Search Results (24)

Anaerobic digestion (AD) has long been valued for producing a biogas–digestate pair, yet its profitability is tightening. Next-generation AD biorefineries now position syngas both as a supplementary feedstock and as a springboard to capture high-value intermediates, hydrogen (H₂) and volatile fatty acids (VFA). This review dissects how complex natural consortia “decide” between hydrogenogenesis and acetogenesis when CO, H₂, and CO₂ co-exist in the feedstocks, bridging molecular mechanisms with process-scale levers. The map of the bioenergetic contest between the biological water–gas shift reaction and Wood–Ljungdahl pathways is discussed, revealing how electron flow, thermodynamic thresholds, and enzyme inhibition dictate microbial “decision”. Kinetic evidence from pure and mixed cultures is integrated with practical operating factors (gas composition and pressure, pH–temperature spectrum, culture media composition, hydraulic retention time, and cell density), which can bias consortia toward the desired product. Full article

Metabolism, the network of biochemical reactions that powers life, arose under conditions radically different from those on Earth today. Investigating its origins reveals how initially simple chemical processes gradually integrated nucleic acid and then protein catalysts, becoming progressively more complex and regulated until they evolved into the enzyme-rich systems observed in modern organisms. Here, we integrate multiple perspectives on the origin of metabolism, focusing primarily on an evolutionary trajectory from an RNA-based world, where ribozymes, metal ions, coenzymes, small peptides, and other small organic molecules worked in concert, to enzyme-driven metabolic networks. We also address the longstanding debates on whether these early metabolic pathways were largely autotrophic or heterotrophic, and consider so-called “pre-metabolisms” (non-enzymatic networks) as an alternative conceptual framework. We discuss key examples such as the Wood–Ljungdahl (W–L) pathway and the reverse tricarboxylic acid (TCA) cycle, both posited to function under early Earth conditions. Finally, we examine how the environment (e.g., minerals, clays, hydrothermal vents) shaped early metabolism, describe unresolved questions about the Last Common Ancestor’s catalytic repertoire and propose future directions that link geochemical insights with molecular biology and synthetic approaches. Full article

This study compared the performance of Clostridium ljungdahlii and Clostridium aceticum in the fermentation of fructose and C1-gasses (CO, CO₂, N₂) to produce valuable products such as ethanol and acetic acid. In heterotrophic fermentation (fructose), C. ljungdahlii yielded high ethanol concentrations (350 mg/L) and acetic acid (500 mg/L), with optimal production at pH 8 on the first day of fermentation. Although autotrophic fermentation (C1-gasses) resulted in lower ethanol levels (200 mg/L), it remained a viable option. Conversely, C. aceticum predominantly produced acetic acid in both fermentation modes, with higher concentrations in the heterotrophic fermentation (1600 mg/L) than the autotrophic fermentation (380 mg/L). These findings demonstrate the versatility of both microorganisms for producing valuable metabolites. C. ljungdahlii shows promise for bioethanol production, while C. aceticum excels at generating acetic acid, a crucial component in bioplastics and various industrial processes. Full article

Two thermophilic spore-forming sulfate-reducing strains, 435^T and 781, were isolated from oil and gas reservoirs in Western Siberia (Russia) about 50 years ago. Both strains were found to be neutrophilic, chemoorganotrophic, anaerobic bacteria, growing at 45–70 °C (optimum, 55–60 °C) and with 0–4.5% (w/v) NaCl (optimum, 0.5–1% NaCl). The major fatty acids were iso-C_15:0, iso-C_17:0, C_16:0, and C_18:0. In sulfate-reducing conditions, the strains utilized H₂/CO₂, formate, lactate, pyruvate, malate, fumarate, succinate, methanol, ethanol, propanol, butanol, butyrate, valerate, and palmitate. In 2005, based on phenotypic characteristics and a 16S rRNA gene sequence analysis, the strains were described as ‘Desulfotomaculum salinum’ sp. nov. However, this species was not validly published because the type strain was not deposited in two culture collections. In this study, a genomic analysis of strain 435^T was carried out to determine its taxonomic affiliation. The genome size of strain 435^T was 2.886 Mb with a 55.1% genomic G + C content. The average nucleotide identity and digital DNA–DNA hybridization values were highest between strain 435^T and members of the genus Desulfofundulus, 78.7–93.3% and 25.0–52.2%, respectively; these values were below the species delineation cut-offs (<95–96% and <70%). The cumulative phenotypic and phylogenetic data indicate that two strains represent a novel species within the genus Desulfofundulus, for which the name Desulfofundulus salinus sp. nov. is proposed. The type strain is 435^T (=VKM B-1492^T = DSM 23196^T). A genome analysis of strain 435^T revealed the genes for dissimilatory sulfate reduction, autotrophic carbon fixation via the Wood–Ljungdahl pathway, hydrogen utilization, methanol and organic acids metabolism, and sporulation, which were confirmed by cultivation studies. Full article

The depletion of fossil fuel resources and the CO₂ emissions coupled with petroleum-based industrial processes present a relevant issue for the whole of society. An alternative to the fossil-based production of chemicals is microbial fermentation using acetogens. Acetogenic bacteria are able to metabolize CO or CO₂ (+H₂) via the Wood–Ljungdahl pathway. As isopropanol is widely used in a variety of industrial branches, it is advantageous to find a fossil-independent production process. In this study, Acetobacterium woodii was employed to produce isopropanol via plasmid-based expression of the enzymes thiolase A, CoA-transferase, acetoacetate decarboxylase and secondary alcohol dehydrogenase. An examination of the enzymes originating from different organisms led to a maximum isopropanol production of 5.64 ± 1.08 mM using CO₂ + H₂ as the carbon and energy source. To this end, the genes thlA (encoding thiolase A) and ctfA/ctfB (encoding CoA-transferase) of Clostridium scatologenes, adc (encoding acetoacetate decarboxylase) originating from C. acetobutylicum and sadH (encoding secondary alcohol dehydrogenase) of C. beijerinckii DSM 6423 were employed. Since bottlenecks in the isopropanol production pathway are known, optimization of the strain was investigated, resulting in a 2.5-fold increase in isopropanol concentration. Full article

The methanogenic strain Mx-05^T was isolated from the human fecal microbiome. A phylogenetic analysis based on the 16S rRNA gene and protein marker genes indicated that the strain is affiliated with the order Methanomassiliicoccales. It shares 86.9% 16S rRNA gene sequence identity with Methanomassiliicoccus luminyensis, the only member of this order previously isolated. The cells of Mx-05^T were non-motile cocci, with a diameter range of 0.4–0.7 μm. They grew anaerobically and reduced methanol, monomethylamine, dimethylamine, and trimethylamine into methane, using H₂ as an electron donor. H₂/CO₂, formate, ethanol, and acetate were not used as energy sources. The growth of Mx-05^T required an unknown medium factor(s) provided by Eggerthella lenta and present in rumen fluid. Mx-05^T grew between 30 °C and 40 °C (optimum 37 °C), over a pH range of 6.9–8.3 (optimum pH 7.5), and between 0.02 and 0.34 mol.L⁻¹ NaCl (optimum 0.12 mol.L⁻¹ NaCl). The genome is 1.67 Mbp with a G+C content of 55.5 mol%. Genome sequence annotation confirmed the absence of the methyl branch of the H₄MPT Wood–Ljungdahl pathway, as described for other Methanomassiliicoccales members. Based on an average nucleotide identity analysis, we propose strain Mx-05^T as being a novel representative of the order Methanomassiliicoccales, within the novel family Methanomethylophilaceae, for which the name Methanomethylophilus alvi gen. nov, sp. nov. is proposed. The type strain is Mx-05^T (JCM 31474T). Full article

The anaerobic oxidation of fatty acids and alcohols occurs near the thermodynamic limit of life. This process is driven by syntrophic bacteria that oxidize fatty acids and/or alcohols, their syntrophic partners that consume the products of this oxidation, and the pathways for interspecies electron exchange via these products or direct interspecies electron transfer (DIET). Due to the interdependence of syntrophic microorganisms on each other’s metabolic activity, their isolation in pure cultures is almost impossible. Thus, little is known about their physiology, and the only available way to fill in the knowledge gap on these organisms is genomic and metabolic analysis of syntrophic cultures. Here we report the results of genome sequencing and analysis of an obligately syntrophic alkaliphilic bacterium ‘Candidatus Contubernalis alkaliaceticus’. The genomic data suggest that acetate oxidation is carried out by the Wood–Ljungdahl pathway, while a bimodular respiratory system involving an Rnf complex and a Na⁺-dependent ATP synthase is used for energy conservation. The predicted genomic ability of ‘Ca. C. alkaliaceticus’ to outperform interspecies electron transfer both indirectly, via H₂ or formate, and directly, via pili-like appendages of its syntrophic partner or conductive mineral particles, was experimentally demonstrated. This is the first indication of DIET in the class Dethiobacteria. Full article

Biotechnology has a high potential to substantially contribute to a low-carbon society. Several green processes are already well established, utilizing the unique capacity of living cells or their instruments. Beyond that, the authors believe that there are new biotechnological procedures in the pipeline which have the momentum to add to this ongoing change in our economy. Eight promising biotechnology tools were selected by the authors as potentially impactful game changers: (i) the Wood–Ljungdahl pathway, (ii) carbonic anhydrase, (iii) cutinase, (iv) methanogens, (v) electro-microbiology, (vi) hydrogenase, (vii) cellulosome and, (viii) nitrogenase. Some of them are fairly new and are explored predominantly in science labs. Others have been around for decades, however, with new scientific groundwork that may rigorously expand their roles. In the current paper, the authors summarize the latest state of research on these eight selected tools and the status of their practical implementation. We bring forward our arguments on why we consider these processes real game changers. Full article

Foods contain dietary fibers which can be classified into soluble and insoluble forms. The nutritional composition of fast foods is considered unhealthy because it negatively affects the production of short-chain fatty acids (SCFAs). Dietary fiber is resistant to digestive enzymes in the gut, which modulates the anaerobic intestinal microbiota (AIM) and fabricates SCFAs. Acetate, butyrate, and propionate are dominant in the gut and are generated via Wood–Ljungdahl and acrylate pathways. In pancreatic dysfunction, the release of insulin/glucagon is impaired, leading to hyperglycemia. SCFAs enhance insulin sensitivity or secretion, beta-cell function, leptin release, mitochondrial function, and intestinal gluconeogenesis in human organs, which positively affects type 2 diabetes (T2D). Research models have shown that SCFAs either enhance the release of peptide YY (PYY) and glucagon-like peptide-1 (GLP-1) from L-cells (entero-endocrine), or promotes the release of leptin hormone in adipose tissues through G-protein receptors GPR-41 and GPR-43. Dietary fiber is a component that influences the production of SCFAs by AIM, which may have beneficial effects on T2D. This review focuses on the effectiveness of dietary fiber in producing SCFAs in the colon by the AIM as well as the health-promoting effects on T2D. Full article

Aquifex aeolicus is a microaerophilic hydrogen- and sulfur -oxidizing bacterium that assimilates CO₂ via the reverse tricarboxylic acid cycle (rTCA). Key enzymes of this pathway are pyruvate:ferredoxin oxidoreductase (PFOR) and 2-oxoglutarate:ferredoxin oxidoreductase (OGOR), which are responsible, respectively, for the reductive carboxylation of acetyl-CoA to pyruvate and of succinyl-CoA to 2-oxoglutarate, two energetically unfavorable reactions that require a strong reduction potential. We have confirmed, by biochemistry and proteomics, that A. aeolicus possesses a pentameric version of these enzyme complexes ((αβγδε)₂) and that they are highly abundant in the cell. In addition, we have purified and characterized, from the soluble fraction of A. aeolicus, two low redox potential and oxygen-stable [4Fe-4S] ferredoxins (Fd6 and Fd7, E⁰ = −440 and −460 mV, respectively) and shown that they can physically interact and exchange electrons with both PFOR and OGOR, suggesting that they could be the physiological electron donors of the system in vivo. Shotgun proteomics indicated that all the enzymes assumed to be involved in the rTCA cycle are produced in the A. aeolicus cells. A number of additional enzymes, previously suggested to be part of a putative partial Wood-Ljungdahl pathway used for the synthesis of serine and glycine from CO₂ were identified by mass spectrometry, but their abundance in the cell seems to be much lower than that of the rTCA cycle. Their possible involvement in carbon assimilation is discussed. Full article

The key microbial group involved in anaerobic methane oxidation is anaerobic methanotrophic archaea (ANME). From a terrestrial mud volcano, we enriched a microbial community containing ANME-2a, using methane as an electron donor, Fe(III) oxide (ferrihydrite) as an electron acceptor, and anthraquinone-2,6-disulfonate as an electron shuttle. Ferrihydrite reduction led to the formation of a black, highly magnetic precipitate. A significant relative abundance of ANME-2a in batch cultures was observed over five subsequent transfers. Phylogenetic analysis revealed that, in addition to ANME-2a, two bacterial taxa belonging to uncultured Desulfobulbaceae and Anaerolineaceae were constantly present in all enrichments. Metagenome-assembled genomes (MAGs) of ANME-2a contained a complete set of genes for methanogenesis and numerous genes of multiheme c-type cytochromes (MHC), indicating the capability of methanotrophs to transfer electrons to metal oxides or to a bacterial partner. One of the ANME MAGs encoded respiratory arsenate reductase (Arr), suggesting the potential for a direct coupling of methane oxidation with As(V) reduction in the single microorganism. The same MAG also encoded uptake [NiFe] hydrogenase, which is uncommon for ANME-2. The MAG of uncultured Desulfobulbaceae contained genes of dissimilatory sulfate reduction, a Wood–Ljungdahl pathway for autotrophic CO₂ fixation, hydrogenases, and 43 MHC. We hypothesize that uncultured Desulfobulbaceae is a bacterial partner of ANME-2a, which mediates extracellular electron transfer to Fe(III) oxide. Full article

The KEGG Orthology (KO) database is a widely used molecular function reference database which can be used to conduct functional annotation of most microorganisms. At present, there are many KEGG tools based on the KO entries for annotating functional orthologs. However, determining how to efficiently extract and sort the annotation results of KEGG still hinders the subsequent genome analysis. There is a lack of effective measures used to quickly extract and classify the gene sequences and species information of the KEGG annotations. Here, we present a supporting tool: KEGG_Extractor for species-specific genes extraction and classification, which can output the results through an iterative keyword matching algorithm. It can not only extract and classify the amino acid sequences, but also the nucleotide sequences, and it has proved to be fast and efficient for microbial analysis. Analysis of the ancient Wood Ljungdahl (WL) pathway through the KEGG_Extractor reveals that ~226 archaeal strains contained the WL pathway-related genes. Most of them were Methanococcus maripaludis, Methanosarcina mazei and members of the Methanobacterium, Thermococcus and Methanosarcina genus. Using the KEGG_Extractor, the ARWL database was constructed, which had a high accuracy and complement. This tool helps to link genes with the KEGG pathway and promote the reconstruction of molecular networks. Availability and implementation: KEGG_Extractor is freely available from the GitHub. Full article

Methanogens are archaea that grow by producing methane as a catabolic end product and thrive in diverse anaerobic habitats, including soil, sediments, oil reservoirs, digestive tracts, and anaerobic digesters. Methanogens have typically been classified into three types—namely, hydrogenotrophic, acetoclastic, and methylotrophic methanogens. In addition, studies have found methanogens that require both hydrogen/CO₂ and organics, such as acetate, for growth. Genomic analyses have shown that these methanogens lack genes for carbon monoxide dehydrogenase/acetyl-CoA synthase (Codh/Acs), one of the oldest enzymes that catalyzes the central step in the Wood–Ljungdahl pathway. Since these methanogens have been found dominant in such habitats as digestive tracts and anaerobic digesters, it is suggested that the loss of Codh/Acs confers ecological advantages on methanogens in these habitats. Comparisons in genomes of methanogens suggest the possibility that these methanogens have emerged recently in anaerobic digesters and are currently under the process of prevalence. We propose that an understanding of the genetic and ecological processes associated with the emergence and prevalence of these methanogens in anaerobic digesters would offer novel evolutionary insights into microbial ecology. Full article

Syngas fermentation via the Wood-Ljungdahl (WL) pathway is a promising approach for converting gaseous pollutants (CO and CO₂) into high-value commodities. Because the WL involves several enzymes with trace metal components, it requires an adequate supply of micronutrients in the fermentation medium for targeted bioprocessing such as bioethanol production. Plackett-Burman statistical analysis was performed to examine the most efficient trace elements (Ni, Mg, Ca, Mn, Co, Cu, B, W, Zn, Fe, and Mo) and their concentrations for Clostridium ljungdahlii on ethanol production. Overall, 1.5 to 2.5 fold improvement in ethanol production could be achieved with designed trace element concentrations. The effects of tungsten and copper on ethanol and biomass production were determined to be the most significant, respectively. The model developed was statistically significant and has the potential to significantly decrease the cost of trace element solutions by 18–22%. This research demonstrates the critical importance of optimizing the medium for syngas fermentation in terms of product distribution and economic feasibility. Full article

Recycling residual industrial gases and residual biomass as substrates to biofuel production by fermentation is an important alternative to reduce organic wastes and greenhouse gases emission. Clostridium carboxidivorans can metabolize gaseous substrates as CO and CO₂ to produce ethanol and higher alcohols through the Wood-Ljungdahl pathway. However, the syngas fermentation is limited by low mass transfer rates. In this work, a syngas fermentation was carried out in serum glass bottles adding different concentrations of Tween® 80 in ATCC® 2713 culture medium to improve gas-liquid mass transfer. We observed a 200% increase in ethanol production by adding 0.15% (v/v) of the surfactant in the culture medium and a 15% increase in biomass production by adding 0.3% (v/v) of the surfactant in the culture medium. The process was reproduced in stirred tank bioreactor with continuous syngas low flow, and a maximum ethanol productivity of 0.050 g/L.h was achieved. Full article