Flexible regression model for predicting the dissemination of Candidatus Liberibacter asiaticus under variable climatic conditions.

Greening, or Huanglongbing (HLB), poses a severe threat to global citrus cultivation, affecting various citrus species and compromising fruit production. Primarily transmitted by psyllids during phloem feeding, the bacterium Candidatus Liberibacter induces detrimental symptoms, including leaf yellowing and reduced fruit quality. Given the limitations of conventional control strategies, the search for innovative approaches, such as resistant genotypes and early diagnostic methods, becomes essential for the sustainability of citrus cultivation. The development of predictive models, such as the one proposed in this study, is essential as it enables the estimation of the bacterium's concentration and the vulnerability of healthy plants to infection, which will be instrumental in determining the risk of HLB. This study proposes a prediction model utilizing environmental factors, including temperature, humidity, and precipitation, which play a decisive role in greening epidemiology, influencing the complex interaction among the pathogen, vector, and host plant. In the proposed modeling, it addresses non-linear relationships through cubic smoothing splines applications and tackles imbalanced categorical predictor variables, requiring the use of a random-effects regression model, incorporating a random intercept to account for variability across different groups and mitigate the risk of biased predictions. The model's ability to predict HLB incidence under varying climatic conditions provides a significant contribution to disease management, offering a strategic tool for early intervention and potentially reducing the spread of HLB. Using climatological and environmental data, the research aims to develop a predictive model, assessing the influence of these variables on the spread of Candidatus Liberibacter asiaticus, essential for effective disease management. The proposed flexible model demonstrates robust predictions for both training and test data, identifying climatological and environmental predictors influencing the dissemination of Candidatus Liberibacter asiaticus, the vascular bacterium associated with Huanglongbing (HLB) or greening.

Methanotrophic Communities and Cultivation of Methanotrophs from Rice Paddy Fields Fertilized with Pig-livestock Biogas Digestive Effluent and Synthetic Fertilizer in the Vietnamese Mekong Delta.

Biogas digestive effluent (BDE) has been applied to rice fields in the Vietnamese Mekong Delta (VMD). However, limited information is available on the community composition and isolation of methanotrophs in these fields. Therefore, the present study aimed (i) to clarify the responses of the methanotrophic community in paddy fields fertilized with BDE or synthetic fertilizer (SF) and (ii) to isolate methanotrophs from these fields. Methanotrophic communities were detected in rhizospheric soil at the rice ripening stage throughout 2 cropping seasons, winter-spring (dry) and summer-autumn (wet). Methanotrophs were isolated from dry-season soil samples. Although the continued application of BDE markedly reduced net methane oxidation potential and the copy number of pmoA genes, a dissimilarity ordination ana-lysis revealed no significant difference in the methanotrophic community between BDE and SF fields (P=0.167). Eleven methanotrophic genera were identified in the methanotrophic community, and Methylosinus and Methylomicrobium were the most abundant, accounting for 32.3-36.7 and 45.7-47.3%, respectively. Type-I methanotrophs (69.4-73.7%) were more abundant than type-II methanotrophs (26.3-30.6%). Six methanotrophic strains belonging to 3 genera were successfully isolated, which included type I (Methylococcus sp. strain BE1 and Methylococcus sp. strain SF3) and type II (Methylocystis sp. strain BE2, Methylosinus sp. strain SF1, Methylosinus sp. strain SF2, and Methylosinus sp. strain SF4). This is the first study to examine the methanotrophic community structure in and isolate several methanotrophic strains from BDE-fertilized fields in VMD.

Evaluating Bacterial Viability in Faecal Microbiota Transplantation: A Comparative Analysis of In Vitro Cultivation and Membrane Integrity Methods.

BACKGROUND: Faecal microbiota transplantation (FMT) is a developing therapy for disorders related to gut dysbiosis. Despite its growing application, standardised protocols for FMT filtrate preparation and quality assessment remain undeveloped. The viability of bacteria in the filtrate is crucial for FMT's efficacy and for validating protocol execution. We compared two methods-in vitro cultivation and membrane integrity assessment-for their accuracy, reproducibility and clinical applicability in measuring bacterial viability in frozen FMT stool filtrate. METHODS: Bacterial viability in stool filtrate was evaluated using (i) membrane integrity through fluorescent DNA staining with SYTO9 and propidium iodide, followed by flow cytometry and (ii) culturable bacteria counts (colony-forming units, CFU) under aerobic or anaerobic conditions. RESULTS: Using different types of samples (pure bacterial culture, stool of germ-free and conventionally bred mice, native and heat-treated human stool), we refined the bacterial DNA staining protocol integrated with flow cytometry for assessment of bacterial viability in frozen human stool samples. Both the membrane integrity-based and cultivation-based methods exhibited significant variability in bacterial viability across different FMT filtrates, without correlation. The cultivation-based method showed a mean coefficient of variance of 30.3%, ranging from 7.4% to 60.1%. Conversely, the membrane integrity approach yielded more reproducible results, with a mean coefficient of variance for viable cells of 6.4% ranging from 0.2% to 18.2%. CONCLUSION: Bacterial viability assessment in stool filtrate using the membrane integrity method offers robust and precise data, making it a suitable option for faecal material evaluation in FMT. In contrast, the cultivation-dependent methods produce inconsistent outcomes.

Leveraging genomic information to predict environmental preferences of bacteria.

Genomic information is now available for a broad diversity of bacteria, including uncultivated taxa. However, we have corresponding knowledge on environmental preferences (i.e. bacterial growth responses across gradients in oxygen, pH, temperature, salinity, and other environmental conditions) for a relatively narrow swath of bacterial diversity. These limits to our understanding of bacterial ecologies constrain our ability to predict how assemblages will shift in response to global change factors, design effective probiotics, or guide cultivation efforts. We need innovative approaches that take advantage of expanding genome databases to accurately infer the environmental preferences of bacteria and validate the accuracy of these inferences. By doing so, we can broaden our quantitative understanding of the environmental preferences of the majority of bacterial taxa that remain uncharacterized. With this perspective, we highlight why it is important to infer environmental preferences from genomic information and discuss the range of potential strategies for doing so. In particular, we highlight concrete examples of how both cultivation-independent and cultivation-dependent approaches can be integrated with genomic data to develop predictive models. We also emphasize the limitations and pitfalls of these approaches and the specific knowledge gaps that need to be addressed to successfully expand our understanding of the environmental preferences of bacteria.

New insight into Clostridium butyricum-ferroferric oxide hybrid system in exogenous carbon dioxide-assisted anaerobic fermentation for acetate and butyrate production.

Mixotrophic cultivation, utilizing both gas and organic substances, is commonly employed to minimize the carbon loss during anaerobic fermentation of bulk chemicals. Herein, a novel Clostridium butyricum-ferroferric oxide (Fe3O4) hybrid system, enhanced by exogenous carbon dioxide (CO2), was proposed to improve carbon recovery and optimize metabolite production. The results demonstrated that exogenous CO2 improved metabolite selectivity towards acetate/butyrate, while also accelerating CO2 fixation. Compared to pure Clostridium butyricum, the hybrid system significantly increased carbon conversion to primary metabolites, boosting butyrate and acetate production by 18.7 % and 18.4 %, respectively. Enzyme activity assays revealed that Fe3O4 and exogenous CO2 acted synergistically, enhancing the activities of key enzymes involved in CO2 assimilation. Additionally, Fe3O4 facilitated intra- and extracellular electron transfer, further improving the fermentation process. This study offers new insights into the combined effects of exogenous CO2 and Fe3O4 on anaerobic fermentation, providing an efficient strategy for carbon recovery and selective acetate/butyrate production.

Green mould contamination of Pleurotus pulmonarius cultivation in Malaysia: Unravelling causal agents and water source as critical factors.

Green mould contamination causes a significant challenge to mushroom growers in Malaysia leading to reduced yields and economic losses in the widely cultivated and marketed edible grey oyster mushroom, Pleurotus pulmanorius. This study aimed to identify the causal agents of green mould contaminants and determine the critical points in the cultivation process in the farm that contribute to green mould contamination. Samples of mushroom substrate (sawdust), spawn substrate (corn), environmental sources and tools were collected at different stages of mushroom cultivation. As results, the causal agents of green mould contamination were identified as Trichoderma pleuroti, T. harzianum and T. ghanese. Prior to steam pasteurisation and after steam pasteurisation, the spawn substrate and mushroom substrate were found to be free of Trichoderma. However, Trichoderma was detected in water, air within the production house and on cleaning tools. This findings suggests that water could serve as the source of green mould introduction in mushroom farms, while cultivation practices such as watering and scratching during the harvesting cycle may contribute to adverse green mould. Understanding these critical points and causal agents provides information to mitigate the green mould contamination throughout the grey oyster mushroom cultivation process.

Laser Aggregometry Assessment of Blood Microrheology in a Slit Fluidic Channel Covered With Endothelial Cells.

The blood rheology in vitro in glass or plastic microfluidic chips is different from that in vivo in blood vessels with similar geometry. Absence of vascular endothelium is suggested to cause these discrepancies. This work aims to perform in vitro measurements of blood microrheologic parameters in a slit microfluidic channel covered with endothelial cells (HUVEC). The laser aggregometry was employed to measure the intensity of laser light, backscattered from the blood flow, as a function of shear stress to evaluate the hydrodynamic strength of red blood cells (RBC) aggregates in terms of critical shear stress (CSS). The results demonstrated a decrease in CSS accompanied by an increase in the accuracy of its measurement at similar shear stresses when endothelial cells were present in the channel. The findings hold valuable implications for advanced approaches for endothelization of microfluidic devices, facilitating the study of blood flow dynamics in physiologically more relevant environment.

Morphological responses of filamentous fungi to stressful environmental conditions.

The filamentous growth mode of fungi, with its modular design, facilitates fungal adaptation to stresses they encounter in diverse terrestrial and anthropogenic environments. Surface growth conditions elicit diverse morphological responses in filamentous fungi, particularly demonstrating the remarkable adaptability of mycelial systems to metal- and mineral-rich environments. These responses are coupled with fungal biogeochemical activity and can ameliorate hostile conditions. A tessellated agar tile system, mimicking natural environmental heterogeneity, revealed negative chemotropism to toxic metals, distinct extreme growth strategies, such as phalanx and guerrilla movements and transitions between them, and the formation of aggregated re-allocation structures (strands, cords, synnemata). Other systems showed intrahyphal growth, intense biomineralization, and extracellular hair-like structures. Studies on submerged mycelial growth, using the thermophilic fungus Thielavia terrestris as an example, provided mechanistic insights into the morphogenesis of two extreme forms of fungal submerged culture-pelleted and dispersed growth. It was found that the development of fungal pellets was related to fungal adaptation to unfavorable stressful conditions. The two key elements affecting morphogenesis leading to the formation of either pelleted or dispersed growth were found to be (1) a lag phase (or conidia swelling stage) as a specific period of fungal morphogenesis when a certain growth form is programmed in response to morphogenic stressors, and (2) cAMP as a secondary messenger of cell signaling, defining the implementation of the particular growth strategy. These findings can contribute to knowledge of fungal-based biotechnologies, providing a means for controllable industrial processes at both morphological and physiological levels.

Manufacturing of the highly active thermophile PETases PHL7 and PHL7mut3 using Escherichia coli.

BACKGROUND: The global plastic waste crisis requires combined recycling strategies. One approach, enzymatic degradation of PET waste into monomers, followed by re-polymerization, offers a circular economy solution. However, challenges remain in producing sufficient amounts of highly active PET-degrading enzymes without costly downstream processes. RESULTS: Using the growth-decoupled enGenes eX-press V2 E. coli strain, pH, induction strength and feed rate were varied in a factorial-based optimization approach, to find the best-suited production conditions for the PHL7 enzyme. This led to a 40% increase in activity of the fermentation supernatant. Optimization of the expression construct resulted in a further 4-fold activity gain. Finally, the identified improvements were applied to the production of the more active and temperature stable enzyme variant, PHL7mut3. The unpurified fermentation supernatant of the PHL7mut3 fermentation was able to completely degrade our PET film sample after 16 h of incubation at 70 °C at an enzyme loading of only 0.32 mg enzyme per g of PET. CONCLUSIONS: In this research, we present an optimized process for the extracellular production of thermophile and highly active PETases PHL7 and PHL7mut3, eliminating the need for costly purification steps. These advancements support large-scale enzymatic recycling, contributing to solving the global plastic waste crisis.

Organic fertilizer improved the lead and cadmium metal tolerance of Eucalyptus camaldulensis by enhancing the uptake of potassium, phosphorus, and calcium.

Phytoremediation is a strategy for the amelioration of soil heavy metal contamination that aligns with ecological sustainability principles. Among the spectrum of phytoremediation candidates, woody plants are considered particularly adept for their substantial biomass, profound root systems, and non-participation in the food chain. This study used Eucalyptus camaldulensis-a tree species characterized for its high biomass and rapid growth rate-to assess its growth and metal uptake in mining tailings. The results were as follows: exposure to heavy metals reduced the E. camaldulensis uptake of potassium (K), phosphorus (P), and calcium (Ca). Heavy metal stress negatively affected the biomass of E. camaldulensis. Lead (Pb) primarily accumulated in the roots, while cadmium (Cd) predominantly accumulated in the stems. The application of organic fertilizers bolstered the stress tolerance of E. camaldulensis, mitigating the adverse impacts of heavy metal stress. A synergistic effect occurred when organic fertilizers were combined with bacterial fertilizers. The plant's enrichment capacity for Cd and its tolerance to Pb was augmented through the concurrent application of bacterial and organic fertilizers. Collectively, the application of organic fertilizers improved the heavy metal tolerance of E. camaldulensis by enhancing the uptake of K, P, and Ca and elevating the content of glutathione peroxidase (GPX) and gibberellin acid (GA) in roots. These findings provided nascent groundwork for breeding E. camaldulensis with enhanced heavy metal tolerance. Moreover, this proved the potentiality of E. camaldulensis for the management of heavy metal-contaminated tailings and offers a promising avenue for future environmental restoration.

A comprehensive review of current practices, challenges, and future perspectives in Koi fish (Cyprinus carpio var. koi) cultivation.

The Koi fish (Cyprinus carpio var. koi) is an ornamental fish with a high selling value because of its attractive colors, color patterns, body shape, and swimming motion. Koi fish is extensively traded in the international fish market because of their popularity among hobbyists from numerous countries worldwide. This review discusses various aspects of Koi fish cultivation, including genetic involvement, selective breeding strategies, and management systems. By examining crucial factors such as water parameters, technological innovations, and evolving cultivation methods, this review explored their influence on the quality of Koi fish. Breakthrough technologies, such as ornamental fish warehousing and recirculation aquaculture systems, enhance breeding efficiency and profitability. Molecular sexing, feed optimization, and color enhancement strategies are central to pursuing superior Koi fish. Reproduction management, disease prevention, and risk reduction during transport underscore ongoing efforts to ensure their survival. Despite notable progress, several challenges remain, including limited genetic studies, gaps in disease research, and unexplored herbal alternatives. The active involvement of hobbyists and breeders in research initiatives is a pivotal force in unlocking the untapped potential. The holistic approaches to enhance production efficiency and improve care standards require further exploration, paving the way for a sustainable future in the evolving management of Koi fish cultivation.

Effect of irrigation regimes on nutrient uptake and nitrate leaching in maize (Zea mays L.) production at Birr-Farm, Upper Blue Nile, Ethiopia.

Sustainably managed irrigation water is essential to agriculture. In order to identify the best irrigation strategies for maximizing agricultural productivity and environmental health, this study examines the effects of various irrigation depths on nutrient uptake, nitrate leaching, and maize yield. The study was carried out at Birfarm, in the Jabitehnan District, Amhara, Ethiopia, throughout the irrigation periods of 2022/23 and 2023/24. The experiment used a (RCBD) with three replications testing five application depths to apply irrigation (50 %, 75 %, 100 %, 125 % and 150 % ETc). ANOVA was performed to determine the influences of irrigation levels on nutrient uptake and nitrate leaching. Irrigation levels significantly impacted N, P and K uptake. Maximum nutrient uptake occurred at 150 % ETc with higher nutrient uptake observed in the second experimental season. Irrigation levels significantly affected nitrate leaching, with the highest leaching at 150 % ETc. Excessive irrigation increased nitrate leaching, aligning with findings from other studies. Maize yield, thousand grain weight (TGW) and above-ground biomass yield (ABY) were significantly influenced by irrigation depth. Optimal irrigation (100 % ETc) produced the maximum yield of 6.08 and 5.83 tha-1, the maximum thousand grain weight of 682.51 g and 685.12 g, and the highest above-ground biomass yield of 31.41 and 32.74 tha-1 in the second and first experiments, respectively, while excessive and deficit irrigation reduced yield. The study highlights the importance of optimizing irrigation depth for nutrient uptake, nitrate leaching and maize yield. While increased irrigation improved nutrient uptake and yield, excessive irrigation led to higher nitrate leaching, emphasizing the need for balanced irrigation practices to enhance productivity and environmental sustainability. Farmers should implement 100%ETc to enhance productivity, ensure efficient nutrient utilization, and protect the environment from the adverse effects of nitrate leaching.

Secondary Metabolites of Fomitopsis betulina: Chemical Structures, Biological Activity and Application Prospects.

Fomitopsis betulina, as a macrofungus with both medicinal and dietary applications, is renowned for its rich content of bioactive substances. The recent advancements in research have significantly enhanced our understanding of its polysaccharides, cellulose-degrading enzymes, and wide range of secondary metabolites. This paper provides a comprehensive review of the artificial cultivation techniques and the chemical profiling of over 100 secondary metabolites identified in F. betulina, including terpenoids, phenols, and various other classes. These compounds exhibit notable pharmacological activities, such as anti-cancer, anti-inflammatory, antimicrobial, antiviral, and anti-malarial effects. Moreover, this review delves into the genomic analysis of F. betulina, focusing on the prediction and classification of terpene synthases, which play a crucial role in the biosynthesis of these bioactive compounds. This insight is instrumental for potentially facilitating future biochemical studies and pharmaceutical applications. Through this review, we aim to solidify the foundation for future in-depth studies and the development of new drugs derived from this promising natural resource.

A Review of Laboratory Requirements to Culture Lichen Mycobiont Species.

Lichens are symbiotic associations between fungi (the mycobiont) and algae or cyanobacteria (the photobionts). They synthesize a large number of secondary metabolites, many of which are potential sources of novel molecules with pharmacological and industrial applications. The advancement of in vitro culture methods of lichen-forming fungi would allow the comprehensive application of these compounds at large scales, enable improvements in the synthesis, facilitate understanding of the role of the partners in the synthesis of these compounds and increase our knowledge about the genes associated with secondary metabolites production. The aim of this work is to summarize the nutritional and physicochemical requirements that have been used to date to culture different lichen-forming fungi species. In total, the requirements for the cultivation of 110 species are presented. This review can provide a starting point for future experiments and help advance the methods of culturing lichenized fungi. The type of diaspore selected to isolate the mycobiont, the composition of the isolation and culture media and the corresponding physicochemical parameters are essential in designing an efficient lichen culture system, allowing the achievement of a suitable growth of lichen-forming fungi and the subsequent production of secondary metabolites.

Integrated bioprocessing and genetic strategies to enhance soluble expression of anti-HER2 immunotoxin in E. Coli.

Immunotoxins are widely applied for cancer therapy. However, bacterial expression of immunotoxins usually leads to the formation of insoluble and non-functional recombinant proteins. This study was aimed to improve soluble expression of a novel anti-HER2 immunotoxin under the regulation of the trc promoter in Escherichia coli by optimization of the cultivation conditions using response surface methodology (RSM). To conduct RSM, four cultivation variables (i.e., inducer concentration, post-induction time, post-induction temperature, and medium recipe), were selected for statistical characterization and optimization using the Box-Behnken design and Design Expert software. Based on the developed model using the Box-Behnken design, the optimal cultivation conditions for soluble expression of anti-HER2 immunotoxin were determined to be 0.1 mM IPTG for induction in the LB medium at 33 °C for 18 h. The expressed immunotoxin was successfully purified using affinity chromatography with more than 90% purity and its bioactivity was confirmed using cell-based ELISA. Technical approach developed in this study can be generally applied to enhance the production yield and quality of recombinant proteins using E. coli as the gene expression system.

First Report of Fusarium oxysporum f. sp. fragariae Causing Fusarium Wilt on Strawberry (Fragaria × ananassa) in Saudi Arabia.

Recently, Saudi growers have expanded their production of organic, soilless-grown strawberries (Fragaria × ananassa Duch.), but their production shows many difficulties associated with disease susceptibility. In October 2021, 45% of strawberry plants cv. "Festival" organically cultivated in Dammam city, Saudi Arabia (26°31'34.5"N 50°00'51.0"E) showed wilting symptoms. Typical symptoms were yellowing, rapid wilting, death of older leaves, stunting, and decreased roots. Vascular bundle necrosis and crown and root rot were also observed; plants eventually collapsed and died. Twenty symptomatic strawberry plants were sampled to isolate the pathogen. Pieces (4 × 4 mm) of the symptomatic tissues from crowns and roots were sanitized with 1% NaOCl (90 s), submerged in 70% alcohol (20 s), rinsed with sterile water (2x 30 s), placed on potato dextrose agar (PDA; Scharlau Chemie, Spain) and incubated at 25°C for 6 days. Next, we prepared single-spore cultures on PDA and synthetic nutrient-poor agar (SNA). On PDA media, pure cultures produced abundant aerial mycelium, with light pink or purple pigmentation in the medium after incubation at 25°C for 7 days. On SNA media, aerial microconidia were abundant cylindrical to ellipsoid hyaline with zero to one septate (3.8 - 5.9 × 1.3 - 2.5 µm, n = 50). Macroconidia were few, hyaline and falcate, with slightly curved apexes and 2 to 4 septate (18.9 - 27.5 × 3.3 - 4.6 µm, n = 50). Chlamydospores were roundish and terminal or intercalary. As Leslie and Summerell (2006) described, such morphological characteristics are typical of F. oxysporum. The isolates' identities were established by extracting DNA using the DNeasy Plant Mini kit (QIAGEN, Hilden, Germany). This was followed by amplification and sequencing of the internal transcribed spacer (ITS) (White et al., 1990), elongation factor 1-α (TEF1-α) (O'Donnell et al., 1998), and the ribosomal RNA intergenic spacer (IGS) (Canizares et al., 2015). The ITS, TEF1-α, and IGS sequences of an isolate Fof-10 were submitted to GenBank (PP564462, PP703242, and PP784894, respectively). BLAST analysis confirmed 99.71 and 100% identities to the ITS, TEF-1α, and IGS sequences of F. oxysporum (KU931552.1, OR640020.1, and FJ985519.1), respectively. All isolates tested were confirmed at the forma specialis fragariae, level using the specific primers FofraF/FofraR (Suga et al. 2013). The ∼239 bp amplicon was sequenced and submitted to GenBank (PP703243). Two-month-old healthy strawberry plants of cultivars "Festival," "Marquis," and "Monterey" were inoculated by dipping the roots in the spore suspension (107 conidia ml-1) for 15 min (Henry et al. 2017). There were five replicates for each cultivar. Plants dipped in water were used as a control treatment. The plants were transplanted in sterilized soil and placed in a greenhouse at 30/26°C (day/night). Within 4 to 6 weeks, inoculated plants showed severe wilting and discoloration of the internal crown tissue, while control plants were symptomless. The pathogen was re-isolated from the discolored vascular tissue onto PDA and identified morphologically and molecularly as the original one, thus fulfilling Koch's postulates. The test was repeated twice. This report confirms F. oxysporum f. sp. fragariae as a causal agent of Fusarium wilt of strawberries in Saudi Arabia. This pathogen was previously reported to cause the Fusarium wilt of strawberries in California (Dilla-Ermita et al., 2023). This disease has been observed in several hydroponic strawberry greenhouses in Saudi Arabia, with incidence ranging from 25% to 45% across multiple locations. Given this, proper strategies are needed to manage this disease and to be compatible with organic farming.

Rapid discrimination between wild and cultivated Ophiocordyceps sinensis through comparative analysis of label-free SERS technique and mass spectrometry.

Ophiocordyceps sinensis is a genus of ascomycete fungi that has been widely used as a valuable tonic or medicine. However, due to over-exploitation and the destruction of natural ecosystems, the shortage of wild O. sinensis resources has led to an increase in artificially cultivated O. sinensis. To rapidly and accurately identify the molecular differences between cultivated and wild O. sinensis, this study employs surface-enhanced Raman spectroscopy (SERS) combined with machine learning algorithms to distinguish the two O. sinensis categories. Specifically, we collected SERS spectra for wild and cultivated O. sinensis and validated the metabolic profiles of SERS spectra using Ultra-Performance Liquid Chromatography coupled with Orbitrap High-Resolution Mass Spectrometry (UPLC-Orbitrap-HRMS). Subsequently, we constructed machine learning classifiers to mine potential information from the spectral data, and the spectral feature importance map is determined through an optimized algorithm. The results indicate that the representative characteristic peaks in the SERS spectra are consistent with the metabolites identified through metabolomics analysis, confirming the feasibility of the SERS method. The optimized support vector machine (SVM) model achieved the most accurate and efficient capacity in discriminating between wild and cultivated O. sinensis (accuracy = 98.95%, 5-fold cross-validation = 98.38%, time = 0.89s). The spectral feature importance map revealed subtle compositional differences between wild and cultivated O. sinensis. Taken together, these results are expected to enable the application of SERS in the quality control of O. sinensis raw materials, providing a foundation for the efficient and rapid identification of their quality and origin.

The effect of novel biotechnological vermicompost on tea yield, plant nutrient content, antioxidants, amino acids, and organic acids as an alternative to chemical fertilizers for sustainability.

In this study, the performance of a novel organic tea compost developed for the first time in the world from raw tea waste from tea processing factories and enriched with worms, beneficial microorganisms, and enzymes was tested in comparison to chemical fertilizers in tea plantations in Rize and Artvin provinces, where the most intensive tea cultivation is carried out in Turkey. In the field trials, the developed organic tea vermicompost was incorporated into the root zones of the plants in the tea plantations in amounts of 1000 (OVT1), 2000 (OVT2) and 4000 (OVT4) (kg ha-1). The experimental design included a control group without OVT applications and positive controls with chemical fertilizers (N: P: K 25:5:10, (CF) 1200 kg ha-1) commonly used by local growers. The evaluation included field trials over two years. The average yields obtained in two-year field trials in five different areas were: Control (6326), OVT1 (7082), OVT2 (7408), OVT4 (7910), and CF (8028) kg ha-1. Notably, there was no significant statistical difference in yields between the organic (at 4000 kg ha-1 ) and chemical fertilizers (at 1200 kg ha-1). The highest nutrient contents were obtained when CF and OVT4 were applied. According to the average values across all regions, the application of OVT4 increased the uptake of 63% N, 18% K, 75% P, 21% Mg, 19% Na, 29% Ca, 28% Zn, 11% Cu and 24% Mn compared to the control group. The application of chemical fertilizers increased the uptake of 75% N, 21% K, 75% P, 21% Mg, 28% Na, 27% Ca, 30% Zn, 18% Cu and 31% Mn compared to the control group. The organic fertilizer treatment had the lowest levels of antioxidants compared to the control groups and the chemical fertilizers. It was also found that the organic fertilizer increased the levels of amino acids, organic acids and chlorophyll in the tea plant. Its low antioxidant activity and proline content prepared them for or protected them from stress conditions. With these properties, the biotechnologically developed organic tea compost fertilizer has proven to be very promising for tea cultivation and organic plant production.

Gut microbiota-derived butyrate selectively interferes with growth of carbapenem-resistant Escherichia coli based on their resistance mechanism.

We investigated consequences of resistance acquisition in Escherichia coli clinical isolates during anaerobic (continuous culture) growth and examined their sensitivity to butyrate, a hallmark metabolite of healthy gut microbiota. Strains were stratified based on carrying either a carbapenemase (CARB) or displaying porin malfunctioning (POR). POR displayed markedly altered growth efficiencies, lower membrane stability and increased sensitivity to butyrate compared with CARB. Major differences in global gene expression between the two groups during anaerobic growth were revealed involving increased expression of alternative substrate influx routes, the stringent response and iron acquisition together with lower expression of various stress response systems in POR. Longitudinal analyses during butyrate wash-in showed common responses for all strains as well as specific features of POR that displayed strong initial "overshoot" reactions affecting various stress responses that balanced out over time. Results were partly reproduced in a mutant strain verifying porin deficiencies as the major underlying mechanism for results observed in clinical isolates. Furthermore, direct competition experiments confirmed butyrate as key for amplifying fitness disadvantages based on porin malfunctioning. Results provide new (molecular) insights into ecological consequences of resistance acquisition and can assist in developing measures to prevent colonization and infection based on the underlying resistance mechanism.

Effects of different trophic conditions on total fatty acids, amino acids, pigment and gene expression profiles in Euglena gracilis.

Euglena gracilis is a unique microalga that lacks a cell wall and is able to grow under different trophic culture conditions. In this study, cell growth, biomass production, and changes in the ultrastructure of E. gracilis cells cultivated photoautotrophically, mixotrophically, and under sequential-heterotrophy-photoinduction (SHP) were assessed. Mixotrophy induced the highest cell growth and biomass productivity (6.27 ± 0.59 mg/L/d) in E. gracilis, while the highest content of fatty acids, 2.69 ± 0.04% of dry cell weight (DCW) and amino acids, 38.16 ± 0.08% of DCW was obtained under SHP condition. E. gracilis also accumulated significantly higher saturated fatty acids and lower unsaturated fatty acids when cultivated under SHP condition. Transcriptomic analysis showed that the expression of photosynthetic genes (PsbA, PsbC, F-type ATPase alpha and beta) was lower, carbohydrate and protein synthetic genes (glnA, alg14 and fba) were expressed higher in SHP-culture cells when compared to other groups. Different trophic conditions also induced changes in the cell ultrastructure, where paramylon and starch granules were more abundant in SHP-cultured cells. The findings generated in this study illustrated that aerobic SHP cultivation of E. gracilis possesses great potential in human and animal feed applications.