Old acetogens, new light

Basics of genome-scale metabolic modeling and applications on C1-utilization

It is fundamental to understand the relationship between genotype and phenotype in biology. This requires comprehensive knowledge of metabolic pathways, genetic information and well-defined mathematic modeling. Integration of knowledge on metabolism with mathematical modeling results in genome-scale metabolic models which have proven useful to investigate bacterial metabolism and to engineer bacterial strains capable of producing value-added biochemical. Single carbon substrates such as methane and carbon monoxide have drawn interests and they assumed one of next-generation feedstocks because of their high abundance and low price. The methylotroph and acetogen-based biorefineries hold promises for bioconversion of C1 substrates into biofuels and high value compounds. As an effort on expanding our knowledge on C1 utilization approaches, in silico computational framework of C1-metabolism in methylotrophic and acetogenic bacteria has been developed. In this review, genome-scale metabolic models for C1-utilizing bacteria and well-established analysis tools are presented for potential uses for study of C1 metabolism at the genome scale and its application in metabolic engineering.

Draft Genome Sequences of Two Thermophilic Moorella sp. Strains, Isolated from an Acidic Hot Spring in Japan

The thermophilic Moorella sp. strains E308F and E306M were isolated from an acidic hot spring in Japan. Here, we report the draft genome sequences of E308F (3.06 Mbp; G+C content, 54.0%) and E306M (2.99 Mbp; G+C content, 54.4%), to advance the genomic information available on the genus Moorella.

The thermophilic Moorella sp. strains E308F and E306M were isolated from an acidic hot spring in Japan. Here, we report the draft genome sequences of E308F (3.06 Mbp; G+C content, 54.0%) and E306M (2.99 Mbp; G+C content, 54.4%), to advance the genomic information available on the genus Moorella.

MtpB, a member of the MttB superfamily from the human intestinal acetogen Eubacterium limosum, catalyzes proline betaine demethylation

The trimethylamine methyltransferase MttB is the founding member of a widely distributed superfamily of microbial proteins. Genes encoding most members of the MttB superfamily lack the codon for pyrrolysine that distinguishes previously characterized trimethylamine methyltransferases, leaving the function(s) of most of the enzymes in this superfamily unknown. Here, investigating the MttB family member MtpB from the human intestinal isolate Eubacterium limosum ATCC 8486, an acetogen that excretes N-methyl proline during growth on proline betaine, we demonstrate that MtpB catalyzes anoxic demethylation of proline betaine. MtpB along with MtqC (a corrinoid protein) and MtqA (a methylcorrinoid:tetrahydrofolate methyltransferase) was much more abundant in E. limosum cells grown on proline betaine than on lactate. We observed that recombinant MtpB methylates Co(I)-MtqC in the presence of proline betaine and that other quaternary amines are much less preferred substrates. MtpB, MtqC, and MtqA catalyze tetrahydrofolate methylation with proline betaine, thereby forming a key intermediate in the Wood-Ljungdahl acetogenesis pathway. To our knowledge, MtpB methylation of Co(I)-MtqC for the subsequent methylation of tetrahydrofolate represents the first described anoxic mechanism of proline betaine demethylation. The activities of MtpB and associated proteins in acetogens or other anaerobes provide a possible mechanism for the production of N-methyl proline by the gut microbiome. MtpB's activity characterized here strengthens the hypothesis that much of the MttB superfamily comprises quaternary amine-dependent methyltransferases.

Reversing an Extracellular Electron Transfer Pathway for Electrode-Driven Acetoin Reduction

Microbial electrosynthesis is an emerging technology with the potential to simultaneously store renewably generated energy, fix carbon dioxide, and produce high-value organic compounds. However, limited understanding of the route of electrons into the cell remains an obstacle to developing a robust microbial electrosynthesis platform. To address this challenge, we leveraged the native extracellular electron transfer pathway in Shewanella oneidensis MR-1 to connect an extracellular electrode with an intracellular reduction reaction. The system uses native Mtr proteins to transfer electrons from an electrode to the inner membrane quinone pool. Subsequently, electrons are transferred from quinones to NAD⁺ by native NADH dehydrogenases. This reverse functioning of NADH dehydrogenases is thermodynamically unfavorable; therefore, we added a light-driven proton pump (proteorhodopsin) to generate proton-motive force to drive this activity. Finally, we use reduction of acetoin to 2,3-butanediol via a heterologous butanediol dehydrogenase (Bdh) as an electron sink. Bdh is an NADH-dependent enzyme; therefore, observation of acetoin reduction supports our hypothesis that cathodic electrons are transferred to intracellular NAD⁺. Multiple lines of evidence indicate proper functioning of the engineered electrosynthesis system: electron flux from the cathode is influenced by both light and acetoin availability, and 2,3-butanediol production is highest when both light and a poised electrode are present. Using a hydrogenase-deficient S. oneidensis background strain resulted in a stronger correlation between electron transfer and 2,3-butanediol production, suggesting that hydrogen production is an off-target electron sink in the wild-type background. This system represents a promising step toward a genetically engineered microbial electrosynthesis platform and will enable a new focus on synthesis of specific compounds using electrical energy.

Genomic reconstruction of σ54 regulons in Clostridiales

Background

The σ⁵⁴ factor controls unique promoters and interacts with a specialized activator (enhancer binding proteins [EBP]) for transcription initiation. Although σ⁵⁴ is present in many Clostridiales species that have great importance in human health and biotechnological applications, the cellular processes controlled by σ⁵⁴ remain unknown.

Results

For systematic analysis of the regulatory functions of σ⁵⁴, we performed comparative genomic reconstruction of transcriptional regulons of σ⁵⁴ in 57 species from the Clostridiales order. The EBP-binding DNA motifs and regulated genes were identified for 263 EBPs that constitute 39 distinct groups. The reconstructed σ⁵⁴ regulons contain the genes involved in fermentation and amino acid catabolism. The predicted σ⁵⁴ binding sites in the genomes of Clostridiales spp. were verified by in vitro binding assays. To our knowledge, this is the first report about direct regulation of the Stickland reactions and butyrate and alcohols synthesis by σ⁵⁴ and the respective EBPs. Considerable variations were demonstrated in the sizes and gene contents of reconstructed σ⁵⁴ regulons between different Clostridiales species. It is proposed that σ⁵⁴ controls butyrate and alcohols synthesis in solvent-producing species, regulates autotrophic metabolism in acetogenic species, and affects the toxin production in pathogenic species.

Conclusions

This study reveals previously unrecognized functions of σ⁵⁴ and provides novel insights into the regulation of fermentation and amino acid metabolism in Clostridiales species, which could have potential applications in guiding the treatment and efficient utilization of these species.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5918-4) contains supplementary material, which is available to authorized users.

Electrosynthesis of acetate from inorganic carbon (HCO3-) with simultaneous hydrogen production and Cd(II) removal in multifunctional microbial electrosynthesis systems (MES)

The simultaneous production of acetate from bicarbonate (from CO₂ sequestration) and hydrogen gas, with concomitant removal of Cd(II) heavy metal in water is demonstrated in multifunctional metallurgical microbial electrosynthesis systems (MES) incorporating Cd(II) tolerant electrochemically active bacteria (EAB) (Ochrobactrum sp. X1, Pseudomonas sp. X3, Pseudomonas delhiensis X5, and Ochrobactrum anthropi X7). Strain X5 favored the production of acetate, while X7 preferred the production of hydrogen. The rate of Cd(II) removal by all EAB (1.20-1.32 mg/L/h), and the rates of acetate production by X5 (29.4 mg/L/d) and hydrogen evolution by X7 (0.0187 m³/m³/d) increased in the presence of a circuital current. The production of acetate and hydrogen was regulated by the release of extracellular polymeric substances (EPS), which also exhibited invariable catalytic activity toward the reduction of Cd(II) to Cd(0). The intracellular activities of glutathione (GSH), catalase (CAT), superoxide dismutase (SOD) and dehydrogenase were altered by the circuital current and Cd(II) concentration, and these regulated the products distribution. Such understanding enables the targeted manipulation of the MES operational conditions that favor the production of acetate from CO₂ sequestration with simultaneous hydrogen production and removal/recovery of Cd(II) from metal-contaminated and organics-barren waters.

Energy conservation by a hydrogenase-dependent chemiosmotic mechanism in an ancient metabolic pathway

The ancient reductive acetyl-CoA pathway is employed by acetogenic bacteria to form acetate from inorganic energy sources. Since the central pathway does not gain net ATP by substrate-level phosphorylation, chemolithoautotrophic growth relies on the additional formation of ATP via a chemiosmotic mechanism. Genome analyses indicated that some acetogens only have an energy-converting, ion-translocating hydrogenase (Ech) as a potential respiratory enzyme. Although the Ech-encoding genes are widely distributed in nature, the proposed function of Ech as an ion-translocating chemiosmotic coupling site has neither been demonstrated in bacteria nor has it been demonstrated that it can be the only energetic coupling sites in microorganisms that depend on a chemiosmotic mechanism for energy conservation. Here, we show that the Ech complex of the thermophilic acetogenic bacterium Thermoanaerobacter kivui is indeed a respiratory enzyme. Experiments with resting cells prepared from T. kivui cultures grown on carbon monoxide (CO) revealed CO oxidation coupled to H₂ formation and the generation of a transmembrane electrochemical ion gradient ([Formula: see text]). Inverted membrane vesicles (IMVs) prepared from CO-grown cells also produced H₂ and ATP from CO (via a loosely attached CO dehydrogenase) or a chemical reductant. Finally, we show that Ech activity led to the translocation of both H⁺ and Na⁺ across the membrane of the IMVs. The H⁺ gradient was then used by the ATP synthase for energy conservation. These data demonstrate that the energy-converting hydrogenase in concert with an ATP synthase may be the simplest form of respiration; it combines carbon dioxide fixation with the synthesis of ATP in an ancient pathway.

Kinetic Study on Heterotrophic Growth of Acetobacterium woodii on Lignocellulosic Substrates for Acetic Acid Production

Extensive research has been done on examining the autotrophic growth of Acetobacterium woodii with gaseous substrates (hydrogen and carbon dioxide) to produce acetic acid. However, only limited work has been performed on the heterotrophic growth of A. woodii using pure sugars or lignocellulosic feedstocks-derived sugars as substrates. In this study, we examine the growth kinetics and acetic acid production of A. woodii on glucose and xylose. While good growth was observed with glucose as substrate, no significant growth was obtained on xylose. Kinetic studies were performed in batch culture using different concentrations of glucose, ranging from 5 g/L to 40 g/L. The highest acetate production of 6.919 g/L with a product yield of 0.76 g acetic acid/g glucose was observed with 10 g/L glucose as initial substrate concentration. When testing A. woodii on corn stover hydrolysate (CSH) and wheat straw hydrolysate (WSH) formed after pretreatment and enzymatic hydrolysis, we found that A. woodii showed acetic acid production of 7.64 g/L and a product yield of 0.70 g acetic acid/g of glucose on WSH, while the acetic acid production was 7.83 g/L with a product yield of 0.65 g acetic acid/g of glucose on CSH. These results clearly demonstrate that A. woodii performed similarly on pure substrates and hydrolysates, and that the processes were not inhibited by the heterogenous components present in the lignocellulosic feedstock hydrolysates.

Reductive metabolism of the important atmospheric gas isoprene by homoacetogens

Isoprene is the most abundant biogenic volatile organic compound (BVOC) in the Earth's atmosphere and plays important roles in atmospheric chemistry. Despite this, little is known about microbiological processes serving as a terrestrial sink for isoprene. While aerobic isoprene degrading bacteria have been identified, there are no known anaerobic, isoprene-metabolizing organisms. In this study an H₂-consuming homoacetogenic enrichment was shown to utilize 1.6 μmoles isoprene h^-1 as an electron acceptor in addition to HCO₃^-. The isoprene-reducing community was dominated by Acetobacterium spp. and isoprene was shown to be stoichiometrically reduced to three methylbutene isomers (2-methyl-1-butene (>97%), 3-methyl-1-butene (≤2%), 2-methyl-2-butene (≤1%). In the presence of isoprene, 40% less acetate was formed suggesting that isoprene reduction is coupled to energy conservation in Acetobacterium spp. This study improves our understanding of linkages and feedbacks between biogeochemistry and terrestrial microbial activity.

Effects of reductive acetogenic bacteria and lauric acid on in vivo ruminal fermentation, microbial populations, and methane mitigation in Hanwoo steers in South Korea

Animal science nutrition studies are increasingly focusing on finding solutions to reduce methane (CH4) emissions. In the present study, we evaluated the effect of reductive acetogenic bacteria [acetogen probiotics (AP)] and lauric acid (LA) on in vivo rumen fermentation and microbial populations in Hanwoo steers. Four cannulated Hanwoo steers (392 ± 14 kg) were analyzed in a 4 × 4 Latin square design and were placed in hood-type chambers. They were fed similar amounts of concentrate and rice straw within and experimental design as follows: control (Con; 40 g DM basal feed, nonaddition of AP or LA), T1 = LA (40 g DM basal feed mixed with 40 g LA), T2 = AP (40 g DM basal feed, fermented with AP), and T3 = LA + AP (40 g DM basal feed, fermented with AP and mixed with 40 g LA). The animals were acclimatized to the diet for 15 d, followed by 6 d of the experimental period. Rumen fluid samples for metabolite and molecular analyses were collected 6 h after the morning feeding, with 2-h collection intervals. The enteric CH4 production was monitored on the last 2 d of the experimental period. Concentrations of total volatile fatty acids increased with the increase in time after feeding. Acetate, propionate, and butyrate concentrations were observed to be higher in the treatments than in Con. The addition of LA and AP reduced CH4 emission compared with that of Con (P < 0.01). Nuclear magnetic resonance spectroscopy results revealed no correlation between the LA and Con groups, but AP showed a correlation with LA and Con. Reduction in the number of protozoa which was accompanied by a decrease, because methanogens live symbiotically with protozoa. Supplementation of AP or LA alone and in combination decreased (P < 0.05) the methanogen population, whereas supplementation of LA alone significantly increased (P < 0.05) Ruminococcus flavefaciens and slightly increased total fungi. Thus, dietary supplementation of LA and AP has inhibitory effects on CH4 production in Hanwoo cattle. If the effects of this method can be maintained, reductive acetogens could become an important part of strategies to lower ruminant CH4 emissions.

AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences

Acetogenic bacteria are imperative to environmental carbon cycling and diverse biotechnological applications, but their extensive physiological and taxonomical diversity is an impediment to systematic taxonomic studies. Acetogens are chemolithoautotrophic bacteria that perform reductive carbon fixation under anaerobic conditions through the Wood-Ljungdahl pathway (WLP)/acetyl-coenzyme A pathway. The gene-encoding formyltetrahydrofolate synthetase (FTHFS), a key enzyme of this pathway, is highly conserved and can be used as a molecular marker to probe acetogenic communities. However, there is a lack of systematic collection of FTHFS sequence data at nucleotide and protein levels. In an attempt to streamline investigations on acetogens, we developed AcetoBase - a repository and database for systematically collecting and organizing information related to FTHFS sequences. AcetoBase also provides an opportunity to submit data and obtain accession numbers, perform homology searches for sequence identification and access a customized blast database of submitted sequences. AcetoBase provides the prospect to identify potential acetogenic bacteria, based on metadata information related to genome content and the WLP, supplemented with FTHFS sequence accessions, and can be an important tool in the study of acetogenic communities. AcetoBase can be publicly accessed at https://acetobase.molbio.slu.se.

Methanogenesis on Early Stages of Life: Ancient but Not Primordial

Of the six known autotrophic pathways, the Wood-Ljungdahl pathway (WL) is the only one present in both the acetate producing Bacteria (homoacetogens) and the methane producing Archaea (hydrogenotrophic methanogens), and it has been suggested that WL is one of the oldest metabolic pathways. However, only the so-called carbonyl branch is shared by Archaea and Bacteria, while the methyl branch is different, both in the number of reactions and enzymes, which are not homologous among them. In this work we show that some parts of the methyl branch of archaeal Wood-Ljungdahl pathway (MBWL) are present in bacteria as well as in non-methanogen archaea, although the tangled evolutionary history of MBWL cannot be traced back to the Last Common Ancestor. We have also analyzed the different variants of methanogenesis (hydrogenotrophic, acetoclastic and methylotrophic pathways), and concluded that each of these pathways, and every different enzyme or subunit (in the case of multimeric enzymes), has their own intricate evolutionary history. Our study supports the scenario of hydrogenotrophic methanogenesis being older than the other variants, albeit not old enough to be present in the last archaeal common ancestor.

Alanine, a Novel Growth Substrate for the Acetogenic Bacterium Acetobacterium woodii

Acetogenic bacteria are an ecophysiologically important group of strictly anaerobic bacteria that grow lithotrophically on H2 plus CO2 or on CO or heterotrophically on different substrates such as sugars, alcohols, aldehydes, or acids. Amino acids are rarely used. Here, we describe that the model acetogen Acetobacterium woodii can use alanine as the sole carbon and energy source, which is in contrast to the description of the type strain. The alanine degradation genes have been identified and characterized. A key to alanine degradation is an alanine dehydrogenase which has been characterized biochemically. The resulting pyruvate is further degraded to acetate by the known pathways involving the Wood-Ljungdahl pathway. Our studies culminate in a metabolic and bioenergetic scheme for alanine-dependent acetogenesis in A. woodiiIMPORTANCE Peptides and amino acids are widespread in nature, but there are only a few reports that demonstrated use of amino acids as carbon and energy sources by acetogenic bacteria, a central and important group in the anaerobic food web. Our finding that A. woodii can perform alanine oxidation coupled to reduction of carbon dioxide not only increases the number of substrates that can be used by this model acetogen but also raises the possibility that other acetogens may also be able to use alanine. Indeed, the alanine genes are also present in at least two more acetogens, for which growth on alanine has not been reported so far. Alanine may be a promising substrate for industrial fermentations, since acid formation goes along with the production of a base (NH3) and pH regulation is a minor issue.

Genome-scale analysis of syngas fermenting acetogenic bacteria reveals the translational regulation for its autotrophic growth

Background

Acetogenic bacteria constitute promising biocatalysts for the conversion of CO₂/H₂ or synthesis gas (H₂/CO/CO₂) into biofuels and value-added biochemicals. These microorganisms are naturally capable of autotrophic growth via unique acetogenesis metabolism. Despite their biosynthetic potential for commercial applications, a systemic understanding of the transcriptional and translational regulation of the acetogenesis metabolism remains unclear.

Results

By integrating genome-scale transcriptomic and translatomic data, we explored the regulatory logic of the acetogenesis to convert CO₂ into biomass and metabolites in Eubacterium limosum. The results indicate that majority of genes associated with autotrophic growth including the Wood-Ljungdahl pathway, the reduction of electron carriers, the energy conservation system, and gluconeogenesis were transcriptionally upregulated. The translation efficiency of genes in cellular respiration and electron bifurcation was also highly enhanced. In contrast, the transcriptionally abundant genes involved in the carbonyl branch of the Wood-Ljungdahl pathway, as well as the ion-translocating complex and ATP synthase complex in the energy conservation system, showed decreased translation efficiency. The translation efficiencies of genes were regulated by 5′UTR secondary structure under the autotrophic growth condition.

Conclusions

The results illustrated that the acetogenic bacteria reallocate protein synthesis, focusing more on the translation of genes for the generation of reduced electron carriers via electron bifurcation, rather than on those for carbon metabolism under autotrophic growth.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5238-0) contains supplementary material, which is available to authorized users.

Direct cell-to-cell exchange of matter in a synthetic Clostridium syntrophy enables CO2 fixation, superior metabolite yields, and an expanded metabolic space

In microbial fermentations at least 33% of the sugar-substrate carbon is lost as CO₂ during pyruvate decarboxylation to acetyl-CoA, with the corresponding electrons lost in the form of H₂. Previous attempts to reduce this carbon and electron loss focused on engineering of a single organism. In nature, most microorganisms live in complex communities where syntrophic interactions result in superior resource utilization. Here, we show that a synthetic syntrophy consisting of the solventogen Clostridium acetobutylicum, which converts simple and complex carbohydrates into a variety of chemicals, and the acetogen C. ljungdahlii which fixes CO₂, achieved carbon recoveries into C2-C4 alcohols almost to the limit of substrate-electron availability, with minimal H₂ and CO₂ release. The syntrophic co-culture produced robust metabolic outcomes over a broad range of starting population ratios of the two organisms. We show that direct cell-to-cell interactions and material exchange among the two microbes enabled unforeseen rearrangements in the metabolism of the individual species that resulted in the production of non-native metabolites, namely isopropanol and 2,3-butanediol. This was accomplished by pathway-specific alterations of gene expression brought about by one organism on the other, and vice versa. While some of these gene-expression alterations can be explained by the exchange of metabolites that induce specific gene expression patterns, others, as demonstrated by co-culture setup in a transwell system, cannot. The latter, for now, would be attributed to complex direct physical interactions among the two organisms, thus providing a glimpse of the potential microbial complexity of simple or multicomponent microbiomes. Such direct material-transfer phenomena have not been documented in the literature. Furthermore, our study shows that syntrophic cultures offer a flexible platform for metabolite production with superior carbon recovery that can also be applied to electron-enhanced fermentations enabling even higher carbon recoveries.

Regulation of lactate metabolism in the acetogenic bacterium Acetobacterium woodii

Acetogenic bacteria compete in an energy-limited environment by coupling different metabolic routes to their central metabolism of CO₂ fixation. The underlying regulatory mechanisms are often still not understood. In this work, we analysed how lactate metabolism is regulated in the model acetogen Acetobacterium woodii. Construction of a ΔlctCDEF mutant and growth analyses demonstrated that the genes are essential for growth on lactate. Subsequent bridging PCR and quantitative PCR analyses revealed that the lctBCDEF genes form an operon that was expressed only during lactate metabolism. The lctA gene was cloned, expressed in Escherichia coli and purified. LctA bound to the intergenic DNA region between lctA and the lct operon in electromobility shift assays, and binding was revoked in the presence of lactate. Further restriction site protection analyses consolidated the lactate-dependent binding of LctA and identified the binding site within the DNA. Cells grew mixotrophically on lactate and another energy source and showed no diauxic growth. From these data, we conclude that the catabolic lactate metabolism is encoded by the lct operon and its expression is negatively regulated by the DNA-binding repressor LctA.

The Rnf Complex Is an Energy-Coupled Transhydrogenase Essential To Reversibly Link Cellular NADH and Ferredoxin Pools in the Acetogen Acetobacterium woodii

The Rnf complex is a respiratory enzyme that catalyzes the oxidation of reduced ferredoxin to the reduction of NAD⁺, and the negative free energy change of this reaction is used to generate a transmembrane ion gradient. In one class of anaerobic acetogenic bacteria, the Rnf complex is believed to be essential for energy conservation and autotrophic growth. We describe here a methodology for markerless mutagenesis in the model bacterium of this class, Acetobacterium woodii, which enabled us to delete the rnf genes and to test their in vivo role. The rnf mutant did not grow on H₂ plus CO₂, nor did it produce acetate or ATP from H₂ plus CO₂, and ferredoxin:NAD⁺ oxidoreductase activity and Na⁺ translocation were also completely lost, supporting the hypothesis that the Rnf complex is the only respiratory enzyme in this metabolism. Unexpectedly, the mutant also did not grow on low-energy substrates, such as ethanol or lactate. Oxidation of these substrates is not coupled to the reduction of ferredoxin but only of NAD⁺, and we speculated that the growth phenotype is caused by a loss of reduced ferredoxin, indispensable for biosynthesis and CO₂ reduction. The electron-bifurcating hydrogenase of A. woodii reduces ferredoxin, and indeed, the addition of H₂ to the cultures restored growth on ethanol and lactate. This is consistent with the hypothesis that endergonic reduction of ferredoxin with NADH is driven by reverse electron transport catalyzed by the Rnf complex, which renders the Rnf complex essential also for growth on low-energy substrates.IMPORTANCE Ferredoxin and NAD⁺ are key electron carriers in anaerobic bacteria, but energetically, they are not equivalent, since the redox potential of ferredoxin is lower than that of the NADH/NAD⁺ couple. We describe by mutant studies in Acetobacterium woodii that the main function of Rnf is to energetically link cellular pools of ferredoxin and NAD⁺ When ferredoxin is greater than NADH, exergonic electron flow from ferredoxin to NAD⁺ generates a chemiosmotic potential. This is essential for energy conservation during autotrophic growth. When NADH is greater than ferredoxin, Rnf works in reverse. This reaction is essential for growth on low-energy substrates to provide reduced ferredoxin, indispensable for biosynthesis and CO₂ reduction. Our studies put a new perspective on the cellular function of the membrane-bound ion-translocating Rnf complex widespread in bacteria.

Production of alkanes from CO2 by engineered bacteria

BACKGROUND

Microbial biosynthesis of alkanes is considered a promising method for the sustainable production of drop-in fuels and chemicals. Carbon dioxide would be an ideal carbon source for these production systems, but efficient production of long carbon chains from CO₂ is difficult to achieve in a single organism. A potential solution is to employ acetogenic bacteria for the reduction of CO₂ to acetate, and engineer a second organism to convert the acetate into long-chain hydrocarbons.

RESULTS

In this study, we demonstrate alkane production from CO₂ by a system combining the acetogen Acetobacterium woodii and a non-native alkane producer Acinetobacter baylyi ADP1 engineered for alkane production. Nine synthetic two-step alkane biosynthesis pathways consisting of different aldehyde- and alkane-producing enzymes were combinatorically constructed and expressed in A. baylyi. The aldehyde-producing enzymes studied were AAR from Synechococcus elongatus, Acr1 from A. baylyi, and a putative dehydrogenase from Nevskia ramosa. The alkane-producing enzymes were ADOs from S. elongatus and Nostoc punctiforme, and CER1 from Arabidopsis thaliana. The performance of the pathways was evaluated with a twin-layer biosensor, which allowed the monitoring of both the intermediate (fatty aldehyde), and end product (alkane) formation. The highest alkane production, as indicated by the biosensor, was achieved with a pathway consisting of AAR and ADO from S. elongatus. The performance of this pathway was further improved by balancing the relative expression levels of the enzymes to limit the accumulation of the intermediate fatty aldehyde. Finally, the acetogen A. woodii was used to produce acetate from CO₂ and H₂, and the acetate was used for alkane production by the engineered A. baylyi, thereby leading to the net production of long-chain alkanes from CO₂.

CONCLUSIONS

A modular system for the production of drop-in liquid fuels from CO₂ was demonstrated. Among the studied synthetic pathways, the combination of ADO and AAR from S. elongatus was found to be the most efficient in heterologous alkane production in A. baylyi. Furthermore, limiting the accumulation of the fatty aldehyde intermediate was found to be beneficial for the alkane production. Nevertheless, the alkane productivity of the system remained low, representing a major challenge for future research.

Managing microbial communities in membrane biofilm reactors

Membrane biofilm reactors (MBfRs) deliver gaseous substrates to biofilms that develop on the outside of gas-transfer membranes. When an MBfR delivers electron donors hydrogen (H₂) or methane (CH₄), a wide range of oxidized contaminants can be reduced as electron acceptors, e.g., nitrate, perchlorate, selenate, and trichloroethene. When O₂ is delivered as an electron acceptor, reduced contaminants can be oxidized, e.g., benzene, toluene, and surfactants. The MBfR's biofilm often harbors a complex microbial community; failure to control the growth of undesirable microorganisms can result in poor performance. Fortunately, the community's structure and function can be managed using a set of design and operation features as follows: gas pressure, membrane type, and surface loadings. Proper selection of these features ensures that the best microbial community is selected and sustained. Successful design and operation of an MBfR depends on a holistic understanding of the microbial community's structure and function. This involves integrating performance data with omics results, such as with stoichiometric and kinetic modeling.

A novel process for volatile fatty acids production from syngas by integrating with mesophilic alkaline fermentation of waste activated sludge

The present study proposed and demonstrated a novel process for the bioconversion of syngas (mainly CO and H₂) to valuable volatile fatty acids (VFA) by integrating with mesophilic alkaline fermentation of waste activated sludge (WAS). The results showed that although pH 9 was suitable for VFA production from WAS, 62.5% of the consumed CO was converted to methane due to the presence of hydrogenogenic pathway for CO conversion. The increase of pH from 9 to 9.5 inhibited the methane production from CO because of the possible presence of only acetogenic pathway for CO conversion. However, methane was still produced from H₂ contained in syngas through hydrogenotrophic methanogenesis, and around 32-34% of the consumed syngas was converted to methane. At both pH 9 and 9.5, methane was produced by hydrogenotrophic methanogens Methanobacteriales. Further increase of pH to 10 effectively inhibited methane production from syngas, and efficient VFA (mainly acetate with the concentration of around 135 mM) production by simultaneous conversion of syngas and WAS was achieved. High acetate concentrations (>150 mM) were shown to have serious negative effects on the conversion of syngas. The addition of syngas to the mesophilic alkaline fermentation of WAS at pH 10 not only resulted in the enrichment of some known bacteria related with syngas conversion, but also changed the microbial community compositions for the fermentation of WAS.

Clostridium bovifaecis sp. nov., a novel acetogenic bacterium isolated from cow manure

A strictly anaerobic, Gram-staining-positive, spore-forming rod-shaped bacterium, and designated BXX^T, was isolated from cow manure. Colonies on DSMZ medium 311c agar plates were cream, circular, opaque and lustrous. Growth occurred at 20-45 °C with a pH range of 5.0-10.0 and at NaCl concentrations of up to 2 % (w/v). The optimum temperature, pH and NaCl concentration for growth were 30 °C, pH 7 and 1 % (w/v), respectively. The major cellular fatty acids were C16 : 0 (26.8 %), C14 : 0 (22.8 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (16.4 %) and C16 : 1ω9c (10.7 %). The main polar lipids of BXX^T were diphosphatidylglycerol, phosphatidylethanolamine, unidentified aminolipids, an unidentified phospholipid and unidentified lipids. Acetate was mainly produced from H2/CO2, H2/CO2/CO (4/3/3, v/v/v), formate, glycerol, 1,2-propanediol, pyruvate, d-fructose and 2-methoxyethanol. BXX^T is most closely related to Clostridium thermobutyricumDSM 4928^T, Clostridiumhomopropionicum DSM 5847^T and Clostridium thermopalmarium DSM 5974^T with 16S rRNA gene sequence similarities of 96.9, 96.6 and 96.5 %, respectively. The DNA G+C content of BXX^T was 33.7 mol%, which was lower than that of C. thermobutyricum DSM 4928^T (37.0 mol%) and C. thermopalmarium DSM 5974^T (35.7 mol%). In addition, DSM 4928^T and DSM 5974^Tare thermophilic members of the genus Clostridium. The absence of C15 : 0 also distinguished BXX^T from Clostridium thermobutyricum. On the basis of phylogenetic, phenotypic and chemotaxonomic evidence, the novel isolate represents a novel species within the genus Clostridium, for which the name Clostridium bovifaecis sp. nov is proposed. The type strain of the type species is BXX^T (=JCM 32382^T=CGMCC 1.5228^T).

Bile acid oxidation by Eggerthella lenta strains C592 and DSM 2243T

Strains of Eggerthella lenta are capable of oxidation-reduction reactions capable of oxidizing and epimerizing bile acid hydroxyl groups. Several genes encoding these enzymes, known as hydroxysteroid dehydrogenases (HSDH) have yet to be identified. It is also uncertain whether the products of E. lenta bile acid metabolism are further metabolized by other members of the gut microbiota. We characterized a novel human fecal isolate identified as E. lenta strain C592. The complete genome of E. lenta strain C592 was sequenced and comparative genomics with the type strain (DSM 2243) revealed high conservation, but some notable differences. E. lenta strain C592 falls into group III, possessing 3α, 3β, 7α, and 12α-hydroxysteroid dehydrogenase (HSDH) activity, as determined by mass spectrometry of thin layer chromatography (TLC) separated metabolites of primary and secondary bile acids. Incubation of E. lenta oxo-bile acid and iso-bile acid metabolites with whole-cells of the high-activity bile acid 7α-dehydroxylating bacterium, Clostridium scindens VPI 12708, resulted in minimal conversion of oxo-derivatives to lithocholic acid (LCA). Further, Iso-chenodeoxycholic acid (iso-CDCA; 3β,7α-dihydroxy-5β-cholan-24-oic acid) was not metabolized by C. scindens. We then located a gene encoding a novel 12α-HSDH in E. lenta DSM 2243, also encoded by strain C592, and the recombinant purified enzyme was characterized and substrate-specificity determined. Genomic analysis revealed genes encoding an Rnf complex (rnfABCDEG), an energy conserving hydrogenase (echABCDEF) complex, as well as what appears to be a complete Wood-Ljungdahl pathway. Our prediction that by changing the gas atmosphere from nitrogen to hydrogen, bile acid oxidation would be inhibited, was confirmed. These results suggest that E. lenta is an important bile acid metabolizing gut microbe and that the gas atmosphere may be an important and overlooked regulator of bile acid metabolism in the gut.

Growth of sedimentary Bathyarchaeota on lignin as an energy source

Members of the archaeal phylum Bathyarchaeota are among the most abundant microorganisms on Earth. Although versatile metabolic capabilities such as acetogenesis, methanogenesis, and fermentation have been suggested for bathyarchaeotal members, no direct confirmation of these metabolic functions has been achieved through growth of Bathyarchaeota in the laboratory. Here we demonstrate, on the basis of gene-copy numbers and probing of archaeal lipids, the growth of Bathyarchaeota subgroup Bathy-8 in enrichments of estuarine sediments with the biopolymer lignin. Other organic substrates (casein, oleic acid, cellulose, and phenol) did not significantly stimulate growth of Bathyarchaeota Meanwhile, putative bathyarchaeotal tetraether lipids incorporated ¹³C from ¹³C-bicarbonate only when added in concert with lignin. Our results are consistent with organoautotrophic growth of a bathyarchaeotal group with lignin as an energy source and bicarbonate as a carbon source and shed light into the cycling of one of Earth's most abundant biopolymers in anoxic marine sediment.

Status and prospects in higher alcohols synthesis from syngas

Higher alcohols are important compounds with widespread applications in the chemical, pharmaceutical and energy sectors. Currently, they are mainly produced by sugar fermentation (ethanol and isobutanol) or hydration of petroleum-derived alkenes (heavier alcohols), but their direct synthesis from syngas (CO + H₂) would comprise a more environmentally-friendly, versatile and economical alternative. Research efforts in this reaction, initiated in the 1930s, have fluctuated along with the oil price and have considerably increased in the last decade due to the interest to exploit shale gas and renewable resources to obtain the gaseous feedstock. Nevertheless, no catalytic system reported to date has performed sufficiently well to justify an industrial implementation. Since the design of an efficient catalyst would strongly benefit from the establishment of synthesis-structure-function relationships and a deeper understanding of the reaction mechanism, this review comprehensively overviews syngas-based higher alcohols synthesis in three main sections, highlighting the advances recently made and the challenges that remain open and stimulate upcoming research activities. The first part critically summarises the formulations and methods applied in the preparation of the four main classes of materials, i.e., Rh-based, Mo-based, modified Fischer-Tropsch and modified methanol synthesis catalysts. The second overviews the molecular-level insights derived from microkinetic and theoretical studies, drawing links to the mechanisms of Fischer-Tropsch and methanol syntheses. Finally, concepts proposed to improve the efficiency of reactors and separation units as well as to utilise CO₂ and recycle side-products in the process are described in the third section.

Reaction engineering analysis of the autotrophic energy metabolism of Clostridium aceticum

Acetogenesis with CO2:H2 or CO via the reductive acetyl-CoA pathway does not provide any net ATP formation in homoacetogenic bacteria. Autotrophic energy conservation is coupled to the generation of chemiosmotic H+ or Na+ gradients across the cytoplasm membrane using either a ferredoxin:NAD+ oxidoreductase (Rnf), a ferredoxin:H+ oxidoreductase (Ech) or substrate-level phosphorylation via cytochromes. The first isolated acetogenic bacterium Clostridium aceticum shows both cytochromes and Rnf complex, putting it into an outstanding position. Autotrophic batch processes with continuous gas supply were performed in fully controlled stirred-tank bioreactors to elucidate energy metabolism of C. aceticum. Varying the initial Na+ concentration in the medium showed sodium-dependent growth of C. aceticum with a growth optimum between 60 and 90 mM Na+. The addition of the Na+-selective ionophore ETH2120 or the protonophore CCCP or the H+/cation-antiporter monensin revealed that an H+ gradient is used as primary energy conservation mechanism, which strengthens the exceptional position of C. aceticum as acetogenic bacterium showing an H+-dependent energy conservation mechanism as well as Na+-dependent growth.

Quantitative analysis of tetrahydrofolate metabolites from clostridium autoethanogenum

INTRODUCTION

Quantification of tetrahydrofolates (THFs), important metabolites in the Wood-Ljungdahl pathway (WLP) of acetogens, is challenging given their sensitivity to oxygen.

OBJECTIVE

To develop a simple anaerobic protocol to enable reliable THFs quantification from bioreactors.

METHODS

Anaerobic cultures were mixed with anaerobic acetonitrile for extraction. Targeted LC-MS/MS was used for quantification.

RESULTS

Tetrahydrofolates can only be quantified if sampled anaerobically. THF levels showed a strong correlation to acetyl-CoA, the end product of the WLP.

CONCLUSION

Our method is useful for relative quantification of THFs across different growth conditions. Absolute quantification of THFs requires the use of labelled standards.

Advances in metabolic engineering in the microbial production of fuels and chemicals from C1 gas

The future sustainable production of chemicals and fuels from non-petrochemical sources, while at the same time reducing greenhouse gas (GHG) emissions, represent two of society's greatest challenges. Microbial chassis able to grow on waste carbon monoxide (CO) and carbon dioxide (CO₂) can provide solutions to both. Ranging from the anaerobic acetogens, through the aerobic chemoautotrophs to the photoautotrophic cyanobacteria, they are able to convert C1 gases into a range of chemicals and fuels which may be enhanced and extended through appropriate metabolic engineering. The necessary improvements will be facilitated by the increasingly sophisticated gene tools that are beginning to emerge as part of the Synthetic Biology revolution. These tools, in combination with more accurate metabolic and genome scale models, will enable C1 chassis to deliver their full potential.

A Genetic System for the Thermophilic Acetogenic Bacterium Thermoanaerobacter kivui

Thermoanaerobacter kivui is one of the very few thermophilic acetogenic microorganisms. It grows optimally at 66°C on sugars but also lithotrophically with H2 + CO2 or with CO, producing acetate as the major product. While a genome-derived model of acetogenesis has been developed, only a few physiological or biochemical experiments regarding the function of important enzymes in carbon and energy metabolism have been carried out. To address this issue, we developed a method for targeted markerless gene deletions and for integration of genes into the genome of T. kivui The strain naturally took up plasmid DNA in the exponential growth phase, with a transformation frequency of up to 3.9 × 10-6 A nonreplicating plasmid and selection with 5-fluoroorotate was used to delete the gene encoding the orotate phosphoribosyltransferase (pyrE), resulting in a ΔpyrE uracil-auxotrophic strain, TKV002. Reintroduction of pyrE on a plasmid or insertion of pyrE into different loci within the genome restored growth without uracil. We subsequently studied fructose metabolism in T. kivui The gene fruK (TKV_c23150) encoding 1-phosphofructosekinase (1-PFK) was deleted, using pyrE as a selective marker via two single homologous recombination events. The resulting ΔfruK strain, TKV003, did not grow on fructose; however, growth on glucose (or on mannose) was unaffected. The combination of pyrE as a selective marker and the natural competence of the strain for DNA uptake will be the basis for future studies on CO2 reduction and energy conservation and their regulation in this thermophilic acetogenic bacterium.IMPORTANCE Acetogenic bacteria are currently the focus of research toward biotechnological applications due to their potential for de novo synthesis of carbon compounds such as acetate, butyrate, or ethanol from H2 + CO2 or from synthesis gas. Based on available genome sequences and on biochemical experiments, acetogens differ in their energy metabolism. Thus, there is an urgent need to understand the carbon and electron flows through the Wood-Ljungdahl pathway and their links to energy conservation, which requires genetic manipulations such as deletion or overexpression of genes encoding putative key enzymes. Unfortunately, genetic systems have been reported for only a few acetogenic bacteria. Here, we demonstrate proof of concept for the genetic modification of the thermophilic acetogenic species Thermoanaerobacter kivui The genetic system will be used to study genes involved in biosynthesis and energy metabolism, and may further be applied to metabolically engineer T. kivui to produce fuels and chemicals.

Bacterial Anaerobic Synthesis Gas (Syngas) and CO2+H2 Fermentation

Anaerobic bacterial gas fermentation gains broad interest in various scientific, social, and industrial fields. This microbial process is carried out by a specific group of bacterial strains called acetogens. All these strains employ the Wood-Ljungdahl pathway but they belong to different taxonomic groups. Here we provide an overview of the metabolism of acetogens and naturally occurring products. Characteristics of 61 strains were summarized and selected acetogens described in detail. Acetobacterium woodii, Clostridium ljungdahlii, and Moorella thermoacetica serve as model organisms. Results of approaches such as genome-scale modeling, proteomics, and transcriptomics are discussed. Metabolic engineering of acetogens can be used to expand the product portfolio to platform chemicals and to study different aspects of cell physiology. Moreover, the fermentation of gases requires specific reactor configurations and the development of the respective technology, which can be used for an industrial application. Even though the overall process will have a positive effect on climate, since waste and greenhouse gases could be converted into commodity chemicals, some legislative barriers exist, which hamper successful exploitation of this technology.

Effects of zinc on the production of alcohol by Clostridium carboxidivorans P7 using model syngas

Renewable energy, including biofuels such as ethanol and butanol from syngas bioconversed by Clostridium carboxidivorans P7, has been drawing extensive attention due to the fossil energy depletion and global eco-environmental issues. Effects of zinc on the growth and metabolites of C. carboxidivorans P7 were investigated with model syngas as the carbon source. The cell concentration was doubled, the ethanol content increased 3.02-fold and the butanol content increased 7.60-fold, the hexanol content increased 44.00-fold in the medium with 280 μM Zn2+, when comparing with those in the control medium [Zn2+, (7 μM)]. Studies of the genes expression involved in the carbon fixation as well as acid and alcohol production in the medium with 280 μM Zn2+ indicated that fdhII was up-regulated on the second day, acs A, fdhII, bdh35 and bdh50 were up-regulated on the third day and bdh35, acsB, fdhI, fdhIII, fdhIV, buk, bdh10, bdh35, bdh40 and bdh50 were up-regulated on the fourth day. The results indicated that the increased Zn2+ content increased the alcohol production through increase in the gene expression of the carbon fixation and alcohol dehydrogenase.

An Adaptive Laboratory Evolution Method to Accelerate Autotrophic Metabolism

Adaptive laboratory evolution (ALE) is an approach enabling the development of novel characteristics in microbial strains via the application of a constant selection pressure. This method is also an efficient tool to acquire insights on molecular mechanisms responsible for specific phenotypes. ALE experiments have mainly been conducted with heterotrophic microbes to study, for instance, cell metabolism with different multicarbon substrates, tolerance to solvents, pH variation, and high temperature. Here, we describe employing an ALE method to generate Sporomusa ovata strains growing faster autotrophically and reducing CO₂ into acetate more efficiently. Strains developed via this ALE method were also used to gain knowledge on the autotrophic metabolism of S. ovata as well as other acetogenic bacteria.

Homoacetogenesis in Deep-Sea Chloroflexi, as Inferred by Single-Cell Genomics, Provides a Link to Reductive Dehalogenation in Terrestrial Dehalococcoidetes

The deep marine subsurface is one of the largest unexplored biospheres on Earth and is widely inhabited by members of the phylum Chloroflexi. In this report, we investigated genomes of single cells obtained from deep-sea sediments of the Peruvian Margin, which are enriched in such Chloroflexi. 16S rRNA gene sequence analysis placed two of these single-cell-derived genomes (DscP3 and Dsc4) in a clade of subphylum I Chloroflexi which were previously recovered from deep-sea sediment in the Okinawa Trough and a third (DscP2-2) as a member of the previously reported DscP2 population from Peruvian Margin site 1230. The presence of genes encoding enzymes of a complete Wood-Ljungdahl pathway, glycolysis/gluconeogenesis, a Rhodobacter nitrogen fixation (Rnf) complex, glyosyltransferases, and formate dehydrogenases in the single-cell genomes of DscP3 and Dsc4 and the presence of an NADH-dependent reduced ferredoxin:NADP oxidoreductase (Nfn) and Rnf in the genome of DscP2-2 imply a homoacetogenic lifestyle of these abundant marine Chloroflexi. We also report here the first complete pathway for anaerobic benzoate oxidation to acetyl coenzyme A (CoA) in the phylum Chloroflexi (DscP3 and Dsc4), including a class I benzoyl-CoA reductase. Of remarkable evolutionary significance, we discovered a gene encoding a formate dehydrogenase (FdnI) with reciprocal closest identity to the formate dehydrogenase-like protein (complex iron-sulfur molybdoenzyme [CISM], DET0187) of terrestrial Dehalococcoides/Dehalogenimonas spp. This formate dehydrogenase-like protein has been shown to lack formate dehydrogenase activity in Dehalococcoides/Dehalogenimonas spp. and is instead hypothesized to couple HupL hydrogenase to a reductive dehalogenase in the catabolic reductive dehalogenation pathway. This finding of a close functional homologue provides an important missing link for understanding the origin and the metabolic core of terrestrial Dehalococcoides/Dehalogenimonas spp. and of reductive dehalogenation, as well as the biology of abundant deep-sea Chloroflexi.

The deep marine subsurface is one of the largest unexplored biospheres on Earth and is widely inhabited by members of the phylum Chloroflexi. In this report, we investigated genomes of single cells obtained from deep-sea sediments and provide evidence for a homacetogenic lifestyle of these abundant marine Chloroflexi. Moreover, genome signature and key metabolic genes indicate an evolutionary relationship between these deep-sea sediment microbes and terrestrial, reductively dehalogenating Dehalococcoides.

Thermophilic ethanol fermentation from lignocellulose hydrolysate by genetically engineered Moorella thermoacetica

A transformant of Moorella thermoacetica was constructed for thermophilic ethanol production from lignocellulosic biomass by deleting two phosphotransacetylase genes, pdul1 and pdul2, and introducing the native aldehyde dehydrogenase gene (aldh) controlled by the promoter from glyceraldehyde-3-phosphate dehydrogenase. The transformant showed tolerance to 540mM and fermented sugars including fructose, glucose, galactose and xylose to mainly ethanol. In a mixed-sugar medium of glucose and xylose, all of the sugars were consumed to produce ethanol at the yield of 1.9mol/mol-sugar. The transformant successfully fermented sugars in hydrolysate prepared through the acid hydrolysis of lignocellulose to ethanol, suggesting that this transformant can be used to ferment the sugars in lignocellulosic biomass for ethanol production.

A genetic approach for microbial electrosynthesis system as biocommodities production platform

Microbial electrosynthesis is a process that can produce biocommodities from the reduction of substrates with microbial catalysts and an external electron supply. This process is expected to become a new application of a cell factory for novel chemical production, wastewater treatment, and carbon capture and utilization. However, microbial electrosynthesis is still subject to several problems that need to be overcome for commercialization, so continuous development such as metabolic engineering is essential. The development of microbial electrosynthesis can open up new opportunities for sustainable biocommodities production platforms. This review provides significant information on the current state of MES development, focusing on extracellularly electron transfer and metabolic engineering.

Acetate-assisted increase of butyrate production by Eubacterium limosum KIST612 during carbon monoxide fermentation

The acetate-assisted cultivation of Eubacterium limosum KIST612 was found to provide a way for enhancing cell mass, the carbon monoxide (CO) consumption rate, and butyrate production using CO as an electron and energy source. Cell growth (146%), μ_max (121%), and CO consumption rates (151%) increased significantly upon the addition of 30mM acetate to microbial cultures. The main product of CO fermentation by E. limosum KIST612 shifted from acetate to butyrate in the presence of acetate, and 5.72mM butyrate was produced at the end of the reaction. The resting cell experimental conditions indicated acetate uptake and an increase in the butyrate concentration. Three routes to acetate assimilation and energy conservation were suggested based on given experimental results and previously genome sequencing data. Acetate assimilation via propionate CoA-transferase (PCT) was expected to produce 1.5mol ATP/mol butyrate, and was thus anticipated to be the most preferred route.

Production of long chain alkyl esters from carbon dioxide and electricity by a two-stage bacterial process

Microbial electrosynthesis (MES) is a promising technology for the reduction of carbon dioxide into value-added multicarbon molecules. In order to broaden the product profile of MES processes, we developed a two-stage process for microbial conversion of carbon dioxide and electricity into long chain alkyl esters. In the first stage, the carbon dioxide is reduced to organic compounds, mainly acetate, in a MES process by Sporomusa ovata. In the second stage, the liquid end-products of the MES process are converted to the final product by a second microorganism, Acinetobacter baylyi in an aerobic bioprocess. In this proof-of-principle study, we demonstrate for the first time the bacterial production of long alkyl esters (wax esters) from carbon dioxide and electricity as the sole sources of carbon and energy. The process holds potential for the efficient production of carbon-neutral chemicals or biofuels.