Metagenomics-guided analysis of microbial chemolithoautotrophic phosphite oxidation yields evidence of a seventh natural CO2 fixation pathway

Redox metabolism for improving whole-cell P450-catalysed terpenoid biosynthesis

The growing preference for producing cytochrome P450-mediated natural products in microbial systems stems from the challenging nature of the organic chemistry approaches. The P450 enzymes are redox-dependent proteins, through which they source electrons from reducing cofactors to drive their activities. Widely researched in biochemistry, most of the previous studies have extensively utilised expensive cell-free assays to reveal mechanistic insights into P450 functionalities in presence of commercial redox partners. However, in the context of microbial bioproduction, the synergic activity of P450- reductase proteins in microbial systems have not been largely investigated. This is mainly due to limited knowledge about their mutual interactions in the context of complex systems. Hence, manipulating the redox potential for natural product synthesis in microbial chassis has been limited. As the potential of redox state as crucial regulator of P450 biocatalysis has been greatly underestimated by the scientific community, in this review, we re-emphasize their pivotal role in modulating the in vivo P450 activity through affecting the product profile and yield. Particularly, we discuss the applications of widely used in vivo redox engineering methodologies for natural product synthesis to provide further suggestions for patterning on P450-based terpenoids production in microbial platforms.

Phosphine Generation Pathways on Rocky Planets

The possibility of life in the venusian clouds was proposed in the 1960s, and recently this hypothesis has been revived with the potential detection of phosphine (PH₃) in Venus' atmosphere. These observations may have detected ∼5-20 ppb phosphine on Venus (Greaves et al., 2020), which raises questions about venusian atmospheric/geochemical processes and suggests that this phosphine could possibly be generated by biological processes. In such a claim, it is essential to understand the abiotic phosphorus chemistry that may occur under Venus-relevant conditions, particularly those processes that may result in phosphine generation. Here, we discuss two related abiotic routes for phosphine generation within the atmosphere of Venus. Based on our assessment, corrosion of large impactors as they ablate near Venus' cloud layer, and the presence of reduced phosphorus compounds in the subcloud layer could result in production of phosphine and may explain the phosphine detected in Venus' atmosphere or on other rocky planets. We end on a cautionary note: although there may be life in the clouds of Venus, the detection of a simple, single gas, phosphine, is likely not a decisive indicator.

Determination of phosphite (HPO3-2) by a new IC/MS/MS method using an 18O-labeled HPO3-2 internal standard

A new method has been developed to determine trace amounts of phosphite (HPO₃^-2) in environmental samples using ion chromatography with electrospray tandem mass spectrometry (IC-ESI/MS/MS). The method includes the production and use of an ¹⁸O-labeled HPO₃^-2 internal standard (IS). This isotopically labeled IS significantly improved sensitivity and could account for matrix suppression. The method detection limit (MDL) was determined as 0.017 and 0.034 μg L^-1 of HPO₃^-2 (6.5 and 13 ng P L^-1) using a 500 and 25 μL injection loop, respectively. Precision (1-10%) and accuracy (recoveries = 96-106%) were established for a range of environmental samples using known (spiked) addition. The impact of ionic interferences was investigated by evaluating the response of the internal standard in the presence of common anions with respect to distilled deionized water. The most significant interference was due to nitrate (100 mg-NO₃^- L^-1) with a 99.99% reduction in IS intensity. The method was successfully applied to wastewater effluent, surface water, tap water, and soil samples. Relatively low concentrations <0.25 μg HPO₃^-2 L^-1 were measured in tap water, surface water and wastewater effluent, and ~1.6 μg kg^-1 HPO₃^-2 in soil samples, using both injection loops. Limited suppression was observed for all matrices. The largest IS peak area suppression (~98%) was observed in WW effluent with 500 μL injection loop; however, this method was able to quantify HPO₃^-2 with good recoveries and precision despite the mentioned suppression, supporting the ability of the proposed method to quantify HPO₃^-2 in different environmental matrices.

The curious consistency of carbon biosignatures over billions of years of Earth-life coevolution

The oldest and most wide-ranging signal of biological activity (biosignature) on our planet is the carbon isotope composition of organic materials preserved in rocks. These biosignatures preserve the long-term evolution of the microorganism-hosted metabolic machinery responsible for producing deviations in the isotopic compositions of inorganic and organic carbon. Despite billions of years of ecosystem turnover, evolutionary innovation, organismic complexification, and geological events, the organic carbon that is a residuum of the global marine biosphere in the rock record tells an essentially static story. The ~25‰ mean deviation between inorganic and organic 13C/12C values has remained remarkably unchanged over >3.5 billion years. The bulk of this record is conventionally attributed to early-evolved, RuBisCO-mediated CO2 fixation that, in extant oxygenic phototrophs, produces comparable isotopic effects and dominates modern primary production. However, billions of years of environmental transition, for example, in the progressive oxygenation of the Earth's atmosphere, would be expected to have accompanied shifts in the predominant RuBisCO forms as well as enzyme-level adaptive responses in RuBisCO CO2-specificity. These factors would also be expected to result in preserved isotopic signatures deviating from those produced by extant RuBisCO in oxygenic phototrophs. Why does the bulk carbon isotope record not reflect these expected environmental transitions and evolutionary innovations? Here, we discuss this apparent discrepancy and highlight the need for greater quantitative understanding of carbon isotope fractionation behavior in extant metabolic pathways. We propose novel, laboratory-based approaches to reconstructing ancestral states of carbon metabolisms and associated enzymes that can constrain isotopic biosignature production in ancient biological systems. Together, these strategies are crucial for integrating the complementary toolsets of biological and geological sciences and for interpretation of the oldest record of life on Earth.

The diversity and evolution of microbial dissimilatory phosphite oxidation

Phosphite is the most energetically favorable chemotrophic electron donor known, with a half-cell potential (Eo') of -650 mV for the PO43-/PO33- couple. Since the discovery of microbial dissimilatory phosphite oxidation (DPO) in 2000, the environmental distribution, evolution, and diversity of DPO microorganisms (DPOMs) have remained enigmatic, as only two species have been identified. Here, metagenomic sequencing of phosphite-enriched microbial communities enabled the genome reconstruction and metabolic characterization of 21 additional DPOMs. These DPOMs spanned six classes of bacteria, including the Negativicutes, Desulfotomaculia, Synergistia, Syntrophia, Desulfobacteria, and Desulfomonilia_A Comparing the DPO genes from the genomes of enriched organisms with over 17,000 publicly available metagenomes revealed the global existence of this metabolism in diverse anoxic environments, including wastewaters, sediments, and subsurface aquifers. Despite their newfound environmental and taxonomic diversity, metagenomic analyses suggested that the typical DPOM is a chemolithoautotroph that occupies low-oxygen environments and specializes in phosphite oxidation coupled to CO2 reduction. Phylogenetic analyses indicated that the DPO genes form a highly conserved cluster that likely has ancient origins predating the split of monoderm and diderm bacteria. By coupling microbial cultivation strategies with metagenomics, these studies highlighted the unsampled metabolic versatility latent in microbial communities. We have uncovered the unexpected prevalence, diversity, biochemical specialization, and ancient origins of a unique metabolism central to the redox cycling of phosphorus, a primary nutrient on Earth.

Reductive Glycine Pathway: A Versatile Route for One-Carbon Biotech

Hong et al. heterologously expressed the metabolic core of the reductive glycine pathway (rGlyP) as a sink for the anaerobic conversion of glycerol. This recent study concludes several reports in 2020 on the ATP-efficient, one-carbon-assimilating rGlyP. Its engineering in diverse hosts could help the transformation toward renewable, one-carbon-based bioproduction.

A Comprehensive Modeling Analysis of Formate-Mediated Microbial Electrosynthesis*

Mediated microbial electrosynthesis (MES) represents a promising strategy for the capture and conversion of CO₂ into carbon-based products. We describe the development and application of a comprehensive multiphysics model to analyze a formate-mediated MES reactor. The model shows that this system can achieve a biomass productivity of ∼1.7 g L^-1  h^-1 but is limited by a competitive trade-off between O₂ gas/liquid mass transfer and CO₂ transport to the cathode. Synthetic metabolic strategies are evaluated for formatotrophic growth, which can enable an energy efficiency of ∼21 %, a 30 % improvement over the Calvin cycle. However, carbon utilization efficiency is only ∼10 % in the best cases due to a futile CO₂ cycle, so gas recycling will be necessary for greater efficiency. Finally, separating electrochemical and microbial processes into separate reactors enables a higher biomass productivity of ∼2.4 g L^-1  h^-1 . The mediated MES model and analysis presented here can guide process design for conversion of CO₂ into renewable chemical feedstocks.

Recent Advances in Developing Artificial Autotrophic Microorganism for Reinforcing CO2 Fixation

With the goal of achieving carbon sequestration, emission reduction and cleaner production, biological methods have been employed to convert carbon dioxide (CO2) into fuels and chemicals. However, natural autotrophic organisms are not suitable cell factories due to their poor carbon fixation efficiency and poor growth rate. Heterotrophic microorganisms are promising candidates, since they have been proven to be efficient biofuel and chemical production chassis. This review first briefly summarizes six naturally occurring CO2 fixation pathways, and then focuses on recent advances in artificially designing efficient CO2 fixation pathways. Moreover, this review discusses the transformation of heterotrophic microorganisms into hemiautotrophic microorganisms and delves further into fully autotrophic microorganisms (artificial autotrophy) by use of synthetic biological tools and strategies. Rapid developments in artificial autotrophy have laid a solid foundation for the development of efficient carbon fixation cell factories. Finally, this review highlights future directions toward large-scale applications. Artificial autotrophic microbial cell factories need further improvements in terms of CO2 fixation pathways, reducing power supply, compartmentalization and host selection.

Synthetic Biology on Acetogenic Bacteria for Highly Efficient Conversion of C1 Gases to Biochemicals

Synthesis gas, which is mainly produced from fossil fuels or biomass gasification, consists of C1 gases such as carbon monoxide, carbon dioxide, and methane as well as hydrogen. Acetogenic bacteria (acetogens) have emerged as an alternative solution to recycle C1 gases by converting them into value-added biochemicals using the Wood-Ljungdahl pathway. Despite the advantage of utilizing acetogens as biocatalysts, it is difficult to develop industrial-scale bioprocesses because of their slow growth rates and low productivities. To solve these problems, conventional approaches to metabolic engineering have been applied; however, there are several limitations owing to the lack of required genetic bioparts for regulating their metabolic pathways. Recently, synthetic biology based on genetic parts, modules, and circuit design has been actively exploited to overcome the limitations in acetogen engineering. This review covers synthetic biology applications to design and build industrial platform acetogens.

The reductive glycine pathway allows autotrophic growth of Desulfovibrio desulfuricans

Six CO2 fixation pathways are known to operate in photoautotrophic and chemoautotrophic microorganisms. Here, we describe chemolithoautotrophic growth of the sulphate-reducing bacterium Desulfovibrio desulfuricans (strain G11) with hydrogen and sulphate as energy substrates. Genomic, transcriptomic, proteomic and metabolomic analyses reveal that D. desulfuricans assimilates CO2 via the reductive glycine pathway, a seventh CO2 fixation pathway. In this pathway, CO2 is first reduced to formate, which is reduced and condensed with a second CO2 to generate glycine. Glycine is further reduced in D. desulfuricans by glycine reductase to acetyl-P, and then to acetyl-CoA, which is condensed with another CO2 to form pyruvate. Ammonia is involved in the operation of the pathway, which is reflected in the dependence of the autotrophic growth rate on the ammonia concentration. Our study demonstrates microbial autotrophic growth fully supported by this highly ATP-efficient CO2 fixation pathway.

Phosphorylation and acylation transfer reactions: Clues to a dual origin of metabolism

Many theories of the origin of life focus on only one primitive polymer as an archetype of a world paradigm. However, life would have emerged within more complex scenarios where a variety of molecules and diverse polymers interconnected by a few similar chemical reactions. Previous work suggested that the ancestors of all major biopolymers would have arisen from abiotic template independent replication processes. They would have been organized in two closed sets of polymerization cycles: polysaccharides, polyribonucleotides and polyphosphates on one site; and peptides, fatty acids and polyhydroxyalkanoates on the other site. Then, these polymerization reaction cycles integrated into a minimal organization closure. Here, the purpose was to explore which kind of reactions could have supported the chemical networks that led to the early (bio)polymers. As a result, the proposed overview suggests that phosphorylation and acylation transfer reactions would have arisen independently and forged two distinct chemical systems that provided the phosphorylated and carboxylated intermediates used for the synthesis of the corresponding polymers. In this sense, modern metabolism may still reflect its dual nature, probably relying on these two reaction networks from the beginnings.

Lists of names of prokaryotic Candidatus taxa

We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.

Metagenomic- and Cultivation-Based Exploration of Anaerobic Chloroform Biotransformation in Hypersaline Sediments as Natural Source of Chloromethanes

Chloroform (CF) is an environmental contaminant that can be naturally formed in various environments ranging from forest soils to salt lakes. Here we investigated CF removal potential in sediments obtained from hypersaline lakes in Western Australia. Reductive dechlorination of CF to dichloromethane (DCM) was observed in enrichment cultures derived from sediments of Lake Strawbridge, which has been reported as a natural source of CF. No CF removal was observed in abiotic control cultures without artificial electron donors, indicating biotic CF dechlorination in the enrichment cultures. Increasing vitamin B₁₂ concentration from 0.04 to 4 µM in enrichment cultures enhanced CF removal and reduced DCM formation. In cultures amended with 4 µM vitamin B₁₂ and ¹³C labelled CF, formation of ¹³CO₂ was detected. Known organohalide-respiring bacteria and reductive dehalogenase genes were neither detected using quantitative PCR nor metagenomic analysis of the enrichment cultures. Rather, members of the order Clostridiales, known to co-metabolically transform CF to DCM and CO₂, were detected. Accordingly, metagenome-assembled genomes of Clostridiales encoded enzymatic repertoires for the Wood-Ljungdahl pathway and cobalamin biosynthesis, which are known to be involved in fortuitous and nonspecific CF transformation. This study indicates that hypersaline lake microbiomes may act as a filter to reduce CF emission to the atmosphere.

Functional cooperation of the glycine synthase-reductase and Wood-Ljungdahl pathways for autotrophic growth of Clostridium drakei

Despite sharing the first four reactions, coutilization of the Wood–Ljungdahl pathway (WLP) with the glycine synthase-reductase pathway (GSRP) and reductive glycine pathway (RGP) to fix C1 compounds has remained unknown. In this study, using Clostridium drakei, we elucidated the role of the GSRP and RGP in the presence of the WLP, via a genome-scale metabolic model, RNA-seq, ¹³C isotope-based metabolite-tracing experiments, biochemical assays, and heterologous expression. Overall, the data suggested the pathways are functional under autotrophic conditions. Along with the WLP, GSRP and RGP convert CO₂ to glycine and then to acetyl-phosphate and serine, which then obtain ATP by producing acetate and operate with limited reducing power. This is a unique coutilization of the pathways under autotrophic conditions in acetogens.

Among CO₂-fixing metabolic pathways in nature, the linear Wood–Ljungdahl pathway (WLP) in phylogenetically diverse acetate-forming acetogens comprises the most energetically efficient pathway, requires the least number of reactions, and converts CO₂ to formate and then into acetyl-CoA. Despite two genes encoding glycine synthase being well-conserved in WLP gene clusters, the functional role of glycine synthase under autotrophic growth conditions has remained uncertain. Here, using the reconstructed genome-scale metabolic model iSL771 based on the completed genome sequence, transcriptomics, ¹³C isotope-based metabolite-tracing experiments, biochemical assays, and heterologous expression of the pathway in another acetogen, we discovered that the WLP and the glycine synthase pathway are functionally interconnected to fix CO₂, subsequently converting CO₂ into acetyl-CoA, acetyl-phosphate, and serine. Moreover, the functional cooperation of the pathways enhances CO₂ consumption and cellular growth rates via bypassing reducing power required reactions for cellular metabolism during autotrophic growth of acetogens.

Growth of E. coli on formate and methanol via the reductive glycine pathway

Engineering a biotechnological microorganism for growth on one-carbon intermediates, produced from the abiotic activation of CO₂, is a key synthetic biology step towards the valorization of this greenhouse gas to commodity chemicals. Here we redesign the central carbon metabolism of the model bacterium Escherichia coli for growth on one-carbon compounds using the reductive glycine pathway. Sequential genomic introduction of the four metabolic modules of the synthetic pathway resulted in a strain capable of growth on formate and CO₂ with a doubling time of ~70 h and growth yield of ~1.5 g cell dry weight (gCDW) per mol-formate. Short-term evolution decreased doubling time to less than 8 h and improved biomass yield to 2.3 gCDW per mol-formate. Growth on methanol and CO₂ was achieved by further expression of a methanol dehydrogenase. Establishing synthetic formatotrophy and methylotrophy, as demonstrated here, paves the way for sustainable bioproduction rooted in CO₂ and renewable energy.

Phosphine as a Biosignature Gas in Exoplanet Atmospheres

A long-term goal of exoplanet studies is the identification and detection of biosignature gases. Beyond the most discussed biosignature gas O₂, only a handful of gases have been considered in detail. In this study, we evaluate phosphine (PH₃). On Earth, PH₃ is associated with anaerobic ecosystems, and as such, it is a potential biosignature gas in anoxic exoplanets. We simulate the atmospheres of habitable terrestrial planets with CO₂- and H₂-dominated atmospheres and find that PH₃ can accumulate to detectable concentrations on planets with surface production fluxes of 10¹⁰ to 10¹⁴ cm^-2 s^-1 (corresponding to surface concentrations of 10s of ppb to 100s of ppm), depending on atmospheric composition and ultraviolet (UV) irradiation. While high, the surface flux values are comparable to the global terrestrial production rate of methane or CH₄ (10¹¹ cm^-2 s^-1) and below the maximum local terrestrial PH₃ production rate (10¹⁴ cm^-2 s^-1). As with other gases, PH₃ can more readily accumulate on low-UV planets, for example, planets orbiting quiet M dwarfs or with a photochemically generated UV shield. PH₃ has three strong spectral features such that in any atmosphere scenario one of the three will be unique compared with other dominant spectroscopic molecules. Phosphine's weakness as a biosignature gas is its high reactivity, requiring high outgassing rates for detectability. We calculate that tens of hours of JWST (James Webb Space Telescope) time are required for a potential detection of PH₃. Yet, because PH₃ is spectrally active in the same wavelength regions as other atmospherically important molecules (such as H₂O and CH₄), searches for PH₃ can be carried out at no additional observational cost to searches for other molecular species relevant to characterizing exoplanet habitability. Phosphine is a promising biosignature gas, as it has no known abiotic false positives on terrestrial planets from any source that could generate the high fluxes required for detection.

"Candidatus Galacturonibacter soehngenii" Shows Acetogenic Catabolism of Galacturonic Acid but Lacks a Canonical Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase Complex

Acetogens have the ability to fixate carbon during fermentation by employing the Wood-Ljungdahl pathway (WLP), which is highly conserved across Bacteria and Archaea. In a previous study, product stoichometries in galacturonate-limited, anaerobic enrichment cultures of “Candidatus Galacturonibacter soehngenii,” from a novel genus within the Lachnospiraceae, suggested the simultaneous operation of a modified Entner-Doudoroff pathway for galacturonate fermentation and a WLP for acetogenesis. However, a draft metagenome-assembled genome (MAG) based on short reads did not reveal homologs of genes encoding a canonical WLP carbon-monoxide-dehydrogenase/acetyl-Coenzyme A synthase (CODH/ACS) complex. In this study, NaH¹³CO₃ fed to chemostat-grown, galacturonate-limited enrichment cultures of “Ca. G. soehngenii” was shown to be incorporated into acetate. Preferential labeling of the carboxyl group of acetate was consistent with acetogenesis via a WLP in which the methyl group of acetate was predominately derived from formate. This interpretation was further supported by high transcript levels of a putative pyruvate-formate lyase gene and very low transcript levels of a candidate gene for formate dehydrogenase. Reassembly of the “Ca. G. soehngenii” MAG with support from long-read nanopore sequencing data produced a single-scaffold MAG, which confirmed the absence of canonical CODH/ACS-complex genes homologs. However, high CO-dehydrogenase activities were measured in cell extracts of “Ca. G. soehngenii” enrichment cultures, contradicting the absence of corresponding homologs in the MAG. Based on the highly conserved amino-acid motif associated with anaerobic Ni-CO dehydrogenase proteins, a novel candidate was identified which could be responsible for the observed activities. These results demonstrate operation of an acetogenic pathway, most probably as a yet unresolved variant of the Wood-Ljungdahl pathway, in anaerobic, galacturonate-limited cultures of “Ca. G. soehngenii.”

Novel syntrophic bacteria in full-scale anaerobic digesters revealed by genome-centric metatranscriptomics

Short-chain fatty acid (SCFA) degradation is an important process in methanogenic ecosystems, and is usually catalyzed by SCFA-oxidizing bacteria in syntrophy with methanogens. Current knowledge of this functional guild is mainly based on isolates or enrichment cultures, but these may not reflect the true diversity and in situ activities of the syntrophs predominating in full-scale systems. Here we obtained 182 medium to high quality metagenome-assembled genomes (MAGs) from the microbiome of two full-scale anaerobic digesters. The transcriptomic response of individual MAG was studied after stimulation with low concentrations of acetate, propionate, or butyrate, separately. The most pronounced response to butyrate was observed for two MAGs of the recently described genus Candidatus Phosphitivorax (phylum Desulfobacterota), expressing a butyrate beta-oxidation pathway. For propionate, the largest response was observed for an MAG of a novel genus in the family Pelotomaculaceae, transcribing a methylmalonyl-CoA pathway. All three species were common in anaerobic digesters at Danish wastewater treatment plants as shown by amplicon analysis, and this is the first time their syntrophic features involved in SCFA oxidation were revealed with transcriptomic evidence. Further, they also possessed unique genomic features undescribed in well-characterized syntrophs, including the metabolic pathways for phosphite oxidation, nitrite and sulfate reduction.

Dark carbon fixation and chemolithotrophic microbial community in surface sediments of the cascade reservoirs, Southwest China

Dark carbon fixation (DCF) by chemolithotrophic microbes can make considerable contribution to inorganic carbon fixation in aquatic ecosystems. However, little is known about the importance and diversity of chemolithotrophic microbes in cascade reservoir sediments. In this study, we determined the potential DCF rates of sediments of three cascade reservoirs in Wujiang River basin by carbon isotopic labeling. The results showed that the DCF rates of the surface sediments ranged from 1.5 to 14.7 mmol C m^-2 d^-1. The ratio of DCF to mineralization rate of sediment organic matter of surface sediment was between 11.6%~60.9%. High-throughput sequencing analysis of cbbL and cbbM genes involved in Calvin Benson Cycle indicated that cbbL-carrying CO₂-assimilating bacteria included diverse functional groups, while cbbM type was mostly involved in sulfur oxidation. The sediments of Hongfeng (HF) reservoir, which has much longer hydraulic residence time (HRT) and locates in most upstream of a major tributary of Wujiang River, have substantially higher DCF rates. The cbbL and cbbM communities in HF were dominated by sulfur oxidizing bacteria, and were largely different from that in the other two reservoirs. Our results suggested that chemolithotrophy plays an important role in carbon cycling of sediments in cascade reservoir. Meanwhile, HRT and relative location of cascade reservoirs are the key control factors of both DCF and composition of autotrophic microbial communities in cascade reservoir sediments.

Revolutionizing agriculture with synthetic biology

Synthetic biology is here to stay and will transform agriculture if given the chance. The huge challenges facing food, fuel and chemical production make it vital to give synthetic biology that chance-notwithstanding the shifts in mindset, training and infrastructure investment this demands. Here, we assess opportunities for agricultural synthetic biology and ways to remove barriers to their realization.

H2 Metabolism revealed by metagenomic analysis of subglacial sediment from East Antarctica

Subglacial ecosystems harbor diverse chemoautotrophic microbial communities in areas with limited organic carbon, and lithological H₂ produced during glacial erosion has been considered an important energy source in these ecosystems. To verify the H₂-utilizing potential there and to identify the related energy-converting metabolic mechanisms of these communities, we performed metagenomic analysis on subglacial sediment samples from East Antarctica with and without H₂ supplementation. Genes coding for several [NiFe]-hydrogenases were identified in raw sediment and were enriched after H₂ incubation. All genes in the dissimilatory nitrate reduction and denitrification pathways were detected in the subglacial community, and the genes coding for these pathways became enriched after H₂ was supplied. Similarly, genes transcribing key enzymes in the Calvin cycle were detected in raw sediment and were also enriched. Moreover, key genes involved in H₂ oxidization, nitrate reduction, oxidative phosphorylation, and the Calvin cycle were identified within one metagenome-assembled genome belonging to a Polaromonas sp. As suggested by our results, the microbial community in the subglacial environment we investigated consisted of chemoautotrophic populations supported by H₂ oxidation. These results further confirm the importance of H₂ in the cryosphere.

Renewable methanol and formate as microbial feedstocks

Methanol and formate are attractive microbial feedstocks as they can be sustainably produced from CO₂ and renewable energy, are completely miscible, and are easy to store and transport. Here, we provide a biochemical perspective on microbial growth and bioproduction using these compounds. We show that anaerobic growth of acetogens on methanol and formate is more efficient than on H₂/CO₂ or CO. We analyze the aerobic C₁ assimilation pathways and suggest that new-to-nature routes could outperform their natural counterparts. We further discuss practical bioprocessing aspects related to growth on methanol and formate, including feedstock toxicity. While challenges in realizing sustainable production from methanol and formate still exist, the utilization of these feedstocks paves the way towards a truly circular carbon economy.

Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria)

Most autotrophs use the Calvin–Benson–Bassham (CBB) cycle for carbon fixation. In contrast, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts (“Candidatus Thiobarba”) of deep-sea mussels that have acquired a complete CBB cycle and may have lost most key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB cycle genes suggest they were acquired in multiple transfers from Gammaproteobacteria closely related to sulfur-oxidizing endosymbionts associated with the mussels, as well as from Betaproteobacteria. We hypothesize that “Ca. Thiobarba” switched from the rTCA cycle to a fully functional CBB cycle during its evolution, by acquiring genes from multiple sources, including co-occurring symbionts. We also found key CBB cycle genes in free-living Campylobacterota, suggesting that the CBB cycle may be more widespread in this phylum than previously known. Metatranscriptomics and metaproteomics confirmed high expression of CBB cycle genes in mussel-associated “Ca. Thiobarba”. Direct stable isotope fingerprinting showed that “Ca. Thiobarba” has typical CBB signatures, suggesting that it uses this cycle for carbon fixation. Our discovery calls into question current assumptions about the distribution of carbon fixation pathways in microbial lineages, and the interpretation of stable isotope measurements in the environment.

Core Catalysis of the Reductive Glycine Pathway Demonstrated in Yeast

One-carbon (C1) compounds are attractive microbial feedstocks as they can be efficiently produced from widely available resources. Formate, in particular, represents a promising growth substrate, as it can be generated from electrochemical reduction of CO₂ and fed to microorganisms in a soluble form. We previously identified the synthetic reductive glycine pathway as the most efficient route for aerobic growth on formate. We further demonstrated pathway activity in Escherichia coli after expression of both native and foreign genes. Here, we explore whether the reductive glycine pathway could be established in a model microorganism using only native enzymes. We used the yeast Saccharomyces cerevisiae as host and show that overexpression of only endogenous enzymes enables glycine biosynthesis from formate and CO₂ in a strain that is otherwise auxotrophic for glycine. We find the pathway to be highly active in this host, where 0.125 mM formate is sufficient to support growth. Notably, the formate-dependent growth rate of the engineered S. cerevisiae strain remained roughly constant over a very wide range of formate concentrations, 1–500 mM, indicating both high affinity for formate use and high tolerance toward elevated concentration of this C1 feedstock. Our results, as well the availability of endogenous NAD-dependent formate dehydrogenase, indicate that yeast might be an especially suitable host for engineering growth on formate.

Widespread soil bacterium that oxidizes atmospheric methane

The global atmospheric level of methane (CH4), the second most important greenhouse gas, is currently increasing by ∼10 million tons per year. Microbial oxidation in unsaturated soils is the only known biological process that removes CH4 from the atmosphere, but so far, bacteria that can grow on atmospheric CH4 have eluded all cultivation efforts. In this study, we have isolated a pure culture of a bacterium, strain MG08 that grows on air at atmospheric concentrations of CH4 [1.86 parts per million volume (p.p.m.v.)]. This organism, named Methylocapsa gorgona, is globally distributed in soils and closely related to uncultured members of the upland soil cluster α. CH4 oxidation experiments and 13C-single cell isotope analyses demonstrated that it oxidizes atmospheric CH4 aerobically and assimilates carbon from both CH4 and CO2 Its estimated specific affinity for CH4 (a0s) is the highest for any cultivated methanotroph. However, growth on ambient air was also confirmed for Methylocapsa acidiphila and Methylocapsa aurea, close relatives with a lower specific affinity for CH4, suggesting that the ability to utilize atmospheric CH4 for growth is more widespread than previously believed. The closed genome of M. gorgona MG08 encodes a single particulate methane monooxygenase, the serine cycle for assimilation of carbon from CH4 and CO2, and CO2 fixation via the recently postulated reductive glycine pathway. It also fixes dinitrogen and expresses the genes for a high-affinity hydrogenase and carbon monoxide dehydrogenase, suggesting that atmospheric CH4 oxidizers harvest additional energy from oxidation of the atmospheric trace gases carbon monoxide (0.2 p.p.m.v.) and hydrogen (0.5 p.p.m.v.).

New environmental model for thermodynamic ecology of biological phosphine production

We present a new model for the biological production of phosphine (PH₃). Phosphine is found globally, in trace amounts, in the Earth's atmosphere. It has been suggested as a key molecule in the phosphorus cycle, linking atmospheric, lithospheric and biological phosphorus chemistry. Phosphine's production is strongly associated with marshes, swamps and other sites of anaerobic biology. However the mechanism of phosphine's biological production has remained controversial, because it has been believed that reduction of phosphate to phosphine is endergonic. In this paper we show through thermodynamic calculations that, in specific environments, the combined action of phosphate reducing and phosphite disproportionating bacteria can produce phosphine. Phosphate-reducing bacteria can capture energy from the reduction of phosphate to phosphite through coupling phosphate reduction to NADH oxidation. Our hypothesis describes how the phosphate chemistry in an environmental niche is coupled to phosphite generation in ground water, which in turn is coupled to the phosphine production in water and atmosphere, driven by a specific microbial ecology. Our hypothesis provides clear predictions on specific complex environments where biological phosphine production could be widespread. We propose tests of our hypothesis in fieldwork.

An Oxidative Pathway for Microbial Utilization of Methylphosphonic Acid as a Phosphate Source

Methylphosphonic acid is synthesized by marine bacteria and is a prominent component of dissolved organic phosphorus. Consequently, methylphosphonic acid also serves as a source of inorganic phosphate (Pi) for marine bacteria that are starved of this nutrient. Conversion of methylphosphonic acid into Pi is currently only known to occur through the carbon-phosphorus lyase pathway, yielding methane as a byproduct. In this work, we describe an oxidative pathway for the catabolism of methylphosphonic acid in Gimesia maris DSM8797. G. maris can use methylphosphonic acid as Pi sources despite lacking a phn operon encoding a carbon-phosphorus lyase pathway. Instead, the genome contains a locus encoding homologues of the non-heme Fe(II) dependent oxygenases HF130PhnY* and HF130PhnZ, which were previously shown to convert 2-aminoethylphosphonic acid into glycine and Pi. GmPhnY* and GmPhnZ1 were produced in E. coli and purified for characterization in vitro. The substrate specificities of the enzymes were evaluated with a panel of synthetic phosphonates. Via ³¹P NMR spectroscopy, it is demonstrated that the GmPhnY* converts methylphosphonic acid to hydroxymethylphosphonic acid, which in turn is oxidized by GmPhnZ1 to produce formic acid and Pi. In contrast, 2-aminoethylphosphonic acid is not a substrate for GmPhnY* and is therefore not a substrate for this pathway. These results thus reveal a new metabolic fate for methylphosphonic acid.

Genetic Evidence for Two Carbon Fixation Pathways (the Calvin-Benson-Bassham Cycle and the Reverse Tricarboxylic Acid Cycle) in Symbiotic and Free-Living Bacteria

Primary production on Earth is dependent on autotrophic carbon fixation, which leads to the incorporation of carbon dioxide into biomass. Multiple metabolic pathways have been described for autotrophic carbon fixation, but most autotrophic organisms were assumed to have the genes for only one of these pathways. Our finding of a cultivable bacterium with two carbon fixation pathways in its genome, the rTCA and the CBB cycle, opens the possibility to study the potential benefits of having these two pathways and the interplay between them. Additionally, this will allow the investigation of the unusual and potentially very efficient mechanism of electron flow that could drive the rTCA cycle in these autotrophs. Such studies will deepen our understanding of carbon fixation pathways and could provide new avenues for optimizing carbon fixation in biotechnological applications.

Very few bacteria are able to fix carbon via both the reverse tricarboxylic acid (rTCA) and the Calvin-Benson-Bassham (CBB) cycles, such as symbiotic, sulfur-oxidizing bacteria that are the sole carbon source for the marine tubeworm Riftia pachyptila, the fastest-growing invertebrate. To date, the coexistence of these two carbon fixation pathways had not been found in a cultured bacterium and could thus not be studied in detail. Moreover, it was not clear if these two pathways were encoded in the same symbiont individual, or if two symbiont populations, each with one of the pathways, coexisted within tubeworms. With comparative genomics, we show that Thioflavicoccus mobilis, a cultured, free-living gammaproteobacterial sulfur oxidizer, possesses the genes for both carbon fixation pathways. Here, we also show that both the CBB and rTCA pathways are likely encoded in the genome of the sulfur-oxidizing symbiont of the tubeworm Escarpia laminata from deep-sea asphalt volcanoes in the Gulf of Mexico. Finally, we provide genomic and transcriptomic data suggesting a potential electron flow toward the rTCA cycle carboxylase 2-oxoglutarate:ferredoxin oxidoreductase, via a rare variant of NADH dehydrogenase/heterodisulfide reductase in the E. laminata symbiont. This electron-bifurcating complex, together with NAD(P)⁺ transhydrogenase and Na⁺ translocating Rnf membrane complexes, may improve the efficiency of the rTCA cycle in both the symbiotic and the free-living sulfur oxidizer.

IMPORTANCE Primary production on Earth is dependent on autotrophic carbon fixation, which leads to the incorporation of carbon dioxide into biomass. Multiple metabolic pathways have been described for autotrophic carbon fixation, but most autotrophic organisms were assumed to have the genes for only one of these pathways. Our finding of a cultivable bacterium with two carbon fixation pathways in its genome, the rTCA and the CBB cycle, opens the possibility to study the potential benefits of having these two pathways and the interplay between them. Additionally, this will allow the investigation of the unusual and potentially very efficient mechanism of electron flow that could drive the rTCA cycle in these autotrophs. Such studies will deepen our understanding of carbon fixation pathways and could provide new avenues for optimizing carbon fixation in biotechnological applications.

DNA-Functionalized Nanoceria for Probing Oxidation of Phosphorus Compounds

Chemical reactions without an obvious optical signal change, such as fluorescence or color, are difficult to monitor. Often, more advanced analytical techniques such as high-performance liquid chromatography and mass spectroscopy are needed. It would be useful to convert such reactions to those with changes in optical signals. In this work, we demonstrate that fluorescently labeled DNA oligonucleotides adsorbed on nanomaterials can probe such reactions, and oxidation of phosphorus-containing species was used as an example. Various metal oxides were tested, and CeO2 nanoparticles were found to be the most efficient for this purpose. Among phosphate, phosphite, and hypophosphite, only phosphate produced a large signal, indicating its strongest adsorption on CeO2 to displace the DNA. This was further used to screen oxidation agents to convert lower oxidation-state compounds to phosphate, and bleach was found to be able to oxidize phosphite. Canonical discriminant analysis was performed to discriminate various phosphorus species using a sensor array containing different metal oxides. On the basis of this, glyphosate was studied for its adsorption and oxidation. Although this method is not specific enough for selective biosensors, it is useful as a tool to produce sensitive optical signals to follow important chemical transformations.

A role for phosphorus redox in emerging and modern biochemistry

Phosphorus is a major biogeochemical element controlling growth in many ecosystems. It has presumably been an important element since the onset of life. In most chemical and biochemical considerations, phosphorus is synonymous with phosphates, a pentavalent oxidation state that includes the phosphate backbone of DNA and RNA, as well as major metabolites such as ATP. However, redox processing of phosphates to phosphites and phosphonates, and to even lower oxidation states provides a work-around to many of the problems of prebiotic chemistry, including phosphorus's low solubility and poor reactivity. In addition, modern phosphorus cycling has increasingly identified reduced P compounds as playing a role, sometimes significant, in biogeochemical processes. This suggests that phosphorus is not redox-insensitive and reduced P compounds should be considered as part of the phosphorus biogeochemical cycle.

Assimilation of formic acid and CO2 by engineered Escherichia coli equipped with reconstructed one-carbon assimilation pathways

Gaseous one-carbon (C1) compounds or formic acid (FA) converted from CO2 can be an attractive raw material for bio-based chemicals. Here, we report the development of Escherichia coli strains assimilating FA and CO2 through the reconstructed tetrahydrofolate (THF) cycle and reverse glycine cleavage (gcv) pathway. The Methylobacterium extorquens formate-THF ligase, methenyl-THF cyclohydrolase, and methylene-THF dehydrogenase genes were expressed to allow FA assimilation. The gcv reaction was reversed by knocking out the repressor gene (gcvR) and overexpressing the gcvTHP genes. This engineered strain synthesized 96% and 86% of proteinogenic glycine and serine, respectively, from FA and CO2 in a glucose-containing medium. Native serine deaminase converted serine to pyruvate, showing 4.5% of pyruvate-forming flux comes from FA and CO2 The pyruvate-forming flux from FA and CO2 could be increased to 14.9% by knocking out gcvR, pflB, and serA, chromosomally expressing gcvTHP under trc, and overexpressing the reconstructed THF cycle, gcvTHP, and lpd genes in one vector. To reduce glucose usage required for energy and redox generation, the Candida boidinii formate dehydrogenase (Fdh) gene was expressed. The resulting strain showed specific glucose, FA, and CO2 consumption rates of 370.2, 145.6, and 14.9 mg⋅g dry cell weight (DCW)-1⋅h-1, respectively. The C1 assimilation pathway consumed 21.3 wt% of FA. Furthermore, cells sustained slight growth using only FA and CO2 after glucose depletion, suggesting that combined use of the C1 assimilation pathway and C. boidinii Fdh will be useful for eventually developing a strain capable of utilizing FA and CO2 without an additional carbon source such as glucose.

In Vivo Assimilation of One-Carbon via a Synthetic Reductive Glycine Pathway in Escherichia coli

Assimilation of one-carbon compounds presents a key biochemical challenge that limits their use as sustainable feedstocks for microbial growth and production. The reductive glycine pathway is a synthetic metabolic route that could provide an optimal way for the aerobic assimilation of reduced C1 compounds. Here, we show that a rational integration of native and foreign enzymes enables the tetrahydrofolate and glycine cleavage/synthase systems to operate in the reductive direction, such that Escherichia coli satisfies all of its glycine and serine requirements from the assimilation of formate and CO₂. Importantly, the biosynthesis of serine from formate and CO₂ does not lower the growth rate, indicating high flux that is able to provide 10% of cellular carbon. Our findings assert that the reductive glycine pathway could support highly efficient aerobic assimilation of C1-feedstocks.