Search Results (112)

Coenzyme Q₁₀ (CoQ₁₀) has attracted widespread attention in recent years due to its momentous physiological functions. Microbial fermentation is the major method in CoQ₁₀ industrial production, and Rhodobacter sphaeroides is the main strain for the production of CoQ₁₀ by fermentation. Optimization of the culture medium is a popular solution to improve the metabolite production. Culture medium is the material basis for microbial growth and product synthesis, of which inorganic salts are a key ingredient. Uniform design (UD), artificial neural network (ANN), and genetic algorithm (GA) are the main research methods. Through uniform design (UD) and artificial neural network/genetic algorithm (ANN-GA) progressive optimization, an optimal formulation of the inorganic salts in fermentation medium was obtained (g·L⁻¹): MgSO₄ 12, NaCl 2.5, FeSO₄ 1.6, KH₂PO₄ 0.8, MnSO₄ 0.1, CaCl₂ 0.1. Ultimately, the fermentation yield of CoQ₁₀ could reach 255.36 mg·L⁻¹. ANN-GA exhibited a superior prediction capability compared to UD. Compared to UD, the optimization results of ANN-GA had a smaller relative error (ANN-GA 1.23%; UD 3.01%) and a higher increase rate in the fermentation level of CoQ₁₀ (ANN-GA 4.1%; UD 2.04%). R. sphaeroides had a high demand for Mg²⁺. Full article

Phage Lydia, a newly isolated siphovirus infecting Pseudomonas aeruginosa, was characterized with respect to its basic kinetic properties and subjected to comparative bioinformatic analysis with related phages. The phage exhibited a restricted host range, with lytic activity observed against 7 of 30 tested isolates. The genome of phage Lydia consists of a 61,986 bp dsDNA molecule and contains 89 predicted genes. Bioinformatic analysis suggests the presence of a DNA modification system, but no apparent genes associated with lysogeny or antibiotic resistance were identified. Taxonomic classification places Lydia within the Mesyanzhinovviridae family, Rabinowitzvirinae subfamily, and Yuavirus genus, with the closest relation to Pseudomonas virus M6. Comprehensive bioinformatic studies, including structural modelling and analysis of phage proteins, as well as comparative taxonomic, phylogenomic, and pangenomic analyses of the Mesyanzhinovviridae family, revealed relationships between proteins of Mesyanzhinovviridae phages, proteins from other phage groups, encapsulins, and a gene transfer agent (GTA) particle from Rhodobacter capsulatus. These analyses uncovered patterns of evolutionary history within the family, characterized by genetic exchange events alongside the maintenance of a common genomic architecture, leading to the emergence of new groups within the family. Full article

The overuse of chemical fertilizers under adverse conditions endangers the sustainability of agriculture. A biological approach should be investigated to address this issue. Therefore, this study aimed to detect the potency of purple non-sulfur bacteria that can fix nitrogen (N) (PNSB-fN) Rhodobacter sphaeroides in soil N fertility, plant N uptake, growth, and rice yield. In brief, an experiment was conducted to check whether the biofertilizer containing PNSB-fN strains can improve rice yield and soil fertility under a highly saline acidic condition. A randomized complete block design was used with four replicates on saline soil in An Bien-Kien Giang, Vietnam. The first factor was the N fertilizer level, i.e., (i) 100%, (ii) 75%, (iii) 50%, and (iv) 0%; the second factor was the PNSB-fN (R. sphaeroides), i.e., (i) the control, (ii) S01, (iii) S06, and (iv) combined S01–S06. In the results, supplying PNSB-fN increased NH₄⁺ compared with the control, i.e., 104.7–112.0 mg NH₄⁺ kg⁻¹ compared with 94.0 mg NH₄⁺ kg⁻¹ in season 1 and 35.9–38.0 mg NH₄⁺ kg⁻¹ compared with 34.2 mg NH₄⁺ kg⁻¹ in season 2. Additionally, by supplying each PNSB-fN strain, the soil Na⁺ and plant Na in culm leaf and grain were decreased in comparison with those in treatments without PNSB-fN. The total N uptake was also enhanced by the PNSB-fN compared with the control. Moreover, supplying PNSB-fN improved the crop height, panicle length, panicle quantity pot⁻¹, grain quantity panicle⁻¹, filled spikelet rate, and grain yield compared with the control. Ultimately, in extremely saline soil, the mixture of PNSB-fN not only improved soil fertility and reduced soil salinity but also replaced 25% of chemical N fertilizer to ensure sustainable agriculture. This newly developed biofertilizer was potent in not only improving the rice and soil health in the locality but also performing the same under similar conditions around the globe. Full article

This study developed a semi-passive treatment system for manganese (Mn)- and zinc (Zn)-containing mine water by repurposing a neutralization tank into a biologically active stirred reactor. Laboratory-scale experiments demonstrated efficient removal of Mn²⁺ (>97%) and Zn²⁺ (>80%) with hydraulic retention times (HRTs) as short as 6 h—significantly faster than traditional passive systems. XRD and XANES analyses identified the predominant formation of birnessite, a layered Mn oxide, during Mn²⁺ oxidation, with Zn co-treatment promoting the precipitation of Zn-containing carbonates. Despite decreasing crystallinity of birnessite over time, microbial activity, dominated by Mn-oxidizing genera, such as Sphingomonas, Pseudonocardia, Sphingopyxis, Nitrospira, and Rhodobacter, persisted in the presence of Zn²⁺, ensuring system stability. Importantly, the low leachability of Mn and Zn from the resulting sludge in TCLP tests confirmed its environmental safety and potential for reuse. By leveraging existing infrastructure and microbial biomineralization, this system bridges the gap between passive and active treatments, significantly reducing treatment footprints and operational costs. These findings highlight the potential of repurposing mine water treatment tanks as a scalable, cost-effective solution for sustainable mine water remediation. Full article

Aedes aegypti is a key vector in the transmission of arboviral diseases in the Colombian Amazon. This study aimed to characterize microbiota composition using DNA extracted from water in artificial breeding sites, immature stages, and adults of Ae. aegypti in Leticia, Amazonas. Additionally, the physicochemical water variables were correlated with the bacterial communities present. Eight artificial breeding sites were identified, with bucket, plant pot, and tire being the most frequent. The breeding sites exhibited similar physicochemical profiles, with significant temperature and salinity differences (p-value < 0.03). The most representative bacterial genera included Ottowia (82%), Xanthobacter (70.59%), and Rhodocyclaceae (92.78%) in breeding site water; Aquabacterium (61.07%), Dechloromonas (82.85%), and Flectobacillus (58.94%) in immature stages; and Elizabethkingia (70.89%) and Cedecea (39.19%) in males and females of Ae. aegypti. Beta diversity analysis revealed distinct clustering between adults and the water and immature communities (p-value < 0.001). Multivariate analysis showed strong correlations among bacterial communities, breeding sites, and physicochemical variables such as tire and drum cover which exhibited high levels of total dissolved solids, conductivity, and salinity associated with Flectobacillus, Leifsonia, Novosphingobium, Ottowia, and Rhodobacter. Bacterial genera such as Mycobacterium, Escherichia, Salmonella, and Clostridium, present in artificial breeding sites, are associated with public health relevance. This study provides insights into bacterial community dynamics across Ae. aegypti’s life cycle and underscores the importance of water physicochemical and biological characteristics for developing new vector control strategies. Full article

Carotenoids are crucial for photosynthesis, playing key roles in light harvesting and photoprotection. In this study, spheroidene and bacteriochlorophyll a (Bchl a) were reconstituted into the chromatophores of the carotenoidless mutant Rhodobacter sphaeroides R26.1, resulting in the preparation of high-quality LH2 complexes. Global and target analyses of transient absorption data revealed that incorporating B800 Bchl a significantly enhances excitation energy transfer (EET) efficiency from carotenoids to Bchl a. EET predominantly occurs from the carotenoid S₂ state, with additional pathways from the S₁ state observed in native LH2. Unique relaxation dynamics were identified, including the generation of the carotenoid S* state in reconstituted LH2 with both spheroidene and B800 Bchl a and the formation of the carotenoid T₁ state in reconstituted LH2. These findings underscore the critical influence of pigment composition and spatial organization on energy transfer mechanisms. They provide valuable insights into the molecular interplay that governs excitation energy transfer in photosynthetic light-harvesting systems. Full article

Disaccharide trehalose has been proven in many cases to be particularly effective in preserving the functional and structural integrity of biological macromolecules. In this work, we studied its effect on the electron transfer reactions that occur in the chromatophores of the photosynthetic bacterium Cereibacter sphaeroides. In the presence of a high concentration of trehalose, following the activation of the photochemistry by flashes of light, a slowdown of the electrogenic reactions related to the activity of the photosynthetic reaction center and cytochtome (cyt) bc₁ complexes is observable. The kinetics of the third phase of the electrochromic carotenoid shift, due to electrogenic events linked to the reduction in cyt b_H heme via the low-potential branch of the cyt bc₁ complex and its oxidation by quinone molecule on the Q_i site, is about four times slower in the presence of trehalose. In parallel, the reduction in oxidized cyt (c₁ + c₂) and high-potential cyt b_H are strongly slowed down, suggesting that the disaccharide interferes with the electron transfer reactions of the high-potential branch of the bc₁ complex. A slowing effect of trehalose on the kinetics of the electrogenic protonation of the secondary quinone acceptor Q_B in the reaction center complex, measured by direct electrometrical methods, was also found, but was much less pronounced. The direct detection of carbohydrate content indicates that trehalose, at high concentrations, permeates the membrane of chromatophores. The possible mechanisms underlying the observed effect of trehalose on the electron/proton transfer process are discussed in terms of trehalose’s propensity to form strong hydrogen bonds with its surroundings. Full article

The pH dependence of the free energy level of the flash-induced primary charge pair P⁺I_A⁻ was determined by a combination of the results from the indirect charge recombination of P⁺Q_A⁻ and from the delayed fluorescence of the excited dimer (P*) in the reaction center of the photosynthetic bacterium Rhodobacter sphaeroides, where the native ubiquinone at the primary quinone binding site Q_A was replaced by low-potential anthraquinone (AQ) derivatives. The following observations were made: (1) The free energy state of P⁺I_A⁻ was pH independent below pH 10 (–370 ± 10 meV relative to that of the excited dimer P*) and showed a remarkable decrease (about 20 meV/pH unit) above pH 10. A part of the dielectric relaxation of the P⁺I_A⁻ charge pair that is not insignificant (about 120 meV) should come from protonation-related changes. (2) The single exponential decay character of the kinetics proves that the protonated/unprotonated P⁺I_A⁻ and P⁺Q_A⁻ states are in equilibria and the rate constants of protonation k_on^H +k_off^H are much larger than those of the charge back reaction k_back ~10³ s⁻¹. (3) Highly similar pH profiles were measured to determine the free energy states of P⁺Q_A⁻ and P⁺I_A⁻, indicating that the same acidic cluster at around Q_B should respond to both anionic species. This was supported by model calculations based on anticooperative proton distribution in the cluster with key residues of GluL212, AspL213, AspM17, and GluH173, and the effect of the polarization of the aqueous phase on electrostatic interactions. The larger distance of I_A⁻ from the cluster (25.2 Å) compared to that of Q_A⁻ (14.5 Å) is compensated by a smaller effective dielectric constant (6.5 ± 0.5 and 10.0 ± 0.5, respectively). (4) The P* → P⁺Q_A⁻ and I_A⁻Q_A → I_AQ_A⁻ electron transfers are enthalpy-driven reactions with the exemption of very large (>60%) or negligible entropic contributions in cases of substitution by 2,3-dimethyl-AQ or 1-chloro-AQ, respectively. The possible structural consequences are discussed. Full article

As a typical pathogen-associated molecular pattern (PAMP), β-1,3-glucan can engage with pattern recognition receptors (PRRs) to initiate an immune response. In this study, we investigated the effects of dietary β-1,3-glucan on growth performance, antioxidant capacity, immune response, intestinal health, and bacterial resistance in juvenile Macrobrachium nipponense. Prawns were fed with five experimental diets containing 0%, 0.05%, 0.1%, 0.2%, and 0.4% β-1,3-glucan for eight weeks. The findings demonstrated that the inclusion of β-1,3-glucan improved weight gain and survival rate in prawns. Prawns fed with β-1,3-glucan exhibited elevated activities of hepatopancreatic ACP (acid phosphatase), AKP (alkaline phosphatase), and SOD (superoxide dismutase), while MDA (malondialdehyde) content was reduced. Expression levels of PRRs related genes including LGBP (lipopolysaccharide and β-1,3-glucan binding protein), lectin, and LBP (lipopolysaccharide-binding protein) were significantly increased in prawns fed with β-1,3-glucan. Intestinal flora analysis revealed suppression of Cyanobacteria abundance at the Phylum level and enhancement in Rhodobacter abundance at the genus level in prawns fed with a 0.2% β-1,3-glucan diet. Furthermore, prawns fed with 0.1%, 0.2%, and 0.4% β-1,3-glucan demonstrated significantly higher survival rates following Aeromonas hydrophila infection. In conclusion, β-1,3-glucan can activate PRRs to improve immune responses in M. nipponese. Within the range of β-1,3-glucan concentrations set in this experiment, it is recommended to add 0.18% of β-1,3-glucan to the diet, taking into account the positive effect of β-1,3-glucan on the survival rate of M. nipponensecu. Full article

p-Coumaric acid (p-CA) is a valuable compound with applications in food additives, cosmetics, and pharmaceuticals. However, traditional production methods are often inefficient and unsustainable. This study focuses on enhancing p-CA production efficiency through the heterologous expression of tyrosine ammonia-lyase (TAL) from Rhodobacter sphaeroides in Pseudomonas putida KT2440. TAL catalyzes the conversion of L-tyrosine into p-CA and ammonia. We engineered P. putida KT2440 to express TAL in a fed-batch fermentation system. Our results demonstrate the following: (i) successful integration of the TAL gene into P. putida KT2440 and (ii) efficient bioconversion of L-tyrosine into p-CA (1381 mg/L) by implementing a pH shift from 7.0 to 8.5 during fed-batch fermentation. This approach highlights the viability of P. putida KT2440 as a host for TAL expression and the successful coupling of fermentation with the pH-shift-mediated bioconversion of L-tyrosine. Our findings underscore the potential of genetically modified P. putida for sustainable p-CA production and encourage further research to optimize bioconversion steps and fermentation conditions. Full article

Ecological floating beds, with their compact footprint and mobility, offer a promising solution for sustainable surface water remediation in rural areas. However, low removal efficiency and instability still limit its application. In this study, iron–carbon-based fillers were integrated into ecological floating beds to investigate their impact and mechanisms in removing pollutants, including carbon, nitrogen, phosphorus, and heavy metals. Results indicate that all five fillers (activated carbon, iron–carbon fillers, sponge iron, activated carbon + iron–carbon fillers, and activated carbon + sponge iron) can completely remove orthophosphate, and the sponge iron filler system can completely remove nitrate. Then, fillers were applied to ecological floating beds, and the iron–carbon microelectrolysis (activated carbon + sponge iron filler)-enhanced ecological floating bed showed superior removal efficiency for pollutants. It achieved 95% removal of NH₄⁺-N, 85% removal of NO₃⁻-N, 75% removal of total phosphorus, 90% removal of chemical oxygen demand, and 90% removal of heavy metals. Typical nitrifying bacteria Nitrospira, denitrifying bacteria Denitratisoma, and a variety of bacterial genera with denitrification functions (e.g., Rhodobacter, Dechloromonas, Sediminibacterium, and Novosphingobium) coexisted in the system, ensuring efficient and robust nitrogen removal performance. These findings will provide support for the sustainable treatment of surface water in rural areas. Full article

Rhodobacter sphaeroides is a facultative phototrophic bacterium that performs aerobic respiration when oxygen is available. Only when oxygen is present at low concentrations or absent are pigment–protein complexes formed, and anoxygenic photosynthesis generates ATP. The regulation of photosynthesis genes in response to oxygen and light has been investigated for decades, with a focus on the regulation of transcription. However, many studies have also revealed the importance of regulated mRNA processing. This study analyzes the phenotypes of wild type and mutant strains and compares global RNA-seq datasets to elucidate the impact of ribonucleases and the small non-coding RNA StsR on photosynthesis gene expression in Rhodobacter. Most importantly, the results demonstrate that, in particular, the role of ribonuclease E in photosynthesis gene expression is strongly dependent on growth phase. Full article

Bacterial cytoplasmic organelles are diverse and serve many varied purposes. Here, we employed Rhodobacter sphaeroides to investigate the accumulation of carbon and inorganic phosphate in the storage organelles, polyhydroxybutyrate (PHB) and polyphosphate (PP), respectively. Using cryo-electron tomography (cryo-ET), these organelles were observed to increase in size and abundance when growth was arrested by chloramphenicol treatment. The accumulation of PHB and PP was quantified from three-dimensional (3D) segmentations in cryo-tomograms and the analysis of these 3D models. The quantification of PHB using both segmentation analysis and liquid chromatography and mass spectrometry (LCMS) each demonstrated an over 10- to 20-fold accumulation of PHB. The cytoplasmic location of PHB in cells was assessed with fluorescence light microscopy using a PhaP-mNeonGreen fusion-protein construct. The subcellular location and enumeration of these organelles were correlated by comparing the cryo-ET and fluorescence microscopy data. A potential link between PHB and PP localization and possible explanations for co-localization are discussed. Finally, the study of PHB and PP granules, and their accumulation, is discussed in the context of advancing fundamental knowledge about bacterial stress response, the study of renewable sources of bioplastics, and highly energetic compounds. Full article

The culture of mandarin fish using artificial feed has been gaining increasing attention in China. Ensuring good water quality in the ponds is crucial for successful aquaculture. Recently, the trial of pond-based rice floating beds (PRFBs) in aquaculture ponds has shown promising results. This research assessed the impact of PRFBs on the microbial community structure and overall quality of the aquaculture pond, thereby enhancing our understanding of its functions. The results revealed that the PRFB group exhibited lower levels of NH₄⁺-N, NO₂⁻-N, NO₃⁻-N, TN, TP, and Alk in pond water compared to the control group. The microbial diversity indices in the PRFB group showed a declining trend, while these indices were increasing in the control group. At the phylum level, there was a considerable increase in Proteobacteria abundance in the PRFB group throughout the culture period, suggesting that PRFBs may promote the proliferation of Proteobacteria. In the PRFB group, there was a remarkable decrease in bacterial populations related to carbon, nitrogen, and phosphorus metabolism, including genera Rhodobacter, Rhizorhapis, Dinghuibacter, Candidatus Aquiluna, and Chryseomicrobium as well as the CL500_29_marine_group. Overall, the research findings will provide a basis for the application of aquaculture of mandarin fish fed an artificial diet and rice floating beds. Full article

The intestine of living organisms harbors different microbiota associated with the biological functioning and health of the host and influences the process of ecological adaptation. Here, we studied the intestinal microbiota’s composition and functional differences using 16S rRNA and metagenomic analysis in the wild, farm, and released Chinese three-keeled pond turtle (Mauremys reevesii). At the phylum level, Bacteroidota dominated, followed by Firmicutes, Fusobacteriota, and Actinobacteriota in the wild group, but Chloroflexi was more abundant in the farm and released groups. Moreover, Chryseobacterium, Acinetobacter, Comamonas, Sphingobacterium, and Rhodobacter were abundant in the released and farm cohorts, respectively. Cetobacterium, Paraclostridium, Lysobacter, and Leucobacter showed an abundance in the wild group. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed that the relative abundance of most pathways was significantly higher in the wild turtles (carbohydrate metabolism, lipid metabolism, metabolism of cofactors, and vitamins). The comprehensive antibiotic resistance database (CARD) showed that the antibiotic resistance gene (ARG) subtype macB was the most abundant in the farm turtle group, while tetA was higher in the wild turtles, and srpYmcr was higher in the released group. Our findings shed light on the association between the intestinal microbiota of M. reevesii and its habitats and could be useful for tracking habitats to protect and conserve this endangered species. Full article