A primordial and reversible TCA cycle in a facultatively chemolithoautotrophic thermophile

Natural carbon fixation and advances in synthetic engineering for redesigning and creating new fixation pathways

BACKGROUND

Autotrophic carbon fixation is the primary route through which organic carbon enters the biosphere, and it is a key step in the biogeochemical carbon cycle. The Calvin-Benson-Bassham pathway, which is predominantly found in plants, algae, and some bacteria (mainly cyanobacteria), was previously considered to be the sole carbon-fixation pathway. However, the discovery of a new carbon-fixation pathway in sulfurous green bacteria almost two decades ago encouraged further research on previously overlooked ancient carbon-fixation pathways in taxonomically and phylogenetically distinct microorganisms.

AIM OF REVIEW

In this review, we summarize the six known natural carbon-fixation pathways and outline the newly proposed additions to this list. We also discuss the recent achievements in synthetic carbon fixation and the importance of the metabolism of thermophilic microorganisms in this field.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Currently, at least six carbon-fixation routes have been confirmed in Bacteria and Archaea. Other possible candidate routes have also been suggested on the basis of emerging "omics" data analyses, expanding our knowledge and stimulating discussions on the importance of these pathways in the way organisms acquire carbon. Notably, the currently known natural fixation routes cannot balance the excessive anthropogenic carbon emissions in a highly unbalanced global carbon cycle. Therefore, significant efforts have also been made to improve the existing carbon-fixation pathways and/or design new efficient in vitro and in vivo synthetic pathways.

Turning around Cycles: An Approach Based on Selected Problems/Cases to Stimulate Collaborative Learning about Krebs and His Four Metabolic Cycles

Metabolism is a challenging subject for bioscience students due to the intrinsic complexity of the metabolic network, as well as that of the overlapping mechanisms of metabolic regulation. Collaborative learning based on a problem-based learning approach can help students to successfully learn and understand metabolism. In the present article, we propose a selection of exercises, problems, and cases aimed to focus students' attention on the scientific work made by Sir Hans Krebs and his collaborators to elucidate four main metabolic cycles, as well as on the study of these cycles, their regulation, and their metabolic integration. The objectives, the tools, and the implementation of this proposal are described, and the results obtained during its first implementation with volunteer students enrolled in two courses on metabolic regulation at our university are presented and discussed. These volunteer students signed a learning contract and were randomly distributed in small groups (3-4 students each). Application of this collaborative learning activity to our classrooms has been very satisfactory, as evidenced by an improvement in the volunteers' academic performance and a very positive perception by most of them, who declared to be "very satisfied" or "satisfied" with their experience and felt that they had learned more.

Culturable Bacterial Diversity from the Basaltic Subsurface of the Young Volcanic Island of Surtsey, Iceland

The oceanic crust is the world's largest and least explored biosphere on Earth. The basaltic subsurface of Surtsey island in Iceland represents an analog of the warm and newly formed-oceanic crust and offers a great opportunity for discovering novel microorganisms. In this study, we collected borehole fluids, drill cores, and fumarole samples to evaluate the culturable bacterial diversity from the subsurface of the island. Enrichment cultures were performed using different conditions, media and temperatures. A total of 195 bacterial isolates were successfully cultivated, purified, and identified based on MALDI-TOF MS analysis and by 16S rRNA gene sequencing. Six different clades belonging to Firmicutes (40%), Gammaproteobacteria (28.7%), Actinobacteriota (22%), Bacteroidota (4.1%), Alphaproteobacteria (3%), and Deinococcota (2%) were identified. Bacillus (13.3%) was the major genus, followed by Geobacillus (12.33%), Enterobacter (9.23%), Pseudomonas (6.15%), and Halomonas (5.64%). More than 13% of the cultured strains potentially represent novel species based on partial 16S rRNA gene sequences. Phylogenetic analyses revealed that the isolated strains were closely related to species previously detected in soil, seawater, and hydrothermal active sites. The 16S rRNA gene sequences of the strains were aligned against Amplicon Sequence Variants (ASVs) from the previously published 16S rRNA gene amplicon sequence datasets obtained from the same samples. Compared with the culture-independent community composition, only 5 out of 49 phyla were cultivated. However, those five phyla accounted for more than 80% of the ASVs. Only 121 out of a total of 5642 distinct ASVs were culturable (≥98.65% sequence similarity), representing less than 2.15% of the ASVs detected in the amplicon dataset. Here, we support that the subsurface of Surtsey volcano hosts diverse and active microbial communities and that both culture-dependent and -independent methods are essential to improving our insight into such an extreme and complex volcanic environment.

Genomic and transcriptomic dissection of Theionarchaea in marine ecosystem

Theionarchaea is a recently described archaeal class within the Euryarchaeota. While it is widely distributed in sediment ecosystems, little is known about its metabolic potential and ecological features. Here, we used metagenomics and metatranscriptomics to characterize 12 theionarchaeal metagenome-assembled genomes, which were further divided into two subgroups, from coastal mangrove sediments of China and seawater columns of the Yap Trench. Genomic analysis revealed that apart from the canonical sulfhydrogenase, Theionarchaea harbor genes encoding heliorhodopsin, group 4 [NiFe]-hydrogenase, and flagellin, in which genes for heliorhodopsin and group 4 [NiFe]-hydrogenase were transcribed in mangrove sediment. Further, the theionarchaeal substrate spectrum may be broader than previously reported as revealed by metagenomics and metatranscriptomics, and the potential carbon substrates include detrital proteins, hemicellulose, ethanol, and CO2. The genes for organic substrate metabolism (mainly detrital protein and amino acid metabolism genes) have relatively higher transcripts in the top sediment layers in mangrove wetlands. In addition, co-occurrence analysis suggested that the degradation of these organic compounds by Theionarchaea might be processed in syntrophy with fermenters (e.g., Chloroflexi) and methanogens. Collectively, these observations expand the current knowledge of the metabolic potential of Theionarchaea, and shed light on the metabolic strategies and roles of these archaea in the marine ecosystems.

Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation

Although there is now an extensive understanding of the diversity of microbial life on earth through culture-independent metagenomic DNA sequence analyses, the isolation and cultivation of microbes remains critical to directly study them and confirm their metabolic and physiological functions, and their ecological roles. The majority of environmental microbes are as yet uncultured however; therefore, bringing these rare or poorly characterized groups into culture is a priority to further understand microbiome functions. Moreover, cultivated isolates may find utility in a range of applications, such as new probiotics, biocontrol agents, and agents for industrial processes. The growing abundance of metagenomic and meta-transcriptomic sequence information from a wide range of environments provides more opportunities to guide the isolation and cultivation of microbes of interest. In this paper, we discuss a range of successful methodologies and applications that have underpinned recent metagenome-guided isolation and cultivation of microbe efforts. These approaches include determining specific culture conditions to enrich for taxa of interest, to more complex strategies that specifically target the capture of microbial species through antibody engineering and genome editing strategies. With the greater degree of genomic information now available from uncultivated members, such as via metagenome-assembled genomes, the theoretical understanding of their cultivation requirements will enable greater possibilities to capture these and ultimately gain a more comprehensive understanding of the microbiomes. Video Abstract.

Into the darkness: the ecologies of novel 'microbial dark matter' phyla in an Antarctic lake

Uncultivated microbial clades ('microbial dark matter') are inferred to play important but uncharacterized roles in nutrient cycling. Using Antarctic lake (Ace Lake, Vestfold Hills) metagenomes, 12 metagenome-assembled genomes (MAGs; 88%-100% complete) were generated for four 'dark matter' phyla: six MAGs from Candidatus Auribacterota (=Aureabacteria, SURF-CP-2), inferred to be hydrogen- and sulfide-producing fermentative heterotrophs, with individual MAGs encoding bacterial microcompartments (BMCs), gas vesicles, and type IV pili; one MAG (100% complete) from Candidatus Hinthialibacterota (=OLB16), inferred to be a facultative anaerobe capable of dissimilatory nitrate reduction to ammonia, specialized for mineralization of complex organic matter (e.g. sulfated polysaccharides), and encoding BMCs, flagella, and Tad pili; three MAGs from Candidatus Electryoneota (=AABM5-125-24), previously reported to include facultative anaerobes capable of dissimilatory sulfate reduction, and here inferred to perform sulfite oxidation, reverse tricarboxylic acid cycle for autotrophy, and possess numerous proteolytic enzymes; two MAGs from Candidatus Lernaellota (=FEN-1099), inferred to be capable of formate oxidation, amino acid fermentation, and possess numerous enzymes for protein and polysaccharide degradation. The presence of 16S rRNA gene sequences in public metagenome datasets (88%-100% identity) suggests these 'dark matter' phyla contribute to sulfur cycling, degradation of complex organic matter, ammonification and/or chemolithoautotrophic CO2 fixation in diverse global environments.

Promotion of Carbon Dioxide Biofixation through Metabolic and Enzyme Engineering

Carbon dioxide is a major greenhouse gas, and its fixation and transformation are receiving increasing attention. Biofixation of CO2 is an eco–friendly and efficient way to reduce CO2, and six natural CO2 fixation pathways have been identified in microorganisms and plants. In this review, the six pathways along with the most recent identified variant pathway were firstly comparatively characterized. The key metabolic process and enzymes of the CO2 fixation pathways were also summarized. Next, the enzymes of Rubiscos, biotin-dependent carboxylases, CO dehydrogenase/acetyl-CoA synthase, and 2-oxoacid:ferredoxin oxidoreductases, for transforming inorganic carbon (CO2, CO, and bicarbonate) to organic chemicals, were specially analyzed. Then, the factors including enzyme properties, CO2 concentrating, energy, and reducing power requirements that affect the efficiency of CO2 fixation were discussed. Recent progress in improving CO2 fixation through enzyme and metabolic engineering was then summarized. The artificial CO2 fixation pathways with thermodynamical and/or energetical advantages or benefits and their applications in biosynthesis were included as well. The challenges and prospects of CO2 biofixation and conversion are discussed.

Tracking the Reversed Oxidative Tricarboxylic Acid Cycle in Bacteria

Different pathways for autotrophic CO₂ fixation can be recognized by the presence of genes for their specific key enzymes. On this basis, (meta)genomic, (meta)transcriptomic, or (meta)proteomic analysis enables the identification of the role of an organism or a distinct pathway in primary production. However, the recently discovered variant of the reductive tricarboxylic acid (rTCA) cycle, the reverse oxidative tricarboxylic acid (roTCA) cycle, lacks unique enzymes, a feature that makes it cryptic for bioinformatics analysis. This pathway is a reversal of the widespread tricarboxylic acid (TCA) cycle. The functioning of the roTCA cycle requires unusually high activity of citrate synthase, the enzyme responsible for citrate cleavage, as well as elevated CO₂ partial pressures. Here, we present a detailed description of the protocol we used for the identification of the roTCA cycle in members of Desulfurellaceae. First, we describe the anaerobic cultivation of Desulfurellaceae at different CO₂ concentrations with a method that can be adapted to the cultivation of other anaerobes. Then, we explain how to measure activities of enzymes responsible for citrate cleavage, malate dehydrogenase reaction, and the crucial carboxylation step of the cycle catalyzed by pyruvate synthase in cell extracts. In conclusion, we describe stable isotope experiments that allow tracking of the roTCA cycle in vivo, through the position-specific incorporation of carbon-13 into amino acids. The label is provided to the organism as ¹³CO₂ or [1-¹³C]glutamate. The same key methodology can be used for the reliable evaluation of the functioning of the roTCA cycle in any organism under study. This pathway is likely to participate, completely unseen, in the metabolism of various microorganisms. Graphic abstract.

Cyanide as a primordial reductant enables a protometabolic reductive glyoxylate pathway

Investigation of prebiotic metabolic pathways is predominantly based on abiotically replicating the reductive citric acid cycle. While attractive from a parsimony point of view, attempts using metal/mineral-mediated reductions have produced complex mixtures with inefficient and uncontrolled reactions. Here we show that cyanide acts as a mild and efficient reducing agent mediating abiotic transformations of tricarboxylic acid intermediates and derivatives. The hydrolysis of the cyanide adducts followed by their decarboxylation enables the reduction of oxaloacetate to malate and of fumarate to succinate, whereas pyruvate and α-ketoglutarate themselves are not reduced. In the presence of glyoxylate, malonate and malononitrile, alternative pathways emerge that bypass the challenging reductive carboxylation steps to produce metabolic intermediates and compounds found in meteorites. These results suggest a simpler prebiotic forerunner of today's metabolism, involving a reductive glyoxylate pathway without oxaloacetate and α-ketoglutarate-implying that the extant metabolic reductive carboxylation chemistries are an evolutionary invention mediated by complex metalloproteins.

Microorganisms harbor keys to a circular bioeconomy making them useful tools in fighting plastic pollution and rising CO2 levels

The major global and man-made challenges of our time are the fossil fuel-driven climate change a global plastic pollution and rapidly emerging plant, human and animal infections. To meet the necessary global changes, a dramatic transformation must take place in science and society. This transformation will involve very intense and forward oriented industrial and basic research strongly focusing on (bio)technology and industrial bioprocesses developments towards engineering a zero-carbon sustainable bioeconomy. Within this transition microorganisms-and especially extremophiles-will play a significant and global role as technology drivers. They harbor the keys and blueprints to a sustainable biotechnology in their genomes. Within this article, we outline urgent and important areas of microbial research and technology advancements and that will ultimately make major contributions during the transition from a linear towards a circular bioeconomy.

Improvement of glycine biosynthesis from one-carbon compounds and ammonia catalyzed by the glycine cleavage system in vitro

Glycine cleavage system (GCS) plays a central role in one-carbon (C1) metabolism and receives increasing interest as a core part of the recently proposed reductive glycine pathway (rGlyP) for assimilation of CO2 and formate. Despite decades of research, GCS has not yet been well understood and kinetic data are barely available. This is to a large degree because of the complexity of GCS, which is composed of four proteins (H, T, P, and L) and catalyzes reactions involving different substrates and cofactors. In vitro kinetics of reconstructed microbial multi-enzyme glycine cleavage/synthase system is desired to better implement rGlyP in microorganisms like Escherichia coli for the use of C1 resources. Here, we examined in vitro several factors that may affect the rate of glycine synthesis via the reverse GCS reaction. We found that the ratio of GCS component proteins has a direct influence on the rate of glycine synthesis, namely higher ratios of P protein and especially H protein to T and L proteins are favorable, and the carboxylation reaction catalyzed by P protein is a key step determining the glycine synthesis rate, whereas increasing the ratio of L protein to other GCS proteins does not have significant effect and the ratio of T protein to other GCS proteins should be kept low. The effect of substrate concentrations on glycine synthesis is quite complex, showing interdependence with the ratios of GCS component proteins. Furthermore, adding the reducing agent dithiothreitol to the reaction mixture not only results in great tolerance to high concentration of formaldehyde, but also increases the rate of glycine synthesis, probably due to its functions in activating P protein and taking up the role of L protein in the non-enzymatic reduction of Hox to Hred. Moreover, the presence of some monovalent and divalent metal ions can have either positive or negative effect on the rate of glycine synthesis, depending on their type and their concentration.

Emerging Role of TCA Cycle-Related Enzymes in Human Diseases

The tricarboxylic acid (TCA) cycle is the main source of cellular energy and participates in many metabolic pathways in cells. Recent reports indicate that dysfunction of TCA cycle-related enzymes causes human diseases, such as neurometabolic disorders and tumors, have attracted increasing interest in their unexplained roles. The diseases which develop as a consequence of loss or dysfunction of TCA cycle-related enzymes are distinct, suggesting that each enzyme has a unique function. This review aims to provide a comprehensive overview of the relationship between each TCA cycle-related enzyme and human diseases. We also discuss their functions in the context of both mitochondrial and extra-mitochondrial (or cytoplasmic) enzymes.

Optical/electrochemical methods for detecting mitochondrial energy metabolism

This review highlights the biological importance of mitochondrial energy metabolism and the applications of multiple optical/electrochemical approaches to determine energy metabolites. Mitochondria, the main sites of oxidative phosphorylation and adenosine triphosphate (ATP) biosynthesis, provide the majority of energy required by aerobic cells for maintaining their physiological activity. They also participate in cell growth, differentiation, information transmission, and apoptosis. Multiple mitochondrial diseases, caused by internal or external factors, including oxidative stress, intense fluctuations of the ionic concentration, abnormal oxidative phosphorylation, changes in electron transport chain complex enzymes and mutations in mitochondrial DNA, can occur during mitochondrial energy metabolism. Therefore, developing accurate, sensitive, and specific methods for the in vivo and in vitro detection of mitochondrial energy metabolites is of great importance. In this review, we summarise the mitochondrial structure, functions, and crucial energy metabolic signalling pathways. The mechanism and applications of different optical/electrochemical methods are thoroughly reviewed. Finally, future research directions and challenges are proposed.

The existence of a nonclassical TCA cycle in the nucleus that wires the metabolic-epigenetic circuitry

The scope and variety of the metabolic intermediates from the mitochondrial tricarboxylic acid (TCA) cycle that are engaged in epigenetic regulation of the chromatin function in the nucleus raise an outstanding question about how timely and precise supply/consumption of these metabolites is achieved in the nucleus. We report here the identification of a nonclassical TCA cycle in the nucleus (nTCA cycle). We found that all the TCA cycle-associated enzymes including citrate synthase (CS), aconitase 2 (ACO2), isocitrate dehydrogenase 3 (IDH3), oxoglutarate dehydrogenase (OGDH), succinyl-CoA synthetase (SCS), fumarate hydratase (FH), and malate dehydrogenase 2 (MDH2), except for succinate dehydrogenase (SDH), a component of electron transport chain for generating ATP, exist in the nucleus. We showed that these nuclear enzymes catalyze an incomplete TCA cycle similar to that found in cyanobacteria. We propose that the nTCA cycle is implemented mainly to generate/consume metabolic intermediates, not for energy production. We demonstrated that the nTCA cycle is intrinsically linked to chromatin dynamics and transcription regulation. Together, our study uncovers the existence of a nonclassical TCA cycle in the nucleus that links the metabolic pathway to epigenetic regulation.

Evolution of glutamatergic signaling and synapses

Glutamate (Glu) is the primary excitatory transmitter in the mammalian brain. But, we know little about the evolutionary history of this adaptation, including the selection of l-glutamate as a signaling molecule in the first place. Here, we used comparative metabolomics and genomic data to reconstruct the genealogy of glutamatergic signaling. The origin of Glu-mediated communications might be traced to primordial nitrogen and carbon metabolic pathways. The versatile chemistry of L-Glu placed this molecule at the crossroad of cellular biochemistry as one of the most abundant metabolites. From there, innovations multiplied. Many stress factors or injuries could increase extracellular glutamate concentration, which led to the development of modular molecular systems for its rapid sensing in bacteria and archaea. More than 20 evolutionarily distinct families of ionotropic glutamate receptors (iGluRs) have been identified in eukaryotes. The domain compositions of iGluRs correlate with the origins of multicellularity in eukaryotes. Although L-Glu was recruited as a neuro-muscular transmitter in the early-branching metazoans, it was predominantly a non-neuronal messenger, with a possibility that glutamatergic synapses evolved more than once. Furthermore, the molecular secretory complexity of glutamatergic synapses in invertebrates (e.g., Aplysia) can exceed their vertebrate counterparts. Comparative genomics also revealed 15+ subfamilies of iGluRs across Metazoa. However, most of this ancestral diversity had been lost in the vertebrate lineage, preserving AMPA, Kainate, Delta, and NMDA receptors. The widespread expansion of glutamate synapses in the cortical areas might be associated with the enhanced metabolic demands of the complex brain and compartmentalization of Glu signaling within modular neuronal ensembles.

Kinetics of the ancestral carbon metabolism pathways in deep-branching bacteria and archaea

The origin of life is believed to be chemoautotrophic, deriving all biomass components from carbon dioxide, and all energy from inorganic redox couples in the environment. The reductive tricarboxylic acid cycle (rTCA) and the Wood-Ljungdahl pathway (WL) have been recognized as the most ancient carbon fixation pathways. The rTCA of the chemolithotrophic Thermosulfidibacter takaii, which was recently demonstrated to take place via an unexpected reverse reaction of citrate synthase, was reproduced using a kinetic network model, and a competition between reductive and oxidative fluxes on rTCA due to an acetyl coenzyme A (ACOA) influx upon acetate uptake was revealed. Avoiding ACOA direct influx into rTCA from WL is, therefore, raised as a kinetically necessary condition to maintain a complete rTCA. This hypothesis was confirmed for deep-branching bacteria and archaea, and explains the kinetic factors governing elementary processes in carbon metabolism evolution from the last universal common ancestor.

Microbial diversity in tropical marine sediments assessed using culture-dependent and culture-independent techniques

The microbial communities associated with marine sediments are critical for ecosystem function yet remain poorly characterized. While culture-independent (CI) techniques capture the broadest perspective on community composition, culture-dependent (CD) methods can select for low abundance taxa that are missed using CI approaches. This study aimed to assess microbial diversity in tropical marine sediments at five shallow-water sites in Belize using both CD and CI techniques. The CD methods captured approximately 3% of the >800 genera detected across all sites using the CI approach. Additionally, 39 genera were only detected in culture, revealing rare taxa that were missed with the CI approach. Significantly different communities were detected across sites, with rare taxa playing an important role in distinguishing among communities. This study provides important baseline data describing shallow-water sediment microbial communities, evidence that standard cultivation techniques may be more effective than previously recognized, and the first steps towards identifying new taxa that are amenable to agar plate cultivation.

Chemical Basis of Carbon Fixation Autotrophic Paleometabolism

Abstract

On the basis of biomimetic, phylometabolic, and thermodynamic analysis of modern CO2 assimilation pathways, a paleophenotypic reconstruction of ancient autotrophic metabolism systems was carried out. As a chemical basis for CO2 fixation paleometabolism, metabolic networks capable of self-reproduction and evolution are considered, and the reversibility of the transformation reactions of its intermediates is the most important factor in self-development of this network. The substances of the C–H–O system, paragenetically associated with hydrocarbons, create a phase space, which is a set of universal intermediates of the autotrophic paleometabolism chemical network. The concept of two strategies for the origin and development of autotrophic carbon fixation paleometabolism in the oxidized (CO2) and reduced (CH4) redox regimes of degassing of the ancient Earth is proposed. It was shown that P, T, and the redox conditions of hydrothermal systems of the early Archean were favorable for the development of primary methanotrophic metabolism.

Diversity and Metabolic Potential of the Terrestrial Mud Volcano Microbial Community with a High Abundance of Archaea Mediating the Anaerobic Oxidation of Methane

Terrestrial mud volcanoes (TMVs) are important natural sources of methane emission. The microorganisms inhabiting these environments remain largely unknown. We studied the phylogenetic composition and metabolic potential of the prokaryotic communities of TMVs located in the Taman Peninsula, Russia, using a metagenomic approach. One of the examined sites harbored a unique community with a high abundance of anaerobic methane-oxidizing archaea belonging to ANME-3 group (39% of all 16S rRNA gene reads). The high number of ANME-3 archaea was confirmed by qPCR, while the process of anaerobic methane oxidation was demonstrated by radioisotopic experiments. We recovered metagenome-assembled genomes (MAGs) of archaeal and bacterial community members and analyzed their metabolic capabilities. The ANME-3 MAG contained a complete set of genes for methanogenesis as well as of ribosomal RNA and did not encode proteins involved in dissimilatory nitrate or sulfate reduction. The presence of multiheme c-type cytochromes suggests that ANME-3 can couple methane oxidation with the reduction of metal oxides or with the interspecies electron transfer to a bacterial partner. The bacterial members of the community were mainly represented by autotrophic, nitrate-reducing, sulfur-oxidizing bacteria, as well as by fermentative microorganisms. This study extends the current knowledge of the phylogenetic and metabolic diversity of prokaryotes in TMVs and provides a first insight into the genomic features of ANME-3 archaea.

Candidatus Eremiobacterota, a metabolically and phylogenetically diverse terrestrial phylum with acid-tolerant adaptations

Candidatus phylum Eremiobacterota (formerly WPS-2) is an as-yet-uncultured bacterial clade that takes its name from Ca. Eremiobacter, an Antarctic soil aerobe proposed to be capable of a novel form of chemolithoautotrophy termed atmospheric chemosynthesis, that uses the energy derived from atmospheric H₂-oxidation to fix CO₂ through the Calvin-Benson-Bassham (CBB) cycle via type 1E RuBisCO. To elucidate the phylogenetic affiliation and metabolic capacities of Ca. Eremiobacterota, we analysed 63 public metagenome-assembled genomes (MAGs) and nine new MAGs generated from Antarctic soil metagenomes. These MAGs represent both recognized classes within Ca. Eremiobacterota, namely Ca. Eremiobacteria and UBP9. Ca. Eremiobacteria are inferred to be facultatively acidophilic with a preference for peptides and amino acids as nutrient sources. Epifluorescence microscopy revealed Ca. Eremiobacteria cells from Antarctica desert soil to be coccoid in shape. Two orders are recognized within class Ca. Eremiobacteria: Ca. Eremiobacterales and Ca. Baltobacterales. The latter are metabolically versatile, with individual members having genes required for trace gas driven autotrophy, anoxygenic photosynthesis, CO oxidation, and anaerobic respiration. UBP9, here renamed Ca. Xenobia class. nov., are inferred to be obligate heterotrophs with acidophilic adaptations, but individual members having highly divergent metabolic capacities compared to Ca. Eremiobacteria, especially with regard to respiration and central carbon metabolism. We conclude Ca. Eremiobacterota to be an ecologically versatile phylum with the potential to thrive under an array of "extreme" environmental conditions.

Cooccurring Activities of Two Autotrophic Pathways in Symbionts of the Hydrothermal Vent Tubeworm Riftia pachyptila

Genome and proteome data predict the presence of both the reductive citric acid cycle (rCAC; also called the reductive tricarboxylic acid cycle) and the Calvin-Benson-Bassham cycle (CBB) in "Candidatus Endoriftia persephonae," the autotrophic sulfur-oxidizing bacterial endosymbiont from the giant hydrothermal vent tubeworm Riftia pachyptila. We tested whether these cycles were differentially induced by sulfide supply, since the synthesis of biosynthetic intermediates by the rCAC is less energetically expensive than that by the CBB. R. pachyptila was incubated under in situ conditions in high-pressure aquaria under low (28 to 40 μmol · h^-1) or high (180 to 276 μmol · h^-1) rates of sulfide supply. Symbiont-bearing trophosome samples excised from R. pachyptila maintained under the two conditions were capable of similar rates of CO₂ fixation. Activities of the rCAC enzyme ATP-dependent citrate lyase (ACL) and the CBB enzyme 1,3-bisphosphate carboxylase/oxygenase (RubisCO) did not differ between the two conditions, although transcript abundances for ATP-dependent citrate lyase were 4- to 5-fold higher under low-sulfide conditions. δ¹³C values of internal dissolved inorganic carbon (DIC) pools were varied and did not correlate with sulfide supply rate. In samples taken from freshly collected R. pachyptila, δ¹³C values of lipids fell between those collected for organisms using either the rCAC or the CBB exclusively. These observations are consistent with cooccurring activities of the rCAC and the CBB in this symbiosis. IMPORTANCE Previous to this study, the activities of the rCAC and CBB in R. pachyptila had largely been inferred from "omics" studies of R. pachyptila without direct assessment of in situ conditions prior to collection. In this study, R. pachyptila was maintained and monitored in high-pressure aquaria prior to measuring its CO₂ fixation parameters. Results suggest that ranges in sulfide concentrations similar to those experienced in situ do not exert a strong influence on the relative activities of the rCAC and the CBB. This observation highlights the importance of further study of this symbiosis and other organisms with multiple CO₂-fixing pathways, which recent genomics and biochemical studies suggest are likely to be more prevalent than anticipated.

Pseudodesulfovibrio alkaliphilus, sp. nov., an alkaliphilic sulfate-reducing bacterium isolated from a terrestrial mud volcano

The diversity of anaerobic microorganisms in terrestrial mud volcanoes is largely unexplored. Here we report the isolation of a novel sulfate-reducing alkaliphilic bacterium (strain F-1^T) from a terrestrial mud volcano located at the Taman peninsula, Russia. Cells of strain F-1^T were Gram-negative motile vibrios with a single polar flagellum; 2.0-4.0 µm in length and 0.5 µm in diameter. The temperature range for growth was 6-37 °C, with an optimum at 24 °C. The pH range for growth was 7.0-10.5, with an optimum at pH 9.5. Strain F-1^T utilized lactate, pyruvate, and molecular hydrogen as electron donors and sulfate, sulfite, thiosulfate, elemental sulfur, fumarate or arsenate as electron acceptors. In the presence of sulfate, the end products of lactate oxidation were acetate, H₂S and CO_2. Lactate and pyruvate could also be fermented. The major product of lactate fermentation was acetate. The main cellular fatty acids were anteiso-C_15:0, C_16:0, C_18:0, and iso-C_17:1ω8. Phylogenetic analysis revealed that strain F-1^T was most closely related to Pseudodesulfovibrio aespoeensis (98.05% similarity). The total size of the genome of the novel isolate was 3.23 Mb and the genomic DNA G + C content was 61.93 mol%. The genome contained all genes essential for dissimilatory sulfate reduction. We propose to assign strain F-1^T to the genus Pseudodesulfovibrio, as a new species, Pseudodesulfovibrio alkaliphilus sp. nov. The type strain is F-1^T (= KCTC 15918^T = VKM B-3405^T).

Biochemical unity revisited: microbial central carbon metabolism holds new discoveries, multi-tasking pathways, and redundancies with a reason

For a long time, our understanding of metabolism has been dominated by the idea of biochemical unity, i.e., that the central reaction sequences in metabolism are universally conserved between all forms of life. However, biochemical research in the last decades has revealed a surprising diversity in the central carbon metabolism of different microorganisms. Here, we will embrace this biochemical diversity and explain how genetic redundancy and functional degeneracy cause the diversity observed in central metabolic pathways, such as glycolysis, autotrophic CO2 fixation, and acetyl-CoA assimilation. We conclude that this diversity is not the exception, but rather the standard in microbiology.

Growth Enhancement Facilitated by Gaseous CO2 through Heterologous Expression of Reductive Tricarboxylic Acid Cycle Genes in Escherichia coli

The enzymatic mechanisms of carbon fixation by autotrophs, such as the reductive tricarboxylic acid cycle (rTCA), have inspired biotechnological approaches to producing bio-based chemicals directly through CO2. To explore the possibility of constructing an rTCA cycle in Escherichia coli and to investigate their potential for CO2 assimilation, a total of ten genes encoding the key rTCA cycle enzymes, including α-ketoglutarate:ferredoxin oxidoreductase, ATP-dependent citrate lyase, and fumarate reductase/succinate dehydrogenase, were cloned into E. coli. The transgenic E. coli strain exhibited enhanced growth and the ability to assimilate external inorganic carbon with a gaseous CO2 supply. Further experiments conducted in sugar-free medium containing hydrogen as the electron donor and dimethyl sulfoxide (DMSO) as the electron acceptor proved that the strain is able to undergo anaerobic respiration, using CO2 as the major carbon source. The transgenic stain demonstrated CO2-enhanced growth, whereas the genes involved in chemotaxis, flagellar assembly, and acid-resistance were upregulated under the anaerobic respiration. Furthermore, metabolomic analysis demonstrated that the total concentrations of ATP, ADP, and AMP in the transgenic strain were higher than those in the vector control strain and these results coincided with the enhanced growth. Our approach offers a novel strategy to engineer E. coli for assimilating external gaseous CO2.

Evolutionary History of Plant Metabolism

Tremendous chemical diversity is the hallmark of plants and is supported by highly complex biochemical machinery. Plant metabolic enzymes originated and were transferred from eukaryotic and prokaryotic ancestors and further diversified by the unprecedented rates of gene duplication and functionalization experienced in land plants. Unlike microbes, which have frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO₂ and have experienced very few, if any, gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner and on existing networks under various evolutionary constraints. This review aims to take a broader view of plant metabolic evolution and lay a framework to further explore evolutionary mechanisms of the complex metabolic network. Understanding the underlying metabolic and genetic constraints is also an empirical prerequisite for rational engineering and redesigning of plant metabolic pathways.

New technologies for developing phage-based tools to manipulate the human microbiome

Gut bacteria play an essential role in the human body by regulating multiple functions, producing essential metabolites, protecting against pathogen invasion, and much more. Conversely, changes in their community structure are linked to several gastrointestinal (GI) and non-GI conditions. Fortunately, these bacteria are amenable to external perturbations, but we need specific tools for their safe manipulation as nonspecific changes can cause unpredicted long-term consequences. Here, we mainly discuss recent advances in cultivation-independent technologies and argue their relevance to different key steps, that is, identifying the modulation targets and developing phage-based tools to precisely modulate gut bacteria and restore a sustainable microbiome in humans. We finally suggest multiple modulating strategies for different dysbiosis-associated diseases.

A rooted phylogeny resolves early bacterial evolution

A rooted bacterial tree is necessary to understand early evolution, but the position of the root is contested. Here, we model the evolution of 11,272 gene families to identify the root, extent of horizontal gene transfer (HGT), and the nature of the last bacterial common ancestor (LBCA). Our analyses root the tree between the major clades Terrabacteria and Gracilicutes and suggest that LBCA was a free-living flagellated, rod-shaped double-membraned organism. Contrary to recent proposals, our analyses reject a basal placement of the Candidate Phyla Radiation, which instead branches sister to Chloroflexota within Terrabacteria. While most gene families (92%) have evidence of HGT, overall, two-thirds of gene transmissions have been vertical, suggesting that a rooted tree provides a meaningful frame of reference for interpreting bacterial evolution.

Minerals Determined a Special Ecological Niche and Selectively Enriched Microbial Species from Bulk Water Communities in Hot Springs

Minerals provide physical niches and supply nutrients or serve as electron donors/acceptors for microorganism survival and growth, and thus minerals and microbes co-evolved. Yet, little is known about how sediment minerals impact microbial community assembly in hot springs and to what extent mineralogical composition influences microbial community composition and diversity. Here the influences of minerals on thermophiles in Tengchong hot springs were revealed by network analysis of field samples, as well as in-situ microcosm experiments with minerals. A molecular ecological network was constructed based on high throughput sequencing data of 16S rRNA gene, with a combination of water geochemistry and sedimentary mineralogical compositions. Six modules were identified and this highly modular network structure represents the microbial preference to different abiotic factors, consequently resulting in niche partitioning in sedimentary communities in hot springs. Diverse mineralogical compositions generated special niches for microbial species. Subsequently, the in-situ microcosm experiments with four minerals (aragonite, albite, K-feldspar, and quartz) and spring water were conducted in a silicate-hosted alkaline spring (i.e., Gmq) and a carbonate-hosted neutral hot spring (i.e., Gxs) for 70 days. Different microbial preferences were observed among different mineral types (carbonate versus silicate). Aragonite microcosms in Gmq spring enriched archaeal genera Sulfophobococcus and Aeropyrum within the order Desulfurococcales by comparison with both in-situ water and silicate microcosms. Sulfophobococcus was also accumulated in Gxs aragonite microcosms, but the contribution to overall dissimilarity is much lower than that in Gmq spring. Besides, Caldimicrobium was a bacterial genus enriched in Gxs aragonite microcosms, in contrast to in-situ water and silicate microcosms, whereas Candidatus Kryptobacter and Thermus were more abundant in silicate microcosms. The differences in microbial accumulations among different mineral types in the same spring implied that mineral chemistry may exert extra deterministic selective pressure in drawing certain species from the bulk water communities, in addition to stochastic absorption on mineral surface. Taken together, our results highlight the special niche partitioning determined by mineralogical compositions and further confirm that minerals could be used as “fishing bait” to enrich certain rare microbial species.

Microorganisms from deep-sea hydrothermal vents

With a rich variety of chemical energy sources and steep physical and chemical gradients, hydrothermal vent systems offer a range of habitats to support microbial life. Cultivation-dependent and independent studies have led to an emerging view that diverse microorganisms in deep-sea hydrothermal vents live their chemolithoautotrophic, heterotrophic, or mixotrophic life with versatile metabolic strategies. Biogeochemical processes are mediated by microorganisms, and notably, processes involving or coupling the carbon, sulfur, hydrogen, nitrogen, and metal cycles in these unique ecosystems. Here, we review the taxonomic and physiological diversity of microbial prokaryotic life from cosmopolitan to endemic taxa and emphasize their significant roles in the biogeochemical processes in deep-sea hydrothermal vents. According to the physiology of the targeted taxa and their needs inferred from meta-omics data, the media for selective cultivation can be designed with a wide range of physicochemical conditions such as temperature, pH, hydrostatic pressure, electron donors and acceptors, carbon sources, nitrogen sources, and growth factors. The application of novel cultivation techniques with real-time monitoring of microbial diversity and metabolic substrates and products are also recommended.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-020-00086-4.

Metagenomic Insights into the Metabolic and Ecological Functions of Abundant Deep-Sea Hydrothermal Vent DPANN Archaea

DPANN archaea show high distribution in the hydrothermal system, although they display small genome size and some incomplete biological processes. Exploring their metabolism is helpful to understand how such small forms of life adapt to this unique environment and what ecological roles they play.

Due to their unique metabolism and important ecological roles, deep-sea hydrothermal archaea have attracted great scientific interest. Among these archaea, DPANN superphylum archaea are widely distributed in hydrothermal vent environments. However, DPANN metabolism and ecology remain largely unknown. In this study, we assembled 20 DPANN genomes among 43 reconstructed genomes obtained from deep-sea hydrothermal vent sediments. Phylogenetic analysis suggests 6 phyla, comprised of Aenigmarchaeota, Diapherotrites, Nanoarchaeota, Pacearchaeota, Woesearchaeota, and a new candidate phylum we have designated Kexuearchaeota. These are included in the 20 DPANN archaeal members, indicating their broad diversity in this special environment. Analyses of their metabolism reveal deficiencies due to their reduced genome size, including gluconeogenesis and de novo nucleotide and amino acid biosynthesis. However, DPANN archaea possess alternate strategies to address these deficiencies. DPANN archaea also have the potential to assimilate nitrogen and sulfur compounds, indicating an important ecological role in the hydrothermal vent system.

IMPORTANCE DPANN archaea show high distribution in the hydrothermal system, although they display small genome size and some incomplete biological processes. Exploring their metabolism is helpful to understand how such small forms of life adapt to this unique environment and what ecological roles they play. In this study, we obtained 20 high-quality metagenome-assembled genomes (MAGs) corresponding to 6 phyla of the DPANN group (Aenigmarchaeota, Diapherotrites, Nanoarchaeota, Pacearchaeota, Woesearchaeota, and a new candidate phylum designated Kexuearchaeota). Further metagenomic analyses provided insights on the metabolism and ecological functions of DPANN archaea to adapt to deep-sea hydrothermal environments. Our study contributes to a deeper understanding of their special lifestyles and should provide clues to cultivate this important archaeal group in the future.

Innovations to culturing the uncultured microbial majority

Despite the surge of microbial genome data, experimental testing is important to confirm inferences about the cell biology, ecological roles and evolution of microorganisms. As the majority of archaeal and bacterial diversity remains uncultured and poorly characterized, culturing is a priority. The growing interest in and need for efficient cultivation strategies has led to many rapid methodological and technological advances. In this Review, we discuss common barriers that can hamper the isolation and culturing of novel microorganisms and review emerging, innovative methods for targeted or high-throughput cultivation. We also highlight recent examples of successful cultivation of novel archaea and bacteria, and suggest key microorganisms for future cultivation attempts.

High CO2 levels drive the TCA cycle backwards towards autotrophy

It has recently been shown that in anaerobic microorganisms the tricarboxylic acid (TCA) cycle, including the seemingly irreversible citrate synthase reaction, can be reversed and used for autotrophic fixation of carbon^1,2. This reversed oxidative TCA cycle requires ferredoxin-dependent 2-oxoglutarate synthase instead of the NAD-dependent dehydrogenase as well as extremely high levels of citrate synthase (more than 7% of the proteins in the cell). In this pathway, citrate synthase replaces ATP-citrate lyase of the reductive TCA cycle, which leads to the spending of one ATP-equivalent less per one turn of the cycle. Here we show, using the thermophilic sulfur-reducing deltaproteobacterium Hippea maritima, that this route is driven by high partial pressures of CO₂. These high partial pressures are especially important for the removal of the product acetyl coenzyme A (acetyl-CoA) through reductive carboxylation to pyruvate, which is catalysed by pyruvate synthase. The reversed oxidative TCA cycle may have been functioning in autotrophic CO₂ fixation in a primordial atmosphere that is assumed to have been rich in CO₂.

Microbe-Mineral Interaction and Novel Proteins for Iron Oxide Mineral Reduction in the Hyperthermophilic Crenarchaeon Pyrodictium delaneyi

Understanding iron reduction in the hyperthermophilic crenarchaeon Pyrodictium delaneyi provides insight into the diversity of mechanisms used for this process and its potential impact in geothermal environments. The ability of P. delaneyi to reduce Fe(III) oxide minerals through direct contact potentially using a novel cytochrome respiratory complex and a membrane-bound molybdopterin respiratory complex sets iron reduction in this organism apart from previously described iron reduction processes.

Dissimilatory iron reduction by hyperthermophilic archaea occurs in many geothermal environments and generally relies on microbe-mineral interactions that transform various iron oxide minerals. In this study, the physiology of dissimilatory iron and nitrate reduction was examined in the hyperthermophilic crenarchaeon type strain Pyrodictium delaneyi Su06. Iron barrier experiments showed that P. delaneyi required direct contact with the Fe(III) oxide mineral ferrihydrite for reduction. The separate addition of an exogenous electron shuttle (anthraquinone-2,6-disulfonate), a metal chelator (nitrilotriacetic acid), and 75% spent cell-free supernatant did not stimulate growth with or without the barrier. Protein electrophoresis showed that the c-type cytochrome and general protein compositions of P. delaneyi changed when grown on ferrihydrite relative to nitrate. Differential proteomic analyses using tandem mass tagged protein fragments and mass spectrometry detected 660 proteins and differential production of 127 proteins. Among these, two putative membrane-bound molybdopterin-dependent oxidoreductase complexes increased in relative abundance 60- to 3,000-fold and 50- to 100-fold in cells grown on iron oxide. A putative 8-heme c-type cytochrome was 60-fold more abundant in iron-grown cells and was unique to the Pyrodictiaceae. There was also a >14,700-fold increase in a membrane transport protein in iron-grown cells. For flagellin proteins and a putative nitrate reductase, there were no changes in abundance, but a membrane nitric oxide reductase was more abundant on nitrate. These data help to elucidate the mechanisms by which hyperthermophilic crenarchaea generate energy and transfer electrons across the membrane to iron oxide minerals.

IMPORTANCE Understanding iron reduction in the hyperthermophilic crenarchaeon Pyrodictium delaneyi provides insight into the diversity of mechanisms used for this process and its potential impact in geothermal environments. The ability of P. delaneyi to reduce Fe(III) oxide minerals through direct contact potentially using a novel cytochrome respiratory complex and a membrane-bound molybdopterin respiratory complex sets iron reduction in this organism apart from previously described iron reduction processes. A model is presented where obligatory H₂ oxidation on the membrane coupled with electron transport and either Fe(III) oxide or nitrate reduction leads to the generation of a proton motive force and energy generation by oxidative phosphorylation. However, P. delaneyi cannot fix CO₂ and relies on organic compounds from its environment for biosynthesis.

The Autotrophic Core: An Ancient Network of 404 Reactions Converts H2, CO2, and NH3 into Amino Acids, Bases, and Cofactors

The metabolism of cells contains evidence reflecting the process by which they arose. Here, we have identified the ancient core of autotrophic metabolism encompassing 404 reactions that comprise the reaction network from H₂, CO₂, and ammonia (NH₃) to amino acids, nucleic acid monomers, and the 19 cofactors required for their synthesis. Water is the most common reactant in the autotrophic core, indicating that the core arose in an aqueous environment. Seventy-seven core reactions involve the hydrolysis of high-energy phosphate bonds, furthermore suggesting the presence of a non-enzymatic and highly exergonic chemical reaction capable of continuously synthesizing activated phosphate bonds. CO₂ is the most common carbon-containing compound in the core. An abundance of NADH and NADPH-dependent redox reactions in the autotrophic core, the central role of CO₂, and the circumstance that the core’s main products are far more reduced than CO₂ indicate that the core arose in a highly reducing environment. The chemical reactions of the autotrophic core suggest that it arose from H₂, inorganic carbon, and NH₃ in an aqueous environment marked by highly reducing and continuously far from equilibrium conditions. Such conditions are very similar to those found in serpentinizing hydrothermal systems.

Complete Genome Sequence of Geobacter sp. Strain FeAm09, a Moderately Acidophilic Soil Bacterium

A moderately acidophilic Geobacter sp. strain, strain FeAm09, was isolated from forest soil. The complete genome sequence is 4,099,068 bp, with an average GC content of 61.1%. No plasmids were detected. The genome contains a total of 3,843 genes and 3,608 protein-coding genes, including genes supporting iron and nitrogen biogeochemical cycling.

A moderately acidophilic Geobacter sp. strain, FeAm09, was isolated from forest soil. The complete genome sequence is 4,099,068 bp with an average GC content of 61.1%. No plasmids were detected. The genome contains a total of 3,843 genes and 3,608 protein-coding genes, including genes supporting iron and nitrogen biogeochemical cycling.

Rethinking the Citric Acid Cycle: Connecting Pyruvate Carboxylase and Citrate Synthase to the Flow of Energy and Material

In 1937, Sir H. A Krebs first published the Citric Acid Cycle, a unidirectional cycle with carboxylic acids. The original concept of the Citric Acid Cycle from Krebs’ 1953 Nobel Prize lecture illustrates the unidirectional degradation of lactic acid to water, carbon dioxide and hydrogen. Here, we add the heart lactate dehydrogenase•proton-linked monocarboxylate transporter 1 complex, connecting the original Citric Acid Cycle to the flow of energy and material. The heart lactate dehydrogenase•proton-linked monocarboxylate transporter 1 complex catalyses the first reaction of the Citric Acid Cycle, the oxidation of lactate to pyruvate, and thus secures the provision of pyruvic acid. In addition, we modify Krebs’ original concept by feeding the cycle with oxaloacetic acid. Our concept enables the integration of anabolic processes and allows adaption of the organism to recover ATP faster.

The coenzyme/protein pair and the molecular evolution of life

Covering: up to 2020What was first? Coenzymes or proteins? These questions are archetypal examples of causal circularity in living systems. Classically, this "chicken-and-egg" problem was discussed for the macromolecules RNA, DNA and proteins. This report focuses on coenzymes and cofactors and discusses the coenzyme/protein pair as another example of causal circularity in life. Reflections on the origin of life and hypotheses on possible prebiotic worlds led to the current notion that RNA was the first macromolecule, long before functional proteins and hence DNA. So these causal circularities of living systems were solved by a time travel into the past. To tackle the "chicken-and-egg" problem of the protein-coenzyme pair, this report addresses this problem by looking for clues (a) in the first hypothetical biotic life forms such as protoviroids and the last unified common ancestor (LUCA) and (b) in considerations and evidence of the possible prebiotic production of amino acids and coenzymes before life arose. According to these considerations, coenzymes and cofactors can be regarded as very old molecular players in the origin and evolution of life, and at least some of them developed independently of α-amino acids, which here are evolutionarily synonymous with proteins. Discussions on "chicken-and-egg" problems open further doors to the understanding of evolution.

Awakening a latent carbon fixation cycle in Escherichia coli

Carbon fixation is one of the most important biochemical processes. Most natural carbon fixation pathways are thought to have emerged from enzymes that originally performed other metabolic tasks. Can we recreate the emergence of a carbon fixation pathway in a heterotrophic host by recruiting only endogenous enzymes? In this study, we address this question by systematically analyzing possible carbon fixation pathways composed only of Escherichia coli native enzymes. We identify the GED (Gnd-Entner-Doudoroff) cycle as the simplest pathway that can operate with high thermodynamic driving force. This autocatalytic route is based on reductive carboxylation of ribulose 5-phosphate (Ru5P) by 6-phosphogluconate dehydrogenase (Gnd), followed by reactions of the Entner-Doudoroff pathway, gluconeogenesis, and the pentose phosphate pathway. We demonstrate the in vivo feasibility of this new-to-nature pathway by constructing E. coli gene deletion strains whose growth on pentose sugars depends on the GED shunt, a linear variant of the GED cycle which does not require the regeneration of Ru5P. Several metabolic adaptations, most importantly the increased production of NADPH, assist in establishing sufficiently high flux to sustain this growth. Our study exemplifies a trajectory for the emergence of carbon fixation in a heterotrophic organism and demonstrates a synthetic pathway of biotechnological interest.

TCA cycle signalling and the evolution of eukaryotes

A major question remaining in the field of evolutionary biology is how prokaryotic organisms made the leap to complex eukaryotic life. The prevailing theory depicts the origin of eukaryotic cell complexity as emerging from the symbiosis between an α-proteobacterium, the ancestor of present-day mitochondria, and an archaeal host (endosymbiont theory). A primary contribution of mitochondria to eukaryogenesis has been attributed to the mitochondrial genome, which enabled the successful internalisation of bioenergetic membranes and facilitated remarkable genome expansion. It has also been postulated that a key contribution of the archaeal host during eukaryogenesis was in providing 'archaeal histones' that would enable compaction and regulation of an expanded genome. Yet, how the communication between the host and the symbiont evolved is unclear. Here, we propose an evolutionary concept in which mitochondrial TCA cycle signalling was also a crucial player during eukaryogenesis enabling the dynamic control of an expanded genome via regulation of DNA and histone modifications. Furthermore, we discuss how TCA cycle remodelling is a common evolutionary strategy invoked by eukaryotic organisms to coordinate stress responses and gene expression programmes, with a particular focus on the TCA cycle-derived metabolite itaconate.

A plausible metal-free ancestral analogue of the Krebs cycle composed entirely of α-ketoacids

Efforts to decipher the prebiotic roots of metabolic pathways have focused on recapitulating modern biological transformations, with metals typically serving in place of cofactors and enzymes. Here we show that the reaction of glyoxylate with pyruvate under mild aqueous conditions produces a series of α-ketoacid analogues of the reductive citric acid cycle without the need for metals or enzyme catalysts. The transformations proceed in the same sequence as the reverse Krebs cycle, resembling a protometabolic pathway, with glyoxylate acting as both the carbon source and reducing agent. Furthermore, the α-ketoacid analogues provide a natural route for the synthesis of amino acids by transamination with glycine, paralleling the extant metabolic mechanisms and obviating the need for metal-catalysed abiotic reductive aminations. This emerging sequence of prebiotic reactions could have set the stage for the advent of increasingly sophisticated pathways operating under catalytic control.

The Microbial Composition in Circumneutral Thermal Springs from Chignahuapan, Puebla, Mexico Reveals the Presence of Particular Sulfur-Oxidizing Bacterial and Viral Communities

Terrestrial thermal springs are widely distributed globally, and these springs harbor a broad diversity of organisms of biotechnological interest. In Mexico, few studies exploring this kind of environment have been described. In this work, we explore the microbial community in Chignahuapan hot springs, which provides clues to understand these ecosystems' diversity. We assessed the diversity of the microorganism communities in a hot spring environment with a metagenomic shotgun approach. Besides identifying similarities and differences with other ecosystems, we achieved a systematic comparison against 11 metagenomic samples from diverse localities. The Chignahuapan hot springs show a particular prevalence of sulfur-oxidizing bacteria from the genera Rhodococcus, Thermomonas, Thiomonas, Acinetobacter, Sulfurovum, and Bacillus, highlighting those that are different from other recovered bacterial populations in circumneutral hot springs environments around the world. The co-occurrence analysis of the bacteria and viruses in these environments revealed that within the Rhodococcus, Thiomonas, Thermonas, and Bacillus genera, the Chignahuapan samples have specific species of bacteria with a particular abundance, such as Rhodococcus erytropholis. The viruses in the circumneutral hot springs present bacteriophages within the order Caudovirales (Siphoviridae, Myoviridae, and Podoviridae), but the family of Herelleviridae was the most abundant in Chignahuapan samples. Furthermore, viral auxiliary metabolic genes were identified, many of which contribute mainly to the metabolism of cofactors and vitamins as well as carbohydrate metabolism. Nevertheless, the viruses and bacteria present in the circumneutral environments contribute to the sulfur cycle. This work represents an exhaustive characterization of a community structure in samples collected from hot springs in Mexico and opens opportunities to identify organisms of biotechnological interest.

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.

Direct reversible decarboxylation from stable organic acids in dimethylformamide solution

Many classical and emerging methodologies in organic chemistry rely on carbon dioxide (CO₂) extrusion to generate reactive intermediates for bond-forming events. Synthetic reactions that involve the microscopic reverse-the carboxylation of reactive intermediates-have conventionally been undertaken using very different conditions. We report that chemically stable C(sp³) carboxylates, such as arylacetic acids and malonate half-esters, undergo uncatalyzed reversible decarboxylation in dimethylformamide solution. Decarboxylation-carboxylation occurs with substrates resistant to protodecarboxylation by Brønsted acids under otherwise identical conditions. Isotopically labeled carboxylic acids can be prepared in high chemical and isotopic yield by simply supplying an atmosphere of ¹³CO₂ to carboxylate salts in polar aprotic solvents. An understanding of carboxylate reactivity in solution enables conditions for the trapping of aldehydes, ketones, and α,β-unsaturated esters.

Older Than Genes: The Acetyl CoA Pathway and Origins

For decades, microbiologists have viewed the acetyl CoA pathway and organisms that use it for H2-dependent carbon and energy metabolism, acetogens and methanogens, as ancient. Classical evidence and newer evidence indicating the antiquity of the acetyl CoA pathway are summarized here. The acetyl CoA pathway requires approximately 10 enzymes, roughly as many organic cofactors, and more than 500 kDa of combined subunit molecular mass to catalyze the conversion of H2 and CO2 to formate, acetate, and pyruvate in acetogens and methanogens. However, a single hydrothermal vent alloy, awaruite (Ni3Fe), can convert H2 and CO2 to formate, acetate, and pyruvate under mild hydrothermal conditions on its own. The chemical reactions of H2 and CO2 to pyruvate thus have a natural tendency to occur without enzymes, given suitable inorganic catalysts. This suggests that the evolution of the enzymatic acetyl CoA pathway was preceded by-and patterned along-a route of naturally occurring exergonic reactions catalyzed by transition metal minerals that could activate H2 and CO2 by chemisorption. The principle of forward (autotrophic) pathway evolution from preexisting non-enzymatic reactions is generalized to the concept of patterned evolution of pathways. In acetogens, exergonic reduction of CO2 by H2 generates acyl phosphates by highly reactive carbonyl groups undergoing attack by inert inorganic phosphate. In that ancient reaction of biochemical energy conservation, the energy behind formation of the acyl phosphate bond resides in the carbonyl, not in phosphate. The antiquity of the acetyl CoA pathway is usually seen in light of CO2 fixation; its role in primordial energy coupling via acyl phosphates and substrate-level phosphorylation is emphasized here.

Autotrophic carbon fixation pathways along the redox gradient in oxygen-depleted oceanic waters

Anoxic marine zones (AMZs), also known as 'oxygen-deficient zones', contribute to the loss of fixed nitrogen from the ocean by anaerobic microbial processes. While these microbial processes associated with the nitrogen cycle have been extensively studied, those linked to the carbon cycle in AMZs have received much less attention, particularly the autotrophic carbon fixation - a crucial component of the carbon cycle. Using metagenomic and metatranscriptomic data from major AMZs, we report an explicit partitioning of the marker genes associated with different autotrophic carbon fixation pathways along the redox gradient (from oxic to anoxic conditions) present in the water column of AMZs. Sequences related to the Calvin-Benson-Bassham cycle were found along the entire gradient, while those related to the reductive Acetyl-CoA pathway were restricted to suboxic and anoxic waters. Sequences putatively associated with the 3-hydroxypropionate/4-hydroxybutyrate cycle dominated in the upper and lower oxyclines. Genes related to the reductive tricarboxylic acid cycle were represented from dysoxic to anoxic waters. The taxonomic affiliation of the sequences is consistent with the presence of microorganisms involved in crucial steps of biogeochemical cycles in AMZs, such as the gamma-proteobacteria sulfur oxidisers, the anammox bacteria Candidatus Scalindua and the thaumarcheota ammonia oxidisers of the Marine Group I.

The hidden chemolithoautotrophic metabolism of Geobacter sulfurreducens uncovered by adaptation to formate

Multiple Fe(III)-reducing Geobacter species including the model Geobacter sulfurreducens are thought to be incapable of carbon dioxide fixation. The discovery of the reversed oxidative tricarboxylic acid cycle (roTCA) for CO₂ reduction with citrate synthase as key enzyme raises the possibility that G. sulfurreducens harbors the metabolic potential for chemolithoautotrophic growth. We investigate this hypothesis by transferring G. sulfurreducens PCA serially with Fe(III) as electron acceptor and formate as electron donor and carbon source. The evolved strain T17-3 grew chemolithoautotrophically with a 2.7-fold population increase over 48 h and a Fe(III) reduction rate of 417.5 μM h^-1. T17-3 also grew with CO₂ as carbon source. Mutations in T17-3 and enzymatic assays point to an adaptation process where the succinyl-CoA synthetase, which is inactive in the wild-type, became active to complete the roTCA cycle. Deletion of the genes coding for the succinyl-CoA synthetase in T17-3 prevented growth with formate as substrate. Enzymatic assays also showed that the citrate synthase can perform the necessary cleavage of citrate for the functional roTCA cycle. These results demonstrate that G. sulfurreducens after adaptation reduced CO₂ via the roTCA cycle. This previously hidden metabolism can be harnessed for biotechnological applications and suggests hidden ecological functions for Geobacter.

In Vivo Thermodynamic Analysis of Glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Using 13C and 2H Tracers

Thermodynamics constitutes a key determinant of flux and enzyme efficiency in metabolic networks. Here, we provide new insights into the divergent thermodynamics of the glycolytic pathways of C. thermocellum and T. saccharolyticum, two industrially relevant thermophilic bacteria whose metabolism still is not well understood. We report that while the glycolytic pathway in T. saccharolyticum is as thermodynamically favorable as that found in model organisms, such as E. coli or Saccharomyces cerevisiae, the glycolytic pathway of C. thermocellum operates near equilibrium. The use of a near-equilibrium glycolytic pathway, with potentially increased ATP yield, by this cellulolytic microbe may represent an evolutionary adaptation to growth on cellulose, but it has the drawback of being highly susceptible to product feedback inhibition. The results of this study will facilitate future engineering of high-performance strains capable of transforming cellulosic biomass to biofuels at high yields and titers.

Clostridium thermocellum and Thermoanaerobacterium saccharolyticum are thermophilic anaerobic bacteria with complementary metabolic capabilities that utilize distinct glycolytic pathways for the conversion of cellulosic sugars to biofuels. We integrated quantitative metabolomics with ²H and ¹³C metabolic flux analysis to investigate the in vivo reversibility and thermodynamics of the central metabolic networks of these two microbes. We found that the glycolytic pathway in C. thermocellum operates remarkably close to thermodynamic equilibrium, with an overall drop in Gibbs free energy 5-fold lower than that of T. saccharolyticum or anaerobically grown Escherichia coli. The limited thermodynamic driving force of glycolysis in C. thermocellum could be attributed in large part to the small free energy of the phosphofructokinase reaction producing fructose bisphosphate. The ethanol fermentation pathway was also substantially more reversible in C. thermocellum than in T. saccharolyticum. These observations help explain the comparatively low ethanol titers of C. thermocellum and suggest engineering interventions that can be used to increase its ethanol productivity and glycolytic rate. In addition to thermodynamic analysis, we used our isotope tracer data to reconstruct the T. saccharolyticum central metabolic network, revealing exclusive use of the Embden-Meyerhof-Parnas (EMP) pathway for glycolysis, a bifurcated tricarboxylic acid (TCA) cycle, and a sedoheptulose bisphosphate bypass active within the pentose phosphate pathway.

IMPORTANCE Thermodynamics constitutes a key determinant of flux and enzyme efficiency in metabolic networks. Here, we provide new insights into the divergent thermodynamics of the glycolytic pathways of C. thermocellum and T. saccharolyticum, two industrially relevant thermophilic bacteria whose metabolism still is not well understood. We report that while the glycolytic pathway in T. saccharolyticum is as thermodynamically favorable as that found in model organisms, such as E. coli or Saccharomyces cerevisiae, the glycolytic pathway of C. thermocellum operates near equilibrium. The use of a near-equilibrium glycolytic pathway, with potentially increased ATP yield, by this cellulolytic microbe may represent an evolutionary adaptation to growth on cellulose, but it has the drawback of being highly susceptible to product feedback inhibition. The results of this study will facilitate future engineering of high-performance strains capable of transforming cellulosic biomass to biofuels at high yields and titers.

Diverse Asgard archaea including the novel phylum Gerdarchaeota participate in organic matter degradation

Asgard is an archaeal superphylum that might hold the key to understand the origin of eukaryotes, but its diversity and ecological roles remain poorly understood. Here, we reconstructed 15 metagenomic-assembled genomes from coastal sediments covering most known Asgard archaea and a novel group, which is proposed as a new Asgard phylum named as the "Gerdarchaeota". Genomic analyses predict that Gerdarchaeota are facultative anaerobes in utilizing both organic and inorganic carbon. Unlike their closest relatives Heimdallarchaeota, Gerdarchaeota have genes encoding for cellulase and enzymes involved in the tetrahydromethanopterin-based Wood-Ljungdahl pathway. Transcriptomics showed that most of our identified Asgard archaea are capable of degrading organic matter, including peptides, amino acids and fatty acids, occupying ecological niches in different depths of layers of the sediments. Overall, this study broadens the diversity of the mysterious Asgard archaea and provides evidence for their ecological roles in coastal sediments.