Search Results (125)

A novel species of the genus Methylocystis is proposed based on polyphasic evidence from strain SC2^T, isolated from the heavily polluted Saale River near Wichmar, Germany. Digital DNA–DNA hybridization and phylogenomic analyses demonstrate that strain SC2^T represents a distinct species within the genus, clearly separated from its closest relatives, namely Methylocystis suflitae NLS-7^T, Methylocystis rosea SV97^T, Methylocystis silviterrae FS^T, and Methylocystis hirsuta CSC1^T. As is typical of the family Methylocystaceae, cells possess intracytoplasmic membranes arranged parallel to the cytoplasmic membrane, and the dominant fatty acids are C18:1ω8c and C18:1ω7c. The strain grows aerobically on methane as the primary carbon and energy source and expresses both low- and high-affinity particulate methane monooxygenase (pMMO), but lacks the soluble form. The species epithet reflects the strain’s ability to utilize hydrogen as an alternative energy source. A further feature is its use of asparagine as an osmoprotectant, enhancing salt tolerance. Genomic analysis reveals complete pathways for nitrogen fixation, denitrification, and hydrogen oxidation. These genetic and physiological characteristics support the designation of a novel species, for which the name Methylocystis hydrogenophila sp. nov. is proposed. The type strain is SC2^T (=DSM 114506 = NCIMB 15437). Full article

The production of green hydrogen by microalgae is a promising strategy to convert energy of sun light into a carbon-free fuel. Many problems must be solved before large-scale industrial applications. One solution is to find a microalgal species that is easy to grow, easy to manipulate, and that can produce hydrogen open-air, thus in the presence of oxygen, for periods of time as long as possible. In this work we investigate by means of predictive computational models, the [FeFe] hydrogenase enzyme of Nannochloropsis salina, a promising microcalga already used to produce high-value products in salt water. Catalysis of water reduction to hydrogen by [FeFe] hydrogenase occurs in a peculiar iron-sulfur cluster (H-cluster) contained into a conserved H-domain, well represented by the known structure of the single-domain enzyme in Chlamydomonas reinhardtii (457 residues). By combining advanced deep-learning and molecular simulation methods we propose for N. salina a two-domain enzyme architecture hosting five iron-sulfur clusters. The enzyme organization is allowed by the protein size of 708 residues and by its sequence rich in cysteine and histidine residues mostly binding Fe atoms. The structure of an extended F-domain, containing four auxiliary iron-sulfur clusters and interacting with both the reductant ferredoxin and the H-domain, is thus predicted for the first time for microalgal [FeFe] hydrogenase. The structural study is the first step towards further studies of the microalga as a microorganism producing pure hydrogen gas. Full article

Biohydrogen, a low-carbon footprint technology, can play a significant role in decarbonizing the energy system. It uses existing infrastructure, is easily transportable, and produces no greenhouse gas emissions. Four technologies can be used to produce biohydrogen: photosynthetic biohydrogen, dark fermentation (DF), photo-fermentation, and microbial electrolysis cells (MECs). DF produces more biohydrogen and is flexible with organic substrates, making it a sustainable method of waste repurposing. However, low achievable biohydrogen yields are a common issue. To overcome this, catalytic mechanisms, including enzymatic systems such as [Fe-Fe]- and [Ni-Fe]-hydrogenases in DF and electroactive microbial consortia in MECs, alongside advanced electrode catalysts which collectively surmount thermodynamic and kinetic constraints, and the two stage system, such as DF connection to photo-fermentation and anaerobic digestion (AD) to microbial electrolysis cells (MECs), have been investigated. MECs can generate biohydrogen at better yields by using sugars or organic acids, and combining DF and MEC technologies could improve biohydrogen production. As such, this review highlights the challenges and possible solutions for coupling DF–MEC while also offering knowledge regarding the technical and microbiological aspects. Full article

Extreme acidophiles from the Acidithiobacillia class thrive in highly acidic environments where they rely on diverse regulatory mechanisms for adaptation. These mechanisms include sigma factors, transcription factors (TFs), and transcription factor binding sites (TFBS), which control essential pathways. Comparative genomics and bioinformatics analyses identified sigma factors and TFs in Acidithiobacillia, showing similarities but key differences from reference neutrophiles. This study highlights sigma54-dependent one- and two-component systems that are crucial for survival in energy acquisition from sulfur compounds and hydrogen as well as nutrient assimilation. Furthermore, the data suggested evolutionary divergence in regulatory elements distinguishes S-oxidizing from Fe-S-oxidizing members of Acidithiobacillia. Conservation of gene clusters, synteny, and phylogenetic analyses supported the expected phenotypes in each species. Notable examples include HupR’s role in hydrogenase-2 oxidation in Fe-S-oxidizers, TspR/TspS regulation of the sulfur oxidation complex, and FleR/FleS control of flagellar motility in S-oxidizers. These regulatory mechanisms act as master controllers of bacterial activity, reflecting adaptation to distinct metabolic needs within Acidithiobacillia. Full article

Direct interspecies electron transfer (DIET) is a syntrophic metabolism wherein free electrons are directly transferred between microorganisms without the mediation of intermediates such as molecular hydrogen or formate. Previous research has demonstrated that Methanothrix harundinacea 6Ac is capable of reducing carbon dioxide through DIET. However, the mechanisms underlying electron uptake in M. harundinacea 6Ac during DIET remain poorly understood. This study aims to elucidate the electron and proton flux in M. harundinacea 6Ac during DIET and to propose a model for electron uptake in this organism, primarily based on the analysis of gene transcript levels, genomic characteristics of M. harundinacea 6Ac, and the pathways generating fully reduced ferridoxin (Fd_red²⁻), reduced coenzyme F₄₂₀ (F₄₂₀H₂), coenzyme M (CoM-SH), and coenzyme B (CoB-SH) during DIET. The findings suggest that membrane-bound heterodisulfide reductase (HdrED), F₄₂₀H₂-dehydrogenase lacking subunit F (Fpo⁻), and cytoplasmic heterodisulfide reductase (HdrABC)-subunit B of F₄₂₀-reducing hydrogenase (FrhB) complex play critical roles in electron uptake in M. harundinacea 6Ac during DIET. Specifically, Fpo⁻ is responsible for generating Fd_red²⁻ with reduced methanophenazine (MPH₂), driven by a proton motive force, while HdrED facilitates the reduction of heterodisulfide of coenzyme M and coenzyme B (CoM-S-S-CoB) to CoM-SH and CoB-SH using MPH₂. Additionally, cytoplasmic heterodisulfide reductase HdrABC and subunit B of coenzyme F₄₂₀-hydrogenase complex (HdrABC-FrhB complex) catalyzes the reduction of oxidized coenzyme F₄₂₀ (F₄₂₀) to F₄₂₀H₂, utilizing CoM-SH, CoB-SH, and Fd_red²⁻. This study represents the first genetics-based functional characterization of electron and proton flux in M. harundinacea 6Ac during DIET, providing a model for further investigation of electron uptake in Methanosaeta species. Furthermore, it deepens our understanding of the mechanisms underlying electron uptake in methanogens during DIET. Full article

The genus Skermanella comprises important soil bacteria that are often associated with the crop rhizospheres, but its physiological traits remain poorly understood. This study characterizes Skermanella sp. TT6^T, isolated from human skin, with a focus on its metabolic and environmental adaptations. Genome sequencing and phylogenomic analyses revealed that the strain TT6^T is most closely related to S. rosea M1^T, with average nucleotide identity and digital DNA–DNA hybridization values of 94.14% (±0.5%) and 64.7%, respectively. Comparative genomic analysis showed that the strains TT6^T, S. rosea M1^T and S. mucosa 8-14-6^T share the Calvin cycle, and possess photosynthetic genes associated with the purple bacteria-type photosystem II. The strains TT6^T and S. rosea M1^T exhibited growth in a nitrogen-free medium under microaerobic conditions, which were generated in test tubes containing 0.1% soft agar. Under these conditions, with nitrate as a nitrogen source, S. rosea M1^T formed gases, indicating denitrification. Strain TT6^T also contains gene clusters involved in trehalose and carotenoid biosynthesis, along with salt-dependent colony morphology changes, highlighting its adaptive versatility. Genomic analyses further identified pathways related to hydrogenase and sulfur oxidation. Phenotypic and chemotaxonomic traits of strain TT6^T were also compared with closely related type strains, confirming its genotypic and phenotypic distinctiveness. The new species, Skermanella cutis sp. nov., is proposed, with TT6^T (=KCTC 82306^T = JCM 34945^T) as the type strain. This study underscores the agricultural and ecological significance of the genus Skermanella. Full article

Synthetic mimics of the active site of [FeFe]-hydrogenase enzymes are important in the context of catalytic hydrogen production for future energetic applications. Providing a detailed quantum chemical description of the catalytic center of such mimics contributes to a better understanding of their behavior in hydrogen production processes. In this work, the analysis of bonds in the butterfly [2Fe2S] core in a series of complexes based on recently synthesized [FeFe]-hydrogenase mimics has been carried out using a wide range of quantum chemical topological methods. This series includes hexacarbonyl diiron dithiolate-bridged complexes with the bridging ligand bearing a five-membered carbon ring functionalized with diverse groups. The quantum theory of atoms in molecules (QTAIM) and the electron localization function (ELF) provided detailed characteristics of Fe–Fe and Fe–S bonds in the [2Fe2S] core of the complexes. A relatively small amount of strongly delocalized electron charge is attributed to the Fe–Fe bond. It was established how the topological parameters of the Fe–Fe and Fe–S bonds are affected by the five-membered carbon ring and its functionalization in the bridging dithiolate ligand. Next, one of the first applications of the interacting quantum atoms (IQA) method to [FeFe]-hydrogenase mimics was presented. The pairwise interaction between the metal centers in the [2Fe2S] core turns out to be destabilizing in contrast to the Fe–S interactions responsible for the stabilization of the entire core. Full article

Anaerobic digestion is a critical technology for pollution control, resource capacity enhancement, and sludge management, necessitating improvements in its efficiency. Formate serves as an electron carrier in syntrophic oxidation of volatile fatty acids (VFAs) during anaerobic digestion. The accumulation of formate can exert an inhibitory effect on the anaerobic digestion process. However, the stress concentration and the mechanism of the formate are not as simple as theoretical calculations based on thermodynamics. Thus, we investigated the response to different concentrations of formate in the syntrophic oxidation of propionate. The anaerobic sludge system and syntrophic co-culture system were applied. The propionate showed more stable degradation when formate dosage ranged from 5 to 10 mM. However, when the formate dosage reached 50 mM, the concentration of propionate was significantly higher than that of CK group, and the propionate metabolism was significantly inhibited. The reduction in functional flora and homogeneous metabolic pathways were found to be unfavorable for the stable progression of syntrophic propionate metabolism. Thus, the enhancement of homoacetogenesis can be a strategy adopted by the sludge system to alleviate formate stress. The methylmalonyl-CoA (MMC) pathway was inhibited under formate stress; the downregulation of RNA transcription of formate dehydrogenase (FDH) and hydrogenase (Hyd) related to MMC pathway may be the main reason for the inhibition of syntrophic propionate oxidation. The anaerobic sludge experiment and the co-culture experiment elucidated the mechanism of action of formate from both macroscopic rules and microscopic molecular mechanisms, respectively. Full article

Due to environmental pollution and the depletion of fossil fuels, there is growing interest in the development and use of biofuels as environmentally friendly alternatives. One of the most promising biofuels is biohydrogen, hydrogen produced through sustainable processes using microorganisms such as bacteria and algae. One of the most interesting bacteria for hydrogen production is Ralstonia eutropha H16, known for its ability to produce oxygen-tolerant hydrogenases. These enzymes play a crucial role in biohydrogen metabolism and production. The aim of this work was to determine the optimal conditions (reactor type and synthetic medium composition) for the cultivation of R. eutropha H16. The culture media contained different concentrations of fructose and glycerol (mono- or double-substrate cultivation) and the experiments were carried out in a batch reactor. The initial experiments were carried out with 4 g/L fructose or glycerol in the culture medium at pH 7, T = 30 °C, and 120 rpm. The mathematical model, consisting of the growth kinetics (described by the Monod’s model) and the corresponding mass balances, was proposed. The developed model was validated using two independent experiments with different initial substrate concentrations: 2 g/L glycerol and fructose in one medium and 4 g/L fructose and 1 g/L glycerol in the second. In order to propose the optimal cultivation procedure for future research, the mathematical model simulations were performed for different reactor types (batch, fed-batch, and continuous stirred tank reactors) and different initial substrate concentrations. The most successful experiment was the one with 4 g/L glycerol, where γ_X = 0.485 ± 0.001 g/L of biomass was achieved. Further calculations showed that the most biomass would be produced at higher glycerol concentrations (at γ_G = 6.358 g/L, γ_X = 1.311 g/L should be achieved after 200 h of cultivation) and when using a fed-batch reactor (γ_X = 0.944 g/L after 200 h of cultivation). Full article

Dark fermentation is a promising method for hydrogen (H₂) production utilizing the metabolic pathways of diverse microbial communities. This process can be carried out without the need for light, making it easier and more efficient to operate in different environments and at a lower cost. It also utilizes a wide range of substrates, making it highly adaptable to waste-to-energy applications. Clostridium spp. are particularly favored in this method due to their versatile metabolism, ability to utilize a wide range of substrates, and high H₂ yields. Anaerobes and facultative anaerobes are mostly used in studies due to their efficient hydrogenase enzyme activity and metabolic pathways. A pH range of 5.5–6.5 and a temperature of 30–37 °C for mesophiles and 55–60 °C for thermophiles are usually preferred in addition to the other parameters such as hydraulic retention time and substrate used. The highest H₂ yield of 9.39 mol H₂/mol sucrose consumed was obtained by C. beijerinckii using sucrose as a substrate under batch mode conditions at 37 °C and pH 6–7. The review analyzes different bacterial species and examines the influence of optimized parameters required on H₂ yield in different bioreactor operating modes. Full article

The first discovery of methanogens led to the formation of a new domain of life known as Archaea. The Archaea domain exhibits properties vastly different from previously known Bacteria and Eucarya domains. However, for a certain multi-step process, a syntrophic relationship between organisms from all domains is needed. This process is called methanogenesis and is defined as the biological production of methane. Different methanogenic pathways prevail depending on substrate availability and the employed order of methanogenic Archaea. Most methanogens reduce carbon dioxide to methane with hydrogen through a hydrogenotrophic pathway. For hydrogen activation, a group of enzymes called hydrogenases is required. Regardless of the methanogenic pathway, electrons are carried between microorganisms by hydrogen. Naturally occurring processes, such as methanogenesis, can be engineered for industrial use. With the growth and emergence of new industries, the amount of produced industrial waste is an ever-growing environmental problem. For successful wastewater remediation, a syntrophic correlation between various microorganisms is needed. The composition of microorganisms depends on wastewater type, organic loading rates, anaerobic reactor design, pH, and temperature. The last step of anaerobic wastewater treatment is production of biomethane by methanogenesis, which is thought to be a cost-effective means of energy production for this renewable biogas. Full article

The abscission of fruits has a significant impact on yield, which in turn has a corresponding effect on economic benefits. In order to better understand the molecular mechanism of early coconut fruit abscission, the morphological and structural characteristics, cell wall hydrolysis and oxidase activities, phytohormones, and transcriptomes were analyzed in the abscission zone (AZ) from early-abscised coconut fruits (AFs) and non-abscised coconut fruits (CFs). These results indicated that the weight and water content of AFs are significantly lower than those of CFs, and the color of AFs is a grayish dark red, with an abnormal AZ structure. Cellulase (CEL), polygalacturonase (PG), pectinesterase (PE), and peroxidase (POD) activities were significantly lower than those of CFs. The levels of auxin (IAA), gibberellin (GA), cytokinins (CKs), and brassinosteroid (BR) in AFs were significantly lower than those in CFs. However, the content of abscisic acid (ABA), ethylene (ETH), jasmonic acid (JA), and salicylic acid (SA) in AFs was significantly higher than in CFs. The transcriptome analysis results showed that 3601 DEGs were functionally annotated, with 1813 DEGs upregulated and 1788 DEGs downregulated. Among these DEGs, many genes were enriched in pathways such as plant hormone signal transduction, carbon metabolism, peroxisome, pentose and gluconate interconversion, MAPK signaling pathway—plant, and starch and sucrose metabolism. Regarding cell wall remodeling-related genes (PG, CEL, PE, POD, xyloglucan endoglucosidase/hydrogenase (XTH), expansin (EXP), endoglucanase, chitinase, and beta-galactosidase) and phytohormone-related genes (IAA, GA, CKs, BR, ABA, JA, SA, and ETH) were significantly differentially expressed in the AZ of AFs. Additionally, BHLH, ERF/AP2, WRKY, bZIP, and NAC transcription factors (TFs) were significantly differently expressed, reflecting their crucial role in regulating the abscission process. This study’s results revealed the molecular mechanism of early fruit abscission in coconuts. This provided a new reference point for further research on coconut organ development and abscission. Full article

In the green alga Chlamydomonas reinhardtii, hydrogen production is catalyzed via the [FeFe]-hydrogenases HydA1 and HydA2. The electrons required for the catalysis are transferred from ferredoxin (FDX) towards the hydrogenases. In the light, ferredoxin receives its electrons from photosystem I (PSI) so that H₂ production becomes a fully light-driven process. HydA1 and HydA2 are highly O₂ sensitive; consequently, the formation of H₂ occurs mainly under anoxic conditions. Yet, photo-H₂ production is tightly coupled to the efficiency of photosynthetic electron transport and linked to the photosynthetic control via the Cyt b₆f complex, the control of electron transfer at the level of photosystem II (PSII) and the structural remodeling of photosystem I (PSI). These processes also determine the efficiency of linear (LEF) and cyclic electron flow (CEF). The latter is competitive with H₂ photoproduction. Additionally, the CBB cycle competes with H₂ photoproduction. Consequently, an in-depth understanding of light-driven H₂ production via photosynthetic electron transfer and its competition with CO₂ fixation is essential for improving photo-H₂ production. At the same time, the smart design of photo-H₂ production schemes and photo-H₂ bioreactors are challenges for efficient up-scaling of light-driven photo-H₂ production. Full article

The design of iron clusters featuring a bimetallic core and several protonation sites in the second coordination sphere of the metal centers is important for modeling the activity of polymetallic active sites such as the H-cluster of [FeFe]-hydrogenases. For this purpose, the syntheses of complexes [Fe₃(CO)₅(κ²-P^Ph₂N^R₂)(μ-pdt)₂] (R = Ph (1), Bn (2)) and [Fe₃(CO)₅(κ²-P^Ph₂N^R₂)(μ-adt^Bn)(μ-pdt)] (R = Ph (3), Bn (4)) were carried out by reacting hexacarbonyl precursors [Fe₂(CO)₆(µ-xdt)] (xdt = pdt (propanedithiolate), adt^Bn (azadithiolate) with mononuclear complexes [Fe(κ²-pdt)(CO)₂(κ²-P^Ph₂N^R₂)] (P^Ph₂N^R₂ = (P^PhCH₂N^RCH₂)₂, R = Ph, Bn) in order to introduce amine functions, through well-known P^Ph₂N^R₂ diphosphine, into the vicinity of the triiron core. The investigation of the reactivity of these triiron species towards the proton (in the presence of CF₃SO₃H) and the influence of the pendant amines on the redox properties of these complexes were explored using spectroscopic and electrochemical methods. The protonation sites in such triiron clusters and their relationships were identified. The orientation of the first and second protonation processes depends on the arrangement of the second coordination sphere. The similarities and differences, due to the extended metal nuclearity, with their dinuclear counterparts [Fe₂(CO)₄(κ²-P^Ph₂N^R₂)(μ-pdt)], were highlighted. Full article

Molecular hydrogen (H₂) is crucial for agricultural microbial systems. However, the mechanisms underlying its influence on crop yields is yet to be fully elucidated. This study observed that H₂-based irrigation significantly increased strawberry (Fragaria × ananassa Duch.) yield with/without nutrient fertilization. The reduction in soil available nitrogen (N), phosphorus (P), potassium (K), and organic matter was consistent with the increased expression levels of N/P/K-absorption-related genes in root tissues at the fruiting stage. Metagenomics profiling showed the alterations in rhizosphere microbial community composition achieved by H₂, particularly under the conditions without fertilizers. These included the enrichment of plant-growth-promoting rhizobacteria, such as Burkholderia, Pseudomonas, and Cupriavidus genera. Rhizobacteria with the capability to oxidize H₂ (group 2a [NiFe] hydrogenase) were also enriched. Consistently, genes related to soil carbon (C) fixation (i.e., rbcL, porD, frdAB, etc.), dissimilar nitrate reduction (i.e., napAB and nrfAH), and P solublization, mineralization, and transportation (i.e., ppx-gppA, appA, and ugpABCE) exhibited higher abundance. Contrary tendencies were observed in the soil C degradation and N denitrification genes. Together, these results clearly indicate that microbe-mediated soil C, N, and P cycles might be functionally altered by H₂, thus increasing plant nutrient uptake capacity and horticultural crop yield. Full article