Frontiers in bioscience (Elite edition)最新文献

Background: Klebsiella pneumoniae possesses a range of virulence factors that enable this bacterium to colonize, persist, adhere to host tissues, invade, and cause disease. The pathogen poses a significant risk to immunocompromised individuals and those with pre-existing health conditions. This research focused on assessing the virulence traits and biofilm-forming abilities of K. pneumoniae isolates in Nigeria.

Methods: Clinical samples were collected from 420 patients across seven tertiary hospitals in Southwestern Nigeria between February 2018 and July 2019. Standard microbiological procedures were employed to identify Klebsiella isolates. The presence of six specific virulence genes was determined using polymerase chain reaction (PCR): fimH, kfu, rmpA, uge, wcaG, and aero_1. Additionally, PCR was utilized to identify capsular serotypes K1, K2, and K5.

Results: A substantial proportion (82%) of K. pneumoniae isolates demonstrated the ability to form biofilms. Of these, 51 isolates (39.8%) were classified as strong biofilm producers, 54 (42.2%) as moderate, and 23 (17.9%) showed no biofilm production. Among the virulence genes detected, uge was the most common (68.0%), followed by fimH (65.6%), aero_1 (63.3%), kfu (29.7%), rmpA (28.1%), and wcaG (14.1%). Statistically significant correlations were found between biofilm formation and the presence of aero_1, fimH, kfu, and rmpA. In terms of capsular serotypes, the majority of isolates were non-K1/K2/K5 (84.4%), with lower frequencies observed for K2 (7.0%), K1 (5.5%), and K5 (3.1%).

Conclusions: This study highlights that the aero_1, fimH, and uge genes are frequently present in K. pneumoniae isolates from this region, and that these strains often carry multiple virulence genes. The strong virulence potential and biofilm-forming capacity of these isolates underscore a significant public health threat, particularly in vulnerable populations.

Background: Red clover (Trifolium pratense L.) is an important forage crop throughout the world due to its high forage quality, nitrogen fixation capacity and beneficial effects on the soil fertility. But aluminum (Al) toxicity limits significantly red clover production in acid soils, which represent more than one third of the world's agricultural lands. Natural variation for Al³⁺ ions resistance has been identified in many crop species so development of tolerant accessions and varieties is a promising approach for red clover breeding. In this context the objectives of this article were to select in vitro and evaluate using different DNA markers the tolerant to toxic aluminum breeding samples of red clover.

Methods: Seeds of the experimental hybrid population were germinated under various aluminum concentrations, including control without aluminum. Epicotyls of seedlings without roots and with roots not less than 4-5 mm were subcultivated on agar's medium of Gamborg B5 with 2 mg/L of 6-benzylaminopurine and 100 mg/L of Al³⁺ and then planted in the cassettes with soil. Seedlings and adult plants F₂, tolerant to 50 and 100 mg/L of Al³⁺ were selected, grown in vegetative pots and used further for molecular analyses. Genetic variability between tolerant and susceptible red clover genotypes was evaluated based on DNA markers: sequence-related amplified polymorphism (SRAP), retrotransposon microsatellite amplified polymorphism (REMAP) and inter-primer binding site polymorphism (iPBS).

Results: Aluminum-tolerant red clover samples were obtained by in vitro selection on the medium with toxic aluminum ions. F₂ seedlings in the variants with 50 mg/L and 100 mg/L of Al³⁺ were characterized by longer length and roots size compared with F₁ seedlings and variety-standard at the same aluminum concentration. Subsequent molecular analysis showed that REMAP and iPBS were efficient markers to detect distinguishes among red clover accessions. The average level of polymorphism was identified as 45.8 using REMAP and 68.2% with iPBS; the average values of polymorphism information content (PIC) were 0.764 and 0.746 accordingly, higher compared to SRAP (0.741).

Conclusions: Combination of the biotechnology methods and the current DNA-technologies based on REMAP and iPBS markers is effective approach to improve precision and reliability of selection and assessing of red clover genotypes with tolerance to toxic aluminum ions (Al³⁺). Breeding samples identified in this study, can be used as a promising initial material for development the new varieties with stable inheritability of the aimed trait.

Background: Low retinal blood flow and/or vasospasm represent major risk factors for the development of glaucomatous optic neuropathy (GON), a potentially blinding eye disease. Bradykinin (BK), a nonapeptide, is endogenously produced and released, which can cause smooth muscles to contract and relax in different tissues depending on the physiological/pathological situation and the presence or absence of vascular tone. Several reports have shown the presence of BK receptor mRNAs, and in some cases, B1- and B2-receptor proteins, in ocular tissues, including the retina. However, the function of these receptors remains to be determined, especially in retinal blood vessels.

Methods: We pharmacologically characterized the ability of BK and any related peptide agonists to promote the contraction of isolated bovine posterior ciliary arteries (PCAs) in an organ bath setup using a cumulative compound addition and tension development recording process. Receptor-selective kinin agonists and subtype-selective BK receptor antagonists were utilized to define the possible heterogeneity in the functional BK receptors for PCAs.

Results: All agonist kinin peptides concentration-dependently contracted the PCA rings bi-phasically over a 5-log unit range (0.1 nM-10 μM). The relative potencies (EC₅₀ values; n = 4-5) regarding the high-affinity receptor site were: Lys-BK = 0.9 ± 0.4 nM; Des-Arg⁹-BK = 0.9 ± 0.4 nM; RMP-7 = 1.1 ± 0.6 nM; Met-Lys-BK = 1.3 ± 0.5 nM; Hyp³-BK = 2.7 ± 0.5 nM; BK = 3.0 ± 0.7 nM. The low-affinity receptor site activated by these peptides mostly exhibited EC₅₀ values ranging from 0.3 μM to 3 μM. The concentration-response curves to Des-Arg⁹-BK (B1-selective agonist) were shifted to the left in the presence of increasing concentrations of a B1-receptor antagonist (R715: 1-10 μM; n = 3). Similarly, WIN-64338 (a B2-receptor antagonist: 1-10 μM; n = 3) moved the BK concentration-response curves to the left.

Conclusions: The pharmacological characteristics of BK and analog-induced contractions, and their inhibition by receptor-selective antagonists, indicated the presence of both B1- and B2-receptors, and perhaps another subtype, which mediate the PCA contractions. These results have potential implications for the involvement of heterogeneous kinin receptors, narrowing PCA diameters in vivo, restricting blood flow to the retina, causing GON, and subsequent visual impairment that can eventually cause blindness.

Pesticides spread into the air, contaminate soil and water, and can affect various objects, contributing to secondary pollution regardless of the employed type or application method. Currently, organophosphorus pesticides (OPs) are widely utilized in agriculture, forestry, and livestock farming worldwide. These chemicals enter the body through multiple exposure routes and can harm the nervous system, endocrine system, and other organs. Owing to the environmental persistence and elevated toxicity exhibited by these pesticides, certain OPs are difficult to break down biologically, thus posing serious threats to human health and ecosystems. Disinfection or destruction of those pesticides remaining in the environment represents one of the important tasks scientists face. This review presents information on OPs, some of their properties, environmental impacts, and mechanisms for the effective decomposition of these pesticide residues by microorganisms. Bacteria and fungi isolated from samples contaminated with various OPs were analyzed. New metabolites formed during OP degradation by these microorganisms, as well as microbial enzymes involved in OP degradation and the molecular mechanisms of the process, are presented. The methods used in these studies and recommendations for future research are also detailed.

Background: Ligninolytic fungi are promising organisms in developing bioremediation technologies due to their ability to degrade various pollutants. Fungi and their extracellular enzymes in soil inevitably collide with metabolites produced by other organisms. Here, we investigated the effect of some natural metabolites on the degradation of a model mixture of polycyclic aromatic hydrocarbons (PAHs) by the fungus Pleurotus ostreatus var. Florida.

Methods: Fungus was grown in the liquid medium containing PAHs with or without the addition of natural metabolites. The degraded PAHs and the identification of metabolites were checked using high-performance liquid chromatography (HPLC). Enzymatic activities were measured spectrophotometrically using test substrates. The metabolite effects on the pure laccase and versatile peroxidase were also checked. All experimental treatments were analyzed using Excel 2019 (Microsoft Office 2019, USA).

Results: Indole-3-acetic acid (IAA) and salicylic acid increased PAH degradation by 25-70%. However, tryptophan, a precursor to IAA biosynthesis, slightly increased the degradation of only three-ring PAHs. The tested flavonoids reduced the PAH degradations, which may have resulted from the inhibition of mycelial growth by these compounds. Ferulic and cinnamic acids, precursors to lignin biosynthesis, also inhibited PAH degradation. Of the tested fungal metabolites, only veratryl alcohol promoted PAH degradation: the four-ring PAHs became more accessible to fungal degradation (43.5 and 38.1% for fluoranthene and pyrene, respectively). Oxalic and malonic acids, the most actively produced fungal organic acids, reduced the degradation of all PAHs but fluoranthene. HPLC led us to identify 9,10-phenanthrenequinone, 9,10-anthraquinone, and 9-fluorenone as the main metabolites of PAH degradation. P. ostreatus is a strong producer of extracellular laccases and peroxidases, whose involvement in PAH degradation is also well known. In our study, the most vigorous laccase inducers were tryptophan and ferulic acid (40 and 60%, respectively), whereas IAA and salicylic acid were weaker inducers (about 20%). Ferulic and salicylic acids increased versatile peroxidase activity by 1.5-2 times, whereas other effectors reduced it to varying degrees.

Conclusions: These results are important for developing environmental biotechnologies that combine phyto- and mycoremediation.

Background: The tolerance and productivity of soybeans under the current climate change conditions can be increased by providing these crops with the necessary macro- and microelements. This can be achieved using effective Bradyrhizobium strains for seed inoculation and adding chelated trace elements.

Methods: Soybean Bradyrhizobium japonicum symbioses were cultivated by adding chelates of trace elements, such as iron (Fe), germanium (Ge), and molybdenum (Mo), to the culture medium, after which microbiological and biochemical analyses were performed.

Results: The addition of chelated forms of Fe or Ge to the Bradyrhizobium culture medium promoted a change in the pro-oxidant-antioxidant balance in soybean nodules under different water supply conditions. This is due to the production of hydrogen peroxide in the nodules (an increase of 12.9%), as well as a twofold increase in the ascorbate peroxidase activity and a decrease in the levels of superoxide dismutase (by 40%) and catalase (by 50%) under water stress. Stimulation of nodulation and nitrogen fixation in soybeans (by 40.1 and 73.0%) and an increase in grain productivity (by 47.5 and 58%) were observed when using Bradyrhizobium inoculant containing Fe or Ge chelates. The inoculation of soybeans with Bradyrhizobium modified using Mo chelate causes similar changes in antioxidant processes as Fe or Ge chelates, but the soybean symbiotic capacity decreases under water stress.

Conclusion: Chelated forms of Fe or Ge as additional components in the Bradyrhizobium culture medium are effective in regulating the antioxidant status of soybeans under drought conditions and can simultaneously contribute to increased nitrogen fixation and grain productivity. These findings are important in expanding the current technologies used to grow this legume in risky farming areas caused by climate change.

Background: Antibiotic resistance is a contemporary public health issue that poses significant environmental and public health concerns. The presence of antimicrobial-resistant (AMR) microbes has been reported across media irrespective of geography and landscape. This study aimed to analyze the antibiotic susceptibility of Bacillus subtilis obtained from the Indian Sector of the Southern Ocean (39°19' S, 57°30' E to 66°38' S, 76°22' E).

Methods: Bacillus subtilis was revived and cultured on Mannitol Yolk Polymyxin Agar. Antibiotic susceptibility was assessed via the agar well diffusion assay against 10 therapeutically significant antibiotics. Whole-genome sequencing was performed to identify the presence of AMR genes. A total of 12 AMR genes were identified via the Comprehensive Antibiotic Resistance Database (CARD). A comparative genomics approach was employed to investigate the global distribution of AMR genes from 2014 to 2024.

Results: Antibiotic susceptibility testing indicated complete resistance to metronidazole, while the isolates remained susceptible to ampicillin, doxycycline, tetracycline, ciprofloxacin, norfloxacin, cefixime, azithromycin, meropenem, and cotrimoxazole. Whole-genome sequencing and comparative analysis identified 12 AMR genes, including aadK, vanT (within the vanG cluster), ykkC, ykkD, vanW (within the vanI cluster), FosBx1, qacJ, qacG, tet(45), vanY (within the vanM cluster), and blt. The observed resistance mechanisms included antibiotic efflux, target modification, and enzymatic inactivation. Comparative genomic analysis of 15 closely related strains revealed variability in the distribution of AMR genes, with B. subtilis strain MB415 carrying all 12 resistance genes.

Conclusion: The detection of antibiotic-resistant B. subtilis in the Southern Ocean suggests potential anthropogenic influences on microbial communities, underscoring the need for continuous surveillance of AMR in remote marine environments to prevent its proliferation and mitigate its ecological consequences.

Background: Lignocellulosic materials, such as soybean hulls, possess a complex and recalcitrant structure that requires efficient pretreatment or enzymatic processing for effective conversion into valuable products. However, pretreatment processes often generate inhibitory byproducts (e.g., furfural, hydroxymethyl furfural (HMF), phenols, and lignin degradation products), which can impede enzymatic activity and increase overall production costs. This study explores soybean hulls, a byproduct of oil and meal production, as a potential high-carbohydrate biorefinery resource, assessing their chemical composition, fermentable sugar recovery, and bioethanol production potential.

Methods: Soybean hulls (5%, w/v dry basis) were subjected to enzymatic hydrolysis at 50 °C for 72 hours, utilizing a dual impeller mixing system at 250 rpm. An enzyme load of 45 mg enzyme protein per gram of solids was applied using a combination of commercial enzyme preparations, including Cellulase Blend and Multifect Pectinase. Conversion of cellulose, xylan, and arabinan into fermentable sugars was quantified. A moderate enzyme loading of 10 mg enzyme protein/g solids was also tested for comparison. Microbial fermentation was carried out using the xylose-fermenting Escherichia coli FBR5 strain to produce bioethanol.

Results: Hydrolysis of untreated soybean hulls resulted in conversion yields of 94.4% for glucan, 72.6% for xylan, and 69.3% for arabinan into glucose, xylose, and arabinose, respectively. In comparison, control experiments without cellulolytic enzymes showed significantly lower conversion yields (14.2%, 20.1%, and 15.5% for glucose, xylose, and arabinose, respectively). A moderate enzyme loading of 10 mg enzyme protein per gram of solids achieved a cellulose conversion of 90.6%, which was nearly equivalent to the conversion obtained with 45 mg enzyme protein/g solids. Microbial fermentation with E. coli FBR5 resulted in 94% theoretical ethanol yield, with a production rate of 0.33 g/L/h and a productivity of 0.48 g ethanol/g sugar.

Conclusions: The study demonstrates that enzymatic hydrolysis of soybean hulls, which are rich in cellulose and hemicellulose, can be effectively conducted without the need for pretreatment. The moderate enzyme load used in this study provides a promising platform for efficient sugar release and bioethanol production, presenting a cost-effective and viable approach for utilizing soybean hulls in biorefinery applications.

Recently, the importance of biocatalysis in bioenergy has been noted, with policymakers and regulatory authorities intervening at the technological level to establish more efficient, varied, and vast-scale exploitations of biocatalysis. These approaches leverage natural catalysts, primarily enzymes, to facilitate the breakdown of larger organic compounds into simpler molecules, which can be further biochemically transformed into biofuels, such as ethanol, biodiesel, and biogas, using improved versions of metabolic enzymes. Advances in enzyme engineering have significantly enhanced the stability, specificity, and activity of key enzymes involved in biofuel synthesis, such as cellulases, oxidoreductases, xylanases, glucose isomerases, butanol dehydrogenase, acetoacetate decarboxylase, ferredoxin oxidoreductases, etc. Further, synthetic biological approaches have allowed the construction of microbial cell factories with restructured integrated biocatalytic pathways, capable of converting the raw biomass directly into biofuels. Despite these advancements, challenges remain, such as the cost of enzymes, their robustness, and the scalability of their production and biotransformation processes. Ongoing research is focused on overcoming these hurdles through innovative biocatalyst design, metabolic engineering, in silico modeling, and optimization. However, changes in government policies and reduced regulatory frameworks are expected to leverage biofuel production and competitiveness with fossil fuels and gradually replace them completely. This review highlights the recent advances in the field of biocatalysis related to the production of biofuels. This review also discusses the current challenges, sustainability, promotional initiatives performed at the government level, and future directions in the field of biofuels.

Background: Bacillus bacteria are often used in the production of biopreparations. Moreover, these bacteria can be used in agriculture as probiotics or starters for manufacturing fodder preserved by fermentation (silage). The ability of Bacillus bacteria to produce many biologically active molecules and metabolites with antimicrobial activity means that these bacteria can stimulate plant growth and restore the balance of the microbiome in the digestive system of certain animals.

Methods: Using molecular biological analysis, bioinformatic annotation, and metabolic profiling of whole genome sequences, we analyzed two promising candidates for creating biopreparations, i.e., two Bacillus strains, namely B. mucilaginosus 159 and B. subtilis 111. We compared the genomes of these two strains and characterized both their microbiomic and metabolomic features.

Results: We demonstrated that both strains lacked elements contributing to the formation of toxic and virulent properties; however, both exhibited potential in the biosynthesis of B vitamins and siderophores. Additionally, these strains could synthesize many antimicrobial substances of different natures and spectrums of action. B. mucilaginosus 159 could synthesize macrolactin H (an antibiotic from the polyketide group), mersacidin (a class II lanthipeptide), and bacilysin. Meanwhile, B. subtilis 111 could synthesize andalusicin (a class III lanthipeptide), bacilysin, macrolactin H, difficidin, bacillaene (a polyene antibiotic), fengycin (a lipopeptide with antifungal activity), and surfactin (another lipopeptide). Further, a unique pathway of intracellular synthesis of the osmoprotectant glycine betaine was identified in B. subtilis 111, with the participation of betaine aldehyde dehydrogenase (BetB); this is not widely represented in bacteria of the genus Bacillus. These compounds can increase osmotic stability, which may be key for manufacturing biological starters for silage preparation.

Conclusions: These two Bacillus strains are safe for use as probiotic microorganisms or starters in producing preserved fodder. However, B. subtilis 111 may be preferable due to a wider spectrum of synthesized antimicrobial substances and vitamins. Our findings exemplify using genomic technologies to describe the microbiomic and metabolomic characteristics of significant bacterial groups such as Bacillus species.