of NUE-related DEGs were enriched in glyoxylate and dicarboxylate metabolism, as well as carbon fixation in photosynthetic organisms. Several genes in these two pathways were identified as hub genes in the two sets of NUE-related DEGs. This study offers new insights into the molecular mechanism of rice NUE under drought in agricultural practices and provides potential genes for breeding drought-resistant crops with high NUE.

Microbiome associated to an H2-emitting zone in the São Francisco basin Brazil

BACKGROUND

Dihydrogen (H₂) natural gas is a clean and renewable energy source of significant interest in the transition to sustainable energy. Unlike conventional petroleum-based fuels, H₂ releases only water vapor upon combustion, making it a promising alternative for reducing carbon footprints in the future. However, the microbial impact on H₂ dynamics in H2-emitting zones remains unclear, as does the origin of H2 - whether it is produced at greater depths or within shallow soil layers. In the São Francisco Basin, soil hydrogen concentrations of approximately 200 ppm were identified in barren ground depressions. In this study, we investigated the microbiome associated with this area using the 16S rRNA gene sequencing, with a focus on metabolic processes related to H₂ consumption and production. Soil samples were collected from two monitored (< 1 m) depths - 10 cm and 1 m - in the emission zone, which is predominantly covered with pasture vegetation, and from an adjacent area with medium and small trees.

RESULTS

Our findings suggest that the H2-emitting zone significantly influences the composition and function of the microbiome, with Bacillus emerging as the dominant genus. In contrast to typical Cerrado soil, we observed a higher prevalence of Actinobacteriota (∼ 40%) and Firmicutes (∼ 20%). Additionally, we identified an abundance of sporulating bacteria and taxonomic groups previously described as H2-oxidizing bacteria.

CONCLUSIONS

The H2-emitting zone in the São Francisco Basin presents a unique opportunity to deepen our understanding of the impact of H₂ on microbial communities. This study is the first to characterize a natural H2-associated bacterial community in Cerrado soil using a culture-independent approach.

Aquificae overcomes competition by archaeal thermophiles, and crowding by bacterial mesophiles, to dominate the boiling vent-water of a Trans-Himalayan sulfur-borax spring

Trans-Himalayan hot spring waters rich in boron, chlorine, sodium and sulfur (but poor in calcium and silicon) are known based on PCR-amplified 16S rRNA gene sequence data to harbor high diversities of infiltrating bacterial mesophiles. Yet, little is known about the community structure and functions, primary productivity, mutual interactions, and thermal adaptations of the microorganisms present in the steaming waters discharged by these geochemically peculiar spring systems. We revealed these aspects of a bacteria-dominated microbiome (microbial cell density ~8.5 × 104 mL-1; live:dead cell ratio 1.7) thriving in the boiling (85°C) fluid vented by a sulfur-borax spring called Lotus Pond, situated at 4436 m above the mean sea-level, in the Puga valley of eastern Ladakh, on the Changthang plateau. Assembly, annotation, and population-binning of >15-GB metagenomic sequence illuminated the numeral predominance of Aquificae. While members of this phylum accounted for 80% of all 16S rRNA-encoding reads within the metagenomic dataset, 14% of such reads were attributed to Proteobacteria. Post assembly, only 25% of all protein-coding genes identified were attributable to Aquificae, whereas 41% was ascribed to Proteobacteria. Annotation of metagenomic reads encoding 16S rRNAs, and/or PCR-amplified 16S rRNA genes, identified 163 bacterial genera, out of which 66 had been detected in past investigations of Lotus Pond's vent-water via 16S amplicon sequencing. Among these 66, Fervidobacterium, Halomonas, Hydrogenobacter, Paracoccus, Sulfurihydrogenibium, Tepidimonas, Thermus and Thiofaba (or their close phylogenomic relatives) were presently detected as metagenome-assembled genomes (MAGs). Remarkably, the Hydrogenobacter related MAG alone accounted for ~56% of the entire metagenome, even though only 15 out of the 66 genera consistently present in Lotus Pond's vent-water have strains growing in the laboratory at >45°C, reflecting the continued existence of the mesophiles in the ecosystem. Furthermore, the metagenome was replete with genes crucial for thermal adaptation in the context of Lotus Pond's geochemistry and topography. In terms of sequence similarity, a majority of those genes were attributable to phylogenetic relatives of mesophilic bacteria, while functionally they rendered functions such as encoding heat shock proteins, molecular chaperones, and chaperonin complexes; proteins controlling/modulating/inhibiting DNA gyrase; universal stress proteins; methionine sulfoxide reductases; fatty acid desaturases; different toxin-antitoxin systems; enzymes protecting against oxidative damage; proteins conferring flagellar structure/function, chemotaxis, cell adhesion/aggregation, biofilm formation, and quorum sensing. The Lotus Pond Aquificae not only dominated the microbiome numerically but also acted potentially as the main primary producers of the ecosystem, with chemolithotrophic sulfur oxidation (Sox) being the fundamental bioenergetic mechanism, and reductive tricarboxylic acid (rTCA) cycle the predominant carbon fixation pathway. The Lotus Pond metagenome contained several genes directly or indirectly related to virulence functions, biosynthesis of secondary metabolites including antibiotics, antibiotic resistance, and multi-drug efflux pumping. A large proportion of these genes being attributable to Aquificae, and Proteobacteria (very few were ascribed to Archaea), it could be worth exploring in the future whether antibiosis helped the Aquificae overcome niche overlap with other thermophiles (especially those belonging to Archaea), besides exacerbating the bioenergetic costs of thermal endurance for the mesophilic intruders of the ecosystem.

Methanothermobacter thermautotrophicus and Alternative Methanogens: Archaea-Based Production

Methanogenic archaea convert bacterial fermentation intermediates from the decomposition of organic material into methane. This process has relevance in the global carbon cycle and finds application in anthropogenic processes, such as wastewater treatment and anaerobic digestion. Furthermore, methanogenic archaea that utilize hydrogen and carbon dioxide as substrates are being employed as biocatalysts for the biomethanation step of power-to-gas technology. This technology converts hydrogen from water electrolysis and carbon dioxide into renewable natural gas (i.e., methane). The application of methanogenic archaea in bioproduction beyond methane has been demonstrated in only a few instances and is limited to mesophilic species for which genetic engineering tools are available. In this chapter, we discuss recent developments for those existing genetically tractable systems and the inclusion of novel genetic tools for thermophilic methanogenic species. We then give an overview of recombinant bioproduction with mesophilic methanogenic archaea and thermophilic non-methanogenic microbes. This is the basis for discussing putative products with thermophilic methanogenic archaea, specifically the species Methanothermobacter thermautotrophicus. We give estimates of potential conversion efficiencies for those putative products based on a genome-scale metabolic model for M. thermautotrophicus.

Volatile Organic Compound Metabolism on Early Earth

Biogenic volatile organic compounds (VOCs) constitute a significant portion of gas-phase metabolites in modern ecosystems and have unique roles in moderating atmospheric oxidative capacity, solar radiation balance, and aerosol formation. It has been theorized that VOCs may account for observed geological and evolutionary phenomena during the Archaean, but the direct contribution of biology to early non-methane VOC cycling remains unexplored. Here, we provide an assessment of all potential VOCs metabolized by the last universal common ancestor (LUCA). We identify enzyme functions linked to LUCA orthologous protein groups across eight literature sources and estimate the volatility of all associated substrates to identify ancient volatile metabolites. We hone in on volatile metabolites with confirmed modern emissions that exist in conserved metabolic pathways and produce a curated list of the most likely LUCA VOCs. We introduce volatile organic metabolites associated with early life and discuss their potential influence on early carbon cycling and atmospheric chemistry.

Navigating the archaeal frontier: insights and projections from bioinformatic pipelines

Archaea continues to be one of the least investigated domains of life, and in recent years, the advent of metagenomics has led to the discovery of many new lineages at the phylum level. For the majority, only automatic genomic annotations can provide information regarding their metabolic potential and role in the environment. Here, genomic data from 2,978 archaeal genomes was used to perform automatic annotations using bioinformatics tools, alongside synteny analysis. These automatic classifications were done to assess how good these different tools perform in relation to archaeal data. Our study revealed that even with lowered cutoffs, several functional models do not capture the recently discovered archaeal diversity. Moreover, our investigation revealed that a significant portion of archaeal genomes, approximately 42%, remain uncharacterized. In comparison, within 3,235 bacterial genomes, a diverse range of unclassified proteins is obtained, with well-studied organisms like Escherichia coli having a substantially lower proportion of uncharacterized regions, ranging from <5 to 25%, and less studied lineages being comparable to archaea with the range of 35-40% of unclassified regions. Leveraging this analysis, we were able to identify metabolic protein markers, thereby providing insights into the metabolism of the archaea in our dataset. Our findings underscore a substantial gap between automatic classification tools and the comprehensive mapping of archaeal metabolism. Despite advances in computational approaches, a significant portion of archaeal genomes remains unexplored, highlighting the need for extensive experimental validation in this domain, as well as more refined annotation methods. This study contributes to a better understanding of archaeal metabolism and underscores the importance of further research in elucidating the functional potential of archaeal genomes.

No signs of microbial-influenced corrosion of cast iron and copper in bentonite microcosms after 400 days

High-level radioactive waste needs to be safely stored for a long time in a deep geological repository by using a multi-barrier system. In this system, suitable barrier materials are selected that ideally show long-term stability to prevent early radionuclide release into the biosphere. In this study, different container matals (copper and cast iron) and pore water compositions (Opalinus Clay pore water and saline cap rock solution) were combined with Bavarian bentonite in static batch experiments to investigate microbial-influenced corrosion. The increasing concentration of iron and copper in the solution as well as detected corrosion products on the metal surface are indicative of anaerobic corrosion of the respective metals during an incubation of 400 days at 37 °C. However, although the intrinsic microbial bentonite community was stimulated with either lactate or H2, an acceleration of cast iron- and copper corrosion did not occur. Furthermore, neither corrosive bacteria nor conventional bacterial corrosion products, such as metal sulfides, were detected in any of the analyzed samples. The analyses of geochemical parameters (e.g. ferrous iron-, iron-, copper- and potassium concentrations as well as redox potentials) showed significant changes in some cast iron- and copper-containing setups, but these changes did not correlate with the microbial community structure in the respective microcosms, as confirmed by statistical analyses. Hence, the analyzed Bavarian bentonite (type B25) showed no significant contribution to cast iron and copper corrosion under the applied conditions after 400 days of incubation. From this perspective, bentonite B25 could be a suitable candidate as a geotechnical barrier in future repositories.

Rethinking life and predicting its origin

The definition, origin and recreation of life remain elusive. As others have suggested, only once we put life into reductionist physical terms will we be able to solve those questions. To that end, this work proposes the phenomenon of life to be the product of two dissipative mechanisms. From them, one characterises extant biological life and deduces a testable scenario for its origin. The proposed theory of life allows its replication, reinterprets ecological evolution and creates new constraints on the search for life.

Covariation of hot spring geochemistry with microbial genomic diversity, function, and evolution

The geosphere and the microbial biosphere have co-evolved for ~3.8 Ga, with many lines of evidence suggesting a hydrothermal habitat for life's origin. However, the extent that contemporary thermophiles and their hydrothermal habitats reflect those that likely existed on early Earth remains unknown. To address this knowledge gap, 64 geochemical analytes were measured and 1022 metagenome-assembled-genomes (MAGs) were generated from 34 chemosynthetic high-temperature springs in Yellowstone National Park and analysed alongside 444 MAGs from 35 published metagenomes. We used these data to evaluate co-variation in MAG taxonomy, metabolism, and phylogeny as a function of hot spring geochemistry. We found that cohorts of MAGs and their functions are discretely distributed across pH gradients that reflect different geochemical provinces. Acidic or circumneutral/alkaline springs harbor MAGs that branched later and are enriched in sulfur- and arsenic-based O2-dependent metabolic pathways that are inconsistent with early Earth conditions. In contrast, moderately acidic springs sourced by volcanic gas harbor earlier-branching MAGs that are enriched in anaerobic, gas-dependent metabolisms (e.g. H2, CO2, CH4 metabolism) that have been hypothesized to support early microbial life. Our results provide insight into the influence of redox state in the eco-evolutionary feedbacks between thermophiles and their habitats and suggest moderately acidic springs as early Earth analogs.

Chemical Antiquity in Metabolism

Life is an exergonic chemical reaction. The same was true when the very first cells emerged at life's origin. In order to live, all cells need a source of carbon, energy, and electrons to drive their overall reaction network (metabolism). In most cells, these are separate pathways. There is only one biochemical pathway that serves all three needs simultaneously: the acetyl-CoA pathway of CO2 fixation. In the acetyl-CoA pathway, electrons from H2 reduce CO2 to pyruvate for carbon supply, while methane or acetate synthesis are coupled to energy conservation as ATP. This simplicity and thermodynamic favorability prompted Georg Fuchs and Erhard Stupperich to propose in 1985 that the acetyl-CoA pathway might mark the origin of metabolism, at the same time that Steve Ragsdale and Harland Wood were uncovering catalytic roles for Fe, Co, and Ni in the enzymes of the pathway. Subsequent work has provided strong support for those proposals.In the presence of Fe, Co, and Ni in their native metallic state as catalysts, aqueous H2 and CO2 react specifically to formate, acetate, methane, and pyruvate overnight at 100 °C. These metals (and their alloys) thus replace the function of over 120 enzymes required for the conversion of H2 and CO2 to pyruvate via the pathway and its cofactors, an unprecedented set of findings in the study of biochemical evolution. The reactions require alkaline conditions, which promote hydrogen oxidation by proton removal and are naturally generated in serpentinizing (H2-producing) hydrothermal vents. Serpentinizing hydrothermal vents furthermore produce natural deposits of native Fe, Co, Ni, and their alloys. These are precisely the metals that reduce CO2 with H2 in the laboratory; they are also the metals found at the active sites of enzymes in the acetyl-CoA pathway. Iron, cobalt and nickel are relicts of the environments in which metabolism arose, environments that still harbor ancient methane- and acetate-producing autotrophs today. This convergence indicates bedrock-level antiquity for the acetyl-CoA pathway. In acetogens and methanogens growing on H2 as reductant, the acetyl-CoA pathway requires flavin-based electron bifurcation as a source of reduced ferredoxin (a 4Fe4S cluster-containing protein) in order to function. Recent findings show that H2 can reduce the 4Fe4S clusters of ferredoxin in the presence of native iron, uncovering an evolutionary precursor of flavin-based electron bifurcation and suggesting an origin of FeS-dependent electron transfer in proteins. Traditionally discussed as catalysts in early evolution, the most common function of FeS clusters in metabolism is one-electron transfer, also in radical SAM enzymes, a large and ancient enzyme family. The cofactors and active sites in enzymes of the acetyl-CoA pathway uncover chemical antiquity in metabolism involving metals, methyl groups, methyl transfer reactions, cobamides, pterins, GTP, S-adenosylmethionine, radical SAM enzymes, and carbon-metal bonds. The reaction sequence from H2 and CO2 to pyruvate on naturally deposited native metals is maximally simple. It requires neither nitrogen, sulfur, phosphorus, RNA, ion gradients, nor light. Solid-state metal catalysts tether the origin of metabolism to a H2-producing, serpentinizing hydrothermal vent.

Stratified Effects of Tillage and Crop Rotations on Soil Microbes in Carbon and Nitrogen Cycles at Different Soil Depths in Long-Term Corn, Soybean, and Wheat Cultivation

Understanding the soil bacterial communities involved in carbon (C) and nitrogen (N) cycling can inform beneficial tillage and crop rotation practices for sustainability and crop production. This study evaluated soil bacterial diversity, compositional structure, and functions associated with C-N cycling at two soil depths (0-15 cm and 15-30 cm) under long-term tillage (conventional tillage [CT] and no-till [NT]) and crop rotation (monocultures of corn, soybean, and wheat and corn-soybean-wheat rotation) systems. The soil microbial communities were characterized by metabarcoding the 16S rRNA gene V4-V5 regions using Illumina MiSeq. The results showed that long-term NT reduced the soil bacterial diversity at 15-30 cm compared to CT, while no significant differences were found at 0-15 cm. The bacterial communities differed significantly at the two soil depths under NT but not under CT. Notably, over 70% of the tillage-responding KEGG orthologs (KOs) associated with C fixation (primarily in the reductive citric acid cycle) were more abundant under NT than under CT at both depths. The tillage practices significantly affected bacteria involved in biological nitrogen (N2) fixation at the 0-15 cm soil depth, as well as bacteria involved in denitrification at both soil depths. The crop type and rotation regimes had limited effects on bacterial diversity and structure but significantly affected specific C-N-cycling genes. For instance, three KOs associated with the Calvin-Benson cycle for C fixation and four KOs related to various N-cycling processes were more abundant in the soil of wheat than in that of corn or soybean. These findings indicate that the long-term tillage practices had a greater influence than crop rotation on the soil bacterial communities, particularly in the C- and N-cycling processes. Integrated management practices that consider the combined effects of tillage, crop rotation, and crop types on soil bacterial functional groups are essential for sustainable agriculture.

Cadaverine and putrescine exposure influence carbon and nitrogen cycling genes in water and sediment of the Yellow River

The response patterns of microbial functional genes involved in biogeochemical cycles to cadaver decay is a central topic of recent environmental sciences. However, the response mechanisms and pathways of the functional genes associated with the carbon (C) and nitrogen (N) cycling to cadaveric substances such as cadaverine and putrescine remain unclear. This study explored the variation of functional genes associated with C fixation, C degradation and N cycling and their influencing factors under cadaverine, putrescine and mixed treatments. Our results showed only putrescine significantly increased the alpha diversity of C fixation genes, while reducing the alpha diversity of N cycling genes in sediment. For the C cycling, the mixed treatment significantly decreased the total abundance of reductive acetyl-CoA pathway genes (i.e., acsB and acsE) and lig gene linked to lignin degradation in water, while only significantly increasing the hydroxypropionate-hydroxybutylate cycle (i.e., accA) gene abundance in sediment. For the N cycling, mixed treatment significantly decreased the abundance of the nitrification (i.e., amoB), denitrification (i.e., nirS3) genes in water and the assimilation pathway gene (i.e., gdhA) in sediment. Environmental factors (i.e., total carbon and total nitrogen) were all negatively associated with the genes of C and N cycling. Therefore, cadaverine and putrescine exposure may inhibit the pathway in C fixation and N cycling, while promoting C degradation. These findings can offer some new insight for the management of amine pollution caused by animal cadavers.

Coupling CO2 Reduction and Acetyl-CoA Formation: The Role of a CO Capturing Tunnel in Enzymatic Catalysis

The bifunctional CO-dehydrogenase/acetyl-CoA synthase (CODH/ACS) complex couples the reduction of CO2 to the condensation of CO with a methyl moiety and CoA to acetyl-CoA. Catalysis occurs at two sites connected by a tunnel transporting the CO. In this study, we investigated how the bifunctional complex and its tunnel support catalysis using the CODH/ACS from Carboxydothermus hydrogenoformans as a model. Although CODH/ACS adapted to form a stable bifunctional complex with a secluded substrate tunnel, catalysis and CO transport is even more efficient when two monofunctional enzymes are coupled. Efficient CO channeling appears to be ensured by hydrophobic binding sites for CO, which act in a bucket-brigade fashion rather than as a simple tube. Tunnel remodeling showed that opening the tunnel increased activity but impaired directed transport of CO. Constricting the tunnel impaired activity and CO transport, suggesting that the tunnel evolved to sequester CO rather than to maximize turnover.

Wood-Ljungdahl pathway encoding anaerobes facilitate low-cost primary production in hypersaline sediments at Great Salt Lake, Utah

Little is known of primary production in dark hypersaline ecosystems despite the prevalence of such environments on Earth today and throughout its geologic history. Here, we generated and analyzed metagenome-assembled genomes (MAGs) organized as operational taxonomic units (OTUs) from three depth intervals along a 30-cm sediment core from the north arm of Great Salt Lake, Utah. The sediments and associated porewaters were saturated with NaCl, exhibited redox gradients with depth, and harbored nitrogen-depleted organic carbon. Metabolic predictions of MAGs representing 36 total OTUs recovered from the core indicated that communities transitioned from aerobic and heterotrophic at the surface to anaerobic and autotrophic at depth. Dark CO2 fixation was detected in sediments and the primary mode of autotrophy was predicted to be via the Wood-Ljungdahl pathway. This included novel hydrogenotrophic acetogens affiliated with the bacterial class Candidatus Bipolaricaulia. Minor populations were dependent on the Calvin cycle and the reverse tricarboxylic acid cycle, including in a novel Thermoplasmatota MAG. These results are interpreted to reflect the favorability of and selectability for populations that operate the lowest energy requiring CO2-fixation pathway known, the Wood-Ljungdahl pathway, in anoxic and hypersaline conditions that together impart a higher energy demand on cells.

Reasons why life on Earth rarely makes fluorine-containing compounds and their implications for the search for life beyond Earth

Life on Earth is known to rarely make fluorinated carbon compounds, as compared to other halocarbons. We quantify this rarity, based on our exhaustive natural products database curated from available literature. We build on explanations for the scarcity of fluorine chemistry in life on Earth, namely that the exclusion of the C-F bond stems from the unique physico-chemical properties of fluorine, predominantly its extreme electronegativity and strong hydration shell. We further show that the C-F bond is very hard to synthesize and when it is made by life its potential biological functions can be readily provided by alternative functional groups that are much less costly to incorporate into existing biochemistry. As a result, the overall evolutionary cost-to-benefit balance of incorporation of the C-F bond into the chemical repertoire of life is not favorable. We argue that the limitations of organofluorine chemistry are likely universal in that they do not exclusively apply to specifics of Earth's biochemistry. C-F bonds, therefore, will be rare in life beyond Earth no matter its chemical makeup.

The radical impact of oxygen on prokaryotic evolution-enzyme inhibition first, uninhibited essential biosyntheses second, aerobic respiration third

Molecular oxygen is a stable diradical. All O2-dependent enzymes employ a radical mechanism. Generated by cyanobacteria, O2 started accumulating on Earth 2.4 billion years ago. Its evolutionary impact is traditionally sought in respiration and energy yield. We mapped 365 O2-dependent enzymatic reactions of prokaryotes to phylogenies for the corresponding 792 protein families. The main physiological adaptations imparted by O2-dependent enzymes were not energy conservation, but novel organic substrate oxidations and O2-dependent, hence O2-tolerant, alternative pathways for O2-inhibited reactions. Oxygen-dependent enzymes evolved in ancestrally anaerobic pathways for essential cofactor biosynthesis including NAD+, pyridoxal, thiamine, ubiquinone, cobalamin, heme, and chlorophyll. These innovations allowed prokaryotes to synthesize essential cofactors in O2-containing environments, a prerequisite for the later emergence of aerobic respiratory chains.

Fusion/fission protein family identification in Archaea

The majority of newly discovered archaeal lineages remain without a cultivated representative, but scarce experimental data from the cultivated organisms show that they harbor distinct functional repertoires. To unveil the ecological as well as evolutionary impact of Archaea from metagenomics, new computational methods need to be developed, followed by in-depth analysis. Among them is the genome-wide protein fusion screening performed here. Natural fusions and fissions of genes not only contribute to microbial evolution but also complicate the correct identification and functional annotation of sequences. The products of these processes can be defined as fusion (or composite) proteins, the ones consisting of two or more domains originally encoded by different genes and split proteins, and the ones originating from the separation of a gene in two (fission). Fusion identifications are required for proper phylogenetic reconstructions and metabolic pathway completeness assessments, while mappings between fused and unfused proteins can fill some of the existing gaps in metabolic models. In the archaeal genome-wide screening, more than 1,900 fusion/fission protein clusters were identified, belonging to both newly sequenced and well-studied lineages. These protein families are mainly associated with different types of metabolism, genetic, and cellular processes. Moreover, 162 of the identified fusion/fission protein families are archaeal specific, having no identified fused homolog within the bacterial domain. Our approach was validated by the identification of experimentally characterized fusion/fission cases. However, around 25% of the identified fusion/fission families lack functional annotations for both composite and split states, showing the need for experimental characterization in Archaea.IMPORTANCEGenome-wide fusion screening has never been performed in Archaea on a broad taxonomic scale. The overlay of multiple computational techniques allows the detection of a fine-grained set of predicted fusion/fission families, instead of rough estimations based on conserved domain annotations only. The exhaustive mapping of fused proteins to bacterial organisms allows us to capture fusion/fission families that are specific to archaeal biology, as well as to identify links between bacterial and archaeal lineages based on cooccurrence of taxonomically restricted proteins and their sequence features. Furthermore, the identification of poorly characterized lineage-specific fusion proteins opens up possibilities for future experimental and computational investigations. This approach enhances our understanding of Archaea in general and provides potential candidates for in-depth studies in the future.

Synergistic Effects of Silica-Supported Iron-Cobalt Catalysts for CO2 Reduction to Prebiotic Organics

To test the ability of geochemical surfaces in serpentinizing hydrothermal systems to catalyze reactions from which metabolism arose, we investigated H2-dependent CO2 reduction toward metabolic intermediates over silica-supported Co-Fe catalysts. Supported catalysts converted CO2 to various products at 180 °C and 2.0 MPa. The liquid product phase included formate, acetate, and ethanol, while the gaseous product phase consisted of CH4, CO, methanol, and C2-C7 linear hydrocarbons. The 1/1 ratio CoFe alloy with the same composition as the natural mineral wairauite yielded the highest concentrations of formate (6.0 mM) and acetate (0.8 mM), which are key intermediates in the acetyl-coenzyme A (acetyl-CoA) pathway of CO2 fixation. While Co-rich catalysts were proficient at hydrogenation, yielding mostly CH4, Fe-rich catalysts favored the formation of CO and methanol. Mechanistic studies indicated intermediate hydrogenation and C-C coupling activities of alloyed CoFe, in contrast to physical mixtures of both metals. Co in the active site of Co-Fe catalysts performed a similar reaction as tetrapyrrole-coordinated Co in the corrinoid iron-sulfur (CoFeS) methyl transferase in the acetyl-CoA pathway. In a temperature range characteristic for deeper regions of serpentinizing systems, oxygenate product formation was favored at lower, more biocompatible temperatures.

Why pyridoxal phosphate could be a functional predecessor of thiamine pyrophosphate and speculations on a primordial metabolism

The account attempts to substantiate the hypothesis that, from an evolutionary perspective, the coenzyme couple pyridoxal phosphate and pyridoxamine phosphate preceded the coenzyme thiamine pyrophosphate and acted as its less efficient chemical analogue in some form of early metabolism. The analysis combines mechanism-based chemical reactivity with biosynthetic arguments and provides evidence that vestiges of "TPP-like reactivity" are still found for PLP today. From these thoughts, conclusions can be drawn about the key elements of a primordial form of metabolism, which includes the citric acid cycle, amino acid biosynthesis and the pentose phosphate pathway.

A prebiotic Krebs cycle analog generates amino acids with H2 and NH3 over nickel

Hydrogen (H2) has powered microbial metabolism for roughly 4 billion years. The recent discovery that it also fuels geochemical analogs of the most ancient biological carbon fixation pathway sheds light on the origin of metabolism. However, it remains unclear whether H2 can sustain more complex nonenzymatic reaction networks. Here, we show that H2 drives the nonenzymatic reductive amination of six biological ketoacids and glyoxylate to give the corresponding amino acids in good yields using ammonium concentrations ranging from 6 to 150 mM. Catalytic amounts of nickel or ground meteorites enable these reactions at 22°C and pH 8. The same conditions promote an H2-dependent ketoacid-forming reductive aldol chemistry that co-occurs with reductive amination, producing a continuous reaction network resembling amino acid synthesis in the metabolic core of ancient microbes. The results support the hypothesis that the earliest biochemical networks could have emerged without enzymes or RNA.

The Impact of Aboveground Epichloë Endophytic Fungi on the Rhizosphere Microbial Functions of the Host Melica transsilvanica

In nature, the symbiotic relationship between plants and microorganisms is crucial for ecosystem balance and plant growth. This study investigates the impact of Epichloë endophytic fungi, which are exclusively present aboveground, on the rhizosphere microbial functions of the host Melica transsilvanica. Using metagenomic methods, we analyzed the differences in microbial functional groups and functional genes in the rhizosphere soil between symbiotic (EI) and non-symbiotic (EF) plants. The results reveal that the presence of Epichloë altered the community structure of carbon and nitrogen cycling-related microbial populations in the host's rhizosphere, significantly increasing the abundance of the genes (porA, porG, IDH1) involved in the rTCA cycle of the carbon fixation pathway, as well as the abundance of nxrAB genes related to nitrification in the nitrogen-cycling pathway. Furthermore, the presence of Epichloë reduces the enrichment of virulence factors in the host rhizosphere microbiome, while significantly increasing the accumulation of resistance genes against heavy metals such as Zn, Sb, and Pb. This study provides new insights into the interactions among endophytic fungi, host plants, and rhizosphere microorganisms, and offers potential applications for utilizing endophytic fungi resources to improve plant growth and soil health.

Regulation on C2-C8 carboxylic acid biosynthesis from anaerobic CO2 fermentation

Bioconversion of CO2 into liquid fuels or chemicals, preferred medium chain carboxylic acids (caproic and caprylic acid), is an attractive CO2 utilization technology. The present study aims to investigate the effects of different ratios of H2/CO2 on regulating the distribution of C2-C8 carboxylic acid products, while the headspace pressure of 1.5 bar was set to amplify the effect of different ratios. The H2/CO2 ratio of 4:1 was more suitable for preparing acetic acid, where the highest acetic acid yield was 17.5 g/L. And the H2/CO2 ratio of 2:1 showed excellent chain elongation ability with the highest n-caprylic yield of 2.4 g/L. Additionally, the actual H2/CO2 ratios of 4:1 reactors were higher than that in 2:1 may be course chain elongation often accompanied by H2 production. The 16S rRNA genes analysis shows that the genus Terrisporobacter and Coriobacteriales may be related to acetic acid production enriched in H2/CO2 ratio 4:1 reactors, and the genus Clostridium and Paenibacillaceae may associate with the chain elongation pathway were enriched in H2/CO2 ratio 2:1 reactors.

Primitive purine biosynthesis connects ancient geochemistry to modern metabolism

An unresolved question in the origin and evolution of life is whether a continuous path from geochemical precursors to the majority of molecules in the biosphere can be reconstructed from modern-day biochemistry. Here we identified a feasible path by simulating the evolution of biosphere-scale metabolism, using only known biochemical reactions and models of primitive coenzymes. We find that purine synthesis constitutes a bottleneck for metabolic expansion, which can be alleviated by non-autocatalytic phosphoryl coupling agents. Early phases of the expansion are enriched with enzymes that are metal dependent and structurally symmetric, supporting models of early biochemical evolution. This expansion trajectory suggests distinct hypotheses regarding the tempo, mode and timing of metabolic pathway evolution, including a late appearance of methane metabolisms and oxygenic photosynthesis consistent with the geochemical record. The concordance between biological and geological analyses suggests that this trajectory provides a plausible evolutionary history for the vast majority of core biochemistry.

Long-term conservation tillage increase cotton rhizosphere sequestration of soil organic carbon by changing specific microbial CO2 fixation pathways in coastal saline soil

Coastal saline soil is an important reserve resource for arable land globally. Data from 10 years of continuous stubble return and subsoiling experiments have revealed that these two conservation tillage measures significantly improve cotton rhizosphere soil organic carbon sequestration in coastal saline soil. However, the contribution of microbial fixation of atmospheric carbon dioxide (CO2) has remained unclear. Here, metagenomics and metabolomics analyses were used to deeply explore the microbial CO2 fixation process in rhizosphere soil of coastal saline cotton fields under long-term stubble return and subsoiling. Metagenomics analysis showed that stubble return and subsoiling mainly optimized CO2 fixing microorganism (CFM) communities by increasing the abundance of Acidobacteria, Gemmatimonadetes, and Chloroflexi, and improving composition diversity. Conjoint metagenomics and metabolomics analyses investigated the effects of stubble return and subsoiling on the reverse tricarboxylic acid (rTCA) cycle. The conversion of citrate to oxaloacetate was inhibited in the citrate cleavage reaction of the rTCA cycle. More citrate was converted to acetyl-CoA, which enhanced the subsequent CO2 fixation process of acetyl-CoA conversion to pyruvate. In the rTCA cycle reductive carboxylation reaction from 2-oxoglutarate to isocitrate, synthesis of the oxalosuccinate intermediate product was inhibited, with strengthened CO2 fixation involving the direct conversion of 2-oxoglutarate to isocitrate. The collective results demonstrate that stubble return and subsoiling optimizes rhizosphere CFM communities by increasing microbial diversity, in turn increasing CO2 fixation by enhancing the utilization of rTCA and 3-hydroxypropionate/4-hydroxybutyrate cycles by CFMs. These events increase the microbial CO2 fixation in the cotton rhizosphere, thereby promoting the accumulation of microbial biomass, and ultimately improving rhizosphere soil organic carbon. This study clarifies the impact of conservation tillage measures on microbial CO2 fixation in cotton rhizosphere of coastal saline soil, and provides fundamental data for the improvement of carbon sequestration in saline soil in agricultural ecosystems.

Biotic and Abiotic Regulations of Carbon Fixation into Lacustrine Sediments with Different Nutrient Levels

Lake sediments play a critical role in organic carbon (OC) conservation. However, the biogeochemical processes of the C cycle in lake ecosystems remain limitedly understood. In this study, Fe fractions and OC fractions, including total OC (TOC) and OC associated with iron oxides (TOCFeO), were measured for sediments from a eutrophic lake in China. The abundance and composition of bacterial communities encoding genes cbbL and cbbM were obtained by using high-throughput sequencing. We found that autochthonous algae with a low C/N ratio together with δ13C values predominantly contributed to the OC burial in sediments rather than terrigenous input. TOCFeO served as an important C sink deposited in the sediments. A significantly positive correlation (r = 0.92, p < 0.001) suggested the remarkable regulation of complexed FeO (Fep) on fixed TOC fractions, and the Fe redox shift triggered the loss of deposited OC. It should be noted that a significant correlation was not found between the absolute abundance of C-associating genera and TOC, as well as TOCFeO, and overlying water. Some rare genera, including Acidovora and Thiobacillus, served as keystone species and had a higher connected degree than the genera with high absolute abundance. These investigations synthetically concluded that the absolute abundance of functional genes did not dominate CO2 fixation into the sediments via photosynthesis catalyzed by the C-associating RuBisCO enzyme. That is, rare genera, together with high-abundance genera, control the C association and fixation in the sediments.

Engineering RuBisCO-based shunt for improved cadaverine production in Escherichia coli

The process of biological fermentation is often accompanied by the release of CO2, resulting in low yield and environmental pollution. Refixing CO2 to the product synthesis pathway is an attractive approach to improve the product yield. Cadaverine is an important diamine used for the synthesis of bio-based polyurethane or polyamide. Here, aiming to increase its final production, a RuBisCO-based shunt consisting of the ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and phosphoribulate kinase (PRK) was expressed in cadaverine-producing E. coli. This shunt was calculated capable of increasing the maximum theoretical cadaverine yield based on flux model analysis. When a functional RuBisCO-based shunt was established and optimized in E. coli, the cadaverine production and yield of the final engineered strain reached the highest level, which were 84.1 g/L and 0.37 g/g Glucose, respectively. Thus, the design of in situ CO2 fixation provides a green and efficient industrial production process.